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    Why Psychiatry Needs Neuroscience

    Scientific American Mind 28, 81 (2017). doi:10.1038/scientificamericanmind0717-81

    Author: Daniel Barron

    An influential subset of psychiatrists argue—absurdly—that neuroscience has little clinical relevance

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    How the Science of “Blue Lies” May Explain Trump's Support

    Scientific American Mind 28, 77 (2017). doi:10.1038/scientificamericanmind0717-77

    Author: Jeremy Adam Smith

    They are a very particular form of deception that can build solidarity within groups

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Does Living in Crowded Places Drive People Crazy?

    Scientific American Mind 28, 74 (2017). doi:10.1038/scientificamericanmind0717-74

    Authors: Oliver Sng, Steven Neuberg, Michael Varnum & Douglas Kenrick

    A new theoretical tool called life history theory offers an answer

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    How to Prevent Suicide with an Opioid

    Scientific American Mind 28, 70 (2017). doi:10.1038/scientificamericanmind0717-70

    Author: Anne Skomorowsky

    Fascinating study suggests treating “psychache”

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Cross-Cultural Evidence for the Genetics of Homosexuality

    Scientific American Mind 28, 7 (2017). doi:10.1038/scientificamericanmind0717-7

    Author: Debra W. Soh

    Mexico's third gender sheds light on the biological correlates of sexual orientation

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Lonely but Never Alone

    Scientific American Mind 28, 62 (2017). doi:10.1038/scientificamericanmind0717-62

    Author: Anna von Hopffgarten

    Space travel: How does the brain react to the isolation encountered in outer space?

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Schizophrenia's Unyielding Mysteries

    Scientific American Mind 28, 50 (2017). doi:10.1038/scientificamericanmind0717-50

    Author: Michael Balter

    Gene studies were supposed to reveal the disorder's roots. That didn't happen. Now scientists are broadening the search

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Listen between the Cries

    Scientific American Mind 28, 44 (2017). doi:10.1038/scientificamericanmind0717-44

    Author: Janosch Deeg

    Researchers try to decipher the hidden messages in babies' wailing

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    How Gut Bacteria Tell Their Hosts What to Eat

    Scientific American Mind 28, 4 (2017). doi:10.1038/scientificamericanmind0717-4

    Author: Knvul Sheikh

    By suppressing or increasing cravings, microbes help the brain decide what foods the body “needs”

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Deciphering the Language of Love

    Scientific American Mind 28, 35 (2017). doi:10.1038/scientificamericanmind0717-35

    Author: Sue Johnson

    Attachment science is helping couples master communication and connection—and getting through conflict

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections?

    Scientific American Mind 28, 27 (2017). doi:10.1038/scientificamericanmind0717-27

    Author: Bret Stetka

    New evidence hints that bariatric surgery changes the dialogue between bowel and brain

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Meditation's Calming Effects Pinpointed in the Brain

    Scientific American Mind 28, 24 (2017). doi:10.1038/scientificamericanmind0717-24

    Author: Diana Kwon

    A new mouse study reveals a set of neurons that may point to physiological roots for the benefits of breathing control

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Your Brain Remembers Languages You Think You Forgot

    Scientific American Mind 28, 22 (2017). doi:10.1038/scientificamericanmind0717-22

    Author: Jane C. Hu

    Kids adopted in a new country have an advantage in learning their native tongue as adults, even if they have not heard it since birth

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Welcome to the New Scientific American Mind

    Scientific American Mind 28, 2 (2017). doi:10.1038/scientificamericanmind0717-2

    Author: Mariette DiChristina

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    The Genius of Pinheads: When Little Brains Rule

    Scientific American Mind 28, 17 (2017). doi:10.1038/scientificamericanmind0717-17

    Author: Erik Vance

    Bigger brains are not always better

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    This is Your Brain on Poverty

    Scientific American Mind 28, 13 (2017). doi:10.1038/scientificamericanmind0717-13

    Author: Amanda Montañez

    Data visualizations highlight the surprising connections between income and brain structure

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Don't Forget: You, Too, Can Acquire a Super Memory

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    Scientific American Mind 28, 10 (2017). doi:10.1038/scientificamericanmind0717-10

    Author: Catherine Caruso

    Learning a memorization technique used by elite memory athletes leads to widespread changes in brain wiring

    in Scientific American Mind on July 08, 2017 12:00 AM.

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    Thoughts on Essays

    I've recently been doing some of every academic's favorite activity - marking student essays (papers). Here's a few observations on essays and on marking them. 1. Marking Essays is Subjective This is a bit of a truism: it's fairly obvious that not everyone will agree on how to grade an essay down to the exact mark. Unlike with, say, a multiple-choice exam, marking an essay is not a mechanical process. But it's easy to forget this when the marks are there in black and white (or r

    in Discovery magazine - Neuroskeptic on June 26, 2017 07:39 PM.

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    Soon-to-be-ex-rector of top Belgium university blames coverage of misconduct case for ouster

    May was quite a month for Rik Torfs, the rector of a prominent university in Belgium. On May 9, Torfs lost his re-election campaign for rector of KU Leuven by a slim margin—out of more than 2100 votes, he lost by a mere 48. And just 20 days later, on May 29, Torfs wrote his […]

    The post Soon-to-be-ex-rector of top Belgium university blames coverage of misconduct case for ouster appeared first on Retraction Watch.

    in Retraction watch on June 26, 2017 02:00 PM.

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    Latest stats are just a start in preventing gun injuries in kids

    New stats on firearm deaths and injuries are disturbing, but the picture to make policy is far from complete, researchers say.

    in Science News on June 26, 2017 02:00 PM.

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    “Searching our souls”: Authors retract paper after researcher admits to fabricating data

    Researchers at a prominent Japanese university have retracted a 2016 paper in a chemistry journal after the first author admitted to scientific misconduct. According to the notice, Kyushu University investigated and verified that the first author had committed scientific misconduct. We requested a copy of the misconduct report, which revealed that the researcher, Prasenjit Mahato, a […]

    The post “Searching our souls”: Authors retract paper after researcher admits to fabricating data appeared first on Retraction Watch.

    in Retraction watch on June 26, 2017 12:00 PM.

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    Sound-reflecting shelters inspired ancient rock artists

    Ancient Europeans sought rock art sites where sounds carried.

    in Science News on June 26, 2017 12:00 PM.

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    Earth’s dry zones support a surprising number of trees

    A Google Earth-based estimate of dryland forests adds serious leafage to Earth’s total tree count.

    in Science News on June 26, 2017 11:00 AM.

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    A channel for neuroscientists on Gitter

    As opposed to the free software community, where I've been around long enough to know what's where, I'm still relatively new to the neuroscience community. Over the two years that I've been doing my PhD, I've found a few neuroscience related mailing lists, but not any chat channels. Various teams tend to use Slack or another platform for internal communications, but nothing seems to be set up for the community in general - an open for all channel.

    Mailing lists are extremely useful, but by design they are suited to particular types of tasks. They are very well suited for longer discussions, and general queries that are not time sensitive, for example. On the other hand, they do not work well for urgent queries, and of course, sometimes sending e-mails back and forth is quite an overhead for simpler tasks or collaborative development.

    Most open source communities have both mailing lists and chat channels. I figured it'd be nice to have one for the neuroscience community too. There's the question of what platform was best suited, of course. We use Slack for our internal communication, but Slack only works well for small teams. It isn't designed for larger communities. The IRC is ideal for larger communities, but on the flip side, the IRC is not very user friendly.

    The third option, and the popular alternative to IRC and Slack, is Gitter - it's been recently acquired by GitLab and will be completely open sourced soon. It's completely free to use unlike Slack where one needs to pay more as the number of group members increases, and is designed for large communities that number in the thousands. One can login using either Github or Twitter - so that's quite convenient too. There's even an IRC gateway for more technical users.

    So here's the channel then - https://gitter.im/neuroscience-central/Lobby. I hope it'll be useful, and if it doesn't, well no harm done :)

    in Ankur Sinha on June 26, 2017 09:30 AM.

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    If high self-control has a downside, these psychologists couldn’t find it

    kettlebell balance demonstrationBy Emma Young

    Self-control has been dubbed a “master virtue” – one which enables so many others, such as selflessness and perseverance. Indeed, better control of short-term impulses in conflict with long-term goals is linked to everything from greater health to greater wealth. It’s no surprise, then, that schools are adopting strategies designed to improve their students’ self-control, under the assumption that there is no downside. But is there…?

    Some researchers have argued that there might be. High levels of self-control might promote obsessive-compulsive tendencies, or a dysfunctional kind of perfectionism, in which a person rigidly strives for unreachable standards. Another potential downside has been suggested: “Too much” self-control might lead to “frequent and sometimes unnecessary regulation of emotions, thoughts and behaviours, resulting in a life marked by rigidity and blandness, thereby lowering subjective wellbeing” note the authors of a new paper on the topic, published in the Journal of Personality. 

    To date, there’s been little actual research to investigate the interplay between changing levels of self-control and wellbeing. So the team – led by Christopher Wiese at Purdue University and including Roy Baumeister of willpower fame and Angela Duckworth, known for her work on “grit” –  ran a series of six studies involving a total of more than 5,000 schoolchildren, college undergraduates and adults aged up to 55.

    In the first study, middle-school children (aged 10-14) completed a questionnaire about their impulsivity, their teachers also rated the kids’ self-control, and the children also reported their subjective wellbeing, including how often they experienced positive and negative moods and their overall life satisfaction. This allowed the researchers to see if having especially high or low self-control was related to feelings of well being.

    Further studies with university students and a community sample of adults were similar, but in one case there was a real-world test of the ability to resist temptation, which involved persisting with a boring computer task while resisting fun distractions. Another of the studies used a “day reconstruction method”, in which participants recalled how much self-control they had exercised during different activities in a given day, and how they had felt during each activity.

    The results of all these investigations? In the researchers’ words, “Self-control enhances subjective wellbeing with little to no apparent downside of too much self-control.” The “little” cost to well being that they did find related to the giving up of immediate pleasures for future gain. Since “these [future] benefits outweigh the loss of in-the-moment pleasures,” the net result was  “overall higher [subjective wellbeing],” the researchers wrote.

    There were a few limitations with the research. Perhaps most glaring was the lack of longitudinal data (the same participants were not followed over time) or any kind of experimental test to see the consequences of exercising different levels of self-control. This meant the researchers couldn’t explore, for example, whether people may start to feel less good about repeatedly exerting self-control in the long term. It also means it’s not possible to say based on this research whether over periods of weeks, months and years, self-control affects well being levels, or if happier people simply tend to exert more self-control. However, the researchers said they believe their results provide “preliminary support” for promoting self-control among school-aged children, as well as in adults.

    Too much of a good thing? Exploring the inverted-U relationship between self-control and happiness

    Emma Young (@EmmaELYoung) is Staff Writer at BPS Research Digest


    in The British Psychological Society - Research Digest on June 26, 2017 08:53 AM.

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    The South West Indian Ocean islands shelter a unique and novel African sub-lineage honeybee

    The western honeybee Apis mellifera is probably one of the most famous pollinators and has a key role in the terrestrial ecosystem. Humans have domesticated honeybees for perhaps more than 9000 years, but wild populations still exist. As beekeeping became more global, honeybees were moved out their native area and are now nearly cosmopolitan. Their wide geographic distribution shows that honeybees have the ability to adapt to very different new environments.

    Originally, Apis mellifera was distributed only in Europe, Africa, the Middle East, and some parts of Asia. The exact point of origin of the western honeybee is still hard to identify, but over the last decades, five major evolutionary groups have been defined. The evolutionary complexity does not stop there, as honeybees have evolved no less than 31 recognized subspecies that can readily hybridize. The most famous example to date is the Africanized honeybee, the result of admixture between the divergent African and European lineages.

    Example of beehives in an apiary on La Réunion © M. TECHER

    Given its intimate relationship with human movements, it can be rather hard to be sure about the honeybee presence in some regions. This difficulty is even more relevant for young isolated island systems in which the natural history before human arrival is often unclear or non-exhaustive. One illustration of such a case is the honeybee populations from the South West Indian Ocean islands (SWIO).

    In this area, Madagascar and three archipelagos form one of the major hotspots of biodiversity with a high proportion of endemic species. In 1804, Pierre André Latreille described a honeybee subspecies Apis mellifera unicolor that is endemic to Madagascar. It is open to debate as to whether honeybees were present in the Mascarene, Seychelles and Comoros archipelagos before humans.

    Concerns about its status were raised because of reported importations in the Mascarene and Seychelles archipelagos. Indeed, the influence of beekeeping was previously proven in Rodrigues (the far-eastern island of the Mascarenes) as a genetic study showed the exclusive presence of European Carnolian and Italian honeybees. However, this situation was exceptional as Seychelles honeybees were African and genetically related to A. m. unicolor from Madagascar.

    Apis mellifera unicolor worker © A. FRANCK – CIRAD

    Given such contrasting patterns, it seemed rather complicated to predict which lineages or subspecies were present in the rest of the SWIO islands. In our latest mitochondrial study, the ancestral genetic identity of honeybees from the Mascarene and Comoros was partly unraveled. Using one of the largest sampling efforts conducted for honeybees in African regions, we helped to retrace the maternal ancestry lineage using two markers. The genetic diversity observed was compared to potential source populations like Madagascar and 19 continental countries.

    Interestingly, the results showed that SWIO honeybees mainly presented Apis mellifera unicolor sequences in 10 islands out of the 11 targeted (all except Rodrigues). Not only were the honeybees from the archipelagos more closely related to Madagascar, but they formed with it a novel African mitochondrial group. One way for these honeybees to reach these isolated islands despite the ocean barrier would have been via human importations.

    Evolutionary lineages transition within Apis mellifera native range using COI-COII region and distribution in the South West Indian Ocean archipelagos. See article for full details.
    Techer et al. 2017

     

    New private A. m. unicolor derivated sequences found in each of the SWIO islands suggested an alternative hypothesis. This finding more likely points towards a long independent evolution among islands after colonization. It is not new that species that originated from Madagascar were able to cross the ocean barrier and colonize nearby islands. The distance between the islands could have been reduced with sea level fluctuations and/or hurricanes. As the Comoros archipelago diversity suggests, honeybees could have progressively colonized the islands, beginning with the nearest island to the mainland before moving from one neighbouring island to the next.

    All these elements support the theory that honeybees could be native to the SWIO archipelagos. Still, European lineage was also retrieved in different frequencies in the Mascarene archipelago, revealing human impact. Until recently, honeybees from these islands were preserved from major worldwide pests such as Varroa destructor thanks to importation restrictions. The diversity of honeybees in the SWIO islands constitutes a unique heritage that deserves special attention.

    The post The South West Indian Ocean islands shelter a unique and novel African sub-lineage honeybee appeared first on BMC Series blog.

    in BMC Series blog on June 26, 2017 06:00 AM.

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    Elsevier and CWTS release report on data sharing perceptions and practices among researchers

    Findings spark conversation at Research Data Alliance meeting about closing the gap between data sharing policies and best practice among researchers

    in Elsevier Connect on June 26, 2017 03:50 AM.

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    Scientists in limbo as US Supreme Court allows modified travel ban

    Justices overturn lower court rulings on policy targeting people from six majority-Muslim countries.

    Nature News doi: 10.1038/nature.2017.22190

    in Nature News & Comment on June 26, 2017 12:00 AM.

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    Intuition harnessed in the name of particle packing

    From avalanches to pharmaceuticals, the physics of powders relies on a much-maligned talent.

    Nature 546 575 doi: 10.1038/546575b

    in Nature News & Comment on June 26, 2017 12:00 AM.

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    Electron cryo-microscopy structure of the mechanotransduction channel NOMPC

    Mechanosensory transduction for senses such as proprioception, touch, balance, acceleration, hearing and pain relies on mechanotransduction channels, which convert mechanical stimuli into electrical signals in specialized sensory cells. How force gates mechanotransduction channels is a central question in the field, for which there are two major models. One is the membrane-tension model: force applied to the membrane generates a change in membrane tension that is sufficient to gate the channel, as in the bacterial MscL channel and certain eukaryotic potassium channels. The other is the tether model: force is transmitted via a tether to gate the channel. The transient receptor potential (TRP) channel NOMPC is important for mechanosensation-related behaviours such as locomotion, touch and sound sensation across different species including Caenorhabditis elegans, Drosophila and zebrafish. NOMPC is the founding member of the TRPN subfamily, and is thought to be gated by tethering of its ankyrin repeat domain to microtubules of the cytoskeleton. Thus, a goal of studying NOMPC is to reveal the underlying mechanism of force-induced gating, which could serve as a paradigm of the tether model. NOMPC fulfils all the criteria that apply to mechanotransduction channels and has 29 ankyrin repeats, the largest number among TRP channels. A key question is how the long ankyrin repeat domain is organized as a tether that can trigger channel gating. Here we present a de novo atomic structure of Drosophila NOMPC determined by single-particle electron cryo-microscopy. Structural analysis suggests that the ankyrin repeat domain of NOMPC resembles a helical spring, suggesting its role of linking mechanical displacement of the cytoskeleton to the opening of the channel. The NOMPC architecture underscores the basis of translating mechanical force into an electrical signal within a cell.

    Nature doi: 10.1038/nature22981

    in Nature Biological Sciences Research on June 26, 2017 12:00 AM.

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    Every breath you take contains a molecule of history

    In 'Caesar’s Last Breath', best-selling author Sam Kean tells vivid stories about the gases we can’t see.

    in Science News on June 25, 2017 11:00 AM.

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    Weekend reads: Death penalty for scientific fraud?; Why criticism is good; Cash for publishing

    The week at Retraction Watch featured revelations about a case of misconduct at the University of Colorado Denver, and the case of a do-over that led to a retraction. Here’s what was happening elsewhere: “An eye for an eye, a tooth for a tooth — a life for a lab book?” A Chinese court recommends […]

    The post Weekend reads: Death penalty for scientific fraud?; Why criticism is good; Cash for publishing appeared first on Retraction Watch.

    in Retraction watch on June 24, 2017 01:30 PM.

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    NPR features Elsevier Foundation winner as world's most "unstoppable scientist"

    Dr. Eqbal Dauqan became a refugee after winning the 2014 Elsevier Foundation Award for Women Scientists in the Developing World

    in Elsevier Connect on June 23, 2017 03:53 PM.

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    Can a tracking system for peer reviewers help stop fakes?

    The problem of fake peer reviews never seems to end — although the research community has known about it since 2014, publishers are still discovering new cases. In April, one journal alone retracted 107 papers after discovering the review process had been compromised. By tracking individual reviewers’ contributions, Publons — recently purchased by Clarivate Analytics — […]

    The post Can a tracking system for peer reviewers help stop fakes? appeared first on Retraction Watch.

    in Retraction watch on June 23, 2017 02:00 PM.

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    Vulnerability: Newly arrived immigrant and refugee children and the right to good health

    Migrant children are at risk of a variety of physical and mental health problems as a result of their limited access to quality health care, the increased prevalence of infectious diseases in their home countries and the difficult conditions they experience during the process of migration. Many of these conditions are manageable, and if undiagnosed or left untreated, could lead to significant unfavorable health outcomes.

    For more than two decades, Greece has been experiencing increased mobility of various populations across its borders. However, there are limited data and information with regards to their health particularly in the case of children.

    In our recently published  study in BMC Pediatrics (Clinical and laboratory evaluation of new immigrant and refugee children arriving in Greece), we prospectively examined all immigrant and refugee children that attended a special outpatient clinic at a large tertiary Children’s Hospital, in Athens, Greece to obtain a health evaluation, within three months of their arrival in the country.

    Lack of vaccination records and bad oral health were the most prevalent clinical issues

    Immigrants were defined as children of parents with long-term residence permit entering for family reunification while refugees, asylum seekers or irregular migrants were defined as refugees. Among both groups, we identified distinct clinical problems and certain laboratory abnormalities that differed according to their migration status, age and region of origin.

    Inadequate immunization status (insufficient number, inadequate serologic response due to improper storage of vaccinations, or severe malnutrition) places migrant children at risk for vaccine-preventable diseases. 80% of the children in the study had no documentation of vaccination, and this was more prominent among the population of refugees, while bad oral health and especially caries was found in more than 20% of them. A number of children presented with respiratory and skin infections and additional clinical conditions requiring intervention.

    Photo from the recent vaccination campaign in Greece for refugee children by Médecins Sans Frontières (MSF).

    More than 40% of migrant children presented lack of protective antibodies to hepatitis B surface antigen (anti-HBs ≥ 10 IU/L), nevertheless, no child was found to be a chronic HBsAg carrier. Latent tuberculosis was detected in 2.7% of our study individuals, and all received BCG vaccination.

    Lack of protective antibodies against hepatitis B virus, Lead exposure, eosinophilia, anemia and low ferritin were the most common laboratory abnormalities

    It is well recognized that Lead exposure is the most widespread exposure among migrant children and may have deleterious, long term neurotoxic effects. In one third of our study population, we identified elevated blood lead levels and the odds were increased among younger children, immigrants and those originating from Asia. Additionally, younger children had increased probability of anemia and low ferritin levels.

    The volume, speed, and diversity of migration in Greece amid the current socioeconomic crisis are additional challenges we face in providing access to health care services to all migrants. It is evident that collaboration with nongovernmental institutions and health providers at national as well as at international levels is essential.

    The post Vulnerability: Newly arrived immigrant and refugee children and the right to good health appeared first on BMC Series blog.

    in BMC Series blog on June 23, 2017 02:00 PM.

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    Instead of retracting a flawed study, a journal let authors re-do it. It got retracted anyway.

    When a journal discovers elementary design flaws in a paper, what should it do? Should it retract immediately, or are there times when it makes sense to give the researchers time to perform a “do-over?” These are questions the editors at Scientific Reports recently faced with a somewhat controversial 2016 paper, which reported that microRNAs […]

    The post Instead of retracting a flawed study, a journal let authors re-do it. It got retracted anyway. appeared first on Retraction Watch.

    in Retraction watch on June 23, 2017 12:00 PM.

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    This glass frog wears its heart for all to see

    A newly discovered glass frog species has skin so clear that it reveals most of the animal’s internal organs, including the heart.

    in Science News on June 23, 2017 11:00 AM.

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    Euthanasia for people with psychiatric disorders or dementia

     

    Euthanasia, i.e. the ending of a patient’s life by a physician on explicit patient request, on the grounds of unbearable suffering caused by mental illness is legal only in Belgium, the Netherlands and Luxembourg. Strict due care and procedural criteria are set out to ensure careful practice.

    The option of euthanasia is increasingly being considered and discussed in a growing number of countries. Euthanasia remains however a controversial issue, especially when it concerns people suffering from a mental illness, such as major depressive disorder or dementia.

    The number of euthanasia cases in Belgium has been increasing year by year since implementation of the euthanasia law in 2002. Euthanasia is most common in cancer patients: in 2015 68% of all reported cases involved people diagnosed with cancer. In previous years, we found a notable increase in deaths from euthanasia in people with conditions other than cancer, and in those without terminal illness, including people with mental illness.

    Taking into account the specific difficulties associated with handling euthanasia requests expressed by people suffering from mental illness, a thorough examination of the practice is vital. Our study adds to and informs the international debate on medically assisted dying in general and in people with mental illness specifically.

    One of the procedural criteria for careful euthanasia practice is an obligation of the attending physician to report the euthanasia case for review to the Federal Control and Evaluation Committee for Euthanasia. Information on the euthanasia cases is collected through a standardized registration form.

    The Committee collects the anonymous information from the registration forms in a database, which we were allowed to use for research purposes. In our article, we report these data from the start of legalization of euthanasia in 2002 until 2013, which are the latest available data.

    Our study shows that the number and proportion of euthanasia cases with a psychiatric disorder or dementia diagnosis has increased from 2008 onwards to 3.0% of all cases reported in 2013 (54 cases in 2013). This increase is particularly visible in cases with a diagnosis of mood disorder. In comparison with the total number of reported cases, euthanasia for these specific patient groups remains a limited practice.

    The increase in the absolute number of cases is particularly evident in cases with a mood disorder diagnosis. The majority of euthanasia cases with a psychiatric disorder or dementia diagnosis concerned women, ranging from 58.1% in people with dementia to 77.1% in people suffering from mood disorders. All notified cases were judged to comply with the due care criteria specified in the Belgian euthanasia law by the Committee.

    Given the highly controversial nature of the practice and the specific complexities associated with handling euthanasia requests expressed by people with mental illness, we strongly recommend more in-depth research on patients’ reasons and physicians’ procedures, as well as on the impact on the family and health care professionals involved.

    The evaluation of a euthanasia request is a complex and challenging task for physicians, particularly when a request is based on psychological or existential suffering. Therefore, development of relevant practice guidelines is necessary.

    Our article studying euthanasia in the most controversial of patient groups suggests that the legal possibilities of euthanasia legislation are being explored more broadly and have become more and more accepted over the past years in Belgium.

     

     

    The post Euthanasia for people with psychiatric disorders or dementia appeared first on BMC Series blog.

    in BMC Series blog on June 23, 2017 09:00 AM.

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    Researchers are figuring out how sense of self develops differently in autistic teens

    Teenage woman looking at herself in a mirrorBy guest blogger Dan Carney

    Our autobiographical memory is fundamental to the development of our sense of self. However, according to past research, it may be compromised in autism, together with other skills that are also vital for self understanding, such as introspection and the ability to attribute mental states to others (known as mentalising).

    For example, experiments involving autistic children have highlighted retrieval difficulties, “impoverished narratives”, and a greater need for prompting, while also suggesting that semantic recall (facts from the past) may be impaired in younger individuals.

    Now a UK research team, led by Sally Robinson from London’s St. Thomas’ Hospital, has published the first attempt to assess the nature of – and relationships between – autobiographical memory, mentalising and introspection in autism. Reporting their findings in Autism journal, the group hope their results will shed more light on the way that autistic children and teens develop a sense of self.

    The researchers compared the performance of 24 autistic participants (age range: 11-18; 4 girls) and 24 age- and gender-matched neurotypical participants on three tasks. The first, designed to tap semantic and episodic aspects of autobiographical memory, required them to recall what kind of personality they showed in different contexts (at school, with the family, when happy etc) and to describe specific episodes from their lives in which they’d behaved as that kind of person.

    A second, interview task measured introspection and mentalising: participants rated both their own ability, and that of a nominated comparison individual (such as a friend or relative), to recognise both their own and the other person’s internal/external traits, such as tiredness (internal trait) or smartness of dress (external). For example, in relation to tiredness, participants rated “How well do you know when you feel tired?”; “How well does X know when you are tired?”; “How well do you know when X feels tired?”; and “How well does X know when he/she feels tired?”.

    The final task was the widely used mentalising measure, the Reading The Mind In The Eyes Task for children, which involved participants looking at pictures showing only the eye region of person’s face and inferring their mental state.

    Overall, the results demonstrated impaired and preserved abilities in the autistic group, while suggesting atypical relationships between skills. In terms of autobiographical memory, the autistic children and teens: a) produced fewer self-descriptive personality traits than the neurotypical group, b) required more prompting to generate specific episodic memories, c) provided fewer memories containing either emotional or sensory detail, but d) did not differ in terms of the number or type of episodic memories recalled.

    That the autistic group recalled a typical number of episodic memories, albeit with greater prompting and atypicality of content, is broadly in line with previous work. The recall of fewer own personality traits, however, is a new finding, and is worth investigating further. This may suggest that autistic individuals’ self-concept is atypical.

    Meanwhile, on the introspection and mentalising interview, the autistic children and teens (a) rated themselves poorer at knowing about another’s mental state than did the neurotypical group, and b) more surprisingly, they rated others as having more knowledge about their own external/behavioural traits than they did themselves. The researchers suggested that this last finding may betray a lack of confidence in making objective/comparative behavioural judgments – as opposed to subjective internal ones – about the self in relation to others.

    Related to this, among the autistic children and teens only, if they rated themselves as having a high level of self-knowledge, they were also more likely to rate others as having a higher knowledge of them. The researchers pointed out that this may highlight the use of introspection as a compensatory strategy in autism, when attributing mental states to others, and that this may play a role in autistic individuals’ documented tendency to over-attribute their own beliefs and knowledge to others.

    As expected, the autistic children and teens were poorer than controls on the Eyes Task, another indication of compromised mentalising skills.

    There was also a group difference in how the various skills related to each other. In the neurotypical group, performance correlated across the tasks: semantic/episodic autobiographical memory, introspecting and mentalising, which indicates how, in typical development, autobiographical memory has a reciprocal relationship with other aspects of the self-concept. In the autistic children and teens, these correlations were absent, suggesting that this reciprocity between mental processes may be impaired.

    Although this study is exploratory and more work is needed, it provides a finer-grained glimpse at how skills associated with self-understanding may interact in autism, and how this may differ from the equivalent processes in typical development.

    The new findings may also have implications for autistic children undertaking Cognitive Behavioural Therapy (CBT), an approach where the recall of autobiographical events is important. CBT is commonly used with autistic people to address anxiety and social skill development. In the new research, the autistic group generated as many episodic memories as controls, after having first described their own personality traits. This may suggest that in CBT with autism, accurate episodic retrieval could be supported by first encouraging individuals to reflect on their own personalities in a more general sense.

    Personality traits, autobiographical memory and knowledge of self and others: A comparative study in young people with autism spectrum disorder

    Dan Carney headshotPost written for BPS Research Digest by Dr. Dan Carney. Dan is a UK researcher specialising in developmental disorders. He undertook his post-doctoral research fellowship at London South Bank University, finishing in 2013. His published work to date has examined cognition, memory, and inner speech processes in Williams syndrome and Down syndrome, as well as savant skills in autism.


    in The British Psychological Society - Research Digest on June 23, 2017 08:04 AM.

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    The secrets of a top salary in science

    The highest-earning academics aren’t necessarily those who do the most research.

    Nature 546 576 doi: 10.1038/546576a

    in Nature News & Comment on June 23, 2017 12:00 AM.

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    Scientists spy on the secret inner life of bacteria

    New images reveal the inner workings of bacteria.

    in Science News on June 22, 2017 06:00 PM.

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    Flight demands may have steered the evolution of bird egg shape

    An analysis of nearly 50,000 bird eggs finds a link between a species’ egg shape and flight ability.

    in Science News on June 22, 2017 06:00 PM.

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    Journal retracts two papers by authors who lifted others’ data

    A journal has retracted two 2014 papers after the editors discovered the authors used data from other research groups without permission. The papers, both published in the same issue of Cell Biochemistry and Biophysics and retracted in May, suffered from similar issues—the authors published data that was not theirs. The authors are all based at […]

    The post Journal retracts two papers by authors who lifted others’ data appeared first on Retraction Watch.

    in Retraction watch on June 22, 2017 03:30 PM.

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    You need to get out more. Occupation could be a major risk factor in vitamin D deficiency

    This week in the UK we’ve been experiencing a heat wave which has left many sweltering in the sun and seeking any available shade. We all know the dangers of sun exposure to our skin but we perhaps overlook the important benefits that it provides through vitamin D synthesis.

    Vitamin D is important for the body in several ways and possessing inadequate amounts has been linked to autoimmune conditions; metabolic, respiratory, cardiovascular and psychiatric disorders; as well as cancers and osteoporosis.

    We can obtain vitamin D through our diets but an estimated 90% is produced endogenously in healthy adults. To do this our bodies synthesize vitamin D from solar ultraviolet B radiation, making sunlight an essential factor in obtaining recommended vitamin D levels.

    Vitamin D deficiency

    Vitamin D deficiency is prevalent worldwide and even those in sunny locations are at risk of being deficient. Modern occupations trending towards indoor work are likely to play a big role in this as decreased time spent outdoors would be expected to lead to decreased vitamin D levels.

    In order to more fully understand the role that occupations play on vitamin D levels and identify those groups at the greatest risk, researchers at the University of Alberta,  Canada performed a systematic review of 71 papers with large population based cohorts that defined occupational groups.

    Vitamin D deficiency was most prevalent in shift workers (80%) closely followed by indoor workers (77%) and healthcare students (72%).

    It was found that across all occupational groups, serum 25-(OH)D levels (a measure of vitamin D status in individuals) were below recommendations for optimal levels that are recommended by the Endocrine Society.

    Vitamin D deficiency was most prevalent in shift workers (80%) closely followed by indoor workers (77%) and healthcare students (72%). Deficiency levels for practicing physicians, nurses and a group termed ‘other healthcare employees’ were all below 50%.

    The findings of the study are consistent with an assumption that workers in an indoor environment would display lower levels of vitamin D compared to those working in outdoor environments.

    The author’s state that the high prevalence of vitamin D deficiency in healthcare students and medical residence (72% and 65% respectively) could be due to long working hours combined with additional time spent studying, leading to considerable time spent indoors. This is an alarming find given low vitamin D in young adults may decrease bone density, increasing the risk of osteoporosis later in life.

    Perhaps the most worrying statistic is the high levels of vitamin D deficiency seen in shift workers. This deficiency has previously been suggested to be associated with shift workers’ predisposition for musculoskeletal, cardiovascular diseases and cancer. However drawing conclusions on this is complicated given that shift workers may work at various times of the day and may spend more time in daylight outside of conventional working hours.

    Clinical implications

    For predominantly indoor occupations such as office work, more encouragement could be given to employees to take breaks outside.

    Given the high prevalence vitamin D deficiency in shift workers, the authors call for regular screenings of these and other high risk groups to be considered in future clinical practice guidelines. They also call for education on the importance of healthy vitamin D levels, both through sun exposure and dietary intake, to be incorporated into workplace wellness programs.

    For predominantly indoor occupations such as office work, more encouragement could be given to employees to take breaks outside, giving their skin more exposure to UV light. This could be aided by revised work schedules allowing for such breaks.

    So whether you’re parked by a fan in the midst of a heat wave or confining yourself to an office all day, provided that you avoid excessive exposure, it may be a good idea to venture outside and soak up some sun.

    The post You need to get out more. Occupation could be a major risk factor in vitamin D deficiency appeared first on BMC Series blog.

    in BMC Series blog on June 22, 2017 02:03 PM.

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    No new math: Journal pulls math paper with “already known” results

    A mathematics journal has withdrawn a paper after discovering that the results were not new. The paper, published online in March in Communications in Algebra, explored the properties of group rings, a discipline of algebra. According to editor-in-chief of the journal, Jason Bell, author Francis E. A. Johnson, a professor of mathematics at the University […]

    The post No new math: Journal pulls math paper with “already known” results appeared first on Retraction Watch.

    in Retraction watch on June 22, 2017 01:30 PM.

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    New Cell Press journal will unite researchers in sustainable energy

    Drawing on the editor’s work in the developing world, Joule will tackle one of the biggest challenges facing humanity

    in Elsevier Connect on June 22, 2017 01:09 PM.

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    Celebrating one librarian’s commitment to global health

    University of Michigan’s global health informationist Gurpreet Rana wins the MLA’s T. Mark Hodges International Service Award

    in Elsevier Connect on June 22, 2017 01:09 PM.

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    The bumpy transition from student to junior doctor – an unseen struggle

    Stepping up from medical student to junior doctor is known to be a daunting and challenging transition. Though being stretched and ‘thrown in the deep end’ can be beneficial to their learning experience, it also increases stress. While getting to grips with the role in long shifts, they are also responsible for patient care. Can their job role and commitment for patient care be associated with poorer self-care?

    This question was investigated by researchers at the Faculty of Medicine, University of Queensland, in a study led by Dr. Sturman, who reported the experiences junior doctors had during their career development.

    Junior doctors were recruited from a range of hospital settings, and interviewed to find out about their experiences when adjusting from the role of medical student to junior doctor. After this process, two clinical academics and an intern conducted a descriptive analysis of the information collected.

    There’s incredible self-doubt when you become an intern that you don’t have as a medical student.

    As a result, some persistent concepts arose. Three main themes were ‘steep learning curve’, ‘relationships and team’ and ‘seeking help’. “There’s incredible self-doubt when you become an intern that you don’t have as a medical student” one interviewee said. Overall, the participants described the transition as physically, mentally and emotionally draining.

    Key experiences were a decrease in confidence, self-care and social wellbeing. It seems that while the juniors were focused on caring for others, and were happy to raise patient related concerns  with senior staff members, there was an unwillingness to voice their own personal problems.

    To try and understand the cause for this, the researchers suggest some key factors in the professionals’ working environment, which may contribute to these negative impacts.

    You’re both at the bottom and somewhere up in the middle of the food chain at the same time because you are making decisions and directing patient care, but at the same time you’re at the very, very bottom of that chain.

    The supportive team structure which can alleviate the stress of this experience may be hindered by a divide being in place between senior staff and the junior doctors, as one participant implied – “You’re both at the bottom and somewhere up in the middle of the food chain at the same time because you are making decisions and directing patient care, but at the same time you’re at the very, very bottom of that chain”.

    Disconnection between the staff can be further exacerbated by the movement of professionals to and from various teams within the hospital. As shallow relationships are maintained, not only the social wellbeing of the junior doctors, but their skills could be affected.

    This study speaks out to medical educators to raise awareness of the personal detriments experienced by junior doctors in this phase of learning, and suggests that improved team support systems and teaching methods could help smooth the bumpy transition from student to professional.

    The advice that I would give is don’t be afraid, everyone is there to help you and everyone is there to guide you along.

    It also voices the lessons learnt by junior doctors who have been through this stressful change, as one interviewee said “The advice that I would give is don’t be afraid, everyone is there to help you and everyone is there to guide you along, don’t be afraid to ask questions because ultimately it’s all in the best interest of the patient.”

    If the wellbeing of junior doctors were to improve, perhaps this could also have a positive impact on their colleagues, and even the patients that they treat.

    The post The bumpy transition from student to junior doctor – an unseen struggle appeared first on BMC Series blog.

    in BMC Series blog on June 22, 2017 01:00 PM.

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    When should babies sleep in their own rooms?

    A new study offers support to sleep-starved parents by suggesting that babies age 6 months and older sleep longer when in their own bedroom.

    in Science News on June 22, 2017 11:00 AM.

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    More than 50 years on, the murder of Kitty Genovese is still throwing up fresh psychological revelations

    KittyGenovese-2By Christian Jarrett

    The horrific killing of Catherine “Kitty” Genovese in New York in 1964 inspired research into what’s known in social psychology as the Bystander Phenomenon – our increased disinclination to intervene when in the company of others. That’s because early reports told how 38 witnesses to Genovese’s murder did nothing to help. But in fact it’s now clear that several people did intervene. So the tragedy that inspired research into the Bystander Phenomenon is actually a bad example of that real phenomenon.

    But it’s not time yet to leave the sad story alone. As psychologist Saul Kassin documents in Perspectives on Psychological Science, hidden in the story in plain sight all these decades is an example of another important psychological principle: the power of false confessions. Moreover, in another twist, details have emerged recently of how a few days after her murder, Genovese’s killer, Winston Moseley, was initially detained by members of the public – ironically, given how the Genovese case inspired research into bystander apathy, these bystanders chose to act.

    Kassin’s perspective on all this is that he has spent years studying the psychology of false confessions, including the surprising number of people who make them, as shown for example by the high proportion of people exonerated by new DNA evidence whose past confessions turn out to have been false. His research has also shown the power of false confessions to sway jurors and witnesses (for instance, on hearing a false confession, witnesses for the defence often lose faith in their own testimony).

    This ties into the murder of Kitty Genovese because it seems highly likely that her killer, Winston Moseley, was also responsible for the murder of 15-year-old Barbara Kralik a year earlier, a crime for which high-school drop-out Alvin Mitchell was already on trial.

    Mitchell had confessed to Kralik’s murder – so he must have done it, right? Well, his confession came following more than 50 hours of interrogation and he soon recanted it. His first trial ended in a hung jury (11 votes for acquittal, 1 for conviction). However, the power of a confession, even one that’s retracted, does not fade easily. On retrial, Mitchell was found guilty and served 12 years, 8 months in prison. He insisted on his innocence throughout his prison stay and does so today.

    Kassin makes a highly persuasive case for Mitchell being innocent of Kralik’s murder and the case being an exemplar of the power of false confessions (if you can get access, it’s worth reading Kassin’s entire article to appreciate the full detail of the seemingly flawed case against Mitchell).

    Kassin believes Moseley is the true killer of Kralik. Relevant here is that after his arrest for killing Genovese, Mosely also confessed to two more murders. He said he had killed 24-year-old Annie Mae Johnson one month earlier (this confession was corroborated in dramatic fashion after his account of the murder matched the wounds to Johnson’s body), and he said he had killed Kralik. Crucially, Moseley confessed with the same certainty and detail to both these additional murders while he steadfastly denied being responsible for another double-murder that was unsolved at the time time. Mosely repeated his confession to Kralik’s murder in Michell’s first trial. However, for some reason, he refused to provide the same testimony in the re-trial.

    In 2014, Kassin travelled to rural Vermont to meet Michell, now in his 70s. Mitchell recalled how he was threatened and intimidated during the police interrogations. “I would have confessed to killing the president because them people had scared me to death,” he said.

    “There are lessons to be learned from this part of the [Kitty Genovese] story,” writes Kassin. “The scientific study of police interrogations and confessions is well grounded in basic psychology … Collectively, this research has shown that innocent people can be induced to confess crimes they did not commit, that judges and juries have difficulty assessing confessions as a matter of common sense, and that reforms are needed to mitigate both sets of problems.”

    What of the public bystanders who detained Moseley? This, says Kassin, is the “irony that slipped through the cracks”. Five days after he killed Genovese, Mosely was attempting to burgle a home in New York in broad daylight. A neighbour confronted him and disbelieving his excuse (Mosely said he was helping the owners move house) he incapacitated Moseley’s van and alerted another neighbour. This second neighbour called the police and Moseley was soon apprehended by officers nearby; within hours he had confessed to a string of burglaries and three murders, writes Kassin.

    “Somehow this part of the Genovese story went unnoticed and without fanfare,” says Kassin. “In a most fitting, if not ironic, conclusion to Moseley’s crime spree, the perpetrator whose actions spawned the narrative of the non responsive urban bystander was capture precisely because of the intervention of urban bystanders!”

    The Killing of Kitty Genovese: What Else Does This Case Tell Us?

    Image: This photograph of Kitty Genovese was used in newspaper reports at the time of her death, and Kassin notes that it is actually the mug shot taken of Genovese from when she had been arrested for a minor gambling offence. In a strange coincidence, the lawyer who represented Genovese for that offence, Sidney Sparrow, went on to be Winston Moseley’s assigned counsel.

    Christian Jarrett (@Psych_Writer) is Editor of BPS Research Digest


    in The British Psychological Society - Research Digest on June 22, 2017 08:27 AM.

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    Battling antimicrobial resistance at ASM Microbe 2017

    ASM Microbe 2017 kicked off with an exciting opening session featuring Julie Theriot, Lalita Ramakrishnan, and ASM Microbe Lecturer, Nick Lane, who were engaging and thought-provoking! It was a great chance to learn more about how the physical and the mechanical properties of bacteria can impact their behaviour (link), about how the zebrafish model can be used to study tuberculosis pathogenesis (link) and about the distinctions between the three domains of life: bacteria, archaea and eukaryotes, from a bioenergetics basis (link).

    AMR, AMR… oh and AMR

    The single most central theme on ASM Microbe 2017 was antimicrobial resistance (AMR) – and rightly so. This was evident first from the address by ASM President Susan Sharp, who spoke about the urgency for a global “one health” solution on AMR. She discussed her representation of ASM at the 2016 United Nations General Assembly focused on AMR, where world leaders expressed concerns ranging from the basic needs of clean water and sanitation, access to effective antibiotics in lower income nations, to overutilization and misutilization of antibiotics in developed countries. ASM has established a multi-stakeholder initiative convening key experts to share and analyse the current status of AMR. We look forward to seeing how this unfolds in the medium term.

    However the address on AMR did not end there. A session with the theme “Global response to antimicrobial resistance: can humans win this war?” offered further insight into the dissemination and control of AMR. Teresa Coque from the Ramón y Cajal University Hospital gave a thorough talk on the environmental dimension of AMR. She spoke about antimicrobial use, the absence of official legislation, about how the farm can affect hospitals and about the factors that influence antibiotic effects. Michihico Goto from the University of Iowa presented a high level strategy on how to control transmission of AMR in humans. Naturally, the talk focused heavily on hand hygiene and environmental/hospital cleanliness and really made us wonder: “how clean is clean enough?”. Finally, we attended a fantastic talk on positive stewardship interventions to reverse AMR and hospital acquired infections (HAIs) by Ian Gould from the University of Aberdeen. His talk ended with him presenting an interesting re-make of the song ‘Knocking on Heavens Door’ by Bob Dylan. Jump to the end of this blog to read the lyrics!

    BMC Microbiology recognises the trend on AMR and plans to respond soon with a new special issue on a very relevant and important topic – stay tuned!

    A keynote address… out of this world!

    NASA astronaut and virologist Dr. Kate Rubins delivered an inspiring keynote address about her journey through space. Her story about how it all started never seizes to amaze:

    “I was procrastinating while applying for a grant when one of my friends found a federal government job posting for astronaut applications and encouraged me to apply for fun.”

    She ended up being selected by NASA in 2009 between 18,000 applications. She then participated on an intense three year training course, which involved survival training in water and land, flying a T-38 supersonic fighter jet trainer (!), as well as learning how to do a spacewalk. Dr. Rubins completed her first spaceflight on Expedition 48/49, where she became the first person to sequence DNA in space. She spent 115 days in space and conducted two spacewalks.

    NASA

    Her stories about her time sequencing DNA at the International Space Station in the absence of gravity, paired with her knowledge on real-time data analysis, the importance of microbial environments in orbit, and emerging technologies, was a fascinating look into the power of the microbial sciences.

    Dr. Rubins also spoke about the international nature of the team of astronauts and cosmonauts with which she spent countless hours training and working tirelessly as a unit, before and during their space trip. She sent a clear message against discrimination and she promoted unity, values that should rightly be elevated, especially in our times. It was very well received.

    You can find some photos of her time in space here.

    Great turnout at our Springer Nature exhibition booths!

    2017 marks the first year where Nature, BioMed Central and Springer joined forces in ASM Microbe and exhibited together as Springer Nature; and this was very well received! We were delighted to interact with authors from all over the world and across disciplines, with funders and with government officials.

    We wish we had brought more copies of BMC Microbiology’s latest review by Section Editor Prof. Raffaele Zarrilli and Associate Editor Dr. Asad Khan on the New Delhi Metallo-β-lactamase and of Microbiome’s article by Section Editor Prof. Marco Ventura and Associate Editors Dr. Christian Milani and Dr. Francesca Turroni on the ancient bacteria of the Ötzi’s microbiome.

    We were excited to experience first-hand the impact that Open Access is having on the publishing industry. BMC Microbiology strives to fulfil BioMed Central’s values by being open and inclusive and it motivates us to see that the research community is endorsing our efforts.

    The Springer Nature team and BMC Microbiology can’t wait for ASM Microbe 2018 in Atlanta!

     

    ‘Knocking on the pharmacist’s door’

    Nebot and Lawes (21/01/2016), presented by Ian Gould at ASM Microbe 2017.

     

    “Mama, take the old cephalosporins off me

    ‘Cause I can’t use them anymore

    There’s ESBL in every pee

    Colonizing every corridor

     

    Knock, knock, knocking on the pharmacist’s door

    Knocking on the microbiologist’s door

    Knocking the infectious disease specialist’s door

    Infection prevention and control team door

     

    Mama, put the quinolones in the ground

    ‘Cause they’re not useful anymore

    SAPG is coming down

    Lock the carbapenems in the store

     

    Mama, take clindamycin off me

    And take the co-amoxiclav too

    ‘Cause there is C diff everywhere I see

    And MRSA is nothing new

     

    Mama, put the macrolides in the ground

    It’s a viral illness anyway

    You know your judgement is really sound

    So send you patients on their way

     

    Mama, take ciprofloxacin off of me

    ‘Cause it is always over-kill

    Not much from GSK or Eli-Lilly

    If we can’t save them, then no-one will”

     

    Related blogs:

    Our human destiny in the post-antibiotic era

    Assessing real-time Zika risk in the United States

    Will my children survive antimicrobial resistance?

    Looking for the needle in a haystack – or how to find mycobacterial DNA in animal tissue samples

    The post Battling antimicrobial resistance at ASM Microbe 2017 appeared first on BMC Series blog.

    in BMC Series blog on June 22, 2017 06:00 AM.

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    US court grants Elsevier millions in damages from Sci-Hub

    Some doubt that the publishing giant will see any money from the pirate site.

    Nature News doi: 10.1038/nature.2017.22196

    in Nature News & Comment on June 22, 2017 12:00 AM.

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    Solar System survey casts doubt on mysterious 'Planet Nine'

    Orbits of four newfound objects show no signs of gravitational pull from proposed giant planet.

    Nature News doi: 10.1038/nature.2017.22177

    in Nature News & Comment on June 22, 2017 12:00 AM.

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    Air guns used in offshore oil exploration can kill tiny marine life

    Lethal effects from pulses of sound used to probe the sea floor can travel over a kilometre.

    Nature News doi: 10.1038/nature.2017.22167

    in Nature News & Comment on June 22, 2017 12:00 AM.

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    Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

    Heterochromatic DNA domains play important roles in regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway1–9. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and tri-methylation (H3K9me2 and H3K9me3, respectively) and heterochromatin formation10–17. H3K9me is in turn required for recruitment of RNAi to chromatin to promote sRNA amplification11,15,18. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast S. pombe homolog of mammalian SUV39H H3K9 methyltransferases, we designed active site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing (CTGS) at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defense.

    Nature doi: 10.1038/nature23267

    in Nature Biological Sciences Research on June 22, 2017 12:00 AM.

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    Bones make hormones that communicate with the brain and other organs

    Bones send out hormone signals that chat with other parts of the body, studies in mice show. What influence these hormones have in people, though, remain a mystery.

    in Science News on June 21, 2017 07:00 PM.

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    Protein in Parkinson’s provokes the immune system

    The immune system recognizes parts of a protein linked to Parkinson’s disease as foreign, triggering an autoimmune response.

    in Science News on June 21, 2017 05:25 PM.

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    12 years after researcher found guilty of misconduct, journal retracts paper

    In 2005, the U.S. Office of Research Integrity found an obesity researcher had engaged in scientific misconduct. More specifically, the ORI report revealed that Eric Poehlman, then based at the University of Vermont, had “falsified and fabricated” data in 10 papers. The 2005 report asked that the journals issue retractions or corrections to the papers. […]

    The post 12 years after researcher found guilty of misconduct, journal retracts paper appeared first on Retraction Watch.

    in Retraction watch on June 21, 2017 03:45 PM.

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    Child Health: Facing the future together

    Children and the Sustainable Development Goals

    Children are central to the 2030 Agenda for Sustainable Development. The 2030 agenda consists of 17 global goals with 169 targets between them which is measured by 230 specific indicators. 50 of these indicators are directly related to children. In 2015, child mortality for those aged under 5 was 5.9 million, which is almost 16,000 a day. It has been found that 83% of these deaths were due to infectious, neonatal, and nutritional conditions. China has seen a decline in under-5 mortality rate in the past 3 decades and it is one of the few countries to have achieved Millennium Development Goals (MDG) 4 (reduce child mortality) and 5 (improve maternal health). Certain provinces in China have also been reported to have achieved this decrease in under-5 mortality rates twice as fast as the MDG 4 target rate. It has been reported that Chinese children’s health status has improved remarkably and the rate of infant mortality and under-five mortality continue to decline.

    Image by Flickr user Micah Sittig (CC BY 2.0)

    However, large disparities have also been found across the region. Although some provinces rivals the best results in the world with relation to under-5 mortality, the reality is very different in other provinces. Preterm birth, low birth weight, birth asphyxia, childhood pneumonia, and diarrhoea are amongst the major threats to infants in some areas of China. Efforts are therefore needed to address this disparity and to close such gaps in subnational units seen within China.

    Nutrition

    A healthy diet and adequate nutrition is necessary to ensure optimum growth and development of children. About one third of child deaths worldwide are linked to malnutrition. This is a major health problem seen in China as well. Climate change also poses a new challenge in the control of undernutrition in this region, a matter which is already a concern particularly in poor rural areas.

    Chronic nutritional deficiency during the first 1,000 days of a child’s life can result in stunting where the damage caused to the child’s development is irreversible. It is estimated that in China, 12.7 million children are stunted, which is equivalent to the population size of Tokyo. A national survey carried out in China in 2013 showed that 8.1%, 2.4% and 1.9% of children under 5 years of age were stunted, underweight, and wasted, respectively. Results from a community based cross-sectional survey carried out by Jiang and colleagues in 84 villages in mid-western provinces of China in 2010 showed that malnutrition is a major public health problem among children and the prevalence of stunting and severe stunting was 27.0% and 13.2%, respectively. Location has been found to have a large impact on nutritional status in China. The risk of underweight and stunting is 3-4 times higher for children in rural areas than for those in cities.

    Over the years improvements in these figures emerging from China can be seen. The level of undernourishment in the country was reduced from 23.9% in 1990 – 1992 to 9.3% in 2014 – 2016. Mortality in children under the age of 5 due to malnutrition also dropped from 22% to 13% between 2000 and 2010. Although the data illustrates that progress has been made resulting in a decline in stunting, underweight and wasting amongst children, the prevalence of undernutrition remains high for children under 5 in rural areas.

     

    Air pollution

    © wusuowei / Fotolia

    China is the world’s largest greenhouse-gas emitter. It has been reported that the peak in China’s emissions of such gases could come by 2025, if not sooner. At the United Nations climate summit which took place in 2015, China committed to halting the growth in its greenhouse gas emissions by 2030 where the new plans call for a reduction of 18% in carbon dioxide emission and a 15% decrease in energy consumption. Children are particularly vulnerable to the effects of air pollution. China has seen an increase of childhood asthma and there are studies emerging which demonstrate a positive correlation between high levels of outdoor pollution with children’s respiratory symptoms.

     

    It is evident that the world cannot reach a number of the SDG targets in the 2030 agenda unless the specific needs of children are monitored and addressed. Although improvements and progress have been seen in certain circumstances, there is still more that needs to be done to ensure that children are provided with the necessary to live healthy lives and achieve their full potential. More needs to be done to ensure that no child is left behind.

    © Syda Productions / Fotolia

    If you are interested in reading more on this topic, please visit the BMC Pediatrics website. The journal welcomes submissions on all aspects of child health including neonates, children and adolescents, as well as related molecular genetics, pathophysiology, and epidemiology studies. Related papers can be submitted to the journal here.

    The post Child Health: Facing the future together appeared first on BMC Series blog.

    in BMC Series blog on June 21, 2017 02:50 PM.

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    Journal alerts readers to “technical criticism” of CRISPR study

    A Nature journal has posted a editor’s note to a recent letter on potential unintended consequences of CRISPR gene editing, after an executive at a company trying to commercialize the technology said the paper should be retracted. The original article, published on May 30 as a correspondence in Nature Methods, suggested that using CRISPR in mice […]

    The post Journal alerts readers to “technical criticism” of CRISPR study appeared first on Retraction Watch.

    in Retraction watch on June 21, 2017 02:05 PM.

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    SDG Resource Centre sheds light on sustainable development

    Interactive platform features multimedia content and research by scientific, legal and business experts

    in Elsevier Connect on June 21, 2017 01:26 PM.

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    Six ways Elsevier supports sustainability

    Two years after the UN ratified its Sustainable Development Goals, we share some exciting projects we are working on

    in Elsevier Connect on June 21, 2017 01:26 PM.

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    A baby’s DNA may kick off mom’s preeclampsia

    A large genetic analysis points to a protein made by the fetus that may trigger preeclampsia in the mom.

    in Science News on June 21, 2017 11:00 AM.

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    Time as it could be measured in artificial living systems

    Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the presented paper, we consider the most minimal abstract pure clocks and investigate their characteristics with respect to their ability to measure time. Amongst others we find fundamentally diametral clock characteristics, such as oscillatory behaviour for local time measurement or decay-based clocks measuring time periods in scales global to the problem. We also include cascades of independent clocks ("clock bags") and composite clocks with controlled dependency; the latter show various regimes of markedly different dynamics.

    Date: 23/06/2017
    Time: 16:00
    Location: LB252

    in UH Biocomputation group on June 21, 2017 10:39 AM.

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    Reviewer 2 is not your nemesis – how to revise and resubmit

    This is a blog piece is written with Sue Fletcher-Watson, a colleague of supreme wisdom and tact, ideally qualified for this particular post. It is a follow-up to our previous joint post about peer-review. We now turn our attention to the response to reviewers.

    16198_10155276140165640_8482032632772318289_n

    As with the role of reviewer, junior scientists submitting their work as authors are given little (if any) guidance on how to interact with their reviewers. Interactions with reviewers are an incredibly valuable opportunity to improve your manuscript and find the best way of presenting your science. However, all too often responding to reviewers is seen as an onerous chore, which partly reflects the attitude we take into the process. These exchanges largely happen in private and even though they play a critical role in academia, we rarely talk about them in public. We think this needs to change – here are some pointers for how to interact with your reviewers.

    • Engage with the spirit of the review

    Your reviewers will be representative of a portion of your intended readership. Sometimes when reading reviewers’ comments we can find ourselves asking “have they even read the paper?!”. But if the reviewer has misunderstood some critical aspect of the paper then it is entirely possible that a proportion of the broader readership will also. An apparently misguided review, whilst admittedly frustrating, should be taken as a warning sign. Give yourself a day or two to settle your temper, and then recognise that this is your opportunity to make your argument clearer and more convincing.

    Similarly, resist the temptation to undertake the minimal possible revisions in order to get your paper past the reviewers. If a reviewer makes a good point and you can think of ways of using your data to address it, then go for it, even if this goes beyond what they specified. Remember – this is your last chance to make this manuscript as good as it can be.

    • Be grateful and respectful. But don’t be afraid to disagree with your reviewers.

    Writing a good review takes time. Thank the reviewers for their efforts. Be polite and respectful, even if you think a review is not particularly constructive. But don’t be afraid to disagree with reviewers. Sometimes reviewers ask you to do things that you don’t think are valid or wise, and it’s important to defend your work. No one wants a dog’s dinner of a paper… a sort of patchwork of awkwardly combined paragraphs designed to appease various reviewer comments. As the author you need to retain ownership of the work. This will mean that sometimes you need to explain why a recommendation has not been actioned. You can acknowledge the importance of a reviewer’s point, without including it in your manuscript.

    We have both experienced reviewers who have requested changes we don’t feel are legitimate. Examples include the reviewer who requested a correlational analysis on a sub-group with a sample size of n=17. Or the reviewer who asked Sue to describe how her results, from a study with participants aged 18 and over, might relate to early signs of autism in infancy (answer: they have no bearing whatsoever and I’m not prepared to speculate in print). Or the reviewer who asked for inclusion of variables in a regression analysis which did not correlate with the outcome, (despite that being a clearly-stated criterion for inclusion in the analysis), on the basis of their personal hunch. In these cases, politely but firmly refusing to make a change may be the right thing to do, though you can nearly always provide some form of concession. For example, in the last case, you might include an extra justification, with a supporting citation, for your chosen regression method.

    • Give your response a clear and transparent structure

    With any luck, your revised manuscript will go out to the same people who reviewed it the first time.  If you do a particularly good job of addressing their comments – and if the original comments themselves were largely minor – your editor may even decide your manuscript doesn’t need peer review a second time. In any case, to maximise the chances of a good result it is essential that you present your response clearly, concisely and fluently.

    Start by copying and pasting the reviewer comments into a document.  Organise them into numbered lists, one for each reviewer.  This might mean breaking down multi-part comments into separate items, and you may also wish to paraphrase to make your response a bit more succinct.  However, beware of changing the reviewer’s intended meaning!

    Then provide your responses under each numbered point, addressed to the editor (“The reviewer makes an excellent point and…”). In each case, try to: acknowledge the validity of what the reviewer is saying; briefly mention how you have addressed the point; give a page reference.  This ‘response to reviewers’ document should be accompanied by an updated manuscript in which any significant areas of new text , or heavily edited text, are highlighted something like this. Don’t submit a revised manuscript with tracked changes – these are too detailed and messy for a reviewer to have to navigate – and don’t feel the need to highlight every changed word.

    If it’s an especially complicated or lengthy response, then it is sometimes a good idea to include a (very) pithy summary up top for the Editor, before you get to the reviewer-specific response. A handful of bullet points can help orient the Editor to the major changes that they can expect to find in the new version of your manuscript.

    • The response letter can be a great place to include additional analyses that didn’t make it into the paper

    Often when exploring the impact of various design choices or testing the impact of assumptions on your analysis, additional comparisons can be very useful. We both often include additional analyses in our ‘response to reviewer’ letters. This aids transparency and can also be a useful way of showing reviewers that your findings are solid. Sometimes these will be analyses that have been explicitly asked for, but on other occasions you may well want to do this from your initiative. As reviewers we are both greatly impressed when authors use their own data to address a point, even if we didn’t explicitly ask them to do this.

    One word of warning here, however. Remember that you don’t want to put an important piece of information or line of reasoning only in your response letter, if it ought also to be in the final manuscript. If you’ve completed an extra analysis as part of your consideration of a reviewer point, consider whether this might also have relevance to your readership when the paper is published.  It might be important to leave it out – you don’t want to include ‘red herring’ analyses or look like you are scraping the statistical barrel by testing ‘til the cows come home. But on the other hand, if the analysis directly answers a question which is likely to be in your reader’s mind, consider including it.  This could be as a supplement, linked online data set, or a simple statement: e.g. “we repeated all analyses excluding n=2 participants with epilepsy and results were the same”.

    • Sometimes you may need the nuclear option

    We have both had experiences where we have been forced to make direct contact with the Action Editor. A caveat to all the points above is that there are occasions where reviewers attempt to block the publication of a manuscript unreasonably. Duncan had an experience of a reviewer who simply cut and paste their original review, and reused it across multiple subsequent rounds of revision. Duncan thought that his team had done a good job of addressing the reviewer’s concerns, where possible, but without any specific guidance from the reviewer they were at a loss to identify what they should do next. Having already satisfied two other reviewers, he decided to contact the Action Editor and explain the situation. They accepted the paper. Sue has blogged before about a paper reporting on a small RCT which was rejected for the simple reason that it reported a null result. She approached the Editor with her concern and it was agreed that the paper should be re-submitted as a new manuscript and sent out again for a fresh set of reviews. This shouldn’t be necessary, but sadly sometimes it is.

    Editors will not be happy with authors trying to circumvent the proper review process, but in our experience they are sympathetic to authors when papers are blocked by unreasonable reviewers. After all, we have all been there. If this is the situation you find yourself in, be as diplomatic as possible and outline your concerns to the Editor.

    In conclusion, much of what we want to say can probably be summed up with the following: This is not a tick-box exercise, but the last opportunity to improve your paper before it reaches your audience. Engage with your reviewers, be open-minded, and don’t be afraid to rethink.

    Really, when it comes to responding to reviewers, the clue is in the name.  It’s a response, not a reaction – so be thoughtful, be engaged and be a good scientist.


    in Forging Connections on June 21, 2017 07:00 AM.

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    Modified viruses deliver death to antibiotic-resistant bacteria

    Engineered microbes turn a bacterium's immune response against itself using CRISPR.

    Nature News doi: 10.1038/nature.2017.22173

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Protect funding for US earthquake early-warning system

    Donald Trump’s proposed cuts to ShakeAlert puts the west coast at risk.

    Nature 546 451 doi: 10.1038/nature.2017.22162

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Track batteries degrading in real time

    Monitor deforming electrodes to speed development of renewable-energy storage, write Liqiang Mai, Mengyu Yan and Yunlong Zhao.

    Nature 546 469 doi: 10.1038/546469a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    The fight to save thousands of lives with sea-floor sensors

    Geophysicists are ramping up their efforts to monitor major undersea faults for movement, and search for signs of the next catastrophic quake.

    Nature 546 466 doi: 10.1038/546466a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    China’s genomics giant to make stock-market debut

    Once the world's biggest DNA sequencer for research, BGI is now looking to medical applications to boost profits.

    Nature 546 461 doi: 10.1038/546461

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    New journal blacklist, palm-oil ban and the world’s top supercomputers

    The week in science: 16–22 June 2017.

    Nature 546 456 doi: 10.1038/546456a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Immunology: The patterns of T-cell target recognition

    The binding of T-cell receptors to peptide molecules not normally present in the body can trigger an immune response. Predicting which peptide a T-cell receptor will bind to — a difficult feat — has now been achieved.

    Nature doi: 10.1038/nature23091

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Immunology: Gut sensor halts viral attack

    Intestinal infection with rotavirus is a major cause of diarrhoea in infants, and can be fatal. The identification of immune sensor proteins that detect and restrict this viral infection now illuminates the body's defence system.

    Nature doi: 10.1038/nature23090

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Molecular biology: A liquid reservoir for silent chromatin

    The protein HP1 mediates compaction of DNA into a repressive structure called heterochromatin. Analysis reveals that HP1 has liquid-like properties, offering a fresh perspective on genome organization.

    Nature doi: 10.1038/nature23089

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Infectious diseases: Predictions of virus spillover across species

    Most human infectious diseases are initially transmitted from animals. An analysis of all known mammalian viruses improves our understanding of such cross-species spillover, with potential benefits for public health.

    Nature doi: 10.1038/nature23088

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Phase separation drives heterochromatin domain formation

    Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

    Nature doi: 10.1038/nature22989

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Identifying specificity groups in the T cell receptor repertoire

    T cell receptor (TCR) sequences are very diverse, with many more possible sequence combinations than T cells in any one individual. Here we define the minimal requirements for TCR antigen specificity, through an analysis of TCR sequences using a panel of peptide and major histocompatibility complex (pMHC)-tetramer-sorted cells and structural data. From this analysis we developed an algorithm that we term GLIPH (grouping of lymphocyte interactions by paratope hotspots) to cluster TCRs with a high probability of sharing specificity owing to both conserved motifs and global similarity of complementarity-determining region 3 (CDR3) sequences. We show that GLIPH can reliably group TCRs of common specificity from different donors, and that conserved CDR3 motifs help to define the TCR clusters that are often contact points with the antigenic peptides. As an independent validation, we analysed 5,711 TCRβ chain sequences from reactive CD4 T cells from 22 individuals with latent Mycobacterium tuberculosis infection. We found 141 TCR specificity groups, including 16 distinct groups containing TCRs from multiple individuals. These TCR groups typically shared HLA alleles, allowing prediction of the likely HLA restriction, and a large number of M. tuberculosis T cell epitopes enabled us to identify pMHC ligands for all five of the groups tested. Mutagenesis and de novo TCR design confirmed that the GLIPH-identified motifs were critical and sufficient for shared-antigen recognition. Thus the GLIPH algorithm can analyse large numbers of TCR sequences and define TCR specificity groups shared by TCRs and individuals, which should greatly accelerate the analysis of T cell responses and expedite the identification of specific ligands.

    Nature doi: 10.1038/nature22976

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Host and viral traits predict zoonotic spillover from mammals

    The majority of human emerging infectious diseases are zoonotic, with viruses that originate in wild mammals of particular concern (for example, HIV, Ebola and SARS). Understanding patterns of viral diversity in wildlife and determinants of successful cross-species transmission, or spillover, are therefore key goals for pandemic surveillance programs. However, few analytical tools exist to identify which host species are likely to harbour the next human virus, or which viruses can cross species boundaries. Here we conduct a comprehensive analysis of mammalian host–virus relationships and show that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable. After controlling for research effort, the proportion of zoonotic viruses per species is predicted by phylogenetic relatedness to humans, host taxonomy and human population within a species range—which may reflect human–wildlife contact. We demonstrate that bats harbour a significantly higher proportion of zoonotic viruses than all other mammalian orders. We also identify the taxa and geographic regions with the largest estimated number of ‘missing viruses’ and ‘missing zoonoses’ and therefore of highest value for future surveillance. We then show that phylogenetic host breadth and other viral traits are significant predictors of zoonotic potential, providing a novel framework to assess if a newly discovered mammalian virus could infect people.

    Nature doi: 10.1038/nature22975

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Crystal structure of the potassium-importing KdpFABC membrane complex

    Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cell shape and turgor under conditions in which potassium is limiting. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. Although there is considerable structural and functional information about members of both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA and a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. On the basis of these observations, we propose a mechanism that repurposes protein channel architecture for active transport across biomembranes.

    Nature doi: 10.1038/nature22970

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells

    Rotavirus, a leading cause of severe gastroenteritis and diarrhoea in young children, accounts for around 215,000 deaths annually worldwide. Rotavirus specifically infects the intestinal epithelial cells in the host small intestine and has evolved strategies to antagonize interferon and NF-κB signalling, raising the question as to whether other host factors participate in antiviral responses in intestinal mucosa. The mechanism by which enteric viruses are sensed and restricted in vivo, especially by NOD-like receptor (NLR) inflammasomes, is largely unknown. Here we uncover and mechanistically characterize the NLR Nlrp9b that is specifically expressed in intestinal epithelial cells and restricts rotavirus infection. Our data show that, via RNA helicase Dhx9, Nlrp9b recognizes short double-stranded RNA stretches and forms inflammasome complexes with the adaptor proteins Asc and caspase-1 to promote the maturation of interleukin (Il)-18 and gasdermin D (Gsdmd)-induced pyroptosis. Conditional depletion of Nlrp9b or other inflammasome components in the intestine in vivo resulted in enhanced susceptibility of mice to rotavirus replication. Our study highlights an important innate immune signalling pathway that functions in intestinal epithelial cells and may present useful targets in the modulation of host defences against viral pathogens.

    Nature doi: 10.1038/nature22967

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

    Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.

    Nature doi: 10.1038/nature22822

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    T cells from patients with Parkinson’s disease recognize α-synuclein peptides

    Genetic studies have shown the association of Parkinson’s disease with alleles of the major histocompatibility complex. Here we show that a defined set of peptides that are derived from α-synuclein, a protein aggregated in Parkinson’s disease, act as antigenic epitopes displayed by these alleles and drive helper and cytotoxic T cell responses in patients with Parkinson’s disease. These responses may explain the association of Parkinson’s disease with specific major histocompatibility complex alleles.

    Nature doi: 10.1038/nature22815

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase

    Ribosomes have the capacity to selectively control translation through changes in their composition that enable recognition of specific RNA elements. However, beyond differential subunit expression during development, evidence for regulated ribosome specification within individual cells has remained elusive. Here we report that a poxvirus kinase phosphorylates serine/threonine residues in the human small ribosomal subunit protein, receptor for activated C kinase (RACK1), that are not phosphorylated in uninfected cells or cells infected by other viruses. These modified residues cluster in an extended loop in RACK1, phosphorylation of which selects for translation of viral or reporter mRNAs with 5′ untranslated regions that contain adenosine repeats, so-called polyA-leaders. Structural and phylogenetic analyses revealed that although RACK1 is highly conserved, this loop is variable and contains negatively charged amino acids in plants, in which these leaders act as translational enhancers. Phosphomimetics and inter-species chimaeras have shown that negative charge in the RACK1 loop dictates ribosome selectivity towards viral RNAs. By converting human RACK1 to a charged, plant-like state, poxviruses remodel host ribosomes so that adenosine repeats erroneously generated by slippage of the viral RNA polymerase confer a translational advantage. Our findings provide insight into ribosome customization through trans-kingdom mimicry and the mechanics of species-specific leader activity that underlie poxvirus polyA-leaders.

    Nature doi: 10.1038/nature22814

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Quantifiable predictive features define epitope-specific T cell receptor repertoires

    T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαβ sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse ‘outlier’ sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.

    Nature doi: 10.1038/nature22383

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Zanos et al. reply

    Nature 546 E4 doi: 10.1038/nature22085

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Effects of a ketamine metabolite on synaptic NMDAR function

    Nature 546 E1 doi: 10.1038/nature22084

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Memories to come

    Is this the real life?

    Nature 546 570 doi: 10.1038/546570a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Genomics: The feline line

    Nature 546 480 doi: 10.1038/546480a

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    50 & 100 Years Ago

    Nature 546 478 doi: 10.1038/546478a

    in Nature Biological Sciences Research on June 21, 2017 12:00 AM.

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    Ecology: Document India's floral biodiversity

    Nature 546 474 doi: 10.1038/546474d

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Counterfeit drugs: Fight fake reagents with digital tools

    Nature 546 474 doi: 10.1038/546474c

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Philosophy: Religion's openness towards science

    Nature 546 474 doi: 10.1038/546474b

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Consent: Data-sharing for indigenous peoples

    Nature 546 474 doi: 10.1038/546474a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Botany: He made plants a profession

    Jim Endersby revisits the legacy of trailblazing botanist Joseph Dalton Hooker.

    Nature 546 472 doi: 10.1038/546472a

    in Nature News & Comment on June 21, 2017 12:00 AM.

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    Here’s why your wheelie suitcase wobbles

    Physicists explain why roller suitcases rock back and forth as you dash through the terminal.

    in Science News on June 20, 2017 11:05 PM.

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    Satellite trio will hunt gravitational waves from space

    The European Space Agency has green-lighted the Laser Interferometer Space Antenna, expected to launch in 2034.

    in Science News on June 20, 2017 08:58 PM.

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    New material could filter water contaminants that others miss

    A new polymer offers a better way to pull fluorine-containing pollutants out of drinking water.

    in Science News on June 20, 2017 08:23 PM.

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    5 Reasons It’s So Hard To Think Like A Scientist

    Maria Goeppert MayerBy Christian Jarrett

    Thinking like a scientist is really hard, even for scientists. It requires putting aside your own prior beliefs, evaluating the quality and meaning of the evidence before you, and weighing it in the context of earlier findings. But parking your own agenda and staying objective is not the human way.

    Consider that even though scientific evidence overwhelming supports the theory of evolution, a third of Americans think the theory is “absolutely false”. Similarly, the overwhelming scientific consensus is that human activity has contributed to climate change, yet around a third of Americans doubt it.

    We Brits are just as blinkered. In a recent survey, over 96 per cent of teachers here said they believed pupils learn better when taught via their preferred learning style, even though scientific support for the concept is virtually non-existent. Why is it so hard to think like a scientist? In a new chapter in the Psychology of Learning and Motivation book series, Priti Shah at the University of Michigan and her colleagues have taken a detailed look at the reasons, and here we pull out five key insights:

    We’re swayed by anecdotes
    When making everyday decisions, such as whether to begin a new treatment or sign up to a particular class at uni, most of us are influenced more powerfully by personal testimony from a single person than by impersonal ratings or outcomes averaged across many people. This is the power of anecdote to dull our critical faculties. In a study published last year Fernando Rodriguez and his colleagues asked dozens of students to evaluate scientific news reports that drew inappropriate conclusions from weak evidence. Some of the reports opened with an anecdote supporting the inappropriate conclusion, other reports lacked an anecdote and acted as a control condition. Regardless of their level of university training or knowledge of scientific concepts, the students were less competent at critically evaluating the reports when they opened with an anecdote. “Anecdotal stories can undermine our ability to make scientifically driven judgements in real-world contexts,” the researchers said. Of course much health and science news in the mainstream media is delivered via anecdotes, increasing the likelihood that news consumers will swallow any claims whole.

    We’re overconfident
    Confronted with a scientific claim, another reason many of us find it hard to reflect on it scientifically is that we overestimate our comprehension of the science. A study from 2003 asked hundreds of university students to read several science news stories, to interpret them and rate their understanding. The students made many interpretative errors – for example, confusing correlation for causation – even though they thought they had a good understanding. This is redolent of a survey from the 1980s of thousands of British and American citizens: nearly 60 per cent stated they were moderately or very well-informed about new science findings and yet far fewer were able to answer easy questions about elementary science. Part of the problem seems to be that we infer our understanding of scientific text based on how well we have comprehended the language used. This means that popular science stories written in layman’s language can contribute to false confidence. This “fluency bias” can also apply to science lectures: a recent study found that students overestimated the knowledge they’d derived from a science lecture when it was delivered by an engaging speaker.

    We’re biased by our prior beliefs
    This obstacle to scientific objectivity was demonstrated by a now-classic study from the 1970s in which participants were asked to evaluate scientific research that either supported or conflicted with their prior beliefs. For instance, one of the to-be-evaluated studies supposedly showed that murder rates tended to be lower in US states with the death penalty. Participants demonstrated an obvious bias in their evaluations. For example, if they supported capital punishment, they tended to evaluate the death penalty study favourably, whereas if they were against capital punishment, they were more likely to see the studies’ flaws. Scientific skills offer little protection against this bias, in fact they can compound it. A 2013 study asked participants to evaluate a piece of research on gun control. Participants with greater numeracy skills were especially biased: if the findings supported their existing beliefs, they were generous in their evaluation, but if the findings went against their beliefs, they used their skills to (in the words of Shah et al) “slam” the findings – a phenomenon dubbed “identity-protective cognition”.

    We’re seduced by graphs, formulas and meaningless neuroscience
    It doesn’t take a lot to dazzle the average newspaper or magazine reader using the superficial props of science, be that formulas, graphics or jargon. Consider a study due for publication soon (Ibrahim et al, cited in the new chapter): researchers asked their participants to consider a news story about a correlational study into genetically modified foods that was either consistent with the bulk of past research showing that they are safe, or was inconsistent, suggesting that they are harmful. Additionally, the story was either accompanied or not by a scatterplot of the new findings. When the news story had a graphic visualisation of the correlational evidence, which was inconsistent with the weight of past research (i.e. it implied a possibility of harm), participants were far more likely to interpret the new evidence as showing genetically modified foods cause harm, than if they had read the same story without a graphic. “This is especially worrisome,” write Shah et al, “since it demonstrates how easily people can be convinced by new data, regardless of the actual scientific merit of the result.” Similar research into readers’ critical skills has shown that they are blinded in a comparable manner by gratuitous neuroscience jargon and meaningless formulas.

    Being smart isn’t enough
    Even expert researchers suffer from the human foibles that undermine scientific thinking. Their critical faculties are contaminated by their agenda, by their ultimate motives for doing their experiments. This is why the open science revolution occurring in psychology is so important: when researchers make their methods and hypotheses transparent, and they pre-register their studies, it makes it less likely that they will be diverted, even corrupted by, confirmation bias (seeking out evidence to support their existing beliefs).

    Take the example of systematic views in psychotherapy research: a recent analysis found that the conclusions of many are spun in a way that supports the researchers’ own biases. Other times, the whole scientific publishing community, from journals editors down to science journalists, seem to switch off their critical faculties because they happen to agree with the message to emerge from a piece of research.

    In their chapter, Shah and her colleagues point out that raw cognitive ability (IQ) is not a good predictor of a person’s ability to think like a scientist. More relevant is mental attitude, such as a person’s “need for cognition” and their ability or motivation to override gut instinct and reflect deeply. On a positive note, these mental dispositions may be more malleable, that is more trainable, than basic intelligence. But we’ll need plenty of solid evidence to test that.

    What Makes Everyday Scientific Reasoning So Challenging?

    Image: Dr. Maria Goeppert Mayer of the University of California was named a co-winner of the 1963 Nobel Prize for Physics (Getty Images).

    Christian Jarrett (@Psych_Writer) is Editor of BPS Research Digest


    in The British Psychological Society - Research Digest on June 20, 2017 03:56 PM.

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    German institute sanctions director after finding him guilty of misconduct

    The executive board of the Leibniz Association in Germany has reprimanded the director of its institute on aging for “grossly negligent scientific misconduct.” Besides a written reprimand, the executive board has removed Karl Lenhard Rudolph’s “passive voting rights” in association committees, and excluded the institute under his leadership from receiving funds from a multi-million Euro internal […]

    The post German institute sanctions director after finding him guilty of misconduct appeared first on Retraction Watch.

    in Retraction watch on June 20, 2017 03:39 PM.

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    Big corrections usually weaken findings. But a recent NEJM one strengthened them, author says

    A 2016 study in New England Journal of Medicine has received a substantial correction, which affected several aspects of the article. Typically, an error that affects so much of a paper would undermine the results (and possibly lead to a retraction). But in this case, the revised dose calculations actually strengthened the findings, according to […]

    The post Big corrections usually weaken findings. But a recent NEJM one strengthened them, author says appeared first on Retraction Watch.

    in Retraction watch on June 20, 2017 01:55 PM.