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    Ring ripples reveal how long a day lasts on Saturn

    Clues in Saturn’s rings divulge the planet’s rotation rate: 10 hours, 33 minutes, 38 seconds.

    in Science News on January 22, 2019 09:59 PM.

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    Microcircuits and their interactions in epilepsy: is the focus out of focus?

    Julia Goncharenko's journal club session, where she will present the paper "Microcircuits and their interactions in epilepsy, is the focus out of focus? (Jeanne Paz and John Huguenard, 2015)".


    Epileptic seizures represent dysfunctional neural networks dominated by excessive and/or hypersynchronous activity. Recent progress in the field has outlined two concepts regarding mechanisms of seizure generation, or ictogenesis. First, all seizures, even those associated with what have historically been thought of as ‘primary generalized’ epilepsies, appear to originate in local microcircuits and then propagate from that initial ictogenic zone. Second, seizures propagate through cerebral networks and engage microcircuits in distal nodes, a process that can be weakened or even interrupted by suppressing activity in such nodes. We describe various microcircuit motifs, with a special emphasis on one that has been broadly implicated in several epilepsies: feed-forward inhibition. Furthermore, we discuss how, in the dynamic network in which seizures propagate, focusing on circuit ‘choke points’ remote from the initiation site might be as important as that of the initial dysfunction, the seizure ‘focus’.

    Date: 25/01/2019
    Time: 16:00
    Location: LB250

    in UH Biocomputation group on January 22, 2019 09:18 PM.

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    Being messy on the inside keeps metamaterials from folding under stress

    Inspiration from disordered arrangements of atoms in crystalline metals may lead to longer-lasting, next-gen materials.

    in Science News on January 22, 2019 05:00 PM.

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    ‘Good to Go’ tackles the real science of sports recovery

    In ‘Good to Go,’ science writer Christie Aschwanden puts science — and herself — to the test for the sake of sports recovery.

    in Science News on January 22, 2019 01:00 PM.

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    Showdown over a study of abortion policy leads to a retraction, and leaves no one happy

    A paper in Contraception that purported to show serious flaws in an earlier study of abortion laws and maternal health has been retracted, after the authors of the original study found what were apparently significant flaws in the study doing the debunking. That’s the short version of this story. The longer version involves years of … Continue reading Showdown over a study of abortion policy leads to a retraction, and leaves no one happy

    in Retraction watch on January 22, 2019 11:00 AM.

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    Physicists aim to outdo the LHC with this wish list of particle colliders

    Proposed new accelerators could solve mysteries of the Higgs boson.

    in Science News on January 22, 2019 11:00 AM.

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    Your Perfect New Excuse For Ordering Unhealthy Food And Drink: “Altruistic Indulgence”

    GettyImages-593325418.jpgBy Christian Jarrett

    On the way to meet your friend at a cafe you’re confident about sticking to your resolutions for healthier living. It soon goes awry though – no, not because of your weak willpower, but due to your excess empathy.

    Your friend orders first and plumps for the super indulgent Winter Warmer Chocca Mocha with added marshmallows. You follow suit, sensing that if you’d stuck with your original plans for a skinny coffee, you’d have made your friend feel awful. There is now a name for this behaviour: You just engaged in “altruistic indulgence”, the most appealing of excuses for a naughty lapse, described for the first time in a paper in Social Influence.

    The researchers led by Youjae Yi at Seoul National University first conducted a field study at a university cafe. They obtained the till receipts for 649 transactions and looked to see whether customers had ordered a low-calorie or high-calorie coffee.

    Around half the lone customers ordered a healthy option and half opted for high calorie. Similarly, among the customers who were in a pair and who had ordered first, there was again roughly a 50/50 split in choosing healthy or unhealthy.

    In striking contrast, among customers who ordered second, their rate of ordering unhealthy leapt to 80 per cent if their companion had ordered a high-calorie drink (conversely, if the first-ordering companion plumped for a healthy drink, the rate of choosing healthy among those choosing second was only 60 per cent, which is statistically not a significant difference from the average rate of choosing healthy among lone customers or first-order customers).

    Put differently, when following a companion who made an unhealthy order, the average rate of choosing unhealthy among customers choosing second increased by 33 per cent; in contrast, when following a companion who made a healthy order, the average rate of choosing healthy among customers choosing second increased by just 8 per cent.

    “The modelling behaviour for unhealthy choices was much stronger than that for healthy choices,” the researchers said, adding that this result is consistent with their theory that if our companion orders an unhealthy option, we are often motivated to copy them so as to avoid making them feel bad.

    To test this idea further, Yi and his team conducted an online experiment in which they asked 174 women in the US to imagine meeting a friend or a rival at a burger bar and that their companion had ordered first and had chosen the more indulgent, higher-calorie burger of the two on offer. Next, the participants were asked to say which kind of burger meal they would order – the healthier or the more indulgent. The researchers reasoned that if altruistic indulgence is a real phenomenon then participants would be more likely to choose the unhealthy option if they were dining with a friend (based on the logic that you are more likely to feel altruistic concern for a friend than a rival).

    Participants asked to imagine dining with a friend were indeed more likely to follow their companion’s lead and opt for the high-calorie burger (51 per cent chose this option, compared with 29 per cent in the rival condition). Moreover, the researchers asked the participants about the motives influencing their choice – concern for their companion’s feelings or a desire to be liked and accepted.  In statistical terms, the higher rate of choosing the unhealthy burger in the friend scenario was entirely explained by the participants in this condition (compared with the rival condition) being more motivated by concern for their companion’s feelings, not by any greater desire to be liked or accepted.

    “Typically indulgence is regarded as an egoistic choice associated with short-term pleasure for the self and engaged via loss of self-control,” the researchers said. “However, we show that altruistic indulgence is associated with self-sacrifice (forgoing one’s preference and health) … [as a way to protect the feelings of one’s companion].”

    Yi and his team said future studies could look into the circumstances that might increase or decrease altruistic indulgence (they predicted that it might be greater when dining with a heavier companion who chooses an unhealthy food or drink option, “… because people should believe that a healthy choice will make a heavier individual feel particularly guilty”) and studies could also investigate how people feel after engaging in altruistic indulgence – will they feel happy that they protected their friend’s feelings or bad that they ate or drank unhealthily?

    Altruistic indulgence: people voluntarily consume high-calorie foods to make other people feel comfortable and pleasant

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

    in The British Psychological Society - Research Digest on January 22, 2019 09:12 AM.

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    What Can Brain Imaging Tell Us About Violent Extremism?


    Before answering that question, I'll tell you about an incredibly impressive ethnographic study and field survey. For a one year period, the investigators (Pretus, Hamid et al., 2018) conducted field work within the community of young Moroccan men in Barcelona, Spain. As the authors explain, the Moroccan diaspora is an immigrant community susceptible to jihadist forms of radicalization:
    Spain hosts Europe’s second largest Moroccan diaspora community (after France) and its least integrated, whereas Catalonia hosts the largest and least integrated Moroccan community in Spain. Barcelona ... was most recently the site of a mass killing ... by a group of young Moroccan men pledging support for the Islamic State. According to a recent Europol’s latest annual report on terrorism trends, Spain had the second highest number of jihadist terrorism-related arrests in Europe (second only to France) in 2016...

    After months of observation in selected neighborhoods, the researchers approached prospective participants about completing a survey, with the assurance of absolute anonymity. No names were exchanged, and informed consent procedures were performed orally, to prevent any written record of participation. The very large sample included 535 respondents (average age 23.47 years, range 18–42), who were all Sunni Muslim Moroccan men.

    The goal of the study was to look at sacred values in these participants, and whether these values might affect their willingness to engage in violent extremism. “Sacred values are immune or resistant to material tradeoffs and are associated with deontic (duty-bound) reasoning...” (Pretus, Hamid et al., 2018). The term sacred values doesn't necessarily refer to religious beliefs. One of the most common is the basic human value, “it is wrong to kill another human being.” But theoretically speaking, we could include statements such as, “it is wrong to kill endangered species for sport (or for any other reason).”

    In this study, Sacred Values included:
    • Palestinian right of return
    • Western military forces being expelled from all Muslim lands
    • Strict sharia as the rule of law in all Muslim countries
    • Armed jihad being waged against enemies of Muslims
    • Forbidding of caricatures of Prophet Mohammed
    • Veiling of women in public

    What were the Nonsacred Values? We don't know. I couldn't find examples anywhere in the paper. It's crucial that we know what these were, to help understand the “sacralization” of nonsacred values, which was observed in an fMRI experiment (described later). So I turned to the Supplemental Material of Berns et al. (2012), inferring that the statements below are good examples of nonsacred values in a population of adults in Atlanta.
    • You are a dog person.
    • You are a cat person.
    • You are a Pepsi drinker.
    • You are a Coke drinker.
    • You believe that Target is superior to Walmart.
    • You believe that Walmart is superior to Target.

    But what if the nonsacred values in the present study of violent extremism were a little more contentious and meaningful?
    • You are a fan of FC Barcelona.
    • You are a fan of AC Milan.

    Anyway, to choose participants for the fMRI experiment, the investigators first divided the entire group into those who were more (n=267) or less (n=268) vulnerable to recruitment into violent extremism (see Appendix for details). An important comparison would have been to directly contrast brain activity in these two groups, but that wasn't done here. Out of the 267 men more vulnerable to violent extremism, 38 agreed to participate in the fMRI study. These 38 were more likely to Endorse Militant Jihadism (score 4.24 out of 7) than the general fMRI pool (3.35) and the non-fMRI pool (2.43).1 

    A battery of six sacred and six nonsacred values was constructed individually for each person and presented in the scanner, along with a number of grammatical variants, for a list of 50 different items per condition. The 38 participants were randomly assigned to one of two manipulations in a between-subjects design: exclusion (n=19) and inclusion (n=19) in the ever-popular ball-tossing video game of Cyberball. [PDF]2



    Unfortunately, this reduced the study's statistical power. Nonetheless, a major goal of the experiment was to examine how social exclusion affects the processing of sacred values. I don't know if Cyberball studies are ever conducted in a within-subjects design (perhaps with an intervening task), or if exposure to one of the two conditions is too “contaminating”. At any rate, in real life, discrimination against Muslim immigrants is isolating and causes exclusion from social and economic benefits. Feelings of marginalization can result in greater radicalization and support for (and participation in) extremist groups. At this point in time, I don't think neuroimaging can add to the extensive knowledge gained from years of field work.

    Nevertheless, the investigators wanted to extend the findings of Berns et al. (2012) to a very different population. The earlier study wanted to determine whether sacred values are processed in a deontological way (based on strict rules of right and wrong) or in a utilitarian fashion (based on cost/benefit analysis of outcome). As interpreted by those authors, processing sacred values was associated with increased activation of left temporoparietal junction (semantic storage) and left ventrolateral prefrontal cortex (semantic retrieval). Berns et al. suggested that “sacred values affect behaviour through the retrieval and processing of deontic rules and not through a utilitarian evaluation of costs and benefits.” Based on those results, the obvious prediction in the present study is that sacred values should activate left temporoparietal junction (L TPJ) and left ventrolateral prefrontal cortex (L VLPFC).


    Fig. 3A (Pretus, Hamid et al., 2018).


    Fig. 3A shows that only the latter half of that prediction was observed, and there was no explanation for the lack of activation in L TPJ. Instead, there was a finding in R TPJ in the excluded group which I won't discuss further.

    Of note, the excluded participants rated themselves as being more likely to fight and die for nonsacred values, compared to the included participants. This was termed “sacralization” and now you can see why it's so important to know the nonsacred values. Are we talking about fighting and dying for Pepsi vs. Coke? For FC Barcelona vs. AC Milan? Not to be glib, but this would help us understand why social exclusion (in an artificial experimental setting) would radicalize these participants (in an artificial experimental setting).



    Fig. 3B (Pretus, Hamid et al., 2018). Nonsacred values activate Left Inferior Frontal Gyrus (IFG, aka VLPFC) in the excluded group, but not in the included group. This was interpreted as a neural correlate of “sacralization”.


    Another interpretation of Fig. 3B is that the exclusion manipulation was distracting, making it more difficult for these participants to process stimuli expressing nonsacred values (due to increased encoding demands, syntactic processing, etc.). Exclusion increased emotional intensity ratings, and decreased feelings of belongingness and being in control. This distraction could have carried over to the task of rating one's willingness to fight and die in defense of values.

    Even if we say the brain imaging results weren't especially informative, the extensive ethnographic study and field surveys were a highly valuable source of data on a marginalized group of young Muslim men at risk of recruitment by violent extremist groups. It's a vicious cycle: terrorist attacks result in greater discrimination and persecution of innocent Muslim men, which has the unintended effect of further radicalization in some of the most vulnerable individuals. To conclude, I acknowledge that my comments may be out of turn because I have no authority or expertise, and because I'm from a country with an appalling record of discriminating against Muslims.


    Footnotes

    1 I was a bit confused by some of these scores, because they changed from one paragraph to the next, and differed from what was in Table 1. Perhaps one was a composite score, and the other from an individual questionnaire.

    2 I've written extensively about whether Cyberball is a valid proxy for social exclusion, but I won't get into that here.


    References

    Berns GS, Bell E, Capra CM, Prietula MJ, Moore S, Anderson B, Ginges J, Atran S. (2012). The price of your soul: neural evidence for the non-utilitarian representation of sacred values. Philos Trans R Soc Lond B Biol Sci. 367(1589):754-62.

    Pretus C, Hamid N, Sheikh H, Ginges J, Tobeña A, Davis R, Vilarroya O, Atran S. (2018). Neural and Behavioral Correlates of Sacred Values and Vulnerability to Violent Extremism. Front Psychol. 9:2462.


    Appendix


    Modified from Table 1 (Pretus, Hamid et al., 2018).

    [The] measures included (1) a modified inventory on general radicalization (support for violence as a political tactic) based on a prior longitudinal study on violent extremist attitudes among Swiss adolescents (Nivette et al., 2017); (2) a scale on personal grievances and previously used on imprisoned Islamist militants in the Philippines, and Tamil Tigers in Sri Lanka (Webber et al., 2018); (3) a scale on collective narcissism which has been shown to shape in-group authoritarian identity and support for military aggression against outgroups (de Zavala et al., 2009); (4) a self-report delinquency inventory adapted from Elliott et al. (1985), based on the disproportionate number of Muslim European delinquents who join jihadist terrorist groups (Basra and Neumann, 2016); and (5) a series of items assessing endorsement of militant jihadism (“The fighting of the Taliban, Al Qaida, ISIS is justified,” “The means of jihadist groups are justified,” “Attacks against Western nations by jihadist groups are justified,” “Attacks against Muslim nations by jihadist groups are justified,” “Attacks against civilians by jihadist groups are justified,” “Spreading Islam using force is every part of the world is an act of justifiable jihad,” and “A Caliphate must be resurrected even by force”) that we combined into a reliable composite score, “Endorsement of Militant Jihadism”...

    in The Neurocritic on January 22, 2019 04:31 AM.

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    Insights on representational similarity in neural networks with canonical correlation

    For this week’s journal club, we covered “Insights on representational similarity in neural networks with canonical correlation” by Morcos, Raghu, and Bengio, NeurIPS, 2018.  To date, many different convolutional neural networks (CNNs) have been proposed to tackle the object recognition … Continue reading

    in Pillow Lab on January 21, 2019 07:26 PM.

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    Nerd Food: Tooling in Computational Neuroscience - Part II: Microscopy

    Nerd Food: Tooling in Computational Neuroscience - Part II: Microscopy

    Research is what I'm doing when I don't know what I'm doing.
    Wernher von Braun

    Welcome to the second instalment of our second series on Computational Neuroscience for lay people. You can find the first post of the previous series here, and the first post of the current series here. As you'd expect, this second series is slightly more advanced, and, as such, it is peppered with unavoidable technical jargon. Having said that, we shall continue to pursue our ambitious target of making things as easy to parse as possible (but no easier). If you read the first series, the second should hopefully make some sense.1

    Our last post discussed Computational Neuroscience as a discipline, and the kind of things one may want to do in this field. We also spoke about models and their composition, and the desirable properties of a platform that runs simulations of said models. However, it occurred to me that we should probably build some kind of "end-to-end" understanding; that is, by starting with the simulations and models we are missing a vital link with the physical (i.e. non-computational) world. To put matters right, this part attempts to provide a high-level introduction on how data is acquired from the real world and can then be used - amongst other things - to inform the modeling process.

    Macro and Micro Microworlds

    For the purposes of this post, the data gathering process starts with the microscope. Of course, keep in mind that we are focusing only on the morphology at present - the shape and the structures that make up the neuron - so we are ignoring other important activities in the lab. For instance, one can conduct experiments to measure voltage in a neuron, and these measurements provide data for the functional aspects of the model. Alas, we will skip these for now, with the promise of returning to them at a later date2.

    So, microscopes then. Microscopy is the technical name for the observation work done with the microscope. Because neurons are so small - some 4 to 100 microns in size - only certain types of microscopes are suitable to perform neuronal microscopy. To make matters worse, the sub-structures inside the neuron are an important area of study and they can be ridiculously small: a dentritic spine - the minute protrusions that come out of the dendrites - can be as tiny as 500 nanometres; the lipid bylayer itself is only 2 or 3 nanometres thick, so you can imagine how incredibly small ion channels and pumps are. Yet these are some of the things we want to observe and measure. Lets call this the "micro" work. On the other hand, we also want to understand connectivity and other larger structures, as well as perform observations of the evolution of the cell and so on. Lets call this the "macro" work. These are not technical terms, by the by, just so we can orient ourselves. So, how does one go about observing these differently sized microworlds?

    F1.large.jpg

    Figure 1: Example of measurements one may want to perform on a dendrite. Source: Reversal of long-term dendritic spine alterations in Alzheimer disease models

    Optical Microscopy

    The "macro" work is usually done using the Optical "family" of microscopes, which is what most of us think of when hearing the word microscope. As it was with Van Leeuwenhoek's tool in the sixteen hundreds, so it is that today's optical microscopes still rely on light and lenses to perform observations. Needless to say, things did evolve a fair bit since then, but standard optical microscopy has not completely removed the shackles of its limitations. These are of three kinds, as Wikipedia helpfully tells us: a) the objects we want to observe must be dark or strongly refracting - a problem, since the internal structures of the cell are transparent; b) visible light's diffraction limit means that we cannot go much lower than 200 nanometres - pretty impressive, but unfortunately not quite low enough for detailed sub-structure analysis; and c) out of focus light hampers image clarity.

    Workarounds to these limitations have been found in the guise of techniques, with the aim of augmenting the abilities of standard optical microscopy. There are many of these techniques. There is the Confocal Microscopy3 - improving resolution and contrast; the Fluorescence microscope, which uses a sub-diffraction techniqueto reconstruct some of the detail that is missing due to diffraction; or the incredible-looking movies produced by Multiphoton Microscopy. And of course, it is possible to combine multiple techniques in a single microscope, as is the case with the Multiphoton Fluorescence Microscopes (MTMs) and many others.

    In fact, given all of these developments, it seems there is no sign of optical microscopy dying out. Presumably some of this is due to the relative lower cost of this approach as well as to the ease of use. In addition, optical microscopy is complementary to the other more expensive types of microscopes; it is the perfect tool for "macro" work that can then help to point out where to do "micro" work. For example, you can use an optical microscope to assess the larger structures and see how they evolve over time, and eventually decide on specific areas that require more detailed analysis. And when you do, you need a completely different kind of microscope.

    Electron Microscopy

    When you need really high-resolution, there is only one tool to turn to: the Electron Microscope (EM). This crazy critter can provide insane levels of magnification by using a beam of electrons instead of visible light. Just how insane, you ask? Well, if you think that an optical microscope lives in the range of 1500x to 2000x - that is, can magnify a sample up to two thousand times - an EM can magnify as much as 10 million times, and provide a sub-nanometre resolution4. It is mind boggling. If fact, we've already seen images of atoms using EM in part II, but perhaps it wasn't easy to appreciate just how amazing a feat that is.

    Of course, EM is itself a family - and a large one at that, with many and diverse members. As with optical microscopy, each member of the family specialises on a given technique or combination of techniques. For example, the Scanning Electron Microscope (SEM) performs a scan of the object under study, and has a resolution of 1 nanometre or higher; the Scanning Confocal Electron Microscope (SCEM)uses the same confocal technique mentioned above to provide higher depth resolution; and Transmission Electron Microscopy (TEM) has the ability to penetrate inside the specimen during the imagining process, given samples with thickness of 100 nanometres or less.

    A couple of noteworthy points are required at this juncture. First, whilst some of these EM techniques may sound new and exciting, most have been around for a very long time; it just seems they keep getting better and better as they mature. For example, TEM was used in the fifties to show that neurons communicate over synaptic junctions but its still wildly popular today. Secondly, its important to understand that the entire imaging process is not at all trivial - certainly not for TEM, nor EM in general and probably not for Optical Microscopy either. It just is a very labour intensive and veryspecialised process - most likely done by an expert human neuroanatomist - and the difficulties range from the chemical preparation of the samples all the way up to creating the images. The end product may give the impression it was easy to produce, but easy it was not.

    At any rate, whatever the technical details, the fact is that the imagery that results from all these advances is truly evocative - haunting, even. Take this image produced by SEM:

    Personally, I think it is incredibly beautiful; simultaneously awe-inspiring and depressing because it really conveys the messiness and complexity of wetware. By way of contrast, look at the neatness of man-made micro-structures:

    bluegeneq%20x%20420.jpg

    Figure 3: The BlueGene/Q chip. Source: IBM plants transactional memory in CPU

    Stacks and Stacks of 'Em

    Technically, pictures like the ones above are called micrographs. As you can see in the neuron micrograph, these images provide a great visual description of the topology of the object we are trying to study. You also may notice a slight coloration of the cell in that picture. This is most likely due to the fact that the people doing the analysis stain the neuron to make it easier to image. Now, in practice - at least as far as I have seen, which is not very far at all, to be fair - 2D grayscale images are preferred by researchers to the nice, Public Relations friendly pictures like the one above; those appear to be more useful for magazine covers. The working micrographs are not quite as exciting to the untrained eye but very useful to the professionals. Here's an example:

    fetch.php?w=900&tok=d88a10&media=wiki:biomed-neurons.jpg

    Figure 4: The left-hand side shows the original micrograph. On the right-hand side it shows the result of processing it with machine learning. Source: Deep Neural Networks Segment Neuronal Membranes in Electron Microscopy Images

    Let's focus on the left-hand side of this image for the moment. It was taken using ssTEM - serial-section TEM, an evolutionary step in TEM. The ss part of ssTEM is helpful in creating stacks of images, which is why you see the little drawings on the left of the picture; they are there to give you the idea that the top-most image is one of 30 in a stack5. The process of producing the images above was as follows: they started off with a neuronal tissue sample, which is prepared for observation. The sample had 1.5 micrometres and was then sectioned into 30 slices of 50 nanometres. Each of these slices was imaged, at a resolution of 4x4 nanometres per pixel.

    As you can imagine, this work is extremely sensitive to measurement error. The trick is to ensure there is some kind of visual continuity between images so that you can recreate a 3D model from the 2D slices. This means for instance that if you are trying to figure out connectivity, you need some way to relate a dendrite to it's soma and say to the axon of the neuron it connects to - and that's one of the reasons why the slices have to be so thin. It would be no good if the pictures miss this information out as you will not be able to recreate the connectivity faithfully. This is actually really difficult to achieve in practice due to the minute sizes involved; a slight tremor that displaces the sample by some nanometres would cause shifts in alignment; even with the high-precision the tools have, you can imagine that there is always some kind of movement in the sample's position as part of the slicing process.

    Images in a stack are normally stored using traditional formats such as TIFF6. You can see an example of the raw images in a stack here. Its worth noticing that, even though the images are 2D grey-scale, since the pixel size is only a few nanometres wide (4x4 in this case), the full size of an image is very large. Indeed, the latest generation of microscopes produce stacks on the 500 Terabyte range, making the processing of the images a "big-data" challenge.

    What To Do Once You Got the Images

    But back to the task at hand. Once you have the stack, the next logical step is to try to figure out what's what: which objects are in the picture. This is called segmentation and labelling, presumably because you are breaking the one big monolithic picture into discrete objects and give them names. Historically, segmentation has been done manually, but its a painful, slow and error-prone process. Due to this, there is a lot of interest in automation, and it has recently become feasible to do so - what with the abundance of cheap computing resources as well as the advent of "useful" machine learning (rather than the theoretical variety). Cracking this puzzle is gaining traction amongst the programming herds, as you can see by the popularity of challenges such as this one: Segmentation of neuronal structures in EM stacks challenge - ISBI 2012. It is from this challenge we sourced the stack and micrograph above; the right-hand side is the finished product after machine learning processing.

    There are also open source packages to help with segmentation. A couple of notable contenders are Fiji and Ilastik. Below is a screenshot of Ilastik.

    Figure-2-a.png

    Figure 5: Source: Ilastik gallery.

    An activity that naturally follows on from segmentation and labelling is reconstruction. The objective of reconstruction is to try to "reconstruct" morphology given the images in the stack. It could involve inferring the missing bits of information by mathematical means or any other kind of analysis which transforms the set of discrete objects spotted by segmentation into something looking more like a bunch of connected neurons.

    Once we have a reconstructed model, we can start performing morphometric analysis. As wikipedia tells us, Morphometry is "the quantitative analysis of form"; as you can imagine, there are a lot of useful things one may want to measure in the brain structures and sub-structures such as lengths, volumes, surface area and so on. Some of these measurements can of course be done in 2D, but life is made easier if the model is available in 3D. One such tool is NeuroMorph. It is an open source extension written in Python for the popular open source 3D computer graphics software Blender.

    Conclusion

    This post was a bit of a world-wind tour of some of the sources of real world data for Computational Neuroscience. As I soon found out, each of these sections could have easily been ten times bigger and still not provide you with a proper overview of the landscape; having said that, I hope that the post at least gives some impression of the terrain and its main features.

    From a software engineering perspective, its worth pointing out the lack of standardisation in information exchange. In an ideal world, one would want a pipeline with components to perform each of the steps of the complete process, from data acquisition off of a microscope (either opitical or EM), to segmentation, labelling, reconstruction and finally morphometric analysis. This would then be used as an input to the models. Alas, no such overarching standard appears to exist.

    One final point in terms of Free and Open Source Software (FOSS). On one hand, it is encouraging to see the large number of FOSS tools and programs being used. Unfortunately - at least for the lovers of Free Software - there are also some proprietary tools that are widely used such as NeuroLucida. Since the software is so specialised, the fear is that in the future, the better funded commercial enterprises will take over more and more of the space.

    That's all for now. Don't forget to tune in for the next instalment!

    Footnotes:

    1

    As it happens, what we are doing here is to apply a well-established learning methodology called the Feynman Technique. I was blissfully unaware of its existence all this time, even though Feynman is one of my heroes and even though I had read a fair bit about the man. On this topic (and the reason why I came to know about the Feynman Technique), its worth reading Richard Feynman: The Difference Between Knowing the Name of Something and Knowing Something, where Feynman discusses his disappointment with science education in Brazil. Unfortunately the Portuguese and the Brazilian teaching systems have a lot in common - or at least they did when I was younger.

    2

    Nor is the microscope the only way to figure out what is happening inside the brain. For example, there are neuroimagining techniques which can provide data about both structure and function.

    3

    Patented by Marvin Minsky, no less - yes, he of Computer Science and AI fame!

    4

    And, to be fair, sub-nanometre just doesn't quite capture just how low these things can go. For an example, read Electron microscopy at a sub-50 pm resolution.

    5

    For a more technical but yet short and understandable take, read Uniform Serial Sectioning for Transmission Electron Microscopy.

    6

    On the topic of formats: its probably time we mention the Open Microscopy Environment (OME). The microscopy world is dominated by hardware and as such its the perfect environment for corporations, their proprietary formats and expensive software packages. The OME guys are trying to buck the trend by creating a suite of open source tools and protocols, and by looking at some of their stuff, they seem to be doing alright.

    Created: 2015-11-30 Mon 23:12

    Emacs 24.5.1 (Org mode 8.2.10)

    Validate

    in Marco Craveiro on January 21, 2019 04:22 PM.

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    Chinese university hospital denounces “malicious attack” by Western vaccine industry

    Manipulated data in 17 papers from one cancer research lab in China gets flagged on PubPeer. It ends with the university hospital in Wuhan issuing a secret statement accusing the US pharma giant a Merck of a conspiracy to slander a Chinese Academy member, Dr Ding Ma.

    in For Better Science on January 21, 2019 12:26 PM.

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    “We were very uncomfortable with this situation:” French group loses aging paper for “overlap”

    The authors of a 2017 paper on how chronic inflammation might hasten aging have retracted the work because it turned out to be a collage of previously published articles. The paper, “Chronic Inflammation: Accelerator of Biological Aging,” appeared in  The Journals of Gerontology: Series A, an Oxford University Press title. It has been cited 41 … Continue reading “We were very uncomfortable with this situation:” French group loses aging paper for “overlap”

    in Retraction watch on January 21, 2019 11:00 AM.

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    Teenagers’ Lack Of Insight Into Some Of Their Abilities Has Implications For Career Counselling

    GettyImages-472404164.jpg
    By Christian Jarrett

    How much insight do you have into your own mental and emotional abilities, such as verbal intelligence, spatial cognition and interpersonal skills? Might your friends have a better idea of your strengths and weaknesses than you do? In a new paper in the journal Heliyon, a team led by Aljoscha Neubauer explain that while such questions of self- vs. other-insight have already been looked at in the context of the main personality traits and general IQ, theirs is the first investigation in the context of more specific abilities. It’s an important issue for young people, they add, since choosing career paths that play to our abilities can increase the chances of later success – but it remains an open question whether and for which abilities people should rely on their own judgments or seek the advice of others.

    The researchers recruited 233 participants in their mid-teens (average age 14) and 215 participants in their late teens (average age 18). Participants completed six tests, including: established measures of their verbal, numerical and spatial abilities; a test of divergent creativity (thinking up novel uses for an umbrella, plastic bottle and shoe); and a questionnaire tapping their intra- and interpersonal emotional management (based on the participants’ selection of the best way to deal with various social and emotional scenarios).

    Immediately after completing the tests, the participants filled out an additional questionnaire asking them to reflect on and estimate their own abilities in the various domains that had been tested. Finally, they also completed the same questionnaire in relation to the abilities of one or more of their school classmates (such that each participant rated themselves and was also rated by two of their classmates).

    The participants were very poor at judging their own verbal ability and their judgments of their peers’ verbal abilities were not much better – a result that the researchers described as their “most puzzling”, considering you’d think such abilities would be apparent both to oneself and one’s peers, especially in a school context. One possible explanation is that the teenagers’ conception of verbal intelligence “might not correspond” with the researchers’ conception and the way it was tested; another explanation, the researchers suggested, is that the participants verbal IQ was perhaps rather low and “individuals of lower verbal ability might be particularly weak at self- and peer estimating because this might require exactly what they are missing: a good verbal ability”.

    In contrast with verbal intelligence, participants had some accurate insight into their own creativity, and even more insight into the creativity of their peers.

    Meanwhile, for spatial ability an age difference emerged. At age 14, as with verbal ability, participants were poor at judging their own and each other’s spatial ability. By age 18, by contrast, participants had some accuracy at judging their own spatial abilities, but not their peers’ abilities.

    In relation to interpersonal competence, the participants had a degree of insight into their own abilities, but not each other’s (perhaps because they simply scored how much they liked the person they were rating rather than offering an unbiased estimate of their social and emotional skills). One detail here is that their ability to estimate their peers’ interpersonal skills increased “considerably” at age 18, compared with 14, albeit that this accuracy was still relatively poor.

    Finally, as the researchers expected, the participants’ were able to estimate their own intra-personal abilities with some accuracy, but not the intra-personal abilities of their peers (presumably because our inner emotional worlds are hidden to an extent).

    Neubauer and his colleagues said their findings have “important practical implications”, particularly in the context of young people choosing their career paths. While they acknowledged their findings need replicating, they suggested that for some domains, especially verbal IQ, young people appear to have surprising ignorance of their own ability (or lack of ability). Even for those abilities where participants had more insight (into themselves and their peers), it’s worth noting that this was relatively modest, with their judgments accounting for only between 15 and 20 per cent of the variance in ability between participants.

    Future research could test other age groups, and look at the judgments made by other informants besides participants’ peers, such as family members, to see if they would have greater insight into participants’ abilities. (The current study included a measure of friendship closeness but found no evidence that this affected the participants’ accuracy in judging their peers’ abilities.)

    The researchers concluded that “As young people might have biased views of their own but also of their peers’ abilities, scientifically based career counselling should include not only tests for interests but also performance tests to avoid erroneous vocational decisions.”

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

    The self–other knowledge asymmetry in cognitive intelligence, emotional intelligence, and creativity

    in The British Psychological Society - Research Digest on January 21, 2019 09:26 AM.

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    Bullied Into Bad Science?

    There's been an interesting discussion on Twitter about senior scientists who pressure their students or postdocs into scientific misconduct or otherwise poor science: Bullying students into providing the "right" results: research misconduct by proxy? This is probably among the worst but receives little attention — Simon Eickhoff (@INM7_ISN) January 19, 2019 Today, I was made aware of a site called Bullied Into Bad Science which aims to tackle this problem. Founded by behavior

    in Discovery magazine - Neuroskeptic on January 20, 2019 09:22 PM.

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    Our fascination with robots goes all the way back to antiquity

    In the book ‘Gods and Robots,’ a scholar recounts how early civilizations explored artificial life through myths.

    in Science News on January 20, 2019 01:00 PM.

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    Weekend reads: #MeToo in a political science journal; 15 articles that challenged dogma in 2018; an entire editorial board resigns

    Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, we could really use your help. Would you consider a tax-deductible donation to support Weekend Reads, and our daily work? Thanks in advance. The week at Retraction Watch featured a sixth retraction for a researcher cleared of misconduct; a … Continue reading Weekend reads: #MeToo in a political science journal; 15 articles that challenged dogma in 2018; an entire editorial board resigns

    in Retraction watch on January 19, 2019 02:13 PM.

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    Cryptic remains of tiny animals have turned up in an Antarctic lake

    Researchers were surprised to find vestiges of what appear to be tiny animals in mud from Antarctica’s ice-covered Lake Mercer.

    in Science News on January 18, 2019 10:35 PM.

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    Prosecco production takes a toll on northeast Italy’s environment

    The soil in Northern Italy’s prosecco vineyards is washing away.

    in Science News on January 18, 2019 06:28 PM.

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    This honeybee parasite may be more of a fat stealer than a bloodsucker

    Inventing decoy bee larvae prompts a back-to-basics rethink of a mite ominously named Varroa destructor.

    in Science News on January 18, 2019 06:15 PM.

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    Max Planck Florida Institute for Neuroscience enters Partnership with Zeiss

    The Max Planck Florida Institute for Neuroscience (MPFI) announces a new “labs@location” partnership agreement between the MPFI Electron Microscopy (EM) Core Facility and Germany-based microscopy company ZEISS, known for its cutting-edge imaging technologies. As a “labs@location” partner institution, MPFI will have access to state-of-the-art ZEISS technology before it is commercially available, providing researchers with innovative imaging tools that will empower their search for new insights into how the brain works. MPFI is the only the third institution in the United States to earn the labs@location designation.

    “ZEISS and MPFI have a long-standing relationship—we have been closely cooperating to push the boundaries of visualizing the brain ultrastructure since MPFI was established in 2012,” said Dr. Naomi Kamasawa, Head of EM Facility. “Our facility might be small compared to other institutions, but the scientific excellence and technology feedback we provided, together with the continuous effort and passion to push boundaries in our research, made us a special partner for ZEISS.”

    Kirk J. Czymmek, Head of the Global ZEISS Microscopy Customer Centers praised the EM Lab in his remarks, saying “The team that you have here is special, and they are internationally recognized for their expertise.”

    MPFI and ZEISS launched the partnership on January 17, 2019 at an event that included lectures focused on Correlative Light-Electron Microscopy (CLEM), facility tours, and a partnership signing and reception held in MPFI’s Dreyfoos Atrium.

    The first piece of equipment made available to MPFI scientists is known as the “Focal Charge Compensation module (FCC)”, which is integrated onto a Serial Block Face Scanning Electron Microscope system. The FCC introduces a local stream of nitrogen gas onto the sample inside the microscope, which absorbs unwanted electrical charges that interfere with imaging. “This new technology results in much higher quality images and allows us to collect data from even more challenging samples,” Dr. Kamasawa explained. “Anything that allows us to better visualize the structure of neurons and correlate it to their function will allow us to achieve a more complete understanding of neural networks, and ultimately, of the brain itself.” MPFI received the FCC equipment in August of this year, and was the first institution in the United States to use the technology after ZEISS made a number of significant improvements to the current commercially available model.

    “The role of high-resolution imaging in unraveling the functional complexity of the brain cannot be overstated. This partnership is a great recognition of the unique know-how and research expertise provided by our electron microscopy facility. It underlines the importance of connecting core facilities, scientists and commercial partners, providing MPFI access to cutting edge technologies to push the boundaries of neuroscience research” said Dr. David Fitzpatrick, Scientific Director and CEO of MPFI.

     “Science is transitioning to utilizing 3D data sets and correlative microscopy, to this end we are pleased to partner with Max Planck Florida. These types of relationships are vital for us to better understand the issues and advantages of our hardware and software,” said James A. Sharp, President Carl Zeiss Microscopy LLC.

    In attendance were: Abdel Barraj, Head of Sales at ZEISS Microscopy North America; Kirk J. Czymmek, Head of the Global ZEISS Microscopy Customer Centers; Geoff Perumal, Academia Life Science EM/XRM Specialist at ZEISS Microscopy; Roger Unger, Regional Sales Manager, ZEISS; Oliver Tress, Systems Specialist, 3D Imaging, ZEISS; Robert Celestine, Area Manager, MICRO OPTICS OF FLORIDA, INC.

    in Max Plank Florida Institute for Neuroscience on January 18, 2019 03:07 PM.

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    “Nobody agrees on what AI is” – How Elsevier’s report used AI to define the undefinable

    Our colleagues came up with a new way to analyze the complex research field of artificial intelligence

    in Elsevier Connect on January 18, 2019 12:20 PM.

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    A new gravitational wave detector is almost ready to join the search

    Buried deep underground, Japan’s KAGRA detector relies on components cooled to just 20 degrees above absolute zero.

    in Science News on January 18, 2019 12:00 PM.

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    “This is something that we have never seen before in any study:” Group loses two more papers

    A group of rheumatology researchers in Egypt that lost a paper in 2016 for a variety of problems has lost two more. The authors common to the two papers, Anna Abou-Raya and Suzan Abou-Raya, are based at the University of Alexandria, which did not find evidence of scientific misconduct, according to one of the retraction … Continue reading “This is something that we have never seen before in any study:” Group loses two more papers

    in Retraction watch on January 18, 2019 11:00 AM.

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    Young Men Who Endorse The Masculine Ideal of Success Enjoy Greater Psychological Wellbeing

    GettyImages-901574552.jpgBy Christian Jarrett

    Recently it’s been difficult to avoid the mantra that masculinity is toxic. There’s that viral Gillette advert encouraging men to be nicer (provoking a mix of praise, scorn and outrage); and the claim from the American Psychological Association (APA), in its promotion for its new guidelines on working with men and boys, that “traditional masculinity—marked by stoicism, competitiveness, dominance and aggression—is, on the whole, harmful” – a message welcomed by some, but criticised by many others, including Steven Pinker who dubbed it “ludicrous” and the British clinical neuropsychologist Vaughan Bell, who described the campaign as “an amazing misfire“.

    The APA report has been criticised on many grounds, including its oversight of the biological roots of masculinity, but the most frequently mentioned issue is with the overly simplistic, sweeping nature of the “masculinity is toxic” message. Traditional masculinity clearly reflects a host of values, beliefs and behaviours, some of which may indeed be harmful in certain circumstances, but some of which may also be beneficial, at least some of the time. Coincidentally, a paper in the January issue of the APA journal Psychology of Men and Masculinity captures just a little of this complexity.

    Responding to the lack of longitudinal research on this topic, and the concerns that potential positive aspects of masculinity have been overlooked, the new study measured nearly 300 young male college students’ endorsement of traditional masculinity at one time point, in the spring of their freshman year, and then measured their wellbeing six months later.

    The findings are mixed, but given the recent cultural emphasis on toxic masculinity, one result stands out: young men who, on the “Conformity to Masculine Norms” scale, more strongly endorsed the masculine ideal of “success and winning” (they agreed with statements like “In general, I will do anything to win”), tended to score higher on psychological wellbeing six months later. “Men who adhere to this norm may experience a sense of mastery and achievement through their accomplishments,” said the researchers, led by Aylin Kaya at the University of Maryland, “which can in turn boost their eudaemonic well-being.”

    In contrast, and more in keeping with the message emanating from Gillette/the APA and others, the men who endorsed the masculine “Playboy” ideal (they agreed strongly that “If I could, I would frequently change sexual partners”) and/or the “power” ideal (“In general, I control the women in my life”) tended to report lower wellbeing six months later.

    At the study start, the men also completed the “Gender Role Conflict” questionnaire (a scale developed in the 1980s ostensibly to explore problems arising from men’s aversion to femininity) and those who scored highly on the Restricted Emotionality sub-scale – for instance, they agreed “I have difficulty expressing my emotional needs to my partner” – also tended to report lower wellbeing six months later.

    However, critics might point out that this correlation is almost inevitable as the items related to Restricted Emotionality are phrased in a negative way that assumes emotional control is a problem, such that it would be odd if a high score on this sub-scale was not associated with subsequent reduced wellbeing. A stronger case against traditional masculinity would be made by results showing that men who felt they successfully and deliberately controlled their emotions went on to experience diminished wellbeing, but such a finding seems highly unlikely given the shelves of evidence documenting the positive consequences of having more mental and emotional self-control.

    It’s worth noting that the men’s endorsement, or not, of the majority of the norms that were measured by the “Conformity to Masculine Norms” scale did not, on their own, have a statistically significant association with their wellbeing six months on (positive or negative), including: “heterosexual-presentation” (being concerned to be perceived as straight); “self-reliance” (not wanting to seek help); “violence” (endorsing violence as a suitable response in some situations); “risk” (willingness to put oneself in risky situations); and “emotional control”.

    Kayla and her colleagues said that the negative associations of the “Playboy” and “power” masculine norms with later wellbeing supported earlier cross-sectional work linking the endorsement of these norms with negative mental health outcomes in men. However, they added that the positive association between endorsing the “winning” norm and later wellbeing “is consistent with our hypothesis and with previous research that has indicated in certain contexts, adherence to dominant masculine norms may contribute to positive mental health.”

    Of course, these new results come with their own important caveats – they may not generalise to other groups beyond young American men at college, and they are based entirely on participants’ self-reports of their own values and wellbeing. Clearly more longitudinal research is needed, arguably using scales that are not phrased with an inherent bias against traditional masculine values, and also including outcome measures not only for the men themselves, but also for those people who live and work with them.

    However, these results do provide a more nuanced take on the simplistic idea that traditional masculinity is entirely toxic, a point worth considering alongside the weight of research showing the benefit to children of having a father involved in their upbringing (a point that, hidden behind the “toxic masculinity” headlines, is acknowledged fully in the new APA report; pdf).

    The role of masculine norms and gender role conflict on prospective well-being among men

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

    in The British Psychological Society - Research Digest on January 18, 2019 09:22 AM.

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    The moon’s craters suggest Earth hasn’t erased lots of past impacts

    A new look at moon craters suggests the Earth and moon suffered more impacts in the last 290 million years, and the Earth retains its biggest scars.

    in Science News on January 17, 2019 07:06 PM.

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    New ways to image and control nerve cells could unlock brain mysteries

    Methods that target single nerve cells in mice and fruit fly brains are starting to tease apart the brain’s complexity.

    in Science News on January 17, 2019 07:00 PM.

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    Boosting Open Science Hardware in an academic context: opportunities and challenges

    Written by: Jenny Molloy (University of Cambridge), Juan Pedro Maestre (University of Texas, Austin)

    Experimental science is typically dependent on hardware: equipment, sensors and machines. Open Science Hardware means sharing designs for this equipment that anyone can reuse, replicate, build upon or sell so long as they attribute the developers on whose shoulders they stand. Hardware can also be expanded to encompass other non-digital input to research such as chemicals, cell lines and materials and a growing number of open science initiatives are actively sharing these with few or no restrictions on use.

    A growing number of academics are developing and using open hardware for research and education in addition to sharing their papers, data and software through broader open research practices. This brought a large cohort to the Gathering for Open Science Hardware (GOSH) in Shenzhen China during October 2018, an four day event which convened over 110 of the most active users and developers of open science hardware from 34 countries and multiple backgrounds including academia, industry, community organising, NGOs, education, art and more. PLOS kindly supported an unconference session during GOSH 2018 where students and researchers shared the following opportunities and challenges to boosting open science hardware in an academic context and planned a course of action to forward the goal of the Global Open Science Hardware Roadmap to make open science hardware ubiquitous by 2025.

    Opportunities for open science hardware in academia

    Open science hardware has some important intrinsic benefits. Firstly, it can reduce the cost of research, democratising opportunity and enabling limited budgets to stretch further. Joshua Pearce of Michigan Tech University has calculated a return on investment of hundreds to thousands of percent for funders of open hardware through a drastic reduction in lab costs. Secondly, it reduces duplication of effort by building on the work of others and thirdly, it provides opportunities to customise hardware to suit your optimal experimental design, rather than designing your experiment to fit the limitations of available hardware. Moreover, sharing more details of experimental designs facilitates replicability in science. This is needed more than ever given current lack of trust towards science in some societal contexts and fears within several scientific communities of a “reproducibility crisis”.

    Gaining additional credit, citations and collaborations are all significant potential opportunities for academics developing open science hardware and are necessary to incentivise those activities. However, cultural change is required within existing systems of academic publication and reward to realise the opportunities. Change is coming, for example the recently established Journal of Open Hardware and HardwareX encourage formal publication of research advances and designs that well documented and appropriately licensed, while the PLOS Open Source Toolkit channel highlights and rewards open hardware publications. We know that open approaches can reap rewards but there is room for further evidence in the hardware context. Open access publications and shared datasets can confer a citation advantage and many projects developing open research tools projects report high numbers of collaborations and significant funding that may not have been possible without their culture of sharing. The Structural Genomics Consortium is involved in publishing over two papers per week, partially a result of hundreds of collaborations through making data and tools freely available. Research funders can be responsive to openness as a strategy to maximise impact: UK-based research centre OpenPlant was awarded £12m to make open technologies for plant synthetic biology and two open source projects on diagnostics for infectious diseases were awarded >£1m from the UK’s Global Challenges Research Fund.

    Educational use of open science hardware also reaps both tangible and intangible benefits for universities. It represents an opportunity to increase the quality of teaching and learning by providing access to instruments that would otherwise be too expensive in the numbers required for effective teaching. It also contributes to building critical thinking skills and breaking open the “black box” of laboratory equipment. There are many academics in the GOSH Community involving their students directly in developing open science hardware, such as air quality sensors at the University of Texas Austin or biological instrumentation through the Biomaker Challenge in Cambridge. Still others such as the Centro de Tecnologia Acadêmica at UFRGS in Brazil are using open hardware tools extensively in student lab practicals and research projects.

    Challenges to address if open science hardware is to become ubiquitous

    There are several barriers to wider adoption of open science hardware in academia. One stumbling block is institutional buy-in and support: in these times of limited funding, many universities have become conservative about approaches to intellectual property and patenting of inventions. Encouraging an open approach to maximising societal and scientific impacts through technology and knowledge transfer requires a compelling narrative. This includes reassurance that openness is contextual. In some cases the traditional route of IP protection and restrictive licensing may be optimal to achieve intended outcomes, in others it is not and  open approaches should be considered a strategic option. It is also important to emphasise that open does not equal non-commercial. Indeed there are many examples of entrepreneurial academics and companies spinning off to sell open hardware back into academia but also to industry, non-profits, educational institutions and directly to the public.

    Funding for ongoing support and scaling of open science hardware efforts is a perennial and important topic of discussion at GOSH. In the case of open science hardware, private investors may not consider open designs as maximizing profit opportunities but they can still be profitable and generate significant social and scientific returns. A major task for the GOSH academic working group formed at the unconference session is therefore to compile justification for a diverse range of funders including private philanthropists, social impact investors and venture funds to support open science hardware and further the goal of making it ubiquitous and widely used by 2025.

    The final topic of discussion during our session was creating awareness among the scientific community both online and offline at major scientific conferences. Offering community-level incentives, support and guidelines to document and share open science hardware is feasible and there is much low-hanging fruit. However, we have seen in other areas of open research that to obtain ubiquity these community efforts need to be backed by formal incentives and rewards. In other words, the value of open approaches has to be recognised in decisions around funding, promotions and hiring decisions.

    Furthering open science hardware through community action

    Four priority actions emerged which correspond closely to recommendations in the Global Open Science Hardware Roadmap: i) leverage the GOSH Community and network to produce guidance and case studies for universities, funders and other stakeholders; ii) put open science hardware on the agenda at large disciplinary conference; iii) raise awareness through mainstream academic channels; and iv) take the initiative within our own institutions to experiment with ideas and build local communities.

    We invite anyone who are interested in open science hardware to join this work to ensure that more researchers, students and those outside of academia have access to vital enabling technologies for science. You can sign the GOSH manifesto, join the GOSH Forum to share your projects and contact organizers@openhardware.science for more information.

    NOTE: The PLOS Open Source Toolkit collects papers from across publishers that describe software and hardware with research applications. The site is curated and managed by five active researchers, including the author of this blog post, Jenny Molloy. Meet all the editors here and here.  We’re on a mission to make exciting, cost-effective, and high-utility tools accessible to all researchers to eliminate barriers to scientific innovation and increase reproducibility. We post new content monthly. Subscribe for notifications. Currently featured: an open source K-mer based machine for subtyping HIV-1 genomes.

    Acknowledgements

    Many thanks to PLOS for their kind support enabling people in need of financial support to attend GOSH and to the participants in the unconference session: Juan Pedro Maestre (University of Texas, Austin), Pierre Padilla (UPCH), Andre Chagas (University of Sussex), Jenny Molloy (University of Cambridge), Moritz Riede (University of Oxford), Benjamin Pfaffhausen (Freie Universität Berlin), Marina de Freitas (CTA-UFRGS), Minerva Castellanos Morales (Scintia), Tobias Wenzel (EMBL), Anne-Pia Marty (University of Geneva), Alex Kutschera (Technical University of Munich), Eduardo Padilha (University of São Paulo).

    Image Credit:

    GOSH 2018: https://www.flickr.com/photos/goshcommunity/44847829654/in/dateposted/

     

     

    in The Official PLOS Blog on January 17, 2019 05:09 PM.

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    Overdose deaths tied to antianxiety drugs like Xanax continue to rise

    Benzodiazepines, widely used but addictive drugs to treat anxiety and insomnia, are contributing to a growing number of overdose deaths.

    in Science News on January 17, 2019 01:00 PM.

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    Journal flags papers about radiation exposure following Fukushima disaster

    A physicist and a radiation health expert have had two papers about people’s exposure to radiation following the Fukushima nuclear plant disaster subject to expressions of concern. The authors of the two papers are Makoto Miyazaki, a of the department of radiation health management at Fukushima Medical University, and Ryugo Hayano, a professor of physics … Continue reading Journal flags papers about radiation exposure following Fukushima disaster

    in Retraction watch on January 17, 2019 11:00 AM.

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    This rediscovered Bolivian frog species survived deadly chytrid fungus

    Scientists recently rediscovered a frog species in Bolivia that hasn’t been seen in 10 years — and it could be used to better understand a frog-killing fungus.

    in Science News on January 17, 2019 11:00 AM.

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    Asking Patients To Draw Their Illness Can Be Surprisingly Revealing

    Screenshot 2019-01-17 at 09.55.46.png“an adult’s perceptions of how the heart has been affected by damage and blockages following a heart attack” – from Broadbent et al 2018 / 2004

    By Christian Jarrett

    Asking patients to draw the parts of their body affected by illness (and similar drawing challenges) can provide insights into how they think about their illness, the seriousness of their condition, and how well they are likely to cope, among other things. For instance, when people who had experienced a heart attack were asked on repeated occasions to draw their heart, an increase in the size of their drawings over time correlated with more anxiety and a slower return to work.

    This example and many others feature in a new paper in Health Psychology Review that’s charted the use of patient drawings in peer-reviewed research, finding that the approach has increased in popularity in recent years. From 1970 to 2002, the average number of papers involving patient drawings published per year was 0.5, whereas that increased to an average of 5.9 per year between 2003 and 2016. In all, Elizabeth Broadbent at the University of Auckland, and her colleagues found 101 relevant studies covering 27 categories of illness (most often cancer) and involving participants from 29 different countries, from Canada to Zimbabwe. “We can utilise patients’ drawings to improve our understanding of the illness experience and inform our clinical interventions,” they said.

    Besides assessing drawing size, other approaches used in this field include identifying themes in drawings; looking for distortions or omissions; studying drawing styles, such as use of colour; and analysing facial expressions.

    Other study examples that feature in the review include research with brain injury survivors in which those who drew greater damage on their brain also tended to experience a longer recovery time and a worse quality of life; research with kidney transplant patients in which those who drew their kidneys larger tended to have higher anxiety and lower feelings of control; research comparing the drawings of healthy and sick children, which found sick children’s drawings featured fewer human figures; and research with AIDS-affected children that showed their drawings featured more bed-ridden people and less beauty and more distress.

    There has also been drawing-based research involving people diagnosed with mental health conditions – for instance, a paper published in the 1970s found that drawings by people with depression “had less colour … and more emptiness and amorphousness than other diagnostic groups.”

    While the research in this area is fascinating, it has suffered from a lack of methodological consistency such that Broadbent and her team were unable to conduct a meta-analysis (an analysis of findings combined from multiple prior studies). For example, there was great variation from one study to another in terms of the drawing instructions given to participants. This methodological variation also makes it difficult to establish the reliability and validity of using drawings as a research tool.

    However, Broadbent’s team are optimistic: they recommend future research use drawing instructions that are as explicit as possible, and they believe patient drawings can offer insights missed by traditional health psychology questionnaires, thus helping to improve and personalise health psychology interventions (that are intended to help patients better understand and cope with their illness and treatment). For a flavor of this approach, here is one of their suggestions:

    “One way in which drawings could be used to personalise interventions is for the person delivering the intervention to discuss the patient’s drawing with the patient. Where misconceptions about pathophysiology are evident, these could be pointed out, and patients’ scans or x-rays, or medical test results could be discussed with the aim to correct misconceptions. Where emotions have been drawn, the drawing could be a good starting point for a discussion about how the patient has been emotionally affected by the illness.”

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

    A systematic review of patients’ drawing of illness: implications for research using the Common Sense Model

    in The British Psychological Society - Research Digest on January 17, 2019 09:53 AM.

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    Bacterial compounds may be as good as DEET at repelling mosquitoes

    A bacterium’s metabolic by-products are as effective as DEET in deterring Aedes aegypti mosquitoes.

    in Science News on January 16, 2019 07:18 PM.

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    An ancient child from East Asia grew teeth like a modern human

    Choppers from a youngster with an unknown evolutionary background indicate that hominids evolved a humanlike life span in East Asia by 100,000 years ago.

    in Science News on January 16, 2019 07:12 PM.

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    These robots can follow how-to diagrams

    Robots capable of reading diagrams could work in more varied environments and be easier to communicate with.

    in Science News on January 16, 2019 07:00 PM.

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    A four-legged robot hints at how ancient tetrapods walked

    Using fossils, computer simulations and a life-size walking robot, researchers re-created how an early tetrapod may have made tracks.

    in Science News on January 16, 2019 06:27 PM.

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    MPFI Researchers Discover a New Synaptic Logic for Connections Between the Two Hemispheres of the Brain

    Researchers at the Max Planck Florida Institute for Neuroscience have developed a new combination of technologies that allows them to identify the functional properties of individual synapses that link the two hemispheres and determine how they are arranged within a neuron’s dendritic field.

    Each of the 20 billion neurons in the cerebral cortex receives thousands of synaptic connections from other neurons, forming complex neural networks that make sensation, perception, movement, and higher cognitive functions possible.  Ultimately the function of these networks depends on events that occur within a neuron’s dendrite– extensions from the neuron’s cell body that resemble branches of a tree and receive synaptic connections from the axons of other neurons, A critical piece of the puzzle of cortical networks that continues to challenge neuroscientists is understanding the functional organization of synapses within a neuron’s dendritic field. This requires determining the functional properties of the synaptic inputs a neuron receives (what they are communicating), the source of the inputs (where they are coming from), and how they are arranged within the dendrite.  In a new article in Neuron, MPFI researchers detail how they recently devised new methods to answer these questions, revealing a functional order to the arrangement of distant and local synaptic inputs within a neuron’s dendritic field that may play an important role in coordinating network activity.

    Graduate student Kuo-Sheng Lee, along with other members of the Fitzpatrick lab, explored this question in the mouse visual cortex by mapping the synaptic inputs that link the two cortical hemispheres via a fiber bundle called the corpus callosum. This pathway is thought to play a critical role in coordinating the activity of the two cerebral hemispheres, and, for the visual system, unifying our binocular view of the world. They developed an approach that would permit them to visualize the individual dendritic spines of a neuron (small dendritic specializations that receive excitatory synaptic inputs), characterize their functional properties, and determine whether they receive callosal inputs.

    To visualize the activity of individual dendritic spines, Lee et al., used an advanced imaging technique that relies on calcium signals that are detected as changes in fluorescence.  By watching the dendritic spines ‘light up’ with activity in the living brain, they could present different visual stimuli to the animal and determine which was most effective. The dendritic spines, like most of the cells in visual cortex, respond selectively to the orientation of edges in the visual scene, so this was the functional property they chose to define for each spine. Then to determine whether a spine received synaptic input from the callosum, Lee et al. used direct stimulation of the other hemisphere and looked to see which of the dendritic spines would light up.  Having found that a small percentage of spines were reliably and consistently activated by stimulating callosal inputs, then they were ready to address how are they were arranged within the dendritic field.

    One interesting possibility was that the callosal inputs with similar orientation preference might be clustered together within the dendritic field.  Previous results had provided evidence for clustering of synaptic inputs by functional properties and suggested that coactivation of clustered inputs could amplify their impact on the neuron’s response.

    But, when they performed the analysis, they found that close pairs of spines receiving callosal input were no more likely to have similar orientation preference than a random distribution of the spines within the dendritic field. Then they considered another possibility. Perhaps the callosal spines were clustered with non-callosal spines with the same orientation preference, bringing spines with distant and local inputs that have similar orientation preference into close proximity on the dendrite.  When they took pairs of close spines, one a callosal recipient and the other non-callosal recipient, and examined the orientation preference of the pairs, they were excited to find that they were they more similar to each other than would be expected by chance.

    Lee et al. recognized that their conclusions would be strengthened if they could confirm the functional evidence for orderly local and callosal connectivity with another experimental approach: defining the synaptic connections anatomically. To accomplish this, they used a novel technique called expansion microscopy to anatomically visualize the nanoscale synaptic contacts with conventional light microscopy. The results were consistent with the functional stimulation results, demonstrating that callosal inputs and local inputs (derived from the region right around the targeted neuron) that exhibit similar or­ientation preference are clustered within the dendritic field.

    These observations put the concept of functional clustering into a whole new context: ‘birds of a feather flock together’ and ‘opposites attract’.  Functional clustering represents a fine scale spatial pattern of specificity in connections within the dendritic field that can bring together inputs that have similar properties and are derived from different networks.  Combined with the evidence that functional clustering of spines in the dendritic field can amplify their impact on neuronal response, neurons in the visual cortex could use this strategy to generate robust responses to orientation-matched inputs from the two hemispheres, contributing to a seamless perception of the visual world. A similar structure may apply to callosal connections that link other areas of the cortex, a fine-scale organization of synapses within the dendrites of individual neurons that has ramifications for large-scale network function.

    The full article can be found by clicking here.

    in Max Plank Florida Institute for Neuroscience on January 16, 2019 06:27 PM.

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    How belief systems handle contradiction - (I) Empirical contradiction

    In this essay, I will discuss the different ways in which a theory can be contradicted, and how theories react. The scope of this discussion is broader than science, so I will be discussing belief systems, of which scientific theories are a particular kind (although, according to Feyerabend, not that particular). Another kind of belief system is political theories, for example. What is a belief system? Roughly speaking (and it will get more precise in the discussion), it is a set of propositions about the world that have a universal character. In science, this could be the law of gravitation, for example. Those propositions have relations with each other, and thus they form a system. For example, some propositions might logically imply others. In a belief system, there are generally core concepts over which other propositions build upon (examples: the atom; the rational agent of economic theory).

    How do we evaluate belief systems? In philosophy of science, it is generally considered that scientific theories are evaluated empirically, by testing the empirical validity of propositions. That is, we evaluate the extent to which propositions are contradicted by facts. This has been the core target of much of modern philosophy of science, and thus I will start by recapitulating arguments about empirical contradiction, and add a few remarks. What has been less discussed is two other types of contradiction, social and theoretical. By social contradiction, I refer to the fact that at any given time, different people hold contradictory beliefs, even when they are aware of the same empirical body of observations. How is it possible and do such contradictions get solved? By theoretical contradiction, I refer to the possibility that a system is in fact not logically coherent. It seems that in philosophy of knowledge, belief systems are generally seen as a set of logically consistent propositions, but I will argue that this view is not tenable or rather is a normative view, and that belief systems actually are in some sense “archipelagos of knowledge”.

    Empirical contradiction

    Science is largely dominated by empiricism. One version of it is the logical empiricism of the circle of Vienna (or logical positivism), dating from the early 20th century. In a nutshell, it claims that scientific statements are of two types: elementary propositions whose truth can be verified empirically, in other words observations, and propositions that can be logically deduced from those elements. This leads to a bottom-up view of science, where experimental scientists establish facts, and then theoreticians build consistent theories from these facts. As far as I can see in my own field, this view is still held by a large portion of scientists today, even though it has been pretty much demolished by philosophy of science in the course of the 20th century. To give an example, logical empiricism is the philosophical doctrine that underlies the logic of the Human Brain Project, whose core idea is to collect measurements of the brain and then build a model from those.

    Karl Popper objected that, on a logical ground, propositions can in fact never be verified if they have a universal nature. For example, to verify the law of gravitation, you would have to make all apples in the world fall, and you would still be unsure of whether another apple in the future might not fall in the way you expect. Universal propositions can only be contradicted by observations. This leads to falsificationism, the idea that scientific theories can only be falsified, not verified. On this view, at any given time, there are different theories that are consistent with the current body of experimental observations, and science progresses by elimination, by coming up with critical tests of theories. For example, one of the motivations advanced for collecting “big data” in neuroscience, such as the connectome, is that theories are presumed to be insufficiently constrained by current data (Denk et al., 2012). This view is extremely popular in biology today, even though again later work in philosophy of science has also pretty much demolished it.

    Paraphrasing Quine (see Two dogmas of empiricism and the Duhem-Quine thesis), we can object that a theory never gets tested directly, only models specific of a particular situation do. For example, if you wanted to test Newton’s laws, you could let an apple fall and measure its trajectory. But to do this, you would first need to come up with a model of the situation, where for example you would consider the apple as a point of a given mass subject to only the force of gravity. In this case, you would conclude that Newton laws are false. But you would have concluded differently if you had added an auxiliary assumption, that air also exerts a friction force on the apple, for which you would have to come up with a particular model.

    Kuhn and Lakatos have pointed out that in fact, the way empirical contradictions are resolved is almost never by abandoning a theory. The process is rather one of interpretation, that is, of coming up with ways of making the observation congruent with the theory. This could be seen as a rhetorical maneuver, or as a fruitful scientific process. In this example, if you think that Newton laws are valid, then you would actually deduce the laws of friction from the empirical contradiction. Laws of friction are in fact very complicated in general and still an active field of research in physics, which draws on various domains of physics, and to make progress one has to accept the underlying theories.

    The key point is to recognize that interpretation is not a flaw of the scientific process, but a logical necessity to confront a theory to reality. A theory is framed in the discrete structure of language, that is, in formal terms. For it to apply to anything in the world, things in the world must be mapped to the formal structure of the theory. This, in essence, is the process of modeling. In contrast with theory, a model does not have a universal character; it applies to a specific situation. In the example above, we would have to introduce the assumption that the apple is a rigid body, and that friction follows a particular law, for example that the friction force is proportional to speed. This implies that it is actually not possible to either verify or falsify a theory on the basis of an empirical observation.

    This argument does not lead to a relativistic view (all theories have the same epistemic value and it is a question of taste); in this, I would temper some of the conclusions of Feyerabend. Interpretation is in fact not only a logical necessity, but also a key element in scientific progress. Lakatos proposed that it is not theories that compete, but research programs. Some research programs are “degenerate”: they evolve by adding heteroclite ad hoc hypotheses to account for each new observation. Others are “progressive”: they evolve by extending their theoretical core, which then applies to new situations. In scientific practice, this is obtained by dissolving the specific character of interpretations into the universal character of theories. To come back to the apple example, initially we would interpret the empirical contradiction by coming up with an empirical model of friction, which essentially amounts to calling the empirical error “friction”. More precisely, it is an auxiliary hypothesis that makes the observation compatible with the theory. But this could then be turned into theoretical progress: from an analysis of a number of cases of falls of objects, we could then postulate that there is a friction force that is proportional to the speed of the apple and to its size (Stokes law). By doing so, we make parts of the previous interpretations instances of a new theoretical proposition. Note that this proposition only makes sense in the context of Newton’s laws, and thus we are indeed describing a system and not just a set of independent laws. The evaluative situation of the apple fall has now changed: we are evaluating a broader theoretical body (Newton’s laws + Stokes law) by using a narrower interpretative model (the apple is a rigid sphere).

    Thus, interpretation is a key feature of belief systems, both logically necessary and progressive, and it appears to be neglected by the two flavors of empiricism that are broadly observed in science (verificationism and falsificationism). Yet without it, it is impossible to understand why people can disagree, other than by postulating than some must be either idiots or liars. I will address this issue in the next part on social contradiction.

    So far, I have argued that scientists face empirical contradiction by interpretation. Theoretical progress is then made by dissolving interpretations into new theory. What this really means is that the very notion of “empirical contradiction” is in fact quite misleading, because for the person doing the interpretative work, there is no real contradiction, only a more complex situation than expected. I will end this part by drawing on developments of psychology, specifically cognitive dissonance theory, and extending to non-scientific situations.

    Resolving empirical contradiction by interpretation is not at all specific of science, but is a general feature of how people confront their beliefs to facts. In When Prophecy Fails, Leon Festinger and colleagues infiltrated a UFO sect that believed in an imminent apocalypse, and they examined what happened when the predicted end of the world did not happen. Believers did not at all abandon their belief. Instead, the leader claimed that they had managed to postpone the end of the world thanks to their prayers, and she proposed a new date. This is a case of interpretation of the observation within the belief system. But importantly, as discussed above, interpretation is not a flaw of human nature, but a necessary feature of belief systems. In this case, the believers appear to have arbitrarily made up an ad hoc justification, and we are tempted to dismiss it as a hallmark of irrational thinking. But when observe the anomalous trajectory of Jupiter and, to make up for this anomaly, we postulate that there must be an unobserved satellite orbiting around the planet, we are making an interpretative move of the same nature, except in this case it turns out to be correct. Our initial reaction in the former case is that any reasonable person should reject the theory if the prediction is directly contradicted, yet in the latter case we find the same attitude reasonable. In reality, the main difference between the two cases is not in the way empirical contradictions are handled, but in the perceived plausibility of both the prediction and the interpretation. Specifically, we do not believe that prayers can have any visible effect at all and thus the interpretative move appears irrational. But of course, the situation is quite different if the powers of prayer have a prominent role in our belief system. Thus, it is an error to describe the ad hoc interpretation as irrational. It is actually totally rational, in that it follows from logical reasoning (A, the end of the world should have occurred if we had not intervened; B, we have prayed; C, prayers have an impact; conclusion: the end of the world has probably be been prevented by our prayers). Only, rationality is applied within a highly questionable theoretical framework. In the end, we realize that it is not really the non-occurrence of the end of the world that should lead us to abandon the belief system, but rather the empirical contradictions of the belief system in its globality, for example the fact that prayers actually do not work.

    Thus, it should not be surprising that in their field study, the authors find that it takes a number of failed end-of-the-world predictions before the beliefs are finally abandoned. This is what Imre Lakatos called a “degenerative research program”: the theory survives repeated contradictions only by making up an incoherent series of ad hoc assumptions. It ends up being overthrown, but the process can take a very long time (this process of change between scientific theories is well documented also by Thomas Kuhn’s The structure of scientific revolutions).

    This phenomenon is particularly visible in political discourse. Any significant political event or observation will be given a different interpretation depending on the political preferences of the person. It never happens that a right wing person turns left wing upon noticing that wealthy countries have many homeless people. Rather, an interpretation is made that revolves around the notion of personal responsibility.

    To give a contemporary example, recent demonstrations in France have been met by an extraordinarily repressive response, with hundreds of serious injuries caused by police, some on journalists and children, which are documented by hundreds of videos circulating on social media (see @davduf and a recent article in Le Monde). A recent one is a 47 year old voluntary fire man, father of three, who was demonstrating with his wife until they were dispersed by tear gas. He was later found lying alone in an empty street with a head injury, and an amateur video shows that police shot him in the head from behind with a flash-ball gun and launched a grenade in the street. The man is currently in a coma. In any of those cases, on social media there is invariably part of the comments that suggest that the man or woman must have done something bad (this is indeed the official doctrine, as the Minister of Interior has recently claimed that he is not aware of any case of police violence). It is not in itself irrational: simply, the commenter presumes that police do not hurt innocent citizens, deduces that the citizen involved is not innocent, and concludes that the critics are irrational conspiracy seekers.

    There are indeed conspiracy theorists, for example those that claim that the landing on the moon was in fact filmed in Hollywood studios. The fact that it is a conspiracy theory is not itself a reason to discredit it, since there have been conspiracies in History. The theory itself is also not irrational, in that it has logical coherence as well as empirical elements of support. For example, on the video the American flag appears to float in the wind whereas there can be no wind on the moon and in fact the flag should appear folded. Indeed: the flag was made rigid precisely for that reason. But most people do not know this fact, and thus the reasons why the ordinary citizen believes that man actually did land on the moon is that she trusts the source and finds the information plausible. Which attitude is irrational?

    These examples illustrate several points. First, isolated empirical contradictions almost never shake a belief system. In fact, this is precisely what we mean when we say that “extraordinary claims require extraordinary evidence”. This proposition, however, is quite misleading since the notion of what is extraordinary is specific of a particular belief system. There is no objective definition of “extraordinary”. Therefore, rather than being a normative feature of scientific method, it simply expresses the inherent conservativeness of belief systems. As Festinger’s study shows, it can take a large number of empirical contradictions to impact a belief system. As explained previously, this is not necessarily a flaw as those contradictions can (sometimes) be turned into theoretical progress within the belief system.

    But there are other ways in which empirical contradictions are handled by belief systems, which are documented in psychology by cognitive dissonance theory. A major one is simply to avoid being confronted to those contradictions, for example by reading newspapers with the same political views, or by discrediting the source of information without actually examining the information (e.g. social media propagate fake news, therefore the video cannot be trusted). Another is proselytism, that is, trying to convert other people to your belief system.

    These mechanisms explain that at any given moment, mutually contradictory belief systems are held by people who live in the same world and are in contact with each other, and who can even discuss the same empirical observations. The conclusion of our discussion is that the main problematic issue in belief systems is not so much irrationality as dogmatism (but we will come back to irrationality in the third part on theoretical contradiction). Dogmatism arises from two different attitudes: blindness and deafness. Dogmatism is blind in that it actively refuses to see empirical evidence as potentially contradictory: it is not just that it is contradicted by empirical observations (this very notion is questionable), but rather that it dismisses empirical contradiction without seriously trying to accommodate for it in a progressive way (i.e., by strengthening its theoretical core). Dogmatism is deaf in that it refuses to acknowledge for the possibility that other rational belief systems can exist, and may have diverging interpretations of the empirical body of observations. Dogmatism denies the theoretical possibility of disagreement: the opponent is always either an idiot (irrational) or a liar (has ulterior motives). In the next part, I will turn to social contradiction: how different belief systems can co-exist and influence each other.

    in Romain Brette on January 16, 2019 04:31 PM.

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    Forget miracles – how can we gauge the real impact of science?

    It’s a problem research funders everywhere grapple with: evaluating what science can do for society

    in Elsevier Connect on January 16, 2019 01:27 PM.

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    “We regret our delay:” PLOS ONE retracts two papers

    PLOS ONE has retracted two papers for image problems, which we’ve learned were brought to the journal’s attention more than four years ago. The first article came from a group of cancer researchers in China, and it turns out to have a bit more wrong than a few dodgy figures. The second also involved cancer … Continue reading “We regret our delay:” PLOS ONE retracts two papers

    in Retraction watch on January 16, 2019 11:00 AM.

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    New Findings Could Help Explain Why ADHD Is Often Overlooked In Girls

    GettyImages-903669856.jpgBy Emma Young

    For every girl with ADHD, there are three boys with the same diagnosis. But among adults, the gender ratio is more like 1:1. That’s a big discrepancy. So what’s going on? 

    In 2017, Aja Louise Murray and colleagues investigated possible predictors of childhood vs. later (adolescent/adult-onset) ADHD, and they found hints that girls tend to develop ADHD at a later age than boys. Now a team that includes the same researchers has investigated this explicitly and in their paper in Developmental Science, they’ve confirmed it seems to be the case, which could partially explain the discrepancy in the ADHD gender ratio between children and adults. 

    The researchers analysed data on 1,571 children living in Zurich, Switzerland, whose teachers used a standard scale to assess symptoms of inattention and also of hyperactivity/impulsivity every year from age 7 (when the children started school) through to age 15. The two domains of ADHD were assessed separately, as previous work has found that they can develop at different rates.

    When it came to inattention, most of the children (about 60 per cent of boys and girls) had low levels of symptoms between the ages 7 to 15. However, whereas the remaining 40 per cent of the boys had persistently high inattention levels during this period, among the girls there was more variation, and generally lower symptom levels: almost a third had moderate symptoms that declined with increasing age, while the others started out with relatively serious symptoms at age 7, which then declined, but still remained above average at age 15. 

    For hyperactivity/impulsivity, there were also some contrasting developmental profiles between the sexes. Again, the majority of children (81 per cent of the girls and 61 per cent of the boys) started out with low levels of symptoms, which decreased even further into late adolescence. There was also a group (13 per cent of boys and 10 percent of girls), who had mildly elevated symptoms in childhood, followed by a dip around age 11 to 13, but then a rapid increase. “This group could speculatively be characterised as ‘adolescence-triggered’,” the researchers write. Finally, there was also a group of children (24 per cent of boys, versus only 9 per cent of girls) who had high levels of symptoms all the way through the study period. 

    In other words, according to this data, more boys than girls show consistently high levels of hyperactivity/impulsivity – and inattention – symptoms from a young age, whereas proportionately more girls than boys develop high levels of these symptoms (which may lead to a diagnosis of ADHD) only after early adolescence.

    Whatever the reasons for this difference, it could be relevant to the sex difference in diagnosis rates because current ADHD diagnostic criteria for children require symptoms to have begun before the age of 12. This could mean that a greater proportion of girls with ADHD, than boys, are being missed by clinicians. (Exactly why adolescence might be associated with a sudden rise in these symptoms in some children, and especially girls, is not known – it could be to do with hormones, and/or increased social and academic pressures, the researchers note.) 

    “More attention should be paid to early adolescence as a period of risk for hyperactivity/impulsivity symptom onset or worsening,” Murray and her colleagues write.  And, they add: “It should be investigated whether removing the ‘onset before 12’ stipulation in diagnostic tests would help to identify more girls who would benefit from intervention.” 

    Sex differences in ADHD trajectories across childhood and adolescence

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

    in The British Psychological Society - Research Digest on January 16, 2019 09:28 AM.

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    Plan S in chaos at Berlin APE conference

    Plan S, designed by the former EU Commissioner Robert-Jan Smits, became a complete and chaotic mess where everyone, including the members of the signatory cOAlition S of research founders, does whatever they want. I learned all that while participating at the Academic Publishing Europe (APE) conference in Berlin, on 15-16 January.

    in For Better Science on January 15, 2019 10:56 PM.

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    Two daring spacecraft aim to bring asteroid dust back to Earth

    A pair of daredevil spacecraft that aim to bring asteroid dust back to Earth have reached their targets and are scouting for the best sampling spots.

    in Science News on January 15, 2019 07:42 PM.

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    About the resignation of the Journal of Informetrics Editorial Board

    We will appoint a new editorial team and board to continue to drive the development of JOI

    in Elsevier Connect on January 15, 2019 04:10 PM.

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    A new 3-D printed ‘sponge’ sops up excess chemo drugs

    Researchers have created “sponges” that would absorb excess cancer drugs before they spread through the body and cause negative side effects.

    in Science News on January 15, 2019 02:00 PM.

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    “An air of urgency” – why we need ethical governance of AI

    ORBIT’s innovation team writes about a new method to evaluate the use of artificial intelligence and related technologies

    in Elsevier Connect on January 15, 2019 12:40 PM.

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    The first suspected exomoon may remain hidden for another decade

    The discoverers of the first evidence for a moon orbiting a planet around a distant star are still trying to confirm the object’s existence.

    in Science News on January 15, 2019 12:00 PM.

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    After more than a year of back and forth, an accounting journal retracts a paper on tax avoidance

    A pair of business researchers in Pittsburgh has lost a controversial 2017 paper on how institutional stock holdings affect tax strategies amid concerns about the validity of the data. The article, “Governance and taxes: evidence from regression discontinuity,” which appeared in The Accounting Review, was written by Andrew Bird and Stephen Karolyi, of Carnegie Mellon’s … Continue reading After more than a year of back and forth, an accounting journal retracts a paper on tax avoidance

    in Retraction watch on January 15, 2019 11:00 AM.

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    Immediately Re-Watching Lecture Videos Doesn’t Benefit Learning

    GettyImages-485409944.jpgBy Christian Jarrett

    Given a passage of text to study, many students repeatedly re-read it in the hope the information will eventually stick. Psychology research has shown the futility of this approach. Re-reading is a poor strategy, it’s too passive and it leads the mind to wander. Much better to test yourself on what you read, or explain it to yourself or someone else. Now a paper in Experimental Psychology suggests the same is true of lecture videos – immediately re-watching them doesn’t lead to any greater learning.

    Leonardo Martin and his team asked 72 participants to watch two lecture videos, both around 10 minutes long. One was a live recording of a lecture about sanitation in the middle ages; the other consisted of voice over slides and was about problem solving. Some students watched the sanitation video first, the others watched the problem solving video first. Also, all the students watched one of the videos (either the sanitation one or the problem-solving one) just once before being tested on it, whereas they watched the other video twice in succession before being tested on it (nine multiple-choice questions in each case). Finally, while they were watching the videos, the students answered a few prompts about whether they were mind wandering or not.

    If immediately re-watching a lecture video helps improve learning then the students ought to have performed better at the test that followed the video they watched twice. But this wasn’t the case – they averaged 79 per cent accuracy in the test about the video they watched once, compared with 76 per cent accuracy in the test that followed the video they watched twice (a statistically non-significant difference). The students also mind wandered more during the repeat viewing than when watching either of the lectures for the first time.

    One important caveat is that this research was specifically about the effects of immediately re-watching a lecture video (“massed re-watching”, as the researchers put it). Re-watching a video after a sufficient delay could be more effective (akin to a form of distributed practice), although testing yourself is probably still the more favourable strategy.

    “Re-watching a video lecture does not encourage individuals to build a richer representation of the content,” the researchers concluded, “thus leading to a more passive mode of viewing that puts little demands on attentional control, ultimately leading to more mind wandering.”

    Re-watching lectures as a study strategy and its effect on mind wandering

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

    in The British Psychological Society - Research Digest on January 15, 2019 10:13 AM.

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    Easing test anxiety boosts low-income students’ biology grades

    Wealthier students outperform their less advantaged peers in math and science. Decreasing test anxiety may help even the playing field.

    in Science News on January 14, 2019 08:00 PM.

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    A cosmic flare called the ‘Cow’ may reveal a new way that stars die

    A burst of light from far away may have been an odd type of exploding star or a white dwarf being eaten by a black hole.

    in Science News on January 14, 2019 04:12 PM.

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    Desalination pours more toxic brine into the ocean than previously thought

    Desalination plants help offset the world’s growing water needs, but they also produce much more supersalty water than scientists realized.

    in Science News on January 14, 2019 03:17 PM.

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    Study Identifies The Most Effective Mental Strategies That People Use To Get Through Aversive Challenges

    GettyImages-820872910.jpgBy Christian Jarrett

    What strategies do you use to push through a tough challenge, be it a run on a treadmill or a stressful phone call with your boss? Perhaps you remind yourself of what you have to gain from completing the task, or you use distraction, or you think about the bad things that will happen if you give in? For a paper in the European Journal of Personality, a team led by Marie Hennecke at the University of Zurich has conducted what they say is the first ever investigation of these strategies, and others, that people use spontaneously in their everyday lives to “regulate their persistence during aversive activities”.

    The researchers’ main interest was to see whether people with strong self-control differ from flakier types by virtue of their use of more effective strategies. In fact, this was not the case – yes, some strategies were more effective than others (offering hope to those of us with weaker willpower that we might benefit from adopting such strategies), but greater use of effective strategies did not explain the persistence of the grittier types, thus suggesting, as the researchers put it, that “… trait self-control and self-regulatory strategies represent separate routes to good self-regulation”.

    The researchers started with a pilot study in which they presented hundreds of participants with challenging scenarios (such as completing a treadmill run) and asked them to list any strategies they’d typically use to push through to the end. The researchers collapsed the answers into 19 strategies most of which fell under one of two headings: situation modification strategies (e.g. drinking coffee; listening to music while working); and attentional deployment strategies (e.g. motivational self-talk or thinking the finish is near).

    screenshot 2019-01-17 at 20.18.46List of strategies (click to enlarge), from Hennecke et al, 2018

    Next, Hennecke’s team ran another pilot study with North American participants and German-speaking participants in which they asked them to complete a measure of their trait self-control and then to indicate how often they used these 19 different strategies (see left). For the study proper, the researchers then used a week-long “experience sampling method” with over 250 young German-speakers – as well as completing the trait self-control quiz, these participants were prompted multiple times a day to log any aversive challenges they’d recently been engaged in (examples included self-study, lectures, commuting and housework), what strategies they’d used to persist, and whether they’d been successful.

    Across the different types of aversive challenge, the strategies correlated with success were: thinking about the positive consequences of getting to the end (this was also the most popular strategy); monitoring one’s goal progress; thinking that the end is near (the second most popular strategy); and emotion regulation (e.g. trying to stay in a good mood). In contrast, distracting oneself from the aversive challenge was associated with less success – perhaps because distraction makes us more inclined to give in and do something more pleasant (note the contrast with research on resisting temptations, such as in the classic Marshmallow Test studies, in which distraction was found to be effective).

    These new findings are of theoretical interest – for instance, an excessive focus on the potential positive outcomes of challenges has previously been flagged in research as an unhelpful approach because it encourages a dependence on so-called extrinsic motivation. Researchers have previously argued that we are actually more likely to reach our goals if we can find pleasure in the process (intrinsic motivation). Hennecke and her colleagues speculated that perhaps the key factor here is whether the challenge is enjoyable or inherently aversive – if the latter, then perhaps focusing on positive outcomes can be an effective strategy. Further research can test this. Meanwhile, monitoring one’s progress is well-established as an effective self-control strategy; on the other hand, the researchers said the strategy of thinking that the finish is near, while very popular here, has actually not been studied before.

    Returning to Hennecke and her colleagues’ main focus – whether people with more self-control use more effective strategies – yes, two of the effective strategies were used more often by participants higher in trait self-control, namely focusing on positive consequences and emotion regulation (as was a third strategy – goal setting – though this strategy was not correlated with greater success). Crucially, however, as I mentioned above, the greater use of these two effective strategies did not explain why these high trait self-control individuals tended to enjoy greater success at aversive challenges. “It is possible that more automatic processes that individuals may not be able to explicitly report are better candidates for explaining individual differences in self-control,” the researchers said.

    Limitations of the new findings include the reliance on participants’ own estimates of their success at persistence, and the mostly student sample for the main study (for whom the nature of everyday challenges are likely to be different than for non-students). However, this research clearly breaks new ground. As Hennecke and her colleagues put it, “… our findings promote a more comprehensive understanding of self-regulatory success and failure during people’s daily attempts to regulate their persistence during aversive activities.”

    Doing Despite Disliking: Self‐regulatory Strategies in Everyday Aversive Activities

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

    in The British Psychological Society - Research Digest on January 14, 2019 12:22 PM.

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    Your phone could reveal your radiation exposure after a nuclear disaster

    Examining personal electronics may help gauge people’s radiation exposure in the event of a nuclear accident or attack.

    in Science News on January 14, 2019 11:00 AM.

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    An Australian university cleared a cancer researcher of misconduct. He’s now retracted six papers.

    The story of Levon Khachigian’s research is a long and winding tale. One place to start would be in October 2009, when a paper co-authored by Khachigian — whose work at the University of New South Wales (UNSW) has been funded by millions of dollars in funding from the Australian government, and has led to … Continue reading An Australian university cleared a cancer researcher of misconduct. He’s now retracted six papers.

    in Retraction watch on January 14, 2019 11:00 AM.

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    Texas Photoshop Massacre (in Nature)

    The team around the paediatric oncologist Nabil Ahmed at Baylor College of Medicine in Houston, Texas, discovered a way to engineer T-leukocytes to bypass the blood-brain barrier at attack otherwise untreatable brain cancers. Their amazing technology to get this published in Nature was brazenly insolent data fakery.

    in For Better Science on January 14, 2019 06:00 AM.

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    NeuroFedora updated: 2019 week 2

    We had our first meeting of the year. The full logs from our meeting are available here on the Fedora mote application. I have pasted the minutes of the meeting at the end for your convenience.

    The meeting was broadly for the team to come together and discuss a few things. We checked on the status of current tasks, and discussed our future steps. We've got to work on our documentation, for example. There's a lot to do, and a lot of cool new things to learn---in science, computing, and community development. If you'd like to get involved, please get in touch.

    We're continuing our work on including software in NeuroFedora, since that's the major chunk of our work load.


    Meeting summary

    Meeting started by FranciscoD at 14:00:15 UTC.

    Meeting ended at 15:10:43 UTC.


    NeuroFedora documentation is available on the Fedora documentation website. Feedback is always welcome. You can get in touch with us here.

    in Ankur Sinha on January 13, 2019 08:55 PM.

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    A Scientific Song of Consciousness and Self

    In what may be a world first, a peer-reviewed journal, Frontiers in Psychology, has published a song. The musical contribution to science is called 'It's Hard Work Being No One', and it comes from psychologist J. Scott Jordan of the Illinois State University. Here's some of the lyrics, which deal with nothing less than the existential question of identity: I got a ticket on the next train to OZ Gotta see that crazy wizard because Even tin man was an I, just had no heart Scarecrow was

    in Discovery magazine - Neuroskeptic on January 13, 2019 12:55 PM.

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    Weekend reads: Fishy research on fishes; was “Sokal Squared” misconduct?; the misuse of metrics

    Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, we could really use your help. Would you consider a tax-deductible donation to support Weekend Reads, and our daily work? Thanks in advance. The week at Retraction Watch featured a criminology professor who has had four papers retracted for … Continue reading Weekend reads: Fishy research on fishes; was “Sokal Squared” misconduct?; the misuse of metrics

    in Retraction watch on January 12, 2019 02:50 PM.

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    Here’s how the record-breaking government shutdown is disrupting science

    The partial government shutdown is taking many U.S. scientists out of commission and putting up hurdles to their research.

    in Science News on January 12, 2019 01:00 PM.

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    A drill built for Mars is being used to bore into Antarctic bedrock

    An autonomous drill originally designed for work on Mars has its first mission in Antarctica.

    in Science News on January 11, 2019 07:47 PM.

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    How worm blobs behave like a liquid and a solid

    Blobs of worms flow like a fluid, plop like a solid and fascinate scientists.

    in Science News on January 11, 2019 06:11 PM.

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    Group issues model retraction over antibody error

    The authors of a 2013 paper on antibody production in patients with rheumatoid arthritis have retracted the work in what looks to us like a case study in how to handle operator error. The paper, “Monoclonal IgG antibodies generated from joint-derived B cells of RA patients have a strong bias toward citrullinated autoantigen recognition,” was … Continue reading Group issues model retraction over antibody error

    in Retraction watch on January 11, 2019 11:00 AM.

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    Nerve cells from people with autism grow unusually big and fast

    In some forms of autism, nerve cells develop faster than normal, possibly setting the stage for the disorder, a study finds.

    in Science News on January 11, 2019 11:00 AM.

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    Researchers Tried To Explore Why “Stereotype Threat” Harms Performance, But Found It Didn’t Harm Performance At All

    GettyImages-185064122.jpgIs stereotype threat too context-dependent to matter all that much?

    By Jesse Singal

    Stereotype threat is a very evocative, disturbing idea: Imagine if simply being reminded that you are a member of a disadvantaged group, and that stereotypes hold that members of your group are bad at certain tasks, led to a self-fulfilling prophecy in which you performed worse on such tasks than you would otherwise.

    That’s been the claim of stereotype threat researchers since the concept was first introduced in the mid-1990s, and it’s spread far and wide. But as seems to be the case with so many strong psychological claims of late, in recent years the picture has gotten a bit murkier. “A recent review suggested that stereotype threat has a robust but small-to-medium sized effect on performance,” wrote Alex Fradera here at the BPS Research Digest in 2017, “but a meta-analysis suggests that publication bias may be a problem in this literature, inflating the apparent size of the effect.” Adding to the confusion are some results which seem to run exactly opposite to what the theory would suspect, like the one Fradera was reporting on: In that study, female chess players were found to have performed better, not worse, against male opponents, which isn’t what the theory would have predicted.

    Now, another study is poised to complicate things yet further. In a paper to be published in the European Journal of Social Psychology, and available as a preprint, a team led by Charlotte Pennington of UWE Bristol recruited female participants to test two mechanisms (reduced effort and working memory disruption) that have been offered to explain the supposed adverse performance effects of gender-related stereotype threat. They also compared different ways of inducing stereotype threat. Interesting questions, you might think, but in all cases the researchers came up empty.

    Pennington and her colleagues’ study consisted of a pair of experiments in which they asked women to complete eye-tracking (both experiments) tasks, intended to test their inhibitory control, and a mental-arithmetic task (the second experiment only) designed to test their working memory. The participants were split into groups and, prior to their completion of the task, given various stereotype reminders — some, for example, were informed that some research shows “that gender differences exist on visuospatial and mathematical tasks,” and that “females are shown to perform less accurately compared to males.” These reminders were used to provoke two different kinds of stereotype threat – one was “group-as-target”  designed to induce a fear that one’s own performance may be used justify stereotypes about women’s inferior performance; the other, a “self-as-target” threat, involved mentioning that women typically perform worse on the task than men, but with the focus of the results supposedly on their own personal ability. In the second experiment, a group was exposed to a positive stereotype claim, to see if that would improve performance, and in both experiments, a control group wasn’t exposed to any stereotype-laden messaging at all.

    The results of both experiments are easy to sum up: Pennington and her colleagues detected no differences between the groups on the key measures they were testing, either in terms of reduced effort or signs of working memory interference. Simply put, neither experiment provided any evidence for a stereotype effect in this setting, let alone revealing anything about the possible mechanisms or contrasting effects of group- or self-threats. Of course, plenty of other studies have provided evidence for such effects. It’s complicated.

    One paragraph in Pennington et al’s paper shows just how complicated:

    Research has revealed many factors that heighten individuals’ susceptibility to stereotype threat. From a methodological viewpoint, performance decrements are more likely to occur under stereotype threat when the task is difficult … However, a recent meta-analysis casts doubt on task difficulty as a significant moderator of stereotype threat … It is also proposed that stereotype threat effects are more likely to emerge when individuals attribute worth to their social group membership (i.e., group identification…), endorse the stereotype to be accurate (i.e., stereotype endorsement…), and identify strongly with the stereotyped domain … Nguyen and Ryan (2008) report in their meta-analytic review, however, that women with moderate relative to high domain identification are more affected by gender-maths stereotypes, with research further suggesting that individuals do not need to identify with the stereotyped domain or group to experience stereotype threat .… The complexity of these observed findings has led some scholars to theorise that individuals may experience unique forms of stereotype threat, which are moderated by different factors and underpinned by diverse mechanisms … [References, removed here for ease of reading, can be found in the preprint].

    If what all these messy, sometimes contradictory findings suggest is true, and stereotype threat, to the extent it has an effect, is moderated by factors like explicit endorsement (or not) of the stereotype in question, or domain identification (or not), and so on – then who is to say we’ve come close to figuring out all the possible moderators? At a certain point, the simple storyline that caused the concept to spread so virally in the first place just doesn’t quite hold anymore. It’s not “You will be affected by X,” but rather, “You might be affected by X, depending on A, B, and C.”

    That’s the nature of good science, of course: We hone in on the truth by figuring out the complicated ways a given phenomenon works. But sometimes this process is at odds with science communication, and can lead to preemptive, oversimplification popularisation and application. If stereotype threat is so complicated that “individuals may experience unique forms of” it, then what are we left with, exactly?

    Stereotype Threat May Not Impact Women’s Inhibitory Control or Mathematical Performance: Providing Support for the Null Hypothesis

    Post written by Jesse Singal (@JesseSingal) for the BPS Research Digest. Jesse is a contributing writer at BPS Research Digest and New York Magazine. He is working on a book about why shoddy behavioral-science claims sometimes go viral for Farrar, Straus and Giroux.

    in The British Psychological Society - Research Digest on January 11, 2019 09:58 AM.

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    Highlights of the BMC series: December 2018

    BMC International Health and Human Rights: Celebrating Human Rights Day

    Human Rights Day  is held on the 10th December, the date that the United Nations General Assembly adopted the Universal Declaration of Human Rights. To mark this occasion, Professor Siroos Mirzaei, an Associate Editor for BMC International Health and Human rights  and Head of the Department of Nuclear Medicine of the Wilhelminen Hospital in Vienna, with Professor Thomas Wenzel, an Associate Professor from the Medical University of Vienna, were invited to write a blog post on the role that physicians play in upholding human rights and the dangers associated with this.

    The authors explain that physicians are often faced with a variety of different ethical and human right issues. Examples include being requested to violate ethical standards in so called “dual obligations” situations, such as being involved in the planning and observation of torturing prisoners. Physicians can also find themselves at serious risk for upholding legal and ethical standards. Mirzaei and Wenzel then conclude the blog post by discussing the barrage of new ethical challenges that physicals may face, linked, for example, to medical technology or health related aspects of conflicts.

    BMC Health Services Research: State variation in opioid treatment policies and opioid-related hospital readmissions

    A new article, published as part of the ongoing Health Services Research for Opioid Use Disorders thematic series in BMC Health Services Research, investigates different opioid treatment policies in the USA and how these variations may affect opioid-related hospital readmissions in different states

    Such policies include, for example, Good Samaritan laws, the availability of naloxone to reverse the effects of an overdose or the provision of medication-assisted treatment for opioid dependence. Blanchard et al conducted a study to assess whether such state opioid treatment policies had an effect on 90-day opioid-related hospital readmissions.

    Differences in index hospitalization rates suggest that states with opioid treatment policies had a higher level of need for opioid-related intervention; this may be a factor in the higher rates of hospital readmission in these states. This, in turn, also suggests that more research is needed to understand what various opioid treatment policies can be most effective in reducing hospital readmission rates.

    BMC Cancer: Exploring the efficacy of an electronic symptom assessment and self-care intervention to preserve physical function in individuals receiving neurotoxic chemotherapy

    Chemotherapy-induced peripheral neuropathy (CIPN) is a progressive condition experienced by up to 40% of cancer patients undergoing chemotherapy. Symptoms include numbness, tingling and sensitivity to cold in the hands and feet and sometimes in the arms and legs. It can cause sufferers to lose function of the affected limbs.  Diagnosing and treating CIPN quickly may prevent this loss of physical function.

    Chemotherapy-induced peripheral neuropathy (CIPN) is a progressive condition experienced by up to 40% of cancer patients undergoing chemotherapy.

    Knoerl et al recently published the results of a trial whereby self-reported physical function in cancer patients undergoing neurotoxic chemotherapy (chemotherapy known to cause CIPN) is assessed via a newly developed Electronic Symptom Assessment-Cancer (ESRA-C) intervention.  The article reports that the patients experienced significantly less reduction in physical functioning when reporting their symptoms in this way.

    BMC Women’s Health: Is caregiving by baby boomer women related to the presence of depressive symptoms? Evidence from eight national surveys

    Studies have suggested that caregivers can be vulnerable to psychological distress (for example, depression), particularly women. An article has recently been published in BMC Women’s Health that investigates the relationship between caregiving (proving unpaid care to someone who has physical, psychological or developmental needs) and depression amongst Baby Boomer women, using surveys distributed to women from nineteen different countries.

    Baby Boomer women living in countries where a higher proportion of their peers are expected to be in managerial/professional employment and living in countries where women are often in vulnerable employment were found to be at greater risk of displaying symptoms of depression

    The term “Baby Boomer” refers to people born between 1946 and 1964. This group of people benefited from the global revival after World War II, with many becoming more highly educated than the previous generation and therefore more likely to be employed in professional and managerial occupations.  Baby Boomer women living in countries where a higher proportion of their peers are expected to be in managerial/professional employment and living in countries where women are often in vulnerable employment were found to be at greater risk of displaying symptoms of depression.  These findings suggest that the risk of depression amongst Baby Boomer women in a caregiving role is dependent in some degree upon social context and structure and that promoting mental health for this group should therefore be tailored to their situation.

    BMC Energy: Thematic series on Advanced Biofuels for CO2 Mitigation

    BMC Energy is inviting submissions to the newly launched thematic series on “Advanced Biofuels for CO2 Mitigation,” covering topics from  strain development and cultivation to biorefineries of microalgae for biofuels.

    BMC Evolutionary Biology: Image of the month

    Figure 1, Koch et al, https://doi.org/10.1186/s12862-018-1300-4

    This image is taken from an article by Koch et al on the sea urchin tree of life and shows the morphological and taxonomic diversity of echinoids included in this study.

    The post Highlights of the BMC series: December 2018 appeared first on BMC Series blog.

    in BMC Series blog on January 11, 2019 09:23 AM.

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    Medical device company uses Science Exchange to advance bionics into the clinic

    Accelerating bionics from the lab to the real world.

    BIOS is an innovative medical device company that is creating an open standard connection for bionic limbs which can be controlled with thought and respond to sensory inputs. Their R&D programs require integrated, cutting-edge expertise from multiple disciplines, including materials science, machine learning, and neuroscience.

    Download the case study to learn how Science Exchange enabled BIOS to rapidly advance its bionics technologies, bringing these potentially life-changing devices into the clinic where they are now being tested.

     

    BIOS Case study image

    in The Science Exchange Blog on January 11, 2019 12:02 AM.

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    Poison toilet paper reveals how termites help rainforests resist drought

    Novel use of poisoned toilet paper rolls and teabags led to discovery that termites help tropical forests resist droughts.

    in Science News on January 10, 2019 07:00 PM.

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    OSU cancer researcher who has faced misconduct allegations sues to regain lost department chairmanship

    Carlo Croce, the embattled cancer researcher at The Ohio State University (OSU), is suing the institution to reclaim the department chair he lost late last year for reasons that he says are unclear. In a filing with the Franklin County civil court, Croce and his attorneys, from the Columbus firm of James E. Arnold and … Continue reading OSU cancer researcher who has faced misconduct allegations sues to regain lost department chairmanship

    in Retraction watch on January 10, 2019 06:45 PM.

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    Floating seabirds provide a novel way to trace ocean currents

    Seabirds idly drifting with ocean currents provide a novel way to track and understand how these flows change with time and location.

    in Science News on January 10, 2019 02:00 PM.

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    50 years ago, scientists studied orcas in the wild for the first time

    The study of killer whales has come a long way since the capture of seven in 1968 allowed scientists to study the animals in their habitat.

    in Science News on January 10, 2019 01:00 PM.

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    3 challenges faced by female researchers in the developing world

    Women in STEM talk about how international foundations and editorial boards can support gender equality

    in Elsevier Connect on January 10, 2019 12:58 PM.

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    Postdoc free access program helps researchers between positions

    Now the program includes a year of access to Scopus as well as ScienceDirect

    in Elsevier Connect on January 10, 2019 12:29 PM.

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    Even potential participants of a research integrity conference commit plagiarism, organizers learn

    One would hope that researchers submitting abstracts for a meeting on research integrity would be less likely to commit research misconduct. But if the experience of the 6th World Conference on Research Integrity is any indication, that may not be the case. Here, the co-organizers of the conference — Lex Bouter, Daniel Barr, and Mai … Continue reading Even potential participants of a research integrity conference commit plagiarism, organizers learn

    in Retraction watch on January 10, 2019 11:00 AM.

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    ‘Little Foot’ skeleton reveals a brain much like a chimp’s

    An ancient skeleton dubbed Little Foot points to the piecemeal evolution of various humanlike traits in hominids, two studies suggest.

    in Science News on January 10, 2019 11:00 AM.

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    Time For A Fresh Approach To Learning Difficulties? The Cognitive Profile Of Kids Struggling At School Bore No Relation To Their Official Diagnoses

    Screenshot 2019-01-09 at 16.23.06.pngThe study used “machine learning” to organise children into clusters based on their cognitive profiles. (Figure 4 reproduced from Astle et al, 2018. See their open-access paper for description.)

    By Emma Young

    Around 30 per cent of British children fail to meet expected targets in reading or maths at age 11. These children face a future of continuing difficulties in education, as well as poorer mental health and employment success. Understanding why some kids struggle – and providing them with tailored support as early as possible – is clearly vital. Some will be diagnosed with a specific disorder, such as Attention Deficient Hyperactivity Disorder or dyslexia, and get targeted help. But many will not. And even many conventional diagnostic labels may be misleading, and fail to capture the true picture of a child’s problems, according to new work by a team at the MRC Cognition and Brain Sciences Unit at the University of Cambridge, which has come up with a radical, alternative approach. 

    Duncan Astle and his colleagues studied 520 children aged between 5 and 18 years (average age 9) who had been referred to a research clinic at the unit for problems with attention, memory, language or poor school progress in reading or maths. Setting aside these diagnoses, they gave all the children a battery of assessments of their cognitive and learning performance, which included measures of working memory, phonological processing, spelling, reading, and maths. Their communication skills were measured using a separate checklist. A parent or carer also completed behavioural assessments of each child – reporting on their impulse control and emotional regulation, for example. The team then fed the cognitive and learning results for each child into an artificial neural network, which looked for any patterns in the data, grouping kids with distinct similarities into clusters.

    One hundred and eighty-four of these children also had MRI brain scans – as did 36 typically performing children, for comparison – allowing the researchers to look for any group differences in patterns of communication between brain regions.  

    As reported in their open-access paper in Developmental Science, according to the artificial neural network analysis, the children fell into four distinct groups. But these bore no relationship to their previous diagnoses. As the researchers write, “children referred primarily for problems with attention, poor learning or memory were equally likely to be assigned to each group”. This finding is worth stressing. The conventional diagnostic labels already given to the children did not reflect their cognitive profiles identified by the thorough testing in this study: “The four groups cut across any traditional diagnostic groupings that existed within the data,” the researchers wrote.  

    So what did characterise these groups? 

    More than half of the children in the sample fell into two extremes. Those in the “age appropriate” group in fact scored typically for their age on the cognitive tests; they did not have learning difficulties. But they did have an elevated level of behavioural difficulties, which presumably accounted for their problems in school. Meanwhile, members of the “broad cognitive deficits” group had widespread and severe cognitive problems, scoring in the bottom 5 per cent of the population on measures of spelling, reading and maths, and also experiencing difficulties with communication. 

    “Generalised cognitive deficits therefore appear to constrain multiple aspects of learning,” the authors note. Relative to the other groups, kids in this group also showed reduced connectivity between some specific areas of the brain that have previously been identified as playing a role in multiple higher-order cognitive skills (such as problem-solving). “These general struggling learners are rarely studied, but our data suggest that they are common amongst those coming to the attention of children’s specialist services,” the researchers write. 

    Children in the other two groups scored in between the two extremes, overall – but they also showed some specific deficits. 

    One group was particularly poor at phonological processing – processing sounds in words – and verbal short-term and working memory. As might be expected, these children had trouble with speech, syntax and general coherence. And the brain imaging data showed reduced connectivity between regions implicated in language processing, supporting the AI analysis. However, these children were also poor at maths, which was unexpected. Though impaired phonological processing is typically associated with problems with reading, this data suggests that it’s likely to indicate more general learning deficits.

    Members of the fourth group had distinct difficulties in working memory, scoring significantly below average on spatial, short-term memory and on verbal and spatial working memory. (There was no obvious differences in the brain connectivity patterns of these children.) 

    One of the striking findings is that though the two intermediate groups had different specific deficits, their performance at maths and reading were almost identical. This contrasts with earlier research linking phonological problems to reading difficulties (dyslexia) and spatial short-term and working memory problems with trouble with maths (dyscalculia). This may be because previous studies have tended to recruit kids with these specific deficits – i.e. reading but not numeracy problems, for example. According to the new results, such specific learning problems may in fact be relatively rare in the general population of struggling learners (which chimes with a recent study of dyscalculia prevalence that found most children with dyscalculia also had language problems).

    The researchers do acknowledge a few imitations with the study. For example, as a total of only 220 children were included in the neuro-imaging comparison portion of the research, only the largest and most consistent group differences are likely to have been revealed. (Which could explain why the team did not observe brain communication differences in a few of the groups.) 

    But there are clearly potentially important insights here. If, as this work suggests, children can struggle with maths and reading for very different reasons, which do not necessarily align with diagnoses made in the conventional way, then surely the diagnosis and referral process has to be looked at – and the interventions that might help these children will surely have to be differently tailored, too. 

    Remapping the cognitive and neural profiles of children who struggle at school

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

    in The British Psychological Society - Research Digest on January 10, 2019 09:30 AM.

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    PLOS Board Appointments

     

    After a careful search and much consideration, we are excited to share with our community five new appointments we’ve made to the PLOS Board. This is a pivotal time for PLOS, and as you’ll see, each member will bring us a different perspective, which will enable us to expand the ways in which we serve our scientific communities.

    Our new Board Chair is Alastair Adam, currently Co-CEO of innovative digital textbook publisher, FlatWorld, who brings to the role not only a strong understanding of publishing – including scientific journals – but also his business savvy and strategic skills. Alastair joined the Board effective November 1 and assumed the Chair role on January 1, 2019, replacing our longtime Board Chair, Gary Ward (more on Gary a little later).

    We also added Dr. Simine Vazire, who is currently a Professor in the Department of Psychology at UC Davis where her research focuses on one of the oldest and most fundamental questions in psychology: how do we know ourselves? In 2017, she was awarded a Leamer-Rosenthal Prize for Open Social Science in recognition of her efforts to advance reproducibility, openness and credibility in the social sciences. She held a previous role as a senior editor of Collabra: Psychology and Editor-in-Chief of Social Psychological and Personality Science. Her scientific and editorial expertise bring a well-rounded and diverse perspective to our Board, and will help to ensure that working scientists retain a strong voice on our Board.

    Dr. Victoria Coleman joined the Board in May 2018. She is currently the Chief Technology Officer at the Wikimedia Foundation where she sets the organization’s technical roadmap for the evolution, development, and delivery of core platforms and architecture.  Victoria brings valuable technology experience to the Board at a time when PLOS, like many mid-size publishers, faces important and difficult choices about its technology infrastructure. Victoria serves in several advisory roles including the Board of the Santa Clara University Department of Computer Engineering and as Senior Advisor to the Director of the University of California Berkeley’s Center for Information Technology Research in the Interest of Society.

    We also wanted to ensure that we maintain deep experience in PLOS’ core biomedical science fields, and we are very lucky to have Professor Keith Yamamoto of UCSF agree to join us (effective February 1, 2019). Keith is both a highly regarded scientist running his own research lab and has extraordinary experience in the policy arena focusing much of his career on science practice, education, communication, and advocacy including strong and early support for OA. He currently serves as UCSF’s first vice chancellor for Science Policy and Strategy.

    Last but by no means least, Suresh Bhat joined us on November 1, 2018 as incoming Chair of the Finance Committee. Suresh brings to PLOS not only deep financial knowledge but also experience at a top research university and a passion for education. Suresh has headed finance programs for a number of financial institutions. He is currently CFO and Treasurer at the Hewlett Foundation, prior to that, he was CFO at the Haas School of Business at UC Berkeley (and is a Haas and Cal alum).

    I would be remiss if I did not take the opportunity here to express my heartfelt thanks to both Gary Ward, our now former Board Chair, and Mike Eisen, one of the co-founders of PLOS, both of whom left the Board in 2018.  In his seven years as Board Chair, Gary has led the Board with passion, wisdom and integrity, and has been both counsel and friend to many of us in the organization. Mike is of course irreplaceable in every way. His vision, zeal and dedication are a big reason that PLOS not only exists but has had such a deep impact on scientific communication. I have no doubt that Mike will continue to be one of PLOS’ greatest advocates (and yes, let us know when we get it wrong – as good friends do!).

    While goodbyes are never easy, we are excited to embark on this new chapter for PLOS with the fresh wisdom of so many exceptional, dedicated individuals. Please join us in welcoming our new Board members!

    in The Official PLOS Blog on January 10, 2019 12:01 AM.

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    Oft-quoted paper on spread of fake news turns out to be…fake news

    The authors of an much-ballyhooed 2017 paper about the spread of fake news on social media have retracted their article after finding that they’d botched their analysis. The paper, “Limited individual attention and online virality of low-quality information,” presented an argument for why bogus facts seem to gain so much traction on sites such as … Continue reading Oft-quoted paper on spread of fake news turns out to be…fake news

    in Retraction watch on January 09, 2019 10:10 PM.

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    This protein may help explain why some women with endometriosis are infertile

    Infertile women with endometriosis have a reduced amount of a protein found to be important for establishing pregnancy in mice, a study finds.

    in Science News on January 09, 2019 07:53 PM.

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    A new app tracks breathing to detect an opioid overdose

    A smartphone app called Second Chance could help save opioid users who shoot up alone.

    in Science News on January 09, 2019 07:00 PM.

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    Paint specks in tooth tartar illuminate a medieval woman’s artistry

    Tooth tartar unveils an expert female manuscript painter buried at a German monastery.

    in Science News on January 09, 2019 07:00 PM.

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    A second repeating fast radio burst has been tracked to a distant galaxy

    Astronomers have spotted a second repeating fast radio burst, and it looks a lot like the first.

    in Science News on January 09, 2019 06:08 PM.

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    Agrolab A/S Joins Science Exchange to Offer Online Access to its Plant Protection Product (PPP) Services in Europe

    Science Exchange, the world’s leading marketplace for R&D services, announced a collaboration with Agrolab A/S to offer online access to its Registration & Field-Testing solutions – including Dossier preparation, E-Fate and Eco-Tox Risk Assessments and GEP/GLP field trials – to AgChem companies focused on Europe.

    Agrolab A/S is a Denmark-based agricultural C.R.O. Its mission is to ensure the safe production of food by assisting companies with testing, developing and registering PPPs according to EU regulations. In addition to field trials, Agrolab A/S can also conduct greenhouse and other specialty trials; i.e. snails, Collembola, etc.

    Explore their services listed on the Science Exchange Agrolab A/S Provider Profile.

    Agrolab sa joins Science Exchange

    Agrolab A/S is certified to conduct GEP/GLP field/laboratory trials at its field stations in Denmark, Sweden, Latvia, and Lithuania. Agrolab A/S is therefore uniquely situated to provide PPP solutions that cover the entire range of requirements from field trials to registration in Scandinavia and the Baltics. Agrolab can also conduct risk assessments according to guidelines from Central and Southern Europe.

    Furthermore, Agrolab has expertise in biocides, biostimulants, biopesticides and fertilizers.  

    in The Science Exchange Blog on January 09, 2019 04:49 PM.

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    Studies can be in vitro, in vivo and now ‘in fimo’ — in poop

    Scientists have coined a new term — “in fimo” — to describe studies focused on feces.

    in Science News on January 09, 2019 12:00 PM.

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    Cribbing from Kribbe: UK criminology prof loses four papers for plagiarism

    A professor of criminology at Middlesex University London has had four papers retracted because at least three of them cribbed significantly from a PhD thesis written by someone named Kribbe. Three of the four retractions for the professor, Anthony Amatrudo, appear in International Journal of Law in Context. One of the notices reads: It has … Continue reading Cribbing from Kribbe: UK criminology prof loses four papers for plagiarism

    in Retraction watch on January 09, 2019 11:00 AM.

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    Raising the global visibility of local research

    A Colombian university’s Research and Innovation Office and library collaborate with Elsevier to make non-STEM, non-English research more accessible

    in Elsevier Connect on January 09, 2019 09:37 AM.

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    Twitter Study Confirms The Power Of “Affect Labelling” – Emotions Are Calmed By Putting Them Into Words

    GettyImages-1073605034.jpgBy Christian Jarrett

    You might imagine – as prior research suggests many people do – that putting your feelings into words will only intensify them. In fact, many laboratory studies have found the opposite to be true. Stating out loud, or writing down, what you are feeling – a process that psychologists call “affect labelling” – seems to down-regulate emotions, diminishing their intensity.

    Now an intriguing study has explored this phenomenon outside of the lab, analysing over a billion tweets to find examples of when people used a tweet to put their emotional state into words. From analysing the emotional language used in preceding and subsequent tweets, Rui Fan and his colleagues were able to see how the act of affect labelling influenced the course of an emotional state. “We found that, for a majority of individuals, emotional intensity decreased rapidly after their explicit expression in an ‘I feel’ statement,” the researchers write in their paper in Nature Human Behaviour.

    Fan and his team identified over 42,000 English language tweets in which an individual had stated they were feeling a positive emotion (for example, writing “I feel happy” or “I feel awesome”) and another 67,000-plus in which an individual had stated they were experiencing a negative emotion (for example, writing “I feel sad” or “I feel terrible”).

    Next, they used an established algorithm to analyse the emotional language content of any tweets written in the 6 hours prior to the affect labelling tweet, and 6 hours afterwards (the algorithm uses over 7,000 commonly used English words previously scored by human raters in terms of their relative positivity or negativity). The emotional language scores provided by the algorithm allowed the researchers to chart the intensity of the Twitter users’ emotions prior to and after they had explicitly labelled how they were feeling.

    The picture that emerged was that both positive and negative emotions began ramping up prior to an act of affect labelling (captured in the “I feel …” tweet) and then rapidly calmed afterwards. On average, the positive emotional experiences were longer lasting than negative (94 versus 85 minutes). Also, the ramping up and subsequent calming of positive emotions was symmetrical around the peak that coincided with the “I feel …” affect labelling tweet. In contrast, the build up of negative emotions was longer and more gradual prior to the relevant “I feel …” tweet, followed by a faster decline to baseline levels.

    Comparing between the genders, there was a suggestion that the calming power of affect labelling was more striking for women than men, especially for negative emotions.

    The researchers acknowledged their approach has its drawbacks – for instance, to what extent are people’s emotional expressions on social media a performance rather than a true reading of their emotional state? It’s possible too that the findings would vary in other languages or cultures. Also, while analysing vast quantities of data gathered from social media offers many advantages (such as large sample sizes and real-life data), there is a loss of experimental control, and experts often disagree about the meaning of the data and how best to interpret it (see here for an example in a different context). It’s notable that in the current study there was no comparison with how positive and negative emotional states unfold in the absence of affect labelling (i.e. what, in an experimental set-up, would be the control condition).

    These issues aside, in an accompanying commentary on the new research, Matthew Lieberman – a leading research on affect labelling – describes the findings as “remarkable”. He adds: “The authors took a creative approach to studying affect labelling out in the real world and produced some of the strongest and most comprehensive data in support of the role of affect labelling in dampening affective intensity.”

    All of which raises an obvious but relatively unexplored question – why does putting our feelings into words lead to a dampening of those feelings? Hopefully future studies will address the relevant mechanisms, which Lieberman (in a recent review) suggests could include a distracting effect, a reduction of uncertainty, and/or something to do with “symbolic conversion” – the distance and closure created by translating emotions into words.

    The minute-scale dynamics of online emotions reveal the effects of affect labeling

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

    in The British Psychological Society - Research Digest on January 09, 2019 09:37 AM.

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    Succeeding as a woman in biomedical engineering

    Tell us a bit about your career as a scientist and Professor and what a typical day looks like for you. What is the most rewarding part of your role?

    As a scientist and a professor, my typical day is focused on teaching the younger generation of engineering students and expanding on my own research. I teach both undergraduate and graduate students in bioengineering as well as guide the students at my lab, aiming to help them improve their research and methodology skills, and their general understanding of bioengineering.

    Concurrently, I communicate with different researchers and industrial leaders to perform innovative and collaborative research and to pioneer new technological advancements for the benefit of cancer patients. I hope to one day be able to aid these people in their battles with this illness.

    The most satisfactory aspect of my role is the notion that my research and teaching will one day aid the future generation of engineers, fulfil their potential and dreams in this field and ultimately bring societal progress.

    What is it like being a woman in your field? Have you ever had any difficulties in your career due to your gender?

    I strongly suggest that young women engineers are ambitious and actively seek out opportunities that can support their career development and fully grasp everything that is available to them.

    In Korea, it can be difficult to be a woman as an engineer in any of the engineering fields. In fact, the majority of the discipline is heavily outnumbered by men. Although sexual discrimination is gradually decreasing over time with improving awareness to social rights and gender equality, there are various difficulties that I have faced.

    Following your dreams as a woman engineer and mother can be difficult, as you are expected to take care of your children while working. This is particularly challenging in Korea, where social support is lacking. In my case, there was no other engineer in my family, so I had to plan everything by myself and the absence of social support made it very difficult to develop my career. However, I expect a better outcome for younger generations of women engineers as there is a growing number of foundations, communities, and social structures coming into place with an aim to support young women engineers to follow their dreams.

    I always admired the well-established network of male engineers, which easily enabled collaborative research. Therefore, I strongly suggest that young women engineers are more ambitious and actively seek out opportunities that can support their career development and fully grasp everything that is available to them.

    You’ve had an international career and you are currently affiliated with institutions in the US, China and South Korea. What is your experience working for these different regions?

    Source: © Gawrav Sinha / Getty Images / iStock

    Regarding my international career and my affiliation to USA, China, and South Korea as a researcher, there are substantial differences in research methodology and skill level among these countries. USA is still the forerunner of pioneering research and possesses the largest number of global leaders within different academic disciplines.

    The research environment in China is rapidly evolving and is becoming globally recognizable with the quality of research improving exponentially over the last two decades. Strong government support for research expansion and a large pool of engineers will provide strong foundation for China to become a leading figure in the future.

    Lastly, Korea does not possess a similar level of resources as the US or China to perform or produce similar quantity of research. However, the Korean government is strongly backing their bioengineering industry and globally recognizable industry leaders have started to take more active involvement in the field. They have allocated their resource wisely and many of the researchers and engineers still perform outstanding research and development with a continuous trend of growth and improvement.

    What would be your advice for young women who are considering a career in science and engineering?

    With continuous growth in engineering field and improvements in social awareness for gender inequality, I strongly believe that there will be a brighter future for young women engineers. There are many globally recognized women engineers actively working in academia or industry, and these leaders can provide a good example for young women engineers to follow.

    I’ve partaken in various support programs for woman engineers both at my home institution and abroad with a hope of aiding the career development of young women engineers. The growing trend for various supports and opportunities for networking and mentoring is available for young generations and they should utilize these resources to better prepare themselves within engineering field.

    Finally, I would like to once again emphasize for the future woman engineers to be ambitious, fully utilize any resources that are available to them, and to follow their dream as their dreams can come true with hard work.


    About Professor Chae-OK Yun 

    Chae-Ok Yun is currently Professor of Bioengineering at Hanyang University, Seoul, Korea. She is also Adjunct Professor of Pharmaceuticals and Pharmaceutical Chemistry at University of Utah, United States, Affiliate Professor of Medicine at University of Washington, United States, Guest Professor of Sichuan University, China, and Adjunct Professor of Genomics at Yonsei University, Korea.

    She has served as Deputy Editor of Molecular Therapy (2010-), Associate Editor of BMC Cancer (2010-) and Cancer Gene Therapy (2013-), Editorial Board member of Journal of Controlled Release (2010-), Gene Therapy and Regulation (2010-), International Journal of Cancer Research & Diagnosis (2013-), Regenerative Therapy (2016-), and Advanced Drug Delivery Review (2016-), Associate Editor in Chief of Oncolytic Virotherapy (2017-), and an Editorial Advisor of BMC Biomedical Engineering. She is also a Member of The National Academy of Engineering of Korea.

    The post Succeeding as a woman in biomedical engineering appeared first on BMC Series blog.

    in BMC Series blog on January 09, 2019 09:30 AM.

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    Scratchy cancer cure discoveries of Ruben Plentz

    Professor Ruben Plentz chose to focus his career on clinical medicine in Bremen, despite his tremendous academic achievements in cancer research. Was it because malicious critics harassed him with frivolous investigations and corrections, envious at all those peer-reviewed cancer cures the great doctor invented?

    in For Better Science on January 09, 2019 06:00 AM.

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    Webinar Jan. 23 : Innovation-led Procurement with Andrew Bartolini, Ardent Partners

    January 23, 2019 • 9am PST/12pm EST/5pm UTC

    Innovation is a powerful word and a broad concept. It can create markets while generating dilemmas, be an industry “game-changer” or a simple, incremental improvement. Given the level of organizational maturity, it is no surprise that most procurement-led innovation today focuses on the incremental.

    The reality is that many of the enterprise’s larger, longer-term opportunities depend on how well procurement identifies and drives innovation within the enterprise and across the supply chain. 

    Join Ardent Partners Chief Research Officer, Andrew Bartolini, as he discusses the opportunities that procurement has to find, harvest, and deliver innovation in today’s marketplace.

    In this 60-minute session, you’ll learn:

    • How innovative technologies are impacting the procurement function
    • Transformational thinking that will help guide you to improving the performance of your team
    • Custom industry intelligence that reveals new best practices for digitizing procurement organizations

     

    About Our Speaker

    in The Science Exchange Blog on January 08, 2019 11:20 PM.

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    Less than a year after launch, TESS is already finding bizarre worlds

    The TESS exoplanet hunter has spotted eight confirmed worlds in its first four months, and several of them are really weird.

    in Science News on January 08, 2019 09:13 PM.

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    A protein in mosquito eggshells could be the insects’ Achilles’ heel

    A newly discovered protein found exclusively in mosquitoes may one day help control their numbers.

    in Science News on January 08, 2019 07:00 PM.

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    150 years on, the periodic table has more stories than it has elements

    The organized rows and columns of the Periodic Table hide a rich and twisting history.

    in Science News on January 08, 2019 04:29 PM.

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    How the periodic table went from a sketch to an enduring masterpiece

    150 years ago, Russian chemist Dmitrii Mendeleev created the periodic table of the elements, revolutionizing chemistry.

    in Science News on January 08, 2019 04:29 PM.

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    New on Science Exchange: Desktop 3D Bioprinting, Hardware-free Long-read NGS, Rethinking Clinical Trials

    Expand your access to innovation through the Science Exchange Network, as we are continuously adding new services and qualified providers. Here are five recent additions that could inspire your next breakthrough. Visit each provider’s online profile to learn more about the technologies listed.

    From replacement organs on demand to alternative energy generators, the applications of bioprinting are rapidly expanding.

    The Science Exchange Network now includes the 3D bioprinting experts at SE3D, an innovative provider whose services include 3D printed tissue scaffolds in various biomaterials, such as polycaprolactone, collagen and calcium phosphate cement.

    With a mission to make bioprinting widely accessible, SE3D develops bioprinting hardware, biomaterials and bioreactors for customer-specified applications.

    A new NGS technology enables sequencing with a fraction of the error rate of traditional methods, less amplification bias, and at much lower costs than long-read sequencing.

    The service, provided by Loop Genomics, tags DNA/RNA molecules with DNA barcodes and copies and pastes those barcodes throughout long molecules. Libraries are then converted into a standard short-read library and sequenced on any short-read sequencer.

    This sequencing approach is already in frequent use by microbiome researchers and others studying low-abundance species.

    Loop Genomics Longread NGS
    Clinical data Sanguine Biosciences

    Clinical researchers face many challenges, including reaching enough of the right patients, patient retention, and high costs per site. Sanguine Biosciences facilitates clinical trials, including collecting clinical data in patient homes. Through their direct-to-patient approach, they offer recruitment, retention, and consenting services for translational and clinical research.

    Sanguine Biosciences also collects and provides liquid biospecimens for translational and preclinical studies, specializing in trial-matched and geo-specific samples. Their expertise spans multiple therapeutic areas, including lupus, IBD, and rheumatoid arthritis.

    Membrane transporters are important for both understanding PK/ADME and as potential drug targets. However, as with many membrane proteins, understanding their structure and function is still a challenge.

    A unique team of researchers at ProNovus Bioscience has applied their experience in studying difficult-to-obtain membrane proteins to developing cell-based assays for key transporters, including BSEP, BCRP, MDR1 and multiple MRPs, in various species.

    Because of the team’s protein research background, they are also able to purify and characterize membrane fractions downstream of these assays.

    Membrane protein
    Fat cells

    Lipid accumulation assays can be used to identify compounds, including potential PPAR agonists and glucocorticoid analogs, that stimulate cultured human adipocyte differentiation or lipogenesis.

    Lipid accumulation occurs not only in obesity, diabetes and other aspects of metabolic syndrome, but also in alcohol-induced liver injury.

    These assay services, available from ZenBio, can be used in human and non-human primary cells and cell lines.

     

     

     

    in The Science Exchange Blog on January 08, 2019 04:08 PM.

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    Recommenders at Elsevier: a perfect blend of data, algorithms and people

    We take you behind the machine-learning scenes with the data scientists and software engineers on the Recommenders Team

    in Elsevier Connect on January 08, 2019 11:09 AM.

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    How to investigate allegations of research misconduct: A checklist

    Do investigations into research misconduct allegations need better standards? The Association for the Promotion of Research Integrity (APRIN) in Japan, a group of volunteers who “commit themselves to the promotion of research of high integrity” and provide “e-learning material for research ethics education,” thinks so. Today, we present a guest post by Iekuni Ichikawa, who chaired … Continue reading How to investigate allegations of research misconduct: A checklist

    in Retraction watch on January 08, 2019 11:00 AM.

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    People With Advantageous Personality Traits Have More Nerve-Fibre Insulation (Myelination) In Key Brain Areas

    Screenshot 2019-01-08 at 09.48.10.png(a) A post-mortem map of average myelination intensity in the brain created over a century ago (red areas show greater myelin). (b) new estimates of average myelin distribution using brain scan technology (independent of personality, red shows greatest myelination, blue the least). From Toschi and Passamonti, 2018

    By Christian Jarrett

    Researchers are getting closer to understanding the neurological basis of personality. For a new paper in the Journal of Personality, Nicola Toschi and Luca Passamonti took advantage of a recent technological breakthrough that makes it possible to use scans to estimate levels of myelination in different brain areas (until fairly recently this could only be done at postmortem).

    Myelin is a fatty substance that insulates nerve fibres and speeds up information processing in the brain – it tends to be thicker in parts of the cortex involved in movement and perception, while it is lighter in brain regions that evolved later and that are involved in more abstract thought and decision making.

    The new findings, though preliminary, suggest that people with “healthier”, more advantageous, personality traits, such as more emotional stability and greater conscientiousness, may benefit during development from more enhanced myelination in key areas of the brain where the myelination process is particularly prolonged in humans, continuing through adolescence and into the twenties.

    The findings are based on brain scans of over 1000 young men and women (average age 29) who also undertook a personality test tapping the “Big Five” traits. Averaged across the entire sample, the researchers found a pattern of myelination through the cortex that closely matched the pattern first discovered over a hundred years ago (from investigation of post-mortem brains) by the German neuroanatomist Paul Flechsig – see image above.

    Myelination was generally thicker in the sensory and motor cortices and lighter in frontal and parietal regions. The latter support “higher order” mental functions – the neural architecture in these regions tends to be highly complex, and, though lighter, the myelination process here is later and lengthier, continuing way beyond the teenage years.

    While controlling for any differences in intelligence, as well as age, gender and brain volume, the researchers found several links between personality traits and myelination. For instance, lower emotional stability (i.e. higher neuroticism) was correlated with less myelination in the prefrontal cortex, a key brain region for emotional control; higher agreeableness was correlated with greater myelination in orbitofrontal cortex (specifically in the anterior region, previously implicated in prosocial behaviour); and higher conscientiousness correlated with greater myelination in part of the prefrontal cortex (the prefrontal cortex pole, which is associated with the human conscience, among other functions).

    The aforementioned correlations suggest a straight-forward pattern whereby what we would usually consider as more advantageous traits are associated with greater myelination in key brain areas. However, the picture was more complicated than that. For example, both higher conscientiousness and higher trait openness were correlated with less myelination in another frontal brain area (the anterior cingulate cortex, a region involved in monitoring mistakes, among other things), and greater neuroticism with more myelination in a part of the occipital lobe (where the visual cortex is located – it’s not clear why this might be, though one could speculate this might be related to enhanced threat detection).

    Broadly speaking, the findings “improve our understanding of the neurobiological underpinnings of variability in common behavioral dispositions” Toschi and Passamonti wrote. Summarising their results, they added that “The personality‐related variability in the intra‐cortical myelin content … represent[s] an important proxy measure of the underlying neurodevelopmental mechanisms that shape subject‐specific attitudes in cognitive, emotional, and behavioral functions”. It will be interesting to follow up these results with longitudinal research, to see how personality traits and patterns of myelination co-vary over time, and to investigate the factors, such as genes, diet and education, that may have an influence.

    Intra‐cortical myelin mediates personality differences

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

    in The British Psychological Society - Research Digest on January 08, 2019 10:06 AM.

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    Webinar Jan. 31 : 3D Cell Culture Technologies In Drug Development

    Save the date: January 31, 2019 • 9am PST/12pm EST/5pm UTC

    Are your 3D cell cultures truly predictive?

    Learn about human, disease-specific tissue microenvironments for testing drug efficacy and safety from leading provider, zPREDICTA.

    Conventional cell culture models lack tissue microenvironment, and thus, have limited physiological relevance. Emerging 3D culture systems, such as zPREDICTA’s disease models, mimic the native architecture of human tissues in an organ- and disease-specific manner, demonstrating high correlation with clinical response.

    Join this 45-minute session to learn about:

    • Importance of incorporating organ-specific human tissue microenvironment for testing drug efficacy and safety
    • Versatile design of 3D culture models for anticancer drug screening, target discovery, and immuno-oncology
    • Clinical study data demonstrating high correlation of zPREDICTA models with clinical response

    Who should attend:

    • Researchers developing new anticancer drugs
    • Scientists performing screening of anticancer agents
    • Laboratories designing immuno-oncology therapies

     

    About Our Speaker

    in The Science Exchange Blog on January 08, 2019 03:51 AM.

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    A weird type of zirconium soaks up neutrons like a sponge

    Zirconium-88 captures neutrons with extreme efficiency, and scientists don’t yet know why.

    in Science News on January 07, 2019 04:00 PM.

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    Green darner dragonflies migrate a bit like monarch butterflies

    Some dragonflies do a north-south annual migration that takes at least three generations.

    in Science News on January 07, 2019 12:00 PM.