1,750 Matching Annotations
  1. Nov 2015
    1. We founded Lingua 66 years ago.

      According to this blog, this is not true.

    2. transfer ownership of the journal to the collective of editors

      Collection of editors, not an individual editor

    1. And while she can't endorse complete open access, she said her group is aiming for "balance" of the various issues involved.

      I wonder why not?

    2. Libraries can pay for access to Language, the society's flagship journal, for about $300, "a fraction" of what Lingua costs.

      I don't fault a commercial business for making a profit, but as scholars and researchers, we have to ask ourselves about this huge differential in price. If it costs LSA $300 and Elsevier several thousands to publish and maintain a journal, why? What is the research community getting for all that overhead?

  2. Oct 2015
    1. We’re excited to announce a new project funded via the Open Annotation Fund. A grant of $7,300 to Fred Chasen to develop EPUB format integration for Hypothes.is.

      You too can annotate with Hypothes.is

    1. Learning may involve putting something like bit strings into banks of molecular switches found inside individual neurons—rather than rewiring the neural circuits.

      If there is any validity to this, then I suspect that the answer is that the brain uses both and possibly additional strategies.

    2. They are stumped, or refuse to answer

      I find that hard to believe. Why can't a number be a pattern of synaptic connections? For that matter, why can't the brain use both?

    3. A computer does not learn by rewiring itself; it learns by encoding facts into sequences of ‘0s’ and ‘1s’ called bit strings, which it stores in addressable registers.

      What about the years of studies showing rewiring? I'm the first to disbelieve most scientific results, but the evidence of a change in patterns of neuronal activity in response to exercise or enrichment seems quite strong.

    1. Literature

      Add an open questions section (Tom Radman)

    2. Data space

      Entity-related data could be in the data space.

    3. Glutamate

      When I click on any assertion, the evidence for that assertion should be available.

    4. cerebral cortex (not in

      Test

    5. Image gallery

      Domain relationships? With the NIF semantic framework, we can detect when there is a relationship between two types of entities.

    1. AMPK activation led to the activation of Rac GTPase and the phosphorylation of myosin regulatory light chain (MRLC).

      I don't necessarily agree with this.

    1. Pyramidal cell

      Can the hierarchy go back to Neuron?

    2. Literature

      This should be a graph of representation in the literature.

    3. Features One of the main structural features of the pyramidal neuron is the triangular shaped soma, or cell body, after which the neuron is named. Other key structural features of the pyramidal cell are a single axon, a large apical dendrite, multiple basal dendrites, and the presence of dendritic spines.

      Actually, this text contains most of the information from the more structured properties. I am wondering whether sitting behind this text, we can have the neurolex properties. I'll explain what i mean.

    4. Structure

      We can add some of the properties from the Neurolex page:

      Supercategory Has role Neurotransmitter Organism Cell soma size: (we will see if we can get some numbers here from Neuromorpho) Number of primary dendrites (get numbers from Neuromorpho) Dendritic spines: High density

    5. See also

      Related concepts:

      For Pyramidal neuron = neuron For Neocortex pyramidal neuron = Neocortex, neuron

    6. About

      Perhaps call this: Lexicon. Have the URI, the synonyms and the tree.

    7. Physiology

      Add Allen source here per our discussion.

    8. Image gallery

      Would be good to have different types of images here, e.g., EM from CCDB/CIL, morphology also from Allen

    9. Summary

      Can you put in the title of the page here: We should have one page for Pyramidal neuron and another for Neocortex pyramidal neuron. Only Neocortex pyramidal neuron needs to connect to data etc.

    1. To this end,theUniversity has asolemnresponsibilitynotonlyto promotealively andfearlessfreedomof debate anddeliberation,butalsoto protectthatfreedomwhenothersattempttorestrictit.

      More language that I would like to adopt.

    2. n a word,the University’s fundamental commitmentistotheprinciplethatdebateordeliberationmay not besuppressedbecause the ideasputfortharethoughtby some or even by most members of the University communityto beoffensive,unwise,immoral,orwrong-headed.ItisfortheindividualmembersoftheUniversity community, notforthe University as an institution,tomake those judgmentsforthemselves,and to act on those judgments not by seeking to suppress speech,but byopenly and vigorously contestingtheideas that theyoppose. Indeed, fostering the ability of members of the University community to engage in such debate and deliberation in an effective and responsiblemanner is an essential part of the University’s educational mission.

      I think this should be part of any Code of Conduct for conferences.

    3. a genuine threat or harassm

      And I think this can be defined very clearly.

    4. But itis not theproper role ofthe University to attempt to shield individuals from ideasand opinionsthey find unwelcome, disagreeable, or even deeply offensive. Although theUniversity greatly values civility, and althoughall members of the University community share in the responsibilityformaintaininga climate of mutual respect, concerns about civility and mutual respect can never be used as a justification for closing off discussion of ideas, however offensive or disagreeable those ideas may be to some members of ourcommunity.

      I find this very refreshing and inspiring.

    5. t “education should not be intended to make people comfortable, it is meant to make them thin
    1. omething strange is happening at America’s colleges and universities.
    2. But students should also be taught how to live in a world full of potential offenses.
    3. “The presumption that students need to be protected rather than challenged in a classroom is at once infantilizing and anti-intellectual.”
    4. All of these actions teach a common lesson: smart people do, in fact, overreact to innocuous speech, make mountains out of molehills, and seek punishment for anyone whose words make anyone else feel uncomfortable.

      Yes, they do, all assurances to the contrary.

    5. A group of women later vandalized Mahmood’s doorway with eggs, hot dogs, gum, and notes with messages such as “Everyone hates you, you violent prick.”

      I would call that a macro-aggression. In fact, I would call it a crime.

    6. But in 2013, the Departments of Justice and Education greatly broadened the definition of sexual harassment to include verbal conduct that is simply “unwelcome.”

      Can we honestly say that this standard would not be applied to Conference Codes of Conduct?

    7. The book honored student opposition to the Ku Klux Klan when it marched on Notre Dame in 1924. Nonetheless, the picture of a Klan rally on the book’s cover offended at least one of the student’s co-workers (he was a janitor as well as a student), and that was enough for a guilty finding by the university’s Affirmative Action Office.

      Really? This makes me very sad. Not that the charge was brought-can't help that-but that the University capitulated. How could they?

    8. A claim that someone’s words are “offensive” is not just an expression of one’s own subjective feeling of offendedness. It is, rather, a public charge that the speaker has done something objectively wrong. It is a demand that the speaker apologize or be punished by some authority for committing an offense.

      Yes, my main objection to Conference Codes of Conduct.

    9. many seem fragile

      I visited the Biosphere a while back. They originally found that when they planted trees, they grew spindly and sickly. Turns out they needed to be stressed by the wind. Then they grew stronger. I know as a biologist that this is true across scales and species. No stress is just as detrimental as too much.

    10. vindictive protectiveness
    11. It is creating a culture in which everyone must think twice before speaking up, lest they face charges of insensitivity, aggression, or worse.

      And this is why I recently fought against (unsuccessfully) instituting a Conference Code of Conduct. Because eventually when one has speech codes that are enforced, the bar gets lowered so that all speech is stifled. And if they aren't enforced, then why have them in the first place?

    12. And more than the last, this movement seeks to punish anyone who interferes with that aim, even accidentally. You might call this impulse vindictive protectiveness.

      This is the crux of the problem. The only way to counter this extreme sensitivity is exposure; but exposure is met with vindictiveness. Most of us just walk away rather than endure the vitriol as usually our intent was not to offend.

    13. More than the last, it presumes an extraordinary fragility of the collegiate psyche, and therefore elevates the goal of protecting students from psychological harm. The ultimate aim, it seems, is to turn campuses into “safe spaces” where young adults are shielded from words and ideas that make some uncomfortable.

      I find it ironic that our movies, books and TV shows geared towards younger audiences feature plucky and determined young people saving the universe from all kinds of menaces yet in real life, discomfort at the written or spoken word causes swoons.

    1. FORCE11 Member since June 17, 2015

      Uh oh. I think that the dates that everyone joined have reverted to when we were transferred over to the new website. Is there any way to fix this? If not, we should apologize to everyone and post an explanation.

    1. Data Citation Implementation Working Group – Publication

      This should be updated to the Peer Reviewed version: https://peerj.com/articles/cs-1/

      Also on the Groups Working page.

    1. Outcomes from the Community of FORCE11.

      Change to: This section features recommendations and products for improving scholarly communication produced by FORCE11 working groups.

    1. Target Areas

      The original board members: Cameron, Phil, Anita, Ivan, Ed should review these materials and see whether they are still relevant.

    1. FORCE11 Videos

      I'm wondering why we wouldn't just include these under the conference pages? Should it be it's own category?

    1. Community Publications

      Why is this blank? I know we discussed this before, but I can't remember whether this is meant to be articles about FORCE11. In which case, we have several of these around, including the latest editorial currently featured on the home page.

      http://bioscience.oxfordjournals.org/content/65/7/635.full

  3. Sep 2015
    1. 60%

      So if I am reading this table correctly, then the overall percentages are similar to the table in the other report. Although I don't know if the other also included unjustifiable homicides.

    1. Outcomes

      Need the Joint Declaration of Data Citation Principles.

    2. Outcomes

      Need to post Tim's article on Implementing data citations and the RRID article when it is finally published (soon).

    1. In this Opinion Paper, the Science Europe Scientific Committee for the Life, Environmental and Geo Sciences wishes to alert academic employers, promotion and appointment Committees and European and national research funding organisations to the lack of clear evaluation metrics for scientists working in multidisciplinary teams. The absence of such metrics already has a negative impact on career paths, as many scientists hesitate to participate in multidisciplinary research. Therefore, the Committee has devised concrete recommendations to contribute to the elaboration of an appropriate evaluation framework.

      Addressing the problems of credit and attribution. FORCE11 also started a working group for assessing contributions for research objects beyond narrative works.

    1. Established in 2004, t

      I would start with something like:

      NIF has been cataloging and surveying the neuroscience resource landscape since 2006. NIF is an initiative of the NIH Blueprint Consortium, which brings together..." and then go into the rest of it.

    2. NIF has touched people's lives in amazing ways.

      We should remove this sentence. We haven't touched anyone's life!

      But we have done some useful things. We did create a list of papers that reference NIF and we included that in the proposal. Perhaps we should have a list of them here under "Who is using NIF"? We should also point to our publications page. We can point to our testimonials page, although it would be nice if we could update that at some point.

    1. People at NIF

      Add:

      Burak, Tom, Devon, James, Yueling, Yazin.

      Add Thomas Radman from NIDA as our program officer

    2. Anita Bandrowski, Ph.D., Project Lead, UC San Diego

      Past

    3. NIF 2011 All Hands Meeting, June 16-17, UC San Diego

      Delete

    4. Karen Skinner, National Institutes of Health Paul Sternberg, Ph.D., California Institute of Technology David C. Van Essen, Ph.D., Washington University in St. Louis

      Past

    5. Hans-Michael Muller, Ph.D., California Institute of Technology Sridevi Polavaram, George Mason University Xufei Qian, Ontology and Data Engineer, UC San Diego

      Past

    6. Jennifer Lawrence, Administrative, UC San Diego

      Past

    7. Jonathan Cachat, UC San Diego Paolo Ciccarese, Harvard University Tim Clark, Harvard University Christopher Condit, Applications Engineer, UC San Diego Mark Ellisman, UC San Diego Lee G. Hornbrook, M.A., Web support and Communications, UC San Diego Fahim Imam, Ontology Engineer, UC San Diego Stephen Larson, UC San DiegoCliff Lee, UC San Diego

      Past

    8. Vadim Astakhov, Software Engineer, UC San Diego

      Past

    9. Giorgio Ascoli, Ph.D., George Mason University

      Past

    10. Andrea Arnaud, UC San Diego

      Past

    1. In addition to providing feedback and input during planning and implementation phases of the cohort, participants should have significant representation on PMI-CP governance and oversight committees (4.1)

      This is a welcome recommendation, provided that the representatives are not patronized, as I often see in these situations. Every scientist and administrator on the committee should read the Immortal Life of Henrietta Lacks.

    2. The best approach will balance normalization of only the highest value data initially for all participants followed by on-demand data curation of other data as driven by scientific demand. I

      I agree with this; it is the only practical solution. Opportunities here for data curation specialists.

    3. To be useful to the goals of PMI, the Working Group recommends that all potential participants in the PMI cohort must agree to share their health data, provide a biospecimen, and be recontacted for future research (3.1).

      That is asking a lot of people. What will be their benefit?

    4. participant engagement

      Perhaps an opportunity for Hypothesis. We need to lobby that any annotation layer is portable, something that does not happen now.

    5. Coincident with advancing the science of medicine is a changing culture of medical practice and medical research that engages individuals as active partners – not just as patients or research subjects

      Key change.

    6. Precision medicine is an approach to disease treatment and prevention that seeks to maximize effectiveness by taking into account individual variability in genes, environment, and lifestyle.

      Definition of precision medicine.

    1. Normal aging is described as aging not accompanied by behavioral or cognitive dysfunctions associated with the cholinergic basal forebrain system

      I don't think that aging can be defined purely in terms of the cholinergic system.

    2. Cholinergic system research may provide the key to treating and reversing this devastating disease.

      Unsupported statement. There are many good reviews of cholinergic therapies for Alzheimer's disease. But it is also a very long standing theory and so I wouldn't characterize the opportunities as "exciting" as therapies have had modest effects to date.

    3. o send its messages

      Better phrase: "as a neurotransmitter".

    4. Cholinergic neurons provide the primary source of acetylcholine to the cerebral cortex,

      I think what is meant is "cholinergic neurons in the basal forebrain", or "the cerebral cortex receives projections from cholinergic neurons", as we presume that acetylcholine is coming from cholinergic neurons.

    1. WHAT IS FORCE 11?

      FORCE11 is now using Hypothesis as an annotation tool. Sign up for Hypothesis and you can annotate any web page in FORCE11. Annotations can be public or private. Let us know what you think about this!

    1. Rostral anterior cingulate gyrus

      SUMS Query: Anterior Cingulate

    2. Anterior rostral cingulate cortex

      SUMS Query: Anterior Cingulate

    3. Anterior Cingulate Gyrus

      SUMS Query: Anterior Cingulate

    1. Univariate analyses of the preclinical database revealed an essentially random pattern of the rank ordering of individual outcome variables according to injury severity, indicating that the most systematic effects were observed at the multivariate level. These data suggest that univariate analysis (e.g., bivariate correlation/regression, ANOVA, t-tests), used by many fields in preclinical research, have the potential to produce inconsistent ‘votes’ for the significance of experimental effects depending on which outcome variables are analyzed.

      That is a very good explanation.

    2. Despite data heterogeneity, the large size and detailed nature of the dataset enabled data-driven detection of recovery as a graded, emergent pattern defined within the full multivariate syndromic space

      Good quote

    3. We first built an information-rich database containing the total set of detailed behavioral and histological outcomes from 159 rats with various types of experimental cervical SCI and multiple outcome metrics (>15,000 data points).

      Could only really be done with different laboratories providing statistical variation.

    4. This is problematic because translational disease features are often reflected in the association among outcomes rather than on individual measures

      Makes perfect sense.

    1. “Universities have become more corporate than many corporations.”

      I have to agree with this statement, sadly. They are drunk on indirects from federal grants and that helps fuel a lot of the misconduct.

    2. I appreciate your interest, but having been in my position for only the last 1.5 years, I have no personal insights into this case. While there are issues in what can be disclosed, in my case there is simply the absence of knowledge of the case other than through the media

      Really? I understand the need for confidentiality, but this is a very weak answer. "An absence of knowledge about the case..." when it has been festering for so long? Shouldn't Brown have taken an interest?

    3. Martin has been under pressure to retract the paper for years, including from within his own society.

      Was there not even an editorial expression of concern or whatever they call that?

    4. It is often said that science self corrects. But for those who have been calling for a retraction of the Keller paper for many years, the system has failed. None of the paper’s 22 mostly academic university authors, nor the journal’s editors, nor the academic and professional institutions they belong to, have intervened to correct the record.

      Wow. That is a very strong indictment. Big argument for why independent channels on top of the literature are so important.

    5. but by an outside medical writer hired by GSK

      I'm not sure that ghost writing is a bad thing as long as "writer" is not confused with lead scientist. Yet another strong argument for contributor roles rather than authors. https://www.force11.org/blog/are-we-ready-define-scholarly-commons-thoughts-force2015

    1. This is problematic because the article has been influential in the literature supporting the use of antidepressants in adolescents.

      Example of the type of harm that lack of transparency can lead to.

    2. Access to primary data from trials has important implications for both clinical practice and research, including that published conclusions about efficacy and safety should not be read as authoritative. The reanalysis of Study 329 illustrates the necessity of making primary trial data and protocols available to increase the rigour of the evidence base.

      How can anyone argue that science isn't served by making primary data available? We must recognize that more people are harmed by not sharing data than are harmed by data being shared.

  4. test-force-11.gotpantheon.com test-force-11.gotpantheon.com
    1. Maryann Martone

      I mostly create blogs by going to my membership page and clicking on the link that used to be there that something like "Write a blog post". I think it personalizes the experience. So I would vote for elevating blogs on the profile page and making it easy for people to add them and list the ones they've contributed.

    1. Support FORCE11

      I think this should be the heading and it should include both donations and sustaining memberships. Also, I'm hoping that when new members sign up they are encouraged to donate. Haven't checked that yet.

    1. FORCE11 Sustainability Committee

      I would prefer a single category called "Sustainability" where we should link to the report. There may be others.

    1. Member Blog Posts

      I don't think that blogs belongs under news and events. Sometimes people use them to promote them, but primarily I think of them as outputs of the community or as publications.

    1. FORCE11 Videos

      I'm not sure that this was what I was expecting under "Media". I was thinking it was going to be a press kit, perhaps? I would put videos under publications. It isn't really different that presentations, I think. And each of our videos should probably have a DOI.

  5. test-force-11.gotpantheon.com test-force-11.gotpantheon.com
    1. Outcomes from the Community of FORCE11.
    2. Outcomes

      Still not happy with Outcomes here, because it doesn't really capture what is here. Perhaps "Materials", "Reports" , something that indicates there is something concrete here to use. We can look at some other websites, perhaps?

    1. FORCE11 Completed Groups Archive

      Each of the working group pages should indicate that the group has been completed. We shouldn't just have a listing of them on this page.

    1. Resources

      I was expecting there to be a place for FORCE11 products. This looks like the old menu.

    1. a response to frustration at owner absence

      Dogs have owners; cats have staff. I think frustration at not having their needs met is definitely a possibility!

    2. but it is clear that the presence of the owner was not able to ameliorate these effects, which should be the case if they serve as an attachment figure in the original sense of Bowlby [8], as compared to the wider sense used by some authors [47].

      Having had the experience of visiting at least two cats in the hospital, I can attest that at least one of them would not eat for the hospital staff but did eat for me when I was put into a room with her. The other one hid at first, but I was able to coax her out eventually. Maybe the staff would have been able to do the same, but in either case, it probably would have taken a while. So I'm not sure that the time periods used for this test were sufficient to reveal all aspects of behavior.

    3. Thus it seems that in the context of SST, passive behaviour by domestic cats, may be associated more with a state of anxiety rather than comfort, as has been found in other studies

      Again, this points to the need for understanding cat behaviors and not trying to transfer measures used in social animals.

    4. We do not reject that cats may have social preferences, nor that some cats might form this type of attachment in certain circumstances, nor do we wish to imply that cats do not form some form of affectionate social relationship or bond with their owners (a broader sense use of the term “attachment”), only that the relationship with the primary caregiver is not typically characterised by a preference for that individual based on them providing safety and security to the cat

      Again, anecdotal, but when I first got a cat after having dogs growing up, I was struck by the fact that when something scared the cat, I may as well not have existed. The cat did not look to me at all but just tried to get away. My dogs would stand run behind me.

    5. except in the case of level of vocalisation if it is a proxy of distress

      OK. Disregard my annotation above. The authors recognize that we may not know what constitutes distress in a cat without measuring it physiologically (which would cause the cat a lot of distress).

    6. Firstly, relevant aspects of the behaviour of cats are not reliable enough to be used in an evaluation of attachment (i.e. aspects of the test produce unreliable data).

      This conclusion seems to be the main finding: we don't have a good way to measure this!

    7. When all of these episodes are combined to examine the overall effect of absence of owner versus stranger on vocalisation, there was no significant difference.

      But do we assume that this is how a cat shows distress? They are largely solitary animals that hunt by stealth, so after kitten-hood, I'm not sure what the appropriate indicators of distress are.

    8. ‘Marking’ behaviour exhibited an episode-order effect (A2+A8 vs B6+B4, z = 1107.5, p<0.05; A1 vs B5 [marking owner], z = 263.5, p<0.05; A1 vs B5 [marking stranger], z = 251.0, p<0.01), but no test-order effect and so these data were used in comparisons relating to the same episodes in the two conditions where relevant to the assessment of attachment.

      Not a very common behavior though. Would be nice to know how many cats actually engaged in this behavior, not the total amount of seconds.

    9. Any cat subjects who remained in the hiding place throughout the experimental testing procedures were removed from the data analysis, since they provided no useful data.

      That would be my cat!

    10. Two females of similar height, build and appearance were used as the stranger (one for each condition).

      My experience is that cats react differently to males and females. Anecdotal evidence of course, but something to consider in the experimental design.

    11. One female cat and all males had been neutered, and no entire female was in season.

      Editorial comment: Females should be spayed!!!!

    12. 13 males and 7 females

      Surprised they didn't try to gender balance the groups.

    13. with four males and 16 females

      That ratio sounds about right for cat owners.

    14. This meant their data came from 6 minutes of observation of the cat with the owner, 3 minutes with the stranger and 3 minutes when the cat was alone.

      I did not read this study, but this seems a major confound if you are using it to quantify behaviors. Surprised peer review did not catch this.

    15. normal healthy response

      For a social animal perhaps, but I don't think you can define normality for all species in this way.

    16. show signs of pleasure upon their return

      Something very difficult to tell in a cat!

    1. hat our ‘hardware’ is tuneable, at least to some extent

      But why would this be surprising, given all we know about plasticity?

    2. The authors studied two apparently different classes of fast-spiking interneurons, only to discover that they were actually looking at the same piece of ‘hardware’ which had the ability to oscillate between two different ground states

      Why it has been difficult to determine how many types of neurons there are in the brain.

    1. The cortical basket cell is a class of interneurons usually found in layers II-V. They are characterized by specific axonal terminations, which are in the form of pericellular "baskets" around the cell bodies of the target cells. Basket cells are distinct from other types of interneurons in that they have the highest tendency to target somata. Cortical basket cells are further subdivided morphologically and electrophysiologically.

      Text should describe instances, not basket cells as a class. So experimental details should be given.

    2. instance #2

      Instances should only link to primary data, not articles.

    1. The personnel officer of a factory drops a stack of a few thousand employee cards into a selecting machine, sets a code in accordance with an established convention, and produces in a short time a list of all employees who live in Trenton and know Spanish.

      We're still trying to standardize information and concepts so we can do this comprehensively. It is conceptually simple but difficult in practice, at least with current technologies.

    2. here will always be plenty of things to compute in the detailed affairs of millions of people doing complicated things

      Particularly in the modern age of sensors. Sorry "girls".

    3. glasses is a square of fine lines

      Google glass?

    4. There is film in the walnut for a hundred exposures, and the spring for operating its shutter and shifting its film is wound once for all when the film clip is inserted.

      Did not imagine digital but other predictions are not bad.

    5. Two centuries ago Leibnitz invented a calculating machine which embodied most of the essential features of recent keyboard devices, but it could not then come into use. The economics of the situation were against it: the labor involved in constructing it, before the days of mass production, exceeded the labor to be saved by its use, since all it could accomplish could be duplicated by sufficient use of pencil and paper. Moreover, it would have been subject to frequent breakdown, so that it could not have been depended upon; for at that time and long after, complexity and unreliability were synonymous.

      This is something we have to keep in mind when developing technology, particularly in academia. It's not just the technology, but whether it can be put into production in a cost effective and useful manner. And just because the time is not right now, doesn't mean that as capacities change, it can't be done eventually.

    6. as truly significant attainments become lost in the mass of the inconsequential

      But assuming we can tell what is inconsequential and what is significant without the passage of time is a little arrogant.

    7. Professionally our methods of transmitting and reviewing the results of research are generations old and by now are totally inadequate for their purpose.

      And in 2015, they are now another generation older. Or is it two? But now we are in a position to do something about it. FORCE11 Manifesto

    8. The investigator is staggered by the findings and conclusions of thousands of other workers—conclusions which he cannot find time to grasp, much less to remember, as they appear.

      But now we really are bogged down by specialization. Honest. But somehow we progress anyway.

    9. For the biologists, and particularly for the medical scientists, there can be little indecision, for their war has hardly required them to leave the old paths

      But perhaps the current "war" on disease does require them to leave the old paths.

    1. It was transferred to Boehringer-Mannheim as Clone 12H11, resold to Roche and finally bought by Chemicon, and it is now sold as MAB3026.
    1. Big data from small data: data-sharing in the 'long tail' of neuroscience.

      Highlight, annotate and tag specific words or phrases.

    2. so-called long-tail data

      Add formulas, links or images Image Description

    1. Among the voices for reform, hybrid entrepreneurs are opening the way for a reformulation of the current economic order, combining the principles, practices, and logics of modern capitalism with more inclusive humanitarian ideals.

      One might argue that when companies were embedded into the fabric of neighborhoods, such ideals were part of the corporation. But I agree that we have drifted from this (if it ever existed).

    2. compensation systems

      I see this as one of the greatest challenges but also, perhaps, a space where hybrids might have an advantage. Large non-profits get slammed when their executives make large salaries as it seems like people's donations are going to help the executives and not the beneficiaries. But if you are a for profit, the "customers" would probably not expect that employees would work for peanuts. But I suspect that typical Wall Street CEO inflated salaries would be viewed with suspicion. So some happy medium has to be established.

    3. Rather than look for job candidates with experience in either social welfare work or finance, Los Andes hired college graduates with essentially no work experience and then trained them to be microfinance loan officers committed both to the social mission of the organization and to effective operations. The idea was that without social-based or profit-based experience, employees would find it easier to adhere to the hybrid mission. Although this approach constrained the rate of growth at first, it proved to be more sustainable.

      Good thinking!

    4. Like all hybrids, however, these organizations are still subject to the risk of mission drift, as they may give priority to profit seeking over social mission. This drifting may lead them to either start charging higher prices or expand their customer pool by targeting wealthier and more profitable market segments.

      I see this as inevitable. Primary rule of biological organisms and companies: survive or have offspring that survive.

    5. For example, educational programs might increase a child’s future earnings, but organizations cannot recoup the child’s future wealth.

      And I think this situation is true for most scientific data. It's eventual value is far removed from immediate uses.

    6. When consumption yields both revenue and social value, customers and beneficiaries may become indistinguishable

      An ideal situation, if you ask me.

    7. We find that many hybrid entrepreneurs have been able to find supportive capital partners through this type of early stage financing.

      Is this something we need to look into?

    8. venture philanthropists

      I think this is a useful term to know.

    9. To create better options for hybrids, several efforts are under way to establish new types of legal structures. In the United States, there are three such forms: the L3C (Low-Profit Limited Liability Company), the Benefit Corporation, and the Flexible Purpose Corporation.

      Legal structures for hybrids

    10. Indeed, a hybrid that registers as a nonprofit cannot access equity capital markets because it cannot legally sell ownership stakes to investors. But if a hybrid incorporates as a for-profit, it cannot offer the same tax benefits to donors as registered nonprofits can, even if these approaches lead to the most effective social solution.

      Well, that does seem to be a problem.

    11. As we have seen in microfinance and other industries where hybrids have grown, however, the real-world pursuit of the hybrid ideal is fraught with potential missteps. Recent scandals and critiques of microfinance institutions have focused on a drift away from social mission to more typical for-profit priorities—leading many observers to question whether social problems, such as extreme poverty, can be solved through strategies that also produce revenue.

      This type of broad statement requires some references.

    12. More important, the integration of social and commercial value creation enables a virtuous cycle of profit and reinvestment in the social mission that builds large-scale solutions to social problems.

      The profits fund the mission

    13. Hybrids also must strike a delicate balance between social and economic objectives, to avoid “mission drift”—in this case, a focus on profits to the detriment of the social good.

      I would also think that there is a trust issue.

    14. Like hybrid species in nature, hybrid organizational models can be a fountain of innovation. But they also face distinct challenges that may prevent them from thriving. When organizations combine social mission with commercial activities, they create unfamiliar combinations of activities for which a supportive ecosystem may not yet exist.

      Yes. Having a supportive ecosystem can really make things easier once you tap into it. But everything has to start somewhere.

  6. Aug 2015
    1. Many senior researchers resent the idea that an outsider, typically a younger scientist, with less expertise, would critique work that often has taken years of study to pull off.

      There certainly must be a "replication etiquette" that must be developed and these studies themselves are subject to the same caveats, but it is a bit arrogant to say, as some have, "how dare you try to replicate my work"?

    1. some (20th century) scientists don't even think we would benefit from doing away with 20th century peer review!

      I don't think we can think of the functions of peer review in a monolithic way. It does some functions OK; it does others badly. As one of my colleagues said, peer review means that at least two people have read every published paper. But, regardless of whether we have peer review or not (it can be a choice), the idea that peer review does anything more than give a first pass evaluation of research should be discarded. The real peer review happens, as the author says, after the paper is published.

    2. Unfortunately the inertia behind the 20th century system is so large that I don't hold out a huge amount of hope that change will occur (people will do what the funding requires and so long as some major funding sources judge based on "published papers" people will submit to journals)

      Sadly, this is very true with the majority of the research community. But there are a few who are branching out. Of course, if we spent less time on unnecessary 20th century behaviors like out-moded peer review systems and formatting grant proposals references, we'd have time for more scholarly pursuits!

    3. The threat of peer review would still be there.

      Some journals, e.g., F1000Research, are adopting open peer review. It is an interesting experience. The paper is there as soon as it is submitted.

    4. isible at the same site where the paper exists

      Or anywhere the paper exists. If it is a object, it shouldn't matter where it is read.

    1. Archibald MacLeish does, that “A poem should not mean / But be,”

      Of course, not every poet or lyricist agrees with this notion. If they did, then poems would never be studied for more than their structure, would they? But even if a poem were written to be completely void of meaning, it doesn't mean that references or phrases within the poem could not benefit from annotation.

    2. Thus the first of our two theoretical questions could be spelled out as follows: are there any characteristics of texts (content, style, genre, period) that allow for the inference of general principles that help us describe what is to be annotated and in which manner?

      This statement ignores the fact that the reasons why one might annotate a text are varied and depend on the audience and the interest of the annotator.

    3. t is, therefore, even more surprising that this old practice is not provided or backed up with an adequate theory (cf. Assmann, “Text und Kommentar”; Eggert; van Peursen; Drucker; Parry; Sutherland, “Paper-based Editing and the Digital Environment”).

      Does this suggest, perhaps, that a theory isn't really needed?

    4. Firstly, what is the idea of the literary text presupposed by annotation, and what does annotation do to a text, both in its medial and material form and as regards its meaning?

      Regardless of either of these questions, I have a right to scribble in the margins if I want to, for any reason.

    5. The reason for this is the sheer lack of a theory of literary annotation.

      A rather strong statement that could use some support.

    1. Recent studies have suggested a link between delirium in the critically ill and long term cognitive dysfunction through a mechanism hypothesized as delirium acting as a subclinical dementing illness (Hopkins and Jackson 2006).

      Perhaps ask the surgeon about the rate of delirium for this surgery, although if 50% of the staff didn't recognize it, the statistics may not be very accurate.

    2. particularly haloperidol,

      Oh no. Just like a full psychosis.

    3. In patients with mixed motor or hyperactive delirium, agitation may lead to inadvertently pulled tubes, drains or lines.

      As the social worker about the risk of this.

    4. Specific interventions which have been shown to reduce delirium include: (1) an orientation protocol to provide the patient with repeated orientation to their surroundings and care team members, (2) a sleep protocol to provide uninterrupted night time sleep, (3) an early-mobilization protocol to allow for daily ambulation and range of motion, (4) a vision protocol to allow easy access to glasses and other visual aids, and (5) a hearing protocol to provide amplifying devices and other hearing aids (Inouye et al 1999).

      Good thing to check with the staff about.

    5. restless, irritable, combative, or agitated

      That was Mom

    6. Over 50% of delirium on inpatient services is unrecognized by the clinical team (Milisen et al 2002)

      Yes, I found with my mother that they did not recognize it.

    7. n comparison to high surgical risk procedures such as vascular operations which result in delirium in 36% of cases

      I don't know where mastectomy falls on this spectrum, but according to the doctor, it is not considered a big surgery.

    8. Assessing all preoperative risk factors, pre-existing dementia appears to be the strongest predictor for the occurrence of postoperative delirium (Dasgupta and Dumbrell 2006)

      Well, that's not good.

    1. One study found that 88.1% of datasets within the Data Citation Index remained uncited [25]. Another study found that even a national data center rarely could identify formal citations of their data [26].

      Our current methods are inadequate. See below annotation about efforts to change this.

    2. Data Discovery Index Coordination Consortium [38] as they move forward to make biomedical big data more discoverable, accessible, and citable.

      A shame that the authors did not acknowledge the work to advance data citation so that all of this mining will become less necessary. The Resource Identification Initiative is also relevant. Clearly, our current systems are inadequate and need to be updated.

    3. The basic challenge is therefore deciding which data are most worthy of the additional resources and effort that will inevitably be required to make them readily discoverable and accessible. Arguably, useful and manageable data discovery systems should focus on datasets that show potential for reuse or that point to significant findings so that underlying data should be available to others to assess validity and accuracy.

      This ignores the transparency and reproducibility argument. Reuse is not the only reason for publishing data; data should be a primary product of research.

    4. (or were eligible to be)

      Given general repositories like Dryad, why is this so low? Is there a large amount of human protected data that can't be handled?

    5. Few annotators chose to use the controlled list; most preferred to use the “Other” option to describe the datasets they found, highlighting the difficulty in establishing a suitable classification for biomedical data types

      Yes, exactly. At NIF we have said that research resources in general are very difficult to classify.

    6. Combining results from all annotators, we estimate that 87% of the articles involved the collection of new data, and 13% involved the analysis of pre-existing data

      New vs old data use estimates.

    7. (e.g., the acronym RGD for Rat Genome Database

      A major motivation behind using resource identifiers for use of research resources.

    8. This finding strongly suggests that any future reviews should be expanded beyond the Acknowledgements section to the entire text of an article.

      I'm hoping that in the discussion, the authors acknowledge the work to advance data citation so that all of this mining will become less necessary. The Resource Identification Initiative is also relevant.

    9. For example, the Influenza Research Database (IRD), Mouse Genome Informatics (MGI) repository, Database of Interacting Proteins (DIP), and Flybase were the most heavily u

      NIF did a similar analysis and came up with many of the same resources, although we did not distinguish between data deposition and data use.

    10. he most common repositories where data were deposited were ClinicalTrials.gov, Protein Data Bank, Gene Expression Omnibus, and GenBank

      Good statistic to know. Most used (or at least referenced) repositories.

    11. The final procedure used to identify articles that mention the deposit of data was to scan for the same keyword variations and acronyms from the 45 NIH data repositories within the XML full-text data for the remaining articles

      A more effective strategy might have been to search for URL's because generally one is included for many of these repositories.

    12. “DataCite” and “Dryad”

      FIgShare also has a lot of traction, although I don't know what the status of FigShare was in 2011 in terms of use.

    13. We selected the NIH Data Sharing Repositories Web page [22] as our gold standard to gather a list of NIH-specific data repositories, and used keyword variations and acronyms (e.g., Gene Expression Omnibus, GEO, Protein Data Bank, PDB) to search each repository in the Acknowledgments field in PMC with the [ack] search tag for the year 2011.

      The NIF Registry (now SciCrunch Registry) data set would have been really helpful here, as it contains synonyms, variants and a list of URL's that point to the resource.