1,750 Matching Annotations
  1. Jul 2015
    1. Since patients do not have the medical expertise to judge the quality of physicians’ decisions in the short run and are neither capable of evaluating the outcomes of such decisions in the long run, their feedback would be limited to their immediate interaction with medical providers and their staff members.

      Although I haven't yet read the original post, this statement seems over general and just a bit arrogant. The "we know better than you do" is discredited by medical history, where the physician insisted that bleeding was the proper treatment for what ailed. you.

    2. Going with one’s gut is perhaps an imperfect approach, though for many of us it often seems to be the best we can manage.

      To me, prior experience of the physician with a particular type of ailment is key. If the physician has seen the condition before and has successfully treated it, that would be one very strong indicator that I should go to that doctor.

    3. With all due respect to the author, since both the reviews and the CAHPS surveys are largely based on patient experience — and not clinical quality process or outcome measures — the correlation does not seem to undercut Niam’s point. It does not address directly the broader question of whether a patient can be an expert on his or her own condition.

      But as the physician is often incapable of treating the condition, whether or not the patient had a positive experience is also an important outcome.

    4. chronic condition

      I think the issue of chronic conditions is an important one. If I go to the doctor's and I'm given a treatment and am cured, then I trust the doctor's medical expertise. If I'm not, then on what basis can I trust their expertise? A doctor does not have time to delve deeply into every case. An informed citizen can, in fact, provide valuable knowledge.

    1. Galton was also probably the first to use a technique that we now know as a scatterplot.

      It is always hard to believe that with something so obvious and ubiquitous as the scatter plot, that it was, in fact, invented. But the same is true with "Happy Birthday".

    2. Playfair is credited with introducing four fundamental techniques: bar chart and line graph (1786), and pie chart and circle graph (1801

      What a great name for the father of the graph!

    3. Only in the mid- dle of the 19 th century, the meaning of “statistics” changes – it becomes a name for an independent discipline concerned with producing summaries and reasoning about any collections of numbers, as op- posed to only number s important for the states and industry.

      Interesting derivation of the word, in any case.

    4. controlling its human subjects

      Wow. I would argue that almost all social groups of humans are designed to control human behavior. Amazing how this judgement was rendered as part of an article on data and art history.

    5. panopticon

      a building, as a prison, hospital, library, or the like, so arranged that all parts of the interior are visible from a single point.http://dictionary.reference.com/browse/panopticon

    6. Secondly, the features are encoded in such a way that we calculate on them .

      They are actionable.

    7. In this way, analog media is turned into discrete data.

      Perhaps, though, this is a conflation of data with digital. Data pre-existed digital.

    8. Before we can use computers to analyze a phenomena or activity, it has to be represented as a finite set of individual objects and also a finite set of their features. F

      Again, this is an important point. Many in sciences talk about unbiased data collection, but it is always biased as it is not analog and infinite. One makes decisions based on a variety of factors as to what gets into a digital form and what doesn't. And digital, in my view, implies a hard boundary of some sort.

    9. That is, a phenom- enon is constituted by its representations and the conversations about it.

      Almost equivalent to the concept of operational definition in the sciences. That is, the thing is defined by how we measure it.

    10. In natural and social sciences, the most common term is “variable,” an d it is used in the context of experiments. But since in hu- manities we do not do systematic exper- iments like in the sciences, for us the term “features” is better

      I think this is a fair distinction.

    11. In humanities, we usually refer to characteristics that are already availa- ble as part of the data (because somebody already recorded them) and characteris- tics we have added (for example, by tag- ging) as metadata.

      I think this is fairly general, although metadata is data.

    12. Like other approaches that work on data such as classical statistics and data visualization, data science starts with representing some phenomenon or a process in a particular way. This repre- sentation may include numbers, catego- ries, digitized texts, images, audio, spatial locations, or conne ctions between ele- ments (i.e., network relations). Only after such a representation is constructed, we can use computers to work on it.

      Really does go back to basics! Basically, we need actionable data for data science.

    13. lthough the term "data science" is quite recent, it is quite useful as it acts as an umbrella for currently most fre- quently used methods of computational data analysis

      Definition of data science


    1. Joining in the daylong hoopla were the two children of the American astronomer who discovered Pluto in 1930, Clyde Tombaugh. (Some of his ashes are aboard the spacecraft.)

      I think that is just wonderful. What a thrill it must be for his children.

    2. Pluto is just two-thirds the size of Earth's moon.

      Well...maybe it shouldn't be a planet after all. Size does matter.

    3. The picture of Pluto taken on Monday showed a frozen, pockmarked world, peach-colored with a heart-shaped bright spot and darker areas around the equator. It drew oohs and aahs.

      I'm inclined to keep it as a planet, not that anyone asked me. It is quite beautiful.

    1. It is clear from the use of ES2 and RMG-II cell lines that the Atlas Antibodies ARID1A antibody is specific for ARID1A in both Western blots and formalin-fixed paraffin embedded preparations of human origin and, coupled with the literature evidence, that it is validated in human tissue.

      Validation statement RRID:AB_1078205 Summary

    2. A No Primary antibody control (NPA) showed no staining in the epithelial or nuclear compartment (Figure 3B; Dataset e).

      Validation statement RRID:AB_1078205 No primary control

    3. There was no cytoplasmic or extracellular stromal background staining present and the antibody titrated successfully losing the intensity of staining, as expected

      Validation statement RRID:AB_1078205 Titration curve

    4. Control slides, omitting the primary antibody, were negative except for the ER2 condition in the RMG-II cell pellet where a weak cytoplasmic background could be seen (Figure 2; Dataset d). Thus there was minimal background inherent in the staining procedure. It was therefore determined that the antibody showed specificity for formalin-fixed paraffin embedded tissues and could be run on murine tissue.

      Omission of primary antibody

      Validation statement RRID:AB_1078205

    5. Using Western blot and IHC on murine wild-type and knockout tissue we have demonstrated that this antibody to ARID1A correctly stains murine tissue by immunohistochemistry.

      Validation claim

    6. It could be demonstrated that the HPA ARID1A antibody showed positive expression in ES-2 cell lines at the expected size of 270 kDa and no staining for RMG-II.

      Validation statement for RRID:AB_1078205

    1. The IOM has recommended embargoes of up to 18 months from study completion before clinical trialists are required to share data, although this has been criticised for being too long

      I agree. It might be good to make some specific recommendations here for reducing it that can be taken up for discussion.

    2. Indeed, we need real data with which to develop more robust links between non-public datasets and journal articles. We strongly encourage others to contact the editors ( scientificdata@nature.com ), to discuss proposals.

      The NeuroImaging community would be a rich source of these data sets. See NITRC.

    3. The consensus of regulators, industry sponsors and funders of clinical trials is for data access to be granted to suitably qualified researchers with a legitimate reanalysis proposal.

      ADNI should probably be mentioned here, as they have been sharing clinical data for a while.

    4. They should also state if the data are subject to a DUA and where the DUA can be found – ideally, . CC-BY 4.0 International license for this preprint is the author/funder. It is made available under a The copyright holder ; http://dx.doi.org/10.1101/021667 doi: bioRxiv preprint first posted online June 30, 2015; this should be hosted permanently with the landing page of the non - public dataset.

      Why would this not be a requirement?

    5. figshare were represented in our working group

      Isn't Figshare also owned by MacMillan Digital Science and doesn't MacMillan own Nature? Seems that needs to be stated.

    6. SDR and the YODA Project

      Is this article advocating for these two repositories particularly? If so, that should be made clear in the abstract.

    7. Moreover, few repositories provide statistical analysis software (SAS/ R/ STATA) environments for reanalysis of data that is provided by CSDR and the YODA Project

      Most journals don't supply any analysis tools either. I'm not sure that this is a legitimate requirement of a data repository. Some sort of programmatic API is necessary for data access, but the requirement to link analysis tools seems inappropriate to me.

    8. However, few repositories have processes for managing and approving requests to access non-public clinical datasets.

      This is also true of institutional repositories, which are getting into this space. Should be included here.

    9. We recommend that an approved repository for clinical data should include assessing DUAs to ensure there is an appropriate balance between restriction and reuse

      Should be some standards around this; researchers should not have to fill out independent DUA's for every repository. The article should address this.

    10. Datasets in curated, readily consumable formats should increase confidence in the delivered data formats, adding further value to the offerings of data journals.

      Has NSD seen any evidence that the publication of a data paper has had impact on the use of the data? Such statistics are important to start gathering.

    11. Bibliographic databases, particularly the more selective databases such as PubMed/MEDLINE, Web of Science and Scopus, give some assurances of quality and reliability of the included information to their users through journal evaluation and selection procedures.

      Again, given the issues facing biomedicine, I think this statement can be questioned.

    12. This might also be an option for researchers granted secondary access to data whose study of another researchers ’ data did not fit a traditional research article format

      This seems an odd statement to me. Someone else can describe my data?

    13. 10 reques ts to access data.

      That seems rather anemic.

    14. When surveyed about their data sharing attitudes and behaviours, clinical researchers express concerns about inappropriate secondary analysis of their data, and they cite concerns about patient privacy 16 .

      These are the same concerns expressed by all types of scientists when asked to share their data.

    15. ntroduce data sharing statements and transparency statements in published articles

      Without a mechanism to verify and enforce, these types of requirements appear to be largely ineffective. Many such requirements are already in place.

    16. his approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. T

      Assumption here is that journal article publishing is the only legitimate form of scientific communication, a premise which many are questioning.

    1. n contrast to our initial hypothesis, the genetic deletion of HDAC6 did not reduce the weight loss or the deficits in cognitive abilities and nest-building behavior shown by R6/1 mice, and even worsened their social impairments, hypolocomotion in the Y-maze, and reduced ultrasonic vocalizations.
    1. “When you cannot measure it, when you cannot express it in number … you have scarcely, in your thoughts, advanced to the stage of science, whatever the matter may be”.

      A good rule for science; but scientists have made the mistake in the past of claiming that because it cannot be measured and studied, it does not exist. And that is simply untrue.

    2. Dogs may become aggressive, or quiet, or may stop socialising with “their” humans and other dogs. Sheep, on the other hand, may appear largely the same when casually observed.

      Predators vs prey.

    3. We also know that it is not just our dogs and cats that can suffer pain – there is an equally strong evidence base for the presence and negative impact of pain in sheep, cattle, pigs and horses among other species.

      Why are we surprised by this? I have long contended that we cannot claim to be able to use animals as subjects for experiments for humans without giving them the benefit of the doubt when it comes to human experience.

    4. For example, we know that animals and indeed birds with clinical signs of pain (limping) will choose to eat food containing pain-killing drugs (analgesics) over untreated food, and by measures of behaviour, they will improve.

      They want to make it go away.

    5. Animals rely on human observers to recognise pain and to evaluate its severity and impact.

      Animals also have a really, really big incentive not to show pain, as it may indicate a weakness to a predator. Humans gain a lot of sympathy and benefits from showing pain in circumstances other than sporting events or fights, where it can be exploited.

    6. And it is these unpleasant feelings that cause the suffering we humans associate with pain

      One of the things I find most fascinating as a neuroscientist these days, particularly given that I am at my age in chronic pain, is why these feelings are so unpleasant? What is the qualia of pain that makes it unbearable or is it only circuitry? As a neuroscientist, I think, of course, it is the latter.

    1. Based on curation of this article, CTD states that:

      • resveratrol has known or potential therapeutic role in peritonitis
      • an inferred role in peritonitis based on gene C5
    1. RDoCdb is an informatics platform for the sharing of human subjects data related to Mental Health research.

      Add to SciCrunch Registry. We already have RDoC, but not the database. So the two should be related.

    1. Grants of up to $200,000 will be awarded

      For 12-18 months. Would have to be shovel ready to meet this budget and criteria.

    2. Applicants will be a sustainable entity with an ongoing and operational commitment to improve community health and/or wellbeing.

      I'm not sure we fit this description.

    1. Collator

      This information should not appear on the encyclopedia page but on a separate contributor page or at the bottom: contributors.

    2. Instantiations

      Does Uberon have anything to say about the relationship of structures to taxa?

    3. Mammals

      Be consistent in singular and plural. I don' think, however, that the taxon should be in the name of the page unless one has something special to say.

    1. gray matter

      Gray matter should not be in the name here. You cannot distinguish gray matter from white matter tissue preparation in any meaningful sense. The gray matter/white matter distinction should derive from the anatomical structure being assayed.

    1. Communication barriers between disciplines; lack of specific NIH funding streams; barriers to data-sharing and integration.

      The basic problems of biomedicine.

    2. The Alzheimer's field has had its share of clinical trial flops. Now there's a push to learn from past failures. Computational scientists in pharmaceutical companies are guiding clinical trial design by first putting drug candidates through their paces in simulations.

      Henry Markram will be happy.

    1. If the scientists are publishing their work with F1000, they will eventually be able to do so with one click directly from their workspace.

      This did win one of the vision awards at FORCE11.

    2. These authoring tools are accompanied by literature discovery mechanisms, one of which Tracz describes as “a bit of magic that’s quite amazing”:

      I wonder what that is?

    3. They are usually not experts in the subdisciplines of the papers they see, and an editor’s main interest, says Tracz, is the journal—in increasing its impact factor, for example—not necessarily disseminating sound scientific findings.

      Not me, and not the new mega journals. But it is difficult sometimes balancing these needs.

    4. Anonymous peer review involves a conflict of interest, says the F1000 founder. Since peer reviewers are experts in the field of the papers they review, they can be in competition with the authors of those papers and therefore may have an interest in delaying publication.

      But peer review with an engaged editor can work, I believe. I go back and forth on the issue of anonymity.

    5. It is “unbelievable and ridiculous,” he says, “that science information should become available to people who want to know it with a year delay.”

      Hear, hear!

    1. Compared with the granule cell, the basket cell is quite complicated. It receives synapses from parallel fibers and to a limited extent from climbing fibers, but it devotes its entire axonal output to the Purkinje cells with the possible exception of a few contacts on other basket cells and Golgi cells.

      The definition needs to start with the definition of the cell type. "Basket neuron of the cerebellar cortex, or something like that".

    1. Reference Collator

      Don't think these should appear on the page; they should be metadata attached to each statement on a reference page.

    2. layers II-V

      Definition is for cortical cell, but class is somatosensory cortex definition.

    3. They

      Change to singular.

    4. which are in the form of

      "which form"

  2. Jun 2015
    1. Respondents over age 65 in poor health were the least likely to trust, share, and engage using social media

      Which would be the largest group one needs to reach.

    2. HRI’s consumer survey found that Facebook and YouTube are the most commonly used social media channels for viewing health-related informa - tion.

      I am surprised by this. I don't think I would get health information via either of these sources.

    3. If you want to connect with people and be part of their community, you need to go where the community is. You need to be connecting before you are actually needed,” explained Ed Bennett, who oversees social media efforts at the University of Maryland Medical Center.

      Interesting viewpoint.

    4. In health, examples of community sites include Caring Bridge, Daily Strength, and BabyCenter.

      Need to look these up.

    5. ome organi - zations are capturing sentiment and standard volume numbers on various sites, while others know that they need to go beyond capturing “likes” and “followers” to collecting qualita - tive engagement metrics

      Might be a good opportunity for H here.

    6. In f act, c ommunity si tes h ad 2 4 t imes mo re social media activity on average than any of the health industry compa - nies over that one-week timeframe.

      Doesn't surprise me, unless they have a dedicated social media staff.

    7. L ess t han h alf ( 45%) of i ndividuals ages 45–64 would be likely to share via social media, while 56% would be likely to engage in health activities.

      Yet these are likely to be the majority of people with health related issues.

    8. 2 0% h ave jo ined a health forum or community

      That is a large number. I am surprised.

    9. open, two-way dialogue.

      Something that annotations provide.

    1. he identities of neurons in the nervous system of the nematode Caenorhabditis elegans, which is composed of 118 anatomically distinct neuron types, have been well-defined not only on the level of anatomy, but also in terms of lineage and function

      I understand that all have not been characterized equally.

    1. Should there be one URI identifying the content itself, regardless of its format (e.g., whether it is online or offline)? This is akin to the issue of identifying, e.g., a book as a whole, as opposed to its delivery format (i.e., whether it is a printed or electronic).

      An emphatic "yes" to this, recognizing the difficulties in doing this.

    2. A typical, and extremely valuable use case is in academic and scholarly publishing. There are currently several methods for citing online works (disputed among style guides), but there is no standard method for citations to ebooks. Even if a reflowable ebook is by a scholar, she must refer to PDF, paper copy, or HTML version to cite it in her bibliography. EPUB+WEB should enable stable citations.

      Should be extended to the idea of version of a paper and equivalencies, e.g., a preprint service vs a published document.

    3. As outlined in [dpub-latinreq] or [jlreq], the Open Web Platform in general, and CSS in particular, is still lacking solutions for meeting all of the publishers’ expectations on satisfactory typography and layout for digital publications. While improved presentation fidelity will be of paramount importance to the overall success and adoption rate of EPUB+WEB, it is clear that many of these issues are going to be addressed on a case-by-case basis by the CSS WG over a longer period of time. STM publishing, for example, where the faithful representation and rendering of, e.g., mathematical or chemical formulae is of a paramount importance, has particularly severe requirements that must be fulfilled by the Open Web Platform technologies.

      Interesting that something so basic causes problems. But of course, consistent pagination can only be achieved with consistent fonts and layout. It seems to me that we need something completely new here.

    4. Among the various portable document formats available today, there is no equivalent ubiquitous method for identifying a publication that by definition does not have an HTTP address. Within the scholarly publishing industry, for example, initiatives such as DOI and CROSSREF have addressed this problem by providing explicit URN resolver services, but these services are not used by traditional “trade” publishing that rely more on ISBN related services. Also, for a universally applicable portable document format, unconditionally relying on distinct resolver services is suboptimal for a number of use cases, primarily as these may not be free of charge, and may require registration process that is not be applicable to the use case at hand.

      I think this is one of the issues that really confuses the discussions on identifier systems. Would be good if this were addressed more substantially somewhere.

    5. Today’s EPUB supports a mechanism [CFI] for fine-grained references into a publication, but it is not defined in a manner that natively handles transitions between online and offline/portable states.

      An important requirement.

    6. It must be emphasized, however, that EPUB+WEB is not meant to create an offline version of any Web page; the emphasis is on Web documents and not to, so to say, duplicate the Web. For example, it is not the goal of EPUB+WEB to store the page of a Web-based email client. The exact boundaries and limitations will have to be properly specified alongside the work on archival formats.

      Web documents vs web distinction.

    7. Indeed, the original goal for scholarly publisher to make files available online was to enable readers to download and print content directly,

      Hence the name: pdf

    8. The specific means of delivering hybrid and web-technology-based system applications is currently proprietary to specific applications frameworks and/or browser platforms. The point of EPUB+WEB is to increase problem solving momentum in package, metadata, and offline support applicable to both portable documents and installed applications

      I think this is the right approach, if I understand it correctly.

    9. Mobile platform web site use is diminishing in favor of native applications.

      What does this mean?

    1. A shared theme of many of these TFs, dubbed terminal selectors 1 0 , is that their genetic removal results in the loss of many functionally unrelated terminal identity features, such as neurotrans - mitter identity, expression of neurotransmitter receptors, ion chan - nels, etc.; however, generic features shared by all neurons, such as the expression of synaptic vesicle proteins, are generally unaffected.

      Suggests a basic "neuron" pattern onto which is layered specificity.

    2. neurotrans - mitter identities, as assessed by expression of enzymes and trans - porters that synthesize, synaptically package and reuptake a specific neurotransmitter, remain stable in many adult neuron types.

      It is interesting that one of the main examples used to illustrate neuronal plasticity is the ability of sympathetic neurons to change transmitter identify during development. But for most neurons, their neurotransmitter signature appears to be remarkably stable. And that makes sense.

    1. None can be call'd deform'd but the unkind: Virtue is beauty, but the beauteous evil Are empty trunks o'erflourish'd by the devil.

      Perhaps also echoes the treatment of Malvolio.

    2. And though 'tis wonder that enwraps me thus, Yet 'tis not madness.

      Madness again.

    3. He named Sebastian: I my brother know Yet living in my glass; even such and so

      So Antonio serves this one purpose; to let Viola know that Sebastian might be alive.

    4. The man grows mad: away with him! Come, come, sir.

      Madness is introduced in the second part.

    5. It grieves me Much more for what I cannot do for you Than what befalls myself.

      Again, this is the language of a suitor, not an acquaintance.

    6. Haply your eye shall light upon some toy You have desire to purchase; and your store, I think, is not for idle markets, sir.

      OK. He's giving him money to buy pretty things. I would understand if he were buying clothes and necessities, but really.

    7. I could not stay behind you: my desire, More sharp than filed steel, did spur me forth; And not all love to see you, though so much As might have drawn one to a longer voyage, But jealousy what might befall your travel,

      This perhaps provides an explanation other than an attraction of Antonio to Sebastien, although I think it still rather weak.

    8. But, come what may, I do adore thee so, That danger shall seem sport, and I will go.

      Not very subtle at all. I don't think there is any other way to interpret Antonio's character.

    1. of what he said (see Curt Rice’s blog for an up to date summary)

      Not sure what he is linking to here. Couldn't find any blogs on the topic.

    2. Oh, that might be too much to expect.

      But to identify them properly; certainly!

    3. The responsibility here is not even to report true facts, but the deeper truth – as the scholar sees it – that underlies the events they observe

      Given the human need to tell stories, though, this presents a slippery slope for our two categories: fiction and non-fiction. Perhaps we need a 3rd category that is in between the two.

    4. But did we need an outsider to make it public enough and urgent enough to drive real action? Did Bohannan have responsibilities to the Open Access community to tell us more about the problem, to do a proper study, or as a journalist was his responsiblity to publicly expose the issue?

      I don't see how one can claim that his responsibility was to the Open Access community. Journalists can't choose not to do a story because they agree with the cause. I suspect it happens all the time, but I think it is wrong.

    5. It is the tradition that employment should not be at risk when a scholar speaks in their area of expertise

      But is there expectation that the scholar would have adhered to the aforementioned scholarly rigour?

    6. Authority is the ability to be listened to not the ability to speak freely.

      Don't think this quite captures the definition of authority. It's not the ability to be listened to that is authority. It is the possession of title or knowledge that indicates you should be listened to.

    1. The active transcription factor bound to the consensus sequence was incubated with a specific primary antibody (NF-κB p65) a

      Interesting that with the problems reported with NK-kB antibodies, the exact primary antibody is not mentioned here.

      Would like to be able to easily look up an article from Pub Med or Google Scholar and insert the link, as I did below.

    2. specific primary antibody (NF-κB p65)

      No information provided about antibody used here. Concerns about the specificity of many primary antibodies against NF-kB have been documented in:

      Herkenham et al. (2011) doi:10.1186/1742-2094-8-141.

      Slotta et al. 2014: doi:10.1369/0022155413515484

    3. mouse SphK1

      Would like to be able to perform a lookup from the Antibody Registry to see whether this antibody has an RRID. In this case, although not enough information was provided, it is likely that this antibody is: RRID:AB_2271047, as it is the only mouse antibody in Santa Cruz' catalog against this protein. But that is really insufficient information. So perhaps we would we able to open up a channel with the author to ask them to provide more information.

      Would like to be able to automatically insert the link and some language around it, if an RRID is available. See annotation below.

    4. mouse p-p44/42

      This antibody may have RRID:AB_627545 but information may not be accurate as insufficient metadata was provided.

    5. mouse SphK1

      This antibody may have RRID:AB_2271047 but information may not be accurate as insufficient metadata was provided.

    6. resveratrol

      Or could embed the NIF navigator within H:

      NIF has the following type of information available about Resveratrol:

      • Annotation(45,733)
      • Brain Activation Foci(552)
      • Clinical Trials(190)
      • Dataset(114)
      • Disease(1,243,446)
      • Drugs(637,343)
      • Expression(200,724)
      • Grants(444)
      • Images(31)
      • Microarray(200,765)
      • Multimedia(37)
      • Phenotype(8)
    7. resveratrol

      More information on resveratrol can be found at:

      1. CTD
    8. Taken together, this study provides novel insights into the modes of action of RSV by establishing its strong inhibitory effect on SphK1 and PLD activities, as well as ERK1/2 phosphorylation.

      I'm not an expert, so I am taking them at their word. The interesting this is how CTD took the results of this paper and inferred that there was a link between a drug and a disease. It involves a chain of reasoning that says, as best as I can tell in this short exercise: This study shows an effect RSV on pathways involved in C5-induced inflammation, a mouse model of acute peritonitis. Various drugs interact with C5, therefore they are inferred to have an effect on peritonitis. I have to do some more digging, but this will be a challenge to model in an annotation.

    9. rabbit monoclonal SphK1 primary Abs

      The Antibody Registry lists at least 11 antibodies from different vendors that have this description, so could not assign an RRID

    10. goat-polyclonal PLD1 (Santa Cruz Biotechnologies)

      The Antibody Registry currently lists at least 5 different antibodies meeting this description, so cannot annotate to an RRID.

    11. Taken together, these data demonstrate the ability of RSV to block C5a-induced acute inflammatory response.

      Claim 1

    12. According to the NIF annotation database, the Comparative Toxicogenomics Database has annotated this article with 54 chemical-gene associations. I'm going to try to track them down.

    1. Nevertheless, the overall goals are pretty good. They want to evolve to some more HHMI-like stability of funding, an equilibrium of participating scientists to the available budgets and to generally keep the grant process on improving scientific productivity rather than h


    1. I believe it to be valid but what's to stop me from flooding the H database with false connections, or just spam?

      That is a question for the Hypothesis team and will have to be addressed. How do we verity whether channels can be trusted? And if NIF says they are coming from NIF, how can we tell that they really are?

    2. If that's the approach we'd use, should the API afford a more direct method?

      I can see that this type of situation will happen a lot. Isn't this also the same as having an article in multiple forms?

    3. Can this mechanism meet the needs of the H/NIF/ORCID partnership on the Helmsley grant

      I'm not sure I understand why we need to draw equivalence between the SciCrunch resolution service and the vendor's page. Often, these are not one to one, i.e., the same antibody is sold by multiple vendors.

    1. Box 1. Investing in Practical Solutions

      Interesting that they do not mention information technology. We can develop all the best practices we want, but if we don't have automated ways to verify compliance-even semi-automated will do-studies will continue to fall through the gap. Peer reviewers are over burdened as it is.

    2. However, one issue that has shown demonstrable impact on similar challenges in other settings is the expanded development and adoption of standards and best practices [13].

      Yet, the previous sentences indicated that reporting guidelines, which are a standard, have had minimal impact.

    3. o be clear, this does not imply that there was no return on that investment. As noted in a recent paper by Stern et al. [21], even in cases of retracted publications due to scientific misconduct, which is not a major source of irreproducibility [13,22], “it is conceivable that some of the research resulting in a retracted article still provides useful information for other nonretracted studies.”

      This fact, which I believe is quite real, makes the reproducibility problem difficult to address in any sort of shallow way. I sincerely believe that taking advantage of 21st century communication channels to broadcast information more widely and quickly is the best counter to errors.

    4. Extrapolating from 2012 data, an estimated US$114.8B in the United States [18] is spent annually on life sciences research, with the pharmaceutical industry being the largest funder at 61.8%, followed by the federal government (31.5%), nonprofits (3.8%), and academia (3.0%) [20].

      I think this would surprise most people, although when one thinks of the cost of developing a drug, it is always stated in the billions. So give that NIH's budget is around 30 billion, it would make sense that pharma would dwarf that number.

    5. 2) biological reagents and reference materials

      Yes; hence the motivation for the Resource Identification Initiative

    6. From an economic perspective, the system is highly inefficient. While there are several root causes, one overarching source of inefficiency is the continued emphasis on placing responsibility with the researcher—despite the fact that a significant portion of the costs of irreproducibility are ultimately borne by downstream parties in the translation of bench discoveries to bedside therapies [13].

      This is an interesting take on this.

    7. Attempting to achieve total reproducibility would dramatically increase the cost of such studies and radically curb their volume.

      And lead to cautious, pedestrian science. Some might argue that is what we need, but I would argue that emphasis on the routine would grind advancement in science to a halt.

    8. For this paper, we adopt an inclusive definition of irreproducibility that encompasses the existence and propagation of one or more errors, flaws, inadequacies, or omissions (collectively referred to as errors) that prevent replication of results.

      Definition of reproducibility

    1. ut Ive’s point suggests a larger truth about Silicon Valley that Jobs understood well. Ideas rarely, if ever, come from the mind of a single person, but those who go down in lore as visionaries take credit for them as if they do.

      I don't think this is a larger truth of just Silicon Valley; it's true everywhere!

    2. He saw his success as the result of a lot of hard work and also a fair bit of luck, and he wanted to give the people he knew the opportunity to be a part of it. He hired his sister, to stock the kitchens at Twitter; his wife, Sara, was hired to design the new offices; and he employed numerous friends from Google.

      Re my previous comment: apparently, yes.

    3. “What’s the worst thing I can do as C.E.O. to screw the company up?” Campbell responded, “Hire your friends!”

      That is interesting advice, but isn't this not the case in most start up's?

    4. But this access often relies on having a narrative — being an entrepreneur with just the right creation story.

      Like the Great Gatsby

    5. Twitter was a service for people to talk about what was going on around them, to share news and information.

      Yes, that is much more appealing (and true)

    6. Then he gave an unimpressive explanation of his vision for Twitter. Yahoo made a lowball offer and said that it was building a better competitor.

      Don't know why, but it's nice to know that we all make mistakes in these types of situations.

    7. More often than not, the people who come up with company ideas have no understanding of how to run a business or turn a profit.

      i didn't know there were requirements for an entrepreneur: "a person who organizes and operates a business or businesses, taking on greater than normal financial risks in order to do so."

    8. n the Valley, these tales are called “the Creation Myth” because, while based on a true story, they exclude all the turmoil and occasional back stabbing that comes with founding a tech company.

      True of all human endeavor. Hence the ubiquity of creation myths.

    1. Sleep apnea has been associated with a host of adverse outcomes, ranging from increased risk of primary cardiovascular events (including in a previous study by Shah) and dementia to early mortality. Thus, the association with reduced risk of recurrent coronary events was surprising.

      In fact, see this article published just recently in the same venue: http://www.medpagetoday.com/Cardiology/CHF/51973

    1. You should be able to see your reflection in his eye,” Elser said. “If you can’t, he’s probably in some kind of pain. It’ll get a little dull. I

      Hardest thing is to know when the time is right.

    2. Mules generally don’t live much past forty.

      Forty is very old for a horse.

    3. ut Britta Osthaus, the first author of the 2013 paper, questions the use of the phrase “hybrid vigor.” “Mules are definitely ‘better’ in many aspects than their parent species,” she told me in an e-mail. “But this is defined by what humans see as useful (load capacity, sure-footedness, etc.). As they almost always are infertile, there is no benefit for the genes.”

      This paragraph is a good example of where it would be nice to select several unconnected fragments for annotation. I could do the entire paragraph, but that seems excessive and has a lot of things that aren't necessary to highlight.

    4. Don’t leave any more comments or direct messages about how if branding my stock isn’t that painful, then I should brand myself.”

      Well, that's one way to stop the comments. But did he tell us how bad it was or wasn't?

    5. (The animals are crucial to resupplying outposts in federally designated wilderness areas, where motorized and wheeled vehicles are banned.)

      But will they be replaced by drones? That would be a shame!

    1. neocortical basket cells (BCs) are composed of three distinct subclasses: [...] a third subclass, the nest basket cell (NBC).

      This information should probably be in the definition. The number of subclasses should by dynamically generated, as people add new subclasses.

    2. They


    3. interneurons

      Should be singular and not plural.

    4. Potassium channel (Kv)

      This resolves to a specific potassium channel, not the generic class.

    1. A Thousand Acres. By Jane Smiley. New York: Ballantine, 1991. $12.00
    2. The Crossing. By Cormac McCarthy. New York: Random House, 1994. $13.00.
    3. Remember Me. By Laura Hendrie. New York: Henry Holt, 1999. $24.00.
    4. Plainsong. By Kent Haruf. New York: Knopf, 1999. $24.00.
    5. The Meadow. By James Galvin. New York: Henry Holt, 1992. $12.00.
    6. Strange Angels. By Jonis Agee. New York: HarperPerennial, 1993. $12.00.
    1. Displaying 560,936,869 results

      Related categories: Gene, molecule, microarray.

    1. Perma.cc helps scholars, journals and courts create permanent links to the online sources cited in their work.

      Interesting to add, perhaps, to SciCrunch Registry

    1. All formats includes ephemeral forms that are increasingly dominating medical communication (e.g., online journals, blogs, and databas

      That is interesting. Also interesting that they do not mention the BD2K Data Discovery and Software Discovery indices.

    2. ecome programmatic and adminis trative home for the BD2K Initiative and take lead in defining subsequent data science efforts

      This is an interesting statement. What about the Director of Data Science?

    1. kind of avoid conferences. People who go to conferences are chasing old science, actually. If you don't know about it a year ahead of when it's presented at the conference, then you're probably not up to speed on where the technology is.

      That is an interesting statement.

    2. ut most researchers who have great ideas (in their minds, anyway) for treatments, preventives, or diagnostics have only a vague notion how to transform their science projects into “value propositions” that can raise the millions needed to commercialize a concept.

      Interesting that they don't focus on data or algorithms.

    1. mostly federal small business research grants.

      I suspect that most SBIR's go to pharmaceuticals and biotech.

    2. One, you need a business plan that makes sense to Western investors, including how to win FDA [Food and Drug Administration] approval for the drug; and two, don't tell me anything more until Case Western has secured the IP [intellectual property].”

      Does that put us at a disadvantage with open source software?

    3. But it's hard to go out and be an entrepreneur with a Plan B. You gotta tell yourself that this is the only way the company can move forward, and we're going to make that work.”

      Yes, we can't be half hearted.

    4. “Todd was a very good scientist, although he was by no means my best student,” Ying says. “But he had very good business acumen. And that's essential in running a company.”

      What a great thing for your advisor to say! At least she is honest.

    5. And although some scientists leave campus to follow their commercial dreams, most do not. They like research and teaching, for one thing, and may not think they have what it takes to run a company.

      I certainly feel that this is the case.

    6. And although some scientists leave campus to follow their commercial dreams, most do not. They like research and teaching, for one thing, and may not think they have what it takes to run a company.

      I certainly feel that this is the case.

    7. Eight years later, a second company grew out of her participation in I-Corps' 10-week boot camp for would-be academic entrepreneurs. “I-Corps opened my eyes,” Ray says. “It taught me that you need to know the customer, and your value proposition—that is, how you plan to make money.”

      We just finished the iCorp program at UCSD. It was really helpful. If you are thinking of starting a company and you have the opportunity to participate in iCorp, I highly recommend it.

    1. not every media type has a fragment specification

      Do images have a fragment specification?

    2. a single comment that applies to several web pages

      Or a single comment that binds together several discontinuous text fragments.

    1. Third, a well - moderated community will have low costs : it will do its work while making as few demands as possible on the infr a structure and on participants. Costs here include the obvious computational ones — servers, hard drives, network connections, elect ricity, etc . — b ut also include the work r e- quired of participants, such as flagging a post for removal, r e- moving a flagged post, or appealing an incorrectly removed post

      Very important point for scholarly communications.

    2. By “mode ration,” I mean the governance mechanisms that structure partic i pation in a community to facilitate cooperation and pr e vent abuse .

      Good to have a definition for moderation, as we refer to it often in Hypothes.is.


    1. “The referee rejected it because it was a replication and didn’t contain any novel work.”

      How perfect is this?

    1. We've learned that isolationism never was and never will be an acceptable response to tyrannical governments with an expansionist intent.

      Have we? Should we? We say violence is never the answer, but is that in fact true?

    2. The men of Normandy had faith that what they were doing was right, faith that they fought for all humanity, faith that a just God would grant them mercy on this beachhead or on the next. It was the deep knowledge -- and pray God we have not lost it -- that there is a profound, moral difference between the use of force for liberation and the use of force for conquest. You were here to liberate, not to conquer, and so you and those others did not doubt your cause. And you were right not to doubt.

      Reagan's speech on the 40th anniversary of D-day. Today is the 71st anniversary. Easy to forget now, but still one of the most profound acts of bravery in history.

    1. So far, the Reproducibility Initiative has obtained data for 31 of the 50 papers. Some validation experiments have already been conducted, each at a cost of around US$25,000 in materials and time. Costs are closer to $35,000 for mouse studies, Gunn said. The project has a $1.3-million grant from the Laura and John Arnold Foundation of Houston, Texas, to do its work.

      Also supported by the Arnold Foundation

    1. He even helped invent the pop-up ad because corporations were wary of the user content appearing next to their ads

      May he live in infamy.

    2. Many people say that no significant number of users will ever pay directly for Internet services.

      I also think that is not true People who have money generally will pay for additional levels of service, particularly if it saves them time. At some point. for some, time is more valuable than money.

    1. Transcriptomine is a tool for mining tissue-specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling.

      This tool should be in the SciCrunch Registry

  3. May 2015
    1. Biomedical innovation and discovery based on research and development by private and public companies and institutions are essential for advancing medical science and improving clinical care. However, unless stealth research adopts more scientific transparency, investors, physicians, patients, and healthy people will not be able to judge whether some proposed innovation is worth $9 billion, $900 billion, or just $9—let alone if the innovation will improve the health and well-being of individuals.

      Can they do that now though? This is a strange statement coming from this author, given that he has exposed how most published research is wrong.

    2. Theranos is just one example among many for which major efforts and major claims about biomedical progress seem to be happening outside the peer-reviewed scientific literature. Many of these efforts and claims have a biotechnology flavor, and the people involved often include a blend of engineers, physical scientists, and venture capitalists. The main motive appears to be to develop products and services, rather than report new discoveries as research scholarship. Products, services, and profit appear to be more important than scientific publications. For some biotechnology innovators, peer-reviewed publication may be perceived as unnecessary. Publication makes knowledge public and communal, whereas the efforts of some companies build on the spirit of private ultracompetitive entrepreneurship. At a time of increasing recognition of the importance of transparency in laboratory and clinical research, this approach seems paradoxical.

      Papers from people in industry are often mistrusted as well.

    1. We see a future in which scientific information and scholarly communication more generally become part of a global, universal and explicit network of knowledge; where every claim, hypothesis, argument—every significant element of the discourse—can be explicitly represented, along with supporting data, software, workflows, multimedia, external commentary, and information about provenance. In this world of networked knowledge objects, it would be clear how the entities and discourse components are related to each other, including relationships to previous scholarship; learning about a new topic means absorbing networks of information, not individually reading thousands of documents. Adding new elements of scholarly knowledge is achieved by adding nodes and relationships to this network. People could contribute to the network from a variety of perspectives; each contribution would be immediately accessible globally by others. Reviewing procedures, as well as reputation management mechanisms, would provide ways to evaluate and filter information. This vision moves away from the Gutenberg paper-centric model of the scholarly literature, towards a more distributed network-centric model; it is a model far better suited for making knowledge-level claims and supporting digital services, including more effective tracking and interrogation of what is known, not known, or contested.

      Actually, Hypothes.is could deliver this. I believe that a layer of annotation on top of, rather than integrated entirely within, is the way to go.

    1. The genomic predictor was clearly bad (everyone agrees), but I don’t see that this patient was physically hurt because of this trial per se,” said Matthew Goetz, a professor of oncology and pharmacology at Mayo Clinic, who also reviewed Shoffner’s case for The Cancer Letter.

      Excuse me, but how do you know? How do you know she wouldn't have pursued some other treatment instead of this fraudulent one. What if a really promising treatment had come along and she was disqualified because she had participated in this trial?

    2. I don’t approve of lying to patients

      Well I would hope not

    3. Lying, or withholding information from patients is “a very bad idea,”

      That's the strongest statement you can make on this? A very bad idea? How about inexcusable and illegal?

    4. Unbeknownst to Shoffner, Duke had suspended the trials twice, silenced the whistleblower, and overlooked data from other institutions—while she was in touch with her Duke oncologist, Paul Kelly Marcom.


    5. Why did we not at least have honesty? Why was there not some integrity with this when it came to the human life? Why could decent human beings do this to other human beings?”

      Science has to answer this question.

    1. 68,000 postdocs

      More importantly, do we have the oversight and training necessary for these post docs? The recent failures in statistics and power analysis suggest that the universities do not have the capacity to train their graduate students or post docs.

    2. It’s hard not to imagine that all of that competition is pushing some scientists to cut corners, or worse, so they can publish in the top journals, they need to in order to earn tenure.

      I always said that the doubling of the NIH budget was the worse thing that could have happened to biomedical science.

    3. For a decade, science magazines have documented trends in employment of PhDs. According to an article last year in Times Higher Education, for example, there are as many as 68,000 postdocs in the United States at the moment – up from about 28,000 in 1979.

      Wow. That is a huge increase in the number of post docs.

    1. Citation: Ioannidis JPA (2014) How to Make More Published Research True. PLoS Med 11(10): e1001747. doi:10.1371/journal.pmed.1001747