443 Matching Annotations
  1. Last 7 days
    1. As John Dickerson recently put it on Slate, describing his attempt to annotate books on an iPad: “It’s like eating candy through a wrapper.”

      [[similies]]

    1. I like how Dr. Pacheco-Vega outlines some of his research process here.

      Sharing it on Twitter is great, and so is storing a copy on his website. I do worry that it looks like the tweets are embedded via a simple URL method and not done individually, which means that if Twitter goes down or disappears, so does all of his work. Better would be to do a full blockquote embed method, so that if Twitter disappears he's got the text at least. Images would also need to be saved separately.

    1. He notes that authors of such projects should consider the return on investment. It take time to go through community feedback, so one needs to determine whether the pay off will be worthwhile. Nevertheless, if his next work is suitable for community review, he’d like to do it again.

      This is an apropos question. It is also somewhat contingent on what sort of platform the author "owns" to be able to do outreach and drive readers and participation.

    2. A short text "interview" with the authors of three works that posted versions of their books online for an open review via annotation.

      These could be added to the example and experience of Kathleen Fitzpatrick.

    1. I returned to another OER Learning Circle and wrote an ebook version of a Modern World History textbook. As I wrote this, I tested it out on my students. I taught them to use the annotation app, Hypothesis, and assigned them to highlight and comment on the chapters each week in preparation for class discussions. This had the dual benefits of engaging them with the content, and also indicating to me which parts of the text were working well and which needed improvement. Since I wasn't telling them what they had to highlight and respond to, I was able to see what elements caught students attention and interest. And possibly more important, I was able to "mind the gaps', and rework parts that were too confusing or too boring to get the attention I thought they deserved.

      This is an intriguing off-label use case for Hypothes.is which is within the realm of peer-review use cases.

      Dan is essentially using the idea of annotation as engagement within a textbook as a means of proactively improving it. He's mentioned it before in Hypothes.is Social (and Private) Annotation.

      Because one can actively see the gaps without readers necessarily being aware of their "review", this may be a far better method than asking for active reviews of materials.

      Reviewers are probably not as likely to actively mark sections they don't find engaging. Has anyone done research on this space for better improving texts? Certainly annotation provides a means for helping to do this.

    1. Writer and photographer Craig Mod wrote, “There is a gapingopportunity to consolidate our myriad marginalia* into an even morerobust commonplace book. One searchable, always accessible,easily shared and embedded amongst the digital text we consume.”6

      6 Craig Mod, “Post-Artifact Books and Publishing,” craigmod.com, June 2011, https://craigmod.com/journal/post_artifact/.

      It's not just me... I might hope that someone could leverage Hypothes.is' product to create a more explicit digital commonplace book out of their product.

    1. This specification, Open Annotation in EPUB, defines a profile of the W3C Open Annotation specification [OpenAnnotation] for the creation, distribution and rendering of annotations for EPUB® Publications.

      This appendix is informative

      All examples use the same hypothetical publication of Alice in Wonderland, and are given in the collection structure with a single annotation.

      • Commentary Annotation on Publication with URI json-ld { "@context": "http://www.idpf.org/epub/oa/1.0/context.json", "@id": "http://example.org/epub/annotations.json", "@type": "epub:AnnotationCollection", "annotations": [ { "@id": "urn:uuid:E7E3799F-3CD5-4F69-87C6-5478B22873D6", "@type": "oa:Annotation", "hasTarget": { "@type": "oa:SpecificResource", "hasSource": { "@id": "http://www.example.org/ebooks/A1B0D67E-2E81-4DF5/v2.epub", "@type": "dctypes:Text" } }, "hasBody": { "@type": "dctypes:Text", "format": "application/xhtml+xml", "chars": "<div xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'>I love Alice in Wonderland</div>", "language": "en" }, "motivatedBy": "oa:commenting" } ] }

      • Commentary Annotation on Publication without Identifying URI json-ld { "@context": "http://www.idpf.org/epub/oa/1.0/context.json", "@id": "http://example.org/epub/annotations.json", "@type": "epub:AnnotationCollection", "annotations": [ { "@id": "urn:uuid:E7E3799F-3CD5-4F69-87C6-5478B22873D6", "@type": "oa:Annotation", "hasTarget": { "@type": "oa:SpecificResource", "hasSource": { "@type": "dctypes:Text", "uniqueIdentifier": "isbn:123456789x", "originURL": "http://www.example.com/publisher/book/", "dc:identifier": "urn:uuid:A1B0D67E-2E81-4DF5-9E67-A64CBE366809", "dcterms:modified": "2011-01-01T12:00:00Z" } }, "hasBody": { "@type": "dctypes:Text", "format": "application/xhtml+xml", "chars": "<div xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'>I love Alice in Wonderland</div>", "language": "en" }, "motivatedBy": "oa:commenting" } ] }

      • Collection Metadata json-ld { "@context": "http://www.idpf.org/epub/oa/1.0/context.json", "@id": "http://example.org/epub/annotations.json", "@type": "epub:AnnotationCollection", "dc:title": "Alice in Wonderland Annotations", "dc:publisher": "Example Organization", "dc:creator": "Anne O'Tater", "dcterms:modified": "2014-03-17T12:30:00Z", "dc:description": "Anne's collection of annotations on Alice in Wonderland", "dc:rights": [ { "@value": "Quelques droits en Français", "@language": "fr" }, { "@value": "Some Rights in English", "@language": "en" } ], "annotations": [ { "@id": "urn:uuid:E7E3799F-3CD5-4F69-87C6-5478B22873D6", "@type": "oa:Annotation", "hasTarget": { "@type": "oa:SpecificResource", "hasSource": { "@type": "dctypes:Text", "uniqueIdentifier": "isbn:123456789x", "originURL": "http://www.example.com/publisher/book/", "dc:identifier": "urn:uuid:A1B0D67E-2E81-4DF5-9E67-A64CBE366809", "dcterms:modified": "2011-01-01T12:00:00Z" } }, "hasBody": { "@type": "dctypes:Text", "format": "application/xhtml+xml", "chars": "<div xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'>I love Alice in Wonderland</div>", "language": "en" }, "motivatedBy": "oa:commenting" } ] }

      • Annotation with Ancillary Resources in the Zip json-ld { "@context": "http://www.idpf.org/epub/oa/1.0/context.json", "@id": "http://example.org/epub/annotations.json", "@type": "epub:AnnotationCollection", "annotations": [ { "@id": "urn:uuid:E7E3799F-3CD5-4F69-87C6-5478B22873D6", "@type": "oa:Annotation", "hasTarget": { "@type": "oa:SpecificResource", "hasSource": { "@type": "dctypes:Text", "uniqueIdentifier": "isbn:123456789x", "originURL": "http://www.example.com/publisher/book/", "dc:identifier": "urn:uuid:A1B0D67E-2E81-4DF5-9E67-A64CBE366809", "dcterms:modified": "2011-01-01T12:00:00Z" } }, "hasBody": { "@type": "dctypes:Text", "format": "application/xhtml+xml", "chars": "<div xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'>I love Alice in Wonderland! <img src='/imgs/heart.jpg'/></div>" }, "motivatedBy": "oa:commenting" } ] }

      • Styling of Selection

      json-ld { "@context": "http://www.idpf.org/epub/oa/1.0/context.json", "@id": "http://example.org/epub/annotations.json", "@type": "epub:AnnotationCollection", "annotations": [ { "@id": "urn:uuid:E7E3799F-3CD5-4F69-87C6-5478B22873D6", "@type": "oa:Annotation", "styledBy": { "@type": "oa:CssStyle", "format": "text/css", "chars": ".red { border: 1px solid red; }" }, "hasTarget": { "@type": "oa:SpecificResource", "hasSelector": { "@type": "oa:FragmentSelector", "value": "epubcfi(/6/4[chap01ref]!/4[body01]/10[para05]/3:10)" }, "hasSource": { "@type": "dctypes:Text", "uniqueIdentifier": "isbn:123456789x", "originURL": "http://www.example.com/publisher/book/", "dc:identifier": "urn:uuid:A1B0D67E-2E81-4DF5-9E67-A64CBE366809", "dcterms:modified": "2011-01-01T12:00:00Z" }, "styleClass": "red" }, "hasBody": { "@type": "dctypes:Text", "format": "application/xhtml+xml", "chars": "<div xml:lang='en' xmlns='http://www.w3.org/1999/xhtml'>I love this part of the text</div>", "language": "en" }, "motivatedBy": "oa:commenting" } ] }

    1. We use the Web Annotation Protocol to sync bookmarks and last reading position across devices. At a glance it covers all the use cases here, and it's a well-defined protocol with multiple independent implementations. In particular, WAP defines a relation for discovery. Here's how we link to the annotation endpoint for a specific book in an OPDS 1.2 feed. Note the distinctive link relation and media type:
    1. Annotating an in-text reference pointer with a citation function

      ```turtle @prefix : http://www.sparontologies.net/example/ . @prefix cito: http://purl.org/spar/cito/ . @prefix c4o: http://purl.org/spar/c4o/ . @prefix oa: http://www.w3.org/ns/oa# . @prefix per: http://data.semanticweb.org/person/ .

      :annotation a oa:Annotation ; oa:hasBody :citation ; oa:hasTarget :in-text-ref-pointer ; oa:annotatedBy per:silvio-peroni .

      :citation a cito:Citation; cito:hasCitingEntity :paper-a ; cito:hasCitationEvent cito:extends ; cito:hasCitedEntity :paper-b .

      :in-text-ref-pointer a c4o:InTextReferencePointer ; c4o:hasContent "[6]" . ```

    2. Annotating a citation with an additional text-defined citation function

      ```turtle @prefix : http://www.sparontologies.net/example/ . @prefix cito: http://purl.org/spar/cito . @prefix cnt: http://www.w3.org/2011/content# . @prefix oa: http://www.w3.org/ns/oa# .

      :annotation a oa:Annotation; oa:motivatedBy oa:commenting ; oa:hasBody :comment ; oa:hasTarget :citation .

      :comment a cnt:ContentAsText ; cnt:chars "I'm citing that paper because it initiated this whole new field of research." .

      :citation a cito:Citation; cito:hasCitingEntity :paper-a ; cito:hasCitationCharacterization cito:cites ; cito:hasCitedEntity :paper-b . ```

  2. May 2022
    1. <details open> <summary>
      Nanotate Annotations Samples
      </summary> ```json [ { "id":"d5JrdABbEeuatj9X3vvoXw", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:50:41.265044+00:00", "updated":"2020-09-27T00:50:41.265044+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"", "prefix":"for 10 minutes. Wash with PBS3. ", "exact":"Add imaging buffer with desired ratios of Buffer C (500 mM), ethylene carbonate, and IS-CF660R at 1-2 nM final concentration. The exact concentration of IS may need to be adjusted depending on the target and based on the imaging kinetics.", "suffix":"", "start":15158, "end":15396, "tags":[ "step" ], "group":"__world__", "ontologies":[ ] }, { "id":"FrhgjABcEeu5B4dnXgvb_A", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:55:08.276888+00:00", "updated":"2020-10-05T14:15:00.764415+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"my other text modificate", "prefix":"ed ratios of Buffer C (500 mM), ", "exact":"ethylene carbonate", "suffix":"", "start":15219, "end":15237, "tags":[ "reagent" ], "group":"__world__", "ontologies":[ "CHEBI" ], "settings":{ "bio_annotations":[ "" ] } }, { "id":"7Z1sugBbEeu9_wtvk1iAjw", "authority":"__world__", "url":"https://protocolexchange.researchsquare.com/article/pex-1069/v1", "created":"2020-09-27T00:53:59.317703+00:00", "updated":"2020-09-30T00:39:50.822216+00:00", "title":[ "Sample preparation and imaging procedures for fast and multiplexed superresolution microscopy with DNA-PAINT-ERS" ], "refs":[ ], "isReply":false, "isPagenote":false, "user":"acct:miguel.ruano@hypothes.is", "displayName":null, "text":"", "prefix":"10 minutes. Wash with PBS3. Add ", "exact":"imaging buffer", "suffix":"", "start":15162, "end":15176, "tags":[ "reagent" ], "group":"__world__", "ontologies":[ "CHEBI" ], "settings":{ "bio_annotations":[ "http://purl.obolibrary.org/obo/CHEBI_35225" ] } } ] </summary>
    1. Example 2 HTTP/1.1 200 OK Content-Type: application/ld+json; profile="http://www.w3.org/ns/anno.jsonld" Link: <http://www.w3.org/ns/ldp#Resource>; rel="type" ETag: "_87e52ce126126" Allow: PUT,GET,OPTIONS,HEAD,DELETE,PATCH Vary: Accept Content-Length: 287 { "@context": "http://www.w3.org/ns/anno.jsonld", "id": "http://example.org/annotations/anno1", "type": "Annotation", "created": "2015-01-31T12:03:45Z", "body": { "type": "TextualBody", "value": "I like this page!" }, "target": "http://www.example.com/index.html" }
  3. Apr 2022
    1. In the margins of books, in the margins of life as commonly conceived by our culture’s inherited parameters of permission and possibility, I have worked out and continue working out who I am and who I wish to be — a private inquiry irradiated by the ultimate question, the great quickening of thought, feeling, and wonder that binds us all: What is all this?

      A wonderful little poem to the marginalia of life.

    1. ```js document.createAnnotation()

      document.getAnnotations(nodes)

      document.removeAnnotation(annotation) ```

      ```js Annotation#addTarget(target)

      Annotation#addBody(body) ```

    1. solo thinking isrooted in our lifelong experience of social interaction; linguists and cognitivescientists theorize that the constant patter we carry on in our heads is a kind ofinternalized conversation. Our brains evolved to think with people: to teachthem, to argue with them, to exchange stories with them. Human thought isexquisitely sensitive to context, and one of the most powerful contexts of all isthe presence of other people. As a consequence, when we think socially, wethink differently—and often better—than when we think non-socially.

      People have evolved as social animals and this extends to thinking and interacting. We think better when we think socially (in groups) as opposed to thinking alone.

      This in part may be why solo reading and annotating improves one's thinking because it is a form of social annotation between the lone annotator and the author. Actual social annotation amongst groups may add additonal power to this method.

      I personally annotate alone, though I typically do so in a publicly discoverable fashion within Hypothes.is. While the audience of my annotations may be exceedingly low, there is at least a perceived public for my output. Thus my thinking, though done alone, is accelerated and improved by the potential social context in which it's done. (Hello, dear reader! 🥰) I can artificially take advantage of the social learning effects even if the social circle may mathematically approach the limit of an audience of one (me).

    2. A 2019 study published in the Proceedings of the National Academy ofSciences supports Wieman’s hunch. Tracking the intellectual advancement ofseveral hundred graduate students in the sciences over the course of four years,its authors found that the development of crucial skills such as generatinghypotheses, designing experiments, and analyzing data was closely related to thestudents’ engagement with their peers in the lab, and not to the guidance theyreceived from their faculty mentors.

      Learning has been shown to be linked to engagement with peers in social situations over guidance from faculty mentors.

      Cross reference: David F. Feldon et al., “Postdocs’ Lab Engagement Predicts Trajectories of PhD Students’ Skill Development,” Proceedings of the National Academy of Sciences 116 (October 2019): 20910–16


      Are there areas where this is not the case? Are there areas where this is more the case than not?

      Is it our evolution as social animals that has heightened this effect? How could this be shown? (Link this to prior note about social evolution.)

      Is it the ability to scaffold out questions and answers and find their way by slowly building up experience with each other that facilitates this effect?

      Could this effect be seen in annotating texts as well? If one's annotations become a conversation with the author, is there a learning benefit even when the author can't respond? By trying out writing about one's understanding of a text and seeing where the gaps are and then revisiting the text to fill them in, do we gain this same sort of peer engagement? How can we encourage students to ask questions to the author and/or themselves in the margins? How can we encourage them to further think about and explore these questions? Answer these questions over time?

      A key part of the solution is not just writing the annotations down in the first place, but keeping them, reviewing over them, linking them together, revisiting them and slowly providing answers and building solutions for both themselves and, by writing them down, hopefully for others as well.

    1. The bookitself participates in the history it recounts: it has a title page, table of contents,footnotes, a bibliography and an index to assist the reader, while the digitalcopy enables the reader to search for individual words and phrases as well asto copy-and-paste without disfiguring a material object.

      Some scholars study annotations as part of material culture. Are they leaving out too much by solely studying those physically left in the books about which they were made, or should we instead also be looking at other sources like commonplace books, notebooks, note cards, digital spaces like e-readers that allow annotation, social media where texts are discussed, or even digital marginalia in services like Hypothes.is or Perusall?

      Some of these forms of annotation allow a digital version of cut and paste which doesn't cause damage to the original text, which should be thought of as a good thing though it may separate the annotations from the original physical object.

    1. 3. Who are you annotating with? Learning usually needs a certain degree of protection, a safe space. Groups can provide that, but public space often less so. In Hypothes.is who are you annotating with? Everybody? Specific groups of learners? Just yourself and one or two others? All of that, depending on the text you’re annotating? How granular is your control over the sharing with groups, so that you can choose your level of learning safety?

      This is a great question and I ask it frequently with many different answers.

      I've not seen specific numbers, but I suspect that the majority of Hypothes.is users are annotating in small private groups/classes using their learning management system (LMS) integrations through their university. As a result, using it and hoping for a big social experience is going to be discouraging for most.

      Of course this doesn't mean that no one is out there. After all, here you are following my RSS feed of annotations and asking these questions!

      I'd say that 95+% or more of my annotations are ultimately for my own learning and ends. If others stumble upon them and find them interesting, then great! But I'm not really here for them.

      As more people have begun using Hypothes.is over the past few years I have slowly but surely run into people hiding in the margins of texts and quietly interacted with them and begun to know some of them. Often they're also on Twitter or have their own websites too which only adds to the social glue. It has been one of the slowest social media experiences I've ever had (even in comparison to old school blogging where discovery is much higher in general use). There has been a small uptick (anecdotally) in Hypothes.is use by some in the note taking application space (Obsidian, Roam Research, Logseq, etc.), so I've seen some of them from time to time.

      I can only think of one time in the last five or so years in which I happened to be "in a text" and a total stranger was coincidentally reading and annotating at the same time. There have been a few times I've specifically been in a shared text with a small group annotating simultaneously. Other than this it's all been asynchronous experiences.

      There are a few people working at some of the social side of Hypothes.is if you're searching for it, though even their Hypothes.is presences may seem as sparse as your own at present @tonz.

      Some examples:

      @peterhagen Has built an alternate interface for the main Hypothes.is feed that adds some additional discovery dimensions you might find interesting. It highlights some frequent annotators and provide a more visual feed of what's happening on the public Hypothes.is timeline as well as data from HackerNews.

      @flancian maintains anagora.org, which is like a planet of wikis and related applications, where he keeps a list of annotations on Hypothes.is by members of the collective at https://anagora.org/latest

      @tomcritchlow has experimented with using Hypothes.is as a "traditional" comments section on his personal website.

      @remikalir has a nice little tool https://crowdlaaers.org/ for looking at documents with lots of annotations.

      Right now, I'm also in an Obsidian-based book club run by Dan Allosso in which some of us are actively annotating the two books using Hypothes.is and dovetailing some of this with activity in a shared Obsidian vault. see: https://boffosocko.com/2022/03/24/55803196/. While there is a small private group for our annotations a few of us are still annotating the books in public. Perhaps if I had a group of people who were heavily interested in keeping a group going on a regular basis, I might find the value in it, but until then public is better and I'm more likely to come across and see more of what's happening out there.

      I've got a collection of odd Hypothes.is related quirks, off label use cases, and experiments: https://boffosocko.com/tag/hypothes.is/ including a list of those I frequently follow: https://boffosocko.com/about/following/#Hypothesis%20Feeds

      Like good annotations and notes, you've got to put some work into finding the social portion what's happening in this fun little space. My best recommendation to find your "tribe" is to do some targeted tag searches in their search box to see who's annotating things in which you're interested.

    2. Where annotation is not an individual activity, jotting down marginalia in solitude, but a dialogue between multiple annotators in the now, or incrementally adding to annotators from the past.

      My first view, even before any of the potential social annotation angle, is that in annotating or taking notes, I'm simultaneously having a conversation with the author of the work and/or my own thoughts on the topic at hand. Anything beyond that for me is "gravy".

      I occasionally find that if I'm writing as I go that I'll have questions and take a stab only to find that the author provides an answer a few paragraphs or pages on. I can then look back at my thought to see where I got things right, where I may have missed or where to go from there. Sometimes I'll find holes that both the author and I missed. Almost always I'm glad that I spent the time thinking about the idea critically and got to the place myself with or without the author's help. I'm not sure that most others always do this, but it's a habit I've picked up from reading mathematics texts which frequently say things like "we'll leave it to the reader to verify or fill in the gaps" or "this is left as an exercise". Most readers won't/don't do this, but my view is that it's almost always where the actual engagement and learning from the material stems.

      Sometimes I may be writing out pieces to clarify them for myself and solidify my understanding while other times, I'm using the text as a prompt for my own writing. My intention most often is to add my own thoughts in a significantly well-thought out manner such that I can in the near future reuse these annotations/notes in essays or other writing. Some of this comes from broad experience of keeping a commonplace book for quite a while, and some of it has been influenced on reading about the history of note taking practices by others. One of the best summations of the overall practice I've seen thus far is Sönke Ahrens' How to Take Smart Notes (Create Space, 2017), though I find there are some practical steps missing that can only be found by actually practicing his methods in a dedicated fashion for several months before one sees changes in their thought patterns, the questions they ask, and the work that stems from it all. And by work, I mean just that. The whole enterprise is a fair amount of work, though I find it quite fun and very productive over time.

      In my youth, I'd read passages and come up with some brilliant ideas. I might have underlined the passage and written something like "revisit this and expand", but I found I almost never did and upon revisiting it I couldn't capture the spark of the brilliant idea I had managed to see before. Now I just take the time out to write out the entire thing then and there with the knowledge that I can then later revise it and work it into something bigger later. Doing the work right now has been one of the biggest differences in my practice, and I'm finding that projects I want to make progress on are moving forward much more rapidly than they ever did.

    1. https://hypothes.is/a/krnfMl0pEeyvKGMTU02-Lw

      stuhlmueller Dec 14, 2021

      Elicit co-founder here - feel free to leave feedback through hypothesis, we're reading it. :)


      Example in the wild of a company using Hypothes.is to elicit (pun intended) feedback on their product.

    1. Pedagogues considered marginal annotations as the first, optional step towardthe ultimate goal of forming a free-standing collection of excerpts from one’sreading. In practice, of course, readers could annotate their books without takingthe further step of copying excerpts into notebooks.

      Annotations or notes are definitely the first step towards having a collection of excerpts from one's reading. Where to put them can be a useful question though. Should they be in the margins for ease of creation or should they go into a notebook. Both of these methods may require later rewriting/revision or even moving into a more convenient permanent place. The idea "don't repeat yourself" (DRY) in programming can be useful to keep in mind, but the repetition of the ideas in writing and revision can help to quicken the memory as well as potentially surface additional ideas that hadn't occurred upon the notes' original capture.

    2. we have evidencetoo that some users of papyrus rolls made marginal notes, notably introducingsymbols to mark a passage for its content or for future editing.41
    3. An initial stage of annotation might be provided bya professional reader hired to add aids to reading for the owner, including espe-cially mnemonic or meditative aids, or enhancements to the layout, but alsooccasionally self-reflexive or potentially dissenting observations.24 A successionof owner-readers could then add further corrections and comments.

      Stages of annotation in the medieval period


      When is Hypothes.is going to branch out into the business of professional readers to add aids to texts?! :)

      Link this to the professional summary industry that reads books and summarizes them for busy executives

      Link this to the annotations studied by Owen Gingerich in The Book Nobody Read.

  4. Mar 2022
    1. fiber volley amplitudes

      Just because I won't get the chance to ask about it in class: what is a fiber volley amplitude?

    2. stimulus intensities

      What is the stimulus being referred to here? Is it the theta bursts? Is it basically saying that the fEPSP intensity (the slope) in response to theta burst intensity is being recorded? I had a very difficult time interpreting this paragraph because I wasn't sure what the stimulus being discussed here was. Does anyone who is more knowledgeable about this type of research understand what is meant by stimulus?

    3. stationary wheel

      What exactly is a stationary wheel, and how is it different from a regular running wheel? Why would the presence of such a thing cause the mice to gain a significant amount of weight? I looked up the definition of "stationary wheel" and it just seems like an alternative name for a running wheel, but that's clearly not what it is given the differential effects it had on weight gain in female mice.

    4. activity- and experience-dependent patterns of gene expression

      This was very confusing for me. I THINK what it's saying is that the gene expression that controls cell function in specific brain circuits is influenced by certain environmental experiences and activities engaged in, and that gene expression is what drives brain development. Essentially, brain development happens via synaptic plasticity, and that synaptic plasticity is very sensitive to the environment. I could be totally off here but I THINK that's what I think it means.

    5. Exact temporal windows

      This reminds me of the childhood sensitive periods during which synaptic plasticity being higher allows for the acquisition of different languages. Based on the content of this article, it seems like early life plasticity in general allows experiences to seriously alter how the brain develops, so something like exercise has much longer lasting or more permanent positive impact. I wonder if this works the other way, as well. Like, could trauma experienced during early life have a longer-lasting or more permanent negative impact than trauma experienced during adulthood?

    1. I've been using the Hypothesis Obsidian annotator to annotate PDFs in an Obsidian vault—so I have a bunch of annotations as markdown files. I am now attempting to publish the Obsidian vault as a website at movement-ontology.brandazzle.net, but the plugin apparently isn't supported on website, as the annotations do not render. Is there any way I could host the Hypothesis tools on the website and connect my annotations so that viewers can see my annotations?

      Brandon,

      Obsidian Annotator (https://github.com/elias-sundqvist/obsidian-annotator), which I'm presuming you're using, looks like it's working from within Obsidian instead of a web page and is very clever looking, but without some significant work, I don't think it's going to provide you with the results you're looking for. It sounds like you want an all-public chain of work and Obsidian Annotator currently defaults to an all-private chain.

      From my brief perusal of what's going on, the plugin appears to be tied to a single Hypothes.is account (likely the developer's) which defaults all annotations to private (only you) and as a result, even if you had the permalink to the annotations you'd not be able to see them presented on the web as they're all private and you wouldn't have access to the account. You could try filing some issues on the related Github repository to see if the developer might add the ability to make public annotations using your own personal account, which I'm sure would require your personal API key for Hypothes.is to be put into the settings page for the plugin in Obsidian. Another issue I see is that it's taking Hypothesis tags and turning them into Obsidian tags, which is generally fine, but the developer isn't accounting for multi-word tags which is creating unintended tag errors along the way that will need to be manually fixed.

      If you're open to an alternate method of annotating and doing so in public, I can recommend a workflow that will allow you to do what it sounds like you're attempting. It starts with annotating .pdf files (either on the web, or as local files in your browser) in public using your own Hypothes.is account. (Most of this also works with private annotations, but if you want them to appear on public versions of web-hosted .pdf files with the same fingerprints, you'll want them to be public so others can see/interact with them.) Next set up the Hypothesidian script described here: https://forum.obsidian.md/t/retrieve-annotations-for-hypothes-is-via-templater-plugin-hypothes-idian/17225. There are some useful hints further down the thread on that page, so read the whole thing. The Github repository for it is here: https://github.com/SilentVoid13/Templater/discussions/191 if you need it. I've documented a few modifications I've made to the built-in template to suit my particular needs and which might serve as a template if you find it useful: https://boffosocko.com/2021/07/08/hypothes-is-obsidian-hypothesidian-for-easier-note-taking-and-formatting/.

      You can then use the functionality of Hypothesidian to pull in the annotations you want (by day, by document, only your annotations, all the annotations on a document, etc.) For .pdf files, you may require Jon Udell's facet tool https://jonudell.info/h/facet/ to search your personal account for the name of the file or one of the tags you used. When you find it, you can click on it and it will open a new browser window that contains the appropriate urn file "key" you'll need to put into Hypothesidian to grab the annotations from a particular .pdf file. It will be in the general form: urn:x-pdf:1234abcd5678efgh9101112ijkl13. I haven't found an easier means of pulling out the URN/fingerprint of pdf files, though others may have ideas.

      When you pull in your annotations you can also get/find permalinks to the annotations on the web if you like. I usually hide mine in the footnotes of pages with the labels "annotation in situ" and "syndication links", a habit I've picked up from the IndieWeb community (https://indieweb.org/posts-elsewhere). You can see a sample of how this might be done at https://notes.boffosocko.com/where-are-the-empty-spaces-on-the-internet where I've been doing some small scale Hypothes.is/Obsidian/Web experiments. (I'm currently using Blot.im to get [[wikilinks]] to resolve.)

      Another strong option you're probably looking for is to use "via" links (https://web.hypothes.is/blog/meetvia/) on the URLs for your pdf files so that people can automatically see the annotation layer. (This may require whitelisting on Hypothes.is' end depending on where the files are hosted; alternately https://docdrop.org/ may be useful here.) Then if you've annotated those publicly, they'll also be able to see them that way too.

      Another side benefit of this method is that it doesn't require the Data View plugin for Obsidian to render your annotations within Obsidian which also means you'll have cleaner looking pages of annotations in your web published versions. (ie. none of the %% code blocks which don't render properly on the web)

      As I notice you're using some scanned .pdf files which often don't have proper OCR and can make creating annotations with appropriate Hypothes.is anchors, you might also appreciate the functionality of docdrop for this as well.

      Given your reliance on documents and the fact that you've annotated some in what looks like Adobe Acrobat or a similar .pdf program, you might additionally enjoy using Zotero with Obsidian, Zotfile, and mdnotes as outlined here: https://forum.obsidian.md/t/zotero-zotfile-mdnotes-obsidian-dataview-workflow/15536. It's relatively slick, but requires additional set up, reliance on more moving pieces, and isn't as nice an overall user interface in comparison to Hypothes.is. It also misses all of the potential useful social annotation you might get with Hypothes.is.

      Hopefully this is all reasonably clear and helpful. I'd be interested in hearing about options from others who are using Hypothes.is in conjunction with Obsidian or other related note taking tools and publishing them to the web after-the-fact.

      Best, Chris Aldrich

    1. but they would have to find it for it to be of any use to them, and this is something I only have so much energy to advertise.

      This is where widespread awareness of annotations would be useful. A service like Hypothes.is inherently functions as a sort of hub for relaying gossip about a given resource.

    1. A simple request to “move your handsas you explain that” may be all it takes. For children in elementary school, forexample, encouraging them to gesture as they work on math problems leadsthem to discover new problem-solving strategies—expressed first in their handmovements—and to learn more successfully the mathematical concept understudy.

      Given the benefits of gesturing, teachers can improve their pedagogy simply by encouraging their students to move their hands while explaining things or working on problems.

      Studies with elementary school children have shown that if they gesture while solving math problems led them to discover and understand new concepts and problem solving strategies.

      link this with prior idea of handwriting out annotations/notes as well as drawing and sketchnoting ideas from lectures

      Students reviewing over Cornell notes also be encouraged to use their hands while answering their written review questions.

    2. Research shows that people who are asked to write on complex topics,instead of being allowed to talk and gesture about them, end up reasoning lessastutely and drawing fewer inferences.

      Should active reading, thinking, and annotating also include making gestures as a means of providing more clear reasoning, and drawing better inferences from one's material?

      Would gestural movements with a hand or physical writing be helpful in annotation over digital annotation using typing as an input? Is this related to the anecdotal evidence/research of handwriting being a better method of note taking over typing?

      Could products like Hypothes.is or Diigo benefit from the use of digital pens on screens as a means of improving learning over using a mouse and a keyboard to highlight and annotate?

    1. Nice to see someone speaking so joyously about annotations. :) Looks like you've got a heavier analog version of the digital version of what I'm doing. I often use Kindle hightlights/annotations and then import them to Obsidian. Alternately I use Hypothes.is on online .pdf copies and then use Hypothesidian (https://forum.obsidian.md/t/retrieve-annotations-for-hypothes-is-via-templater-plugin-hypothes-idian/17225) to import all my digital notes into Obsidian. I love being able to keep the original context of the text close for either creating literature notes or expanding fleeting notes into permanent ones. When I am in a more analog mode (who doesn't love the feel of a nice fountain pen on paper?) I have a method for doing optical character recognition on my handwritten notes to save the time of typing them out again: https://boffosocko.com/2021/12/20/55799844/

    2. https://www.youtube.com/watch?v=Gvke-vriQbY

      Morgan Eua talks about her active reading practice for fiction and non-fiction and how she transcribes her notes into Obsidian.

    1. I created a tiny app for tracking my studies and adding marginalia to digitally scanned quotes.

      He's an annotations fan!

    1. significantly greater decreases inanxiety over time

      Seems like the control group attenuated to anxiety more effectively than the PI group. Could this maybe be related to habituation? I.e., the controls being in a less stressful environment than the PI group allows them to habituate to negative feelings like anxiety more effectively than the PI group.

    2. unconditioned stimulus(US)

      So, the aversive noise is the US. Am I correct in interpreting the CS as the shape border becoming thicker? Also, this is the terminology used in classical conditioning, but this seems more like operant conditioning, since the participants actually have to do a specific behavior in order for the aversive stimulus to be removed.

    3. enhanced aversive learning

      As an adult with an anxiety disorder...yeah, this is pretty accurate. It's weird to think of anxiety as affording benefits when it's seemingly so maladaptive, but I guess it does make it easier for us to detect potentially harmful situations and avoid them. The problem is really when you begin to experience anxiety when you shouldn't, in response to nonthreatening or neutral stimuli.

    4. Previously institutionalized (PI) youth (i.e., youth who were ini-tially reared in orphanage care)

      This study looking into how stress experienced by orphaned children effects structure and function of mPFC and limbic structures made me curious about how children who go through foster care differ from children who grow up with their biological parents in terms of brain development, since the U.S. foster care system is notorious for child maltreatment. Looking into it, it seems that children who grow up in the foster care system significantly differ from children who grow up with their biological parents in terms of inhibitory control neurocircuitry (Bruce et al., 2013), although it isn't clear to me from skimming the article whether inhibitory control is more robust in foster care children or controls.

    5. amygdala, hippocampus, andmedial prefrontal cortex

      Is it possible that the mPFC, in a sense, "learns" to exert a greater amount of top-down control over the amygdala and hippocampus in individuals with high trait anxiety, since they appear to be overly active in said individuals (particularly the amygdala)? Could it be that spending time in an aversive environment early in development "conditions" these limbic structures to be hyperactive, which in turn leads to strengthened connections with the PFC, since it needs to exert a greater amount of top-down control over them in order to inhibit their overactivity?

  5. Feb 2022
    1. Stay at the forefront of educational innovation

      What about a standard of care for students?

      Bragging about students not knowing how the surveillance technology works is unethical.<br><br>Students using accessibility software or open educational resources shouldn't be punished for accidentally avoiding surveillance. pic.twitter.com/Uv7fiAm0a3

      — Ian Linkletter (@Linkletter) February 22, 2022
      <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

      #annotation https://t.co/wVemEk2yao

      — Remi Kalir (@remikalir) February 23, 2022
      <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
    1. https://en.wikipedia.org/wiki/S._(Dorst_novel)?

      This was mentioned to me at an IndieWebCamp event today.

      Seems interesting with respect to the meta portions of books.

      Looks like the sort of thing that @remikalir and @anterobot may be interested in.

    1. Taking smart notes is the deliberate practice ofthese skills. Mere reading, underlining sentences and hoping toremember the content is not.

      Some of the lighter and more passive (and common) forms of reading, highlighting, underlining sentences and hoping to understand or even remember the content and contexts is far less valuable than active reading, progressive summarization, comparing and contrasting, and extracting smart or permanent notes from one's texts.

    2. Notes build up while you think, read, understand and generateideas, because you have to have a pen in your hand if you want tothink, read, understand and generate ideas properly anyway

      An active reader is always thinking, writing, and annotating. The notes from this process can and could easily be used to facilitate writing and generating new material showing new contexts and new modes of thought.

    1. I would advise you to read with a pen in your hand, and enter in a little book short hints of what you find that is curious or that may be useful; for this will be the best method of imprinting such particulars in your memory, where they will be ready either for practice on some future occasion if they are matters of utility, or at least to adorn and improve your conversation if they are rather points of curiosity.

      Benjamin Franklin letter to Miss Stevenson, Wanstead. Craven-street, May 16, 1760.

      Franklin doesn't use the word commonplace book here, but is actively recommending the creation and use of one. He's also encouraging the practice of annotation, though in commonplace form rather than within the book itself.

  6. Jan 2022
    1. Here’s an even more magical trick. Download that PDF to your file system, load it into a third tab, and annotate again. Now you’ll see all three annotations in all three tabs!

      Since Hypothesis doesn’t know that the local copy of the PDF came from http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0168597&type=printable, or that it’s related to http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168597, how is that possible?

      The answer is that the PDF standard defines a unique identifier, or “fingerprint,” that authoring tools encode into the PDFs they create. When you use the Hypothesis client to annotate web-hosted PDF, it captures the fingerprint and sends it to the server.

    2. It was already the case that you could search Hypothesis for the DOI, like so:

    3. First, here’s a magic trick you might not realize Hypothesis has up its sleeve. Consider this PLOS One article. Annotate it in one tab, then open a second tab and annotate the PDF version there. You’ll see both annotations in both tabs. How is that possible?

      The answer is that when scholarly publishers provide HTML versions of articles, they typically include metadata that points to PDF versions of the same articles. Here’s one way that happens:

      <meta name=”citation_pdf_url” content=”http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0168597&type=printable”>
      

      Hypothesis remembers the correspondence between the HTML and PDF versions, and coalesces annotations across them.

    1. That is why Francis Bacon was rather skeptical about the possibility that excerpts might be shared among scholars. His opinion was that ‘in general, one man’s Notes will little profit another, because one man’s Conceit doth so much differ from another’s; and because the bare Note itself is nothing so much worth, as the suggestion it gives the Reader’.47

      See Bacon’s letter to Greville examined by Vernon Snow, ‘Francis Bacon’s Advice to Fulke Greville on Research Techniques’, Huntington Library Quarterly 23 (1960), 369–78, at 374

      This is similar in tone but for slightly differing reasons to Mortimer J. Adler recommending against loaning one's annotated books to other users. (see: https://hypothes.is/a/6x75DnXBEeyUyEOjgj_zKg)

    1. Underlining (or highlighting): of major points, of important or forceful statements. • Vertical lines at the margin: to emphasize a statement already underlined. • Star, asterisk, or other doo-dad at the margin: to be used sparingly, to emphasize the ten or twenty most important statements in the book. (You may want to fold the bottom comer of each page on which you use such marks. It won't hurt the sturdy paper on which most modern books are printed, and you will be able take the book off the shelf at any time and, by opening it at the folded-corner page, refresh your recollection of the book.)

      These three are all essentially the same thing, just providing differing levels of overall value to Adler somehow. Is there really so much value in highlighting one's highlights?

      Perhaps better would be to rewrite the sections one is highlighting in their own words to provide a stronger signal that one truly understands the concepts one has read.

    2. An incredibly short, but dense essay on annotating books, but one which doesn't go into the same sort of detail as he gets in his book length treatment in How to Read a Book.

      Missing here is the social aspect of annotating a book. In fact, he actively recommends against loaning one's annotated books for fear of losing the details and value in them.

    3. There are all kinds of devices for marking a book intelligently and fruitfully. Here's the way I do it: • Underlining (or highlighting): of major points, of important or forceful statements. • Vertical lines at the margin: to emphasize a statement already underlined. • Star, asterisk, or other doo-dad at the margin: to be used sparingly, to emphasize the ten or twenty most important statements in the book. (You may want to fold the bottom comer of each page on which you use such marks. It won't hurt the sturdy paper on which most modern books are printed, and you will be able take the book off the shelf at any time and, by opening it at the folded-corner page, refresh your recollection of the book.) • Numbers in the margin: to indicate the sequence of points the author makes in developing a single argument. • Numbers of other pages in the margin: to indicate where else in the book the author made points relevant to the point marked; to tie up the ideas in a book, which, though they may be separated by many pages, belong together. • Circling or highlighting of key words or phrases. • Writing in the margin, or at the top or bottom of the page, for the sake of: recording questions (and perhaps answers) which a passage raised in your mind; reducing a complicated discussion to a simple statement; recording the sequence of major points right through the books. I use the end-papers at the back of the book to make a personal index of the author's points in the order of their appearance.

      Mortimer J. Adler's method of annotating a text.

      He's primarily giving the author and their ideas all the power and importance here.

      There is nothing, so far, about immediate progressive summarization. There's also little about the reuse of one's notes for analysis and future synthesis, which I find surprising.

      Earlier in the essay he mentions picking the book up later to refresh one's memory, but there's nothing about linking the ideas from one book to another.

    4. marking up a book is not an act of mutilation but of love.

      —Mortimer J. Adler

    5. You shouldn't mark up a book which isn't yours.

      Killjoy!

    6. You know you have to read "between the lines" to get the most out of anything. I want to persuade you to do something equally important in the course of your reading. I want to persuade you to write between the lines. Unless you do, you are not likely to do the most efficient kind of reading.

      -Mortimer J. Adler

    1. The Annotations API is an extension to the Europeana REST API which allows you to create, retrieve and manage annotations on Europeana objects. Annotations are user-contributed or system-generated enhancements, additions or corrections to (or a selection of) metadata or media. We adopted the Web Annotation Data Model as a base model for the representation of annotations and as a format for exchanging annotations between client applications and the API, but also the Web Annotation Protocol as base HTTP protocol for the API.

      Example:

      {
        "@context": “http://www.w3.org/ns/anno.jsonld”
        "id": "http://data.europeana.eu/annotations/1",
        "type": "Annotation",
        "created": "2015-03-10T14:08:07Z",
        "creator": {
          "type": "Person",
          "name": "John Smith"
        },
        "generated": "2015-04-01T09:00:00Z",
        "generator": {
            "type": "Software",
            "name": "HistoryPin",
            "homepage": "https://www.historypin.org/"
        },
        "motivation": "tagging",
        "bodyValue": "MyBeautifulTag",
        "target": "http://data.europeana.eu/item/92062/BibliographicResource_1000126189360"
      }
      
    1. <small><cite class='h-cite via'> <span class='p-author h-card'> Alexander Wang </span> in Alexander Wang on Twitter: "After discovering the idea of "A Meta-Layer for Notes" (https://t.co/EioyyptzCb), I started to try reading in this way ↓. https://t.co/lOhRyeytXZ" / Twitter (<time class='dt-published'>01/11/2022 09:15:59</time>)</cite></small>

    2. You could imagine employers shipping corporate laptops with pre-installed notes to make it easier to transfer (previously tacit) knowledge and thus improve the onboarding process for new hires.

      Using Hypothes.is as an annotation layer for internal company notes in a private space could be an interesting way for easing on-boarding.

      In some sense, this is a little bit of what the annotated syllabus is doing for students at the beginning of a course (in addition to helping to onboard them to the idea of social annotation at the same time.)

    3. Together, post-its essentially become a notes layer that augments the real world.

      Annotations on Post-It Notes are a form of augmented reality.