1,318 Matching Annotations
  1. Last 7 days
    1. Rank, Mark Robert, Lawrence M. Eppard, and Heather E. Bullock. Poorly Understood: What America Gets Wrong About Poverty. Oxford University Press, 2021.

      Reading as part of Dan Allosso's Book Club

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  2. Sep 2022
    1. Heyde, Johannes Erich. Technik des wissenschaftlichen Arbeitens. (Sektion 1.2 Die Kartei) Junker und Dünnhaupt, 1931.

      (Unknown translation from German into English. v1 TK)

      The overall title of the work (in English: Technique of Scientific Work) calls immediately to mind the tradition of note taking growing out of the scientific historical methods work of Bernheim and Langlois/Seignobos and even more specifically the description of note taking by Beatrice Webb (1926) who explicitly used the phrase "recipe for scientific note-taking".

      see: https://hypothes.is/a/BFWG2Ae1Ee2W1HM7oNTlYg

      first reading: 2022-08-23 second reading: 2022-09-22

    1. Sword, Helen. “‘Write Every Day!’: A Mantra Dismantled.” International Journal for Academic Development 21, no. 4 (October 1, 2016): 312–22. https://doi.org/10.1080/1360144X.2016.1210153

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    1. IntertextsAs Jonathan Culler writes: “Liter-ary works are not to be consideredautonomous entities, ‘organicwholes,’ but as intertextual con-structs: sequences which havemeaning in relation to other textswhich they take up, cite, parody,refute, or generally transform.” ThePursuit of Signs (Ithaca, NY: CornelUniversity Press, 1981), 38.

      Throughout Rewriting: How To Do Things With Texts (Utah State University Press, 2006) Joseph Harris presents highlighted sidebar presentations he labels "Intertexts".

      They simultaneously serve the functions of footnotes, references, (pseudo-)pull quotes, and conversation with his own text. It's not frequently seen this way, but these intertexts serve the function of presenting his annotations of his own text to model these sorts of annotations and intertextuality which he hopes the reader (student) to be able to perform themselves. He explicitly places them in a visually forward position within the text rather than hiding them in the pages' footnotes or end notes where the audience he is addressing can't possibly miss them. In fact, the reader will be drawn to them above other parts of the text when doing a cursory flip through the book upon picking it up, a fact that underlines their importance in his book's thesis.


      This really is a fantastic example of the marriage of form and function as well as modelling behavior.


      cc: @remikalir

    2. Harris, Joseph. Rewriting: How To Do Things With Texts. Logan: Utah State University Press, 2006. https://muse.jhu.edu/book/9248

    1. Courtney, Jennifer Pooler. “A Review of Rewriting: How to Do Things with Texts.” The Journal of Effective Teaching 7, no. 1 (2007): 74–77.

      Review of: Harris, Joseph. Rewriting: How To Do Things With Texts. Logan: Utah State University Press, 2006. https://muse.jhu.edu/book/9248.

    1. Sword, Helen. “‘Write Every Day!’: A Mantra Dismantled.” International Journal for Academic Development 21, no. 4 (October 1, 2016): 312–22. https://doi.org/10.1080/1360144X.2016.1210153.

      Preliminary thoughts prior to reading:<br /> What advice does Boice give? Is he following in the commonplace or zettelkasten traditions? Is the writing ever day he's talking about really progressive note taking? Is this being misunderstood?

      Compare this to the incremental work suggested by Ahrens (2017).

      Is there a particular delineation between writing for academic research and fiction writing which can be wholly different endeavors from a structural point of view? I see citations of many fiction names here.

      Cross reference: Throw Mama from the Train quote

      A writer writes, always.

    1. Bjorn, Genevive A., Laura Quaynor, and Adam J. Burgasser. “Reading Research for Writing: Co-Constructing Core Skills Using Primary Literature.” Impacting Education: Journal on Transforming Professional Practice 7, no. 1 (January 14, 2022): 47–58. https://doi.org/10.5195/ie.2022.237

      Found via:

      #AcademicTwitter I survived crushing reading loads in grad school by creating a straightforward method for analyzing primary literature, called #CERIC. Saved my sanity and improved my focus. @PhDVoice. Here’s the free paper - https://t.co/YehbLQNEqJ

      — Genevive Bjorn (@GeneviveBjorn) September 11, 2022
      <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

      I'm curious how this is similar to the traditions of commonplace books and zettelkasten from a historical perspective.

    1. Eco, Umberto. How to Write a Thesis. Translated by Caterina Mongiat Farina and Geoff Farina. Cambridge, MA, USA: MIT Press, 2015. https://mitpress.mit.edu/books/how-write-thesis

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  3. Aug 2022
    1. Each type of index card should have a dif-ferent color, and should include in the top right corner abbre-viations that cross-reference one series of cards to another,and to the general plan. The result is something majestic.

      Finally a concrete statement about actively cross-linking ideas on note cards together!

    1. German publishers send out so-called book cards to book shops along with their newreleases. On them, bibliographic information is printed. Those book cards are also in postcardsize, i.e. A6, and their textual structure allows for them to be included in the reference filebox.

      Automatic reference cards!

      When did they stop doing this!!!

    1. Allosso, Dan, and S. F. Allosso. How to Make Notes and Write. Minnesota State Pressbooks, 2022. https://minnstate.pressbooks.pub/write/.

      Annotatable .pdf copy for Hypothes.is: https://docdrop.org/pdf/How-to-Make-Notes-and-Write---Allosso-Dan-jzdq8.pdf/

      Nota Bene:

      These annotations are of a an early pre-release draft of the text. One ought to download the most recent revised/final/official draft at https://minnstate.pressbooks.pub/write/.

    1. Jones, Christopher P. “Zettelkasten.” Edited by R. Merkelbach and J. Stauber. The Classical Review 50, no. 1 (2000): 170–72.

      Nothing at all about the titular word zettelkasten, but rather a negative review of a book on inscriptions...

    1. Fickert, Kevin-Steven. “Die Geschichte des Zettelkatalogs : eine historisch-kritische Betrachtung eines Verzeichnismediums und seiner Regelwerke.” Fachhochschule Stuttgart Hochschule der Medien, 2003. https://hdms.bsz-bw.de/frontdoor/index/index/docId/141

      via Ton Zijlstra

    1. Allosso, Dan. US History and Primary Source Anthology, Vol. 1. 2 vols. Minnesota State Pressbooks, 2022. https://minnstate.pressbooks.pub/ushistory1/

    1. Jahraus, Oliver, Armin Nassehi, Mario Grizelj, Irmhild Saake, Christian Kirchmeier, and Julian Müller, eds. Luhmann-Handbuch: Leben – Werk – Wirkung. Springer, 2012. https://link.springer.com/book/10.1007/978-3-476-05271-1

    1. Dutcher, George Matthew. “Directions and Suggestions for the Writing of Essays or Theses in History.” Historical Outlook 22, no. 7 (November 1, 1931): 329–38. https://doi.org/10.1080/21552983.1931.10114595

    2. (see paragraph 28)

      an example within this essay of a cross reference from one note to another showing the potential linkages of individual notes within one's own slipbox.

    3. the slips by the topicalheadings. Guide cards are useful to gdicate the several head-ings and subheadings. Under each heading classif the slipsin writing, discarding any that may not prove useful andmaking cross references for notes which may be needed foruse in more than one lace. This classification will reveal,almost automatically, wiere there are deficiencies in the ma-terials collected which should be remedied. The completedand classified collection of notes then becomes the basis ofcomposition.

      missing some textual context here for full quote...

      Dutcher is recommending arranging notes and cards by topical headings in a commonplace sort of method. He does recommend a sub-arrangement of placing them in logical order for one's writing however. He goes even further and indicates one may "make cross references for notes which may be needed for use in more than one place." Which provides an early indication of linking or cross linking cards to multiple places within in one's card index. (Has this cross referencing (linking) idea appeared in the literature specifically before, or is this an early instantiation of this idea?)

    1. Scheper, Scott P. Antinet Zettelkasten: The Secret Knowledge Development System Evolved By History’s Greatest Minds. Advanced Reader Copy. Greenlamp, 2022.

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    1. Historical Hypermedia: An Alternative History of the Semantic Web and Web 2.0 and Implications for e-Research. .mp3. Berkeley School of Information Regents’ Lecture. UC Berkeley School of Information, 2010. https://archive.org/details/podcast_uc-berkeley-school-informat_historical-hypermedia-an-alte_1000088371512. archive.org.

      https://www.ischool.berkeley.edu/events/2010/historical-hypermedia-alternative-history-semantic-web-and-web-20-and-implications-e.

      https://www.ischool.berkeley.edu/sites/default/files/audio/2010-10-20-vandenheuvel_0.mp3

      headshot of Charles van den Heuvel

      Interface as Thing - book on Paul Otlet (not released, though he said he was working on it)

      • W. Boyd Rayward 1994 expert on Otlet
      • Otlet on annotation, visualization, of text
      • TBL married internet and hypertext (ideas have sex)
      • V. Bush As We May Think - crosslinks between microfilms, not in a computer context
      • Ted Nelson 1965, hypermedia

      t=540

      • Michael Buckland book about machine developed by Emanuel Goldberg antecedent to memex
      • Emanuel Goldberg and His Knowledge Machine: Information, Invention, and Political Forces (New Directions in Information Management) by Michael Buckland (Libraries Unlimited, (March 31, 2006)
      • Otlet and Goldsmith were precursors as well

      four figures in his research: - Patrick Gattis - biologist, architect, diagrams of knowledge, metaphorical use of architecture; classification - Paul Otlet, Brussels born - Wilhelm Ostwalt - nobel prize in chemistry - Otto Neurath, philosophher, designer of isotype

      Paul Otlet

      Otlet was interested in both the physical as well as the intangible aspects of the Mundaneum including as an idea, an institution, method, body of work, building, and as a network.<br /> (#t=1020)

      Early iPhone diagram?!?

      (roughly) armchair to do the things in the web of life (Nelson quote) (get full quote and source for use) (circa 19:30)

      compares Otlet to TBL


      Michael Buckland 1991 <s>internet of things</s> coinage - did I hear this correctly? https://en.wikipedia.org/wiki/Internet_of_things lists different coinages

      Turns out it was "information as thing"<br /> See: https://hypothes.is/a/kXIjaBaOEe2MEi8Fav6QsA


      sugane brierre and otlet<br /> "everything can be in a document"<br /> importance of evidence


      The idea of evidence implies a passiveness. For evidence to be useful then, one has to actively do something with it, use it for comparison or analysis with other facts, knowledge, or evidence for it to become useful.


      transformation of sound into writing<br /> movement of pieces at will to create a new combination of facts - combinatorial creativity idea here. (circa 27:30 and again at 29:00)<br /> not just efficiency but improvement and purification of humanity

      put things on system cards and put them into new orders<br /> breaking things down into smaller pieces, whether books or index cards....

      Otlet doesn't use the word interfaces, but makes these with language and annotations that existed at the time. (32:00)

      Otlet created diagrams and images to expand his ideas

      Otlet used octagonal index cards to create extra edges to connect them together by topic. This created more complex trees of knowledge beyond the four sides of standard index cards. (diagram referenced, but not contained in the lecture)

      Otlet is interested in the "materialization of knowledge": how to transfer idea into an object. (How does this related to mnemonic devices for daily use? How does it relate to broader material culture?)

      Otlet inspired by work of Herbert Spencer

      space an time are forms of thought, I hold myself that they are forms of things. (get full quote and source) from spencer influence of Plato's forms here?

      Otlet visualization of information (38:20)

      S. R. Ranganathan may have had these ideas about visualization too

      atomization of knowledge; atomist approach 19th century examples:S. R. Ranganathan, Wilson, Otlet, Richardson, (atomic notes are NOT new either...) (39:40)

      Otlet creates interfaces to the world - time with cyclic representation - space - moving cube along time and space axes as well as levels of detail - comparison to Ted Nelson and zoomable screens even though Ted Nelson didn't have screens, but simulated them in paper - globes

      Katie Berner - semantic web; claims that reporting a scholarly result won't be a paper, but a nugget of information that links to other portions of the network of knowledge.<br /> (so not just one's own system, but the global commons system)

      Mention of Open Annotation (Consortium) Collaboration:<br /> - Jane Hunter, University of Australia Brisbane & Queensland<br /> - Tim Cole, University of Urbana Champaign<br /> - Herbert Van de Sompel, Los Alamos National Laboratory annotations of various media<br /> see:<br /> - https://www.researchgate.net/publication/311366469_The_Open_Annotation_Collaboration_A_Data_Model_to_Support_Sharing_and_Interoperability_of_Scholarly_Annotations - http://www.openannotation.org/spec/core/20130205/index.html - http://www.openannotation.org/PhaseIII_Team.html

      trust must be put into the system for it to work

      coloration of the provenance of links goes back to Otlet (~52:00)

      Creativity is the friction of the attention space at the moments when the structural blocks are grinding against one another the hardest. —Randall Collins (1998) The sociology of philosophers. Cambridge, MA: Harvard University Press (p.76)

  4. Jul 2022
    1. Bernheim, Ernst. Lehrbuch der historischen Methode und der Geschichtsphilosophie: mit Nachweis der wichtigsten Quellen und Hilfsmittel zum Studium der Geschichte. Leipzig : Duncker & Humblot, 1908. http://archive.org/details/lehrbuchderhist03berngoog.

      Title translation: Textbook of the historical method and the philosophy of history : with reference to the most important sources and aids for the study of history

      A copy of the original 1889 copy can be found at https://digital.ub.uni-leipzig.de/mirador/index.php

    1. Peirce, Charles Sanders. “How to Make Our Ideas Clear.” Popular Science Monthly 12, no. Jan. (January 1878): 286–302.

      see also: - https://cspeirce.omeka.net/items/show/3

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    1. Kidd, Alison. “The Marks Are on the Knowledge Worker.” In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, 186–91. CHI ’94. New York, NY, USA: Association for Computing Machinery, 1994. https://doi.org/10.1145/191666.191740.

  5. Local file Local file
    1. Orwell, George. Nineteen eighty-four. (Mariner, 2008) ISBN 978-0-15-603584-2

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  6. Jun 2022
    1. First!


      What I really mean is: <br /> I'm bookmarking this for my digital notebook https://journals.sagepub.com/doi/abs/10.1177/1474022220915128

      “Something fruitful for all of us”: Social annotation as a signature pedagogy for literature education<br /> Jeffrey Clapp, Matthew DeCoursey, Sze Wah Sarah Lee, et al.<br /> First Published March 29, 2020<br /> https://doi.org/10.1177/1474022220915128

      There's always something suspicious about journal articles about social annotation when there's no public sign of social annotation on them.

      We've remedied this problem...

    1. The Reading Brain in the Digital Age: The Science of Paper versus Screens https://www.scientificamerican.com/article/reading-paper-screens/ by Ferris Jabr Scientific American 2013-04-11 A good overview of reading practices, reading user interfaces, and research literature relevant to it. Lots of abstracts from research which I ought to look at more closely, and thus didn't make note of as much as I'd rather delve into the primary sources.

      Most of the research cited here is preliminary to early e-reading devices and has small sample sizes. Better would be to see how subsequent studies have fared with larger and more diverse groups.

    1. [26]

      There should be a total of 19 references, but this version has 26 due to duplicate references. I have fixed this in a newer version.

    2. [3] - [9], [11] - [17]

      There should be a total of 19 references, but this version has 26 due to duplicate references. I have fixed this in a newer version.

  7. May 2022
    1. Brine, Kevin R., Ellen Gruber Garvey, Lisa M. Gitelman, Steven J. Jackson, Virginia Jackson, Markus Krajewski, Mary Poovey, et al. “Raw Data” Is an Oxymoron. Edited by Lisa M. Gitelman. Infrastructures. MIT Press, 2013. https://mitpress.mit.edu/books/raw-data-oxymoron.

    1. https://interactions.acm.org/archive/view/may-june-2011/between-the-lines-the-social-life-of-marginalia1

      Danzico, Liz. “Between the Lines: The Social Life of Marginalia.” Interactions 18, no. 3 (May 2011): 12–13. https://doi.org/10.1145/1962438.1962443.

      A short synopsis article about marginalia with some simple questions. She's read a fair amount in the space from the 2010s given references, but little I hadn't encountered before. The Robin Sloan tidbit was interesting as well as the etymology of marginalia, though these will need better references.

    1. 32. C. Sagan, O. B. Toon, J. B. Pollack, Science 206, 1363 (1979). 33. S. Manabe and R. F. Strickler, J. Atmos. Sci. 21, 361 (1964).

      Accurate climate models require a thorough understanding of how much light is reflected by clouds and the Earth's surface. These studies shed light on how land cover and clouds impact the global energy balance.

    2. 26. J. Hansen, A. Lacis, P. Lee, W. Wang, Ann. N. Y. Acad. Sci. 338, 575 (1980). 27. H. H. Lamb, Philos. Trans. R. Soc. London Ser. A 255, 425 (1970). 28. S. H. Schneider and C. Mass, Science 190, 741 (1975). 29. J. B. Pollack, O. B. Toon, C. Sagan, A. Summers, B. Baldwin, W. Van Camp, J. Geophys. Res. 81, 1971 (1976). 30. A. Robock, J. Atmos. Sci. 35, 1111 (1978); Science 206, 1402 (1979). 31. W. Cobb, J. Atmos. Sci. 30, 101 (1973); R. Roosen, R. Angione, C. Klemcke, Bull. Am. Meteorol. Soc. 54, 307 (1979).

      Experimental and theoretical investigations of the effect of aerosols, particularly those released during volcanic eruptions, have allowed for the reliable modeling of cooling periods throughout history.

    3. 24. H. Oeschger, U. Siegenthaler, U. Schotterer, A. Gugelmann, Tellus 27, 168 (1975). 25. W. S. Broecker, Science 189, 460 (1975).

      The development of box diffusion models provided a useful, tunable way to represent the exchange of heat between the atmosphere and ocean in climate models.

    4. 14. A. Lacis, W. Wang, J. Hansen, NASA Weather and Climate Science Review (NASA Goddard Space Flight Center, Greenbelt, Md., 1979). 15. R. A. McClatchey et al., U.S. Air Force Cambridge Res. Lab. Tech. Rep. TR-73-0096 (1973). 16. R. E. Roberts, J. E. A. Selby, L. M. Biberman, Appl. Opt.15, 2085 (1976). 17. O. B. Toon and J. B. Pollack, J. Appl. Meteorol. 12, 225 (1976). 18. R. D. Cess, J. Quant. Spectrosc. Radiat. Transfer 14, 861 (1974). 19. W. C. Wang and P. H. Stone, J. Atmos. Sci. 37, 545 (1980). 20. R. D. Cess, ibid. 35, 1765 (1978).

      Experimental studies are vital to the construction of accurate climate models. These studies include measurements of the absorption of radiation by gases, aerosols, and the Earth's surface to supply parameters for programs that predict energy flows through the atmosphere.

    5. 5. W. C. Wang, Y. L. Yung, A. A. Lacis, T. Mo, J. E. Hansen, Science 194, 685 (1976). 6. National Academy of Sciences, Carbon Dioxide and Climate: A Scientific Assessment (Washington, D.C., 1979). This report relies heavily on simulations made with two three-dimensional climate models (7, 8) that include realistic global geography, seasonal insolation variations, and a 70-m mixed-layer ocean with heat capacity but no horizontal transport of heat. 7. S. Manabe and R. J. Stouffer, Nature (London) 282, 491 (1979); J. Geophys. Res. 85, 5529 (1980). 8. J. Hansen, A. Lacis, D. Rind, G. Russell, P. Stone, in preparation. Results of an initial CO2 experiment with this model are summarized in (6). 9. National Academy of Sciences, Understanding Climate Change (Washington, D.C., 1975).

      Hansen, Manabe, and others performed extensive work creating models to represent the atmosphere and predict its response to the emission of greenhouse gases.

    1. T. J. Johnson, D. Ross, L. E. Locascio, Anal. Chem. 10.1021/ac010895d.

      T.J. Johnson and colleagues studied several mixer designs by fabricating a series of slanted wells within a microchannel using a UV excimer laser. These wells generated a high degree of lateral transport within the channel to help induce rapid mixing between two confluent streams undergoing electroosmotic flow.

    2. 11. Jones S. W., Thomas O. M., Aref H., J. Fluid Mech. 209, 335 (1989).

      The authors demonstrated chaotic mixing in a twisted pipe with a circular cross-section.

    3. 23. We qualify the mixing as thorough when the fluorescence appears uniform to within the resolution (∼2 μm) and sensitivity (down to variations of ∼5% of the maximum intensity) of our microscope.

      Because there are many possible solutions to a problem; it is important to choose the design requirements and success criteria for the proposed solution. Here the authors describe their design criteria for thoroughly mixing a solution.

  8. Apr 2022
    1. 16. We made the master structures with two-step photolithography in SU-8 photoresist: The first layer of photolithography defined the channel structure; the second layer defined the pattern of ridges. The pattern of ridges was aligned to lie on top of the channel structure in the first layer. We measured the dimensions of the channel and the ridges using a profilometer. We made molds of the structure in PDMS. To close the channel, we exposed the PDMS to a plasma for 1 min and sealed it to a glass cover slip.

      Here the authors describe the exact steps that they use to create the devices. The techniques (photolithography) and materials (PDMS) described are commonly used in the fabrication of microfluidic devices.

    2. McDonald J. C., et al., Electrophoresis 21, 27 (2000).

      This paper is the first to report the use of PDMS in the fabrication of microdevices and discusses its pros and cons. The paper introduced soft lithography based on PDMS as a novel fabrication method for microfluidic devices, which is commonly used in academic research and industry.

    3. Liu R. H., et al., J. Microelectromech. Syst. 9, 190 (2000)

      This paper shows an alternative form of fluid mixing in microfluidic channels. This method uses curved channels with serpentine geometry to mix fluids by generating chaotic flow similar to the one presented in this paper.

    4. Dunn D. A., Feygin I., Drug Discovery Today 5, S84 (2000)

      This article outlines a common use of microfluidics, that is the miniaturization of assays to run many of them in parallel at the same time ((high throughput assays). This paper addresses one of the main problems in assay miniaturization, which is efficient mixing of assay components.

    5. 30. Supported by Defense Advanced Research Projects Agency grants NSF ECS-9729405 and NSF DMR-9809363 Materials Research Science and Engineering Center (A.D.S., S.K.W.D., H.A.S., and G.M.W.); NIH grant GM51559 (A.D.S., S.K.W.D, and G.M.W.); Army Research Office grant DAAG55-97-1-0114 (H.A.S.); and NSF-9875933, NSF DMS-9803555, and a Sloan Foundation Fellowship (I.M.). S.K.W.D. thanks the Deutsche Forschungsgemeinschaft for a research fellowship.

      Here the authors list where the funding for the research came from. A lot of academic research is funded through government grants (DARPA, NSF, NIH, Military, etc.).

    1. Webb, Beatrice P. (1926). My Apprenticeship. Longmans, Green & Co.

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    1. 27. R. St. Pierre, W. Gosrich, S. Bergbreiter, A 3D-printed 1mg legged microrobot running at 15 body lengths per second, paper presented at Solid-State Sensors, Actuators, and Microsystems Workshop, Hilton Head, SC, 3 to 7 June 2018.

      Prior studies conducted by Pierre et al. have embedded permanent magnets into the soft robot that allow for the generation of a magnetic field. This actuation method allows for faster movement.

    2. 7. A. Rafsanjani, Y. Zhang, B. Liu, S. M. Rubinstein, K. Bertoldi, Kirigami skins make a simple soft actuator crawl. Sci. Robot. 3, eaar7555 (2018).

      Rafsanjani et al. utilized Japanese paper folding techniques to create a soft robot mimicking the crawling motion of a snake.

    3. 24. S.-J. Park, M. Gazzola, K. S. Park, S. Park, V. Di Santo, E. L. Blevins, J. U. Lind, P. H. Campbell, S. Dauth, A. K. Capulli, F. S. Pasqualini, S. Ahn, A. Cho, H. Yuan, B. M. Maoz, R. Vijaykumar, J.-W. Choi, K. Deisseroth, G. V. Lauder, L. Mahadevan, K. K. Parker, Phototactic guidance of a tissue-engineered soft-robotic ray. Science 353, 158–162 (2016).

      Park et al. created a biohybrid system that enables an artificial animal to swim with light stimulation. The device was inspired by batoids (like sting rays), where the researchers reverse-engineered the animal’s musculoskeletal structure and used optical signals to enable steering and turning maneuvers.

    1. In an ever-increasing sphere of digital print, why can't publishers provide readers a digitally programmed selection of footnote references in texts?

      This digital version of Annie Murphy Paul's book has endnotes with links from the endnotes back to the original pages, but the opposite links from the reading don't go to the endnotes in an obvious way.

      I'd love to be able to turn on/off a variety of footnote options so that I can see them on the pages they appear, as pop up modals, or browse through them in the end notes after-the-fact as I choose. This would allow me to have more choice and selection from a text based on what I want to get out of it rather than relying on a publisher to make that choice for me.

      Often in publishing a text written for the broad public will "hide" the footnotes at the end of the text in unintuitive ways where as more scholarly presses will place them closer to their appearance within the text. Given the digital nature of texts, it should be possible to allow the reader to choose where these items appear to suit their reading styles.

    1. Hollier, Denis. “Notes (On the Index Card).” October 112, no. Spring (2005): 35–44. https://www.jstor.org/stable/3397642

      Read: 2022-04-20 15:36

      Interesting material on Barthes' use of note cards, though not in depth. Some interesting discussion on the idea of autobiography from a philosophical perspective.

      The first five sections were interesting to me, the last two a bit denser and not as clear or interesting without additional context.

  9. Mar 2022
    1. 43. M. H. Dickinson, M. S. Tu, The function of dipteran flight muscle. Comp. Biochem. Physiol. 116, 223–238 (1997).

      By studying asynchronous flight systems in flies, Dickinson and Tu concluded that the resonant properties of the thorax (the midsection of an insect) determine the contraction frequency of the muscles.

    2. 26. W. Hu, G. Z. Lum, M. Mastrangeli, M. Sitti, Small-scale soft-bodied robot with multimodal locomotion. Nature 554, 81–85 (2018).

      Hu et al have embedded permanent magnets into the soft robot that allow for the generation of a magnetic field. This actuation method allows for faster movement, but Hu's top speed (213 mm/s) is still one-fourth of the top speed reported for the presented robot.

    3. 12. D. W. Haldane, M. M. Plecnik, J. K. Yim, R. S. Fearing, Robotic vertical jumping agility via series-elastic power modulation. Sci. Robot. 1, eaag2048 (2016).

      On a larger scale, researchers like Haldane et al. have chosen a small primate, galagos, as their model animal which is known for having the highest vertical jumping ability.

    4. 5. J. Aguilar, T. Zhang, F. Qian, M. Kingsbury, B. Mclnroe, N. Mazouchova, C. Li, R. Maladen, C. Gong, M. Travers, R. L. Hatton, H. Choset, P. B. Umbanhowar, D. I. Goldman, A review on locomotion robophysics: The study of movement at the intersection of robotics, soft matter and dynamical systems. Rep. Prog. Phys. 79, 110001 (2016).

      Aguilar et. al define "robophysics" as the pursuit of principles of self-generated motion.

    5. 23. M. Rogóż, H. Zeng, C. Xuan, D. S. Wiersma, P. Wasylczyk, Light-driven soft robot mimics caterpillar locomotion in natural scale. Adv. Optic. Mater. 4, 1689–1694 (2016).

      Rogóz et al. utilizes liquid crystalline elastomers that change shape under light; specifically, a continuous wave green laser beam scans the robot body and a traveling deformation is observed. The robot can perform difficult tasks like walk up a slope and squeeze through a narrow slit, however it is hindered by damage from burning along the laser beam center.

    6. 22. E. Wang, M. S. Desai, S.-W. Lee, Light-controlled graphene-elastin composite hydrogel actuators. Nano Lett. 13, 2826–2830 (2013).

      Wang et al. chooses to use light-driven hydrogel as it allows for wires and electrodes to be avoided, and light can be controlled more easily than other actuation methods. However, the crawling gait was generated by curling and uncurling after exposure to a near infrared laser. This mechanism poses issues due to the constant laser repetition required to move the device.

    7. 13. N. Kagawa, H. Kazerooni, Biomimetic small walking machine, in Proceedings of the 2001 IEEE/ IEEE/ASME International Conference on Advanced Intelligent Mechatronics, Como, Italy, 8 to 12 July 2001 (IEEE, 2001).

      In order to mimic a hop-like pattern, Kagawa et al. have used the movement style and foot path of cockroaches. Unlike the single-leg and later implemented double-leg utilized in this paper, Kagawa uses a four-legged walking machine with dimensions of 2 in x 1 in (50.8 mm x 25.4) which is significantly larger than this 10 mm x 15 mm soft robot.

    8. 8. W. Wang, J.-Y. Lee, H. Rodrigue, S.-H. Song, W.-S. Chu, S.-H. Ahn, Locomotion of inchworm-inspired robot made of smart soft composite (SSC). Bioinspir. Biomim. 9, 046006 (2014).

      Wang et al. employed worm movement patterns to show proper movement of their soft robots. Specifically the looping gait, requires front and back leg anchoring for sequential contracting and stretching. This differs from the four main postures used in this wave-like gait pattern which include aerial, front-touching, back-touching, and both-touching.

    1. 26. X. Wang, L. Dong, H. Zhang, R. Yu, C. Pan, Z. L. Wang, Recent progress in electronic skin. Adv. Sci. 2, 1500169 (2015).

      This paper is a review article focusing on the strategies, technology, and desired performance of electronic skin devices. The paper introduces transduction mechanisms that are commonly used in e-skins. They also write about technical improvements for stretchability, sensitivity, and resolution properties for tactile sensing. They also highlight recent breakthroughs and development trends for e-skin in 2015.

    2. 18. T. Someya, T. Sekitani, S. Iba, Y. Kato, H. Kawaguchi, T. Sakurai, A large-area, flexible pressure sensor matrix with organic field-effect transistors for artificial skin applications. Proc. Natl. Acad. Sci. U.S.A. 101, 9966–9970 (2004).

      This paper focuses on the integration of organic field-effect transistors and rubber pressure sensors fabricated using low cost processing technology. They took pressure images with flexible active matrix drivers with organic transistors. All materials in this device are soft except for the electrodes. The maximum effective device area is 8x8 cm squared, and contains a 32x32 array of pressure sensors. The device is electrically functional, even when wrapped around a cylindrical bar with a diameter of 4 millimeters.

    3. 41. Y. Kim, A. Chortos, W. Xu, Y. Liu, J. Y. Oh, D. Son, J. Kang, A. M. Foudeh, C. Zhu, Y. Lee, S. Niu, J. Liu, R. Pfattner, Z. Bao, T.-W. Lee, A bioinspired flexible organic artificial afferent nerve. Science 360, 998–1003 (2018).

      This paper draws inspiration from sensory (afferent) nerves to make flexible organic electronics. Afferent nerves carry sensations such as touch, pain, and temperature. The authors combined a pressure sensor, ring oscillator, and an ion gel-gated transistor to form an artificial mechanoreceptor. Their artificial nerve can collect pressure information from 1 to 80 kilopascals. It transforms the pressure information into action potentials ranging from 0 to 100 hertz. Their afferent nerve can detect movement, simultaneous pressure inputs, and distinguish braille characters.

    4. 33. A. Miyamoto, et. al, Inflammation-free, gas-permeable, lightweight, stretchable on-skin electronics with nanomeshes. Nat. Nanotechnol. 12, 907–913 (2017).

      This research group focused on using nanomeshes to design a long-lasting skin patch that reduced inflammation and irritation for the user without compromising data collection and accuracy. The fabricated patch is lightweight, ultrathin, stretchable, and has high-air permeability - all factors that promote user comfort. Overall, their device was able to detect temperature, touch, and pressure as well as acquire electromyogram recordings with minimal user discomfort.

    5. B. C.-K. Tee, et. al, A skin-inspired organic digital mechanoreceptor. Science 350, 313–316 (2015).

      This paper talks about a power-efficient skin-inspired mechanoreceptor with a flexible organic transistor circuit that transduces pressure into digital frequency signals directly. Their DiTact system was able to mimic human tactile perception with slow/no frequency oscillation in the absence of pressure stimulation and increasing frequency with increased with pressures applied to the device. Overall, the device was capable of evoking action potentials at frequencies up to 200 Hz for prolonged intervals.

    1. maybe i need to explain that i changed the way i write in rome a little bit 01:23:42 because i um use the blocks as um individual notes so that 01:23:55 the page can become what in the traditional center cast might be a note sequence and if two notes are directly related i might just add another block 01:24:07 because you still have the granularity with the block references um a question would become part of that note sequence and 01:24:19 [Music] they are just a part of the writing itself so i don't have a special question page 01:24:33 i have a lot of questions within the ongoing dialogues and sometimes 01:24:44 um there are the ones that turn into a project and um so they are on top of my mind and um they 01:24:59 might move into the uh shortcut section because i just want to jump right back into that the next day 01:25:13 but there is no sophisticated system to deal with questions they are just part of it

      Sönke Ahrens uses block references in Roam Research as zettels (or atomic notes), but puts them into larger pages almost as if he was pre-building larger project pages, as described in his book.

    1. Cowan, Frank (2005). "Stubbs Earthworks : An Ohio Hopewell "Woodhenge"". In Lepper, Bradley T. (ed.). Ohio Archaeology : An illustrated chronicle of Ohio's Ancient American Indian Cultures. Wilmington, Ohio: Orange Frazer Press. pp. 148–151. ISBN 978-1882203390.
    2. Miller, Gregory L. (2010). Ohio Hopewell Ceremonial Bladelet Use at the Moorehead Circle, Fort Ancient (Masters) (Thesis). Ohio State University.
    3. Gilmore, Zackary I.; O'Donoughue, Jason M., eds. (2015). The Archaeology of Events: Cultural Change and Continuity in the Pre-Columbian Southeast. University of Alabama Press. p. 149. ISBN 978-0817318505.
    4. https://en.wikipedia.org/wiki/Timber_circle

      Some timber circle sites to look into: - Secotan in North Carolina circa 1585 - Poverty Point - Hopewell timber circles (Moorehead Circle and Stubbs Earthworks) in Ohio - Cahokia

    1. Burns M. A., et al., Science 282, 484 (1998)

      Here, Burns and other collaborators developed and integrated a device that can analyze DNA through microfabricated channels, heaters, temperature sensors, and fluorescence detectors. This work was one of the first demonstrations of lab-on-a-chip systems for analyzing biological samples.

  10. Feb 2022
    1. <small><cite class='h-cite via'> <span class='p-author h-card'>Gordon Brander</span> in "Slouching toward Xanadu: a roundup of block reference mechanisms https://t.co/CxSm0bZjHu" (<time class='dt-published'>02/24/2022 17:12:12</time>)</cite></small>

      Discussion of some prior art leading up to Google's text fragment links.

    1. 11. J. Kim, et. al, Stretchable silicon nanoribbon electronics for skin prosthesis. Nat. Commun. 5, 5747 (2014).

      The artificial skin developed in this article had the ability to sense stimuli in highly variable external environments. It also had the ability to sense skin moisture and temperature.

    2. 42. M.-H. Phan, H.-X. Peng, Giant magnetoimpedance materials: Fundamentals and applications. Prog. Mater. Sci. 53, 323–420 (2008).

      This article provides a comprehensive summary of giant magneto-impedance. It covers the fundamental understanding of GMI phenomena, properties of GMI materials, and application of GMI based magnetic sensors. This is a helpful summary to further understand the effect of GMI and application in the current paper.

    3. 31. S. Park, H. Kim, M. Vosgueritchian, S. Cheon, H. Kim, J. H. Koo, T. R. Kim, S. Lee, G. Schwartz, H. Chang, Z. Bao, Stretchable energy-harvesting tactile electronic skin capable of differentiating multiple mechanical stimuli modes. Adv. Mater. 26, 7324–7332 (2014).

      This report demonstrates the first energy-harvesting electronic-skin (EHES) device capable of differentiating and generating energy from stimuli such as normal pressure, lateral strain, bending, and vibration. The authors use the stretchability of their device to measure the change in capacitance and film resistance due to lateral strain. The EHES had a high pressure sensitivity compared to previous capacitive sensors, and was capable of harvesting different mechanical stimuli with voltage and current generation in the range of 10 volts.

    4. 5. J. L. Collinger,  et. al. , Collaborative approach in the development of high-performance brain-computer interfaces for a neuroprosthetic arm: Translation from animal models to human control. Clin. Transl. Sci. 7, 52–59 (2014).

      This paper is interested in developing a brain-computer interface to provide control of a robotic upper limb as well as laying out a road map of resources and procedures for implanted neuroprosthetic devices. Motor BCI's have the potential to assist people with disabling injuries and lost limbs. This is complex and expensive research, and there have been very few clinical trials with implanted BCIs in people with motor impairments.

    5. 2. A. P. Gerratt, H. O. Michaud, S. P. Lacour, Elastomeric electronic skin for prosthetic tactile sensation. Adv. Funct. Mater. 25, 2287–2295 (2015).

      This paper reports on a stretchable electronic skin that is designed to be worn like a glove. The glove monitors live finger movement and registers distributed pressure along the entire length of the finger. The sensory skin is made of elastic materials and does not impede hand movement. Capacitive pressure sensors with stretchable gold thin-film electrodes and porous silicone foam display high sensitivity across the dynamic pressure range of human skin. Pressure sensors in the glove are distributed along the grasping region of the finger, with strain sensors along the back of the finger. The glove is successfully used in grasping and manipulation tasks.

    1. 15. M. Volpert, I. Mezić, C. D. Meinhart, M. Dahleh, Proceedings of the First International Conference on Heat Transfer, Fluid Mechanics, and Thermodynamics, Kruger Park, South Africa, 2001.

      This work lists numerous papers in the field of fluid mechanics and thermodynamics, three of which discuss the use of active mixers in microdevices for applications such as heat transfer mechanisms/analysis and flow cooling in microtechnology.

    2. 12. J. M. Ottino, The Kinematics of Mixing: Stretching, Chaos, and Transport (Cambridge Univ. Press, Cambridge, 1989).

      This book explores fluid mixing from a kinematic viewpoint and provides mechanisms of mixing including stretching and folding that occur in nature and technology.

    3. This condition is based on the following characteristic values: U < 100 cm/s, l ∼ 0.01 cm, ν = 0.01 g/cm·s. For channels, l is typically taken to be the smallest cross-sectional dimension.

      Given these values, the Reynolds number for the microchannel flow described in this work would be less than 100, which indicates laminar flow and dominant viscous forces. It is nearly impossible to generate chaotic flows, which facilitates mixing, in microchannels.

    4. Losey M. W., Schmidt M. A., Jensen K. F., Ind. Eng. Chem. Res. 40, 2555 (2001).

      A microchemical reactor was developed to safely and efficiently fluorinate toluene (a reactive substance found in paint products) as an alternative means to macroscale methods, which could not effectively perform this task.

    5. Jones S. W., Young W. R., J. Fluid Mech. 280, 149 (1994).

      Statistics of axial dispersion through a twisted pipe with diffusive and non-diffusive tracer chaotic advection were analyzed.

    1. Ahrens, Sönke. How to Take Smart Notes: One Simple Technique to Boost Writing, Learning and Thinking – for Students, Academics and Nonfiction Book Writers. Create Space, 2017.

    Tags

    Annotators

  11. Jan 2022
    1. I suspect Grafton translated the actual title, Aurifondina artium et scientiarum omnium excerpendi solerti, omnibus litterarum amantibus monstrata. http://www.worldcat.org/oclc/11169213
    1. Eusebius, a historian and bishop of the coastal city of Caesarea, in Palestine, assembled Christian writings in the local library. He also devised a system of cross-references, known as “canon tables,” that enabled readers to find parallel passages in the four Gospels—a system that the scholar James O’Donnell recently described as the world’s first set of hot links.
  12. Dec 2021
    1. Word

      Capitalized this is a direct reference to Microsoft Word, but I can't help thinking of John 1 "In the beginning was the Word, and the Word was with God, and the Word was God." presumably as the first Word.

    1. Luhmann, Niklas. "Kommunikation mit Zettelkästen." Öffentliche Meinung und sozialer Wandel/Public Opinion and Social Change. VS Verlag für Sozialwissenschaften, 1981. 222-228.

      https://luhmann.surge.sh/communicating-with-slip-boxes

      Note the 1981 original publication date.

    1. 28. P. A. Newman, E. R. Nash, S. R. Kawa, S. A. Montzka, S. M. Schauffler, Geophys. Res. Lett. 33, L12814 (2006).

      Newman et al.'s model predicts the size of the hole in the Antarctic ozone layer based on the level of ozone-depleting substances in the atmosphere.

      Their model predicts that the hole is expected to fully recover around 2068 because the levels of ozone-depleting substances have been declining.

    2. 24. S. Solomon, D. Kinnison, J. Bandoro, R. R. Garcia, J. Geophys. Res. 120, 7958–7974 (2015).

      Solomon et al. used a model to identify key factors influencing chemically induced ozone depletion.

      For example, they found that polar ozone loss is particularly sensitive to temperature and the presence of sulfate aerosols from volcanic eruptions.

      The model's predictions are in good agreement with measured ozone-abundance data.

    3. 13. J. Kuttippurath et al., Atmos. Chem. Phys. 15, 10385–10397 (2015).

      Kuttippurath et al. reported that from 2004 to 2013, the level of ozone-depleting substances was relatively stable. Thus, they conclude that naturally occurring climate variations produced the year-to-year variations in the ozone hole depth.

    4. 12. S. Solomon, Rev. Geophys. 37, 275–316 (1999).

      In this review paper, Solomon explains that human-made chlorofluorocarbons (CFCs) are the primary cause of the hole in the ozone layer.

      Also, the paper emphasizes that more ozone depletion occurs in the Antarctic and Arctic regions due to surface chemistry on cold polar clouds.

    5. 10. J. Kuttippurath et al., Atmos. Chem. Phys. 13, 1625–1635 (2013).

      Kuttippurath et al. reported signs of ozone-layer recovery by using September-to-November averaged data collected from 1979 to 2010.

      They attributed these signs of recovery to the reduction in ozone-depleting substances.

    6. 9. M. L. Salby, E. Titova, L. Deschamps, Geophys. Res. Lett. 38, L09702 (2011).

      Salby et al. demonstrate that naturally occurring changes, or variability, in the ozone layer must be taken into account to observe human-induced changes.<br> Here, they report that after accounting for the naturally occurring changes, a trend of increasing ozone levels is observed.

      Salby et al. look for signs of ozone healing using September-to-November averages, but the current paper by Solomon et al. uses data from September when there is less variability.

    7. 7. T. G. Shepherd et al., Nat. Geosci. 7, 443–449 (2014).

      Shepherd et al. show that in order to predict the effects of human-induced climate change, models must include more than just surface temperature conditions.

      These models must also account for uncertainties arising from circulation, or the movement of air, within the atmosphere.

    8. 2. World Meteorological Organization/United Nations Environment Programme (WMO/UNEP), Scientific Assessment of Ozone Depletion: 2014 (Global Ozone Research and Monitoring Project Report No. 55, WMO, 2014).

      Typically every 4 years, the World Meteorological Organization and the United Nations Environment Programme publish a joint assessment of the state of the ozone layer based on the latest scientific findings. The report helps to guide policy makers in making science-based policy decisions.

      The 2014 assessment concludes that nearly half of the improvement in stratospheric ozone levels since the year 2000 is due to a reduction in ozone-depleting substances.

  13. Nov 2021
    1. https://threadreaderapp.com/thread/1459547762517688327.html

      Anthony Baker experimenting with ideas from Necromant and Eleanor Konik to cross link digital notes with physical paper notes.

      I've thought about doing something similar to this with my physical notebooks in the past, though hadn't done block level linking as a means of potentially pulling in and linking pieces in the future.

      Often for more important linked things, I'll simply import the physical version into my digital copy at the time of first use/reference, but this could be interesting for large bodies of notes which aren't digital.

    1. The Odyssey of Homer translated with an introduction by Richmond Lattimore (Harper, 1965)

      Adobe Digital Edition October 2009 ISBN 978-0-06-176020-4

  14. Oct 2021
    1. F. Lan et al., Nature 449, 689–694 (2007).

      Lan et al. show that JMJD3/KDM6B demethylates H3K27. They find that this demethylation is critical to the expression of body patterning genes during animal development.

    2. J. J. Bull, R. C. Vogt, Science 206, 1186–1188 (1979).

      A formative study from 1979 that showed temperature directly influences sex differentiation of turtle hatchlings, rather than turtle hatchling mortality.

    3. C. Pieau, M. Dorizzi, N. Richard-Mercier, Cell. Mol. Life Sci. 55, 887–900 (1999).

      Pieau, Dorizzi and Richard-Mercier present what was known about temperature-dependent sex determination across species of reptiles in 1999. This review focuses on gene expression that marks temperature-dependent gonad differentiation and the regulation of hormone-producing proteins.

    4. L. Navarro-Martín et al., PLOS Genet. 7, e1002447 (2011).

      Navarro-Martín et al. study the mechanism underlying temperature-dependent sex determination in the European sea bass fish. They show that DNA methylation at the promoter of a gonadal aromatase (estrogen-making protein) is increased at high temperatures, causing female fish to masculinize.

      This supports the idea that there are many epigenetic mechanisms that can govern temperature-dependent sex determination across species and environments.

    5. F. Piferrer, Dev. Dyn. 242, 360–370 (2013).

      Piferrer reviews what is known about the epigenetic mechanisms underlying sex determination in plants, invertebrates, and vertebrates. This includes a discussion of how environment can affect gene expression through changes in histone modifications, DNA methylation, and non-coding RNAs (RNA that does not make protein).

    6. E. T. Wiles, E. U. Selker, Curr. Opin. Genet. Dev. 43, 31–37 (2017).

      Wiles and Selker discuss what is known about the function and how H3K27 methylation is specifically deposited and defined across the genome.

      This review provides good overview of histone modification interactions with gene expression.

    7. R. Yatsu et al., BMC Genomics 17, 77 (2016).

      Yatsu et al. profile the total gene expression of the American alligator with RNA-seq analysis of embryonic gonads at MPT and FPT during multiple timepoints of sex development.

      One of the genes that was predicted as a regulator of sex development at MPT was KDM6B.

    8. I. W. Deveson et al., Sci. Adv. 3, e1700731 (2017).

      Deveson et al. reveals that a single intron change for two epigenetic-related protein transcripts (JARID2 and JMJD3/KDM6B) is specifically induced in high temperature sex reversal in female bearded dragons as opposed to normal bearded dragons. Authors propose that the intron retention changes JARID2 and JMJD3/KDM6B function and overcomes genetic sex-determining with different gene expression at extreme temperatures.

    9. M. Czerwinski, A. Natarajan, L. Barske, L. L. Looger, B. Capel, Dev. Biol. 420, 166–177 (2016).

      Czerwinski et al. completed sequencing for the total RNA in T.scripta embryos at MPT and FPT before gonad development and during gonad development. This allowed authors to classify male- and female-specific gene expression during sex development.

    10. C. Ge et al., Development 144, 2222–2233 (2017).

      Ge et al., shows that Dmrt1 expression is necessary for and a driver of T.scripta temperature-dependent male sex determination.

  15. Sep 2021
    1. S. Culliney, L. Pejchar, R. Switzer, V. Ruiz-Gutierrez, Ecol. Appl. 22, 1718–1732 (2012).

      This study provides evidence that ‘Alalā, an endangered native bird species in Hawaii, displays seed dispersal behaviors and promotes seed germination of various native plants. Based on these results, the authors suggest that ‘Alalā can contribute toward the restoration of native fruiting plants in Hawaiian forest communities.

    2. E. Burgos et al., J. Theor. Biol. 249, 307–313 (2007).

      Nestedness can contribute toward the robustness of a network. If species that share fewer interactions are the first to go extinct, the remaining mutualistic system has a greater chance of survival. The authors also calculate a coefficient as a parameter of a network’s robustness.

    3. H. A. Mooney, E. E. Cleland, Proc. Natl. Acad. Sci. U.S.A. 98, 5446–5451 (2001).

      Mooney and Cleland describe the evolutionary consequences of invasive species on the invaders themselves and on native species. Modifying behavior to adapt to a new environment, competing for similar resources, predation, or creating hybrid progeny by breeding with native species are just a few examples.

    4. N. Blüthgen, F. Menzel, N. Blüthgen, BMC Ecol. 6, 9 (2006).

      Previously, the majority of network analysis was qualitative. Blüthgen et al. introduce two quantitative measurements that use the frequency of interactions to describe specialization at the species level and across a network.

    5. E. L. Rezende, J. E. Lavabre, P. R. Guimarães, P. Jordano, J. Bascompte, Nature 448, 925–928 (2007).

      The phylogenetic or evolutionary relationship between species can predict the types and quantity of interaction patterns they exhibit in a network. Using a simulation of extinction events, the authors also demonstrated that the extinction of one species can result in the extinction of other species that are evolutionarily related.

    6. A. de Almeida, S. B. Mikich, Oikos 127, 184–197 (2018).

      The authors merged data sets from multiple studies investigating fruit-frugivore interactions and illustrated that most networks across various neotropical areas were significantly nested and modular. The authors also concluded that combining results from different studies can be useful for analyzing the ecological structures of broad regions and supporting conservation efforts.

    7. C. G. Chimera, D. R. Drake, Biotropica 42, 493–502 (2010).

      In contrast to Foster, Chimera found that introduced birds in Hawaii dispersed predominately the seeds of non-native plants. Possible explanations could be that the non-native plants produce larger fruit that are more abundant and have a smaller seed size. These qualities are more enticing to birds and enhance the fruit's chances of getting eaten and its seeds later deposited.

    8. J. T. Foster, S. K. Robinson, Conserv. Biol. 21, 1248–1257 (2007).

      Foster and colleagues investigated how often introduced fruit-eating birds on the islands of Hawaii consume and disperse seeds from native plants versus seeds from exotic plants. They found that seeds from native plants made up the majority of the introduced bird species’ diets. This supports the potential of introduced bird species playing a role in the conservation efforts of native habitats.

    9. A. Traveset, D. M. Richardson, Annu. Rev. Ecol. Evol. Syst. 45, 89–113 (2014).

      The authors studied the feeding behaviors of birds in the Galapagos island. They discovered that these birds ate a not just a select few, but a wide variety of plants on the Islands. They called this behavior interaction release, a survival tactic where animals expand their niches.

    10. S. L. Lewis, M. A. Maslin, Nature 519, 171–180 (2015).

      The Anthropocene is defined as the epoch or geological time when human activity significantly impacted the global environment. Based on the criteria for defining a new epoch and supporting geological evidence, the authors propose two possible dates to mark the beginning of the Anthropocene: 1610 and 1964.

    11. J. Vizentin-Bugoni, P. K. Maruyama, C. S. de Souza, F. Ollerton, A. R. Rech, M. Sazima, “Plant-pollinator networks in the tropics: A review,” in Ecological Networks in the Tropics, W. Dáttilo, V. Rico-Gray, Eds. (Springer, 2018), pp. 73–91.

      This review summarizes current research on plant-pollinator networks, stressing the need to include more studies in tropical areas. Tropical areas have a richer diversity in plants and animals than non-tropical areas, resulting in the several network patterns such as low connectance and higher modularity. However, these patterns are overlooked when tropical areas are not equally analyzed, limiting accurate understanding of this relationships.

    12. P. J. Conry, R. Cannarella, “Hawaii statewide assessment of forest conditions and trends: 2010” (Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, 2010).

      This statewide assessment details the forest conditions of Hawaii in hopes of developing strategies towards conservation. It includes information comparing the major changes in vegetation before and after the arrival of humans on the island.

    13. J. Memmott, N. M. Waser, M. V. Price, Proc. R. Soc. London Ser. B 271, 2605–2611 (2004).

      By simulating the network patterns between plants and pollinators, the authors demonstrated that plants were more resistant to extinction with the removal of specialized pollinators versus generalized pollinators. Specialized pollinators only interact with a few plant species, whereas generalized pollinators interact with a larger range of plant species. When a generalized pollinator is lost, more plants are affected.

    14. J. Memmott, N. M. Waser, M. V. Price, Tolerance of pollination networks to species extinctions. Proc. R. Soc. London Ser. B 271, 2605–2611 (2004). doi:10.1098/rspb.2004.2909pmid:15615687

      By simulating the network patterns between plants and pollinators, the authors demonstrated that plants were more resistant to extinction with the removal of specialized pollinators versus generalized pollinators. Specialized pollinators only interact with a few plant species, whereas generalized pollinators interact with a larger range of plant species. When a generalized pollinator is lost, more plants are affected.

    15. N. Blüthgen, F. Menzel, N. Blüthgen, Measuring specialization in species interaction networks. BMC Ecol. 6, 9 (2006). doi:10.1186/1472-6785-6-9pmid:16907983

      Previously, the majority of network analysis was qualitative. Blüthgen et al introduce two quantitative measurements that uses the frequency of interactions to describe specialization at the species level and across a network.

    16. S. Culliney, L. Pejchar, R. Switzer, V. Ruiz-Gutierrez, Seed dispersal by a captive corvid: The role of the ‘Alalā (Corvus hawaiiensis) in shaping Hawai‘i’s plant communities. Ecol. Appl. 22, 1718–1732 (2012). doi:10.1890/11-1613.1pmid:23092010

      This study provides evidence that ‘Alalā, an endangered, native bird species in Hawaii, displays seed dispersal behaviors and promotes seed germination of various native plants. Based on these results, the authors suggest that ‘Alalā can contribute towards the restoration of native fruiting plants in Hawaiian forest communities.

    17. E. C. Fricke, J. J. Tewksbury, E. M. Wandrag, H. S. Rogers, Mutualistic strategies minimize coextinction in plant-disperser networks. Proc. Biol. Sci. 284, 20162302 (2017). doi:10.1098/rspb.2016.2302pmid:28490622

      Fricke et al investigates how well mutualistic systems between plants and animals protect against coextinction. They find that the diversity in partners protects species in mutualistic interactions because they do not rely solely on one or few partners for survival.

    18. ↵ S. L. Lewis, M. A. Maslin, Defining the Anthropocene. Nature 519, 171–180 (2015). doi:10.1038/nature14258pmid:25762280

      The Anthropocene defines the epoch or geological time when human activity significantly impacted the global environment. Based on the criteria for defining a new epoch and supporting geological evidence, the authors propose two possible dates to mark the beginning of the Anthropocene: 1610 and 1964

    19. H. A. Mooney, E. E. Cleland, The evolutionary impact of invasive species. Proc. Natl. Acad. Sci. U.S.A. 98, 5446–5451 (2001). doi:10.1073/pnas.091093398pmid:11344292

      Mooney and Cleland describe the evolutionary consequences of invasive species on the invaders themselves and on native species. Modifying behavior to adapt to a new environment, competing for similar resources, predation, or creating hybrid progeny by breeding with natives species are just a few examples.

    20. A. de Almeida, S. B. Mikich, Combining plant–frugivore networks for describing the structure of neotropical communities. Oikos 127, 184–197 (2018). doi:10.1111/oik.04774

      The authors merged data sets from multiple studies investigating fruit-frugivore interactions and illustrated that most networks across various neotropical areas were significantly nested and modular. The authors also concluded that combining results from different studies can be useful for analyzing the ecological structures of broad regions, and supporting conservation efforts.

    21. E. Burgos, H. Ceva, R. P. J. Perazzo, M. Devoto, D. Medan, M. Zimmermann, A. María Delbue, Why nestedness in mutualistic networks? J. Theor. Biol. 249, 307–313 (2007). doi:10.1016/j.jtbi.2007.07.030pmid:17897679

      Nestedness can contribute towards the robustness of a network. If species that share fewer interactions are the first to go extinct, the remaining mutualistic system have a greater chance of survival. The authors also calculate a coefficient as a parameter of a network’s robustness.

    22. E. L. Rezende, J. E. Lavabre, P. R. Guimarães, P. Jordano, J. Bascompte, Non-random coextinctions in phylogenetically structured mutualistic networks. Nature 448, 925–928 (2007). doi:10.1038/nature05956pmid:17713534

      The phylogenetic or evolutionary relationship between species can predict the types and quantity of interaction patterns they exhibit in a network. Using a simulation of extinction events, the authors also demonstrated that the extinction of one species can result in the extinction of others species that are evolutionarily related.

    23. A. Traveset, J. M. Olesen, M. Nogales, P. Vargas, P. Jaramillo, E. Antolín, M. M. Trigo, R. Heleno, Bird-flower visitation networks in the Galápagos unveil a widespread interaction release. Nat. Commun. 6, 6376 (2015). doi:10.1038/ncomms7376pmid:25757227

      The authors studied the feeding behaviors of birds in the Galapagos island. They discovered that these birds ate a not just a select few, but a wide variety of plants on the island. They called this behavior interaction release, a survival tactic where animals expand their niche.

    24. C. G. Chimera, D. R. Drake, Patterns of seed dispersal and dispersal failure in a Hawaiian dry forest having only introduced birds. Biotropica 42, 493–502 (2010). doi:10.1111/j.1744-7429.2009.00610.x

      In contrast to Foster, Chimera found that introduced birds in Hawaii dispersed predominately the seeds of non-native plants. Possible explanations could be that the non-native plants produce larger fruit, that are more abundant and have a smaller seed size. These qualities are more enticing to birds and enhance the plants’ chances of getting eaten and later deposited.

    25. J. T. Foster, S. K. Robinson, Introduced birds and the fate of Hawaiian rainforests. Conserv. Biol. 21, 1248–1257 (2007). doi:10.1111/j.1523-1739.2007.00781.xpmid:17883490

      Foster and colleagues investigated how often introduced, fruit-eating birds on the islands of Hawaii consume and disperse seeds from native plants versus seeds from exotic plants. They found that seeds from native plants made up the majority of the introduced bird species’ diets. This supports the potential of introduced bird species playing a role in the conservation efforts of native habitats.

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      Wesolowski and the team used mobile phone data to map human mobility in Pakistan in 2013, the year this country saw large dengue outbreaks. They found that human mobility within the country can predict the spread and the timing of epidemics.

    2. K. E. Jones et al., Nature 451, 990-993 (2008).

      The authors analyzed 335 emerging infectious disease incidents between 1940 and 2004 and found that most had originated from wildlife and low-altitude regions. They also revealed an alarming lack of reporting effort in areas that are "hotspots" of these diseases.