55 Matching Annotations
  1. Jul 2022
    1. Famously, Luswig Wittgenstein organized his thoughts this way. Also famously, he never completed his 'big book' - almost all of his books (On Certainty, Philosophical Investigations, Zettel, etc.) were compiled by his students in the years after his death.

      I've not looked directly at Wittgenstein's note collection before, but it could be an interesting historical example.

      Might be worth collecting examples of what has happened to note collections after author's lives. Some obviously have been influential in scholarship, but generally they're subsumed by the broader category of a person's "papers" which are often archived at libraries, museums, and other institutions.

      Examples: - Vincentius Placcius' collection used by his students - Niklas Luhmann's zettelkasten which is being heavily studied by Johannes F.K. Schmidt - Mortimer J. Adler - was his kept? where is it stored?

      Posthumously published note card collections - Ludwig Wittgenstein - Walter Benjamin's Arcades Project - Ronald Reagan's collection at his presidential library, though it is more of an commonplace book collection of quotes which was later published - Roland Barthes' Mourning Diary - Vladimir Nabokov's The Original of Laura - others...

      Just as note collections serve an autobiographical function, perhaps they may also serve as an intellectual autobiographical function? Wittgenstein never managed to complete his 'big book', but in some sense, doesn't his collection of note cards serve this function for those willing to explore it all?

      I'd previously suggested that Scott P. Scheper publish not only his book on note taking, but to actually publish his note cards as a stand-alone zettelkasten example to go with them. What if this sort of publishing practice were more commonplace? The modern day equivalent is more likely a person's blog or their wiki. Not enough people are publicly publishing their notes to see what this practice might look like for future generations.

  2. Jun 2022
    1. u/sscheper in writing your book, have you thought about the following alternative publishing idea which I'm transcribing from a random though I put on a card this morning?

      I find myself thinking about people publishing books in index card/zettelkasten formats. Perhaps Scott Scheper could do this with his antinet book presented in a traditional linear format, but done in index cards with his numbers, links, etc. as well as his actual cards for his index at the end so that readers could also see the power of the system by holding it in their hands and playing with it?

      It could be done roughly like Edward Powys Mathers' Cain's Jawbone or Henry Korn's Pontoon Manifesto? Perhaps numbered consecutively to make it easier to bring back into that format, but also done with your zk numbering so that people could order it and use it that way too? This way you get the book as well as a meta artifact of what the book is about as an example of how to do such a thing for yourself. Maybe even make a contest for a better ordering for the book than the one you published it in ?

      Link to: - https://hyp.is/6IBzkPfeEeyo9Suq-ZmCKg/www.scientificamerican.com/article/reading-paper-screens/

  3. Apr 2022
    1. I was fortunate enough to see—and now share with you—a handful of these diaries from 1977 in their original, hand-written form. (A collection of more than three hundred entries, entitled “Mourning Diary,” will be published by Hill and Wang next month.)

      Hill and Wang published Mourning Diary by Roland Barthes on October 12, 2010. It is a collection of 330 entries which he wrote following the death of his mother Henriette in 1977.

      Kristina Budelis indicates that she saw them in person and reproduced four of them as index card-like notes in The New Yorker (September 2010).

  4. Mar 2022
  5. Nov 2021
  6. Aug 2021
  7. Jul 2021
  8. Jun 2021
  9. May 2021
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      Rosado J, Pelleau S, Cockram C et al. Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study. The Lancet Microbe 2021; doi: 10.1016/S2666-5247(20)30197-X.

    2. doi: 10.1101/2020.06.05.135921.

      Bertoglio F, Meier D, Langreder N et al. SARS-CoV-2 neutralizing human recombinant antibodies selected from –pre-pandemic healthy donors binding at RBD-ACE2 interface. Nature Communications 2021; doi: 10.1038/s41467-021-21609-2.

    3. doi: 10.1101/2020.07.17.20140533.

      Sahin U, Muik A, Derhovnessian E et al. COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T cell repsonses. Nature 2020; doi: 10.1038/s41586-020-2814-7.

    4. doi: 10.1101/2020.06.29.178509.

      Tian J-H, Patel N, Haupt R et al. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice. Nature Communications 2021; doi: 10.1038/s41467-020-20653-8.

    5. doi: 10.1101/2020.06.27.175166.

      Routhu NK, Cheedarla N, Gangadhara S et al. A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs. Immunity 2021; doi: 10.1016/j.immuni.2021.02.001.

    6. doi: 10.1101/2020.08.09.242867.

      Gai J, Ma L, Li G et al. A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential. MedComm 2021; doi: 10.1002/mco2.60.

    7. doi: 10.1101/2020.06.22.20137695.

      Hicks J, Klumpp-Thomas C, Kalish H et al. Serologic Cross-Reactivity of SARS-CoV-2 with Endemic and Seasonal Betacoronaviruses. Journal of Clinical Immunology. 2021. doi: https://doi.org/10.1007/s10875-021-00997-6

    8. doi: 10.1101/2020.07.29.20162917

      Klassan SA, Senefeld, JW, Johnson PW et al. The Effect of Convalescent Plasma Therapy on COVID-19 Patient Mortality: Systematic Review and Meta-analysis. medRxiv 2021; doi: 10.1101/2020.07.29.20162917.

    9. doi: 10.1101/2020.04.28.20083139

      Xiao T, Wang Y, Yuan J et al. Early Viral Clearance and Antibody Kinetics of COVID-19 Among Asymptomatic Carriers. Frontiers in Medicine. 2021. doi:https://doi.org/10.3389/fmed.2021.595773

    10. doi: 10.1101/2020.08.21.261909.

      Gontu A, Srinivasan S, Salazar E et al. Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy. Communications Biology 2021; doi: 10.1038/s42003-021-01813-y.

    11. doi: 10.1101/2020.07.18.20155374.

      Iyer AS, Jones FK, Nodoushania A et al. Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients. Sci Immunol 2020; doi:10.1126/sciimmunol.abe0367.

    1. I like the idea in theory, however it doesn’t feel very robust – you are relying on the layout of the page in question. Many authors regularly revisit articles and add new sections and paragraphs. Now your #h2:3 link points to a previous section. (This is far less likely to happen with IDs.)
  10. Apr 2021
  11. Mar 2021
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      Rebendenne A, Valadão ALC, Tauziet M, Maarifi G, Bonaventure B, McKellar J, Planès R, Nisole S, Arnaud-Arnould M, Moncorgé O, Goujon C. SARS-CoV-2 triggers an MDA-5-dependent interferon response which is unable to control replication in lung epithelial cells. J Virol. 2021 Jan 29:JVI.02415-20 https://doi.org/10.1128/JVI.02415-20

    2. Bayati A , Kumar R , Francis V  et al.   PREPRINT: SARS-CoV-2 uses clathrin-mediated endocytosis to gain access into cells. bioRxiv  2020:2020.07.13.201509. doi:10.1101/2020.07.13.201509.

      Bayati A, Kumar R, Francis V, McPherson PS. SARS-CoV-2 infects cells following viral entry via clathrin-mediated endocytosis. J Biol Chem. 2021 Jan 18;296:100306 https://doi.org/10.1016/j.jbc.2021.100306

    3. Zhou Q , Wei X-S , Xiang X  et al.   PREPRINT: Interferon-a2b treatment for COVID-19. medRxiv  2020:2020.04.06.20042580. doi:10.1101/2020.04.06.20042580.

      Zhou, Q., Chen, V., Shannon, C. P., Wei, X.-S., Xiang, X., Wang, X., Wang, Z.-H., Tebbutt, S. J., Kollmann, T. R., & Fish, E. N. (2020). Interferon-α2b Treatment for COVID-19. Front Immunol, 11(1061) https://doi.org/10.3389/fimmu.2020.01061

    4. Baker SA , Kowk S , Berry GJ  et al.   PREPRINT: Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation. medRxiv  2020:2020.07.05.20140467. doi:10.1101/2020.07.05.20140467.

      Baker SA, Kwok S, Berry GJ, Montine TJ. Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation. PLoS One. 2021 Feb 16;16(2):e0247060 https://doi.org/10.1371/journal.pone.0247060

    5. Wang K , Chen W , Zhou Y-S  et al.   PREPRINT: SARS-CoV-2 invades host cells via a novel route: CD147-spike protein. bioRxiv  2020:2020.03.14.988345. doi:10.1101/2020.03.14.988345.

      Wang, K., Chen, W., Zhang, Z. et al. CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells. Sig Transduct Target Ther 5, 283 (2020). https://doi.org/10.1038/s41392-020-00426-x

    6. Zhang L , Jackson CB , Mou H  et al.   PREPRINT: The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv  2020:2020.06.12.148726. doi:10.1101/2020.06.12.148726.

      Zhang, L., Jackson, C.B., Mou, H. et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun 11, 6013 (2020). https://doi.org/10.1038/s41467-020-19808-4

    7. Lee IT , Nakayama T , Wu C-T  et al.   PREPRINT: Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers. medRxiv  2020:2020.05.08.20092866. doi:10.1101/2020.05.08.20092866.

      Lee, I.T., Nakayama, T., Wu, CT. et al. ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs. Nat Commun 11, 5453 (2020). https://doi.org/10.1038/s41467-020-19145-6

    1. Cerda P , Ribas J , Iriarte A , et al. ; PREPRINT: D-dimer dynamics in hospitalized COVID-19 patients: potential utility for diagnosis of pulmonary embolism. medRxiv  2020:2020.09.21.20193953. doi: 10.1101/2020.09.21.20193953.

      Cerdà P, Ribas J, Iriarte A, Mora-Luján JM, Torres R, Del Río B, Jofre HI, Ruiz Y, Huguet M, Fuset MP, Martínez-Yélamos S, Santos S, Llecha N, Corbella X, Riera-Mestre A. Blood test dynamics in hospitalized COVID-19 patients: Potential utility of D-dimer for pulmonary embolism diagnosis. PLoS One. 2020 Dec 28;15(12):e0243533. https://doi.org/10.1371/journal.pone.0243533

    2. Meizlish ML , Pine AB , Bishai JD  et al.   PREPRINT: a neutrophil activation signature predicts critical illness and mortality in COVID-19. medRxiv  2020. doi:10.1101/2020.09.01.20183897.

      Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun HJ. A neutrophil activation signature predicts critical illness and mortality in COVID-19. Blood Adv. 2021 Mar 9;5(5):1164-1177. https://doi.org/10.1182/bloodadvances.2020003568

    3. Aschenbrenner AC , Mouktaroudi M , Kraemer B  et al.   PREPRINT: disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. medRxiv  2020. doi:10.1101/2020.07.07.20148395.

      Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T; German COVID-19 Omics Initiative (DeCOI). Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med. 2021 Jan 13;13(1):7. https://doi.org/10.1186/s13073-020-00823-5.

    4. Falck-Jones S , Vangeti S , Yu M  et al.   PREPRINT: functional myeloid-derived suppressor cells expand in blood but not airways of COVID-19 patients and predict disease severity. medRxiv  2020. doi:10.1101/2020.09.08.20190272.

      Falck-Jones S, Vangeti S, Yu M, Falck-Jones R, Cagigi A, Badolati I, Österberg B, Lautenbach MJ, Ahlberg E, Lin A, Lepzien R, Szurgot I, Lenart K, Hellgren F, Maecker HT, Sälde J, Albert J, Johansson N, Bell M, Lore K, Färnert A, Smed-Sörensen A. Functional monocytic myeloid-derived suppressor cells increase in blood but not airways and predict COVID-19 severity. J Clin Invest. 2021 Jan 25:144734. https://doi.org/10.1172/JCI144734

    5. Lombardi A , Trombetta E , Cattaneo A  et al.   PREPRINT: early phases of COVID-19 are characterized by a reduction of lymphocyte populations and the presence of atypical monocytes. medRxiv  2020. doi:10.1101/2020.05.01.20087080.

      Lombardi A, Trombetta E, Cattaneo A, Castelli V, Palomba E, Tirone M, Mangioni D, Lamorte G, Manunta M, Prati D, Ceriotti F, Gualtierotti R, Costantino G, Aliberti S, Scaravilli V, Grasselli G, Gori A, Porretti L and Bandera A (2020) Early Phases of COVID-19 Are Characterized by a Reduction in Lymphocyte Populations and the Presence of Atypical Monocytes . Front. Immunol. 11:560330. https://doi.org/10.3389/fimmu.2020.560330

    6. Vietzen H , Zoufaly A , Traugott M  et al.   PREPRINT: NK cell receptor NKG2C deletion and HLA-E variants are risk factors for severe COVID-19. Res Square  2020. doi:10.21203/rs.3.rs-34505/v1.

      Vietzen H, Zoufaly A, Traugott M, Aberle J, Aberle SW, Puchhammer-Stöckl E. Deletion of the NKG2C receptor encoding KLRC2 gene and HLA-E variants are risk factors for severe COVID-19. Genet Med. 2021 Jan 26:1–5. https://doi.org/10.1038/s41436-020-01077-7

    7. Zhou Q , Wei X-S , Xiang X  et al.   PREPRINT: Interferon-a2b treatment for COVID-19. medRxiv  2020:2020.04.06.20042580.

      Zhou Q, Chen V, Shannon CP, Wei X-S, Xiang X, Wang X, Wang Z-H, Tebbutt SJ, Kollmann TR and Fish EN (2020) Interferon-α2b Treatment for COVID-19. Front. Immunol. 11:1061. https://doi.org/10.3389/fimmu.2020.01061

    8. Simadibrata DM , Calvin J , Wijaya AD  et al.   PREPRINT: neutrophil-to-lymphocyte ratio on admission to predict the severity and mortality of COVID-19 patients: a meta-analysis. medRxiv  2020. doi:10.1101/2020.09.14.20191098.

      Simadibrata DM, Calvin J, Wijaya AD, Ibrahim NAA. Neutrophil-to-lymphocyte ratio on admission to predict the severity and mortality of COVID-19 patients: A meta-analysis. The American Journal of Emergency Medicine. 2021; 42: 60– 69. https://doi.org/10.1016/j.ajem.2021.01.006.

    9. Zhang D , Guo R , Lei L  et al.   PREPRINT: COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome. medRxiv  2020. doi:10.1101/2020.03.24.20042655.

      Zhang, D, Guo, R, Lei, L, et al. COVID‐19 infection induces readily detectable morphological and inflammation‐related phenotypic changes in peripheral blood monocytes. J Leukoc Biol. 2021; 109: 13– 22. https://doi.org/10.1002/JLB.4HI0720-470R

  12. Feb 2021
    1. Note: This question has been edited since it was asked. The original title was "Test whether a glob has any matches in bash". The specific shell, 'bash', was dropped from the question after I published my answer. The editing of the question's title makes my answer appear to be in error. I hope someone can amend or at least address this change.
  13. Oct 2020
  14. Aug 2020
  15. Jul 2020
    1. "that text has been removed from the official version on the Apache site." This itself is also not good. If you post "official" records but then quietly edit them over time, I have no choice but to assume bad faith in all the records I'm shown by you. Why should I believe anything Apache board members claim was "minuted" but which in fact it turns out they might have just edited into their records days, weeks or years later? One of the things I particularly watch for in modern news media (where no physical artefact captures whatever "mistakes" are published as once happened with newspapers) is whether when they inevitably correct a mistake they _acknowledge_ that or they instead just silently change things.
  16. Jun 2020
  17. Apr 2017
    1. The letters that were exchanged among the membership of the Royal Society in the mid-17th century, and that were later gathered into journals, gradually accrued formalized processes of review, editing, production, and distribution. In creating this new product —the scholarly journal—learned societies found one part of the financial model that would allow them to serve their larger goals. Scholars were encouraged to join and maintain their memberships in order to receive the journal. In addition to memberships made available to individuals, journal subscriptions were created for libraries, allowing academic institutions to help support the organizations that facilitated, validated, and circulated the work of their faculty members.

      History of journals from letters

  18. Jul 2016
    1. Figure 3 illustrates at what age ceased ‘indie’ journals stopped publishing. Most journals survived the first 2–5 years period, whereas the mortality rate rose in the critical 6–9 years period. After that, the number of journals ceasing dropped sharply, indicating that the surviving journals had found stability.

      Most critical period for journals is 6-9 years. After year ten, the number of journals that stop drops quickly

    2. The development over time of active ‘indie’ OA journals before and after 2002 is shown in Figs. 1A and 1B. A journal was counted as ‘active’ in a particular year if it was still publishing articles in that year. Before 2002 the number of active journals grew very rapidly from a total of 76 journals in 1995 to 207 journals in 2002. The year 2002 was the cut-off year to be included in the studied cohort, meaning that no new journals were added to the data set after this point in time. After 2002, the number of journals in the cohort decreased steadily to the 127 that stayed active in 2014.

      Interesting charts showing the rise and then decline of independent, scholar-published OA journals

    3. The average number of articles published was 31 per year with 74% publishing 0–30 articles, and 9% 60 or more. The study also contains interesting data about the workload done, revenues etc.

      Average numbers of articles in OJS journals: 31

      • 74% publish 0-30
      • 9% 60 or more
    4. “The key question for OA publishing is whether it can be scaled up from a single journal publishing model with relatively few articles published per year to a comprehensive major journal with of the order of 50–100 articles annually.” They further note: “The continuation of the journal relies very heavily on the personal involvement of the editor and is as such a risk to the model. Employing staff to handle, for example, management, layout and copyediting tasks, is a cost-increasing factor that also is a threat to the model.” Both questions are still highly relevant today.

      Key issues facing scholar-published journals: can they ramp up; can they survive succession.

    5. Often the enthusiasm of the founders and their personal network can carry a volunteer-based journal for a few years. But at that same time this type of journal, which lack the support of employed staff and a professional publishing organization, are threatened by many dangers. The editor may change affiliation or retire, or the support of the university hosting the journal might be withdrawn. Authors may stop sending in good manuscripts and it may become more and more difficult to find motivated reviewers. Not being included in the Web of Science, and the impact factor that follows, may in the long run limit the number of submissions severely. On the positive side of the balance the emergence of open source software for publishing (i.e., Open Journals System) and cheap or free hosting services like Latin American Scielo have facilitated the technical parts of publishing.

      Problems with Scholar-published journals

    6. Open Access (OA) is nowadays increasingly being used as a business model for the publishing of scholarly peer reviewed journals, both by specialized OA publishing companies and major, predominantly subscription-based publishers. However, in the early days of the web OA journals were mainly founded by independent academics, who were dissatisfied with the predominant print and subscription paradigm and wanted to test the opportunities offered by the new medium. There is still an on-going debate about how OA journals should be operated, and the volunteer model used by many such ‘indie’ journals has been proposed as a viable alternative to the model adopted by big professional publishers where publishing activities are funded by authors paying expensive article processing charges (APCs). Our longitudinal quantitative study of 250 ‘indie’ OA journals founded prior to 2002, showed that 51% of these journals were still in operation in 2014 and that the median number of articles published per year had risen from 11 to 18 among the survivors. Of these surviving journals, only 8% had started collecting APCs. A more detailed qualitative case study of five such journals provided insights into how such journals have tried to ensure the continuity and longevity of operations.


    7. A longitudinal study of independent scholar-published open access journals

      Björk, Bo-Christer, Cenyu Shen, and Mikael Laakso. 2016. “A Longitudinal Study of Independent Scholar-Published Open Access Journals.” PeerJ 4 (May). peerj.com: e1990. doi:10.7717/peerj.1990.