1,275 Matching Annotations
  1. 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.

  2. 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.



    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.

  3. 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.

  4. 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.



  5. 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.
  6. 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.


      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.

  7. 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

  8. 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.

  9. 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.

    1. A. Wesolowski et al., Proc. Natl. Acad. Sci. U.S.A. 112, 11887-11892 (2015).

      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.

    3. D. Brockmann, D. Helbing, Science 342, 1337-1342 (2013).

      Brockmann and Helbing proposed effective distance, as a replacement for conventional geographic distance, for simplifying the transmission patterns of global epidemics.

      The proposed approach was successfully applied to data on the worldwide 2009 H1N1 influenza pandemic and 2003 SARS epidemic.

    4. S. Chen et al., Lancet 395, 764-766 (2020).

      This comment article summarized the transmission control measures that had been taken in China, suggesting their potential effectiveness. Space is reserved for further quantitative research, though.

    1. En effet, selon nos informations, les autorités ont reçu des alertes deux jours avant le déclenchement de l’attaque qui a conduit à un vol massif de données. Ce n’est pas tout: ce printemps, un rapport externe rédigé par la société BDO pointait du doigt des faiblesses majeures dans le système informatique de la commune

      Societe BDO. Pointe faiblesses majeures de la commune.

    1. 37. N. Butchart, Rev. Geophys. 52, 157–184 (2014).

      Butchart reviews scientific studies of climate change's effect on the stratospheric overturning circulation.

      The review shows that a variety of models agree that greenhouse gas-induced climate change should strengthen the overturning circulation. However, it has been difficult to confirm these models using actual measurements.

    2. 16. R. W. Portmann et al., J. Geophys. Res. 101, 22991–23006 (1996).

      Portmann et al.'s models showed that both colder temperatures and particles from volcanic eruption can delay the healing of the ozone layer.

      Thus, these factors must be accounted for when tracking human-caused ozone depletion.

    3. 15. D. J. Hofmann, S. J. Oltmans,  J. Geophys. Res. 98, 18555–18561 (1993).

      Hofmann and Oltmans demonstrated that the unusually large Antarctic ozone hole in 1992 was most likely caused by the 1991 Pinatubo volcanic eruption.

      They concluded that sulfuric acid droplets released from the eruption were responsible for the abnormally large Antarctic ozone hole.

    4. 14. N. J. Livesey, M. L. Santee, G. L. Manney, Atmos. Chem. Phys.15, 9945–9963 (2015).

      Livesey et al. determined how much polar ozone loss was caused by chemicals versus other sources of ozone variation.

      This was accomplished by tracking how much ozone varies within the same air mass over time.

    5. 1. J. C. Farman, B. G. Gardiner, J. D. Shanklin, Nature 315, 207–210 (1985).

      Farman et al. reported that October Antarctic ozone levels had dropped significantly.

      The authors suggested that Cl based chemicals could play a significant role in the ozone depletion.

  10. Aug 2021
    1. U. T. Bornscheuer et al., Nature 485, 185–194 (2012).

      Bornscheuer discusses the various applications of biocatalysis. Biocatalysts offer a more practical and a green route to synthesis when compared to organometallic catalysts. Professor Arnold's work features the use of biocatalysis as a key step in C-Si bond formation.

    2. Y.-Z. Zhang, S.-F. Zhu, L.-X. Wang, Q.-L. Zhou, Angew. Chem. Int. Ed. 47, 8496–8498 (2008).

      This paper describes how Cu(OTf)2 can be used to catalyze asymmetric carbenoid insertion into a Si-H bond. 22 reactions were run and the product, alpha-silyl esters, was formed in high yields and up to 99% enantiomeric excess. When Professor Arnold's group ran the desired reaction with Cu(OTf)2, a complex mixture of products from Si-H, O-H and N-H insertion reactions was observed.

    3. 10. T. Lee, J. F. Hartwig, Angew. Chem. Int. Ed. 55, 8723–8727 (2016) and references therein.

      This paper discusses the use of rhodium catalysts in the asymmetric, intramolecular silylation reaction of cyclopropyl C-H bonds. The reaction proceeds with high enantiomeric excess. However, when Professor Arnold's group used Rh2(OAc)4 to catalyze C-Si bond formation, they observed that O-H and N-H insertions often dominated over the preferred silylation reactions.

    4. A. K. Franz, S. O. Wilson, J. Med. Chem. 56, 388–405 (2013).

      Silicon, an isostere of carbon, has unique properties. Properties of silicon and application of organosilicon molecules in drug release technology, etc., are discussed. These properties can be used to enhance drug potency and improve pharmacological action.

    1. C. Viboud et al., Science 312, 447-451 (2006).

      Viboud and colleagues found a strong correlation between people's traveling rate between their workplace and home and the spread of infection. A gravity model can describe the workflow.

    2. A. Wesolowski et al., Science 338, 267-270 (2012).

      The authors used mobile phone data to depict the travel patterns of people in Kenya over a year. They found the exportation of malaria from specific regions to others. The finding suggested human mobility as an essential factor in the spread of malaria.

    3. M. U. G. Kraemer et al., Science in press (2020)

      The authors conducted a correlational study using mobility data from Wuhan and case data from different regions of China.

      The spatial distribution of confirmed cases of COVID-19 before the implementation of travel restrictions was found related to the human mobility data. Such correlation was diminished after the implementation, and the growth of COVID-19 in many areas turned to a decline.

    4. C. Wang et al., Lancet 395, 470-473 (2020).

      Wang and co-workers synthesized the up-to-date understandings of COVID-19 by then. They summarized the time of the early-stage outbreak, the characteristics of infected patients, and control measures that had been taken by the time.

    5. R. Lu et al., Lancet 395, 565-574 (2020).

      Lu and the team collected samples from nine patients presenting symptoms of viral pneumonia.

      They then used the samples for DNA sequencing. The full-length sequence reported in this study confirmed the distinction of the newly reported coronavirus from the previously reported ones.

    6. N. Zhu et al., N. Engl. J. Med. 382, 727-733 (2020)

      Zhu and colleagues isolated the virus that had caused the outbreak of an epidemic in Wuhan, China.

      They captured images of the virus and performed DNA sequencing. Based on the results, they reported the identification of a new type of coronavirus.

    1. I'm going to need some significant time delving into and mining this treasure trove of references.


      Burke provides a sort of miniature commonplace book about journal articles and books on commonplaces!

      A great resource for an overview of some of the more recent studies (since year TK?) on commonplace book research.



  11. Jul 2021
    1. V. Tyagi, R. B. Bonn, R. Fasan, Chem. Sci. 6, 2488–2494 (2015).

      This paper discusses the directed evolution via mutation of the amino acids of myoglobin that lead to 49% enantiomeric excess. Engineered myoglobin catalysts are used to synthesize thioethers via a carbene S-H insertion reaction. Conversions as high as 99% and turnover numbers as high as 5400 were observed.

    2. P. J. O’Brien, D. Herschlag, Chem. Biol. 6, R91–R105 (1999)

      O'Brien and Herschlag discuss the evolution of a superfamily of enzymes and the diverse reactions they catalyze. Single point mutations can lead to the evolution of new enzymatic activities. Professor Arnold's work also involves mutations of the WT to alter the reactivity of the enzyme.

    1. Hermann Diels and Walter Kranz have edited the doxography (A) and the existing texts (B) of the Presocratic philosophers in Die Fragmente der Vorsokratiker, Berlin 1951-19526. (A quotation like “DK 12A17” means: “Diels/Kranz, Anaximander, doxographical report no.17”).

      References for many of the pieces in this article.

    1. The miscellanies, numbered and indexed, would often be noted in the margins of his Bible as well, especially if the note was an expansion of an exegetical point.

      Interesting to see that Jonathan Edwards cross referenced his commonplace book to his bible as well.

  12. Jun 2021
    1. A. M. Tondreau et al., Science 335, 567–570 (2012).

      Iron compounds are found abundantly in nature and are cheap. The paper discusses the use of iron complexes as catalysts to add Si-H (hydrosilylation) across alkene double bonds. The catalysis proceeds with high regioselectivity, thereby eliminating the need for product purification.

    2. J. G. Kleingardner, K. L. Bren, Acc. Chem. Res. 48, 1845–1852 (2015).

      The article presents a wealth of information about heme c and cytochrome c. This knowledge is essential for engineering enzymes to catalyze novel reactions.

    3. E. Scharrer, M. Brookhart, J. Organomet. Chem. 497, 61–71 (1995).

      Iron carbene complexes react with organosilanes leading to insertion of carbene in the Si-H bond. This is another example of the use of organometallic catalyst to carry out the insertion reaction.

    4. M. Stelter et al., Biochemistry 47, 11953–11963 (2008)

      This paper presents the crystal structure of cyt c. X-ray crystallography shows that cytochrome c consists of alpha helices wrapped around the compact heme core. In addition, there is a singular alpha helix that wraps around the back of the molecule.

    5. G. A. Showell, J. S. Mills, Drug Discov. Today 8, 551–556 (2003).

      This paper describes how silicon isosteres can be critical to drug discovery success. Professor Arnold's paper uses an approach whose benefits can be applied to drug design.

    6. A. A. Toutov et al., Nature 518, 80–84 (2015).

      This paper describes how potassium tert-butoxide can catalyze the silylation of C-H bonds in aromatic heterocycles. The reaction is one step, occurs under mild conditions and is scalable to ~100 g. This methodology replaces the expensive route of using Rh or Ir complexes.

    1. R. E. Marshall, K. Farahbakhsh, Waste Manag. 33, 988–1003 (2013).

      This article compares and contrasts solid waste management (SWM) practices in developed versus developing countries. SWM practices in industrialized countries are often affected by public health, the environment, resource scarcity, climate change, and public awareness and participation. However, urbanization, inequality, economic growth, and socioeconomic factors often complicate SWM in developing countries.

    2. A. Cózar et al., Proc. Natl. Acad. Sci. U.S.A. 111, 10239–10244 (2014).

      This research examined the sizes and locations of plastic particles found in the world's oceans. When plastic objects in the ocean are exposed to sunlight, they tend to break up into small particles because sunlight weakens the plastic structure and waves provide mechanical force. The small plastic particles are quite durable. Most of the plastic debris recovered and measured during this study was about 2 mm in diameter. The total amount of plastic in the ocean estimated by this study was less than predicted from plastics production and input rates. The "missing" plastics were hypothesized to be removed through one or more of the following processes: shore deposition (being deposited on shore somewhere), nano-fragmentation (breaking up into very small pieces), biofouling (small organisms grow on the plastic particles, and the plastics become heavy enough to sink), and ingestion (being consumed by marine life). The pathway and fate of the "missing" plastic is unknown.

    3. R. W. Obbard et al., Earth’s Future 2, 315–320 (2014).

      When sea ice forms, it traps particulate matter from the water column such as microplastics. When sea ice melts, the particulate matter is released back into the ecosystem. This study examines the concentration of microplastics in Arctic Sea ice and finds that sea ice contains high concentrations of microplastics and other manmade particulates. Melting sea ice has the potential to release large amounts of microplastics back into the ocean.

    4. Materials and methods are available as supplementary materials on Science Online.

      Articles in Science are very brief. Supplementary materials available online can include text or images such as figures and graphs. Supplementary materials can provide additional information about how the research was conducted or additional evidence that supports the article's conclusions.

    5. M. C. Goldstein, D. S. Goodwin, PeerJ 1, e184 (2013).

      An ocean gyre is a circular ocean current formed by Earth’s wind patterns and rotation. The area in the center of a gyre tends to be very calm, and the circulation patterns of the currents draw debris into the stable center, where it becomes trapped. The debris is composed of objects both manmade and natural (i.e., driftwood). Many kinds of sea life live on and near the debris, such as gooseneck barnacles. Goldstein and Goodwin examined the digestive tracts of gooseneck barnacles to see if the barnacles consumed any plastics. One-third of the 385 barnacles examined had plastic particles present in their digestive tracts, and larger barnacles tended to contain more plastic particles. The effects of plastic particle ingestion on the ecosystem are still unknown.

    1. For bibliographic information on this strange memory image, see Bouchot (13).

      Other than filling some space and giving a bit of quirky context, did the text even mention this image? There should have been something.

      There was one later reference to parts of animals, but not specific to this image which could have been tied in better.



  13. Apr 2021
    1. P. Waterhouse et al., Science 270, 985 (1995)

      Waterhouse et al. investigate the effects of deleting CTLA-4 from mice. These "CTLA-4 deficient" mice had disorders of T cell proliferation and quickly died.

    2. J. G. Gribben et al., Proc. Natl. Acad. Sci. U.S.A. 92, 811 (1995)

      Gribben et al. show that CTLA-4 functions to induce cell death of T cells. In biology, many signaling events are also controlled by an off switch that prevents prolonged or out-of-control signaling. CTLA-4 fulfills this role for T cells.

    3. J. F. Brunet et al., Nature 328, 267 (1987)

      Brunet et al. identify the sequence of the CTLA-4 receptor. They note that it is part of immunoglobulin and has hydrophobic flanking sequences reminiscent of a membrane-bound protein. They also show that its expression is restricted to activated lymphocytes (T cells and B cells).

    4. D. L. Mueller, M. K. Jenkins, R. H. Schwartz, Ann. Rev. Immunol. 7, 445 (1989)

      Mueller, Jenkins, and Schwartz review the body of research on T cell costimulatory signaling pathways. In the few years after the discovery of the T-cell receptor, which directly binds the antigen to which a T cell is responding, researchers proposed that other signals are needed for T cells to become fully activated. This led to the two-signal model of T-cell activation described in this review.

    1. I’m resisting the temptation to add bibliographical cards into the Obsidian vault. Niklas Luhmann, you may recall, had a set of cards in his zettelkasten that were source citations. I don’t get the impression from reading his descriptions of his process or Schmidt’s research into it, that these were really an active part of the network of ideas in the boxes, which seem to have been based on his digested reactions to sources.

      I've done some bibliographical cards in the past myself, but find that I never used or revisited them or had great need to have them crosslinked myself. I've been moving away from doing this as well.

  14. Mar 2021
    1. S. Y. Oh, et al., ACS Appl. Mater. Interfaces 10, 13729–13740

      To add on wearable skin electronics, the created sweat glucose and pH sensors. The sensors were created out of carbon nanotubes combined with different polymers.

    2. G. Schwartz, et al., Nat. Commun. 4, 1859

      They have created a flexible pressure sensor which has the capability of non-invasive continuous radial artery pule monitoring. It is stated that this has the capability of being a breakthrough for wearable cardiovascular health monitoring.

    3. H. C. Ko, et al., Nature 454, 748–753

      They created an hemispherical optoelectronic device that can replicate the functions and characteristics of a human eye such as a wide field of view and low aberrations. This electronic device is based off of single-crystalline silicon and is compressible, which enables the hemispherical shape.

    4. S. Choi, et al., Nat. Nanotechnol. 13, 1048–1056

      Here, biocompatable and stretchable materials were tested for implant use. Gold coated silver nanowires within a polymer were tested to see its conductivity. Using this material they were able to fabricate wearable and implantable soft bioelectronic devices that can be conformally integrated with human skin.

    5. J. A. Rogers, T. Someya, Y. Huang. Science 327, 1603–1607

      They reviewed materials that maintain proper electronic properties while having the ability to be stretched, compressed, twisted, bent, and deformed. They discussed different applications for these technologies and possible commercialization.

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      They used transistors with a floating gate embedded in hybrid dielectrics at a nanoscale of size, and created a flexible array of these floating gate transistors. They coupled this with a pressure sensitive rubber sheet, and the result was a matrix that was able to read mechanical pressure and store it as an image.

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      They test a high density, hemispherical image sensor array comprised of an atomically small MoS2 heterostructure that has the capability of releasing strain. They deem this device to be capable of being a soft retinal implant capable of various imaging elements.

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      Stiff-neural implants have very rare compatibility with soft-neural tissues. Therefore an soft-neural implant was configured that is elastic like dura matter (the protective membrane of the spinal cord).

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      An elastomeric camera was created in the likeness of ant and beetle eyes. These cameras have close to full hemispherical shapes, at around 160 degrees. This hopes to copy arthropods who have wide-angle field of view, low aberrations, high acuity to motion and an infinite depth of field which are all difficult to replicate.

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      A self-healing system was created that was capable of automatically repair damage from repeating events. They used a coating-substrate (a substance on which an enzyme acts) to deliver healing agents to cracks within the polymer.

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      They created a thin, comfortable device that can be laminated or stuck to the skin of a person to allow for the monitoring of physiological monitoring for the user. Examples of this could be heart rate or blood pressure. This is also a wireless device.

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      A non-invasive ultra-thin electronic interface was created what is capable of being mounted on tissue using a a protein called fibroin which can be obtained from silk. This protein is capable of being absorbed back into the tissue which results in the mounting of the device. These electronics are capable of neural mapping of the brain.

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      They created a wireless, battery free, touch based electronic system that is capable of being placed onto the skin. This technology has the capability of communicating information through vibrations. They also have the capability of being used for VR.

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      A multiple phase heat sensitive rubber like material was created. This substance is extremely tough and durable while also having the capability of self-healing.

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      An easily foldable and stretchable circuit was created using silicon, a good semi-conductive metal. They combined the silicon with rubber like plastic material to help create the flexibility of the circuit.

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      The chemical way in which bioluminescence works is described in depth, and explained that the factors which control the intensity of this light can vary. Wilson and Hastings also touch on how this can be credited for some bacteria to sense their density and regulate specific genes through chemical communication.

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      Roger Hanlon discusses the use of dynamic camouflage, specifically applied to cephalopods.

      Hanlon discusses that these animals are able to camouflage themselves against almost any background, which is a feat non mastered by any land animals. He also categorizes different camouflage patterns. These patterns help to allow the animals that possess them to stay alive.

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      This paper found that extended release devices, like the one described in this paper, add therapeutic and convenience benefits, without adding any risks.

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      This paper gave the authors the idea for the Leopard Tortoise shell shape to design this pill.

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      This paper showed the authors that microneedles increase bioavailability of a drug and can be safely excreted by the body as seen using a swine model.

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      This source describes the preference of people taking injections or tablets. The authors of that paper found that people preferred tablets over injections. This led the authors of this paper to design a tablet to treat diabetes as an alternative to insulin injections.

  15. Feb 2021
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      This paper details a technique that rivals conventional electrowetting techniques. Here liquid dispersion forces are used in order to pull colored oil out of a reservoir and into an observable area greatly increasing the ability to see color while enhancing contrast.

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      This paper describes the process of electrowetting. This process is a way of taking paper and using electric fields to manipulate water droplets that are found on the surface of the paper. In terms of application this paper uses electrowetting as a way of creating a reflective surface that can be altered.

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      This paper was published in 2003 and highlighted advances in the field of thermal imaging. Specifically advancements in infrared detection was made. Here the author highlights three new techniques to detecting infrared waves.

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      In this piece we start with a review detailing how different studies of color changing organisms has led to what we currently know about camouflage. The paper then goes onto describe how organisms do not only change color based on their background but potentially also the number of predators that are threatening them.

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      Stevens and Merilaita explain the importance of animal camouflage and their implications in science today.

      While other authors focus on the how animal camouflage would work in general, there is more of a focus on defining camouflage strategies and crypsis, or features of physical appearance but also behavioral traits.

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      Robert Shephard, who is an author of this work, teamed up with several of his collages in order to help introduce soft robotics to the world. Here he defines what constitutes as soft robotics and how it can be useful to different fields of study.

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      Cott and Huxley describe general camouflage and warning coloration and mimicking which animals use.

      This knowledge of camouflage can be utilized to be adapted towards soft machines and how to use dynamic coloration. The ability for this type of technology is not commonly used and replicated by using other technologies.


      This word is exactly the point. What if this web page were a public thing within Roam? Then other people's notebooks could comment within their own, but using notifications (via Webmention) could be placed into a comments section at the bottom of one's page or even done inline on the portions they're commenting on using block references.