1,208 Matching Annotations
  1. Last 7 days
  2. 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.
  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.



  8. 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.

  9. 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.



  10. 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.

  11. 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.

    6. T. Sekitani, et al.,Science 326, 1516–1519 (2009)

      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.

    7. C. Choi, et al., Nat. Commun. 8,

      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.

    8. I. R. Minev, et al., Science 347, 159–163 (2015).

      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).

    9. Y. M. Song, Yet al., Nature 497

      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.

    10. 1. W. Gao, et al., Nature 529, 509–514 (2016).

      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.

    11. S. Xu, et al., Science 344, 70–74 (2014).

      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.

    12. D. H. Kim, et al., Nat. Mater

      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.

    13. X. Yu, et al., Nature 575, 473–479 (2019).

      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.

    14. Y. Chen, A. M. Kushner, G. A. Williams, Z. Guan, Nat. Chem

      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.

    15. D.-H. Kim, et al., Science 320, 507–511 (2008).

      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.

    1. 14. T. Wilson, J. W. Hastings, Annu. Rev. Cell Dev. Biol. 14, 197 (1998).

      Wilson and Hastings discuss bioluminescence in this article. This is a very large overview and descriptor of bioluminescence, where it covers what it is and what it does.

      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.

    2. 1. R. T. Hanlon, Curr. Biol. 17, R400 (2007).

      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.

    1. D. M. Bass, M. Prevo, D. S. Waxman, Drug Saf. 25, 1021–1033 (2002).

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

    2. G. Domokos, P. L. Várkonyi, Proc. Biol. Sci. 275, 11–17 (2008).

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

    3. G. Traverso et al., J. Pharm. Sci. 104, 362–367 (2015).

      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.

    4. L. Bolondi et al., Gastroenterology 89, 752–759 (1985).

      This paper showed the authors that direct injection into the stomach lining leads to a more predictable delivery rate when compared to a small intestine injection.

    5. I. P. Vazharov, J. IMAB 18, 273–275 (2012).

      This source showed that there were few injuries after multiple upper endoscopies, which are much more invasive. This was another source that showed the authors that injecting insulin into the GI tract is a safe way to deliver insulin, since it is less invasive than an upper endoscopy.

    6. D. K. Podolsky, J. Gastroenterol. 32, 122–126 (1997).

      This source explains that the mucosal surface in the GI tract is quick healing, giving the authors a good place to inject insulin without causing damage to the GI tract.

    7. T. A. S. Aguirre et al., Adv. Drug Deliv. Rev. 106, 223–241 (2016).

      This source shows that the bioavailability for even the most advanced drugs when taken orally is usually only 1-2%, meaning that very little drug is actually usable by the body, when a pill is taken orally. This led to the authors designing a pill that directly administered insulin directly into the GI tract.

    8. E. Moroz, S. Matoori, J.-C. Leroux, Adv. Drug Deliv. Rev. 101, 108–121 (2016).

      This study was important to the authors to find proper coatings for successful treatments of diabetes via the GI tract.

    9. M. J. Calvert, R. J. McManus, N. Freemantle, Br. J. Gen. Pract. 57, 455–460 (2007).

      This study explained that optimized treatment for Type II diabetes is delayed by, on average, 7.7 years. This meant that people with Type II diabetes were not well monitored or treated.

    10. Diabetes Control and Complications Trial Research Group, N. Engl. J. Med. 329, 977–986 (1993).

      This paper found that intense regular treatments of diabetes led to a decreased rate of progression to diabetic retinopathy (a disease of the eye caused by diabetes).

    11. L. Fallowfield et al., Ann. Oncol. 17, 205–210 (2006).

      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.

  12. Feb 2021
    1. J. Heikenfeld et al., Nat. Photonics 3, 292 (2009)

      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.

    2. R. A. Hayes, B. J. Feenstra, Nature 425, 383 (2003)

      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.

    3. 24. A. Rogalski, Prog. Quantum Electron. 27, 59 (2003).

      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.

    4. D. Stuart-Fox, A. Moussalli, Philos. Trans. R. Soc. B Biol. Sci. 364, 463 (2009)

      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.

    5. 12. M. Stevens, S. Merilaita, Philos. Trans. R. Soc. B Biol. Sci. 364, 423 (2009).

      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.

    6. 6. F. Ilievski, A. D. Mazzeo, R. F. Shepherd, X. Chin, G. M. Whitesides, Angew. Chem. Int. Ed. 50, 1890 (2011)

      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.

    7. 3. H. B. Cott, Adaptive Coloration in Animals (Methuen, London, 1957).

      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.

    8. 7. R. F. Shepherd et al., Proc. Natl. Acad. Sci. U.S.A. 108, 20400 (2011).

      Shepherd and others describe the utilization of a soft robot that is exclusively made of soft polymers.

      This soft quadrupedal robot is utilized as it can produce complex motions. Soft robotics can simplify the more mechanical structures and do not require a mechanically strong and rigid skeleton.


      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.

    1. Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis

      A flexible sensor device was created with the ability to analyze different elements/compounds found within sweat such as glucose and sodium while also monitoring skin temperature. All of this is fully integrated within the system so no outside analysis is needed.

  13. Jan 2021
    1. cellular data recorders offer the capacity to measure biologically relevant signals15,16,17,18,19 in places that are otherwise difficult to access, such as inside the body20,21, and over time22
    2. Recently, redox-responsive biomolecules such as phenazines have been used in several electrochemical strategies to interrogate a range of biological activities30,31 and to control gene expression in living cells32,33, where the redox status of the biomolecules could be measured or manipulated by application of electronic potentials
    1. 19. G. Fatemifar et al., Hum. Mol. Genet. 22, 3807–3817 (2013).

      Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

  14. Nov 2020
  15. Oct 2020
    1. E. E. Evans-Pritchard

      I hear this name and can't help but think about the potential influence on the name of the character from The Dead Poets Society


  16. Jul 2020
    1. 18. M. N. Weedon et al., Nat. Genet. 40, 575–583 (2008).

      Weedon et al. concluded that the HMGA2 gene was one of several that has a role in influencing height in adult humans.

    2. 17. X. Zhou, K. F. Benson, H. R. Ashar, K. Chada, Nature 376, 771–774 (1995).

      Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions.

      When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result is dwarfism. This protein is associated with the HMGA2 gene.

    3. 16. K. Pfannkuche, H. Summer, O. Li, J. Hescheler, P. Dröge, Stem Cell Rev. Rep. 5, 224–230 (2009).

      Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

    4. 15. S. Lamichhaney et al., Nature 518, 371–375 (2015).

      The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 – 300,000 years ago.

    5. 14. A. Abzhanov, M. Protas, B. R. Grant, P. R. Grant, C. J. Tabin, Science 305, 1462–1465 (2004).

      Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed simply showed no correlation whereas other factors showed a correlation with beak size, but not beak shape.

      However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

    6. 11. P. R. Grant, B. R. Grant, Science 313, 224–226 (2006).

      Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. magnirostris. This divergence happened on an isolated Galapagos island 22 years after G. magnirostris arrived to share a habitat with G. fortis.

    1. C. Y. Logan, J. R. Miller, M. J. Ferkowicz, D. R. McClay, Development 126, 345 (1999).

      This work is part of the foundation that the Wnt signaling pathway is well established chemical pathway in embyrogenesis. This is important, because embryos contain stem cells which require direction for migration and differentiation much the the regeneration in adult planarians.

    2. C. E. Rocheleau et al., Cell 90, 707 (1997

      This research was the first to identify the set of genes in C. elegans (a simple nematode invertebrate model) that were used in the experimental RNAi silencing by Alvarado and colleagues. Evidence was also provided that showed a potential role in early embryonic development.

    3. S. Q. Schneider, B. Bowerman, Dev. Cell 13, 73 (2007).

      The data confirm that β-catenin regulates cell fate in two very distant animal species, which suggest that β-catenin has an ancient metazoan origin.

    4. A. H. Wikramanayake et al., Nature 426, 446 (2003).

      The authors in this study show that β-catenin plays a role in cell adhesion and body plan development in sea urchins, a primitive invertebrate animal. This research provides additional evidence the β-catenin is an evolutionarily important molecule and its role has been maintained over time across the animal kingdom.

    5. 1. S. Schneider, H. Steinbeisser, R. M. Warga, P. Hausen, Mech. Dev. 57, 191 (1996).

      The authors used two vertebrate models, zebrafish and frogs, to identify that β-catenin via the Wnt signaling pathway plays a role in dorsal-ventral polarity. This research suggest that β-catenin is an important molecule because it has been found to play similar roles in both vertebrates and invertebrates.

    6. R. Stadeli, R. Hoffmans, K. Basler, Curr. Biol. 16, R378 (2006)

      The data provided insight into how the Wnt signaling pathway and β-catenin target gene activation. This foundational information provided understanding of how RNAi could be used to silence the genes associated with control of this pathway.

    7. H. Yokoyama, H. Ogino, C. L. Stoick-Cooper, R. M. Grainger, R. T. Moon, Dev. Biol. 306, 170 (2007).

      Some amphibian species have the ability to regenerate limbs. The data suggest that Wnt/β-catenin signaling plays an essential role in this process. These results again confirm that β-catenin is present across various animal species. A full understanding of regeneration in vertebrates may lead to potential treatments for human organ regeneration.

    8. T. H. Morgan, Am. Nat. 38, 502 (1904)

      Morgan was a pioneer in the field of genetics. His theory that polarity, or development of two axes in animals was a direct result of the presence of a yet unidentified molecule. This theory has stood the test of time and provides the foundation of this research.

    9. P. W. Reddien, A. Sánchez Alvarado, Annu. Rev. Cell Dev. Biol. 20, 725 (2004).

      Earlier research by Alvarado and colleagues identified the types of tissue that are able to regenerate from a blastema that forms after tissue damage. Without previously identifying this role, the current research would not be possible.

    1. A. R. Adamantidis, F. Zhang, A. M. Aravanis, K. Deisseroth, L. de Lecea, Nature 450, 420 (2007).

      The authors used Channelrhodopsin-2 to selectively photostimulate hypocretin-producing neurons in the lateral hypothalamus and showed a frequency-dependent effect on sleep-to-wakefulness transition. This paper supported optogenetics' ability to stimulate cells and elicit a physiological effect.

    2. V. Gradinaru et al., J. Neurosci. 27, 14231 (2007)

      This paper discusses targeting strategies to selectively express opsins to certain regions or cell types as well as methods to read out expression and activity. Methods include electrophysiology, imaging, and behavior analysis.

    3. F. Zhang et al., Nature 446, 633 (2007).

      A paper describing the first use of halorhodopsin—a chloride pump expressed in an archaeon named Natronomonas pharaonis that expressed temporal optical inhibition of neural activity. The investigators were then able to co-express both NpHR and ChR2 in the same cell and optically control its activity.

    4. V. Gradinaru, K. R. Thompson, K. Deisseroth, Brain Cell Biol. 36, 129 (2008)

      The authors engineered the NpHR from the F. Zhang et al. paper in 2007 to be better expressed at the cell membrane by inserting a membrane-insertion signal and an endoplasmic reticulum export signal. Both interventions created eNpHR (enhanced NpHR) that improved protein trafficking and membrane expression. This was a necessary modification for the current paper published by the same first author. Temporal precision is a key parameter when dealing with neural firing which can occur at millisecond resolution.

    5. F. Zhang et al., Nat. Neurosci. 11, 631 (2008)

      The authors investigated a red-shifted cation-conducting opsin variant from the algae species Volvox carteri that could be stimulated at a wavelength of 595nm. VChR1 can be stimulated by yellow light and offered a third class of microbial opsins.

    1. 29. J. D. Creswell et al., Psychol. Sci. 16, 846 (2005).

      Creswell et al. identified a physical reaction to stereotype threat and found that values affirmation reduces this reaction.

    2. 23. G. L. Cohen, J. Garcia, N. Apfel, A. Master, Science 313, 1307 (2006).

      Cohen et al. performed a large-scale examination of the efficacy of values affirmation in an authentic classroom environment.

      They found that having students complete a short writing exercise, in which they wrote about a value they found important (values affirmation), reduced the gap in performance between African American students and other students.

      A full PDF copy of this research can be found in the Related content tab.

    3. 22. C. Good, J. Aronson, M. Inzlicht, Appl. Dev. Psychol. 24, 645 (2003).

      Good, Aronson, and Inzlicht assessed whether specific kinds of mentoring could reduce the effects of stereotype threat in female, minority, or low-income 7th graders.

      They found that students paired with a college-student mentor who either 1) encouraged them to view intelligence as malleable, or 2) told them to attribute academic difficulties to the novelty of the educational setting, performed much better than students who did not get this framing.

    4. 31. G. L. Cohen, J. Garcia, V. Purdie-Vaughns, N. Apfel, P. Brzustoski, Science 324, 400 (2009).

      Cohen et al. found that an initial values affirmation intervention could have long-lasting positive effects.

  17. Jun 2020
    1. B. Schoene et al., Science 363, 862-866

      S. Burgess stresses that knowledge of the cause or causes of mass extinctions can inform understanding of how the biosphere responds to dramatic environmental change and can help to validate hypotheses about probable outcomes of anthropogenic changes. Both the asteroid impact and large-scale volcanic eruptions as the cause of the K-Pg extinction are credible. Now, with more accurate dating techniques, it appears that most of the large-scale eruptions occurred after the impact, delaying recovery.

    2. P. Hull, Curr. Biol. 25, R941-R952 (2015)

      Mass extinctions often result in the loss of entire branches of the tree of life. Pincelli Hull argues that macroevolution is shaped as much by the species that survive a mass extinction as by those that do not. He contends that more than 99% of all species that have ever lived are now extinct and that the losses have not been random.

    3. 8. P. Wilf, K. R. Johnson, B. T. Huber, Proc. Natl. Acad. Sci. U.S.A. 100, 599-604 (2003).

      Wilf et al. differentiate between climatic change and asteroid impact effects on biodiversity. They determined there was a cooling trend during the final 0.1 m.y. of the Cretaceous. This likely accounts for some loss of biodiversity from its peak during the earlier warm interval and makes inaccurate the observation that the asteroid impact alone resulted in the loss of 70%–90% of macrofossil species.

    4. B. Blonder et al., PLOS Biol. 12, e1001949 (2014).

      The authors tested the hypothesis that an impact winter following the asteroid impact selected against slow-growing evergreen species. Using fossil leaf collections crossing a 2-million-year interval spanning the K-Pg boundary, they assessed both carbon assimilation rate and carbon investment using leaf vein density and leaf mass per area as proxies. They learned that species that survived the K-Pg extinction had fast-growth strategies with high assimilation rates and low carbon investment.

    5. 18. W. C. Clyde et al., Earth Planet. Sci. Lett. 452, 272-280 (2016).

      Clyde et al. used several different dating techniques to more precisely determine the age of volcanic ash deposits across the K-Pg boundary in the Denver Basin. The results were compared to data derived from an analysis of fossil spores and pollen from deposits in the same region. They concluded that the interval between the extinction of the dinosaurs and the appearance of the earliest Cenozoic mammals in the Denver Basin lasted ∼185 k.y. and the "fern spike" lasted ∼1 k.y. after the K–Pg boundary layer was deposited, indicating rapid rates of biotic extinction and initial recovery in the Denver Basin.

    6. G. P. Wilson, "Mammalian extinction, survival, and recovery dynamics across the Cretaceous-Paleogene boundary in northeastern Montana, USA" in Through the End of the Cretaceous in the Type Locality of the Hell Creek Formation in Montana and Adjacent Areas (Geological Society of America Special Paper, ed. 503, 2014), pp. 365-392.

      Wilson’s research concludes that the richness of mammalian species remained relatively stable for most of the last ~1.9 m.y. of the Cretaceous. However, the relative abundance of mammals more closely related to marsupials than to placentals began declining ~500–600 k.y. before the Cretaceous-Paleogene boundary. Based on available fossil evidence, mammalian recovery occurred within ~600–700 k.y. of the Cretaceous-Paleogene event.

    7. 3. R. O. Prum et al., Nature 526, 569-573 (2015).

      Prum and colleagues investigated avian phylogeny with a data set of >390,000 bases of genomic sequence from each of 198 species of living birds. This represents all major avian lineages, and two crocodilian outgroups. The results of their divergence time analyses are congruent with the paleontological record and support a major radiation of crown birds following the Cretaceous–Paleogene (K–Pg) mass extinction.

  18. Apr 2020
    1. S. Lamichhaney, F. Han, J. Berglund, C. Wang, M. S. Almen, M. T. Webster, B. R. Grant, P. R. Grant, L. Andersson, Science 352, 470-474 (2016).

      This paper reports the identification of the importance of the HMGA2 gene in affecting beak shape in Darwin's finches, especially during natural selection that occurred during a drought in 2004-05.

    2. P. R. Grant, B. R. Grant, Evolution 48, 297-316 (1994).

      In this summary of genes and traits of hybridizing finches on Daphne Major, the authors established general patterns found in hybridization of the finches on this island: that hybrids are generally intermediate between parental species and often go on to mate with members of the parental species.

      They discuss hybridization as a source of genetic variation within existing species and suggest that it can happen through new combinations of genes (additive genetic variance) as well as new patterns of dominance or co-dominance among known genes, or even the establishment of new combinations of genes on chromosomes.

      They also note how rare it would be to see hybridization produce birds much larger than parent species, and how unusual occurrences might be necessary to provide the conditions for this to happen.

    3. L. H. Rieseberg, M. A. Archer, R. K Wayne, Heredity 83, 363-372 (1999)

      In this discussion of transgressive segregation, Riesenberg et al. review many studies and conclude that the genetic basis of transgressive segregation is through complementary alleles: new combinations of alleles that provide novel combinations of genotypes.

      They find that transgressive segregation occurs most frequently in crosses between closely related species and that niche separation is the most important factor in favoring the establishment of hybrids.

    4. H. S. Swarth, Occas. Pap. Calif. Acad. Sci. 18, 1-299 (1931)

      Swarth's paper reorganized the classification of Darwin's finches slightly, particularly with regard to the Geospiza genus.

    5. D. L. Lack, Darwin's Finches (Cambridge Univ. Press, 1947)

      Lack's book recounts what he learned about Darwin's finches from a visit to the Galapagos in late 1938-39, one of the first visits to the island focused on the finches since Darwin's time. The work includes the classification of the finches as well as notes on speciation, adaptive radiation, and evolution.

    6. P. R. Grant, B. R. Grant, Philos. Trans. R. Soc. Lond. B Biol Sci. 365, 1065-1076 (2010)

      Grant and Grant use genetic information to quantify the effects of the gene exchange between populations of birds. They explore two situations: genes that enter a population through mating with a bird of the same species (conspecific) but from a different population on another island; and genes that enter a population from a member of a different species (heterospecific). They conclude that while both types of gene flow are rare, they do occur and have measurable effects on the populations that are complex and change through time rather than being steady.

    7. S. Lamichhaney, J. Berglund, M. S. Almen, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerova, C. -J. Rubin, C. Wang, N. Zamani, B. R. Grant, P. R. Grant, M. T. Webster, L. Andersson, Nature 518, 371-375 (2015).

      This paper presents the results of a whole genome study of 120 of Darwin's finches and identifies the ALX1 gene as important in determining beak shape. The study also helps revise the phylogenetic tree of the finches and provides evidence for hybridization as the finches evolved.

    8. P. R. Grant, B. R. Grant, How and Why Species Multiply (Princeton Univ. Press, 2008)

      This book gives a complete evolutionary history of Darwin's finches. Grant and Grant explain the speciation that occurred and the mechanisms that underpin the formation of different species of finches in the Galapagos Islands.

    9. M. Schumer, G. G. Rosenthal, P. Andolfatto, Evolution 68, 1553-1560 (2014)

      In the article "How Common is Homoploid Hybrid Speciation?" Schumer et al. indicate that in the study of this topic future research needs to clarify the mechanisms of this type of event. They also propose criteria by which to judge the strength of evidence for this event, arguing that evidence for hybridization's role in speciation is somewhat limited.

    1. 19. A.-K. Olsson, A. Dimberg, J. Kreuger, L. Claesson-Welsh, Nat. Rev. Mol. Cell Biol. 7, 359–371 (2006).

      Researchers at the Department of Genetics and Pathology in Rudbeck Laboratory studied three vascular endothelial growth-factor receptors (VEGF) responsible for regulating the cardiovascular system. VEGFR1, VEGFR2, and VEGFR3 all function slightly different but together produce cardiovascular development, control endothelial-cell function and the development and survival of blood vessels. They showed the importance of controlling angiogenetic-growth-factors (such as proangiogenic) that are responsible for the formation of blood vessels. Fibronectin is not mentioned by name but other glycoproteins are emphasized for their importance as receptors for VEGF.

    2. 5. D. B. Kolesky, K. A. Homan, M. A. Skylar-Scott, J. A. Lewis, Proc. Natl. Acad. Sci. U.S.A. 113, 3179–3184 (2016).

      Researchers at Harvard were the first to keep a 1cm thick vascularized tissue alive in lab conditions for longer than 6 weeks. They achieved this by co-printing a mixture of bioinks composed of human stem cells, skin cells, cells from umbilical cord vessels, and growth factors. The printed artificial tissue contained a network of embedded blood vessels used for perfusion to keep the tissue alive.

    3. 23. J. S. Miller, PLOS Biol. 12, e1001882 (2014).

      Jordan S. Miller at Rice University highlighted that more clinical trials, proper tissue fabrication sterilization, sufficient vasculature and quality assurance will lead to good manufacturing practice (GMP) and a standard regulatory process. Miller believes overcoming these obstacles will transition the use of 3D printed tissue from research and development to manufacturing and production.

    4. 17. M. Potente, H. Gerhardt, P. Carmeliet, Cell 146, 873–887 (2011).

      Michael Potente, Holger Gerhardt, and Peter Carmeliet worked with endothelial cells in order to grow blood vessels in a scaffold smaller than any needle is capable of printing. The cells naturally line the inner surface of the vessel and are responsible for repair and growth of new vasculature. Under predetermined conditions the cell have genes that will be expressed to grow vasculature; a process known as angiogenesis.

    5. 9. C. Frantz, K. M. Stewart, V. M. Weaver, J. Cell Sci. 123, 4195–4200 (2010).

      Christian Frantz, Kathleen M. Stewart and Valerie M. Weaver compiled information on the extracellular matrix (ECM) and its application in tissue engineering

    6. 8. N. Noor et al., Adv. Sci. 6, 1900344 (2019)

      Dvir and colleagues used a specific type of stem cells called pluripotent stem cells that allowed them to grow and develop vascularization as an embryo would. They are the first to take cells from a patient to print a personalized full size and function heart using bioinks. Bioinks are the printing material that replicates the extracellular matrix and has living cells in it.

    7. 6. H.-W. Kang et al., Nat. Biotechnol. 34, 312–319 (2016).

      HW Kang and others at Wake Forest Institute for Regenerative Medicine used microchannels developed at University of Pennsylvania on an integrated tissue-organ printer (ITOP) so that they can produce human-scale mandible and calvarial bone, cartilage and skeletal muscle.

    8. 4. J. S. Miller et al., Nat. Mater. 11, 768–774 (2012)

      J.S. Miller and others in the Bioengineering Departmnet of University of Pennsylvenia were able to 3D print living cells together to form a tissue. The current problem is that blood and oxygen was unable to get to the center of the tissue leaving a large dead spot in the center called a necrotic core. They solved this problem by engineering in channels for blood to flow as they do through veins to keep a wide variety of cell types alive.

    1. S. Hunt, T. G. McKay, I. A. Anderson, Appl. Phys. Lett. 104, 113701 (2014).

      This paper describes the development of a self healing dielectric elastomer. The actuator contains a layer of oil which allows the actuator to maintain dimensional stability even after being punctured multiple times.

    2. S. J. Dünki, Y. S. Ko, F. A. Nüesch, D. M. Opris, Adv. Funct. Mater. 25, 2467–2475 (2015).

      This paper describes self‐repairable, high permittivity dielectric elastomers with large actuation strains at low electric fields. The actuators can be operated repeatedly and reversibly at voltages below the first breakdown.

    3. W. Yuan et al., Adv. Mater. 20, 621–625 (2008).

      This paper demonstrates the fault-tolerant dielectric elastomer electrodes consisting of elastomers spray coated with carbon nanotubes. The electrodes allows for isolation of the fault after a dielectric breakdown increasing the reliability of the actuator.

    4. R. Pelrine, R. Kornbluh, Q. Pei, J. Joseph, Science 287, 836–839 (2000).

      This paper describes the change in characteristics of elastomers when pre-strained. The resulting elastomers feature double the strength and speed of previous actuators.

    5. R. F. Shepherd et al., Proc. Natl. Acad. Sci. U.S.A. 108, 20400–20403 (2011).

      This paper describes the development of a quadrupedal soft robot that moves through fluid pressure.

    6. P. Polygerinos et al., Adv. Eng. Mater. 19, 1700016 (2017).

      This paper reviews a specific type of soft robot, elastomeric robots, that are powered by fluid pressure.

    7. F. Ilievski, A. D. Mazzeo, R. F. Shepherd, X. Chen, G. M. Whitesides, Angew. Chem. Int. Ed. 50, 1890–1895 (2011).

      This paper defines the characteristics of many types of soft robots. The authors compile a benchmark of these characteristics for future research reference.

    8. S. Kim, C. Laschi, B. Trimmer, Trends Biotechnol. 31, 287–294 (2013).

      This article is a review of the current common designs and applications of "soft-robots". Soft-robots are robots modeled after things that occur in nature. For example, robotics would traditionally use gears and motors to move. .Soft-robotics use designs that mimic human or even insect muscle.

  19. Mar 2020
    1. J. Liu, Y. Pang, S. Zhang, C. Cleveland, X. Yin, L. Booth, J. Lin, Y.-A. L. Lee, H. Mazdiyasni, S. Saxton, A. R. Kirtane, T. von Erlach, J. Rogner, R. Langer, G. Traverso, Triggerable tough hydrogels for gastric resident dosage forms. Nat. Commun. 8, 124 (2017).

      Liu and colleagues created "triggerable tough hydrogels," composed of novel materials that promote a prolonged stay in the gastric system.

      The once-monthly smart birth control pill employs this concept of tough materials that will only disintegrate in the presence of chemical stimuli to ensure the contraceptive will stay in the digestive tract longer.

    2. A. M. Bellinger, M. Jafari, T. M. Grant, S. Zhang, H. C. Slater, E. A. Wenger, S. Mo, Y.-A. L. Lee, H. Mazdiyasni, L. Kogan, R. Barman, C. Cleveland, L. Booth, T. Bensel, D. Minahan, H. M. Hurowitz, T. Tai, J. Daily, B. Nikolic, L. Wood, P. A. Eckhoff, R. Langer, G. Traverso, Oral, ultra–long-lasting drug delivery: Application toward malaria elimination goals. Sci. Transl. Med. 8, 365ra157 (2016).

      Bellinger and colleagues design a long-term drug delivery system for malaria. They accomplish this by designing an oral capsule that stays in the gastric cavity for up to 14 days.

      The smart birth control pill presented in this work builds off of this research and the idea that reducing dosage frequency can be accomplished by increasing the time it stays in the stomach.

    3. A. Hayward, T. Bensel, H. Mazdiyasni, J. Rogner, A. R. Kirtane, Y.-A. L. Lee, T. Hua, A. Bajpayee, J. Collins, S. McDonnell, C. Cleveland, A. Lopes, A. Wahane, R. Langer, G. Traverso, Scalable gastric resident systems for veterinary application. Sci. Rep. 8, 11816 (2018).

      A study was performed to investigate scalable doses and the modulation of drug release in the gastrointestinal system.

      The author's used most of the characteristics of these dosage forms in the manufacturing of the oral contraceptive.

    1. J. Terborgh et al., Science 294, 1923 (2001)

      In this natural experiment, as a result of a hydroelectric dam flooding a rainforest in Venezuela, researchers were able to measure the results of predator removal in isolated communities. Top-down regulation of these communities were discovered and drastic trophic cascades were observed.