1,025 Matching Annotations
  1. Last 7 days
    1. 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.

  2. Feb 2020
    1. T. Hanyu, I. Kaneoka, Nature 390, 273–276 (1997)

      This article reports the helium isotope data from ancient basalts located in three islands in the southern pacific ocean. The HIMU sample collected from this area shows a relatively low and stable helium-3 to helium-4 ratio. While, other enriched samples show a variation in this isotope ratio.

    2. M. G. Jackson, J. G. Konter, T. W. Becker, Nature 542, 340–343 (2017)

      In this paper, the authors have shown that only the hottest hotspots with the slowest wave velocity draw from the ancient reservoirs formed during the early days of planet Earth.

    3. M. J. Walter et al., Science 334, 54–57 (2011)

      There has been a lot of debate regarding the exact location of the chemical reservoirs containing superdeep diamonds. In this research, the authors have done carbon isotope analysis on these diamonds and concluded that the most likely origin is in the lower mantle of Earth.

    4. H. M. Gonnermann, S. Mukhopadhyay, Nature 449, 1037–1040 (2007)

      It has long been debated that He, one of the most volatile element, remains trapped in Earth, relative to other volatile elements, like the chondrites. This is also known as the "Helium Concentration Paradox". This paper aims at self-consistently explain the paradox by measuring the carbon dioxide in mid-ocean ridge basalts (MORBs) and ocean island basalts (OIBs).

    5. D. L. Anderson, Proc. Natl. Acad. Sci. U.S.A. 95, 4822–4827 (1998)

      This research article debunks the popular outcomes of previous geological models of Earth's interior. The author shows data to disprove the previous hypothesis of correlating high R in basalts with excess of helium-3 and existence of primitive gas-rich chemical reservoirs.

    6. M. D. Kurz, J. J. Gurney, W. J. Jenkins, D. E. Lott III, Earth Planet. Sci. Lett. 86, 57–68 (1987)

      In this paper, the authors have performed a series of experiments on diamond samples in order to ascertain the chemical composition and isotope variability of diamonds from the Orapa kimberlite.

    7. F. Kaminsky, Earth Sci. Rev. 110, 127–147 (2012)

      There are several existing models of the Earth's formation. In this research, the author points out the discrepancies in the preconceived models and highlights the fact that the chemical compositions of the upper and lower mantle are different.

    8. J. C. VanDecar, D. E. James, M. Assumpção, Nature 378, 25–31 (1995)

      The author reports a seismic study of old parts of southeast Brazil and provides no concrete evidence of metamorphic rocks which are commonly found in regions occupied by subducted oceanic plates.

    9. M. Broadley et al., Geochem. Perspect. Lett. 8, 26–30 (2018)

      In this research, the authors investigate the geochemical processes involving diamond formation within the Siberian cratonic lithosphere. They particularly study the halogen and noble gas geochemistry of fluids trapped in diamonds sampled from this region.

    10. R. L. Christiansen, G. Foulger, J. R. Evans, Geol. Soc. Am. Bull. 114, 1245–1256 (2002)

      In this research paper, the author presents their data of helium isotope analysis of rock samples from the Yellowstone region. They conclude that the analysis shows no evidence of a deep mantle origin of the collected samples.

    1. 7. United States Food Drug and Administration, Mirena FDA label, (2015); www.accessdata.fda.gov/drugsatfda_docs/label/2015/021225s031lbl.pdf). 8. United States Food Drug and Administration, Liletta FDA label, (2018); www.accessdata.fda.gov/drugsatfda_docs/label/2018/206229s007lbl.pdf). 9. United States Food and Drug Administration, Kyleena FDA label, (2016); www.accessdata.fda.gov/drugsatfda_docs/nda/2016/208224Orig1s000LBL.pdf. 10. United States Food and Drug Administration, Skyla FDA label, (2017); www.accessdata.fda.gov/drugsatfda_docs/label/2017/203159s007lbl.pdf.

      The authors discuss that intrauterine (within the uterus) hormone devices can serve as an alternative contraceptive form, providing protection for 3-6 years.

    2. 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 contraceptive 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.

    3. 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 a prolonged period of time.

      The proposed expanding, oral contraceptive 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. Nov 2019
    1. P. Waterhouse et al., Science 270, 985 (1995)

      Waterhouse et al. investigate the effects of deleting the 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. M. F. Krummel and J. P. Allison, J. Exp. Med. 182, 459 (1995)

      Krummel and Allison study the effect of CTLA-4 engagement. Their anti-CTLA-4 antibody blocks the receptor without engaging it. On its own, blocking the receptor does not have an effect on T-cell responses. Combined with an activation signal, anti-CTLA-4 allows for enhanced proliferation of T cells. The antibodies introduced here are the same ones used in the treatment of mice in this paper.

    4. T. L. Walunas et al., ibid., p. 405

      Walunas et al. show that CTLA-4 is an inhibitor of T cells. Their approach is to cross-link the receptors together, mimicking the cross-linking that would occur naturally upon receptor engagement. The effect of this is inhibition of T cell proliferation.

    5. P. S. Linsley et al., Immunity 1, 793 (1994)

      Linsley et al. study the differences between binding of CD28 and CTLA-4 to B7 molecules. Though they have similar avidities, they bind the B7 surface molecules using different conformations and kinetics.

    6. P. S. Linsley et al., J. Exp. Med. 174, 561 (1991)

      Linsley et al. show that CTLA-4, like CD28, binds B7. Using a soluble version of CTLA-4, they show that it binds to B7 with an affinity of 12 nM.

    7. K. Harper et al., J. Immunol. 147, 1037 (1991)

      Harper et al. present compelling evidence that CTLA-4 and CD28 share a similar function. They found that the receptors share similarities in structure, sequence, gene location, and expression patterns.

    8. 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 the 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).

    9. P. S. Linsley, J. Exp. Med. 182, 289 (1995)

      In this commentary, Linsley speculates on how the evidence for the roles of CD28 and CTLA-4 fits together. T-cell activation is more complex than scientists originally thought.

    10. J. A. Bluestone, ibid. 2, 555 (1995)

      In this minireview, Bluestone summarizes the studies showing the nuances of CD28-mediated signaling. He discusses that different B7 molecules result in differing levels of activation, and that CTLA-4 has an inhibitory effect.

    11. M. K. Jenkins, Immunity 1, 443 (1994)

      In this minireview, Jenkins summarizes the evidence for the role of CTLA-4. It was shown from multiple studies that CTLA-4 has an immunosuppressive effect.

    12. S. Baskar et al., Proc. Natl. Acad. Sci. U.S.A. 90, 5687 (1993)

      Baskar et al. investigate the effect of B7 expression in tumor cells on the helper T cell immune response. They show that engineered tumor cells generate a helper T cell response and tumor rejection.

    13. S. E. Townsend and J. P. Allison, Science 259, 368 (1993)

      Townsend and Allison investigate whether expressing B7 on the surface of a tumor will enhance its rejection. They show that B7 expression results in a cytotoxic T cell immune response.

    14. L. Chen, S. Ashe, W. A. Brady, l. Hellstrom, K. E. Hellstrom et al., Cell 71, 1093 (1992)

      Chen et al. investigate whether expressing B7 on the surface of a tumor will enhance its rejection. They show a B7-dependent immune response by cytotoxic T cells.

    15. C. H. June, J. A. Bluestone, L. M. Nadler, C. B. Thompson, Immunol. Today 15, 321 (1994)

      June, Bluestone, Nadler, and Thompson review the research on B7 and CD28. Though they are the most commonly found members, each of these molecules is part of a larger receptor family of related molecules.

    16. P. S. Linsley and J. A. Ledbetter

      Linsley and Ledbetter summarize the research on CD28 and B7 molecules. The costimulatory signal needed for full T-cell activation is supplied through these surface molecules.

    17. 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 signalling 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. (s. d.)

      Votre référence est bien en bib, mais (hormis l'hyperlien), elle est totalement vide : si vou l'aviez exporté à partir de la bibliographie commune sur Zotero, elle aurait été plus fournie et les indices bib auraient alors fait sens.

    2. article

      c'est moins un article, qu'une partie d'un ouvrage commun

    3. article Chapitre 11. Le livrel et le format ePub

      si c'est un chapitre, c'est un chapitre

    4. sur les Presses de l’Université de Montréal.

      les PUM sont ici la maison d'édition

  4. stylo.ecrituresnumeriques.ca stylo.ecrituresnumeriques.ca
    1. (Fontanille, 2008, p. 23)

      référence qui aurait mérité d'être éditée dans la bibliographie

    2. (1954)

      référence à intégrer dans la bibliographie

    3. Mackenzie

      la référence est ici attendue

    4. Louis Hjelmslev

      l'ajout de la référence aurait été nécessaire ici.

    5. (De Angelis 2018)↩ (De Angelis 2018)↩ (De Angelis 2018)↩ (De Angelis 2018)↩ (De Angelis 2018)↩

      ces références auraient pu être intégrées au corps du texte avec les indices bib (sans appel de note)

    6. revue Signata

      il est conseillé de citer les revues en utilisant l'italique

  5. stylo.ecrituresnumeriques.ca stylo.ecrituresnumeriques.ca
    1. Cet article

      Il s,agit davantage d'un billet de blog

    2. Méchoulan, professeur à l’Université de Montréal au département des littératures de langue française, ou en littérature électronique Doueihi, titulaire de la Chaire d’humanisme numérique à l’Université de Paris-Sorbonne.


    3. Turing, Bush, Nelson, von Neumann.

      des ouvrages de références auraient permi d'enrichir un peu ce passage.

    4. l’hypertextualité, l’interactivité, la collaborativité et l’algorithmicité.

      peut-être des références par éléments ? Comme Bush pour l'hypertextualité.

    1. Bibliographie

      vous avez ici placé la bibliographie du cours, ce qui vous génère une bibliographie immense avec des entrées doubles... Était davantage attendue une bibliographie présentant les ouvrages dont vous vous êtes inspirée pour créer le compte rendu (dont l'ouvrage de référence).

    2. page3]

      même remarque que pour la référence précédente, de plus un espace manquant entre la page et son numéro

    3. [(???); page 1]

      la référence est absente de la bibliographie : elle n'apparaît donc pas correctement

    1. Roger Bautier et Gabriella Giudici, « La question de la démocratie des réseaux socio-numériques », Sciences de la société [En ligne], 91 | 2014, mis en ligne le 16 avril 2015, consulté le 31 octobre 2019. URL : http://journals.openedition.org/sds/931 ; DOI : 10.4000/sds.931

      cette référence doit être éditée dans le module bibliographie

    2. (Bautier, 2014).


    3. (Bautier, 2014).

      cette référence aurait dû être éditée avec un indice bib et se retrouver dans le module bibliographie.

    4. « il n’est de science de ce qui est publié »,

      référence ?

    5. (Le Crosnier, 2004).

      la référence aurait dû être citée avec l'indice bib

    6. Désintermédiation et démocratie

      les articles sont généralement cités entre guillemets

    1. Grenier (2017) , p. 8 et p. 10

      On cite généralement les références entre parenthèse, sans italique, mais cela montre ici que vous vous êtes appropriez l'édition dans stylo !

    2. (Grenier (2017), p. 2)↩

      Vous avez ici placé l'indice bib entre parenthèse : cela créé une double parenthèse. Il faut le laisser entre crochet.

    1. « Google nous rend-il stupide? »

      référence ?

    2. C. Anderson, The Long Tail : How Endless Choice Is Creating Unlimited Demand, Londres, Random House, 2007.↩ S. Firer-Blaess, « Wikipédia : hiérarchie et démocratie », Homo numericus, 2007.↩

      ces références aurait mérités une intégration dans la bibliographie

    3. Communications,

      les revues sont citées en italique

    4. “Édition électronique”

      guillemets français de préférence

    1. Dans le numéro 19 de la revue politique, artistique et philosophique Multitudes, Hervé Le Crosnier, enseignant-chercheur à l’université de Caen et responsable éditorial chez C&F éditions, écrit sur la question de la désintermédiation dans le domaine culturel (Le Crosnier 2004). Il affirme que « ce sont les intermédiaires qui fondent les sociétés ».

      il aurait été attendu que soit citer le titre de l'article.

    2. Multitude

      les revues sont à citer en italique

    1. Claire Clivaz et Jérôme Meizoz

      exemples de références ?

    2. Roger Chartier, Serge Bouchardon, Bourdieu ou encore Christian Vanderdorpe.

      quelques références étaient attendues ici

    3. UNIL - Jérôme Meizoz 

      il y a ici un problème d'encodage (UTF8) dans le bib

    1. Foglia

      le nom de l'auteur aurait pu être ôté dans l'indice bib (avec la présence préalable du tiret)

    2. Voir (Delacroix 2005)↩ Voir (Simondon 1958)↩ Voir (Flower et Hayes 1981)↩ Voir (Caby-Guillet, Guesmi, et Mallard 2009)↩

      ces références auraient pu être intégrées dans le corps du texte avec les indices bib.

    1. (Mounier et Dacos 2011)↩ (Mounier et Dacos 2011)↩

      ces références auraient pu être placées dans le corps du texte

    2. Édition électronique

      on cite en général un article entre guillemets

    3. ouvrage

      il s'agit d'une revue

    1. Johanna Drucker, théoricienne de l’esthétique et artiste livresque, et de Milad Doueihi, historien des religions et titulaire de la chaire d’humanisme numérique à l’université de Paris-Sorbonne.

      des références inclues en bibliographies auraient été attendues.

    1. Doctorante en études littéraires

      où ? quels sont ces notions de réflexions ?

    2. Introduction

      très bonne contextualisation de l'article qui aurait cependant mérité d'être cité (édition, date)

  6. stylo.ecrituresnumeriques.ca stylo.ecrituresnumeriques.ca
    1. De Angelis, Rossana. 2018. « Textes et textures numériques. Le passage de la matérialité graphique à la matérialité numérique ». Signata. Annales des sémiotiques / Annals of Semiotics, nᵒ 9 (décembre):459‑84. https://via.hypothes.is/https://journals.openedition.org/signata/1675. https://journals.openedition.org/signata/267 https://fr.linkedin.com/in/rossana-de-angelis-2390b622

      Cette référence aurait été mieux structurée si elle avait été intégrée dans le module bibliographique.

    2. peut signifier qu’un texte est toujours tissé à un autre

      Vous auriez pu citer le principe d'hypertexte et Bush

    3. De Angelis, Rossana. 2018. « Textes et textures numériques. Le passage de la matérialité graphique à la matérialité numérique ». Signata. Annales des sémiotiques / Annals of Semiotics, nᵒ 9 (décembre):459‑84, paragraphe 45.↩

      à citer dans le corps de texte avec les indices bib

    4. Fontanille


    5. r La stratification du langage de Louis Hjelmslev

      référence nécessaire dans la bibliographie

    6. Thérenty, Laufer et Chartier,

      références nécessaires

    7. Textes et textures numériques écrit par Rossana De Angelis en 2018 est un article tiré de la revue Signata

      Les articles sont cités en règle générale entre guillemets et les revues en italique

    1. La grande conversion numérique

      il aurait été préférable de citer directement Doueihi ici

    2. Le numérique fait maintenant partie intégrante de notre existence.

      Vous auriez pu citer Vitali-Rosati ici, même si cette affirmation peut apparaître comme trop évidente, il vaut mieux toujours la référencer.

    3. Labelle, Sarah. 2009. « Milad Doueihi La grande conversion numérique , 2008, Seuil, Paris, 271 p. » Communication langages N° 160 (2):130‑30. https://www.cairn.info/revue-communication-et-langages1-2009-2-page-130.htm.↩


    4. Assouline, Pierre. 2012. « La métamorphose du lecteur ». Le Debat n° 170 (3):78‑89. https://www.cairn.info/revue-le-debat-2012-3-page-78.htm.↩

      Cette référence aurait due être éditée dans la suite de la phrase avec l'indice bib.

    5. (Le Crosnier, 2004), l’économie de l’attention (Simon, 1971), et le phénomène de la longue traîne (Anderson, 2007)

      Ces références auraient dues être intégrées dans la bibliographie et citées avec les indices bib.

    1. (

      il manque un espace entre le mot et l'indice bib.

    2. Les revues littéraires en ligne : entre éditorialisation et réseaux d’intelligence

      Pour citer un article, on le met en général entre guillemets afin de le différencier du nom de la revue qui est en italique

  7. Sep 2019
    1. D. Berman, A. Erdemir, A. V. Sumant, Carbon 59, 167–175 (2013)

      This study reports the tribological properties of graphene-lubricated 440C steel. At medium loads and under dry nitrogen environments, graphene is found to maximize its performance as a solid lubricant.

    2. Z. Liu et al., Phys. Rev. Lett. 108, 205503 (2012)

      This study details the first experimental evidence of reproducible superlubricity at the microscale under ambient conditions. The self retraction of graphite mesas upon shearing is described as a direct evidence of ultra-low friction between the incommensurate surfaces. The variation in superlubric conditions with contact area is also described. A similar observation is made in the current study as well.

    3. J. Cumings, A. Zettl, Science 289, 602–604 (2000)

      The authors demonstrate an experimental set up for finding friction between multi-walled nanotube layers using a nanomanipulator and insitu TEM imaging. Ultra-low friction is observed between the core and outer nanotube layers in a dry environment, which is similar to the superlubricity conditions in the present study.

    4. Y. Mo, K. T. Turner, I. Szlufarska, Nature 457, 1116–1119 (2009)

      The authors report bridging the gap between macroscale and nanoscale laws of friction. A linear relationship was found to exist between the friction force and contact area at both regimes. In the present study, authors also observed a similar phenomenon.

    5. M. Hirano, K. Shinjo, R. Kaneko, Y. Murata, Phys. Rev. Lett. 78, 1448–1451 (1997).

      This study reports measurements of friction as a function of commensurability of the contacting surfaces using ultra-high vacuum scanning tunneling microscopy. Authors have used atomically clean surfaces to experimentally check the superlubric conditions. They found a match between experimental results and theoretical predictions.

    6. C. Lee et al., Science 328, 76–80 (2010).

      This study compares the nanotribological properties of atomically thin sheets of 2D materials such as graphene, molybdenum disulfide, boron nitride, and niobium diselenide using friction force microscopy. The dependence of friction on the number of atomic sheets and substrate effect are also reported.

    7. A. Z. Szeri, Tribology: Friction, Lubrication, and Wear (Hemisphere, Panama City, Panama, 1980)

      This book provides an overview of the theory and practice of tribology, that is, the science of interacting surfaces in motion.

    1. 18. B. A. Stamoutsos, R. G. Carpenter, L. Grossman, S. P. Grossman, Physiol. Behav. 23, 771–776 (1979).

      The authors show that rats administered with 2-deoxy-D-glucose (2-DG) increase their food intake, whereas this is abolished in animals with ZI lesions. 2-DG is a modified glucose molecule that inhibits the breakdown of glucose, leading to low levels of blood glucose. This increases food intake in order to restore blood glucose levels. The reduced food intake in 2-DG-treated rats with ZI lesions suggests that the ZI is necessary for food intake in response to low blood glucose.

    2. 19. Y. Aponte, D. Atasoy, S. M. Sternson, Nat. Neurosci. 14, 351–355 (2011)

      This paper was one of the first to show that two populations of neurons in the arcuate nucleus of the hypothalamus have opposing effects on food intake. They demonstrated that opotogenetic activation of AgRP-expressing neurons increases food intake, whereas activation of POMC-expressing neurons decreases food intake.

  8. Aug 2019
    1. C. F. Dreyfus, K. A. Markey, M. Goldstein, I. B. Black, Dev. Biol. 97, 48 (1983)

      Dreyfus et al. used locus coeruleus, a region in the brain, to study neurotransmitter expression in brain. His group was able to show that the catecholamines can be expressed both in culture and in animals, making the locus coeruleus an excellent system to study the plasticity in brain.

    2. J. E. Adler and I. B. Black, Science, in press

      Given that the plasticity occurs during development, the authors tested whether the plasticity can be observed in mature neurons as well. The authors performed these experiments in the ganglia of young and old rats and assessed the changes in the neurotransmitter, substance P.

      Substance P had a significant increase in expression at young rats and at 6-month-old rats but not 2-year-old rats.

    3. G. M. Jonakait, K. A. Markey, M. Goldstein, I. B. Black, Dev. Biol. 101, 51 (1984)

      Jonakait et al. show that the loss of expression is not confined to the rat gut, but also observed in the cranial sensory and dorsal root ganglia of the embryonic rats. Here the authors have shown that the expression of catecholamine is lost for a certain time period during the development.

      These studies suggest that, irrespective of embryonic origin, the loss in expression of neurotransmitters, catecholamine, and noradrenergic occur during development.

    4. G. M. Jonakait, J. Wolf, P. Cochard, M. Goldstein, I. B. Black, ibid. 76, 4683 (1979)

      Jonakait et al. used the embryonic neural cells in the rat gut to understand the expression of noradrenergic cells.

      It was shown that these neural cells exhibit several characteristics of noradrenergic cells at embryonic stages. The authors wanted to know if there were a change in expression levels of noradrenergic during the development. For a certain time period during the development, the expression of noradrenergic is lost; however, the uptake system of norepinephrine is present and functional.

    5. P. H. Patterson, Annu. Rev. Neurosci. 1, 1 (1978)

      In this review, Patterson discusses how we can manipulate the neurons’ decision to produce certain chemicals by altering the environmental factors. This manipulation can be performed during development by changing the fluid or culture conditions in which the neurons are growing.

    6. T. Hokfelt, O. Johansson, A. Ljungdahl, J. M. Lundberg, M. Schultzberg, Nature (London) 238, 515 (1980)

      This review by T. Hökfelt et al. discusses the identification of new neurotransmitters that are peptidergic in nature. Peptidergic refers to the neurons that release small peptides as their neurotransmitters.

      The article provides a snapshot of peptidergic neurons identified in the nervous system, namely, the brain, spinal cord, and peripheral nervous system.

  9. Jul 2019
    1. 1. I. Voineagu et al., Nature 474, 380–384 (2011).

      In this paper by Voineagu et al., the authors found that there is lower enrichment of prefrontal genes in autistic brains, suggesting that there's dysregulation in this region.

  10. Jun 2019
    1. 20. T. Schmader, M. Johns, M. Barquissau, Sex Roles 50, 835 (2004).

      Schmader, Johns, and Barquissau found that the level of endorsement of the stereotype that men are better than women at math was a moderating variable for gender performance.

      Women who more strongly endorsed the stereotype performed worse.

    2. 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.

    3. 30. A. Martens, M. Johns, J. Greenberg, J. Schimel, J. Exp. Soc. Psychol. 42, 236 (2006).

      Martens et al. showed that values affirmation was effective under laboratory conditions.

    4. 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.

    5. 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 tested whether a simple intervention could reduce the effects of stereotype threat for African American students. 

      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.

    6. 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 seventh-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.

    7. 13. M. Lorenzo, C. Crouch, E. Mazur, Am. J. Phys. 74, 118 (2006).

      Using more interactive teaching methods has been shown to improve conceptual understanding for students in college-level physics compared to traditional lecture-based teaching.

      Interactive teaching has also been shown to reduce the gap in performance between women and men.

    8. 6. S. J. Pollock, N. D. Finkelstein, L. E. Kost, Phys. Rev. Spec. Top. Phys. Ed. Res. 3, 010107 (2007).

      Kost, Pollock, and Finkelstein performed the initial assessment of the gender achievement gap in college students taking introductory physics at the University of Colorado at Boulder.

      They found that most (but not all) of the gender achievement gap, could be attributed to previous preparation in the field.

    9. 21. T. Schmader, M. Johns, C. Forbes, Psychol. Rev. 115, 336 (2008).

      Schmader, Johns, and Forbes suggest that stereotype threat might affect women's performance through three interconnected mechanisms:

      1) It causes a physical stress response that can impair some aspects of brain function, reducing the baseline level of mental resources.

      2) It causes women to actively monitor their performance, taking valuable mental resources away from the assigned task.

      3) It causes women to actively repress negative feelings and thoughts, which also consumes mental resources.

    10. 18. S. J. Spencer, C. M. Steele, D. M. Quinn, J. Exp. Soc. Psychol. 35, 4 (1999).

      Spencer, Steele, and Quinn performed some of the original experiments showing that the stereotype that men are better at math than women affected women's performance on math tests.

    1. J. A. Kessler, J. E. Adler, M. C. Bohn, I. B. Black, Science 214, 335 (1981); J. A. Kessler, J. E. Adler, W. O. Bell, I. B. Black, Neuroscience 9, 309 (1983)

      In these studies, the authors examined the role of the neurotransmitter substance P in nerve ganglia. The authors confirmed that the activity of substance P is dependent on sodium currents, changes within the cell, and impulsive activity.

    1. D. B. Kandel, Stages and Pathways of Drug Involvement: Examining the Gateway Hypothesis (Cambridge Univ. Press, Cambridge, UK, 2002), pp. 3–15

      The book chapter introduces the concept of gateway hypothesis – a model to inform how teenagers initiate and progress in the usage of illicit drugs. The chapter addresses these crucial questions from various fronts – neurobiology, animal studies, and epidemiological studies.

    2. F. E. Pontieri, G. Tanda, F. Orzi, G. Di Chiara, Effects of nicotine on the nucleus accumbens and similarity to those of addictive drugs. Nature 382, 255–257 (1996).

      The article addresses a fundamental question: is nicotine a habit-forming drug or an addictive drug? The authors performed experiments in mice and concluded that nicotine shares several biological aspects with the drugs of abuse.

    3. J. A. Kauer, R. C. Malenka, Synaptic plasticity and addiction. Nat. Rev. Neurosci. 8, 844–858 (2007)

      The review presents the available evidence that the drugs of abuse can alter the synaptic plasticity mechanisms in the dopaminergic circuit, the key pathway to processing reward in the brain.

    4. A. Kumar, K. H. Choi, W. Renthal, N. M. Tsankova, D. E. Theobald, H. T. Truong, S. J. Russo, Q. Laplant, T. S. Sasaki, K. N. Whistler, R. L. Neve, D. W. Self, E. J. Nestler, Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron 48, 303–314 (2005)

      The authors show that the cocaine, a drug of abuse, can activate genes at core histones, which can lead to a restructuring of chromatin. This restructuring could have an effect on long-lasting changes in the animal, for instance, modulating the body movements

    5. A. A. Levine, Z. Guan, A. Barco, S. Xu, E. R. Kandel, J. H. Schwartz, CREB-binding protein controls response to cocaine by acetylating histones at the fosB promoter in the mouse striatum. Proc. Natl. Acad. Sci. U.S.A. 102, 19186–19191 (2005).

      The authors show that the cAMP response element binding protein (CREB)-binding protein (CBP) acetylate histones at the FosB promoter in the mouse striatum, thereby regulating the responses to cocaine.

      The authors confirmed this finding by repeating this experiment in mice lacking a copy of the CBP gene. These mice exhibited a decrease response to cocaine than the animals that had an intact copy of the CBP gene.

    1. R. T. Paine, Am. Nat. 103, 91 (1969)

      In this letter, Paine notes the importance of predators to community stability not only to the system that he studied (the intertidal of the Pacific Northwest) but also that of other simple or complex systems worldwide.

    2. J. A. Estes, D. O. Duggins, Ecol. Monogr. 65, 75 (1995).

      In this observational study of 153 sites, over the course of 3-15 years, the importance of sea otters to the community structure of the kelp forests of the Aleutian Islands and Alaska. Without sea otters, the kelp forests collapsed due to overgrazing by urchins and other herbivores, leading to implications for numerous other organisms in the system. With sea otter predation on urchins, the kelp system was stable and supported a much higher diversity of organisms at all trophic levels (Fig 3).

    3. R. T. Paine, J. Anim. Ecol. 49, 667 (1980)

      A discussion of food webs, trophic relationships, species connectedness, and whether community structure and stability could be modeled based on these ideas.

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

      In this natural experiment, 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 with drastic trophic cascades observed.

    5. N. G. Hairston, F. E. Smith, L. B. Slobodkin, Am. Nat. 94, 421 (1960)

      The authors highlight 5 lines of reasoning to underscore the importance of predators as top-down controls:

      1) the rate of planetary fossil fuel accumulation over time has not been minuscule as compared to the rate of photosynthesis in the same systems;

      2) given this, decomposers must be food-limited otherwise fossil fuels would build up at higher rates;

      3) in terrestrial systems, plants are typically not herbivore-controlled nor are they regularly destroyed by weather but are controlled by bottom-up factors such as light, water, and nutrients;

      4) terrestrial herbivores are therefore typically not limited by their food supply, even in areas where the primary consumers are overabundant;

      5) herbivore populations are therefore controlled by predators.

    6. M. E. Power, W. J. Matthews, A. J. Stewart, Ecology 66, 1448 (1985)

      This seminal paper on the indirect effects of predation in freshwater rivers demonstrated that the trophic cascades previously seen in marine and terrestrial systems also held true for river ecosystems.

  11. May 2019
    1. K. M. Kendrick, M. R. Hinton, B. A. Baldwin, Brain Res. 550, 165–168 (1991).

      Kendrick and colleagues measured GABA in the ZI in live sheep. They found that in food-deprived animals, GABA was increased in the ZI upon the sight and ingestion of food. This response did not occur when a non-food object was presented.

    2. 13. J. S. Lee, E. Y. Lee, H. S. Lee, Brain Res. 1598, 97–113 (2015).

      The authors performed retrograde mapping from the PVT and showed that neurons in the ZI directly project to the PVT. These cells were shown to express the protein cocaine- and amphetamine-related transcript (CART).

    1. F. H. C. Crick, L. Barnett, S. Brenner, R. J. Watts-Tobin, Nature 192, 1227 (1961)

      In this seminal Nature paper, Crick and co-workers demonstrate that a group of three bases codes for one amino acid; the code does not overlap; the sequence of bases is read from a fixed starting point; and the code is degenerate.

    2. F. H. C. Crick, in Progress in Nucleic Acid Research, J. N. Davidson and Waldo E. Cohn, Eds. (Academic Press, New York, in press).

      This review paper is an extended version of the paper you've read here with sections dedicated to similar questions such as: "Is the code universal?" and "Is the code overlapping?"

    3. G. von Ehrenstein and F. Lipmann, ibid. 47, 941 (1961)

      Von Ehrenstein and Lipmann demonstrate the genetic materials of a rabbit (a mammal) and E. coli (a bacterium) are compatible, suggesting the genetic code is universal!

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

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

    2. 23. P. R. Grant, B. R. Grant, Biol. J. Linn. Soc. London 117, 812–822 (2016).

      Introgression, the movement of a gene from one species into the gene pool of another, has been known to speed up a population's response to an evolutionary selective pressure. It does this by increasing genetic diversity.

      Grant and Grant documented recurring introgressive hybridization between medium ground finches and small ground finches.

    3. 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.

    4. 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 in dwarfism. This protein is associated with the HMGA2 gene.

    5. 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.

    6. 3. W. L. Brown Jr., E. O. Wilson, Syst. Zool. 5, 49–64 (1956).

      Brown and Wilson (1956) argued that character displacement was a common part of geographical speciation. They explained that displacement happened most often as a product of genetic and ecological interaction when species first met.

    7. 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. maguirostris. This divergence happened on an isolated Galapagos island 22 years after G. maguirostris arrived to share a habitat with G. fortis.

    8. 13. P. R. Grant, B. R. Grant, Evolution 48, 297–316 (1994).

      Grant and Grant (1994) explored hybridization among finch species over 17 years. They concluded that hybrid traits were morphologically intermediate, which indicated the parent genes contributed to the offspring phenotype equally. Hybrids also varied more phenotypically.

    9. 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 while 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.

    10. 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.

    1. 20. Y. Zheng, C. Lorenzo, P. A. Beal, Nucleic Acids Res. 45, 3369–3377 (2017)

      The authors showed that ADAR proteins were able to deaminate adenosines not only in RNA duplexes but also in RNA-DNA heteroduplexes.

      While this work was done in vitro, it may help understand the functions of ADAR in the cell, specifically the link between ADAR impairment and the autoimmune disease Aicardi-Goutieres Syndrome (AGS). Also it may be used as a new tool for DNA editing techniques.

    2. 10. O. O. Abudayyeh et al., Science 353, aaf5573 (2016).

      A large group of scientists from several labs conducted an extensive study on the protein C2c2 (now known as Cas13a). They demonstrated that C2c2 was an RNA-guided RNA nuclease and predicted that it would be an important tool for RNA targeting.

      Moreover, they showed that in vitro C2c2 once activated by the target binding could cleave not only the target but also the surrounding mRNA molecules. The authors termed this effect "the collateral cleavage."


    1. A. Erdemir, C. Donnet, J. Phys. D Appl. Phys. 39, R311–R327 (2006).

      This review outlines the synthesis, characterization, and applications of DLC films. The mechanism of friction and wear behaviors of DLC films and the conditions to achieve superlubricity are reported.

  12. Apr 2019
    1. M. Eddaoudi et al., Science 295, 469–472 (2002)

      A systematic study on the influence of the organic linkers on the pore properties of a metal-organic framework. In this work, the authors use the same metallic cluster as a base and demonstrate how the small molecule linkers can be functionnalized to tune its properties.

    1. M. P. Baldwin et al., Geophys. Res. Lett. 21, 1141 (1994).

      Baldwin et al. described the relationship between the stratosphere and the troposphere. Changes to stratospheric circulation can, in turn, affect tropospheric weather patterns. This study notes that the North Atlantic Oscillation (NAO) was the pattern most strongly related to wintertime changes in stratospheric temperatures and circulation.

    2. D. T. Shindell et al., Nature 399, 452 (1999).

      Shindell et al. described the importance of modeling stratospheric atmosphere dynamics to improve predictions of global climate conditions. They also determined that it was possible to program climate models to simulate climate patterns like the Arctic Oscillation when including greenhouse gas concentrations. This suggested that greenhouse gases can influence regional climates.

    3. R. W. Reynolds and T. S. Smith, J. Clim. 7, 929 (1994)

      This was a pivotal paper in helping to develop a method of correcting satellite temperature data. By using satellite measurements over the early 1990s during the time of the Mount Pinatubo eruption, Reynolds and Smith were able to factor out the volcanic aerosols for a more accurate measurement of global temperatures.

    4. R. Dickson, J. Lazier, J. Meincke, P. Rhines, J. Swift, Prog. Oceanogr. 38, 241 (1996).

      This paper reviews the recent history of North Atlantic changes in convection and deep water formation. Waters are mixed downwards in the Greenland and Labrador Seas, but this study found that these locations are currently at opposite convective extremes.

      The authors proposed that atmospheric forcings (such as the North Atlantic Oscillation) are influencing the location and quantity of water sinking into the deep ocean.

    5. J. R. N. Lazier, in Natural Climate Variability on Decade-to-Century Time Scales, D. G. Martinson et al., Eds. (National Academy Press, Washington, DC, 1995), chap. 3, pp. 295–302

      "Approaches to studying the ocean's role in climate can be divided into two types: understanding and modeling the ocean as part of the fully coupled climate system, and observing, quantifying, and modeling the dynamics of the ocean itself."

      This comes from Lazier's chapter "The Oceans" in the book Natural Climate Variability on Decade-to-Century Time Scales, available online: https://www.nap.edu/read/5142/chapter/5#234

    6. K. Hasselmann, R. Sausen, E. Maier-Reimer, R. Voss , Clim. Dyn. 9, 53 (1993)

      One of the elements of a global climate model is a simulation of CO<sub>2</sub> circulation.  However, models that begin in pre-industrial times include so much data that computers take a long time to complete the simulation. To decrease processing time, scientists sometimes set the start date of the simulation later, but this introduces error into the model. The authors of this paper found a way to account for this error (called the "cold-start" error) and discussed the implications for the climate models used by the IPCC. 

    7. S. Levitus , J. Geophys. Res. Oceans 94, 6091 (1989)

      Levitus had previously performed a very similar study that focused on the temperature and salinity of the North Atlantic. More measurements have been collected since this study in 1989, making it possible to examine more of the world's oceans and to update the scientific understanding of what was going on in the North Atlantic.

    8. T. Nitta, S. Yamada, J. Meteorol. Soc. Jpn. 67, 375 (1989)

      Nitta and Yamada used global ocean temperature data to discover that, since the late 1970s, surface temperatures were rising in the tropics, particularly in the eastern Pacific and the Indian Ocean. Their research suggests the changes in ocean temperature may have contributed to a change in climate patterns, affecting the Pacific-North American in particular.

    9. J. I. Antonov , J. Clim. 6, 1928 (1993)

      Antonov investigated temperature changes in the North Atlantic and North Pacific oceans within the depth range of 300 to 3000 meters over the years 1957–1981.

      He found that, while the North Pacific did not change temperature in deeper areas, it cooled between 300 and 500m. On the other hand, over the same period, North Atlantic ocean temperatures increased in the 800 to 2500 meter layer.

    1. Y. Guo, W. Guo, C. Chen, Phys. Rev. B 76, 155429 (2007)

      This study investigates theoretically, the dependence of superlubricity on interlayer distance between graphene sheets and atomic defects on graphene for both commensurate and incommensurate configurations.

    2. D. Berman, A. Erdemir, A. V. Sumant, Carbon 54, 454–459 (2013)

      This earlier study by the current authors identifies and reports the potential of graphene layers in reducing friction and wear at the tribological interface of steel in air.

    1. I. Martínez et al., Cell Rep. 11, 527–538 (2015).

      Martinez and colleagues compared the gut microbiome of individuals from Papua New Guinea and the United States. Individuals from Papua New Guinea had greater bacterial diversity and abundances, suggesting that industrialization may have an impact on the gut microbiome and, consequently, human health.

    2. J. K. Goodrich et al., Cell 159, 789–799 (2014).

      Goodrich and colleagues compared the gut microbiomes from individuals in the TwinsUK population and found that there is a correlation between the host genetics, metabolism, and gut microbiome.

    3. T. Yatsunenko et al., Nature 486, 222–227 (2012).

      Yatsunenko and colleagues sequenced the gut microbiome of three vastly different populations and found that there were pronounced differences between individuals from the United States than from Venezuela or Malawi. They suggest that the gut microbiome may be impacted by human development and Westernization.

    4. F. H. Karlsson et al., Nature 498, 99–103 (2013).

      Karlsson and colleagues characterized the fecal microbiota of European women and found that predictive tools for type-2 diabetes-associated markers could be useful if the age and location of the individual is accounted for.

  13. Mar 2019
    1. 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 its hybridization's role in speciation is somewhat limited.

    2. R. J. Abbott, N. H. Barton, J. M. Good, Mol. Ecol. 25, 2325-2332 (2016).

      Abbott et al. summarize why studying hybridization is important to evolutionary biologists, and how the genomic data now available can help scientists better understand the mechanisms of speciation and the particular genes responsible for maintaining hybrids as separate populations.

      The authors indicate that homoploid hybrid speciation, while theoretically possible, has few strongly supported examples and there is little detail known about how it works. This helps us understand why this research paper is so important and interesting.

    1. 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.

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

      The authors engineered the NpHR from 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.

    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. E. S. Boyden, F. Zhang, E. Bamberg, G. Nagel, K. Deisseroth, Nat. Neurosci. 8, 1263 (2005).

      The first paper describing the algal protein, Channelrhodopsin-2, which was successfully cloned and expressed into mammalian neurons. The authors performed electrophysiological recordings of neurons expressing an opsin and measured the spiking activity.

    1. E. J. Furshpan, P. R. MacLeish, P. H. O'Lague, D. D. Potter, Proc. Natl. Acad. Sci. U.S.A. 73, 4225 (1976)

      In this study, Furshpan et al. were interested in identifying the neurotransmitter that is being released in response to different liquids or drugs. His group noted that neurons release acetylcholine, catecholamine or both in response to the drugs.

  14. Feb 2019
    1. N. Gold, A. M. Colman, B. D. Pulford, Judgm. Decis. Mak. 9, 65–76 (2014).

      This study asked Chinese and U.K. citizens if an individual should be sacrificed to save many.

      Chinese participants were less willing to sacrifice the lone individual, and were less likely to think that it was the more moral choice.

    2. J. A. C. Everett, D. A. Pizarro, M. J. Crockett, J. Exp. Psychol. Gen. 145, 772–787 (2016).

      This paper found a general pattern across all its different studies—that people who decide that something is moral based on rules are considered more trustworthy.

      This paper thus supports the idea that the methods used in "The social dilemma of autonomous vehicles" provide a representative view of the U.S. population, even though the respondents themselves might not entirely represent people in the U.S.

    1. 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 the late 1938-9, 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.

    2. 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.

    3. 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.

    4. 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 2004-5.

    5. P. R. Grant, B. R. Grant, Proc. Natl. Acad. Sci. U.S.A. 106, 20131-20148 (2009)

      In this paper, Grant and Grant report the establishment of the Big Bird lineage and discuss the mechanisms of reproductive isolation that exist for its population.

    6. 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 occured and the mechanisms that underpin the formation of different species of finches in the Galapagos Islands.

    7. B. R. Grant, P. R. Grant, 40 Years of Evolution: Darwin's Finches on Daphne Major Island (Princeton Univ. Press, 2014)

      This book summarizes the evidence for evolution gathered over the entire research project on Daphne Major that the Grants led. It concludes that natural selection occurred repeatedly during that time, and that competition for food in times of drought drove that evolution.

    8. 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 establishments of hybrids.

    9. 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 effect of the exchange of genes 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.

    10. A. W. Nolte, D. Tautz, Trends Genet. 26, 54-58 (2010).

      Nolte and Tautz discuss homoploid hybrid speciation and indicate that there is a need to understand the mechanisms involved in this type of speciation. They argue that the best way to examine these mechanisms is through observing hybrid populations that may or may not be on their way to forming new species, either in natural situations or in experiments.

    11. 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.

    1. From our annotated research papers to our trainings and workshops, we're dedicated to bridging the communication gap between scientists and everyone else.

      Beth, Shelby, and I will be in the AAAS Lounge starting at 10am on Friday.

  15. Jan 2019
    1. 28. K. A. Lehmann, B. L. Bass, Biochemistry 39, 12875–12884 (2000)

      The authors of this work investigated and described the activity of the human ADAR1 and ADAR2 deaminases.

      They showed that ADAR proteins had certain sequence preferences, including the nucleotides around the target and the position of the target relative to the RNA duplex ends. Additionally, they determined that ADARs did not edit all accessible adenosines. That implied these proteins possessed some specificity with unknown mechanism.

    2. 22. S. K. Wong, S. Sato, D. W. Lazinski, RNA 7, 846–858 (2001).

      This paper demonstrated that ADAR deaminases preferentially edit adenosine bases that are mismatched with a cytidine.

    3. 21. A. Kuttan, B. L. Bass, Proc. Natl. Acad. Sci. U.S.A. 109, E3295–E3304 (2012).

      The authors of the paper mutated the ADAR2 protein and, by screening of multiple mutants, identified the E488Q variant that could edit adenosine in all possible triplet targets.

    4. 16. K. Nishikura, Annu. Rev. Biochem. 79, 321–349 (2010).

      A comprehensive review on research into ADAR proteins.

    5. 15. O. O. Abudayyeh et al., Nature 550, 280–284 (2017).

      The authors of this study showed that the Cas13a protein was comparable to RNAi in its efficiency at knocking down RNA, but has superior specificity.

      They also generated a catalytically dead Cas13a and demonstrated that it retained RNA-binding properties. This dCas13a was successfully used for RNA tracking.

      Finally, the authors did not observe cleavage at sites surrounding the target (collateral cleavage) with Cas13a in mammalian cells. This was extremely important as it suggests the nuclease can be safely used to target specific sites without major adverse effects.

    6. 14. J. S. Gootenberg et al., Science 356, 438–442 (2017).

      The authors of the paper presented a new application of the CRISPR-based tools as diagnostic devices. They created a technique called SHERLOCK (Specific High-Sensitivity Enzymatic Reporter UnLOCKing) which was able to detect very small amounts of disease-causing viruses and bacteria, as well as mutations in human DNA.

    7. 9. Y. B. Kim et al., Nat. Biotechnol. 35, 371–376 (2017).

      The same group of researchers that developed the first DNA base editor (7) improved the complex's specificity and expanded its ability to target.

      They improved specificity by making the targeting window smaller, and expanded its ability to target different sequences by fusing the complex to Cas9 proteins that use different PAM sequences.

    8. 7. A. C. Komor, Y. B. Kim, M. S. Packer, J. A. Zuris, D. R. Liu, Nature 533, 420–424 (2016)

      The authors of the study suggested an alternative strategy to genome editing that doesn't use DNA breaks and donor templates. They created a DNA base-editor complex composed of a mutant Cas9 and a cytidine deaminase APOBEC1. This complex was able to convert all C-G pairs into T-A within a narrow targeting window. However, it required additional modules to control the editing.

    9. 8. K. Nishida et al., Science 353, aaf8729 (2016).

      This group of scientists created a DNA base editor consisting of Cas9 and the cytidine deaminase PmCDA1. Similar to other work (7), this editor modified all cytidines in a target window and required an additional protein module for the control of editing.

    1. 17. A. G. Davies, J. C. Bettinger, T. R. Thiele, M. E. Judy, S. L. McIntire, Neuron 42, 731 (2004).

      First paper to establish the relationship between NPF in C. elegans and sensitivity to the effects of ethanol.

    2. 16. T. Wen, C. A. Parrish, D. Xu, Q. Wu, P. Shen, Proc. Natl. Acad. Sci. U.S.A. 102, 2141 (2005).

      First paper to establish the relationship between NPF in fruit flies and sensitivity to the effects of ethanol.

    3. 14. R. S. Hewes, P. H. Taghert, Genome Res. 11, 1126 (2001).

      A comprehensive analysis of the various genes in the Drosophila that pertain to the vast majority of—if not all—neuropeptides and their receptors.