137 Matching Annotations
  1. May 2019
  2. Apr 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 awake 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.

  3. Mar 2019
    1. 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 while activation of POMC-expressing neurons decreases food intake.

    2. 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 while 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.

    3. 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. 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.

    1. She felt out of place.

      Ей было не по себе.

    2. for starters orders

      сигналов стартеров

    3. Of course, we've had our ups and downs

      Конечно, у нас бывало то лучше, то хуже

    4. processed kind

      консервированный

    5. Jean put the ruler down on the conveyor belt.

      Джин положила линейку на конвейер. (Прим.: В западных супермаркетах для экономии времени несколько покупателей выгружают продук­ты на конвейер одновременно. Для того, чтобы кассир видела, где граница, покупатели кладут пластиковую линейку яркого цвета между своими и чужими покупками.)

    6. Think of all the oriental foods you can get into

      Как по­думаешь, каких только ни бывает восточных продуктов

    7. her individual yoghurt seemed to say it all

      казалось, что её единственная упаковка йогурта говорит сама за себя.

    8. a gross offish fingers

      оптовая закупка рыбных па­лочек

    9. You can always tell a person by their shopping

      Всегда можно определить, что за человек перед тобой, по его покупкам

    10. when I turned up?

      когда я бы вдруг пришла?

    11. a see-through tray of tomatoes which fell casualty to the rest.

      прозрачный лоток с помидорами, придавленный другими покупками.

    12. the quick till

      касса-экспресс

    13. Jean felt her patience beginning to itch.

      Джин чувствовала, что её терпение заканчивается.

    14. giving an accompaniment of nods and headshaking at the appropriate parts.

      в такт словам то кивала, то качала го­ловой.

    15. why I should have to put up with her at family occasions.

      с какой стати я должна мириться с её присутствием на се­мейных праздниках.

  4. Feb 2019
    1. RSA ANIMATE: Drive: The surprising truth about what motivates us

      Notes from Video -Group of students and gave them a set of challenges- to incentivize their performance 3 levels of rewards- High, middle, and lower levels of rewards -mechanical skills- bonuses worked as expected- higher pay brought better performance -rudimentary cognitive skills- larger reward led to poorer performance-rewards don't work that way once you get to rudimentary cognitive skills- defies laws of behavioral physics -did the experiment in india- small rewards (2 weeks salary) medium rewards (1 months salary) highest reward (2 months salary)- Higher incentive led to worse performance -replicated over and over again- simple straight forward tasks- rewards work

      • when task get s more complicated and it requres some conceptual, creative thinking- rewards don't work -3 factors lead to better performance- (autonomy)- self direction is better- (mastery)- getting better at stuff- (purpose)- need to have a reason for doing something -more organizatoins want to have a purpose- not money or profit- -if we start treating people like people- we can build organizations to make the world a little better
    1. Understanding by Design

      Notes

      • -prepare you to think in the short-term and long-term teaching
      • -student comment as an entry point on where we want to end up
      • -proactive, autonomous learners
      • -a planning framework
      • -critical and creative thinking- you don't need these skills to make all A's in school
      • -pedagogical effectiveness
      • -critical thinking test- NO GAIN
      • -long-term goals and short-term plan
      • -desired and actual results
      • -strategic thinking- teachers that tell you what to do all the time- doesn't make room for student thought
      • -when we teach, we need to be more goal focused (comment)
      • backward design thinking- long term goal- what follows for assessment (not grading, assessing/ judging how we are doing against the goal, coaching) and what follows for instruction
      • What do we have to do to make our students love what we are teaching them?
      • the textbook is not the course- only used as a resource
      • given our understanding goals, which chapters should be highlighted, skimmed, skipped, re-sequenced?
      • aim for explicit understanding
      • Backward from Goals: Meaning-"I want students to leave having inferred/realized that, now and in the future..."
      • Background from Goals: Transfer - "I want students to leave able to transfer their understanding- on their own- to concrete address current and future situations
      • 3rd day of lesson- textbook is used (not on the first day)
      • the way we do math is bad- this is why people don't like math or they think that they are bad at math- backward design lesson planning expands the pool of interested parties and is differentiatable for individual students
      • it is our jobs as teachers to make the design of the lesson relatable to every student- we are given this backward design plan but we must figure out how to plan our lesson to make sure that every child is learning- DESIGN CHALLENGE
      • Intellectual engagement- finding ways to help students that are uninterested in the content to want to be engaged in the content
      • Incentivize- incentives to learning the information
  5. Jan 2019
    1. they are not meant to be substituted for a recollection that may fail. They constitute, rather, a material and a framework for exercises to be carried out frequently: reading, rereading, meditating, conversing with oneself and with others.

      Looking at one's academic notes in this sense, what if students were taught from a young age to view their notes and note taking as a continuous process which required frequent study and conversation? Even in college, students often only refer to notes as a means of remembering a specific fact, statement or concept.

    1. Artificial Neural Networks

      三大板块:Hopfield 网络+ 监督学习+非监督学习

    1. Measurements are variables that can be quantified. All data in the output above are measurements. Some of these measurements, such as state_percentile_16, avg_score_16 and school_rating, are outcomes; these outcomes cannot be used to explain one another. For example, explaining school_rating as a result of state_percentile_16 (test scores) is circular logic. Therefore we need a second class of variables.
  6. Sep 2018
    1. Create a note by selecting some text and clicking the butto

      Här skriver jag "note" alltså en annotering, kommentarer och feedback till studenten.

  7. Jun 2018
    1. N. G. Hairston, F. E. Smith, L. B. Slobodkin, Am. Nat. 94, 421 (1960)

      The authors highlight 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.

    2. 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.

    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. 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).

    5. 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.

  8. Dec 2017
    1. followed by failure to interbreed when partial connection between the oceans was reestablished

      Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.

    2. Hence, pairs P5-C5 and P6-C6 probably separated during the period of marked shoaling and environmental divergence preceding final closure.

      P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.

    3. 1. E. Mayr, Animal Species and Evolution (Harvard Univ. Press, Cambridge, 1963).

      This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.

    4. D. S. Jordan, Am. Nat. 42, 73 (1908)

      Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.

    5. J. A. Coyne and H. A. Orr, Evolution 43, 362 (1989). W. R. Rice, ibid., p. 223.

      The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)

    6. D. L. Swofford, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1; (Illinois Natural History Survey, Champaign, IL, 1993).

      The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)

    7. J. H. Gillespie, The Causes of Molecular Evolution (Oxford Univ. Press, New York, 1991).

      The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)

    8. Genetic divergence before final closure may have been facilitated by changing oceanographic conditions

      Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)

    1. J. E. K. Byrnes, L. Gamfeldt, F. Isbell, J. S. Lefcheck, J. N. Griffin, A. Hector, B. J. Cardinale, D. U. Hooper, L. E. Dee, J. E. Duffy, Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions. Methods Ecol. Evol. 5, 111–124 (2014).

      Byrne's review focuses on the impacts of assemblage diversity on ecosystem functions.

      This study acknowledges the impact of diversity on resource utilization and thus productivity, however the focus is on the characterization of multi-functionality.

    2. C. Fissore, J. Espeleta, E. A. Nater, S. E. Hobbie, P. B. Reich, Limited potential for terrestrial carbon sequestration to offset fossil-fuel emissions in the upper midwestern US. Front. Ecol. Environ. 8, 409–413 (2010).

      Fissore's review argues that carbon sequester by forests in the mid-west can not off set fossil fuel based carbon dioxide emissions. The study compares hypothetical scenarios necessary to offset significant proportions of the carbon dioxide emissions by converting landscapes into carbon sequestering species.

    3. R. F. Follett, Soil management concepts and carbon sequestration in cropland soils. Soil Tillage Res. 61, 77–92 (2001).

      Follett discusses the role organic soils play in the movement of carbon dioxide from the atmosphere to the soil. This review characterizes terrestrial soils as carbon sinks which is important for crop management.

    4. P. B. Reich, D. Tilman, S. Naeem, D. S. Ellsworth, J. Knops, J. Craine, D. Wedin, J. Trost, Species and functional group diversity independently influence biomass accumulation and its response to CO2 and N. Proc. Natl. Acad. Sci. U.S.A. 101, 10101–10106 (2004).

      Reich compares the role of CO2 and N on species richness and functional group diversity.

      This study compares the roles of functional group diversity and species richness has on biomass accumulation in an elevated carbon dioxide and nitrogen environment.

    5. R. Sedjo, B. Sohngen, Carbon sequestration in forests and soils, in Annual Review of Resource Economics, G. C. Rausser, Ed. (Annual Reviews, Palo Alto, 2012), vol. 4, pp. 126–143

      Sejo discusses the role species richness plays in effecting economic value.

      This review puts emphasis on the role of biodiversity on marginal economic value represented as carbon storage for conservation efforts.

    6. D. A. Fornara, D. Tilman, Plant functional composition influences rates of soil carbon and nitrogen accumulation. J. Ecol. 96, 314–322 (2008).

      Fornara reviews the mechanisms that control carbon and nitrogen accumulation in soils.

      The review covers the relationships between biodiversity and carbon and nitrogen accumulation in soils, with an emphasis on the c3 and c4 grasses.

    7. T. L. Daniels, Integrating forest carbon sequestration into a cap-and-trade program to reduce net CO2 emissions. J. Am. Plann. Assoc. 76, 463–475 (2010).

      Daniels reviews the role forests play in reducing atmospheric carbon dioxide levels. His focus however is primarily advocating for including carbon sequester by forests into management plans or a cap-and-trade program.

    8. A. D. Barnosky, N. Matzke, S. Tomiya, G. O. U. Wogan, B. Swartz, T. B. Quental, C. Marshall, J. L. McGuire, E. L. Lindsey, K. C. Maguire, B. Mersey, E. A. Ferrer, Has the Earth's sixth mass extinction already arrived? Nature 471, 51–57 (2011).

      Barnosky discusses the events known as mass extinctions and compares the rates of extinction for these events to modern rates of extinction. PB

    9. Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2.

      Each additional degree of species richness is worth less than the previous degree of richness in terms of economic value. Therefore, the economic value does not increase in direct proportion with the species richness, although they are correlated.

      SC

    10. B. J. Cardinale, K. L. Matulich, D. U. Hooper, J. E. Byrnes, E. Duffy, L. Gamfeldt, P. Balvanera, M. I. O'Connor, A. Gonzalez, The functional role of producer diversity in ecosystems. Am. J. Bot. 98, 572–592 (2011).

      Cardinale reviews the roles of primary producer biodiversity with respect to ecological processes critical to the functionality and health of terrestrial and marine ecosystems. PB

    1. predicted secondary structure

      Villordo and peers (2015) studied the cycle of how mosquito viruses could quickly adapt to different human host environments. The changes in RNA structures were examined in the dengue virus during host adaptation. The researchers discovered that the 3’UTR of RNA is modified during host adaptation, such as duplicating the structure to accommodate for beneficial mutations.

    2. Musashi-1

      Sakakibara and peers studied the Musashi-1 protein within a mouse and associated the protein with neural development. Musashi-1 was found to be highly enriched within the central nervous system of mammalian cells, regulate stem cell translation, and can differentiate into neurons through regulation.

    3. interferes specifically with fetal brain development

      Li and others (2016) hypothesized that ZIKV can infect not only developing neuronal stem cells, but also adult brain cells. The results seen were that adults can be affected by the ZIKV. The adult would need to be triply deficient in the regulatory factor for interferon to allow the virus to take hold of the stem cells in the brain.

    4. interferes specifically with fetal brain development

      Li and others (2016) hypothesized that ZIKV can infect not only developing neuronal stem cells, but also adult brain cells. The results seen were that adults can be affected by the ZIKV. The adult would need to be triply deficient in the regulatory factor for interferon to allow the virus to take hold of the stem cells in the brain.

    5. effect on fetal neurodevelopment

      Cugola et al., (2016) found that ZIKV infects fetuses, causes intrauterine growth restriction (IUGR), and causes signs of microcephaly in mice. Data demonstrated that the infection of ZIKV into human brain organoids reduced proliferation and disrupted cortical layers. This indicates that ZIKV is able to cross the placenta and cause microcephaly by inducing apoptosis in cortical progenitor cells.

  9. Nov 2017
    1. it in-creases hyperexcitability in Abprecursor protein(APP) transgenic mice

      Side effects of phosphorylation

    2. n-hibition of p38aand p38bimproves Ab-induced

      inhibition may have a short term positive effect

    3. Accordingly, the depletion of tau prevents Abtoxicity in AD models (7–9). Ab-induced neuronalnetwork and synaptic dysfunction is associatedwith aberrant glutamatergic synaptic transmis-sion (10).N-methyl-D-aspartate (NMDA)–typeglutamatergic receptors (NRs) drive glutamate-induced neuronal excitotoxicity (11)andmediateAbtoxicity by downstream responses that pro-mote neuronal dysfunction (12

      The steps that tau tangles interfere with in the transmittance of signals in the brain.

    4. Aberrant tau phosphorylation is the firststep in a cascade leading to its deposition and tocognitive dysfunction (4,5). Abis thought to trig-ger toxic events, including tau phosphorylation

      steps and relevance to Alzheimer's disea

    1. Long-term nutrient enrichment decouples predator and prey production

      This article discusses the effect the addition of nutrients has on an aquatic ecosystem. Originally the author hypothesized an increase of energy transfer from prey to predators because of the increase of nutrients. However, this did not occur because the increase in nutrient led to an increase of predator resistant prey.

    2. Stream nutrient enrichment has a greater effect on coarse than on fine benthic organic matter

      This article discusses how an increase in nutrients affects the levels of coarse and fine organic litter. It was observed that there were higher levels of fine organic material which led to an increase in bacteria. However, in the stream with no nutrients added to it, there was an increase in both fungal and bacterial communities.

    3. Nutrient enrichment alters storage and fluxes of detritus in a headwater stream ecosystem

      This article demonstrates how the addition of nitrogen and phosphorus led to an increase in the production of fine organic compound by more than 300%. The article also mentions that this increase in fine organic compound will have an effect on the entire ecosystem in that area in the long term.

    4. Multiple trophic levels of a forest stream linked to terrestrial litter inputs

      This article discusses the importance of terrestrial litter on an aquatic ecosystem. It was observed that organisms that lived in the stream that was being tested were affected the most by the absence of litter and the same effects could be observed throughout the entire ecosystem. However, terrestrial fauna was not affected meaning that it got its carbon from another source.

    5. Lakes and reservoirs as regulators of carbon cycling and climate.

      This article mentions the that the rate at which inland water sources release carbon dioxide is equivalent to the rate at which carbon is absorbed by the ocean. Methane is also being release in higher levels from lakes which are beginning to thaw because of increasing temperatures from global warming.

    6. Continental-scale effects of nutrient pollution on stream ecosystem functioning

      This experiment was a pan-European research of more than 100 streams in multiple European countries. It helped determine the importance of litter breakdown and states that countries should begin to consider the importance of regulating nutrient levels in aquatic ecosystems.

    7. Ecosystem metabolism and turnover of organic carbon along a blackwater river continuum

      This article discusses the respiration rate of an aquatic ecosystem and uses it to determine patterns of activity found within a river during different seasons. It was observed that there were higher levels of respiration when there were was more organic carbon in the river.

    8. Nutrient co-limitation of primary producer communities

      This article focuses on how nutrients affect the growth of primary producers. The factors that were observed to have the highest effects on the ecosystems were nitrogen and phosphorus levels.

    9. Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem

      This article discusses how the addition of nutrients in an aquatic ecosystem affects secondary production. It was noted that there was an increase in secondary consumers most likely caused because of an increase in prey. There was also an increase of secondary consumer predators. It is mentioned that the increase of nutrients in the two years the survey was done resulted in positive effects for the secondary consumers, however, this might eventually change as the carbon levels in the ecosystem begin to decline because of the higher nutrient levels.

    10. Human influences on nitrogen removal in lakes

      This article discusses how human practices have led to a increase of nitrogen levels in lakes. The article also mentions that an increase of phosphorus in lakes resulted in the extraction of higher levels of nitrogen. However, the author also states that laws pertaining to the concentration of phosphorus in aquatic habitats should not be removed or relaxed because phosphorus can also have a negative effect on an ecosystem if found in high concentrations.

    1. Min, K.-T. and Benzer, S. (1997). Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death. Proc. Natl. Acad. Sci. USA 94, 10792-10796.

      Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.

      GG

    2. Teixeira, L., Ferreira, A. and Ashburner, M. (2008). The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol. 6, e2.

      The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.

      GG

    3. Ponton, F., Wilson, K., Holmes, A., Raubenheimer, D., Robinson, K. L. and Simpson, S. J. (2015). Macronutrients mediate the functional relationship between Drosophila and Wolbachia. Proc. Biol. Sci. 282, 20142029.

      Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.

      GG

    4. Serbus, L. R., White, P. M., Silva, J. P., Rabe, A., Teixeira, L., Albertson, R. and Sullivan, W. (2015). The impact of host diet on Wolbachia titer in Drosophila. PLoS Pathog. 11, e1004777.

      Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.

      GG

    5. Mouton, L., Henri, H., Charif, D., Bouletreau, M. and Vavre, F. (2007). Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis. Biol. Lett. 3, 210-213. Musselman, L. P., Fink, J. L., Narzinski, K., Ramachandran, P. V., Hathiramani, S. S., Cagan, R. L. and Baranski, T. J. (2011). A high-sugar diet produces obesity and insulin resistance in wild-type Drosophila. Dis. Model. Mech. 4, 842-849.

      Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.

      GG

    6. Wang, M. and Wang, C. (1993). Characterization of glucose transport system in Drosophila Kc cells. FEBS Lett. 317,241-244.

      Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.

      GG

    7. Dale, C. and Moran, N. A. (2006). Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453-465

      While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.

      GG

    8. Christensen, S., Pérez Dulzaides, R., Hedrick, V. E., Momtaz, A. J. M. Z., Nakayasu, E. S., Paul, L. N. and Serbus, L. R. (2016). Wolbachia endosymbionts modify Drosophila ovary protein levels in a context-dependent manner. Appl. Environ. Microbiol. 82, 5354-5363

      Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophilaovaries are modified by Wolbachia.

      GG

    9. Bordenstein, S. R. and Bordenstein, S. R. (2011). Temperature affects the tripartite interactions between bacteriophage WO, Wolbachia, and cytoplasmic incompatibility. PLoS ONE 6, e29106. Boyle, L., O'Neill, S. L., Robertson, H. M. and Karr, T. L. (1993). Interspecific and intraspecific horizontal transfer of Wolbachia in Drosophila. Science 260, 1796-1799.

      Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.

      Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.

      GG

    10. Caragata, E. P., Rancès, E., Hedges, L. M., Gofton, A. W., Johnson, K. N., O'Neill, S. L. and McGraw, E. A. (2013).Dietary cholesterol modulates pathogen blocking by Wolbachia. PLoS Pathog. 9, e1003459.

      Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.

      GG

    1. D. S. Jordan, Am. Nat. 42, 73 (1908)

      Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.

    2. E. Mayr, Animal Species and Evolution (Harvard Univ. Press, Cambridge, 1963).

      This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.

    3. Hence, pairs P5-C5 and P6-C6 probably separated during the period of marked shoaling and environmental divergence preceding final closure.

      P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.

    4. followed by failure to interbreed when partial connection between the oceans was reestablished

      Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.

    5. J. A. Coyne and H. A. Orr, Evolution 43, 362 (1989). W. R. Rice, ibid., p. 223.

      The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)

    6. D. L. Swofford, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1; (Illinois Natural History Survey, Champaign, IL, 1993).

      The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)

    7. J. H. Gillespie, The Causes of Molecular Evolution (Oxford Univ. Press, New York, 1991).

      The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)

    8. Genetic divergence before final closure may have been facilitated by changing oceanographic conditions

      Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)

  10. Oct 2017
    1. M. Nei, Genetics 89, 583 (1978)

      Nei found the average heterozygosity and genetic distance from a small number of individuals.This paper explains how biases arise in calculations when small samples are used. However, this paper establishes an average that reduces bias. (JP)

    2. R. W. Rubinoff and 1. Rubinoff, Evolution 25, 88 (1971)

      This paper, through studying 3 different species of Bathygobius, found that morphological divergence is not correlated with reproductive isolation. Their experiment was testing the extent in which these 3 species had evolved reproductive isolation in the Isthmus of Panama. (JP)

    3. 4. E. Bermingham and H. A. Lessios, Proc. Nati. Acad. Sci. U.S.A. 90, 2734 (1993).

      This source demonstrates that mitochondrial DNA is able to provide fairly accurate estimates of times since separation of a species in a 3 million year range. Here they also used organisms from the Isthmus of Panama and gel electrophoresis to deduce the time of speciation. (JP)

    4. A. T. Vawter, R. Rosenblatt, G. C. Gorman, Evolution 34, 705 (1980)

      The authors of this paper found that, through parsimony analysis of the sequence divergence estimates and of sequence polymorphisms of the Holarctic fish's mtDNA, different Holarctic fish species arose from a geographical event that occurred during the beginning of the mid-Pliocene period.

      The authors of this paper cited this source because this source conducts a similar study in deducing a time frame in which speciation of the Holarctic fish occurred. (JP)

    5. H. A. Lessios, Nature 280, 599 (1979)

      This source published in 1979 to Nature tests the reliability of the molecular clock hypothesis by using Panamanian sea urchins. The author argues that the molecular clock hypothesis is not tenable or supportable. (JP)

    1. McCauley, D.J., Young, H.S., Dunbar, R.B., Estes, J.A., Semmens, B.X., and Micheli, F. (2012). Assessing the effects of large mobile predators on ecosystem connectivity. Ecol. Appl. 22, 1711–1717.

      This study states that sharks in the Palmyra Atoll find food in other habitats.

      -RKL

    2. Heithaus, M.R., Frid, A., Wirsing, A.J., and Worm, B. (2008). Predicting ecological consequences of marine top predator declines. Trends Ecol. Evol. 23, 202–210.

      The study explains how the effects of a high cost/ low reward way of life may affect an ecosystem -M.A.S

  11. Sep 2017
    1. Brown, J.H., Gillooly, J.F., Allen, A.P., Savage, V.M., and West, G.B. (2004). Toward a metabolic theory of ecology. Ecology 85, 1771–1789.

      Explains the metabolic equation used in the study -M.A.S.

  12. Dec 2016
    1. What is annotation as a genre? I think what he observed in the annotations was a wide range of reader responses, some highly engaging, others less clearly so.

      This question seems like it should be more specific to disciplines. What is annotation in the legal world? How about for scientists? For beginning readers?

      If I'm annotating a text to make meaning, that's different than if I'm a prof annotating a historical text to provide relevant background. The two notes have only their "noteness" in common, I'd say.

  13. Sep 2016
    1. Unfortunately Evernote stopped its syncing service. Only a pay-account can use syncing across more than two devices. This made it useless for millions of users, who are now forced to export their notes and look for a more contemporary, user-loyal alternative.

  14. May 2016
    1. Headrick, Daniel R. 2000. When Information Came of Age: Technologies of Knowledge in the Age of Reason and Revolution, 1700-1850. Oxford University Press.

      Notes (American spelling).

  15. Nov 2015
    1. Frequency

      Frequency of the note A_x: $$f(A_x) = 440 \cdot 2^{x - 4}$$

      Inverse (octave x of the note A_x from frequency f): $$x = \log_2{\frac{f}{440}} + 4 = \log_2{f} + 4 - \log_2{440}$$

  16. Aug 2015
    1. H. Wang, M. A. Winnik, I. Manners, Synthesis and self-assembly of poly(ferrocenyldimethylsilane- b -2-vinylpyridine) diblock copolymers. Macromolecules 40, 3784 (2007).

      In this paper, the authors developed a new class of diblock copolymers that have a metal-containing hydrophobic block (PFS) and an organic hydrophilic block (P2VP): PFS = poly(ferrocenyldimethylsilane) and P2VP = poly(2-vinylpyridine). The authors of this publication discovered the ability to obtain spherical and cylindrical morphologies simply by using different alcohols. Having established the ability to obtain cylindrical micelles using the PFS-b-P2VP block copolymer system in isopropyl alcohol, the authors modified their approach in the current study to obtain supermicelles.

    2. P. A. Rupar, G. Cambridge, M. A. Winnik, I. Manners, Reversible cross-linking of polyisoprene coronas in micelles, block comicelles, and hierarchical micelle architectures using Pt(0)–olefin coordination. J. Am. Chem. Soc. 133, 16947 (2011).

      This paper established that Karstedt's catalysts ability to cross-link the double bonds in polyisoprene in the absences of silicon-containing molecules. Besides acquiring a variety of morphologies, the authors also investigated their ability to use Karstedt's catalyst to synthesize reversible polymer gel networks.

    3. X. S. Wanget al., Shell-cross-linked cylindrical polyisoprene- b -polyferrocenylsilane (PI- b -PFS) block copolymer micelles: One-dimensional (1D) organometallic nanocylinders. J. Am. Chem. Soc. 129, 5630 (2007).

      This reference investigates the development of 1D nano-structures through the use of cross-linked cylindrical micelles. This paper highlights possible applications for these 1D nanomaterials such as microfluidics.

    4. R. K. O’Reilly, C. J. Hawker, K. L. Wooley, Cross-linked block copolymer micelles: functional nanostructures of great potential and versatility. Chem. Soc. Rev. 35, 1068 (2006).

      This review paper describes the uses and progress made in the field of cross-linked micelles. Concepts covered include stabilization as well chemical modification and functionalization.

    5. W. Zhanget al., Supramolecular linear heterojunction composed of graphite-like semiconducting nanotubular segments. Science 334, 340 (2011).

      References: This paper describes the synthesis of semiconducting nanotubes through a process similar to CDSA by connecting dissimilar junctions, referred to as heterojuntions, to study the behaviors of photocarriers.

    6. Z.-X. Du, J.-T. Xu, Z.-Q. Fan, Micellar morphologies of poly(ε-caprolactone)- b -poly(ethylene oxide) block copolymers in water with a crystalline core. Macromolecules 40, 7633 (2007).

      This paper describes the use of a biodegradable polymer in order to obtain a variety of micelle morphologies. A concept referred to as tethering density is used in this paper to explain unexpected morphologies.

    7. Schmelz, M. Karg, T. Hellweg, H. Schmalz, General pathway toward crystalline-core micelles with tunable morphology and corona segregation. ACS Nano 5, 9523 (2011).

      This paper uses triblock copolymers to synthesize cylindrical and spherical micelles. By carefully controlling crystallization, the authors were able to control the micellar morphology in a highly selective fashion.

    8. T. Gädt, N. S. Ieong, G. Cambridge, M. A. Winnik, I. Manners, Complex and hierarchical micelle architectures from diblock copolymers using living, crystallization-driven polymerizations. Nat. Mater. 8, 144 (2009).

      This paper utilizes CDSA to synthesize noncylindrical block co-micelles. The authors utilized plateletlike micelle and cylindrical micelles in order to form scarflike architectures using platelet-cylindrical and cylindrical-cylindrical connections.

    9. X. S. Wanget al., Cylindrical block copolymer micelles and co-micelles of controlled length and architecture. Science 317, 644 (2007)

      This paper describes the discovery of CDSA. The authors draw a comparison to living polymerization and explain the phenomenon of epitaxial crystallization-induced co-micellization

    10. Y. Xia, B. D. Olsen, J. A. Kornfield, R. H. Grubbs, Efficient synthesis of narrowly dispersed brush copolymers and study of their assemblies: The importance of side chain arrangement. J. Am. Chem. Soc. 131, 18525 (2009).

      This reference describes the synthesis of brush block and random copolymers. The polymers are referred to as a "brush" because pendant groups are dangling off the main chain. The brush polymers synthesized were amphiphilic and demonstrated self-assembly.

    11. Walther, M. Drechsler, A. H. E. Müller, Structures of amphiphilic Janus discs in aqueous media. Soft Matter 5, 385 (2009).

      This paper describes the synthesis of amphiphilic Janus discs using a block terpolymer (three distinct blocks comprised of three distinct monomers). Two different size discs were made where, depending on size, the manner in which the hydrophobic side is "protected" from water can vary. The smaller discs are stabilized by the long hydrophilic polymer chains, protruding out of one side and shielding the hydrophobic side against water. The larger discs undergo aggregation as well as bending to again shield the hydrophobic side from the water by flipping over one part of the structure.

    12. J. Dupont, G. Liu, ABC triblock copolymer hamburger-like micelles, segmented cylinders, and Janus particles. Soft Matter 6, 3654 (2010).

      This reference is an example where triblock copolymers were photo-crosslinked to create Janus particles which were classified as "hamburger-like" micelles.

    13. Walther, A. H. E. Müller, Janus particles. Soft Matter 4, 663 (2008)

      This review paper discusses a class of noncentrosymmetric nanoparticles referred to as the Janus particle. These particles are rather challenging to synthesize because two different chemistries are present on the surface of the particle.

    14. H. Cui, Z. Chen, S. Zhong, K. L. Wooley, D. J. Pochan, Block copolymer assembly via kinetic control. Science 317, 647 (2007).

      This paper utilized charged polymers as well as metal cations and a variety of solvents to kinetically trap unique micelle morphologies. The self-assembly systems were forced down a specific pathway in order to form morphologies that would not have typically occurred without assistance.

    15. L. Zhang, A. Eisenberg, Multiple morphologies of “crew-cut” aggregates of polystyrene-b-poly(acrylic acid) block copolymers. Science 268, 1728 (1995).

      This paper was one of the first papers to establish the ability to form micelles of different morphologies (beyond just spherical) for systems using amphiphilic block copolymers

  17. Jul 2015
    1. J. F. Soderholm, S. L. Bird, P. Kalab, Y. Sampathkumar, K. Hasegawa, M. Uehara-Bingen, K. Weis, R. Heald, Importazole, a small molecule inhibitor of the transport receptor importin-β. ACS Chem. Biol. 6, 700–708 (2011).

      Importazole is a small molecule inhibitor of the transport receptor importin-β. This inhibitor was identified by a screening assay developed by the authors of this paper.

    2. A. J. Firestone, J. S. Weinger, M. Maldonado, K. Barlan, L. D. Langston, M. O’Donnell, V. I. Gelfand, T. M. Kapoor, J. K. Chen, Small-molecule inhibitors of the AAA+ ATPase motor cytoplasmic dynein. Nature 484, 125–129 (2012). doi:10.1038/nature10936 pmid:22425997

      This work reported the discovery of ciliobrevins, the first specific small-molecule antagonists of cytoplasmic dynein.

    3. K. V. Butler, J. Kalin, C. Brochier, G. Vistoli, B. Langley, A. P. Kozikowski, Rational design and simple chemistry yield a superior, neuroprotective HDAC6 inhibitor, tubastatin A. J. Am. Chem. Soc. 132, 10842–10846 (2010). doi:10.1021/ja102758v pmid:20614936

      This paper reported the development of Tubastatin A, a potent and selective HDAC6 inhibitor.

    4. H. Ouyang, Y. O. Ali, M. Ravichandran, A. Dong, W. Qiu, F. MacKenzie, S. Dhe-Paganon, C. H. Arrowsmith, R. G. Zhai, Protein aggregates are recruited to aggresome by histone deacetylase 6 via unanchored ubiquitin C termini. J. Biol. Chem. 287, 2317–2327 (2012).

      This work suggested a novel ubiquitin-mediated signaling pathway, where the exposure of ubiquitin C termini within protein aggregates enables HDAC6 recognition and transport to the aggresome. The authors found that the ubiquitin-binding domain (ZnF-UBP) of HDAC6, instead of recognizing protein aggregates by binding directly to polyubiquitinated proteins, binds exclusively to the unanchored C-terminal diglycine motif of ubiquitin.

    5. Y. Zhang, B. Gilquin, S. Khochbin, P. Matthias, Two catalytic domains are required for protein deacetylation. J. Biol. Chem. 281, 2401–2404 (2006).

      In this report, the authors showed that both HDAC domains are required for the intact deacetylase activity of HDAC-6.

    6. Y. Zhang, S. Kwon, T. Yamaguchi, F. Cubizolles, S. Rousseaux, M. Kneissel, C. Cao, N. Li, H. L. Cheng, K. Chua, D. Lombard, A. Mizeracki, G. Matthias, F. W. Alt, S. Khochbin, P. Matthias, Mice lacking histone deacetylase 6 have hyperacetylated tubulin but are viable and develop normally. Mol. Cell. Biol. 28, 1688–1701 (2008). doi:10.1128/MCB.01154-06 pmid:18180281

      In this study, the author generated HDAC6 knock out mice and investigated the in vivo functions of HDAC6 and the relevance of tubulin acetylation/deacetylation. they observed that HDAC6-deficient mice are viable and fertile and show hyperacetylated tubulin in most tissues.They concluded that mice survive well without HDAC6 and that tubulin hyperacetylation is not detrimental to normal mammalian development.

    7. I. Kemler, G. Whittaker, A. Helenius, Nuclear import of microinjected influenza virus ribonucleoproteins. Virology 202, 1028–1033 (1994).

      
This work showed that when influenza virus ribonucleoproteins (vRNPs), devoid of M1, were introduced into the cytoplasm of cells by microinjection, they were found to be imported into the nucleus, and the RNA was transcribed. Their uptake into the nucleus was ATP-dependent, inhibited by antibodies to the nuclear pore complex, unaffected by the prior acidification of the vRNPs, and not inhibited by an anti-virurs, called amantadine. These experiments demonstrated that for productive infection, all the early stages of the viral entry pathway can be bypassed.

    8. anerjee, Y. Yamauchi, A. Helenius, P. Horvath, High-content analysis of sequential events during the early phase of influenza A virus infection. PLOS ONE 8, e68450 (2013).

      This study provides a powerful high-throughput platform to understand the host cell processes. The authors developed quantitative, imaging-based assays to dissect seven consecutive steps in the early phases of IAV infection in tissue culture cells.

    9. K. S. Matlin, H. Reggio, A. Helenius, K. Simons, Infectious entry pathway of influenza virus in a canine kidney cell line. J. Cell Biol. 91, 601–613 (1981).

      This work investigated the cell fusion process of representatives of 3 families of enveloped viruses. it was discovered that hemagglutinin plays a role for the influenza in the low-pH-dependent membrane fusion activity. Low-pH-induced fusion is a widespread property of enveloped animal viruses and that it may play a role in the infective process.

    10. L. H. Pinto, L. J. Holsinger, R. A. Lamb, Influenza virus M2 protein has ion channel activity. Cell 69, 517–528 (1992).

      The authors of this paper identified the ion channel activity of M2.

    11. J. White, K. Matlin, A. Helenius, Cell fusion by Semliki Forest, influenza, and vesicular stomatitis viruses. J. Cell Biol. 89, 674–679 (1981).

      This work investigated the cell fusion process of representatives of 3 families of enveloped viruses. it was discovered that hemagglutinin plays a role for the influenza in the low-pH-dependent membrane fusion activity. Low-pH-induced fusion is a widespread property of enveloped animal viruses and that it may play a role in the infective process.

    12. K. Martin, A. Helenius, Nuclear transport of influenza virus ribonucleoproteins: The viral matrix protein (M1) promotes export and inhibits import. Cell 67, 117–130 (1991). doi:10.1016/0092-8674(91)90576-K pmid:1913813

      This work described the nuclear transport of influenza virus ribonucleoproteins (vRNPs). Viral matrix protein (M1) associates with newly assembled vRNPs in the nucleus and escorts them to the cytoplasm through the nuclear pores. In contrast, during entry of the virus into a new host cell, M1 protein dissociates from the RNPs, allowing them to enter the nucleus.

    1. G. Larson, J. Burger,Trends Genet.29, 197–205 (2013).

      This study is about animal domestication. It explains that the dog is the only animal domesticated before the advent of agriculture. It also discuss the limits of mtDNA analysis.

  18. Apr 2015
    1. First, the domain is a poor candidate because the domain of all entities relevant to neurobiological function is extremely large, highly fragmented into separate subdisciplines, and riddled with lack of consensus (Shirky, 2005).

      Probably a good thing to add to the Complex Data integration workshop write up

  19. Jan 2015
    1. You can then add your own comments and tags.

      I add my own comments and tags

      Test blockquote.

  20. Dec 2014
    1. It would be wonderful to be able to have pop up GIFs on this page when you scroll over a highlighted word. We should play around with that.

  21. May 2014
  22. futurepress.github.io futurepress.github.io
    1. ncernment where I was to eat and sleep meanwhile. It was a very dubious-looking, nay, a very dark and dismal night, bitingly cold and cheerless. I knew no one in the place. With anxious grapnels I had sounded my pocket, and only brought up a few

      I love notes. Dubious-looking, nay dark and dismal notes.

  23. Sep 2013