1,279 Matching Annotations
  1. Jan 2018
    1. “Probabilistic projections of total population: Median and confidence intervals,” (United Nations, Department of Economic and Social Affairs, New York, 2012); http://esa.un.org/unpd/ppp/Data-Output/ UN_PPP2010_output-data.htm.

      This population growth data from the United Nations was used to predict future amounts of plastic waste entering the ocean from individual countries.

    1. R. B. Widelitz, T.-X. Jiang, J. Lu, C.-M. Chuong, b-catenin in epithelial morphogenesis: Conversion of part of avian foot scales into feather buds with a mutated b-catenin. Dev. Biol. 219, 98–114 (2000).

      Explores the role of β-catenin, which is expressed in the placode.

      When this protein was mutated in chickens, their feet were scaleless and they had abnormal feather growth.

    2. C. Blanpain, E. Fuchs, Epidermal stem cells of the skin. Annu. Rev. Cell Dev. Biol. 22, 339–373 (2006).

      Reviews the development of skin cells that give rise to hairs.

      A hair placode forms, allowing the expression of genes that direct skin cell and hair follicle development.

    3. J. M. Musser, G. P. Wagner, R. O. Prum, Nuclear b-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol. Dev. 17, 185–194 (2015).

      Explores the relationship between feathers and scales.

      Visualization of the location and amount of β-catenin during the development of feathers and scales revealed similar patterns between the two. The authors concluded that feathers and scales share an evolutionary ancestor.

    4. D. Dhouailly, A new scenario for the evolutionary origin of hair, feather, and avian scales. J. Anat. 214, 587–606 (2009).

      Proposed the theory that mammalian hair evolved from glandular structures, whereas reptile and bird skin evolved from a thick protective coating.

    5. P. F. A.Maderson,Mammalian skin evolution: A reevaluation. Exp. Dermatol. 12, 233–236 (2003).

      A revision to a 1972 model of how mammalian hair evolved.

      This new model proposes that the development of hair was caused by mutations in patterning genes, which resulted in hair becoming more useful insulation.

    6. M. C. Milinkovitch, L. Manukyan, A. Debry, N. Di-Poï, S. Martin, D. Singh, D. Lambert, M. Zwicker, Crocodile head scales are not developmental units but emerge from physical cracking. Science 339, 78–81 (2013).

      This paper discusses the way that crocodile head scales form. Unlike feathers, hair, and other scales, crocodile facial scales are formed when growing cells physically crack to form unique patterns.

  2. 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. F. A. Ran et al., Cell 154, 1380–1389 (2013).

      This study investigated offset nicking as a means of reducing off-target modifications. The authors found that by using Cas9 mutants with sgRNAs, a targeted double-stranded break can be performed. Off-target activity was reduced 50- to 1000-fold with this technique.

    2. K. T. Flaherty et al., N. Engl. J. Med. 363, 809–819 (2010).

      This study investigates the BRAF mutation in melanoma and the BRAF protein kinase inhibitor vemurafenib (PLX). The researchers found that PLX reduced tumor growth in cells that had a mutated BRAF gene.

    3. P. Mali et al., Science 339, 823–826 (2013).

      This study demonstrated that Cas9 is effective at introducing specific loss-of-function mutations in the genome and creating specific double-stranded breaks in DNA sequences.

    1. A. A. Ittner, A. Gladbach, J. Bertz, L. S. Suh, L. M. Ittner, p38 MAP kinase-mediated NMDA receptor-dependent suppression of hippocampal hypersynchronicity in a mouse model of Alzheimer’s disease. Acta Neuropathol. Commun. 2, 149 (2014).

      In this study Ittner and others described the parts of the APP23 mouse model through artificial stimulation.

    2. S. Li, M. Jin, T. Koeglsperger, N. E. Shepardson, G. M. Shankar, D. J. Selkoe, Soluble Aβ oligomers inhibit long-term potentiation through a mechanism involving excessive activation of extrasynaptic NR2B-containing NMDA receptors. J. Neurosci. 31, 6627–6638 (2011).

      Li and others studied how amyloid beta affects synaptic plasticity, or the ability of synapse to weaken or strengthen. The amyloid beta increases activation of extrasynaptic NMDARs.

    3. Q. Wang, D. M. Walsh, M. J. Rowan, D. J. Selkoe, R. Anwyl, Block of long-term potentiation by naturally secreted and synthetic amyloid β-peptide in hippocampal slices is mediated via activation of the kinases c-Jun N-terminal kinase, cyclin-dependent kinase 5, and p38 mitogen-activated protein kinase as well as metabotropic glutamate receptor type 5. J. Neurosci. 24, 3370–3378 (2004).

      Mucke and Selkoe show that amyloid beta binds to different parts of plasma membranes and induces neuronal dysfunction and disruption of networks.

    4. L. M. Ittner, Y. D. Ke, F. Delerue, M. Bi, A. Gladbach, J. van Eersel, H. Wölfing, B. C. Chieng, M. J.Christie, I. A. Napier, A. Eckert, M. Staufenbiel, E. Hardeman, J. Götz, Dendritic function of tau mediates amyloid-β toxicity in Alzheimer’s disease mouse models. Cell 142, 387–397 (2010).

      In this article, Ittner and others show that the absence of tau in amyloid beta-forming mice lessens the severity of amyloid beta toxicity. These results suggest that tau and amyloid beta together increase the symptoms and progression of Alzheimer’s disease.

    5. E. D. Roberson, K. Scearce-Levie, J. J. Palop, F. Yan, I. H. Cheng, T. Wu, H. Gerstein, G.-Q. Yu, L. Mucke, Reducing endogenous tau ameliorates amyloid β-induced deficits in an Alzheimer’s disease mouse model. Science 316, 750–754 (2007).

      Roberson and others conducted an experiment on mice to test targeting tau in Alzheimer’s as an effective treatment. The experiment showed that tau reduction can block amyloid beta neuronal dysfunction, showing that tau reduction could be a future effective treatment of Alzheimer’s.

    6. L. M. Ittner, J. Götz, Amyloid-β and tau—a toxic pas de deux in Alzheimer’s disease. Nat. Rev. Neurosci. 12, 67–72 (2011).

      Ittner and Gӧtz review new findings showing the interactions of tau and amyloid beta. Tau can shift from the axon to the dendrite helping to mediate amyloid beta toxicity.

    7. C. Haass, D. J. Selkoe, Soluble protein oligomers in neurodegeneration: Lessons from the Alzheimer’s amyloid β-peptide. Nat. Rev. Mol. Cell Biol. 8, 101–112 (2007).

      C. Haass, D. J. Selkoe,Nat. Rev. Mol. Cell Biol.8, 101–112(2007).: Haass and Selkoe show that in AD, small intermediates of amyloid beta, called oligomers, negatively affects synaptic structure and plasticity.

  3. Nov 2017
    1. 11

      Warming induced early leaf bud bursts, growth, and reproduction but did not effect senescence. Study was performed in multiple sites in the arctic region over a course of four years.

      RW

    2. Arft AM et al. 1999 Responses of tundra plants to experimental warming: meta-analysis of the International Tundra Experiment. E

      Warming induced early leaf bud bursts, growth, and reproduction but did not effect senescence. Study was performed in multiple sites in the arctic region over a course of four years.

      RW

    3. [4

      Sea ice decline due to global warming is effecting plant productivity in arctic regions.

      RW

    4. hatt US et al. 2010 Circumpolar Arctic tundra vegetation change is linked to sea ice decline. Earth Interact. 14, 1-20. (doi:10.1175/ 2010EI315.1

      Sea ice decline due to global warming is effecting plant productivity in arctic regions.

      RW

    5. haver GR, Kummerow J. 1992 Phenology, resource allocation, and growth of Arctic vascular plants. In Arctic ecosystems in a changing climate : an ecophysioiogical perspective (eds FS Chapin, RL Jefferies, JF Reynolds, GR Shaver, J Svoboda), pp. 193-211. San Diego, CA: Academic Pres

      Heat sum increases for flowering and senescence

      RW

    6. [12

      Heat sums have increased over time for flowering and senescence.

      RW

    1. Robbins WD, Hisano M, Connolly SR, Choat JH (2006) Ongoing collapse of coral reef shark populations. Current Biology 16: 2314–2319.

      This paper discusses how inefficient no-take zones are in protecting reef sharks. - Emily

    2. Large-Scale Absence of Sharks on Reefs in the Greater-Caribbean: A Footprint of Human Pressures

      This study was cited to illustrate the effect of marine reserves on the Caribbean sharks. The study found sharks to be less concentrated in areas of high human activity.

    3. Roberts CM, Bohnsack JA, Gell F, Hawkins JP, Goodridge R (2001) Effects of marine reserves on adjacent fisheries. Science 294: 1920–1923.

      The effects of marine reserves on fisheries is discussed in this paper. Marine reserves were sometimes controversial; however, they proved to be a supportive force in the quality and amount of fish caught by adjacent fisheries. - Emily

    4. Heupel MR, Simpfendorfer CA, Fitzpatrick R (2010) Largescale movement and reef fidelity of grey reef sharks. PLoS ONE 5: e9650.

      This article aided in emphasizing the concepts of site fidelity and the effect that migrations have on the density of shark populations in marine reserves. It built upon the idea that reserves increase the overall population of species inhabiting the area due to to the lack of fishing that occurs in these areas in contrast to non preserved locations. -Sindy

    1. Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.

      This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.

      -Otniel Gonzalez

    2. Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.

      This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.

      -Angela Mujica

    1. G. E. Hardingham, H. Bading, Synaptic versus extrasynaptic NMDA receptor signalling: Implications for neurodegenerative disorders. Nat. Rev. Neurosci. 11, 682–696 (2010).

      Hardingham and Bading show that NMDAR responses depend on receptor location. Synaptic NMDARs promotes cell survival, while stimulate of extrasynaptic NMDARs promotes cell death. The unequal stimulation of these receptors neuronal dysfunction, while stimulation of synaptic receptors could be used a protective therapy.

    2. C. Ballatore, V. M. Lee, J. Q. Trojanowski, Tau-mediated neurodegeneration in Alzheimer’s disease and related disorders. Nat. Rev. Neurosci. 8, 663–672 (2007).

      Ballatore, Lee, and Trojanowski review and summarize the recent discoveries of tau-mediated neurodegeneration mechanisms and how they can understand AD progression and discover new drug treatments.

    1. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455–2457.

      For this experiment to occur, there had to be some kind of data to support what is being presented. Datamonkey is a popular-based web suite of phylogenetic analysis tools for use in evolutionary biology. Analysis options fall into many different categories such as algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, etc. For this paper, the data is based on evolution throughout the events and moments shown from these insects. https://academic.oup.com/bioinformatics/article/26/19/2455/228720

    2. Gempe T, Beye M (2011) Function and evolution of sex determination mechanisms, genes and pathways in insects. Bioessays 33:52–60. doi:10.1002/bies.201000043PubMedCentralPubMedCrossRefGoogle Scholar

      The article summarizes all recent findings of the time regarding sexual determination in drosophilids and other non-model insects. The primary concept remains that sexual determination depends on a shared gene switch present in both males and females of the same species. -Eri-Ray

    3. Bopp D, Saccone G, Beye M (2014) Sex determination in insects: variations on a common theme. Sex Dev 8:20–28

      This article explains that holometabolous insects, despite diversity, all generally have the same sex-determining pathway. It also explains how the (tra) goes to the (dsx) gene to go from the on to off position to determine sex of the zygote. - Jake Barbee

    4. Artieri CG, Haerty W, Singh RS (2009) Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila. BMC Biol 7:42. doi

      This article explains that organisms show a much greater divergence during the later stages of development in comparison to the earlier stages of development. Their conclusions proved that an increasing evolutionary rate (divergence) occurred in later developmental stages. -Elder

    1. Hopkins, 1991

      The article written by Carl D. Hopkins provides the author with background informational on B.pinnicaudatus and on the electric organs found within the organism . B.pinnicaudatus is a gymmotiform discovered in French Guinea and can be found throughout South America. This species similar to other electric fish is able to generate a pulse-type electric-organ discharge. The two type of electric discharges generated by electric fish tend to a pulse or a wave. This species is part of the largest family that produce electric pulses . Within this species , the males are able to produce a longer discharge than female within the species. http://pages.nbb.cornell.edu/neurobio/hopkins/Reprints/Hypopomus%20Pinnicaudatus,%20a%20New%20Species.pdf -Michelle Oriana Gomez-Guevara

    2. Synchronized activation along the length of the electric organ implies effective mechanisms for compensation of neuronal propagation delays along the length of the EO (Bennett, 1971)

      Bennett's article analyzes the anatomy and physiology of the electric organs found within these electric fish. The membrane physiology of these electric organs evolved independently into six different groups and resulted in different membrane functions in different electrolyte which affect the electrorecption in the electric organism . Michelle Oriana Gomez-Guevara Note to Nick: I was only able to find a summary of the article and not the entire article. I checked google scholar, tried fiu library data and tried find it @FIU and I still was unable to find access to the article.

    3. (Bastian, 1986),

      This source provides information about how the various regions of neuronal activity in electric fish response differently in response to variance in body movement.

      Specifically, electrosensory pyramidal cells (neurons found in the areas of the brain that are involved in executive functions: memory, emotional responses etc,) activate or discharge electric signals in multiple ways dependent on the re-afferent (sensory information that is received) signals from their external environment.

      https://www.ncbi.nlm.nih.gov/pubmed/7823309

      -Kierra Hobdy

    4. Bullock and Heiligenberg, 1986

      Bullock's and Heiligenberg's article , Electroreception ,gives an in-depth knowledge on electroreception as well as as review on the electric organs that are found within marine vertebrates . This background provide the author with the basic foundation for understanding how electrolocation works and the purposes it serves these marine vertebrates in their natural environment and daily lives. This citation also helps the author introduce the topic of electrogenesis and electroreception in relation to the location of the organs necessary for the process of electrolocation to occur. Michelle Oriana Gomez-Guevara

    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)

    1. Brill, R. W. (1996). Selective advantages conferred by the high performance physiology of tunas, billfishes, and dolphin Fish. Comp. Biochem. Physiol. A Comp. Physiol. 13A, 3-15.doi:10.1016/0300-9629(95)02064-0

      In this review the author talks about the characteristics that give tuna fish high performance. These characteristics include 3 things: high rates of somatic and gonadal growth, rates of digestion, and rates of recovery from exhaustive exercise. This study uses these findings to defy the myth that sailfish and other pelagic fish just have high maximum swimming speeds that allows them to avoid cavitation.

      Mikaela

  4. Oct 2017
    1. L. A. Gilbert et al., Cell 154, 442–451 (2013).

      This study investigated how different Cas9 mutants are more effective for different situations.

    2. S. R. Whittaker et al., Cancer Discovery 3, 350–362 (2013).

      This study investigated PLX drug resistance in A375 cells. The authors found that NF1 is the most common mutation leading to PLX resistance, a finding that is supported by the current study. The Raf inhibitor vemurafenib was used in both studies. The authors in this paper used a pooled RNAi screen that targeted 16500 genes to look at loss-of-function mutations leading to PLX resistance.

    3. A. L. Jackson et al., RNA 12, 1179–1187 (2006).

      This paper investigates some of the unintended consequences of RNAi, such as the lack of specificity. While one sequence may be the target, other sequences could also be silenced in this process. If a sequence shows some complementarity to the target sequence, it may be targeted, as well. The paper predicts that perfect specificity will be difficult to achieve with RNAi.

    4. J. E. Carette et al., Science 326, 1231–1235 (2009).

      This study is another example of a loss-of-function screen. The initial experiment found host factors that were necessary for influenza infection, such as genes important for the synthesis pathway of diphthamide and genes that are necessary for cytolethal distending toxin. The authors knocked these genes out to investigate their effects.

    5. M. Boutros et al., Heidelberg Fly Array Consortium, Science 303, 832–835 (2004).

      This study uses RNAi to screen for loss-of-function alleles. The initial experiment tested the function of 91% of the genome of Drosophila. Testing was done by using an RNAi of the known 19,470 genes involved in cell growth and viability.

    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. J. W. Porter, Science 186, 543 (1974).

      Coral reefs on both the Pacific and Caribbean sides of Panama do not experience extreme weather events such as hurricanes. Coral diversity in Panama is maintained by mechanisms other than extreme weather disturbances, such as predation by the crown-of-thorns seastar, Acanthaster planci.

      Note: many invertebrate zoologists insist on the term "sea star" to communicate that invertebrates are not fish. This is similar to the push to move from "jellyfish" to "sea jelly."

    2. J. P. Sutherland, Am. Nat. 108, 859 (1974).

      Sutherland presents evidence and argues for the existence of "alternative stable states" in several ecosystems—the idea that the history of organisms and physical events in a place can ultimately determine the "final" community. This is opposed to the idea that the community will eventually look the same regardless of which organisms are initially present.

    3. J. B. C. Jackson [Am. Nat. 111, 743 (1977)]

      Colonial animals (animals that grow by budding or that live in close association with each other, e.g. the polyps of corals that live together to form a single coral colony) have unique advantages and well as disadvantages compared to solitary organisms.

      Jackson's paper describes some of the characteristics of colonial marine organisms, their distributions, and the factors that shape their distributions.

    4. T. F. Goreau, Ecology 40, 67 (1959).

      Goreau describes the species of corals found in Jamaica's reefs and the patterns of their distributions. He notes that the northern and southern coasts look different from each other and hypothesizes that these differences are driven by differences in storm frequencies.

  5. Sep 2017
    1. K. Tang, K. R. Thornton, M. Stoneking, A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5, e171 (2007).

      This study develops an approach to detect selective sweeps that is also used in this paper,

    2. C. Mariac et al., Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping. Mol. Ecol. 20, 80 (2011).

      This interesting paper similarly aims to understand the genetic basis of adaptation but look at the crop pearl millet. The authors were able to detect genetic changes associated with changes in the climate.

    3. J. Stapley et al., Adaptation genomics: The next generation. Trends Ecol. Evol. 25, 705 (2010).

      This review discusses how the advance in genomic technologies has helped stimulate research on the genetic basis of adaptation.

    1. N. Knowlton, J. C. Lang, M. C. Rooney, P. Clifford, Nature (London), in press.

      While strong waves and intense pulses of freshwater can cause immediate damage to coral reefs, coral reefs hit by severe tropical storms also experience significant sustained secondary mortality months after the initial impact of tropical storms as a result of less immediate consequences of tropical storms.

      This detailed study of survivorship of Acropora cervicornis after Hurricane Allen showed that later mortality was over ten times more severe than the mortality caused by the storm itself and was caused by disease and coral predators feeding on survivors. This complex pattern may explain why rates of recovery from disturbances may vary widely.

      “In press” means that the paper had not actually been published at the time.

    2. J. H. Connell, Science 199, 1302 (1978).

      Connell describes a mechanism by which the high biodiversity of tropical rain forests and coral reefs is maintained by disturbances, contrary to earlier hypotheses that suggested that tropical environments were very stable.

    3. J. G. Ogg and J. A. Koslow, Pac. Sci. 32, 105 (1978).

      Researchers in Guam describe minimal damage to hard coral reefs after a typhoon and no long-term impact, even in exposed areas. This is likely due in part to the low, rugged profile of reefs in Guam and the fact that they are hit by hurricanes very often.

  6. Aug 2017
    1. S. J. Strich, Shearing of nerve fibres as a cause of brain damage due to head injury: A pathological study of twenty cases. Lancet 2, 443–448 (1961). T. A. Gennarelli, L. E. Thibault, A. K. Ommaya, in Biomechanics of Impact Injury and Injury Tolerances of the Head-Neck Complex, S. H. Backaitis, Ed. (Society of Automotive Engineers Inc., Warrendale, PA, 1993).

      These papers investigate axonal injury in the context of TBI. Strich et al. focused on the clinical neuropathology of axonal injury, and Gennarelli et al. focused on the biomechanics.

      These works support the idea that head acceleration during injury leads to stress that causes damage to nerve fibers and impairs the brain postinjury.

    2. B. Omalu, J. L. Hammers, J. Bailes, R. L. Hamilton, M. I. Kamboh, G. Webster, R. P. Fitzsimmons, Chronic traumatic encephalopathy in an Iraqi war veteran with posttraumatic stress disorder who committed suicide. Neurosurg. Focus 31, E3 (2011).

      Omalu et al. presented a single case of CTE in a military veteran. The authors of the present study investigated a controlled case series comparing blast-exposed military veterans and athletes

      Dr. Omalu is perhaps best known as the subject of the movie Concussion, starring Will Smith.

    3. A. C. McKee, R. C. Cantu, C. J. Nowinski, E. T. Hedley-Whyte, B. E. Gavett, A. E. Budson, V. E. Santini, H. S. Lee, C. A. Kubilus, R. A. Stern, Chronic traumatic encephalopathy in athletes: Progressive tauopathy after repetitive head injury. J. Neuropathol. Exp. Neurol. 68, 709–735 (2009).

      A report of the long-term effects of repetitive head injury linked to American football.

      This paper provides a thorough case study of CTE in athletes and characterizes some of the key features of the disease. The motivation behind the present study came from identifying similar CTE pathology in the brains of military veterans.

      McKee et al. also published a follow-up that includes the largest case series of CTE to date.

    4. C. L. Mac Donald, A. M. Johnson, D. Cooper, E. C. Nelson, N. J. Werner, J. S. Shimony, A. Z. Snyder, M. E. Raichle, J. R. Witherow, R. Fang, S. F. Flaherty, D. L. Brody, Detection of blast-related traumatic brain injury in U.S. military personnel. N. Engl. J. Med. 364, 2091–2100 (2011).

      This study provided evidence for structural brain injury in blast-exposed military veterans. This brought attention to the reality of blast TBI, which was the signature injury of the Operation Enduring Freedom and Operation Iraqi Freedom conflicts.

    5. T. L. Tanielian, L. H. Jaycox, Invisible Wounds of War: Psychological and Cognitive Injuries, Their Consequences, and Services to Assist Recovery (RAND Corporation, Santa Monica, CA, 2008).

      A book by RAND corporation that brought the concept of the "invisible injury[should this be "wounds"?] of war" to a broader audience both in the United States and abroad.

    1. J. J. Palop, J. Chin, L. Mucke, Nature 443, 768 (2006).

      This review was written by members of the same lab in which Dr. Roberson did the work described in this paper.

      It outlines how the symptoms experienced by Alzheimer's patients seem to fluctuate constantly, suggesting that these symptoms cannot just be caused by dying neurons (which would result in symptoms that would get progressively worse).

      The authors discuss known changes in other proteins in the brains of Alzheimer’s patients and how these protein networks might work together to mediate symptoms of Alzheimer’s disease in the brain.

    2. K. SantaCruz et al., Science 309, 476 (2005).

      Santa Cruz and colleagues studied genetically modified mice that had a mutation in the human version of the tau gene, which caused those mice to get tau tangles like those seen in Alzheimer’s disease.

      Knocking out this tau gene allowed the mice to avoid memory and cognitive problems, although the tangles still formed.

    3. A. J. Myers et al., Hum. Mol. Genet. 14, 2399 (2005).

      Myers and colleagues examined patients that had died of progressive supranuclear palsy, a disease caused by a mutation in the tau gene.

      They found that these patients also had an increased risk for Alzheimer’s disease, pointing to an important connection between tau and Alzheimer’s.

    4. R. Tanzi, L. Bertram, Cell 120, 545 (2005).

      Tanzi and Bertram review the "amyloid hypothesis," which is the idea that a build-up of amyloid-β into plaques causes problems in tau, which then form tangles, causing the symptoms of Alzheimer’s disease.

  7. Jun 2017
    1. J. Burgdorf, P. L. Wood, R. A. Kroes, J. R. Moskal, J. Panksepp, Behav. Brain Res. 182, 274–283 (2007).

      The authors show that microstimulation of regions of the brain associated with reward pathways can trigger 50 kHz USVs in rats.

      They also use drug treatments to demonstrate the involvement of dopamine signaling pathways in the prodution of 50 kHz USVs.

    2. E. Bobrov, J. Wolfe, R. P. Rao, M. Brecht, Curr. Biol. 24, 109–115 (2014).

      Activity in the barrel cortex (a region of the somatosensory cortex) of rats is higher during social touch than it is when the rat is touched by an object. This suggests that the somatosensory cortex plays a role in both detecting touch and integrating information about the social context of the touch.

    3. V. Gazzola et al., Proc. Natl. Acad. Sci. U.S.A. 109, E1657–E1666 (2012).

      fMRI imaging shows that the somatosensory cortex plays a role in both the sensory detection of touch and the integration of emotional responses to that touch.

    4. B. Newman, M. A. O’Grady, C. S. Ryan, N. S. Hemmes, Percept. Mot. Skills 77, 779–785 (1993).

      This article describes the use of Pavlovian conditioning in humans to create an "expectation" of tickling. This is offered as an explanation for the tendency of people to respond to tickling gestures in the same way they would respond to actual tickling.

    5. J. Panksepp, J. Burgdorf, Physiol. Behav. 79, 533–547 (2003).

      Panksepp and Burgdorf describe the initial discovery and characterization of 50 kHz calls in the rat and present the case for interpreting these calls as laughter.

    6. C. R. Harris, Am. Sci. 87, 344–351 (1999).

      Harris reviews our current understanding of ticklishness in humans.

      This paper includes descriptions of the two types of tickle, different types of laughter, the physiology of human ticklishness, and the possible evolutionary basis of ticklishness.

    1. C. M. Wahle, Science 209, 689 (1980).

      Millepora spp. fire corals can live detect gorgonians and will actively grow special "attack" branches towards gorgonians and overgrow them.

    2. T. P. Hughes and J. B. C. Jackson, Science 209, 713 (1980).

      In a separate study of corals, small corals were less likely to be injured or damaged, but, when they were, they were much more likely to die.

  8. May 2017
    1. I’m trying an interesting experiment in which I read Dumas’s D’Artagnan romances and Brust’s Khaavren romances alternating, back and forth one after another. I kind of stalled out because The Viscount of Bragelonne is pretty boring. Hopefully Brust’s counterpart of it is more interesting.

      Very interesting, I did not know Brust's novels are connected to Dumas.

    1. J. K. Hartshorne, A. Schachner, Tracking replicability as a method of post-publication open evaluation. Front. Comput. Neurosci. 6, 8 (2012). doi: 10.3389/fncom.2012.00008; pmid: 22403538

      Hartshorne and Schachner suggest that replication success should be traced in a database connecting replication attempts with original studies. Based on this information, a replication success score could be computed, which could be used as a criterion for a journal's quality alongside other indicators such as citation counts.

    2. T. M. Errington et al., An open investigation of the reproducibility of cancer biology research. eLife 3, e04333 (2014). doi: 10.7554/eLife.04333; pmid: 25490932

      Similarly to the reproducibility project in psychology, Errington and colleagues planned to conduct replication attempts on 50 important papers from the field of cancer biology. While the registered reports are already available online, the replication studies themselves are currently still being conducted.

      Read more on eLife:

      https://elifesciences.org/collections/reproducibility-project-cancer-biology

    3. J. P. Simmons, L. D. Nelson, U. Simonsohn, False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol. Sci. 22, 1359–1366 (2011). doi: 10.1177/0956797611417632; pmid: 22006061

      Simmons and colleagues conduct computer simulations and two experiments that show how significant results can easily be achieved for a research hypothesis that is false. They show that flexibility --or as they call it: researcher degrees of freedom --in four areas make it more likely to find significant effects for a false hypothesis:

      1. Flexibility in choosing the dependent variables reported: When researchers flexibly analyze two related dependent variables, this already almost doubles the probability of finding a positive result for a false hypothesis.

      2. Flexibility in choosing the sample size: When researchers stop data collection, find no significant result, and collect additional data before checking for the same effect, this increases the probability of finding a positive result for a false hypothesis by 50%.

      3. Flexibility in the use of additional variables included in the analyses: When researchers include additional variables in the analyses, false positive rates more than double.

      1. Flexibility in the number of experimental conditions reported: When researchers collect data in three experimental conditions and flexibly decide whether to report the result of comparisons between any two conditions or all three, this more than doubles the false positive rate.

      If researchers used research practices where they used all four flexibilities, they would, overall, be more likely to find positive results although the underlying hypothesis was indeed false.

    4. R. Rosenthal, The file drawer problem and tolerance for null results. Psychol. Bull. 86, 638–641 (1979). doi: 10.1037/0033- 2909.86.3.638

      Rosenthal addresses the 'file drawer problem', a questionable research practice where only studies that showed the desired result would be published and all other studies would land in the 'file drawer' and thus unknown to the scientific community.

      In the extreme case, this could mean that, if a specific effect did not exist in reality, the 5% of studies that (due to statistical error allowed) find this effect get published and discussed as if the effect were true, whereas 95% of studies do not (and rightly so) find the effect, but are tucked away in a file drawer. This problem hinders scientific progress, as new studies would build on old, but false, effects.

      Rosenthal introduces a way to assess the size of the file drawer problem, the tolerance to future null results: calculating the number of studies with null results that would have to be in a file drawer before the published studies on this effect would be called into question.

    5. B. A. Nosek, J. R. Spies, M. Motyl, Scientific utopia: II. Restructuring incentives and practices to promote truth over publishability. Perspect. Psychol. Sci. 7, 615–631 (2012). doi: 10.1177/1745691612459058; pmid: 26168121

      Nosek and colleagues argue that scientists are often torn between "getting it right" and "getting it published." While finding out the truth is the ultimate goal of research, more immediately, researchers need to publish their work to be successful in their profession.

      A number of practices, such as the establishment of journals emphasizing reports of non-significant results, are argued to be ill suited for improving research practices. To reconcile the two seemingly-at-odds motives, Nosek and colleagues suggest measures such as lowering the bar for publications and emphasizing scientific rigor over novelty, as well as openness and transparency with regard to data and materials.

    6. L. K. John, G. Loewenstein, D. Prelec, Measuring the prevalence of questionable research practices with incentives for truth telling. Psychol. Sci. 23, 524–532 (2012). doi: 10.1177/ 0956797611430953; pmid: 22508865

      John, Loewenstein and Prelec conducted a survey with over 2,000 psychologists to identify to what extent they used questionable research practices (QPRs). The respondents were encouraged to report their behavior truthfully, as they could increase donations to a charity of their choice by giving more truthful answers.

      Results showed that a high number of psychologists admitted to engaging in QRPs. Almost 70% of all respondents admitting to not reporting results for all dependent measures and around 50% of respondents admitting to reporting only studies that showed the desired results.

      Moreover, results showed that researchers suspected their peers also occasionally engaged in such QRPs, but that psychologists thought that there was generally no good justification for engaging in QRPs.

    7. G. S. Howard et al., Do research literatures give correct answers? Rev. Gen. Psychol. 13, 116–121 (2009). doi: 10.1037/a0015468

      Howard and colleagues examine how the file drawer problem---that is, the tendency of researchers to publish positive results but not negative or inconclusive results--affects a body of research literature. They compare "old," existing bodies of literature that could be suffering from the file drawer problem with a newly constructed body of literature guaranteed to be free of the file drawer problem, which they achieved by conducting new studies.

      This investigation suggests that some bodies of literature are supported as relatively file-drawer-free, while other bodies of literature raise concern and kindle further studies on the effects they include.

    8. A. G. Greenwald, Consequences of prejudice against the null hypothesis. Psychol. Bull. 82, 1–20 (1975). doi: 10.1037/h0076157

      Greenwald examines how research practices discriminate against accepting the null hypothesis (that an effect does not exist). Using a simulation, he suggests that too few publications accept the null hypothesis, and that a high proportion of publications falsely reject the null hypothesis when it would have held.

      Greenwald further debunks traditional arguments about why a null hypothesis should not be accepted, and suggests ways to improve research practices to improve the acceptance of accepting the null hypothesis.

    9. D. Fanelli, “Positive” results increase down the hierarchy of the sciences. PLOS ONE 5, e10068 (2010). doi: 10.1371/journal. pone.0010068; pmid: 20383332

      Fanelli assessed more than 2000 papers from different scientific disciplines and found that the proportion of studies reporting support for their hypotheses is higher in disciplines such as psychology or economics as compared to disciplines such as space science. It is concluded that both the type of hypotheses tested and the rigor applied in these tests differ between fields.

    10. K. S. Button et al., Power failure: Why small sample size undermines the reliability of neuroscience. Nat. Rev. Neurosci. 14, 365–376 (2013). doi: 10.1038/nrn3475; pmid: 23571845

      Button and colleagues study the average statistical power of studies in neuroscience, and conclude that it is low. They highlight that low power does not only mean that studies have a lower chance of detecting a true effect, but that when using such low-powered studies, it is also becomes less likely that a significant effect indeed reflects a true effect.

      It is argued that using studies with low power may seem efficient at the first glance, because less money is spent on subjects. However, because future research could be building on an erroneous line of investigations, low-powered studies are inefficient in the long-run.

    1. Y. Yan, S. Shin, B. S. Jha, Q. Liu, J. Sheng, F. Li, M. Zhan, J. Davis, K. Bharti, X. Zeng, M. Rao, N. Malik, M. C. Vemuri, Efficient and rapid derivation of primitive neural stem cells and generation of brain subtype neurons from human pluripotent stem cells. Stem Cells Transl. Med. 2, 862–870 (2013).

      This study presents an efficient method to produce neural stem cells from human pluripotent stem cells.

      The system presented in this study enables the creation of NSC banks, increasing cell therapy applications.

    2. Z. W. Naing, G. M. Scott, A. Shand, S. T. Hamilton, W. J. van Zuylen, J. Basha, B. Hall, M. E. Craig, W. D. Rawlinson, Congenital cytomegalovirus infection in pregnancy: A review of prevalence, clinical features, diagnosis and prevention. Aust. N. Z. J. Obstet. Gynaecol. 56, 9–18 (2016).

      This study examines the effects on the developing fetus of congenital cytomegalovirus infection.

    3. C. Grief, R. Galler, L. M. C. Côrtes, O. M. Barth, Intracellular localisation of dengue-2 RNA in mosquito cell culture using electron microscopic in situ hybridisation. Arch. Virol. 142, 2347–2357 (1997).

      In this study, Grief et al. used electron microscopy to localize dengue virus in infected mosquito cells.

      They concluded that the smooth membrane structures are an important site for the production of virus particles.

    4. H. Tang, C. Hammack, S. C. Ogden, Z. Wen, X. Qian, Y. Li, B. Yao, J. Shin, F. Zhang, E. M. Lee, K. M. Christian, R. A. Didier, P. Jin, H. Song, G. L. Ming, Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell 18, 1–4 (2016).

      Tang’s article highlights the impact of ZIKV infection on both cell death and dysregulation of the cell cycle.

    5. G. Calvet, R. S. Aguiar, A. S. Melo, S. A. Sampaio, I. de Filippis, A. Fabri, E. S. Araujo, P. C. de Sequeira, M. C. de Mendonça, L. de Oliveira, D. A. Tschoeke, C. G. Schrago, F. L. Thompson, P. Brasil, F. B. Dos Santos, R. M. Nogueira, A. Tanuri, A. M. de Filippis, Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: A case study. Lancet Infect. Dis. (2016).

      In this article, the authors were able to detect the Brazilian Zika virus in amniotic fluid and compare its genome to other Zika strains and flaviviruses. In doing so, they hoped to find out if there had been recombination events between them.

      The authors collected amniotic fluid samples from women whose fetuses were diagnosed with microcephaly, extracted DNA purified virus particles, and analyzed the samples with qRT-PCR.

      They found that the different viruses share 97–100% of their genomes and that there had been no recombination events.

    6. C. G. Woods, J. Bond, W. Enard, Autosomal recessive primary microcephaly (MCPH): A review of clinical, molecular, and evolutionary findings. Am. J. Hum. Genet. 76, 717–728 (2005).

      Woods et al. discuss some clinical aspects of microcephaly but mainly focus on molecular and evolutionary factors.

      From an evolutionary point of view, changes in genes linked to a microcephalic phenotype might have been responsible for the evolution of the human brain size.

      Woods et al. also note that microcephaly is the consequence of a mitotic deficiency in neural precursors.

    7. E. C. Gilmore, C. A. Walsh, Genetic causes of microcephaly and lessons for neuronal development. WIREs Dev. Biol. 2, 461–478 (2013).

      Microcephaly is caused by abnormal cell growth in the brain leading to a reduced brain size.

      Mutations in genes involved in the cell cycle could be one factor causing this phenomenon.

      Here, the authors showed that variations in brain size is more related to the number of connections between neurons.

    1. To game theorists, many situations can be modeled in a similar way to the classic Prisoner’s Dilemma including issues of nuclear deterrence, environmental pollution, corporate advertising campaigns and even romantic dates.

      See The Tragedy of the Commons.

    1. P. Azoulay, J. Graff-Zivin, D. Li, B. Sampat, Public R&D investments and private sector patenting: Evidence from NIH funding rules, NBER working paper 20889 (2013); http://irps.ucsd.edu/assets/001/506033.pdf.

      This paper shows a link between grants and private-sector innovations and created a model to quantify the variation in funding for different fields.

      Their results show an increase in private-sector patents by NIH.

    2. R. K. Merton, Science 159, 56–63 (1968).

      In this article, the sociological expression "the rich get richer and the poor get poorer", also called Matthew effect, is presented in the context of scientific publication.

      Scientists who have received grants in the past are more likely to get more grants and produce results.

    3. W. R. Kerr, The ethnic composition of US inventors, Working Paper 08-006, Harvard Business School (2008); http://www.people.hbs.edu/wkerr/Kerr%20WP08_EthMatch.pdf.

      This study applies an ethnic-name database to individual patent records granted by the United States Patent and Trademark Office to document these trends with greater detail than previously available.

    4. B. A. Jacob, L. Lefgren, J. Public Econ. 95, 1168–1177 (2011).

      The authors of this paper evaluated the impact of NIH grants on publications. They concluded that researchers who did not get an NIH grant but simultaneously applied for others grants saw one more publication (+7%).

    5. J. Berg, Productivity metrics and peer review scores: NIGMS feedback loop blog (2011); https://loop.nigms.nih.gov/2011/ 06/productivity-metrics-and-peer-review-scores.

      This article is a reasonable hypothesis that preliminary data that contribute to receiving an outstanding peer review score likely lead to high visibility publications shortly after the grant is funded.

    6. S. Cole, J. R. Cole, G. A. Simon, Science 214, 881–886 (1981).

      This article is about one negative effect of peer review, that an individual scientist devotes so much time and energy to getting financial support that it takes away from their science.

      Basically, a huge disadvantage of the peer review program is that scientists must spend too much time writing what they intend to research, rather than performing the research.

    7. D. F. Horrobin, JAMA 263, 1438–1441 (1990).

      The main goal of peer review in the biomedical sciences is to facilitate the introduction into medicine of improved ways of curing, relieving, and comforting patients. The achievement of this aim requires both quality control and the encouragement of innovation. If an appropriate balance between the two is lost, then peer review will fail to reach its purpose.

    8. B. Alberts, M. W. Kirschner, S. Tilghman, H. Varmus, Proc. Natl. Acad. Sci. U.S.A. 111, 5773–5777 (2014).

      This study describes the advances in scientific knowledge and human health that have accrued as a result of the long-standing public investment in biomedical research.

  9. Apr 2017
    1. A. H. S. Holbourn, Mechanics of head injuries. Lancet 242, 438–441 (1943).

      Holbourn compared the head to a jar containing gelatin, hypothesizing that if the jar was shaken or violently rotated it would cause a shearing effect. He believed this shearing may be the culprit behind TBI.

    2. F. W. Mott, The effects of high explosives upon the central nervous system. Lancet 187, 331–338, 441–449, 545–553 (1916). War Neuroses and Shell Shock (Frowde, Hodder &Stoughton, London, 1919).

      Mott's investigation of "shell shock" in WWI veterans was the first human clinicopathological analysis of the physical effects of blast exposure on the brain.

      The idea that an explosion could cause damage to the brain, and therefore potentially be responsible for mental deficits, led to a controversial national inquiry into blast exposure and veterans' health.

    3. D. R. Richmond, E. G. Damon, I. G. Bowen, E. R. Fletcher, C. S. White, Air-blast studies with eight species of mammals. Techn Progr Rep DASA 1854. Fission Prod. Inhal. Proj. 1–44 (1967).

      U.S. Department of Defense study that focused on blast-related lung injury and influenced thought behind blast-related injury for nearly half a century.

    4. H. Celander, C. J. Clemedson, U. A. Ericsson, H. I. Hultman, The use of a compressed air operated shock tube for physiological blast research. Acta Physiol. Scand. 33, 6–13 (1955).

      One of the first uses of a compressed gas shock tube to study blast exposure in an animal model.

    5. B. I. Omalu, S. T. DeKosky, R. L. Minster, M. I. Kamboh, R. L. Hamilton, C. H. Wecht, Chronic traumatic encephalopathy in a National Football League player. Neurosurgery 57, 128–134 (2005).

      A report of the long-term effects of repetitive head injury linked to American football.

    6. C. W. Hoge, D. McGurk, J. L. Thomas, A. L. Cox, C. C. Engel, C. A. Castro, Mild traumatic brain injury in U.S. Soldiers returning from Iraq. N. Engl. J. Med. 358, 453–463 (2008).

      An influential paper that drew national attention to mild TBI in military veterans.

    1. Entic's naval history

      A new naval history, or, Compleat view of the British marine... by John Entick was published in London in 1757.

    1. J. L. Robertson, J. Barling, Greening organizations through leaders’ influence on employees’ pro-environmental behaviors. J. Organ. Behav. 34, 176-194 (2013)

      This research examined 139 pairs of leaders and followers in the United States and Canada. What they found is that transformational leadership behaviors positively influence the environmental behavior of followers. "Transformational leaders" are trusted by followers because they have shown themselves to be experts, yet they make followers feel important too. Such leaders energize and empower followers to take on risks and to overcome challenges, trusting them to make good choices and feel confident about it. Perhaps surprisingly, transformational leadership is a teachable skill.

    2. P. W. Schultz, Strategies for promoting proenvironmental behavior: Lots of tools but few instructions. Eur. Psychol. 19, 107-117 (2014)

      Schultz reviews the most common strategies for facilitating more sustainable behaviors. There are quite a variety of tools that can be employed, such as education, prompts, feedback, incentives, social norms, and public commitments. Which ones will prove most useful depends on how high or low the relative barriers and benefits are. This balance is affected by factors such as how challenging, novel, and (un)popular the new behavior is, how deeply ingrained the old habits are, and the relative likelihood of changing the context; for instance, infrastructure often takes a long time to change.

    3. S. van der Linden, E. Maibach, A. Leiserowitz, Improving public engagement with climate change: Five “best practice” insights from psychological science. Perspect. Psychol. Sci. 10, 758–763 (2015)

      American decision-makers have procrastinated about making climate change–related policies because it is hard to see, feel, and understand the effects of climate change. These Yale University researchers use psychological research to describe how to engage people in the urgent task of reducing our climate impacts.

      It is important to: highlight the local and personal impacts of a climate change, connect the proposed activity to behaviors that are already considered normal, highlight the benefits that people will gain, and tap into people’s emotions and values—including the sense of an ethical responsibility to other species, future humans, and the poor and marginalized.

    4. D. M. Kahan, E. Peters, M. Wittlin, P. Slovic, L. L. Ouellette, D. Braman, G. Mandel, The polarizing impact of science literacy and numeracy on perceived climate change risks. Nat. Clim. Change 2, 732-735 (2012)

      Though the scientific community is in overwhelming agreement that climate change is a threat to human well-being, much of the public does not view the issue as a major risk.

      In prior work, the "Cultural Cognition Thesis" proposes that this is because people form their ideas of risk by looking at how others in their identity groups perceive an issue. In contrast, the "Science Comprehension Thesis" proposes that it happens because people are not good at thinking like scientists.

      Research by Kahan and colleagues finds support for the Cultural Cognition Thesis, but no evidence for the Science Comprehension Thesis.

      Learn more at National Public Radio: http://www.npr.org/templates/story/story.php?storyId=124008307

    5. R. B. Cialdini, Influence: The Psychology of Persuasion (Harper Business, New York, revised edition, 2006).

      This classic book reviews six key sources of persuasion:

      1. Reciprocity: People feel compelled to return favors;
      2. Commitment and consistency: People are more likely to agree to do something if they've agreed to something similar in the past;
      3. Social proof: Especially in new situations, we watch what other people do and then copy it;
      4. Authority: We do what a respected authority tells us to do;
      5. Liking: We do what people we like do or tell us to do
      6. Scarcity: We tend to be persuaded to do something if time is running out or if there's a risk that we might miss out.
    6. G. Hardin, The tragedy of the commons. Science 162, 1234-1248 (1968)

      This classic article describes what psychologists call "commons dilemmas." A commons dilemma occurs when individuals are tempted to overuse a shared resource.

      In a commons dilemma, the immediate consequence benefits the individual, but the long-term consequence punishes the group.

    7. M. van Vugt,V. Griskevicius, P. W. Schultz, Naturally green: harnessing stone age psychological biases to foster environmental behavior. Soc. Issues Policy Rev. 8, 1-32 (2014)

      These authors suggest that efforts to get people to behave sustainably are most successful when they harmonize with—rather than deny—our deeply embedded, evolutionary-based human tendencies. They identify five human tendencies and propose solutions that are consistent with them:

      1. We are self-interested. Thus, emphasize benefits to people and their families.
      2. We want to have more status than the people around us. Encouraging friendly competitions can increase motivation because people want to win.
      3. We imitate others. Therefore, it is important to publicly display and communicate expected behavior.
      4. We focus on the present. Thus, emphasize today's consequences.
      5. We ignore what we can't sense. Therefore it is important to make the invisible visible.
    8. S. Bamberg, G. Möser, Twenty years after Hines, Hungerford, and Tomera: A new meta-analysis of psycho-social determinants of pro-environmental behaviour. J. Environ. Psychol. 27, 14–25 (2007)

      Meta-analyses are "studies of studies," meaning that they look at patterns across a large number of research projects that focus on the same topic. This meta-analysis looked at data from 57 different samples. They conclude that psychological variables such as perceived control over a behavior, a sense of moral obligation to act, how difficult the behavior is, and whether their friends and family would support the behavior are connected to whether people intend to behave in pro-environmental ways. The intention to behave in pro-environmental ways, in turn, is the best predictor of actual pro-environmental behavior.

      Another important feature of this article is that it replicates a previous meta-analysis completed 20 years ago and has consistent findings, meaning that even after 20 years, the patterns seem to be the same.

    9. C. Roser-Renouf, E. Maibach, A. Leiserowitz, S. Rosenthal, Global Warming’s Six Americas and the Election (Yale Program on Climate Change Communication, New Haven, CT, 2016)

      A research group at Yale University regularly measures the American public's views on climate change. People have a range of views from those who are extremely worried to those who dismiss climate change as not being real. The six categories are: alarmed, concerned, cautious, disengaged, doubtful, and dismissive. During the 2016 presidential election, only the alarmed group (17% of Americans) considered a candidate's position on climate change to be an important factor when deciding for whom to vote.

    10. J. Mistry, A. Berardi, Bridging indigenous and scientific knowledge. Science 352, 1274-1275 (2016)

      This article discusses how Traditional Ecological Knowledge (TEK) has helped indigenous groups maintain the biodiversity of their land and adapt to climate change. It contrasts TEK with more traditional quantitative experiments and suggests that the two approaches to understanding ecosystems can benefit from each other.

    11. S. Schein, A New Psychology for Sustainability Leadership: The Hidden Power of Ecological Worldviews (Greenleaf, Sheffield, UK, 2015)

      This book is the first to make the case that people who lead sustainability movements within organizations are most effective if they possess an ecologically accurate understanding of how the physical world works.

    12. N. Geiger, J. K. Swim, Climate of silence: Pluralistic ignorance as a barrier to climate change discussion. J. Environ. Psychol. 47, 79-90 (2016)

      This article is the first major publication to apply the well-known psychological phenomenon called "pluralistic ignorance" to discussions about climate change.

      Pluralistic ignorance is when people believe, inaccurately, that the person they are talking to might disagree with them, and decide not to speak up.

      In the case of climate change, most Americans believe that it is occuring and that it is caused by humans, yet this research shows that people fail to speak up about climate change, believing that the person they are talking to might deny climate change exists.

    13. C. Roser-renouf, E. W. Maibach, A. Leiserowitz, X. Zhao, The genesis of climate change activism: From key beliefs to political action. Clim. Change 125, 163-178 (2014)

      This article addresses why people take political action about climate change. Researchers found that people are motivated to act only if they believe that a group effort by humans can reverse the course of climate change. Then, in order to act, people must believe that political actions such as calling elected officials and speaking up at meetings will have an impact on the governmental policies that impact climate change.

    14. A. M. Bliuc, C. McGarty, E. F. Thomas, G. Lala, M. Berndsen, R. Misajon, Public division about climate change rooted in conflicting socio-political identities. Nat. Clim. Change 5, 226-230 (2015)

      Bliuc and colleagues demonstrate that U.S. climate change worriers and skeptics hold very different social identities. These social identities have been formed around their opinion toward climate change (acceptance and concern vs. skepticism toward the science) rather than around demographic characteristics like religion or political party. The authors suggest that opinion about climate change has become a source of inter-group conflict similar to that surrounding the issues of abortion or same-sex marriage.

    15. L. Tay, E. Diener, Needs and subjective well-being around the world. J. Pers. Soc. Psychol. 101, 354-365 (2011)

      Psychologists have proposed for many years that human well-being increases when certain needs are fulfilled. Studies have explored basic physiogical needs, safety and security needs, social needs, and respect and autonomy needs. Little research, however, has examined whether these needs are common to all humans, or whether some of them are culture-specific.

      Tay and Diener looked at the relationship between different kinds of needs and subjective well-being in 123 countries. They found evidence that all human beings share a variety of psychological and social needs in addition to basic needs.

    16. T. Dietz, E. Ostrom, P. C. Stern, The struggle to govern the commons. Science 302, 1907-1912 (2003)

      This classic Science article examines Hardin's Tragedy of the Commons scenario with respect to global environmental commons such as oceans, freshwater, clean air, and the climate and atmosphere.

      Dietz, Ostrom, and Stern suggest that it is difficult to govern global environmental commons because many of the features of historically successful commons management are missing at the global scale. These features include limiting access to the resource, monitoring resource use, promoting frequent face-to-face contact between users, and enforcing rules dictating resource use.

      When it comes to our global environmental commons, the authors are guardedly optimistic that we can implement effective forms of governance and not over-exploit global natural resources.

    17. R. M. Ryan, E. L. Deci, Self-determination theory and the facilitation of intrinsic motivation, social development, and well-being. Am. Psychol. 55, 68–78 (2000). doi:10.1037/0003-066X.55.1.68

      Self-determination theory suggests that people are most motivated by situations that help them fulfill basic needs: autonomy, relatedness, and competence.

      People need autonomy, to feel they have choices and are free to decide what, when, and how to proceed, rather than being forced by rules, deadlines, or evaluation by others. We seek relatedness, a sense of being socially connected and accepted by others. Competence is the need to accomplish an action with grace and achieve the desired outcome, as opposed feeling uninformed, or not having the requisite skills or abilities to achieve success.

    18. R. Gifford, A. Nilsson, Personal and social factors that influence pro-environmental concern and behavior: A review. Int. J. Psychol. 49, 141-157 (2014)

      This is a review article, organizing and summarizing what research has been conducted and suggests what future research should focus on.

      Gifford and Nilsson review 18 factors that influence whether people behave in ways that help rather than hurt the environment. They organize the factors into two basic categories: personal and social.

      The authors also recognize that people sometimes behave in pro-environmental ways because it is practical (such as saving money) and not because of these personal and social factors.

    19. T. Hartig, P. H. Kahn Jr., Living in cities, naturally. Science 19, 938-940 (2016)

      This article reviews how important it is for humans to maintain a connection with nature, especially when living in city environments. Research shows that our emotional and physical health improves when we engage with nature. There are many natural features that can be added to streets and buildings to facilitate keeping connected with nature including urban rivers, parks for play, and rooftop gardens.

  10. Mar 2017
    1. By then end of my PhD, I had over 800 documents in my Sente library incuding journal articles and full books, many with highlights and notes. How am I supposed to find interesting bits related to one concept, idea or topic? My highlights and notes are there somewhere in those documents but there is no easy way of tracking them down and working with them. They are searchable or can be made searchable (see Jeff Pooley’s guide  on Macademic here), but that is often not very helpful. I would for instance like to see them in one place organized according to some logic. My current practice is that I make the highlights in Sente for any potential future use and at the same time I copy the text (quote) to Scrivener with the citation info and keep these snippets organized there. I would for instance have a card for ‘innovation (def.)’ in which I would only collect various definitions of innovation from the sources I read.

      Interesting process. I have tended to export all notes from one reference in a batch, and then organize them in DevonThink. In theory, this process is more efficient (I think) because I can process large numbers of notes in one go without constant app-switching. On the other hand, though, the method outlined is wonderfully direct: when you find information you need, you put it where you're going to need it.

    1. his tradi-tion, in which the theory of invention is reduced to a minimum and interest is focused on the per-suasive aspect of discourse, is represented by such original works as George Campbell's The Philosophy of Rhetoric (1776) and Richard Whately's Elements of Rhetoric (1828)

      Oh, hey, we know those guys. It's been a while since they've been mentioned in our readings, though.

  11. Feb 2017
    1. E. Y. Chiang, A. Hidalgo, J. Chang, P. S. Frenette, Nat. Methods 4, 219–222 (2007).

      This 2007 paper from Chiang et al. presented a new method for looking at the recruitment of different types of white blood cells to the site of an injury, while simultaneously identifying clusters of ligand-receptor couplings.

      All of this can be visualized in live mice!

      From this initial study, PSGL-1 was identified as a promising neutrophil ligand protein.

  12. Jan 2017
    1. T. F. Goreau, Ecology 40, 67 (1959).

      Goreau describes the species of corals found in Jamaica's reefs and the patterns of their distributions. He notes that the north and south coasts look different from each and hypothesizes that these differences are driven by differences in storm frequencies.

    2. J. H. Connell, Science 199, 1302 (1978).

      Connell describes a mechanism by which the high biodiversity of tropical rain forests and coral reefs is maintained by...

    3. N. Knowlton, J. C. Lang, M. C. Rooney, P. Clifford, Nature (London), in press.

      Severe tropical storms can cause widespread mortality in reef corals1,2. The Caribbean staghorn coral, Acropora cervicornis, although dependent on fragmentation for asexual propagation3–5, is particularly vulnerable to hurricane damage6,7. The most important agents of post-hurricane mortality are assumed to be high wave energy6 and change in salinity8, factors which typically soon diminish in intensity. We report here that there was substantial delayed tissue and colony death in A. cervicornis on a Jamaican reef damaged by Hurricane Alien. This previously undocumented degree of secondary mortality, sustained for 5 months and unrelated to emersion9, was over one order of magnitude more severe than that caused by the immediate effects of the storm. The elimination of >98% of the original survivors suggests potentially complex responses to catastrophes, involving disease10,11 and predation, which may explain the widely variable rates of reef recovery previously reported12–15.

    4. J. W. Porter, Science 186, 543 (1974).

      Coral reefs on both the Pacific and Caribbean sides of Panama do not experience extreme weather events such as hurricanes. Coral diversity in Panama is maintained by mechanisms other than extreme weather disturbances, such as predation by the crown-of-thorns seastar, Acanthaster planci.

    5. J. G. Ogg and J. A. Koslow, Pac. Sci. 32, 105 (1978).

      Researchers in Guam describe minimal damage to hard coral reefs after a typhoon and no long-term impact, even in exposed areas. This is likely due in part to the low, rugged profile of reefs in Guam.

    1. T. M. Errington et al., An open investigation of the reproducibility of cancer biology research. eLife 3, e04333 (2014). doi: 10.7554/eLife.04333; pmid 25490932

      Similarly to the reproducibility project in psychology, Errington and colleagues planned to conduct replication attempts on 50 important papers from the field of cancer biology. While the registered reports are already available online, the replication studies themselves are currently still being conducted.

      Read more on eLife: https://elifesciences.org/collections/reproducibility-project-cancer-biology

    2. B. A. Nosek, J. R. Spies, M. Motyl, Scientific utopia: II. Restructuring incentives and practices to promote truth over publishability. Perspect. Psychol. Sci. 7, 615–631 (2012). doi: 10.1177/1745691612459058; pmid 26168121

      Nosek and colleagues argue that scientists are often torn between "getting it right" and "getting it published": while finding out the truth is the ultimate goal of research, more immediately, researchers need to publish their work to be successful in their profession.

      A number of practices, such as the establishment of journals emphasizing reports of non-significant results, are argued to be ill suited for improving research practices. To reconcile the two seemingly-at-odds motives, Nosek and colleagues suggest measures such as lowering the bar for publications and emphasizing scientific rigor over novelty, as well as openness and transparency with regard to data and materials.

    3. L. K. John, G. Loewenstein, D. Prelec, Measuring the prevalence of questionable research practices with incentives for truth telling. Psychol. Sci. 23, 524–532 (2012). doi: 10.1177/ 0956797611430953; pmid 22508865

      John, Loewenstein and Prelec conducted a survey with over 2,000 psychologists to identify to which extent they used questionable research practices (QPRs). The respondents were encouraged to report their behavior truthfully, as they could increase donations to a charity of their choice by giving more truthful answers.

      Results showed that a high number of psychologists admitted to engaging in QRPs such as almost 70% of all respondents admitting to not reporting results for all dependent measures, or around 50% of respondents admitting to reporting only studies that showed the desired results. Moreover, results showed that researchers suspected their peers also occasionally engaged in such QRPs, but that psychologists thought that there was generally no good justification for engaging in QRPs.

    4. D. Fanelli, “Positive” results increase down the hierarchy of the sciences. PLOS ONE 5, e10068 (2010). doi: 10.1371/journal. pone.0010068; pmid 20383332

      Fanelli assessed more than 2000 papers from different scientific disciplines and found that the proportion of studies reporting support for their hypotheses increased in the disciplines such as psychology or economics compared to disciplines such as space science. It is concluded that both the type of hypotheses tested and the rigor applied in these tests differ between fields.

    5. K. S. Button et al., Power failure: Why small sample size undermines the reliability of neuroscience. Nat. Rev. Neurosci. 14, 365–376 (2013). doi: 10.1038/nrn3475; pmid 23571845

      Button and colleagues study the average statistical power of studies in neuroscience, and conclude that it is low. They highlight that low power does not only mean that studies have a lower chance of detecting a true effect, but that when using such low-powered studies, it is also becomes less likely that a significant effect indeed reflects a true effect. It is argued that using studies with low power may seem efficient at the first glance, because less money is spent on subjects, but that indeed, because future research could be building on an erroneous line of investigations, low-powered studies are inefficient in the long-run.

    6. J. K. Hartshorne, A. Schachner, Tracking replicability as a method of post-publication open evaluation. Front. Comput. Neurosci. 6, 8 (2012). doi: 10.3389/fncom.2012.00008; pmid 22403538

      Hartshorne and Schachner suggest that replication success should be traced in a database connecting replication attempts with original studies. Based on this information, a replication success score could be computed, which could be used as a criterion for a journal's quality alongside other indicators such as citation counts.

    7. G. S. Howard et al., Do research literatures give correct answers? Rev. Gen. Psychol. 13, 116–121 (2009). doi 10.1037/a0015468

      Howard and colleagues examine how the file drawer problem affects a research literature. They compare "old", existing bodies of literature that could be suffering from the file drawer problem (i.e., which could include the few studies were an effect was found, while studies yielding non-significant results on the same effect were never published) with a newly constructed body of literature guaranteed to be free of the file drawer problem, which they achieved by conducting new studies. This investigation suggests that some bodies of literature are supported as relatively file-drawer-free, while other bodies of literature raise concern and kindle further studies on the effects they include.

    8. A. G. Greenwald, Consequences of prejudice against the null hypothesis. Psychol. Bull. 82, 1–20 (1975). doi 10.1037/h0076157

      Greenwald examines how research practices discriminate against accepting the null hypothesis (that an effect does not exist). Using a simulation, he suggests that too few publications accept the null hypothesis, and that the proportion of publications which falsely reject the null hypothesis although it would have been true is high.

      Greenwald further debunks traditional arguments why a null hypothesis should not be accepted, and suggests ways to improve research practices to improve the acceptance of accepting the null hypothesis.

    9. J. P. Simmons, L. D. Nelson, U. Simonsohn, False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol. Sci. 22, 1359–1366 (2011). doi: 10.1177/0956797611417632; pmid 22006061

      Simmons and colleagues conduct computer simulations and two experiments that show how significant results can easily be achieved for a research hypothesis that is false. They show that flexibility - or as they call it: researcher degrees of freedom - in four areas contributes to making it more likely to find significant effects for a false hypothesis:

      1. Flexibility in choosing the dependent variables reported: When researchers flexibly analyze two related dependent variables, this already almost doubles the probability of finding a positive result for a false hypothesis. 2. Flexibility in choosing the sample size: When researchers stop data collection, find no significant result, and collect additional data before checking for the same effect, this increases the probability of finding a positive result for a false hypothesis by 50%.
      2. Flexibility in the use of additional variables included in the analyses: When researchers include additional variables in the analyses, false positive rates more than double.
      3. Flexibility in the number of experimental conditions reported: When researchers collect data in three experimental conditions and flexibly decide whether to report the result of comparisons between any two conditions or all three, this more than doubles the false positive rate.

      If researchers used research practices where they used all four flexibilities, they would, overall, be more likely than not to find positive results although the underlying hypothesis was indeed false.

    10. R. Rosenthal, The file drawer problem and tolerance for null results. Psychol. Bull. 86, 638–641 (1979). doi: 10.1037/0033- 2909.86.3.638

      Rosenthal addresses the 'file drawer problem', a questionable research practice where only studies that showed the desired result would be published and all other studies would land in the 'file drawer' and would not be known to the scientific community.

      In the extreme case, this could mean that, if a specific effect did not exist in reality, the 5% of studies that (due to statistical error allowed) find this effect get published and discussed as if the effect were true, whereas 95% of studies do not (and rightly so) find the effect, but are tucked away in a file drawer. This problem hinders scientific progress, as new studies would build on old, but false, effects.

      Rosenthal introduces a way to assess the size of the file drawer problem, the tolerance to future null results: calculating the number of studies with null results that would have to be in a file drawer before the published studies on this effect would be called into question.

    1. V. Vähätalo, M. Salkinoja-Salonen, P. Taalas, K. Salonen, Spectrum of the quantum yield for photochemical mineralization of dissolved organic carbon in a humic lake. Limnol. Oceanogr. 45, 664–676 (2000).

      This study measured sunlight driven conversion of DOC to CO<sub>2</sub> in a lake in southern Finland. They measured lower quantum yields than the authors found in the paper you just read.

  13. Nov 2016
    1. and what shall be the sign

      This line is from the Gospel of Mark.

    2. and the giver of Life

      This line is from the Chaldean Oracles.

    1. Y. Yan, S. Shin, B. S. Jha, Q. Liu, J. Sheng, F. Li, M. Zhan, J. Davis, K. Bharti, X. Zeng, M. Rao, N. Malik, M. C. Vemuri, Efficient and rapid derivation of primitive neural stem cells and generation of brain subtype neurons from human pluripotent stem cells. Stem Cells Transl. Med. 2, 862–870 (2013).

      This study presents an efficient method to produce neural stem cells from human pluripotent stem cells.

      The system presented in this study enables the creation of NSC banks, increasing cell therapy applications.

    2. Z. W. Naing, G. M. Scott, A. Shand, S. T. Hamilton, W. J. van Zuylen, J. Basha, B. Hall, M. E. Craig, W. D. Rawlinson, Congenital cytomegalovirus infection in pregnancy: A review of prevalence, clinical features, diagnosis and prevention. Aust. N. Z. J. Obstet. Gynaecol. 56, 9–18 (2016).

      This study examines the effects on the developing fetus of congenital cytomegalovirus infection.

    3. C. Grief, R. Galler, L. M. C. Côrtes, O. M. Barth, Intracellular localisation of dengue-2 RNA in mosquito cell culture using electron microscopic in situ hybridisation. Arch. Virol. 142, 2347–2357 (1997).

      In this study, Grief et al used electron microscopy to localize dengue virus in infected mosquito cells.

      They concluded that the smooth membrane structures are an important site for the production of virus particles.

    4. H. Tang, C. Hammack, S. C. Ogden, Z. Wen, X. Qian, Y. Li, B. Yao, J. Shin, F. Zhang, E. M. Lee, K. M. Christian, R. A. Didier, P. Jin, H. Song, G. L. Ming, Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell 18, 1–4 (2016).

      Tang’s article highlights the impact of ZIKV infection on both cell death and dysregulation of the cell cycle.

    5. G. Calvet, R. S. Aguiar, A. S. Melo, S. A. Sampaio, I. de Filippis, A. Fabri, E. S. Araujo, P. C. de Sequeira, M. C. de Mendonça, L. de Oliveira, D. A. Tschoeke, C. G. Schrago, F. L. Thompson, P. Brasil, F. B. Dos Santos, R. M. Nogueira, A. Tanuri, A. M. de Filippis, Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: A case study. Lancet Infect. Dis. (2016).

      In this article, the authors were able to detect the Brazilian Zika virus in amniotic fluid and compare its genome to other Zika strains and flaviviruses. In doing so, they hoped to find out if there had been recombination events between them.

      The authors collected amniotic fluid samples from women whose fetuses were diagnosed with microcephaly, extracted DNA purified virus particles, and analyzed the samples with qRT-PCR.

      They found that the different viruses share 97–100% of their genomes and that there had been no recombination events.

    6. C. G. Woods, J. Bond, W. Enard, Autosomal recessive primary microcephaly (MCPH): A review of clinical, molecular, and evolutionary findings. Am. J. Hum. Genet. 76, 717–728 (2005).

      Woods et al. discuss some clinical aspects of microcephaly but mainly focus on molecular and evolutionary factors.

      From an evolutionary point of view, changes in genes linked to a microcephalic phenotype might have been responsible for the evolution of the human brain size.

      Woods et al. also note that microcephaly is the consequence of a mitotic deficiency in neural precursors.

    7. E. C. Gilmore, C. A. Walsh, Genetic causes of microcephaly and lessons for neuronal development. WIREs Dev. Biol. 2, 461–478 (2013).

      Microcephaly is caused by abnormal cell growth in the brain leading to a reduced brain size.

      Mutations in genes involved in the cell cycle could be one factor causing this phenomenon.

      Here, the authors showed that variations in brain size is more related to the number of connections between neurons.

    1. P. Azoulay, J. Graff-Zivin, D. Li, B. Sampat, Public R&D investments and private sector patenting: Evidence from NIH funding rules, NBER working paper 20889

      This paper shows a link between grants and private-sector innovations and created a model to quantify the variation in funding for different fields.

      Their results show an increase in private-sector patents by NIH.

    2. R. K. Merton, Science 159, 56–63 (1968).

      In this article, the sociological expression "the rich get richer and the poor get poorer", also called Matthew effect, is presented in the context of scientific publication.

      Scientists who have received grants in the past are more likely to get more grants and produce results.

    3. B. A. Jacob, L. Lefgren, J. Public Econ. 95, 1168–1177 (2011).

      The authors of this paper evaluated the impact of NIH grants on publications. They concluded that researchers who did not get an NIH grant but simultaneously applied for others grants saw one more publication (+7%).

    4. J. Berg, Productivity metrics and peer review scores: NIGMS feedback loop blog (2011)

      This article is a reasonable hypothesis that preliminary data that contribute to receiving an outstanding peer review score likely lead to high visibility publications shortly after the grant is funded.

    5. S. Cole, J. R. Cole, G. A. Simon, Science 214, 881–886 (1981).

      This article is about one negative effect of peer review, that an individual scientist devotes so much time and energy to getting financial support that it takes away from their science.

      Basically, a huge disadvantage of the peer review program is that scientists must spend too much time writing what they intend to research, rather than performing the research.