1,011 Matching Annotations
  1. Aug 2016
    1. K. S. Gobush, B. M. Mutayoba, S. K. Wasser, Conserv. Biol. 22, 1590–1599 (2008).

      This paper examined the long-term impact of poaching on elephant family structure, stress levels, and reproductive output approximately 15 years after the 1989 ivory ban was implemented. Before the ban, widespread poaching drastically altered the demographic structure of the African elephant family groups by decreasing the number of old adult female elephants.

      The authors specifically examined 218 adult female African elephants from 109 groups that differed in size, age structure, and average genetic relatedness.

      Females from groups that lacked an old matriarch, first-order relatives, and strong social bonds had significantly higher stress hormone levels than females from groups where these features existed. Female elephants from groups disrupted by poaching had significantly lower reproductive output.

      The negative impact of poaching persisted 15 years after the 1989 ivory ban was implemented.

    1. enabling the drongo to steal the abandoned food (11,12)

      In this study, the authors demonstrated that drongos are heartless.

      Melissa can edit as SitC

  2. Jul 2016
    1. A. Jacob, L. Lefgren, Are idle hands the devil's workshop? Incapacitation, concentration, and juvenile crime. Am. Econ. Rev. 93, 1560–1577 (2003).

      Findings from this study suggest that when juveniles are not engaged in supervised activities they are more likely to engage in certain anti-social behaviors; at the same time, the increase in interactions associated with school attendance leads to more interpersonal conflict and violence.

    2. L. Lochner, E. Moretti, The effect of education on crime: Evidence from prison inmates, arrests, and self-reports. Am. Econ. Rev. 94, 155–189 (2004).

      Using Census and FBI data, this study finds that schooling significantly reduces the probability of incarceration and arrest.

    3. P. J. Cook, J. Ludwig, in Controlling Crime: Strategies and Tradeoffs, P. J. Cook, J. Ludwig, J. McCrary, Eds. (University of Chicago Press, Chicago, 2011), pp. 1–39.

      Controlling Crime considers alternative ways to reduce crime that do not sacrifice public safety. Among the topics considered here are criminal justice system reform, social policy, and government policies affecting alcohol abuse, drugs, and private crime prevention.

    4. W. J. Wilson, When Work Disappears: The World of the Urban Poor (Alfred Knopf, New York, 1996).

      In this book, W. J. Wilson persuasively argues that problems endemic to America's inner cities--from fatherless households to drugs and violent crime--stem directly from the disappearance of blue-collar jobs in the wake of a globalized economy

    5. E. I. Knudsen, J. J. Heckman, J. L. Cameron, J. P. Shonkoff, Economic, neurobiological, and behavioral perspectives on building America’s future workforce. Proc. Natl. Acad. Sci. U.S.A. 103, 10155–10162 (2006).

      This paper concludes that the most efficient strategy for strengthening the future workforce, both economically and neurobiologically, and improving its quality of life is to invest in the environments of disadvantaged children during the early childhood years.

    6. C. Uggen, Work as a turning point in the life course of criminals: A duration model of age, employment, and recidivism. Am. Sociol. Rev. 65, 529–546 (2000).

      A brief overview of research on the relationship between work and crime.

    7. Unemployment and criminal involvement: An investigation of reciprocal causal structures. Am. Sociol. Rev. 49, 398–411 (1984)

      This study showed that unemployment and crime mutually influence one another over the individual's life span.

    1. K. A. Oye, K. Esvelt, E. Appleton, F. Catteruccia, G. Church, T. Kuiken, S. B. Lightfoot, J. McNamara, A. Smidler, J. P. Collins , Regulating gene drives. Science 345, 626–628 (2014).

      This and the subsequent reference discuss the concept of and the dangers associated with gene drives.

      Gene drives are techniques that alter genes in such a way that biases their inheritance, making them spread more rapidly than normal through a population.

      Mutagenic chain reaction is an example of a powerful gene drive method. They list several checkpoints that they recommend be completed before the use of gene drive in endogenous populations, such as designing and testing techniques for reversal of the gene drive and long term studies to fully understand the consequences of a gene drive strategy.

  3. Jun 2016
    1. M. Rosel, C. Claas, S. Seiter, M. Herlevsen, M. Zoller, Oncogene 17, 1989 (1998).

      Describes how C4.4, a human GPI-anchored protein, was found.

    2. G. C. Fletcher et al., Br. J. Cancer 88, 579 (2003).

      Identifies hAG-2 and hAG-3 (nAG homologs) as ligands for C4.4, a GPI-anchored protein in humans.

    3. D. A. Thompson, R. J. Weigel, Biochem. Biophys. Res. Commun. 251, 111 (1998).

      hAG-2 (an nAG homolog in humans) is expressed alongside an estrogen receptor in breast-cancer cell lines. The authors propose that hAG may play some role in cancer.

    4. D. B. Drachman, M. Singer, Exp. Neurol. 32, 1 (1971).

      Acetycholine, a neurotransmitter for skeletal muscle, was once thought to be a molecule crucial in limb regeneration. However, this paper shows that when its release is inhibited, the limb still regenerates.

    5. K. Echeverri, E. M. Tanaka, Dev. Biol. 279, 391 (2005).

      Experiments showing the effects of Prod1 overexpression in regeneration are shown. Overexpression causes distal blastema cells to take on a proximal identity and disrupt proper limb patterning.

    6. S. Morais da Silva, P. B. Gates, J. P. Brockes, Dev. Cell 3, 547 (2002).

      This paper shows how Prod1 was discovered in salamanders and provides a basis for this paper, as nAG is ligand.

    7. M. Maden, Nature 295, 672 (1982).

      A research article that shows that vitamin A causes issues with the PD axis during regeneration of salamanders. This paper provides the basis for using vitamin A and other retinoids to disrupt proper limb regeneration.

    8. J. P. Brockes, Science 276, 81 (1997).

      A good overview of limb regeneration, specifically in salamanders. Discusses some molecular mechanisms in regards to limb specification and muscle regeneration.

    1. L. Hartwell, P. Szankasi, C. J. Roberts, A. W. Murray, S. H. Friend, Science 278, 1064 (1997).

      This article discusses the use of genetic profiling in tumors to determine the ideal course of treatment, something that has gained increasing attention as our sequencing technology improved.

    2. A. B. Niculescu et al., Mol. Cell. Biol. 18, 629 (1998).

      This article provided evidence that p21 might play a role in the G2-M checkpoint in addition to its established role at the G1-S checkpoint.

      Additionally, the paper looked at the protein Rb (retinoblastoma) and its role in checkpoint activation. Rb prevents cells from entering S phase when signals from growth factors are absent.

    3. Y. Li, C. W. Jenkins, M. A. Nichols, Y. Xiong, Oncogene 9, 2261 (1994).

      This paper showed that the levels of p21 normally oscillate throughout the cell cycle. However, in cells that did not have functional p53, no p21 was detected, implying that p21 expression is regulated by p53.

    4. A. Paoletti and M. Bornens, Prog. Cell Cycle Res. 3, 285 (1997).

      This paper discusses research on the process of centrosome duplication.

    5. K. Fukasawa, T. Choi, R. Kuriyama, S. Rulong, G. F. Vande Woude, Science 271, 1744 (1996).

      This paper established a role for p53 in the regulation of centrosomes, which enable the cell to separate its chromosomes during mitosis. Cells without functional p53 had abnormal numbers of centrosomes, leading to unequal chromosome segregation.

    6. S. Zhou et al., Proc. Natl. Acad. Sci. U.S.A. 95, 2412 (1998)

      This paper looked at the role of the protein SMAD4 in a pathway called TGF-β signaling. The authors used homologous recombination to disrupt the SMAD4 gene.

    7. H. Hermeking et al., Mol. Cell 1, 3 (1997).

      This article investigated the G2-M checkpoint in irradiated colorectal cancer cells and found that p53 induced the expression of a protein called 14-3-3, which triggers G2 arrest.

    8. D. P. Cahill et al., Nature 392, 300 (1998).

      This paper showed that mitotic checkpoints are often defective in cancer cells, leading to the chromosomal instability that may drive carcinogenesis (the development of cancer).

    9. T. J. McGarry and M. W. Kirschner, Cell 93, 1043 (1998).

      This paper described the protein geminin, which prevents DNA replication from occurring more than once per cell cycle. Geminin accumulates after DNA replication to block repeated replication, and it is degraded in mitosis so that the cell can replicate its DNA in the next S phase.

    10. P. L. Olive, J. P. Banath, R. E. Durand, Radiat. Res. 146, 595 (1996).

      This article looked into the survival of different cell lines treated with radiation. The authors observed the appearance of "giant cells" that had undergone extra rounds of replication, which in turn generated multiple nuclei.

    11. T. Waldman, C. Lengauer, K. W. Kinzler, B. Vogelstein, Nature 381, 713 (1996).

      This paper showed that when cells lacking p21 were treated with DNA-damaging agents, they frequently underwent extra rounds of replication, which led to deformed nuclei and cell death.

    12. J. P. Brown, W. Wei, J. M. Sedivy, Science 277, 831 (1997).

      This paper established a role for p21 in senescence, an age-dependent decline in the cell's ability to divide.

    13. T. Waldman, K. W. Kinzler, B. Vogelstein, Cancer Res. 55, 5187 (1995).

      This paper showed that p21 functioned downstream of p53 in the activation of the G1-S checkpoint.

    14. L. H. Hartwell and M. B. Kastan, Science 266, 1821 (1994); A. B. Niculescu et al., Mol. Cell. Biol. 18, 629 (1998)

      This review discusses what was known at the time about the regulation of the cell cycle and how we could potentially use this information to design new cancer drugs.

    1. M. A. Cuadros, J. Navascués, Prog. Neurobiol. 56, 173 (1998). 

      An early review of microglial origin in birds.

    2. P. Herbomel, B. Thisse, C. Thisse, Dev. Biol. 238, 274 (2001). 

      This study showed that invasion of embryonic tissue by yolk sac macrophages in zebrafish fails in the absence of macrophage colony-stimulating factor-1.

    3. I. M. Samokhvalov, N. I. Samokhvalova, S. Nishikawa, Nature 446, 1056 (2007).

      The authors of this study generated the RUNX1 fate mapping model used in this study and showed that yolk sac cells expressing Runx1 can develop into fetal lymphoid progenitors and adult hematopoietic stem cells (HSCs).

    4. G. Blevins, S. Fedoroff, J. Neurosci. Res. 40, 535 (1995).

      As shown in this paper, microglia are not affected by the autosomal recessive mutation osteopetrosis (op) that leads to a general skeletal sclerosis and decreased numbers of macrophages in various tissues.

    5. V. Chitu, E. R. Stanley, Curr. Opin. Immunol. 18, 39 (2006). 

      A review of the role of the colony-stimulating factor-1, also known as macrophage stimulating factor, in immunity and inflammation.

    6. F. Alliot, I. Godin, B. Pessac, Brain Res. Dev. Brain Res. 117, 145 (1999).

      This study suggested that microglia derive from yolk sac progenitors and actively proliferate in situ.

    7.  K. Liu et al., Science 324, 392 (2009); 10.1126/science.1170540. 

      This study examines the origin and differentiation of dendritic cells.

    8. S. H. Orkin, L. I. Zon, Cell 132, 631 (2008).

      A review of the developmental origins of hematopoietic stem cells and the molecular mechanisms that regulate lineage-specific differentiation.

    9. A. M. Lichanska, D. A. Hume, Exp. Hematol. 28, 601 (2000). 

      In this review of the studies on the origins, phenotype, and function of embryonic phagocytes the authors conclude that yolk sac–derived macrophages constitute a separate lineage.

    10. K. Liu et al., Nat. Immunol. 8, 578 (2007). 

      This study showed that limited recruitment of cells by the recipient in parabiotic models can be attributed to a short half-life of the donor-derived cells in the blood.

    11. A. Mildner et al., Nat. Neurosci. 10, 1544 (2007). 

      In this study the authors identified a unique population of peripheral Ly-6C(hi)CCR2(+) monocytes, which are preferentially recruited into the lesioned brain following irradiation.

    12. B. Ajami, J. L. Bennett, C. Krieger, W. Tetzlaff, F. M. Rossi, Nat. Neurosci. 10, 1538 (2007). 

      Using parabiosis and irradiation in an experimental autoimmune encephalitis mouse model of multiple sclerosis, the authors found that peripheral monocytes infiltrate the brain and contribute to the progression of the disease but do not contribute to the pool of resident microglial cells.

    13. L. J. Lawson, V. H. Perry, S. Gordon, Neuroscience 48, 405 (1992). 

      Yet another early study supporting the hypothesis of microglial turnover via division and recruitment of peripheral monocytes into the brain parenchyma in the absence of the overt blood-brain barrier disruption.

    14. E. A. Ling, J. Anat. 128, 847 (1979). 

      One of the earlier studies of microglial origin, supporting their monocytic origin.

    15. R. M. Ransohoff, V. H. Perry, Annu. Rev. Immunol. 27, 119 (2009). 

      This is a comprehensive review of the ontogeny and functions of microglial cells.

    1. M. Sinha et al., Science 344, 649–652 (2014).

      Similar to this study, which showed that a young systemic factor could improve neurogenesis in old mice, Sinha et al. 2014 tested the same concept in muscle.

      Exposure of GDF-11 in old mice led to improved muscle structure, restored genomic integrity in adult muscle stem cells, increased strength, and increased capacity for exercise.

    2. C. L. Grady et al., Neuroimage 8, 409–425 (1998).

      This study, conducted in 1999, was one of the first to study the effects of age on brain networks. At the time, little was known about the relationship between age and brain mechanisms of changes in memory.

      This study showed that age is related to changes in verbal memory, and not picture memory.

    3. L. Katsimpardi et al., Stem Cells 26, 1796–1807 (2008).

      Neurogenesis is restricted to two main areas of the brain (subventricular zone and dentate gyrus) by precursor cell proliferation and differentiation. BM88/Cend1 is a neuronal lineage specific regulator. In this study, Katsimpardi et al. studied the effects of this regulator in postnatal neurogenesis.

      They found that BM88 is important for cell cycle control and neuronal differentiation in the neonatal subventricular zone, in the transition from neuroblast to mature neurons in mouse brains.

    4. J. Luo, S. B. Daniels, J. B. Lennington, R. Q. Notti, J. C. Conover, Aging Cell 5, 139–152 (2006).

      Here, the authors study the subventricular zone (SVZ) to investigate the decline in neurogenesis during aging. By conducting electron microscopy imaging, and labeling cells, they examine the cytoarchitecture of the SVZ.

      They found a specific dorsolateral aspect of the SVZ, which retains features of a neurogenic stem cell niche in elderly mice.

    5. S. A. Villeda et al., Nature 477, 90–94 (2011).

      This study shows the effects of systemic factors on the decline of age-related neurogenesis. They found that chemokines CCL1/Eotaxin is present in aging mice, and is associated with reduced neurogenesis. Similar to this Katsimpardi et al. study, increasing the levels of the blood-borne factor CCL1 in young mice led to decreased neurogenesis and impaired learning and memory.

    6. H. van Praag, G. Kempermann, F. H. Gage, Nat. Neurosci. 2, 266–270 (1999).

      Exposure to an enriched environment increases neurogenesis in adult mice. Examples of enriched environments include larger housing, voluntary exercise, social interactions, and learning opportunities. Enhanced neurogenesis in enriched environments is also linked to improved spatial memory capabilities.

      This study shows that voluntary exercise alone can improve enhanced neurogenesis in adult mice.

    7. Q. Shen et al., Science 304, 1338–1340 (2004).

      Here, endothelial cells were identified as critical components of the neural stem cell niche.

      Factors derived from endothelial cells promote neural stem cell self-renewal and promotes neurogenesis.

    8. F. S. Loffredo et al., Cell 153, 828–839 (2013).

      Reference 13 describes a study similar to the one described in this paper, where heterochronic parabiotic mouse pairs were generated between young and old mice, to discover a reversal in the process of age-related cardiac hypertrophy.

      In this study, they observed a dramatic reduction in cardiac hypertrophy in old mice, due to being exposed to a blood-borne factor in young mice. In order to identify the special systemic factor, they profiled the proteome of young mice, and found that GDF11 declines with age, and exposure to GDF11 in old mice restored age-related cardiac hypertrophy.

    9. J. S. Snyder, A. Soumier, M. Brewer, J. Pickel, H. A. Cameron, Nature 476, 458 (2011).

      Reference 6 studies the effects of stress and anxiety on neurogenesis.

      Here, they found that a small subset of neurons in the dentate gyrus, which is responsible for the negative control of the hypothalamic-pituitary-adrenal axis. Elevation of stress hormones and anxiety are correlated with decreased neurogenesis.

  4. May 2016
    1. X. Zheng et al., Rev. Sci. Instrum. 83, 125001 (2012)

      This article reports the design of the high-resolution projection microstereolithography technique used by the authors.

      This technique is used in the present article to manufacture the different cellular solids (see Fig.2 A).

    2. W. Y. Jang, S. Kyriakides, A. M. Kraynik, Int. J. Solids Struct. 47, 2872–2883 (2010).

      The authors of this article investigated the compressive behavior of a random cell structure, a metallic foam.

      This structure was also manufactured by the authors of the present article and served for comparison purposes against the new ultralight and ultrastiff structures.

    3. J. D. Renton, Elastic Beams and Frames (Horwood, Chichester, UK, ed. 2, 2002).

      This book presents the basic theory and tools needed to study the behavior of elastic structures.

    4. V. S. Deshpande, N. A. Fleck, M. F. Ashby, J. Mech. Phys. Solids 49, 1747–1769 (2001).

      The goal of this article is to analyze the properties of the octet-truss unit cell using mechanical theory, simulations, and experiments.

      The octet-truss unit cell is the basic building block chosen by the authors of the present article to design their ultralight and ultrastiff materials.

    5. D. Rayneau-Kirkhope, Y. Mao, R. Farr, Phys. Rev. Lett. 109, 204301 (2012).

      In this article, the authors explain the process of manufacturing an ultralight fractal structure to obtain either hollow or solid objects. The potential applications are described.

    6. J. K. Cochran, K. J. Lee, D. McDowell, T. Sanders, Multifunctional metallic honeycombs by thermal chemical processing. In Processsing and Properties of Lightweight Cellular Metals and Structures, A. K. Ghosh, T. H. Sanders, T. D. Claar, Eds. (Minerals, Metals and Materials Society, Seattle, WA, 2002), p. 127–136.

      This chapter of a book describes the processing and the properties of a specific cellular class of solids: the metallic honeycombs.

    7. L. J. Gibson, MRS Bull. 28, 270–274 (2003).

      This text reviews the contents of a special issue of the MRS bulletin, dedicated to cellular solids.

    8. S. O. Kucheyev et al., Adv. Mater. 24, 776–780 (2012).

      This article describes the behavior of nanoporous silica aerogels: these objects are super compressible for ultralow densities.

    9. T. A. Schaedler et al., Science 334, 962–965 (2011)

      In this article, the authors have fabricated ultralight metallic microlattices and have performed mechanical testing on these objects.

      The elasticity of this material is proportional to the square of the density.

      Hence, the linear law desired by the authors of the present paper is not reached in this article.

    10. J. L. Gibson, F. M. Ashby, Cellular Solids: Structure and Properties (Cambridge Univ. Press, Cambridge, 2001).

      This book about cellular solids summarizes the theory needed to understand the structural properties and the mechanical behavior of cellular solids.

      The applications of these kinds of materials are also reviewed.

    11. S. Baudis et al., Biomed. Mater. 6, 055003 (2011).

      In this article, the authors report the design of a new biocompatible material in the vascular tissue engineering field.

    12. O. Y. Kwon, H. J. Ryu, S. Y. Jeong, J. Ind. Eng. Chem. 12, 306 (2006).

      This article describes the use of carbon microlattices as a catalyst support for chemistry applications.

    13. L. Valdevit, A. Pantano, H. A. Stone, A. G. Evans, Int. J. Heat Mass Transfer 49, 3819–3830 (2006).

      This article presents the optimization process in the design of metallic sandwiches for active cooling applications.

    14. T. A. Schaedler et al., Adv. Eng. Mater. 16, 276–283 (2014).

      This article describes the design of metallic microlattices for energy-absorbing applications.

    15. L. Valdevit, A. J. Jacobsen, J. R. Greer, W. B. Carter, J. Am. Ceram. Soc. 94, s15–s34 (2011).

      This article is a review of the manufacturing techniques available to produce microarchitectured materials.

      The conclusion of the review is that the technology is mature for the development, characterization, and optimal design of a novel class of multifunctional materials with the potential to achieve unprecedented combination of properties.

    1. S. R. Clark et al., Nat. Med. 13, 463–469 (2007).

      This paper details the process of how neutrophils, with the help of platelets, are able to trap bacteria in the blood and play an important role in controlling sepsis.

    2. J. J. Miner et al., Blood 112, 2035–2045 (2008).

      In this study, the deltaCD knock-in mice were prepared, whereas the cytoplamsic domain (CD) of PSGL-1 is removed.

    3. K. Szczur, Y. Zheng, M. D. Filippi, Blood 114, 4527–4537 (2009).

      In this paper, the authors show that neutrophils deficient in Cdc42 cannot maintain polarity (distinct leading edge and uropod).

    4. J. W. Semple, J. E. Italiano Jr., J. Freedman, Nat. Rev. Immunol. 11, 264–274 (2011).

      This is a review of the immune functions of platelets, the underdog cell type for most immunologists, This review highlights the essential roles platelets play in several immune functions.

    1. Introduction to Ecological Biochemistry

      An introductory textbook to the subject of "ecological biochemistry." This science is the study of the biochemistry of interactions between animals, plants and the environment, including the effect of plant toxins on animals.

    2. Revealing the paradox of drug reward in human evolution

      It is generally believe that drug abuse is the result of triggering reward systems in the brain. However, the most commonly used drugs are plant neurotoxins that evolved to deter herbivores from eating the plants, not reward them for it. How do we explain this contradiction?

      This paper outlines a few theories to explain this paradox, including the idea that humans may have evolved mechanisms to exploit these plant defenses.

    3. Effects of aging on acute toxicity of nicotine in rats.

      This and the publications listed immediately above and below it are meant to serve as evidence that while caffeine can be a stimulant and have positive effects, it is lethal when ingested at very high doses.

      This study showed that high doses of nicotine was lethal and caused convulsions in rats regardless of age. However, the older the rat was, the longer it took for the nicotine to be lethal. The older rats also had reduced neurobiological responses to the nicotine.

      The authors hypothesized that these effects reflected the older rats' reduced brain sensitivity to nicotine and decreased ability to metabolize nicotine in the liver.

    4. Pest control: Caffeine as a repellent for slugs and snails.

      This study published as a Nature Brief Communication showed that caffeine at high doses is lethal to slugs and snails.

      This and the two publications listed below it are meant to serve as evidence that while caffeine can be a stimulant and have positive effects, it is lethal when ingested at very high doses.

      This study has an important real-world application - as caffeine is a product that is already classified as "GRAS" (Generally Recognized as Safe) by the U.S. Food and Drug Administration, these results suggest caffeine has potential to be used as a safe alternative to some pesticides used on farm crops.

    5. Are we dependent upon coffee and caffeine? A review on human and animal data.

      This paper reviews available data on caffeine dependence, tolerance, reinforcement and withdrawal, including the effects of all of the above on humans and animals.

      It is referred to in this paper to support the idea that low doses of caffeine are mildly rewarding and enhance cognitive performance and memory retention.

    6. A case of fatal caffeine poisoning

      This and the two publications listed above it are meant to serve as evidence that while caffeine can be a stimulant and have positive effects, it is lethal when ingested at very high doses.

      This paper describes the case of a 21-year-old woman who ingested 10,000 mg of caffeine (and incredibly high dose). The woman went into cardiac arrest, and though she was resuscitated, she died in the hospital three days later.

    7. Tropical Agriculture: The value of bees to the coffee harvest.

      This paper counters the previously-held belief that the self-pollinating Coffea arabica plant did not benefit from insect pollinators. It shows that honeybees not only help with pollination, but also ultimately boost crop yields by over 50%.

    8. Economic value of tropical forest to coffee production

      This paper, as its title suggests, outlines an argument for the economic value of tropical forests to coffee production (and so argues against deforestation.) It is cited here to support the claim that plants of the genera Citrus and Coffea produce more fruits and seeds when pollinated by bees.

    9. Materials and methods are available in the supplementary materials in Science Online

      Found here

    10. M. E. Bitterman, R. Menzel, A. Fietz, S. Schafer

      This paper describes the experimental procedure behind the classical conditioning of proboscis extension in honeybees. It appears to be the first paper to do so, indicating its authors first established this protocol.

    11. Caffeine-induced synaptic potentiation in hippocampal CA2 neurons

      This paper shows that caffeine inhibits adenosine receptors and induces long-term potentiation of neurons in the hippocampus. This long-term potentiation of hippocampal neurons is critical for memory formation.

    12. Mushroom body memoir: From maps to models.

      This review discusses insect mushroom bodies. It is cited here as it discusses the evidence that mushroom bodies in insect brains participate in olfactory memory.

    13. Long-term synaptic plasticity in the honeybee.

      This paper describes the first demonstration of long-term synaptic plasticity in the honeybee brain. It is cited to show the long-term potentiation in insect neurons that is associated with memory formation.

    14. Selective impairment of learning and blockade of long-term potentiation by an N-methyl-D-aspartate receptor antagonist, AP5

      This paper showed that blocking long-term potentiation of hippocampal neurons interferes with learning and memory formation.

    15. Phytochemistry

      This paper found that there were significant amounts of caffeine in the pollen and nectar of citrus flowers. They further found that the presence of caffeine and other alkaloids was linked to the time during which the flowers were in full bloom (i.e., when a honeybee would be interested in them.)

    16. Evolution, discovery, and interpretations of arthropod mushroom bodies

      This paper is an overview of the history of research on mushroom bodies. Included in this overview is a discussion of the data showing that insect mushroom bodies are associated with olfactory learning.

    17. The role of extracellular adenosine in chemical neurotransmission in the hippocampus and basal ganglia: Pharmacological and clinical aspects

      This paper is cited here as it shows that caffeine can block A1 receptors (a presynaptic adenosine receptor in the brain).

    18. Associative and non-associative plasticity in kenyon cells of the honeybee mushroom body

      This paper showed that Kenyon Cells undergo associative plasticity after appetitive odor learning (as performed here with the conditioned scent.)

    19. Neural plasticity of mushroom body-extrinsic neurons in the honeybee brain

      This paper describes the first time that associative LTP was found in an interneuron of the insect nervous system (the authors stimulated honeybee Kenyon Cells and looked to see what happened.)

    20. Conditional modulation of spike-timing-dependent plasticity for olfactory learning

      This paper showed that spike-timing-dependent plasticity (STDP), which is responsible for adjustments in the strength of connections between neurons in the brain based on the relative timing of a particular neuron's output and input spikes, plays an important role in associative learning.

    21. Olfactory trace conditioning in Drosophila

      In order to look at the distinctions between the memory of an odor and a memory trace, the authors of this study established a protocol to look specifically at memories after trace conditioning.

    22. Mind the gap: Olfactory trace conditioning in honeybees.

      This study also describes the formation of memory traces that convey information about the initial odor that was used to stimulate the formation of the memory.

    23. Attraction, deterrance, or intoxication of bees (Apis mellifera) by plant allelochemicals.

      This paper tested the effects of certain defense chemicals produced by plants on honeybees. The alkaloids they tested, a group of chemicals that includes caffeine, were toxic and repellent to honeybees at relatively high concentrations.

    24. Consumption of an acute dose of caffeine reduces acquisition but not memory in the honey bee

      The study described in this reference is very similar to the one being performed here with one notable difference: the concentrations of caffeine being used were very high. The study's authors found that honeybees were repelled by very high concentrations of caffeine.

      Interestingly, such high concentrations did have have the same positive effect on the development of olfactory memory that low doses of caffeine had on the honeybees tested in this paper.

    25. Feeding responses of free-flying honeybees to secondary compounds mimicking floral nectars

      This study looked to see how honeybees reacted to compounds found naturally occurring in the nectar of some plants. The authors found that (with one exception) naturally occurring levels of these compounds did not have a repellent effect on the bees.

      However, concentrations of caffeine higher than those seen naturally occurring in floral nectar were repellent to the honeybees.

    26. Parallel reinforcement pathways for conditioned food aversions in the honeybee

      This study showed that honeybees can learn to detect toxins in nectar, remember that toxin and the negative effects it previously had, and in the future will avoid flowers whose nectar contains that toxin.

      This study did not use caffeine, but it proves the point that if caffeine was present in floral nectar at repellant concentrations, the bees would remember to avoid those flowers, which ultimately would have a negative effect on the plant's reproductive success.

    27. Caffeine: A well known but little mentioned compound in plant science

      This review sums up current knowledge of caffeine in the field of plant biology. It is cited here to back up the claim that caffeine has been found in the vegetative and seed tissues (as opposed to nectar and pollen) of plants in the genus Coffea at concentrations as high as 24 mg/mL. These values are quite high relative to the concentrations found in the nectar of these same plants.

    28. The evolution of floral scent: The influence of olfactory learning by insect pollinators on the honest signalling of floral rewards.

      This paper addresses the question of why flowers produce scent by looking at how olfactory learning of pollinators (like honeybees) influences how plants evolve to produce scents and chemicals in their nectar.

    29. Foraging dynamics of bumble bees: Correlates of movements within and between plant species.

      This study examines what conditions influenced foraging bumblebees' decisions to continue foraging from the same species of plant or move to a different species. They found a wide variety of conditions that affect honeybee foraging behavior, but one of the most important determinants was the amount of reward a bee received from a flower (i.e. nectar).

    30. Pollinator-mediated selection on flower color allele drives reinforcement.

      This paper looked at how pollinators, like honeybees, can drive the selection of flower color.

      In short, because honeybees prefer some colors to others, plants with flowers that are that color are more frequently visited by pollinators. Therefore, they are able to reproduce more and become more common.

    31. Sex and the Single Mustard - Population-Density and Pollinator Behavior Effects on Seed-Set.

      This paper showed that mustard plants with larger flowers (which in this case were more attractive to pollinators) had more pollen transferred to pollinators per visit than plants with smaller flowers.

    32. Cholinergic synaptic transmission in insect mushroom bodies in vitro.

      This paper is cited in the supplementary materials as the source of the protocol for making electrophysiological recordings from neurons located in a sensilla on the tip of the honeybee's proboscis.

    33. Distinct electrophysiological properties in subtypes of nonspiking olfactory local interneurons correlate with their cell type-specific Ca2+ current profiles

      This paper is cited in the supplementary materials as the source of the protocol for the bee's sensitivity to bitter compounds.

    34. Variation in complex olfactory stimuli and its influence on odour recognition.

      This paper is cited in the supplementary materials as the source of the protocol for part of their conditioning assay. As in this study, bees were trained by placing them in the conditioning arena and exposing it to a four-second pulse with an odor.

    35. Massed and spaced learning in honeybees: The role of CS, US, the intertrial interval, and the test interval.

      This study was cited in the supplementary materials as the source for the 30 second time interval used between trials during their conditioning experiments.

    1. T. Rudel , Is there a forest transition? Deforestation, reforestation and development. Rural Sociol. 63, 533–552 (1998).

      In reference 23, Thomas Rudel explains how forests change with economies. When an impoverished society's economy starts to grow, the society then cuts down many of the tree in it's surrounding territory.

      Once the economy grows to a certain point, however, the deforestation is replaced with reforestation, and the forest is replanted.

      At this point the forests may then be managed like a crop in cycles of planting and harvesting timber.

    2. S. Rodrigues, S. J. Andelman, M. I. Bakarr, L. Boitani, T. M. Brooks, R. M. Cowling, L. D. Fishpool, G. A. Da Fonseca, K. J. Gaston, M. Hoffmann, J. S. Long, P. A. Marquet, J. D. Pilgrim, R. L. Pressey, J. Schipper, W. Sechrest, S. N. Stuart, L. G. Underhill, R. W. Waller, M. E. Watts, X. Yan , Effectiveness of the global protected area network in representing species diversity. Nature 428, 640–643 (2004).

      In reference 22, Rodriguez and colleagues investigate land/nature reserves around the globe. When added together, 11.5% of Earth's surface is protected in nature reserves.

      They found that although a substantial portion of land is protected, the locations of these reserves do not necessarily cover areas with different types of ecosystems and different types of plant and animal species.

      Therefore, the present state of these land reserves is not optimized to protect as many species of plants and animals as possible.

      Yet, data like what Hansen and colleagues present in this paper could help improve how and where we select new nature reserves to protect more species.

    3. T. M. Brooks, R. A. Mittermeier, G. A. da Fonseca, J. Gerlach, M. Hoffmann, J. F. Lamoreux, C. G. Mittermeier, J. D. Pilgrim, A. S. Rodrigues , Global biodiversity conservation priorities. Science 313, 58–61 (2006).

      In reference 21, Brooks and colleagues review the different management strategies that are used to conserve plant and animal species (e.g., biodiversity).

    4. P. Potapov et al ., Mapping the world’s intact forest landscapes by remote sensing. Ecol. Soc. 13, 51 (2008).

      In reference 20, Potapov and colleagues published a world map that outlines the "Intact Forest Landscapes" (i.e., large areas of undisturbed forest). You can view the map here.

    5. S. S. Saatchi, N. L. Harris, S. Brown, M. Lefsky, E. T. Mitchard, W. Salas, B. R. Zutta, W. Buermann, S. L. Lewis, S. Hagen, S. Petrova, L. White, M. Silman, A. Morel , Benchmark map of forest carbon stocks in tropical regions across three continents. Proc. Natl. Acad. Sci. U.S.A. 108, 9899–9904 (2011). Baccini, S. J. Goetz, W. S. Walker, N. T. Laporte, M. Sun, D. Sulla-Menashe, J. Hackler, P. S. A. Beck, R. Dubayah, M. A. Friedl, S. Samanta, R. A. Houghton , Estimated carbon dioxide emissions from tropical deforestation improved by carbon-density maps. Nature Clim. Change 2, 182–185 (2012). N. L. Harris, S. Brown, S. C. Hagen, S. S. Saatchi, S. Petrova, W. Salas, M. C. Hansen, P. V. Potapov, A. Lotsch , Baseline map of carbon emissions from deforestation in tropical regions. Science 336, 1573–1576 (2012).

      In references 16–18, the authors describe baseline measurements for carbon emissions and stocks in tropical forests/regions.

      Now, what is the difference between a carbon stock and a carbon emission?

      A carbon stock is stored carbon. (Think of a tree trunk made of carbon-rich cellulose and lignin.)

      A carbon emission, however, is carbon that has been released into the atmosphere. (Now, consider a tree trunk that has been burnt to ash, thereby releasing carbon.)

    6. Prishchepov, D. Muller, M. Dubinin, M. Baumann, V. Radeloff , Determinants of agricultural land abandonment in post-Soviet European Russia. Land Use Policy 30, 873–884 (2013).

      Why were agricultural lands abandoned in Eurasian coniferous forests?

      The answer lies in changing political regimes. A large number of farms were abandoned in post-Soviet Russia (after socialism fell) because the economy and institutions of Russia where undergoing a radical change.

    7. J. A. Foley, R. Defries, G. P. Asner, C. Barford, G. Bonan, S. R. Carpenter, F. S. Chapin, M. T. Coe, G. C. Daily, H. K. Gibbs, J. H. Helkowski, T. Holloway, E. A. Howard, C. J. Kucharik, C. Monfreda, J. A. Patz, I. C. Prentice, N. Ramankutty, P. K. Snyder , Global consequences of land use. Science 309, 570–574 (2005).

      Hansen and colleagues reference work from Jonathan Foley and colleagues (2005), which details how harvesting natural resources can have negative effects through a decrease in ecosystem services.

      For example, Foley and colleagues show that "forests in the Yangtze watershed help moderate" water flow, which then supplies a hydroelectric plant with energy (40 million kilowatt hours per year). This energy is valued at $610,000!

      In comparison, this value is roughly 40% of the value of the trees in the forest that are then harvested for timber.

      In comparison, this value is roughly 40% of the value of the trees in the forest that are then harvested for timber. Thus, harvesting resources (in this case timber) can negatively effect other ecosystem services (in this case water flow), which are also important (e.g., worth $610,000 in energy).

      Which came first, the rain or the rainforest? Find out here and discover one of the many ways that forests affect our water supply.

    8. S. Goetz, R. Dubayah , Advances in remote sensing technology and implications for measuring and monitoring forest carbon stocks and change. Carbon Manage. 2, 231–244 (2011).

      In reference 40, Goetz and Dubayah summarize both aircraft and satellite imaging techniques. They also explain how tree canopy height is measured.

      Tree canopy height is measured by light reflectance. First, a laser on a satellite (in this case, NASA's Geoscience Laser Allometry System, or GLAS) is emitted and pointed at the surface of Earth.

      The light from the laser reflects off of Earth's surface and is then received by the satellite. The time that it takes for this to happen can determine the distance from the satellite to Earth's surface.

      When the laser is emitted over a forest, the tree's leaves and branches reflect the energy, yet some of the laser's energy will still reach the ground and will be reflected from the surface of the soil.

      Thus, the satellite receives two main light reflectance measurements: reflectance from the ground and reflectance from the tree canopy.

      Then, the difference in the time it takes for the ground reflectance and canopy reflectance light to reach the satellite determines how tall the trees are.

      For more information, check out Figure 2.

      For Hansen and colleagues' study, they decided that any plant that had a canopy height of 5 m or taller was a tree (rather than a shrub or herbaceous plant).

      Thus, determining canopy height is an important step in processing the satellite images to find where forests are distributed around the world.

    9. P. Gong, J. Wang, L. Yu, Y. Zhao, Y. Zhao, L. Liang, Z. Niu, X. Huang, H. Fu, S. Liu, C. Li, X. Li, W. Fu, C. Liu, Y. Xu, X. Wang, Q. Cheng, L. Hu, W. Yao, H. Zhang, P. Zhu, Z. Zhao, H. Zhang, Y. Zheng, L. Ji, Y. Zhang, H. Chen, A. Yan, J. Guo, L. Yu, L. Wang, X. Liu, T. Shi, M. Zhu, Y. Chen, G. Yang, P. Tang, B. Xu, C. Giri, N. Clinton, Z. Zhu, J. Chen, J. Chen , Finer resolution observation and monitoring of global land cover: First mapping results with Landsat TM and ETM+ data. Int. J. Remote Sens. 34, 2607–2654 (2013).

      In reference 36, Gong and colleagues describe the first study that uses Landsat satellite images that photograph Earth's surface at a 30 m by 30 m resolution.

      With these photos, they characterized Earth's surface into different land types (e.g., agricultural land, forests, grasslands, ice).

      They found that "forests, grasslands, and shrublands cover 28.35%, 13.37%, and 11.49% of the world, respectively. … Inland waterbodies, barren lands, and snow and ice cover 3.56%, 16.51%, and 12.81% of the world, respectively."

    10. M. Hansen, R. S. DeFries, J. R. G. Townshend, M. Carroll, C. Dimiceli, R. A. Sohlberg , Global percent tree cover at a spatial resolution of 500 meters: First results of the MODIS vegetation continuous fields algorithm. Earth Interact. 7, 1–15 (2003).

      In reference 30, Hansen and colleagues look at tree cover using the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument.

      The calculations for tree cover were then used in this current paper to determine forest distribution, loss, and gain.

      Also, note that technology is continuously advancing. Reference 30 was published in 2003. At this time MODIS was the most sophisticated satellite imaging instrument available. Yet, it could take images at a resolution of only 500 meters squared.

      In this paper from 2013, Hansen and colleagues use Landsat data that has a resolution of 30 meters squared.

    11. M. Hansen, A. Egorov, D. P. Roy, P. Potapov, J. Ju, S. Turubanova, I. Kommareddy, T. R. Loveland , Continuous fields of land cover for the conterminous United States using Landsat data: First results from the Web-Enabled Landsat Data (WELD) project. Remote Sens. Letters 2, 279–288 (2011).

      In reference 29, Hansen and colleagues detail the use of Landsat data to look at continent-scale images.

      This initial study helped Hansen and colleagues to then scale up to look at global patterns in land change in the present study.

    12. F. Achard, H. D. Eva, H. J. Stibig, P. Mayaux, J. Gallego, T. Richards, J. P. Malingreau , Determination of deforestation rates of the world’s humid tropical forests. Science 297, 999–1002 (2002).

      In reference 35, Achard and colleagues investigate deforestation in tropical humid forests. To do this, they surveyed 100 sites in Latin America, Africa, Southeast Asia, and India.

      Hansen and colleagues build off of this study by looking at all forests worldwide and do not limit themselves to particular sites.

    1. F. V. Mariani, G. R. Martin, Nature 423, 319 (2003).

      Discusses models of skeletal patterning.

    2. L. Niswander, Nat. Rev. Genet. 4, 133 (2003).

      Review of pattern formation in vertebrates, but more under the sense of development rather than regeneration.

    3. M. Carlson, Principles of Regenerative Biology (Elsevier Inc., London, 2007).

      A "textbook" that provides a basic foundation in regenerative biology. Discusses the dependence of skeletal muscle regeneration on nerves.

    4. G. Lemke, Sci. STKE 2006, pe11 (2006).

      Review article. Describes how Neuregulin-1 is the likely signaling molecule that causes myelin formation.

    5. J. P. Brockes, A. Kumar, Science 310, 1919 (2005).

      Review article. Discusses the field of limb regeneration in vertebrates and its possible contribution to medicine.

    6. T. Endo, S. V. Bryant, D. M. Gardiner, Dev. Biol. 270, 135 (2004).

      Describes a step-wise procedure for examining limb regeneration. However, this paper is referenced in regard to the fact that they demonstrate deviation of the nerve can cause an ectopic blastema.

      A diagram of their protocol can be found here

    1. M. Edwards, P. Scardina, L. S. McNeill, “Enhanced coagulation impacts on water treatment plant infrastructure” [American Water Works Association (AWWA) Research Foundation, Denver, CO, 2004].

      This is a book reference that includes information on experiments and case studies done to compare ferric chloride and aluminum use in water treatment and their effects on concrete corrosion.

    2. AWWA, Dawn of the Replacement Era: Reinvesting in Drinking Water Infrastructure (AWWA, Denver, CO, 2001).

      This reference can be visited in order to get an idea of approaching water infrastructure replacement requirements.

      They estimated that the budget requirement for the replacement of water infrastructures will be about $250 billion in the next 30 years.

    3. Volket al., Impact of enhanced and optimized coagulation on removal of organic matter and its biodegradable fraction in drinking water. Water Res. 34, 3247–3257 (2000).

      This reference investigates the use of an enhanced coagulation process in order to remove not only the particles, but also dissolved organic material in the water, which will help to increase the drinking water quality.

    4. U.S. Environmental Protection Agency, “Technical report: Hydrogen sulfide corrosion in wastewater collection and treatment systems” (publication 430/09-91-010, EPA, Washington, DC, 1991).

      This reference is a technical report by the Environmental Protection Agency.

      It consists of parts including: national assessment of corrosion; effects of industrial pretreatment, detection, prevention, and repair of hydrogen sulfide corrosion damage.

      The reference can be reached by visiting this link

    5. R. Fabris, C. W. K. Chow, M. Drikas, B. Eikebrokk, Comparison of NOM character in selected Australian and Norwegian drinking waters. Water Res. 42, 4188–4196 (2008).

      This study investigates the changes in the natural organic matter (NOM) concentration in raw and conventionally treated drinking waters in two hemispheres. They investigated the characteristics of NOM in Norwegian and Australian waters as well as the effect of coagulation treatment.

    6. M. Elimelech, W. A. Phillip, The future of seawater desalination: Energy, technology, and the environment. Science 333, 712–717 (2011).

      This paper looks in depth into the issue of seawater desalination. It is trying to answer questions such as energy requirements, how new materials/technologies can improve it, and sustainability. In this paper, the reference is used to convey the idea that these technologies still require improvement to compete with conventional drinking water treatment.

  5. Apr 2016
    1. K. M. Esvelt, A. L. Smidler, F. Catteruccia, G. M. Church , Concerning RNA-guided gene drives for the alteration of wild populations. eLife 10.7554/eLife.03401 (2014).

      Esvelt et al. bring up several additional precautions to consider before use of gene drive on native populations, such as determining if gene drives could incorporate into related species and performing field trials of both the gene drive and the gene drive reversal.

    2. J. E. DiCarlo, A. Chavez, S. L. Dietz, K. M. Esvelt, G. M. Church , http://biorxiv.org/content/early/2015/01/16/013896 (2015).

      The DiCarlo et al. study describes a method that can help prevent accidental release of mutagenic chain reaction organisms into the environment.

    3. R. Bassett, C. Tibbit, C. P. Ponting, J. L. Liu , Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4, 220–228 (2013).

      In this reference, the authors designed the gRNA targeting the fly yellow locus that Gantz and Bier used in the current paper. They chose to use this gRNA sequence because the authors in the reference here showed that this gRNA sequence resulted in the highest percentage (88%) of yellow mosaic flies of the 4 gRNAs tested.

    4. S. J. Gratz, F. P. Ukken, C. D. Rubinstein, G. Thiede, L. K. Donohue, A. M. Cummings, K. M. O’Connor-Giles , Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics 196, 961–971 (2014).

      In this paper, the authors use homology-directed repair (the same technique used in the current paper to generate the MCR allele) to introduce foreign DNA sequences at specific genome sites in the fly. This was an important advancement because most other studies have used CRISPR/Cas technology to create insertion or deletion mutations in target genes. The Gratz et al. paper showed that CRISPR/Cas9 could also be used to introduce large DNA sequences into specific sites of the fly genome.

    5. F. Port, H. M. Chen, T. Lee, S. L. Bullock , Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 111, E2967–E2976 (2014).

      In this article, the authors design two transgenic Drosophila melanogaster lines expressing Cas9 protein and guide RNAs that target either the ebony or yellow genes. The gRNAs guide Cas9 to these genes and induce mutations. They determined that their strategy for targeting these genes was highly efficient and specific.

    6. P. D. Hsu, E. S. Lander, F. Zhang , Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262–1278 (2014).

      In this extensive review, Feng Zhang discusses in detail the original use of CRIPSR/Cas in bacteria, the timeline for its use in research, and how it has been used for genome editing.

    7. F. Zhang, Y. Wen, X. Guo , CRISPR/Cas9 for genome editing: Progress, implications and challenges. Hum. Mol. Genet. 23, R40–R46(2014).

      The Feng Zhang lab has been instrumental in the development of CRISPR/Cas technology for use in genome engineering. In this review, Zhang summarizes how the tool works, how it can be used for genome editing, regulating gene expression, and for gene therapy as well as some of the limitations/weaknesses that are associated with the technology.

    1. M. R. Looney, B. M. Gilliss, M. A. Matthay, Curr. Opin. Hematol. 17, 418–423 (2010).

      This is a review of clinical findings that explain the cellular responses in TRALI. They also talk about how the interaction between neutrophils and platelets is essential to trigger TRALI.

    2. M. Phillipson et al., J. Exp. Med. 203, 2569–2575 (2006).

      This paper is a good read to see time-lapse videos of intravital imaging and confocal microscopy. It explains how neutrophils require distinct mechanisms to first bind and then crawl out of the vasculature.

  6. Mar 2016
    1. G. W. Kling, G. W. Kipphut, M. M. Miller, J. W. O’Brien, Integration of lakes and streams in a landscape perspective: The importance of material processing on spatial patterns and temporal coherence. Freshw. Biol. 43, 477–497 (2000).

      This study measured how chemical and biological properties of the water in Toolik Lake and its surrounding streams change over time.

      This paper is cited in the supplemental information because the authors used the same analysis methods in the two papers for measuring water chemistry parameters.

    2. Y. Zhang, W. Chen, D. W. Riseborough, Temporal and spatial changes of permafrost in Canada since the end of the Little Ice Age. J. Geophys. Res. 111, D22103 (2006).

      This study used a model to measure the amount of permafrost decrease that occurred between 1850 and 2002 and found that there was enough change to potentially impact landscape, hydrology, and ecosystems.

    3. G. W. Kling, G. W. Kipphut, M. C. Miller, Arctic lakes and streams as gas conduits to the atmosphere: Implications for tundra carbon budgets. Science 251, 298–301 (1991).

      This study showed that carbon from Arctic soils can be released as carbon dioxide from Arctic surface waters.

    4. J. E. Vonk, Ö. Gustafsson, Permafrost-carbon complexities. Nat. Geosci. 6, 675–676 (2013).

      This letter to the editor makes an argument that transport of permafrost carbon into surface waters and beyond is important to consider when modeling the carbon cycle in the Arctic.

    5. D. McGuire, L. G. Anderson, T. R. Christensen, S. Dallimore, L. Guo, D. J. Hayes, M. Heimann, T. D. Lorenson, R. W. Macdonald, N. Roulet, Sensitivity of the carbon cycle in the Arctic to climate change. Ecol. Monogr. 79, 523–555 (2009).

      This review examines the impacts of climate change on the carbon cycle in the Arctic.

    6. C. Tarnocai, J. G. Canadell, E. A. G. Schuur, P. Kuhry, G. Mazhitova, S. Zimov, Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem. Cycles 23, GB2023 (2009).

      This study reported a higher and more reliable estimate of the total amount of carbon stored in Arctic permafrost relative to previous studies. They included deeper soils and additional pools of carbon.

    7. E. A. G. Schuur, J. G. Vogel, K. G. Crummer, H. Lee, J. O. Sickman, T. E. Osterkamp, The effect of permafrost thaw on old carbon release and net carbon exchange from tundra. Nature 459, 556–559 (2009).

      This study found that on a decadal time scale, melting permafrost is a large source of carbon to the atmosphere, even when increases in carbon dioxide use by new plant life is taken into consideration.

    8. R. M. Cory, B. C. Crump, J. A. Dobkowski, G. W. Kling, Surface exposure to sunlight stimulates CO2 release from permafrost soil carbon in the Arctic. Proc. Natl. Acad. Sci. U.S.A. 110, 3429–3434 (2013).

      This study showed that dissolved organic carbon (DOC) that is exposed to sunlight is more susceptible to being broken down by microbial respiration than DOC that is kept in the dark (i.e., photostimulated bacterial respiration is important).

      The authors cite this paper heavily in their supplemental information. Many of the same methods were used in the two papers, including those for field sampling, light absorption measurements, and measurements of photostimulated bacterial respiration.

    9. E. A. G. Schuur, J. Bockheim, J. G. Canadell, E. Euskirchen, C. B. Field, S. V. Goryachkin, S. Hagemann, P. Kuhry, P. M. Lafleur, H. Lee, G. Mazhitova, F. E. Nelson, A. Rinke, V. E. Romanovsky, N. Shiklomanov, C. Tarnocai, S. Venevsky, J. G. Vogel, S. A. Zimov, Vulnerability of permafrost carbon to climate change: Implications for the global carbon cycle. Bioscience 58, 701–714 (2008).

      This review describes the pathways for permafrost carbon to enter the atmosphere and the changes in Arctic ecosystems that could be caused by permafrost thawing. They conclude that the overall impact of thawing permafrost will be to increase atmospheric carbon and global climate change.

    10. H. MacDougall, C. A. Avis, A. J. Weaver, Significant contribution to climate warming from the permafrost carbon feedback. Nat. Geosci. 5, 719–721 (2012).

      This paper uses a model to measure the feedback between global warming and permafrost melting (i.e., how much additional warming will occur because warming is causing additional carbon dioxide and methane to enter the atmosphere).

    11. V. Vähätalo, K. Salonen, U. Münster, M. Järvinen, R. G. Wetzel, Photochemical transformation of allochthonous organic matter provides bioavailable nutrients in a humic lake. Arch. Hydrobiol. 156, 287–314 (2003).

      This study found that sunlight converted dissolved organic carbon, nitrogen, and phosphorous into forms that are more easily consumed by bacteria and plankton in a lake in Norway. The bacteria and plankton were able to be more productive when grown in sunlight-exposed waters.

    12. R. M. Cory, D. M. McKnight, Y.-P. Chin, P. Miller, C. L. Jaros, Chemical characteristics of fulvic acids from Arctic surface waters: Microbial contributions and photochemical transformations. J. Geophys. Res. 112, G04S51 (2007).

      This paper shows that both sunlight and microbial transformation of dissolved organic carbon (DOC) is important to consider when examining the structure of DOC remaining in surface water. Additionally, it is important to consider how long the DOC has been present in the surface water.

    13. Koehler, T. Landelius, G. A. Weyhenmeyer, N. Machida, L. J. Tranvik, Sunlight-induced carbon dioxide emissions from inland waters. Global Biogeochem. Cycles (2014).

      This study is very similar to the one you just read. These authors studied sunlight-driven dissolved organic carbon degradation in Swedish lakes and found that 12% of the carbon dioxide released by the lakes was from photodegradation.

    14. R. M. Cory, K. McNeill, J. P. Cotner, A. Amado, J. M. Purcell, A. G. Marshall, Singlet oxygen in the coupled photochemical and biochemical oxidation of dissolved organic matter. Environ. Sci. Technol. 44, 3683–3689 (2010).

      This study determined the effect of a specific type of sunlight-driven degradation of dissolved organic carbon (DOC) on the availability of DOC to be eaten by bacteria.

      The authors cite this paper in the supplemental information because they used the same methods for measuring oxygen consumption by bacteria in water samples.

    1. S. E. Taylor, J. D. Brown , Illusion and well-being: A social psychological perspective on mental health. Psychol. Bull. 103, 193–210 (1988).

      In this paper, the authors argue that positive self-biases (overly positive self-evaluations, illusion of personal control, and unrealistic optimism) are characteristic of normal human thought.

      In addition, the authors say that these positive illusions are adaptive and beneficial for mental health, in that they promote more satisfying connections with others, greater productivity, and greater resilience in response to negative feedback.

    2. R. E. Nisbett, T. D. Wilson , Telling more than we can know: Verbal reports on mental processes. Psychol. Rev. 84, 231–259 (1977).

      Here, Nisbett and Wilson review evidence that supports the idea that people generally have relatively little insight into their own psychological/cognitive processes. When it comes to the process of a stimulus causing/influencing a response, people can be unaware of the stimulus itself, unaware of the response, or unaware of how the stimulus influenced the response.

      The authors argue that although people can attempt to report on the mechanisms that underlie their thoughts, decisions, etc., these self-reported explanations are not necessarily accurate, and they rely more on people's lay theories about how cognition should work, as opposed to how it actually does work.

    3. S. P. Wojcik, P. H. Ditto , Motivated happiness: Self-enhancement inflates self-reported subjective well-being. Soc. Psychol. Personal. Sci. 5, 825–834 (2014).

      Here, the authors report on the "happier-than-average effect," which shows that greater self-enhancement (either because of individual differences or experimental manipulation) leads to greater reports of subjective well-being.

    4. J. R. Hibbing, K. B. Smith, J. R. Alford , Differences in negativity bias underlie variations in political ideology. Behav. Brain Sci. 37, 297–307 (2014).

      Hibbing, Smith, and Alford argue that individuals' reactions, both physiological and psychological, to negative events and stimuli underlie a major part of the differences between political liberals and conservatives. Their argument centers around the idea that, compared with liberals, conservatives display greater responses to negativity.

    5. M. H. Kernis , Toward a conceptualization of optimal self-esteem. Psychol. Inq. 14, 1–26 (2003).

      This theoretical paper examines the potential for differences between high self-esteem and "optimal" self-esteem. Kernis makes the argument that high self-esteem can be either fragile (nonoptimal) or secure (optimal), depending on factors such as the defensiveness and stability of that self-esteem.

  7. Dec 2015
    1. K. L. Flanagan, R. van Crevel, N. Curtis, F. Shann, O. Levy, Optimmunize Network,

      Researchers have also noted that there are differences in the gender of the child that can change how protective the Measles vaccine is at protecting against other illnesses.

    2. P. Aaby, T. R. Kollmann, C. S. Benn, Nonspecific effects of neonatal and infant vaccination: Public-health, immunological and conceptual challenges. Nat. Immunol. 15, 895–899 (2014).

      WHO and other researchers have found that the Measles vaccine, and other live vaccines, can have effects of childhood mortality not associated with the vaccine target. This reference is a review of some of the studies done in the past to try and better understand this off target effect.

    3. P. Aaby, A. Bhuiya, L. Nahar, K. Knudsen, A. de Francisco, M. Strong, The survival benefit of measles immunization may not be explained entirely by the prevention of measles disease: A community study from rural Bangladesh. Int. J. Epidemiol. 32, 106–115 (2003).

      Scientists use a sample from Bangladesh to look at data similar to the results of this paper. They also find that Measles vaccinating reduces childhood mortality not due to Measles, specifically from diarrhea and oedema. However, the data used in their analysis is only one sample of a population and is confounded by some study control issues.

  8. Nov 2015
    1. B. Rasch, C. Büchel, S. Gais, J. Born , Odor cues during slow-wave sleep prompt declarative memory consolidation. Science 315, 1426–1429 (2007).

      In this study participants were asked to memorize stimuli and were either presented with a smell during the learning process or not. Then during sleep, participants were either re-exposed to the same smell as during learning, a different new smell, or no smell. Participants that were re-exposed to the same smell as during learning had better memory for the items the following morning than either the participants exposed to a new smell or to no smell during sleep.

    2. J. D. Rudoy, J. L. Voss, C. E. Westerberg, K. A. Paller , Strengthening individual memories by reactivating them during sleep. Science 326, 1079 (2009).

      In this study participants learned where to place pictures on a grid on the computer screen. While they learned the locations, each picture was also associated with a sound (e.g. a picture of a bell was also associated with a bell sound). Then, while participants took a nap, half of the sounds were replayed while they slept. After the nap, participants had a better memory for the picture locations of the sounds that were played during sleep than the sounds that were not played during sleep.

    3. M. A. Wilson, B. L. McNaughton , Reactivation of hippocampal ensemble memories during sleep. Science 265, 676–679 (1994).

      In this a seminal study in the area of sleep and memory. Rats have brain cells called 'place cells' that activate when they are in specific locations in their environment. In a series of experiments these researchers demonstrated that place cells that fired in a specific order as the Rat moved around its environment activated in the same order during sleep.

      This was the first evidence that memories may be replayed during sleep after learning.

    4. M. Weisbuch, K. Pauker, N. Ambady , The subtle transmission of race bias via televised nonverbal behavior. Science 326, 1711–1714 (2009).

      In this study researchers extracted short clips from 11 popular television shows, muted the clip so no sound was produced, erased the character that was being interacted with, and asked participants to rate how the other characters were interacting with the 'invisible' character. Results showed that invisible White characters were interacted with more positively than invisible Black characters.

      These same clips were shown to another group of participants and the results showed that exposure to more racially biased nonverbal clips resulted in more implicit bias.

    5. Olsson, J. P. Ebert, M. R. Banaji, E. A. Phelps , The role of social groups in the persistence of learned fear. Science 309, 785–787 (2005).

      In this study researchers presented participants with two Black faces and two White faces. One of the Black faces and one of the White faces was paired wit a mild electric shock (painful but not hurtful) such that each time the participants saw one of the two shock-associated faces they received a shock.

      The researchers then continued to present the faces but stopped giving the shock and measured the fear response.

      The results showed that participants established a fear response to both Black and White shock-associated faces but the fear of the Black shock-associated face persisted while participants stopped fearing the White shock-associated face sooner. When this study was conducted with Black and White participants, for White participants the Black face continued to show a fear response, for Black participants the White face continued to show a fear response.

    6. Gawronski, R. Deutsch, S. Mbirkou, B. Seibt, F. Strack , When “Just Say No” is not enough: Affirmation versus negation training and the reduction of automatic stereotype activation. J. Exp. Soc. Psychol. 44, 370–377 (2008).

      This study compares two types of counterbias training. In one training. In the first type, participants were supposed to respond "YES" when they saw a counter-stereotype pair (e.g. male and weak or female and strong). In the other type of training participants were supposed to respond "NO" when they saw a stereotypical pair (e.g. male and strong or female and weak).

      The results showed that counter-stereotype training (saying yes to counter-stereotypes) DECREASED implicit bias while stereotype negation training (saying no to stereotypical pairs) INCREASED implicit bias.

    7. S. Crandall, A. Eshleman, L. O’Brien , Social norms and the expression and suppression of prejudice: The struggle for internalization. J. Pers. Soc. Psychol. 82, 359–378 (2002).

      In this study, participants rated how appropriate it would be to express prejudice to over 100 different groups (e.g. Black Americans and White Southerners but also liars, child molesters, drunk drivers, and doctors). Then a separate group of participants were asked to rate their personal feelings toward each of the 100 groups.

      The researchers found that willingness to express personal prejudice against a group was strongly related with how acceptable it was to express prejudice against that group.

    8. A. Nosek, F. L. Smyth, N. Sriram, N. M. Lindner, T. Devos, A. Ayala, Y. Bar-Anan, R. Bergh, H. Cai, K. Gonsalkorale, S. Kesebir, N. Maliszewski, F. Neto, E. Olli, J. Park, K. Schnabel, K. Shiomura, B. T. Tulbure, R. W. Wiers, M. Somogyi, N. Akrami, B. Ekehammar, M. Vianello, M. R. Banaji, A. G. Greenwald , National differences in gender-science stereotypes predict national sex differences in science and math achievement. Proc. Natl. Acad. Sci. U.S.A. 106, 10593–10597 (2009).

      In this study more than 500,000 participants completed the gender and academics Implicit Association Test (a test that measures your unconscious associations between different genders (males and females) and different academic areas (liberal arts and sciences).

      The researchers found that countries where participants had higher

      Nations with higher implicit bias scores (associating males with science and females with liberal arts) had larger differences between males' scores and females' scores on an international standardized 8th grade science test.

    9. D. A. Stanley, P. Sokol-Hessner, M. R. Banaji, E. A. Phelps , Implicit race attitudes predict trustworthiness judgments and economic trust decisions. Proc. Natl. Acad. Sci. U.S.A. 108, 7710–7715 (2011).

      In the trust game, participants were presented with a picture of a face and they had to decide whether to offer the person $10 or not. If the participant gave the person $10, the person received $40 and could either give the participant half (so they each received $20) or could keep it all for themselves. Participants saw 300 faces (100 White, 100 Black, and 100 other race) and made the decision to give $10 or not for each face.

      Researchers found that the amount of implicit bias participants had was correlated with how much more likely they were to offer a White person money than a Black person. This was not related to participants' explicit report of racist attitudes.

    10. A. Moss-Racusin, J. F. Dovidio, V. L. Brescoll, M. J. Graham, J. Handelsman , Science faculty’s subtle gender biases favor male students. Proc. Natl. Acad. Sci. U.S.A. 109, 16474–16479 (2012).

      Over 100 science faculty in research universities across the US were asked to determine a starting salary for and rate the application materials of potential research assistants. There were two versions of each application that were identical except that one had a female name and one had a male name. Each faculty member received one of the two versions for each application.

      Faculty members rated the male applications higher and suggested a higher starting salary than the identical female applications.

    11. J. Correll, B. Park, C. M. Judd, B. Wittenbrink, M. S. Sadler, T. Keesee , Across the thin blue line: Police officers and racial bias in the decision to shoot. J. Pers. Soc. Psychol. 92, 1006–1023 (2007).

      In a first-person-shooter videogame participants were instructed to shoot individuals that held a gun and to refrain from shooting individuals that were holding non-gun objects such as wallets or soda cans.

      This finding remained even when experimenters increased the number of White individuals holding guns and decreased the number of Black individuals holding guns.

  9. Oct 2015
    1. Suspendisse auctor pharetra a et hac mauris nisi magna risus taciti a a interdum turpis gravida eu velit magna aliquet a id dignissim. Mi et parturient venenatis quam nullam suspendisse odio mi hac accumsan arcu adipiscing nullam curae habitasse vestibulum

      Ref test 2

  10. Aug 2015
    1. quality-adjusted frontier analysis are available inEckermann and Coelli (2013).

      *Interesting reference for reviewing!

    2. Details of the estimationprocess can be found in operations research textbooks (e.g., Banker, Charnes,and Cooper 1984; Ramanathran and Ramanathan 2003)

      *Interesting reference for reviewing!



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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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