1,011 Matching Annotations
  1. Dec 2018
    1. Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, et al. 2012. Nature. 490:49–54.

      This paper focuses on the member of the Mollusca phyla, Crassostrea gigas. It goes into depth on how the genome of the oyster reveals how it has been able heat chock protein 70 and apoptosis inhibitors contribute to the organisms ability to survive in very stressful environmental conditions. this contributes to the GIGA project because the genome had to have been coded and that can go towards the GIGA coalition.

    2. Vinson JP, Jaffe DB, O’Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, et al. 2005. Genome Res. 15:1127–1135.

      "Whole-genome assembly is now used routinely to obtain high-quality draft sequence." This supports the main idea of which GIGA stands for. A database for easy access to high- quality sequences of a certain organism.

    3. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, et al..; Taenia solium Genome Consortium. 2013. Nature. 496:57–63.

      This paper speaks of how parasitisms has developed in worms. Scientist have been able to figure this information out using the genome of 3 different tapeworms. They also identify treatments to ride humans of these parasites. This aids with the GIGA project because uses the genetic code of invertebrates, which can be a part of the GIGA database.

    4. Struck TH, Paul C, Hill N, Hartmann S, Hösel C, Kube M, Lieb B, Meyer A, Tiedemann R, Purschke G, et al. 2011. Nature. 471:95–9

      This paper is on ring phylum Annelid. With the information in this study Animal body plan evolution can be more defined which can help researchers better understand the evolution of metazoans. It mentions on how other organisms who were classified under different phyla should actually fall under Annelid. Showing how this paper can help researchers narrow down the evolution of these creatures consisting of invertebrates.

    5. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, et al. 2008. Nature. 454:955–960.

      This study focuses on the Placozoan Trichoplax genome in order to understand the organisms that fall under this category. It focuses in where they stand in categories of animals as one of the first emerging animals. It can be used to study how the first animals ever looked on this earth and their DNA can present a lot more information that can still be found out.

    6. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. 2010. Nature. 463:1079–1083.

      This has to do with how arthropods are more closely related to aquatic invertebrates than other terrestrial invertebrates. This shows how evolution of invertebrates were different then originally thought and with the help of data from this study other scientist can know this and use it for themselves.

    7. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ. 2011. Nature. 470:255

      This paper focuses on how to two taxa are actually very similar to one another. This all contributes to the database for flatworms and the taxa they pertain to.

    8. Mardis ER. 2011. Nature. 470:198–203

      This study focuses on how the Human Genome Project has lead humanity to leap into the future and gain a ton of knowledge. This is more of an example of how the GIGA project can be of use. It goes into detail of what we have learned since the HGP was completed. This is more of a reflection of the possibilities the GIGA project can have for marine invertebrate genome.

    9. Lewin HA, Larkin DM, Pontius J, O’Brien SJ. 2009. Genome Res. 19:1925–1928

      This is an article that is justifying the reasons for mapping a genome and how it can be useful in advancing knowledge, research, and technology.

    10. Jeffery NW, Jardine CB, Gregory TR. 2013. Genome. 56:451–456.

      Focuses on the genome size of an early branching phylum. This is all scarce information so this study is important into better understanding the entire phylum which is pretty wide spread. This is perfect example of what GIGA is trying to prevent. They want to create a global database of information of marine invertebrates especially due to the lack of information on these creatures.

    11. Human Microbiome Project. 2012. Nature. 486:207–214.

      This project is essentially a genomic mapping project of the the microbes that live within humans. Another example of how databases are useful, which supports the reasoning for creating the GIGA project.

    12. Hill CA, Wikel SK. 2005. Trends Parasitol. 21:151–153.

      This is a perfect example of how creating a database of a genome can enhance the spread of information and the use of certain standards and information in order go further into research of the tick genome. Shows how the GIGA initiative can be of use.

    13. Funch P, Kristensen RM. 1995. Nature. 378:711–714

      This is an older paper, published establishing a new phylum Cycliophora. This contributes to database on new discoveries on marine invertebrates. it foes into depth on the larva of the organism and what makes it different form other invertebrates.

    14. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. 2012. Nature. 489:52–55

      This article focuses on the ENCODE project and goes to explain its functions and what it can lead to. It focuses on learning and understanding the functional regions of the human DNA, but it makes you think that if this can work for humans why can it not work for any other species? This shows incentive to the GIGA coalition and what it can mean for researchers in the marine invertebrate field.

    15. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Nature. 439:965–968.

      This paper focuses on how Tunicates are the closest living relatives to vertebrates. This study can assist from en evolutionary standpoint to picture a transition from an invertebrate to vertebrate creatures. This pertains to paper at hand because it will contribute to the database for GIGA.

    16. Davidson EH, Erwin DH. 2006. Science. 311:796–800.

      This article focuses on the evolution of body plans of invertebrates. So due to the nature of the paper it refers to a lot of invertebrates and focuses on their development. The GIGA project focuses on invertebrates

    17. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. 1994. Science. 263:802–805.

      The name of this paper is called "Green Fluorescent Protein as a Marker for Gene Expression." The marine invertebrate mentioned is the Aequorea victoria. This will contribute to the papers database. Can help with focusing on proteins of jelly fish.

    18. C. elegans Sequencing Consortium. 1998. Science. 282:2012–2018.

      This article contains the genome of the nematode C. elegans. The main purpose of GIGA is to obtain and database the genomes and infomration of the genome for others to use so this paper is a perfect candidate that reach this criteria.

    19. Birney E. 2012. Nature. 489:49–51

      This article speaks on the ENCODE project. ENCODE is a mass collection of functional parts of DNA. It focuses on the do's and do not's of database creation. This can serve as a source of how the creators of GIGA can go about creating their database, and steps they should take to ensure its success.

    20. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al. 2009. Nature. 460:352–358.

      "Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries." It contains the genome for this species and goes into depth the characteristics of the genetic code. for instance it says that it contains a large amount of introns. Also shows how the information gathered has led researchers to begin new ideas of possible treatments and regulations of the disease.


      This paper proposes a project so it isn't necessarily a topic that many people have researched. Due to the nature of the paper, the resources and past works will consist of published works that describe the pros of creating a database and examples of the types of works that will contribute to the GIGA project.

    1. Vandegehuchte, M.B., Lemiere, F., Janssen, C.R., 2009. Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 150, 343–348.

      A paper published in 2009, concluding that different exposure histories results in different levels of methylation.

    2. Valdiglesias, V., Fernandez-Tajes, J., Mendez, J., Pasaro, E., Laffon, B., 2013. The marine toxin okadaic acid induces alterations in the expression level of cancer-related genes in human neuronal cells. Ecotoxicol. Environ. Saf. 92,303–311

      A study in which the effect of the marine toxin Okadaic acid (OA) on certain genes that are related to cancer. In the study it was seen that there are alterations to the genes that could explain the relationship of OA to cancer.

    3. Sunda, W.G., Burleson, C., Hardison, D.R., Morey, J.S., Wang, Z., Wolny, J., Corcoran, A.A., Flewelling, L.J., Van Dolah, F.M., 2013. Osmotic stress does not trigger brevetoxin production in the dinoflagellate Karenia brevis. Proc. Natl. Acad. Sci.U. S. A. 110, 10223–10228.

      Sunda has previously concluded that exposure to brevetoxins limit growth

    4. Murrell, R.N., Gibson, J.E., 2009. Brevetoxins 2, 3, 6, and 9 show variability in potency and cause significant induction of DNA damage and apoptosis in Jurkat E6-1 cells. Arch. Toxicol. 83, 1009–1019.

      Murell and Gibsons reviewed the effect of Red Tides on human health, particularly on the effect it has with DNA strands. It further supported their reasoning into investigate on Histone 2 dynamics during the toxic experiment.

    5. Flewelling, L.J., Naar, J.P., Abbott, J.P., Baden, D.G., Barros, N.B., Bossart, G.D., Bottein,M.Y., Hammond, D.G., Haubold, E.M., Heil, C.A., Henry, M.S., Jacocks, H.M.,Leighfield, T.A., Pierce, R.H., Pitchford, T.D., Rommel, S.A., Scott, P.S., Steidinger, K.A., Truby, E.W., Van Dolah, F.M., Landsberg, J.H., 2005. Brevetoxicosis: red tides and marine mammal mortalities. Nature 435, 755–756

      Flewelling published a paper pinpointing areas in which saxitoxin (HABs) were found in food around the world. The Southeastern U.S was one of these areas in which saxitoxins were found. (DZ)

      Also the paper talks about the effect of Karenia brevis's brevetoxins on food webs and the effects.

    6. Dame, R.F., 1972. The ecological energies of growth, respiration, and assimilation in the intertidal American oyster Crassostrea virginica. Mar. Biol. 17, 243–250

      Dame's paper studies the interactions between the grazing of bivalves and their role in their respective environments (specifically, carrying capacity).

    7. Cardozo, K.H., Guaratini, T., Barros, M.P., Falcao, V.R., Tonon, A.P., Lopes, N.P.,Campos, S., Torres, M.A., Souza, A.O., Colepicolo, P., Pinto, E., 2007. Metabolites from algae with economical impact. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 146, 60–78.

      Cardozo focuses on the effects of the biotoxins released by the algae. From these effects the experiment is conducted upon what the toxins do on marine life organism in which the toxic effect is a natural defense mechanism.

    8. Brand, L.E., Campbell, L., Bresnan, E., 2012. Karenia: the biology and ecology of atoxic genus. Harmful Algae 14, 156–178.

      A paper describing the dinoflagellate, karenia brevis. The paper explains the biotoxins released by it, how the biotoxins build up in shellfish, and what damage it does to other marine organisms.

    1. Garwood, N.C., 1983. Ecology 53, 159–181

      Garwood focused on seed germination in tropical environments in Panama. He was looking to help determine primary selective factors that controlled the timing of germination, the significance of seed dormancy, and to identify any major seed germination syndromes. These are all related to the success of a plant population and help scientists better understand and map out conservation efforts for species diversity.

    2. Galetti, M., Dirzo, R., 2013. Biol. Conserv. 163, 1–6.

      Galetti and Dirzo reviewed the anthropogenic drivers of defaunation. They determined that direct drivers include hunting, poaching, and the presence of invasive species. Indirect drivers of defaunation include deforestation and fragmentation as a result of human activities. Some of the many consequences of defaunation are reduced ecosystem services and evolutionary changes in populations.

    3. Bond, W.J., Keeley, J.E., 2005. Trends Ecol. Evol. 20, 387–394. Borchert, R., 1998. Clim. Chang. 39, 381–393.

      Bond and his colleagues reviewed previous research in order to draw parallels between the effects of fire and herbivory on ecosystems. They concluded that, like herbivores, fires select for particular plant traits. For example, small herbaceous plants that require a lot of light for growth and seed establishment are more likely to be wiped out by fires. They also suggested that species that thrive under conditions of repeated defoliation would dominate communities where fires are likely to occur.

    4. Alvarado, S.T., Buisson, E., Rabarison, H., Rajeriarison, C., Birkinshaw, C., Lowry Ii, P.P., Morellato, L.P.C., 2014. S. Afr. J. Bot. 94, 79–87.

      Alvarado and colleagues analyzed the reproductive success of Madagascar sclerophyllous tapia woodlands in relation to fire frequency. They determined that more frequent fires resulted in increased latency of reproductive phenological events (flowering and fruit production in particular). Additionally, frequent fires reduced the overall number of individuals producing flower and fruits. It should be noted that the fires mentioned in this study were related to human activities.

    5. Ali, N.S., Trivedi, C., 2011. Biodivers. Conserv. 20, 295–307.

      Ali and his colleagues focused their studies on the species diversity and conservation of various bird communities in Pakistan. This is important in understanding the relationship between the animal organisms within an ecosystem and their neighboring plants in order to obtain an optimal amount of species diversity within the ecosystem. This helps answer the question: what are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

    6. Alberton, B., Almeida, J., Helm, R., da Torres, S.R., Menzel, A., Morellato, L.P.C., 2014. Ecol. Inform. 19, 62–70.

      Alberton and colleagues tested whether or not digital cameras (used as a near-surface monitoring system) can be used effectively for measuring phenological changes in plants (specifically leaf color change). They determined that digital cameras are a reliable tool to monitor change in regional leafing patterns. This means that on-the-ground phenological observations of individual plants may no longer need to be used. However, the authors suggest that both methods, on-ground and near-surface monitoring through photographs, should be used to collect the most accurate picture of phenological change.

    7. increases in temperature and drought frequency may lead to premature leaf senescence in deciduous forests, affecting the efficiency of nutrient resorption and the length of growing seasons, impacting carbon uptake and ecosystem nutrient cycling (Estiarte & Peñuelas 2015), and therefore management practices (e.g. Eriksson et al., 2015)

      This study looks at how climate change alters the rate of leaf senescence in which drought advances it and warming decreases it. This change affects the flow of nutrients within an ecosystem. This information helps us to understand how shifts in climate activity influences plant phenology, such as losing leaves sooner and disrupting the nutrient cycle.

    1. Kursar, T. A., K. G. Dexter, J. Lokvam, R. T. Pennington, J. E. Richardson, M. G. Weber, E. T. Murakami, C. Drake, R. McGregor, and P. D. Coley. 2009. Proceedings of the National Academy of Sciences USA 106: 18073-18078.

      This paper is a different version of the same type of research. This study provided backup information to further prove what was being stated and identified in this research.

    1. D. Anglesea, C. Veltkamp, G. H. Greenhalgh, The upper cortex of Parmelia saxatilis and other lichen thalli. Lichenologist 14, 29–38 (1982).

      An important paper that shows the role of glue-like polysaccharides in filling the spaces between fungal cells and holding the lichen together. The yeasts described in this paper live in this filler zone.

    2. I. A. Aschenbrenner, T. Cernava, G. Berg, M. Grube, Understanding microbial multi-species symbioses. Front. Microbiol. 7, 180 (2016).

      This paper highlights the possible role bacterial symbionts might play in lichen formation and maintenance.

    3. R. Honegger, Developmental biology of lichens. New Phytol. 125, 659–677 (1993).

      This review discusses how lichens develop, their structure and function, their growth patterns, and how thalli are differentiated.

    4. V. Ahmadjian, The Lichen Symbiosis (John Wiley & Sons, 1993).

      This paper describes the cortex deficiencies of lichens grown from only the two previously known symbiotic partners.

  2. Nov 2018
    1. 19. Y. Lin, R. Jin, D. Cai, S. Yan, X. Li, in 2013 IEEE Conference on Computer Vision and Pattern Recognition (IEEE Computer Society, 2013), pp. 446–451.

      Lin et al. address a known issue in hashing methods, which is that they often require a large number of hash tables to be effective.

      To solve this problem, the authors propose a novel approach called compressed hashing. This approach uses sparse coding and is shown to be more effective than previously known hashing algorithms.

    2. 6. E. A. Hallem, J. R. Carlson, Cell 125, 143–160 (2006).

      Hallem and Carlson analyze how the fly olfactory circuit encodes information about the specific qualities—such as quality, quantity, and duration–of an individual odor.

      They test over 100 different odors and create an "odor space" that shows how the responses of olfactory receptors depend on an odor's chemical class, concentration, and molecular complexity.

    3. 4. A. C. Lin, A. M. Bygrave, A. de Calignon, T. Lee, G. Miesenböck, Nat. Neurosci. 17, 559–568 (2014).

      Lin et al. consider the role of sparse coding in helping organisms remember specific odors.

      They discover that sparsity in the olfactory circuit is controlled by a "negative feedback circuit" involving Kenyon cells and anterior paired lateral neurons. From their results, they suggest that sparse coding is important for helping flies store a large number of odor-specific memories without confusing or overlapping information.

    1. M. S. Bretscher and M. Grunberg-Manago, Nature 195, 283 (1962).

      Bretscher and Grunberg-Manago debunk the hypothesis that all codons must contain uracil by analyzing the coded proteins from poly(C, A).

    1. P. Kersey et al., Nucleic Acids Res. 33, D297–D302 (2005).

      This paper presents intrgr8. Intrgr8 is a database that helps researchers find information about the many different genomes that have been sequenced. Specifically, it links the sequenced genomes to information about that organism's proteins and any papers published about the genome.

    2. 12. C. M. Silva et al., J. Polym. Sci. A Polym. Chem. 43, 2448–2450 (2005).

      Describes the use of a cutinase from Fusarium solani pisi to degrade the surfaces of fibers to make them more hydrophilic and appropriate for use in the clothing industry. They found that the cutinase degraded the surface of a variety of fibers, including PET, to varying extents.

    3. 2. R. J. Müller, I. Kleeberg, W. D. Deckwer, J. Biotechnol. 86, 87–95 (2001).

      In this review, the authors discuss the work to create polymers that are both biodegradable and useful. Historically, most aliphatic polymers did not have the correct properties to be useful and most aromatic polymers were difficult to biodegrade. The review article details different techniques for making copolymers which have portions that are aromatic and portions that are aliphatic, allowing them to be both biodegradable and useful.

    1. 14. S. Schiffels, R. Durbin, Nat. Genet. 46, 919–925 (2014)

      A new technique—multiple sequentially Markovian coalescent (MSMC)—was developed. Eight haplotypes from four individuals can be analysed at the same time to trace lineages until the most recent common ancestor is identified. It is a powerful technique that provides information about population sizes, population splits, and migration patterns. In this study, they analyzed the genomes of nine different human populations and discovered that humans began to migrate out of Africa over 50,000 years ago.

    2. 6. A. H. Freedman et al., PLOS Genet. 10, e1004016 (2014).

      Dogs and wolves diverged 11,000-16,000 years ago, the authors conclude. A severe reduction in the population (a bottleneck) of wolves occurred shorly thereafter. They traced the ancestry of the amylase gene, a gene that allows dogs to eat starchy foods. Their data showed that dogs were mostly carnivores when they were first domesticated, which supports the theory that dogs were domesticated by hunter-gatherers, rather than starch-loving farmers.

    3. 19. P. Savolainen, Y. P. Zhang, J. Luo, J. Lundeberg, T. Leitner, Science 298, 1610–1613 (2002).

      The authors investigate the specific time and place of domestication by using the mitochondrial DNA of over 600 dogs and 38 wolves to trace the maternal lineage.They determine that dogs were domesticated about 15,000 years ago in East Asia, and that dogs were isolated to East Asia for a long time thereafter.

    4. 5. M. Ollivier et al., PLOS One 8, e75110 (2013)

      Scientists traced the ancestry of two genes associated with coat color. They examined DNA from teeth and bones from 28 different sites across Europe and Asia and determined that coat color was lost when dogs were domesticated. Variants in one coat color gene was detected in the early "ancient" breeds, which suggested that a pool of early dogs may have been geographically isolated 14,000-12,000 years ago, maybe as a result of rising sea levels.

    1. V. F. Dvorak, Mon. Weather Rev. 103, 420 (1975)

      The Dvorak scheme is a method of determining storm intensity based off satellite images and certain characteristics. Tropical cyclone patterns used to estimate intensity come from 1) the “shear” pattern, which examines how tilted a hurricane may be from the upper to lower atmosphere, 2) the “curved band” pattern of how the clouds swirl around a cyclone, 3) the “central dense overcast” pattern as in how thick the cloud cover appears, and 4) the “eye” pattern that examines the shape of the storm's center.

      Here is an image presents some of the common patterns seen during tropical cyclone formation along with their Dvorak-assigned intensities: Description

      A Dvorak T-Number of 1.0-2.0 is considered a tropical depression, 2.5-3.5 is a tropical storm, 4.0-4.5 represents a category 1 hurricane, 4.5-5.0 is a category 2, 5.5 is considered a category 3, with 6.0-6.5 representing category 4, and T numbers of 7.0-8.5 correspond to category 5 hurricanes.

    2. W. M. Gray, Mon. Weather Rev. 112, 1649 (1984)

      In this study, William Gray discusses the seasonal variability in Atlantic hurricane frequency.

      He found that during years with strong El Nino conditions in the Pacific, there were fewer hurricanes, hurricane days and tropical storms in the Atlantic. He also discovered that when stratospheric winds (at 30 mb in the atmosphere) were from an easterly direction, there tended to be fewer storms.

      In contrast, more tropical storms and hurricanes occurred during non-El Nino years as well as when stratospheric winds blew from a westerly direction.

      Thus global and regional climate oscillations in addition to upper atmosphere weather dynamics influence hurricane frequency.

    3. T. R. Knutson, R. E. Tuleya, J. Clim. 17, 3477 (2004)

      Knutson and Tuleya explored how the choice of climate model and convective wind parameters simulating hurricanes can impact the model results. By running experiments examining higher carbon dioxide futures using different climate models and different wind and atmospheric assumptions, the authors looked at whether different models produced the same results.

      They found that "nearly all combinations of climate model boundary conditions and hurricane model convection schemes show a CO2-induced increase in both storm intensity and near-storm precipitation rates." They also found a "gradually increasing risk in the occurrence of highly destructive category-5 storms" if global climate continued to warm.

      Based on this study, it appears that most climate models tend to produce similar results regardless of differences in certain background parameters and assumptions.

    4. W. M. Gray, Mon. Weather Rev. 96, 669 (1968)

      For this study, William Gray examined measurements of upper atmospheric conditions which had only recently become available from over the tropical oceans. Using about a decade's worth of airplane and sensor readings, Gray noticed that cyclone storms develop under certain conditions with regard to temperatures and atmospheric moisture content.

      Development of storms appears to be due to the combination of surface winds converging due to frictional forces in addition to conditions inhibiting atmospheric vertical mixing (such as specific wind shear and cloud conditions). Under certain atmospheric conditions, warm oceans and evaporation-condensation reactions of water can concentrate energy into a cyclonic system and cause a hurricane to form.

    5. K. A. Emanuel, Nature 326, 483 (1987).

      Using a simple model that takes the thermodynamic attributes of the atmosphere into account, Emanuel determined that if carbon dioxide concentrations doubled there would be a "40–50% increase in the destructive potential of hurricanes".

      This is due to the well-studied heat-trapping potential of carbon dioxide which contributes to a warming climate and increasing sea surface temperatures. Warmer waters in turn alter atmospheric pressures and wind speeds. Thus on a theoretical basis using knowledge of atmospheric gases and their relationship to temperature, a warmer world is likely to produce more destructive hurricane events.

    6. C. W. Landsea, R. A. Pielke Jr., A. M. Maestas-Nunez, J. A. Knaff, Clim. Change 42, 89 (1999)

      Landsea and coauthors compared the record of hurricane activity in the Atlantic with other climate records of sea level pressures, wind, climate oscillations (like the El Niño-Southern Oscillation), African West Sahel rainfall, and Atlantic sea surface temperatures.

      They found that variability in the background climate state of the region affects the frequency, intensity and duration of Atlantic hurricanes.

      With improved understanding of the large-scale climate conditions of the Atlantic and how regional climate changes over multi-decadal timescales should improve our ability to predict hurricane activity.

    7. K. E. Trenberth et al., Bull. Am. Meteorol. Soc. 84, 1205 (2003)

      Trenberth and coauthors wrote this paper in order to summarize the environmental controls on precipitation events and to point out how climate models were not yet considering all the variables influencing precipitation.

      Since "climate change is certainly very likely to locally change the intensity, frequency, duration, and amounts of precipitation" we need to be developing models which can accurately reproduce these types of changes if we want to accurately predict how the water cycle may vary as climate changes.

    8. K. E. Trenberth, Science 308, 1753 (2005)

      In this perspective piece "Uncertainty in Hurricanes and Global Warming" Trenberth notes that while the effects of human-driven climate change have already begun altering the environment in hurricane formation regions, it is not yet possible to connect changes in climate to the number of storms forming.

      Trenberth suggests that instead of focusing on just the number of storms and the tracks they move along, the bigger scientific question is how hurricane attributes such as intensity and rainfall are changing in today's world.

    9. S. B. Goldenberg, C. W. Landsea, A. M. Maestas-Nunez, W. M. Gray, Science 293, 474 (2001)

      Goldenberg and coauthors studied "The recent increase in Atlantic hurricane activity: causes and implications."

      After examining hurricane data from 1944 to 2000, these authors also found that there has been an increase in cyclone activity and the number of major hurricanes since 1995. They attribute the greater storm activity on increases in North Atlantic sea-surface temperatures and decreases in vertical wind shear.

      These changes in storm activity appear to coincide with changes in the climatic state of the Atlantic, specifically in how the Atlantic responds with regard to El Nino and La Nina conditions that vary on the timescales of a few decades. Due to the current climate of the North Atlantic, Goldenberg and coauthors predict "the present high level of hurricane activity is likely to persist for an additional ∼10 to 40 years."

  3. Oct 2018
    1. 4. K. R. Kaun, R. Azanchi, Z. Maung, J. Hirsh, U. Heberlein, Nat. Neurosci. 14, 612 (2011).

      This paper established the odor-ethanol pairing method for probing motivation and rewarding properties that is used in the current study. It is by the same authors.

    2. 15. T. E. Thiele, D. J. Marsh, L. Ste. Marie, I. L. Bernstein, R. D. Palmiter, Nature 396, 366 (1998).

      First paper to establish the relationship between NPY in mice and ethanol consumption/sensitivity.

    3. 10. W. W. Ja et al., Proc. Natl. Acad. Sci. U.S.A. 104, 8253 (2007).

      The first paper to establish the two-choice preference assay for flies using food, including a method to precisely measure how much food was being consumed at any given time.

    4. 6. G. E. Robinson, R. D. Fernald, D. F. Clayton, Science 322, 896 (2008).

      A review paper highlighting various past studies that have shown that it is possible to establish direct causal links between genetics and behavior.

    5. 1. A. E. Kelley, K. C. Berridge, J. Neurosci. 22, 3306 (2002).

      A landmark review paper outlining how and why addiction occurs. This paper has been cited over 750 times.

    1. 9. S. J. Caron, V. Ruta, L. F. Abbott, R. Axel, Nature 497, 113–117 (2013).

      Caron et al. investigate the specific process by which Kenyon cells integrate information sent to them from glomeruli.

      Their results suggest that the input to KCs is random; that is, there is no discernible organization in how the glomeruli project information to individual KCs.

    2. 17. Z. Allen-Zhu, R. Gelashvili, S. Micali, N. Shavit, Proc. Natl. Acad. Sci. U.S.A. 111, 16872–16876 (2014).

      Zhu et al. consider whether the physical properties of neural tissue are actually conducive to performing Johnson-Lindenstrauss (JL) calculations in the brain. For example, the fact that neurons are either inhibitory or excitatory has certain implications for the signs (+ or -) in a JL matrix.

      They determine that it is indeed possible to construct JL matrices that accurately reflect the physical properties of the brain.

    1. J. C. Clemente, L. K. Ursell, L. W. Parfrey, R. Knight, Cell 148, 1258–1270 (2012).

      Clemente and colleagues review the interactions between microbes in the human gut and their effect on the host's immune system.

    2. J. F. Cryan, T. G. Dinan, Nat. Rev. Neurosci. 13, 701–712 (2012).

      Dinan and Cyran suggest that the gut microbiome may have a role in regulating and influencing brain function and behavior.

    3. E. Le Chatelier et al., Nature 500, 541–546 (2013).

      Le Chatelier and colleagues conduct a similar study on non-obese and obese Danish individuals. They find that they are able to classify subsets of individuals that may be at risk of obesity or associated comorbidities based on variation in the gut microbiota.

    4. J. Qin et al., Nature 490, 55–60 (2012).

      Qin and colleagues conducted a metagenome-wide association study in Chinese individuals. They identified type-2 diabetes-associated markers based on sequencing of the gut microbiome.

    5. M. Rajilić-Stojanović et al., Am. J. Gastroenterol. 110, 278–287 (2015).

      Rajilić-Stojanović and colleagues provide a review of current research on and suggest mechanisms regarding the impact of diet and the intestinal microbiome on irritable bowel syndrome symptoms.

    1. C. L. Schoch, K. A. Seifert, S. Huhndorf, V. Robert, J. L. Spouge, C. A. Levesque, W. Chen, E. Bolchacova, K. Voigt, P. W. Crous, A. N. Miller, M. J. Wingfield, M. C. Aime, K.-D. An, F.-Y. Bai, R. W. Barreto, D. Begerow, M.-J. Bergeron, M. Blackwell, T. Boekhout, M. Bogale, N. Boonyuen, A. R. Burgaz, B.Buyck, L. Cai, Q. Cai, G. Cardinali, P. Chaverri, B. J. Coppins, A. Crespo, P. Cubas, C. Cummings, U. Damm, Z. W. de Beer, G. S. de Hoog, R. Del-Prado, B. Dentinger, J. Dieguez-Uribeondo, P. K. Divakar, B.Douglas, M. Duenas, T. A. Duong, U. Eberhardt, J. E. Edwards, M. S. Elshahed, K. Fliegerova, M. Furtado,M. A. Garcia, Z.-W. Ge, G. W. Griffith, K. Griffiths, J. Z. Groenewald, M. Groenewald, M. Grube, M.Gryzenhout, L.-D. Guo, F. Hagen, S. Hambleton, R. C. Hamelin, K. Hansen, P. Harrold, G. Heller, C.Herrera, K. Hirayama, Y. Hirooka, H.-M. Ho, K. Hoffmann, V. Hofstetter, F. Hognabba, P. M. Hollingsworth,S.-B. Hong, K. Hosaka, J. Houbraken, K. Hughes, S. Huhtinen, K. D. Hyde, T. James, E. M. Johnson, J. E.Johnson, P. R. Johnston, E. B. G. Jones, L. J. Kelly, P. M. Kirk, D. G. Knapp, U. Koljalg, G. M. Kovacs, C. P.Kurtzman, S. Landvik, S. D. Leavitt, A. S. Liggenstoffer, K. Liimatainen, L. Lombard, J. J. Luangsa-ard, H. T. Lumbsch, H. Maganti, S. S. N. Maharachchikumbura, M. P. Martin, T. W. May, A. R. McTaggart, A. S.Methven, W. Meyer, J.-M. Moncalvo, S. Mongkolsamrit, L. G. Nagy, R. H. Nilsson, T. Niskanen, I. Nyilasi, G.Okada, I. Okane, I. Olariaga, J. Otte, T. Papp, D. Park, T. Petkovits, R. Pino-Bodas, W. Quaedvlieg, H. A.Raja, D. Redecker, T. L. Rintoul, C. Ruibal, J. M. Sarmiento-Ramirez, I. Schmitt, A. Schussler, C. Shearer,K. Sotome, F. O. P. Stefani, S. Stenroos, B. Stielow, H. Stockinger, S. Suetrong, S.-O. Suh, G.-H. Sung, M.Suzuki, K. Tanaka, L. Tedersoo, M. T. Telleria, E. Tretter, W. A. Untereiner, H. Urbina, C. Vagvolgyi, A.Vialle, T. D. Vu, G. Walther, Q.-M. Wang, Y. Wang, B. S. Weir, M. Weiss, M. M. White, J. Xu, R. Yahr, Z. L.Yang, A. Yurkov, J.-C. Zamora, N. Zhang, W.-Y. Zhuang, D. Schindel, Fungal Barcoding Consortium,Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. U.S.A. 109, 6241–6246 (2012).

      This paper describes the use of the phylogenetic marker that is used to barcode fungal species. One of the reasons that the yeast symbiotic partner was missed is because this barcode doesn't work for that species.

    2. A. M. Millanes, P. Diederich, M. Wedin, Cyphobasidium gen. nov., a new lichen-inhabiting lineage in the Cystobasidiomycetes (Pucciniomycotina, Basidiomycota, Fungi). Fungal Biol., 10.1016/j.funbio.2015.12.003 (2015).

      This paper describes the discovery of the genus Cyphobasidium.

    3. H. Lindgren, S. Velmala, F. Högnabba, T. Goward, H. Holien, L. Myllys, High fungal selectivity for algal symbionts in the genus Bryoria. Lichenologist 46, 681–695 (2014).

      This paper examines the specificity of fungal and algal partners in the lichen symbosis.

    4. S. Velmala, L. Myllys, P. Halonen, T. Goward, T. Ahti, Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific. Lichenologist 41, 231–242 (2009).

      Genomic data is used to show that the two main species of Bryoria fungi examined in this work are conspecific, that is they are genomically identical to one another.

    5. S. T. Bates, D. Berg-Lyons, C. L. Lauber, W. A. Walters, R. Knight, N. Fierer, A preliminary survey of lichen associated eukaryotes using pyrosequencing. Lichenologist 44, 137–146 (2012).

      This paper used pyrosequencing to look for additional eukaryotic symbiotic partners in lichens, like the one discovered in this paper.

    6. D. L. Hawksworth, The variety of fungal-algal symbioses, their evolutionary significance, and the nature of lichens. Bot. J. Linn. Soc. 96, 3–20 (1988).

      Lichens evolved independently many times as a symbiosis between fungi and algae.

    7. A. Gargas, P. T. DePriest, M. Grube, A. Tehler, Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268, 1492–1495 (1995).

      This is a foundational paper that describes how lichen symbiosis arose multiple times through evolutionary history.

    1. N. E. Klepeis et al., J. Expo. Anal. Environ. Epidemiol. 11, 231–252 (2001).

      Telephone survey that monitored where people in the United States spent the majority of their time. Found that 87% of time was spent in buildings and 6% of time was spent inside of automobiles.

      Since 93% of human activities are indoors, indoor air quality is extremely important.

    2. G. J. Dollard, P. Dumitrean, S. Telling, J. Dixon, R. G. Derwent, Atmos. Environ. 41, 2559–2569 (2007).

      Study analyzed VOC emissions in the United Kingdom from 1993 to 2004. Found that VOC emissions from automobiles were decreasing at a rate of 20% per year due to more stringent automobile emissions regulations.

    3. B. C. McDonald, D. R. Gentner, A. H. Goldstein, R. A. Harley, Environ. Sci. Technol. 47, 10022–10031 (2013).

      Study looked at emissions from automobile traffic in the United States between 1990 and 2010. Found that fuel consumption increased by 10% - 40% during the time period, but emissions such as carbon monoxide and VOCs decreased by 80% - 90% due to increased fuel efficiency and regulations.

    4. Q. Di et al., N. Engl. J. Med. 376, 2513–2522 (2017).

      The United States' air quality standards sets advisable levels for different pollutants. Human health was shown to be negatively impacted even when fine particulate matter and ozone were present at levels below the current air quality standards.

    1. 8. D. Ribitsch et al., Biocatalysis Biotransform. 30, 2–9 (2012).

      Rititsch et al. report cutinases from the bacteria Thermobifida alba. While the reported cutinases don't degrade PET particularly quickly, they do produce a novel degradation product.

      The authors were able to obtain a crystal structure, a type of picture on a molecular scale, of the enzyme degrading PET. This allowed them to identify parts of the enzyme that may be responsible for PET degradation.

    2. 1. V. Sinha, M. R. Patel, J. V. Patel, J. Polym. Environ. 18, 8–25 (2010).

      In this paper, Sinha et al. discuss the current best methods of disposing of and recycling plastic. The authors focus in particular on tertiary recycling techniques. These techniques use chemicals to break down the chemical bonds inside polymers.

    1. K. J. Willis, S. A. Bhagwat, Biodiversity and climate change. Science 326, 806–807 (2009).

      This article is a review about species distribution modeling, or, the ability to predict how species ranges could change under global warming. Authors highlight the fact that models published in the past have overlooked microclimates (small places that provide species with climate different than in the overall area). For example, in a place where heat waves are felt, some species could be able to use the surrounding vegetation to remain cool, and essentially be unaffected by the heat wave. Willis et al. (2009) show how important it is to consider such areas when estimating species’ future ranges under climate change since they could halt or at least slow many species’ extinctions.

    2. J. M. Sunday, A. E. Bates, M. R. Kearney, R. K. Colwell, N. K. Dulvy, J. T. Longino, R. B. Huey, Thermal-safety margins and the necessity of thermoregulatory behavior across latitude and elevation. Proc. Natl. Acad. Sci. U.S.A. 111, 5610–5615 (2014).

      Thermal limits of ectotherms (cold-blooded species) are often much higher than the temperature of the surrounding air. When limits are exceeded however, it was previously thought that organisms internally regulated their body in order to survive. However, this study shows that most ectotherms must use their behavior by retreating to suitable habitat when the air temperature becomes unsuitable (too cold or too hot). These behaviors are costly, obligating ectotherms, like bees, to direct their energy into preserving their heat/cool, instead of directing it into reproduction, feeding, and other essential activities. Extreme temperatures are predicted to happen more often as climate change progresses, and is likely to be problematic to bees.

    3. P. Rasmont, S. Iserbyt, The bumblebee scarcity syndrome: Are heat waves leading to local extinctions of bumblebees (Hymenoptera: Apidae: Bombus)? Ann. Soc. Entomol. Fr. 48, 275–280 (2012).

      Authors discuss the effect of heat waves on bumblebee decline. Heat waves and drought occurrences in France, the United Kingdom, Scandinavia, and Turkey led to bumblebee declines. It highlights that bumblebees are sensitive to extreme temperature events.

      Different aspects of heat waves could be affecting bees, as discussed in this paper. It could be that temperatures are rising above a tolerable threshold killing the bees, the length of the heat wave, the drought that is often associated with heat waves, starvation if bees are overheating and cannot feed themselves properly, or that heat waves are occurring during winter which could interrupt the queens’ hibernation while flowers providing their food are not yet available. Climate change is estimated to increase the probabilities for the occurrence of extreme temperature events in the future, a factor that may further threaten bee decline.

    4. S. J. Leroux, M. Larrivée, V. Boucher-Lalonde, A. Hurford, J. Zuloaga, J. T. Kerr, F. Lutscher, Mechanistic models for the spatial spread of species under climate change. Ecol. Appl. 23, 815–828(2013).

      Authors described an approach to model species’ distributions under climate change which takes into consideration ecological characteristics of species like reproduction, dispersal, and adaptation. We call these “mechanistic” models because they include mechanisms into their predictions.

      Using this approach, they modeled the distribution of 12 butterfly species and found that the ability to colonize unoccupied areas that are newly suitable and maintain populations in these areas is essential for species to track their suitable conditions. Otherwise, species can fall behind the pace of climate change and loose range.

    5. P. R. Whitehorn, S. O’Connor, F. L. Wackers, D. Goulson, Neonicotinoid pesticide reduces bumble bee colony growth and queen production. Science 336, 351–352 (2012).

      Testing for the effect of pesticides was important as field experiments have their negative impacts on bumblebees in the past. Whitehorn et al. (2015) showed that Bombus terrestris colonies exposed to pesticides in a lab had a lower growth rate and produced 85% fewer queens (bees that would eventually leave the colony to start a new colony) than those that were not exposed to the chemical. While this was observed on a small scale, the effect of pesticides was not measurable when Kerr et al. (2015) asked if it affected bumblebees’ wide scale shrinking range.

    6. D. Goulson, E. Nicholls, C. Botías, E. L. Rotheray, Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347, 1255957 (2015).

      This review explains the multiple threats that bees are currently facing. Pesticides and other agrochemicals, parasites spread by humans, climate change, and land use change, are threats that either act on their own or interact, to cause negative effects on bees.

      For the study design, Kerr et al. (2015) took these threats into consideration to measure what effect was responsible for the results that they obtained, and chose to look at pesticides and land-use change; effects which, surprisingly, were not responsible for bumblebee range loss in the south and the inability for them to expand their range in the north. This is not to say pesticides and land-use change cannot create population declines at a smaller scale.

    7. V. Kellermann, J. Overgaard, A. A. Hoffmann, C. Fløjgaard, J. C. Svenning, V. Loeschcke, Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically. Proc. Natl. Acad. Sci. U.S.A. 109, 16228–16233 (2012).

      This study showed that Drosophila (a type of fruit fly species) adapted to hot and dry regions were more resistant to heat. The upper thermal limits tolerated by Drosophila could influence range limits. Authors conducted trait analyses and found that heat tolerance was an ancestral trait, kept over time. Trait-based analyses for bumblebees conducted by Kerr et al. (2015) also correspond to these results.

    8. M. B. Araújo, F. Ferri-Yáñez, F. Bozinovic, P. A. Marquet, F. Valladares, S. L. Chown, Heat freezes niche evolution. Ecol. Lett. 16, 1206–1219 (2013).

      This paper answers the research question “Can species physiologically adapt to climate warming?” They analyzed data from numerous other studies that described the thermal tolerances of species worldwide. Main findings of this study are that tolerance to heat was mostly conserved within closely related species, whereas tolerance to the cold was a trait that could vary.

      Trait-based analyses conducted by Kerr et al. (2015) correspond to these results. The upper thermal limits of bumblebees were found to be an ancestral trait, since it was conserved across closely related species.

    9. I. C. Chen, J. K. Hill, R. Ohlemüller, D. B. Roy, C. D. Thomas, Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).

      Authors conducted a meta-analysis, a type of analysis that looks at a group of studies on the subject. They demonstrate that many terrestrial species shifted their range higher in altitude as well as further north. Chen et al. (2011) found that the rate at which species can shift varies strongly between species. Thus, it is likely for individual species traits to play an important role in their ability to shift.

      Findings by Chen et al. (2011) were important to frame the research question in Kerr et al. (2015). Since species from many different taxa have shifted, it was reasonable to ask if bumblebees are shifting as well.

    10. M. Pacifici, W. B. Foden, P. Visconti, J. E. M. Watson, S. H. M. Butchart, K. M. Kovacs, B. R. Scheffers, D. G. Hole, T. G. Martin, H. R. Akçakaya, R. T. Corlett, B. Huntley, D. Bickford, J. A. Carr, A. A. Hoffmann, G. F. Midgley, P. Pearce-Kelly, R. G. Pearson, S. E. Williams, S. G. Willis, B. Young, C. Rondinini, Assessing species vulnerability to climate change. Nat. Clim. Change 5, 215–224 (2015).

      This paper is a review of the different ways to measure how much species are threatened by climate change, and how they might respond. For instance, you can do this by estimating how a species range could change in the future. Understanding how climate change is affecting specific species is the first step to develop conservation strategies. Kerr et al. (2015) accomplished a first step toward this goal by demonstrating that climate change is linked to widespread losses and an overall shrink in distribution.

    11. C. D. Thomas, A. Cameron, R. E. Green, M. Bakkenes, L. J. Beaumont, Y. C. Collingham, B. F. Erasmus,M. F. De Siqueira, A. Grainger, L. Hannah, L. Hughes, B. Huntley, A. S. Van Jaarsveld, G. F. Midgley, L.Miles, M. A. Ortega-Huerta, A. T. Peterson, O. L. Phillips, S. E. Williams, Extinction risk from climate change. Nature 427, 145–148 (2004).

      It is now clear that climate change has affected species, as shown by endless amounts of papers in the primary literature. This paper estimates sizeable species extinctions by 2050 linked to climate change. They do this with species distribution modeling. This technique uses known species distributions and climatic conditions, and estimates how the distribution could change in the future according to models of future climate. Authors used optimistic and pessimistic estimates of future climate data (since, we do not know how much humans will cut down on activities that aggravate climate change), and even took into account the capacity for some species to move to and colonize other places. They estimated extinctions of 15% to 37% of the species included in their study. Studies that look at future impacts of climate change yield uncertain results since these cannot be verified.

      The IPCC (Intergovernmental Panel on Climate Change) put together a report summarizing climate literature. Refer to the PDF of the synthesis of this report here if you are interested in finding out more information on climate change: https://www.ipcc.ch/pdf/assessment-report/ar4/wg1/ar4-wg1-spm.pdf

    1. S. H. Schneider, Encyclopedia of Climate and Weather (Oxford Univ. Press, 1996

      A comprehensive description of the phenomena responsible for the world's climate and weather events, as well as the history of atmospheric science.

    2. S. Narayanan, S. Yang, H. Kim, E. N. Wang, Int. J. Heat Mass Transfer 77, 288–300 (2014).

      A computational modeling study of adsorption dynamics evaluating how multiple parameters such as vapor pressure and porosity affect the adsorption performance. The simulation results were confirmed experimentally with an adsorbing zeolite.

    3. J. H. Cavka et al., J. Am. Chem. Soc. 130, 13850–13851 (2008).

      The design and characterization of a zirconium-based MOF displaying very high thermal and chemical stability.

    4. H. Furukawa, K. E. Cordova, M. O’Keeffe, O. M. Yaghi, Science 341, 1230444 (2013).

      A review on the preparation of MOFs and their structural properties as well as their applications.

    5. J. Lee et al., Chem. Soc. Rev. 38, 1450–1459 (2009).

      An overview of the usage of the use of MOFs as selective catalyst to perform chemical reactions between substrates.

    6. H. Furukawa et al., J. Am. Chem. Soc. 136, 4369–4381 (2014).

      The same group previously described how to prepare MOF-801 and characterized its water adsorption properties.

    7. R. V. Wahlgren, Water Res. 35, 1–22 (2001).

      A review on existing systems to extract water from the atmosphere.

    8. M. M. Mekonnen, A. Y. Hoekstra, Sci. Adv. 2, e1500323 (2016).

      A study showing that about 4 billion people do not have access to fresh water for at least a month per year, half of them in China and India.

    1. K. D. Ersche et al., Science 335, 601–604 (2012).

      Ersche et al. studied the brain structure and behavior control capacities of 50 sibling pairs where one of the siblings was considered drug dependent, and compared them with 50 volunteer controls. The authors found that both siblings had deficits in regulating behavior with brain structure. They saw a reduction of white matter in drug dependent individuals and their biological siblings, which may predispose to drug use and indicate a genetic component to drug dependency..

    2. F. J. Miles, B. J. Everitt, A. Dickinson, Behav. Neurosci. 117, 927–938 (2003).

      In this study, Miles et al. were interested in looking at how chronic cocaine use in rats affects response to outcome devaluation. His group noted that chronic cocaine users were not responsive to changes.

    3. R. J. Beninger, S. T. Mason, A. G. Phillips, H. C. Fibiger, J. Pharmacol. Exp. Ther. 213, 623–627 (1980).

      Beninger et al. studied the effect of pimozide treatment, a dopamine receptor blocker, to determine if treated rats would avoid the negative outcomes that were previously associated with a particular stimulus.

      They found that treated animals could not avoid the negative outcomes due to their inability to initiate a response to the stimulus.

  4. Sep 2018
    1. C. S. Velden, T. L. Olander, R. M. Zehr, Weather and Forecasting 13, 172 (1998)

      Velden and co-authors came up with an algorithm based technique for examining satellite imagery and cataloging storm systems. Their "Objective Dvorak Technique" is a modified version of the original Dvorak scheme which uses patterns in winds and moisture content to rate a storm on its intensity and characteristics.

      Instead of humans eye-balling characteristics, now computers do the calculations for us to determine storm behavior.

    2. G. J. Holland, Aust. Meteorol. Mag. 29, 169 (1981)

      Greg Holland studied a subset of global data in order to see how enhanced observational technology has improved the detection of intense tropical storms.

      He found that prior to the use of satellite imagery to recognize storms, records tend to underestimate the true number of events. This may be due to the amount of storms which form and remain far offshore which did not make it into historical records. Thus in the 1960's when satellites really started getting widespread usage for tracking weather, scientists "saw" more hurricanes than previously reported.

    1. White TD. 1980. Evolutionary implications of pliocene hominid footprints. Science 208:175–176. doi: 10.1126/science.208.4440.175, PMID: 17745537

      At the time this article was written, the author stated that the 3.6-million-year-old Laetoli footprints were the earliest evidence of bipedalism in human evolution.

    2. Reno PL, Meindl RS, McCollum MA, Lovejoy CO. 2003. Sexual dimorphism in Australopithecus Afarensis was similar to that of modern humans. PNAS 100:9404–9409. doi: 10.1073/pnas.1133180100, PMID: 12878734

      The authors estimated the degree of sexual dimorphism present in Australopithecus afarensis through a systematic, random sampling of skeletal fossils. Simulations using the same sampling strategy with modern humans, chimpanzees, and gorillas confirmed the accuracy of the technique. It was determined that A. afarensis exhibited moderate sexual dimorphism similar to that of modern humans. This, coupled with the presence of a reduced male canine, is consistent with monogamy.

    3. Johanson DC, White TD, Coppens Y. 1978. A new species of the genus Australopithecus (Primates: Hominidae) from the Pliocene of eastern Africa. Kirtlandia 28:1–14.

      A large assortment bones was unearthed in Laetoli, Tanzania and Hadar, Ethiopa. The authors attribute them to a new species of Australopithecus. The soil types and depth of each bone is described and mapped.

    4. Harcourt-Smith WEH. 2005. Did Australopithecus Afarensis make the Laetoli footprint trail? New insights into an old problem. American Journal of Physical Anthropology S40:116. doi: 10.1002/ajpa.20217

      The authors investigated the hotly debated question: "Did early bipeds walk more like humans or more like apes?" Modern humans walk with extended hind limbs whereas apes walk with flexed hind limbs. By comparing the Laetoli trackway prints with those made by modern humans walking along a sand pathway, the authors conclude that A. afarensis walked in an energetically economical way—more like modern humans.

    5. Haile-Selassie Y, Latimer BM, Alene M, Deino AL, Gibert L, Melillo SM, Saylor BZ, Scott GR, Lovejoy CO. 2010. An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. PNAS 107:12121–12126. doi: 10.1073/pnas.1004527107

      The partial skeleton of A. afarensis specimen KSD-VP-1 was studied to learn more about stature, body mass, and bipedality in the species. KSD-VP-1/1 antedates Lucy (A.L.288-1) by about 0.4 million years. Based on measurements of bones it was determined KSD-VP-1/1 is a larger-bodied specimen than Lucy and likely a male. There is evidence of a high degree of sexual dimorphism and a well-developed thorax different from present-day apes.

    6. Gordon AD, Green DJ, Richmond BG. 2008. Strong postcranial size dimorphism in Australopithecus afarensis: results from two new resampling methods for multivariate data sets with missing data.

      There has been much debate over the degree of sexual dimorphism and implied social behavior in Australopithecus afarensis. Previous studies have suffered from limited sample size. The authors present two new resampling techniques that do not rely on template specimen and its associated assumptions. Postcranial size dimorphism is determined measuring the femur, tibia, humerus, and radius in samples of A. afarensis, modern humans, chimpanzees, gorillas, and orangutans. Based on their findings, the authors concluded that postcranial dimorphism in A. afarensis is similar to that of gorillas and orangutans, and significantly greater than in modern humans and chimpanzees. Though not conclusive, the authors feel that there is a strong evidence of behavioral and mating strategies employed by A. afarensis.

    7. Bennett MR, Reynolds SC, Morse SA, Budka M. 2016. Laetoli’s lost tracks: 3D generated mean shape and missing footprints. Scientific Reports 6:21916. doi: 10.1038/srep21916

      The authors employed a new technique, color-rendered optical laser scanning, to decouple the G2/3 Laetoli hominin footprints. Scientists had speculated that the G2/3 print was made by a smaller individual walking in the footsteps of a larger individual. Some had argued that the G2/3 trackway was made by only one individual and not a composite. Until this study, the G2/3 trackway had not been well studied. This article describes how the use of color-rendered optical laser scanning allowed the authors to decouple the G2 and G3 tracks, end the argument, and render the footprints usable for data analyses.

    8. Anton SC, Potts R, Aiello LC. 2014. Human evolution. Evolution of early Homo: an integrated biological perspective. Science 345:1236828. doi: 10.1126/science.1236828, PMID: 24994657

      Three lineages of early Homo evolved between 2.5 and 1.5 million years ago. Evidence collected over the past few decades has resulted in a revision in the thinking about how and when adaptations such as our large, linear bodies, long legs, large brains, and reduced sexual dimorphism first appeared. Originally, it was thought these adaptations occurred as a package. Fossil analysis and environmental data indicate that many of the traits associated with Homo sapiens appeared at different times. Some arose earlier and others later. Environmental changes gave a selective advantage to different traits.

    1. There are several reasons why the Aleutian archipelago provides an ideal large-scale experimental system to study the effects of introduced predators: (i) Most islands are small; (ii) high-latitude floral diversity is relatively low; (iii) there are no native vertebrate herbivores; (iv) the islands are geologically and climatologically homogeneous with similar overall soil properties; (v) the large number of islands in the archipelago provides the opportunity for meaningful replication; (vi) the islands are isolated from anthropogenic nutrient inputs; and (vii) fox introductions were not targeted for particular island types, and the history of introductions is reasonably well known.

      The Aleutian Islands were chosen to be the place of study for many reasons, the main one being the similarity between the individual islands in the chain. The islands are of fair size, with similar soil makeup and weather. There are also numerous islands making the sample size large enough to be used for replication and to ensure the results were not due to chance. There was also the curious distribution of fox introductions that directly lead to a split in islands by type: fox-free vs. fox-infested.

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

      In the paper by Terborgh et al., the different views on trophic cascades are investigated: top-down where predators limit herbivores and therefore prevent large destruction to vegetation, whereas bottom-up looks at the effects of plant defense in keeping predators at bay. This study touched upon the idea of top down interactions with the predation of seabirds by foxes having effects on plant communities, but in a more indirect way.

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

      The paper by N. G. Hairston, F. .E. Smith, and L. B. Slobodkin, "Community structure, Population Control, and Competition," observed what and how organisms are limited by their respective resources. Producers may be limited by an array of variables: light, water, and nutrients. These limiting resources can cause a change in competition throughout the trophic levels. In this paper, the limiting resources are the nutrients from guano. As the foxes prey and decrease the number of seabirds visiting the island, the dispersal of guano also decreases on the island.

    1. 15. S. Dasgupta, A. Gupta, Random Structures Algorithms 22, 60–65 (2003).

      Dasgupta and Gupta prove one result of the Johnson-Lindenstrauss theorem. This proof shows that a set of points in high-dimensional space can be mapped into a smaller dimensional space such that the distance between any two points changes only by a very small amount (1 ± ε).

      This result forms the foundation of many LSH algorithms.

    2. 10. A. Andoni, P. Indyk, Commun. ACM 51, 117 (2008).

      Andoni and Indyk provide an overview of efficient algorithms for nearest neighbor search problems.

      They focus specifically on locality-sensitive hashing algorithms, highlighting one specific option within the LSH family that provides near-optimal performance on nearest neighbor search problems.

    3. 8. S. R. Olsen, V. Bhandawat, R. I. Wilson, Neuron 66, 287–299 (2010).

      Olsen, Bhandawat, and Wilson describe one specific type of computation that occurs in olfactory processing in flies.

      They show that this computation, known as divisive normalization, helps to equalize responses to different input stimuli. This same computation is also known to serve a similar purpose in many parts of the visual system.

    4. 2. D. Owald, S. Waddell, Curr. Opin. Neurobiol. 35, 178–184 (2015).

      Owald and Waddell explore how memories of odors manifest in the fly's olfactory circuit and drive fly behavior

      Specifically, they discover that dopamine plays a key role in this process. During learning, dopaminergic neurons reactivate Kenyon cells associated with specific odor tags. In this way, the fly recalls previously-learned odors.

    5. 1. C. F. Stevens, Proc. Natl. Acad. Sci. U.S.A. 112, 9460–9465 (2015).

      Stevens outlines the three-layer architecture that makes up the fly's olfactory circuit.

      He also presents the idea of a unique odor label, or "tag" that is comprised of a small set of neurons and helps the fly identify distinct odors.

    1. V. Devictor, C. van Swaay, T. Brereton, L. Brotons, D. Chamberlain, J. Heliölä, S. Herrando, R. Julliard,M. Kuussaari, Å. Lindström, J. Reif, D. B. Roy, O. Schweiger, J. Settele, C. Stefanescu, A. Van Strien, C.Van Turnhout, Z. Vermouzek, M. WallisDeVries, I. Wynhoff, F. Jiguet, Differences in the climatic debts of birds and butterflies at a continental scale. Nat. Clim. Change 2, 121–124 (2012).

      This paper demonstrates how bird and butterfly communities have changed over time, and while they shifted through time, they failed to keep up with climate change. They show that northward shifts for bird communities shifted by 37 km, and butterfly communities shifted by 114 km. The climate shifted much faster than this, leaving lags of 212 km for birds, and 135 km for butterflies. These are the distances that birds and butterflies would need to travel to reach temperatures similar to that of their historical range shifts.

  5. Aug 2018
    1. T.C. LaJeunesse, Marine Biology 141, 387–400 (2002).

      Following LaJeunesse and Trench's 2000 publication on DGGE, this work expands on the applications, effectiveness, and usefulness of DGGE -a technique that separates DNA fragments.

    2. T.C. LaJeunesse, Journal of Phycology 37, 866–880 (2001).

      This work was used in this research since it is based on a characteristic molecular region in the Symbiodinium species.

    3. T.C. LaJeunesse, R.K. Trench, Biological Bulletin 199, 126–134 (2000).

      Reviews the technique denaturing gradient gel electrophoresis (DGGE) and how it is used for molecular identification.

    4. R. Rowan, D.A. Powers, Marine Ecology Progress Series 71, 65–73 (1991).

      Gives background information on different types of amplification techniques used to determine molecular identification.

    5. D.L. Taylor, In: Symbiosis in the Sea (ed. Vernberg WB), pp. 245–262. (University of South Carolina Press, South Carolina, 1974).

      Prior to the introduction of molecular techniques, early work such as this reference discusses dinoflagellates and how they were thought to belong to one pandemic species.

    6. X. Pochon, R.D. Gates, Molecular Phylogenetics and Evolution 56, 492–497 (2010).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    7. M.A. Coffroth, S.R. Santos, Protist 156, 19–34 (2005).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    8. H.D. Freudenthal, Journal of Protozoology 9, 45–52 (1962).

      This reference explains why there are so many types of Symbiodinium.

    9. J.H. Connell, Science 199, 1302–1310 (1978).

      This information is used in order to introduce what species this research is going to focus on. Although the focus is on Symbiodinium, this information highlights the importance of this genus.

    1. C.D. Hopkins, Copeia 1991, 151–161 (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 types 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 females.

    2. M.V.L. Bennett, Fish Physiology 5, 347–491 (1971).

      In his paper Electric Organs, Fishes, Bennett explains the various mechanisms behind electric fish organs and how they generate electricity, such as electrocytes and discharge patterns. He also describes several vital functions of electric organs and how they vary depending on the strength of the species' electricity, or the power of its voltage emission. For example, the electric organs of more strongly electric fish, or those who emit higher voltages, emit electricity to defend against predators. Conversely, in more weakly electric fish, their electric organs emit electricity that serves as a method of communication.

      This reference is significant to this paper, Electric organ discharges and electric images during electrolocation, because it gives a broad overview on electric fish, their anatomy, and their functions. It serves as a source of background information and context for this paper, which can be especially helpful for readers who possess limited knowledge on electric fish.

    3. J. Bastian, Electrolocation: behavior, anatomy and physiology.  (New York: Wiley, 1986).

      This source provides information about how the various regions of neuronal activity in electric fish respond differently 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.

    4. E. Knudsen, J. Comp. Physiol. 99, 103–118 (1975).

      This source provides information about how the electrical patterns of small fish work compared to dipolar geometry and how that changes as the fish become larger in size.

      Specifically, the smaller electrical fish, which the author of this article is studying, have electrical currents that work like magnets. These smaller fish are much easier to measure and experiment on since their electrical currents and fields can be predicted. The bigger electrical fish are the more likely the electrical fields are to deviate from a dipole field.

    5. T.H. Bullock, W. Heiligenberg, Electroreception. (New York: Wiley, 1986).

      Bullock's and Heiligenberg's article, Electroreception, gives an in-depth knowledge on electroreception as well as a review on the electric organs that are found within marine vertebrates. This background provides 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.

    1. C. Parmesan, G. Yohe, Nature 421, 37–42 (2003).

      Identifying effects of climate change on recent biological trends is difficult because non-climatic changes greatly influence local, short-term biological changes. Parmesan and Yohe study the differences between climatic and non-climatic effects on over 1700 species. A diagnostic indicator of temporary, geographic shifts was found with confidence for 279 species.

    2. M. H. Williamson, Biological Invasions (Chapman & Hall, 1996).

      A collection of invasive species and the damages they can cause, summarized by an invasive species expert. The focus of the text is on approach to biological control and releasing genetically modified organisms.

    1. National Research Council, “Air quality management in the United States” (2004).

      This document sets standards for ensuring good air quality in the United States. Most of the recommendations focus on transportation and industrial sources. This paper suggests that household VCPs are becoming an ever increasing source of VOCs.

    2. X. M. Wu, M. G. Apte, R. Maddalena, D. H. Bennett, Environ. Sci. Technol. 45, 9075–9083 (2011).

      Monitored air pollution at various small industrial buildings in California. This monitoring included measurements for VOCs.

      This experimental data was used to compare with the model calculations in this study.

    3. California Air Resources Board, “The California Consumer Products Regulation” (2015).

      California looks to regulate the emission of VOCs and thus regulates and keeps records of VOCs in various products. The authors of this paper were able to utilize that database to know what chemicals are present in various products.

    4. J. M. Logue, T. E. McKone, M. H. Sherman, B. C. Singer, Indoor Air 21, 92–109 (2011).

      Compiled results from 77 separate studies to look at typical levels of indoor air pollution in household environments. The study includes VOCs.

      This experimental data was used to compare with the model calculations in this study.

    5. A. Borbon et al., J. Geophys. Res. Atmos. 118, 2041–2057 (2013).

      An experimental study that monitored the presence of VOCs in the outdoor air near Los Angeles, California during 2010.

      This study uses the experimental data by Bordon to compare with their model calculations.

    6. J. L. Jimenez et al., Science 326, 1525–1529 (2009).

      Jimenez and colleagues developed a model to show and predict how VOCs react to turn into aerosol particles in the atmosphere.

      Understanding VOC emissions is important to understanding aerosol formation.

    7. GBD 2016 Risk Factors Collaborators, Lancet 390, 1345–1422 (2017).

      This study compiled a large number of studies on human health to examine various risk factors for disease and death.

      Air pollution was found to be the fifth leading risk factor for human health.

    1. R. J. Müller, H. Schrader, J. Profe, K. Dresler, W. D. Deckwer, Macromol. Rapid Commun.

      The authors reported a hydrolase from Thermobifida fusca. The authors noted that the hydrolase successfully degrades PET. They note that it is helpful that PET has a glass transition temperature near the temperature where the enzyme can be incubated with the plastic.

    2. 3. D. Kint, S. Munoz-Guerra, Polym. Int. 48, 346–352 (1999).

      Discusses the synthetic methods of preparing biodegradable copolymers that include PET as well as the mechanisms that break down the resulting products.

      The review details several areas of research needed if PET copolymers are to become a feasible biodegradable material, including finding a polymer with sufficiently high melting point to be bonded to PET and ensuring the resulting copolymer has the correct properties for practical use.

    3. 5. T. Nimchua, H. Punnapayak, W. Zimmermann, Biotechnol. J. 2, 361–364 (2007).

      This paper took samples of fungi from a variety of tropical locations in Thailand and then tested them for cutinase production. It found 22 samples able to use a cutinase enzyme to degrade PET.

    4. T. Nimchua, D. E. Eveleigh, U. Sangwatanaroj, H. Punnapayak, J. Ind. Microbiol. Biotechnol. 35, 843–850 (2008)

      Reports on a fungus that is capable of turning PET yarn into terephthalic acid (TPA). The enzyme responsible was identified as a hydrolase. PET degradation was measured by the production of TPA and the increasing hydrophilicity of the PET fiber.

    1. Musiba CM, Mabula A, Selvaggio M, Magori CC. 2008. Pliocene animal trackways at laetoli: research and conservation potential. Ichnos 15:166–178. doi: 10.1080/10420940802470383

      The authors discuss the animal tracks at a newly discovered Laetoli exposure and other sites. Animal trackways serve as ecological indicators.

    2. Maslin MA, Shultz S, Trauth MH. 2015. A synthesis of the theories and concepts of early human evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 370:20140064. doi: 10.1098/rstb.2014. 0064

      The authors examine the African paleoclimate and tectonics to determine how climate variability provides a framework within which to understand human evolution. The varying East African climate supports the pulsed climate variability hypothesis. Drying trends punctuated by short periods of high humidity may have driven hominin speciation and migration.

    3. Leakey MD. 1981. Tracks and tools. Philosophical Transactions of the Royal Society B: Biological Sciences 292: 95–102. doi: 10.1098/rstb.1981.0017

      Dr. Leakey and associates discovered the footprints left by three hominins in the Laetoli beds. In this article, it is reported that the trackway extends 27 meters and provides evidence of upright, bipedal locomotion. Radiometric dating places the tracks at 3.6 million years ago. There have been no stone artifacts found in the Laetoli area. The earliest evidence of stone tools in the region was found in Olduvai Gorge and dates to about 2 million years ago. Consequently, it can be inferred that bipedalism evolved prior to formalized tool-making.

  6. Jul 2018
    1. M. C. Goldstein, D. S. Goodwin, PeerJ 1, e184 (2013).

      An ocean gyre is a circular ocean current formed by the Earth’s wind patterns and rotation. The area in the center of a gyre tends to be very calm, and the circulation patterns of the currents draw debris into the stable center, where it becomes trapped. The debris is composed of objects both manmade and natural (i.e. driftwood). Many kinds of sea life live on and near the debris. Gooseneck barnacles are one of these types of organism. Goldstein and Goodwin examined the digestive tracts of gooseneck barnacles to see if the barnacles consumed any plastics. One third of the 385 barnacles examined had plastic particles present in their digestive tracts, and larger barnacles tended to contain more plastic particles. The effects of the plastic particle ingestion on the ecosystem are still unknown.

    1. 17. M. Hosaka et al., Appl. Environ. Microbiol. 79, 6148–6155 (2013).

      This paper reported two genes that code for two separate proteins that sit in a cell membrane and help TPA get into the cell.

  7. Jun 2018
    1. W. Zimmermann, S. Billig, Adv. Biochem. Eng. Biotechnol.

      This is a chapter in a book about biofunctionalization of polymers. The authors focus on how using biological methods to modify PET might make it more hydrophilic and therefore allow it to be used for a greater variety of applications in, for example, engineering and medicine.

      The authors do not focus on the use of methods of degrading polymers for recycling or disposal, however many of the biofunctionalization processes they describe involve degrading portions of PET polymer to give it better properties.

    1. E. A. Posner, C. R. Sunstein, Univ. Chic. Law Rev. 72, 537–598 (2005).

      This article discusses how governments should assign dollar values to human lives when someone dies. One consideration is whether children and adults should be valued differently.

    2. W. Wallach, C. Allen, Moral Machines: Teaching Robots Right from Wrong (Oxford University Press, 2008).

      This book discusses how robots should be able to factor morality and ethics into their decisions, and discusses some ways engineers can program morality into machines.

    3. R. M. Dawes, Annu. Rev. Psychol. 31, 169–193 (1980).

      This study reviews the nature of social dilemmas, investigates potential solutions to social dilemmas, and lists psychological studies that have shed insights on the topic.

    4. K. Spieser et al., in Road Vehicle Automation, G. Meyer, S. Beiker, Eds. (Lecture Notes in Mobility Series, Springer, 2014), pp. 229–245.

      This paper investigates what would happen if personal transportation in Singapore was replaced by self-driving cars. Results suggest that far fewer vehicles would need to be on the road if such a system were implemented.

    5. M. M. Waldrop, Nature 518, 20–23 (2015).

      This feature article describes the rise of driverless cars and the technologies being implemented to make them drive on roads.

      The article argues that self-driving vehicles could help make roads safer, as about 90% of driving accidents are due to human error.

    6. B. Deng, Nature 523, 24–26 (2015).

      This feature article describes the challenges in programming robots to make ethical decisions.

    7. B. Montemerlo et al., J. Field Robot. 25, 569–597 (2008). C. Urmson et al., J. Field Robot. 25, 425–466 (2008).

      References 1 and 2 describe two entries for the DARPA Urban Challenge, which brought together self-driving cars that could navigate realistic city environments.

    1. Acero F., Ackermann M., Ajello M. et al (Fermi-LAT) 2015 arXiv:1501.02003Preprint

      Starting in 2014-2015, AAS/IOP started linking to preprints in reference lists if they were the version cited by the author and an accepted manuscript did not at that time exist.

      Thus we now have built in "categories" for references, which could be expanded to include data/software sections.

    1. Barbary K. 2014 sncosmo Zenodo, 10.5281/zenodo.11938

      This software citation losts its version information. We will have to work on our typsetting and production rules, as well as develop formal JATS/NLM XML schema to contain versioning information.

    1. K. E. Taylor, R. J. Stouffer, G. A. Meehl, An overview of CMIP5 and the experiment design. Bull. Am. Meteorol. Soc. 93, 485–498 (2012)

      Taylor, Stouffer, and Meehl provided an overview of phase five of the Climate Model Intercomparison Project (CMIP5), written while the project was underway. The project aimed to produce a new set of freely available coordinated climate model experiments and data sets. The paper describes the plan for the experiments and a discussion of issues related to interpreting the results.

    2. A. Indermühle, T. F. Stocker, F. Joos, H. Fischer, H. J. Smith, M. Wahlen, B. Deck, D. Mastroianni, J.Tschumi, T. Blunier, R. Meyer, B. Stauffer, Holocene carbon-cycle dynamics based on CO2 trapped in ice at Taylor Dome, Antarctica. Nature 398, 121–126 (1999).

      Indermühle and colleagues developed an atomospheric CO<sub>2</sub> concentration reconstruction for the entire Holocene from ice core samples from the Taylor Dome in Antarctica.

      The ice cores have trapped air bubbles, which were only exposed to atmosphere when the bubbles were at the top (youngest) layer of the ice. The CO<sub>2</sub> concentration of these bubbles were measured using infared spectroscopy. By testing many layers throughout the entire core sample, the researchers reconstructed the atmospheric CO<sub>2</sub> levels throughout the last 11,000 years, to the start of the Holocene.

    3. C. B. Yackulc, J. D. Nichols, J. Reid, R. Der, To predict the niche, model colonization and extinction. Ecology96, 16–23 (2015).

      In this report, Yackulc and colleagues argue that niche-based models, which predict future species distribution using current plant or animal distributions, assume that the observed species are in equilibrium, which may not be a valid assumption for many ecosystems that are in flux. They proposed a process-based model that uses colonization and extinction rates for a given species in a given environment, and use case studies to show the model's applicability.

    4. J. Geophys. Res. 121, 2060–2074 (2016).

      Cook and coauthors analyzed variations in droughts in the Mediterranean region over the past 900 years (1100–2012), using tree-ring data. They found a number of patterns in drought variation and distribution, and also determined a 98% likelihood that the current drought in the Levant region (Cyprus, Israel, Lebanon, Palestine, Syria, and Turkey) is the worst in the past 500 years, and an 89% likelihood that it is the worst in 900 years.

    5. D. Kaniewski, E. Van Campo, H. Weiss, Drought is a recurring challenge in the Middle East. Proc. Natl. Acad. Sci. U.S.A. 109, 3862–3867 (2012).

      In this integrative study, Kaniewski, Van Campo, and Weiss examined the trends of water availability during the Medieval Climate Anomaly (900–1300 CE) and the Little Ice Age (1550–1850 CE) in Northern Mesopotamia, and how those trends affected human systems.

      The study combined archaeological data, climate proxies, and an agricultural record based on pollen. The researchers found that changes in precipitation had an impact on yield and productivity of crops, and these changes were correlated with changes in agriculture and settlement activities.

    6. E. Xoplaki, J. F. González-Rouco, J. Luterbacher, H. Wanner, Wet season Mediterranean precipitation variability: Influence of large-scale dynamics and trends. Clim. Dyn. 23, 63–78 (2004).

      Xoplaki and co-authors examined how different variables affected the wet season patterns across the Mediterranean region for the years 1950–1999. They found that while large-scale atmospheric features had a high influence on the variability, smaller scale factors also impacted the rainfall across the region.

    7. J. Guiot, D. Kaniewski, The Mediterranean Basin and Southern Europe in a warmer world: What can we learn from the past? Front. Earth Sci. 3, 28 (2015)

      Guito and Kaniewski present the "inverted" BIOME4 method of reconstructing climate variables and biomes from pollen core data that is the basis for the current paper.

      They developed a climate data for a small set of gridpoints in the Mediterranean region for two time frames: 1901–2000 and 10,000 years ago to the present. They found that the climate dynamics of 1901–2000 differed from those of the past 10,000 years in several ways, and that the warming pattern in the past decades does not have an equivalent match in the earlier Holocene period.

    8. W. Cramer et al., in Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, C. B. Field et al., Eds. (Cambridge Univ. Press, 2014), pp. 979–1037.

      The Intergovernmental Panel on Climate Change develops reports on climate change that provide information for the United Nations Framework Convention on Climate Change. The Fifth Assessment Report was published in 2014, in advance of the Paris Agreement meeting.

      This report section focuses identifying impacts of climate change that have already happened. The report found more observations of regional climate change impacts than in the past, and reaching all continents, but also found gaps in knowledge of climate change impacts at regional levels.

  8. May 2018
    1. (Feng, C.-L. Chinese Academy of Forestry, personal communication)

      Personal communication was made between the author and other researchers to confirm that this species of orchid is rare and its populations are unknown due to orchid poaching.

    1. Zabierowski SE, Herlyn M. Melanoma stem cells: the dark seed of melanoma. Cancer Lett. 2008;26:2890–93.

      This study investigated the hierarchy of characteristic genes of melanomas with the goal of developing new therapeutic treatments.

    2. Spinella F, Rosano L, Di Castro V, Decandia S, Nicotra MR, Natali PG, Bagnato A. Endothelin-1 and endothelin-3 promote invasive behavior via hypoxia-inducible factor-1alpha in human melanoma cells. Cancer Res. 2007; 67:1725–34.

      The study investigated the interactions between hypoxia, an oxygen deficiency, and the ET axis, or the ET receptors, in primary melanoma cell lines and metastasized melanoma cell lines. Metastasized means that the tumor beyond the tissue initially affected by the tumor.

      The study found that ET-1, ET-3 and the ET(B)R react with HIF-1alpha-dependent molecules to promote melanoma invasion of tissues. The HIF-1alpha is the hypoxia-inducible factor-1alpha, a transcriptional factor that induces a signaling by growth factor receptors and hypoxia.

    3. Shackleton M, Quintana E, Fearon ER, Morrison SJ. Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell. 2009; 138:822–9.

      This study focused on targeting genes present in malignant cancer cells to develop novel therapeutic treatments for cancers.

    4. Schatton T, Murphy GF, Frank NY, Yamaura K, Waaga-Gasser AM, Gasser M, Zhan Q, Jordan S, Duncan LM, Weishaupt C, et al. Identification of cells initiating human melanomas. Nature. 2008; 451:345–9.

      This study was designed to investigate tumor promoting cells, which could have therapeutic benefits if they are targeted with a specific treatment. The targeted cells accumulate in advanced cancers.

    5. Pla P, Larue L. Involvement of endothelin receptors in normal and pathological development of neural crest cells. Int J Dev Biol. 2003; 47:315–25.

      This study examined how mutations that affect neural crest development pathways affect neural crest cells. It also examines how endothelin receptors act during cell development, movement, and differentiation.

    6. Larue L, Beermann F. Cutaneous melanoma in genetically modified animals. Pigment Cell Res. 2007; 20:485–97.

      This study examined the effects of NRAS gene mutations in mouse models and how these mutations affect cancer development. The conclusion reached was that somatic mutations in the NRAS gene are risk factors of primary melanoma in mouse models and in children.

    7. Garcia RJ, Ittah A, Mirabal S, Figueroa J, Lopez L, Glick AB, Kos L. Endothelin 3 induces skin pigmentation in a keratin-driven inducible mouse model. J Invest Dermatol. 2008; 128:131–42.

      This experiment was conducted at Florida International University as well.

      The results indicate the Endothelin 3 originating outside of the nucleus affects melanocyte precursors and differentiated melanocytes. It causes a phenotype similar to dermal melanocytosis to be developed.

      Dermal melanocytosis is a blue-grey pigmentation of the skin that usually occurs in newborn humans.

    8. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000; 406:536–40.

      The authors examined melanoma development in a series of samples with the use of mathematical techniques. A subset of melanomas was discovered with the use of these samples and mathematical models. Many of the genes used to identify this subset are regulated differently in aggressive melanomas that have metastasized.

    9. Bellahcene A, Castronovo V, Ogbureke KU, Fisher LW, Fedarko NS. Small integrin-binding ligand N-linked glycoproteins (SIBLINGs): multifunctional proteins in cancer. Nat Rev Cancer. 2008; 8:212–26.

      The researchers investigated the role of a group of glycophosphoproteins known as SIBLINGs, or small integrin-binding ligand N-linked glycoproteins, in cancer development. The results indicated that the SIBLINGs could be used in therapy development, diagnosing cancers, or predicting prognoses.

    10. Bagnato A, Rosano L, Spinella F, Di Castro V, Tecce R, Natali PG. Endothelin B receptor blockade inhibits dynamics of cell interactions and communications in melanoma cell progression. Cancer Res. 2004;64:1436–43. [PubMed]

      Bagnato investigates the agonists of the endothelin B receptor (ET(B)R), endothelin-1 (ET-1) and ET-3 and the role that they play in tumorigenesis.

      Bagnato states that (ET(B)R) is a marker for tumor progression. This study supported the role of ET-1 and ET-3 to impede the usual interactions between hosts and tumors.

      The ligands also promote development of cutaneous melanoma. Melanoma is a cancer in melanin-producing cells. Cutaneous melanoma is melanoma that occurs on skin.

    1. J. D. Salamone, M. Correa, Behav. Brain Res. 137, 3–25 (2002).

      Salamone and Correa review evidence for the fact that motivation is the main process for reinforcement. They also discuss how low/moderate doses of a dopamine receptor-blocking drug can block some actions but leave other behavior intact.

      This study and others suggest that the behavior in drug addiction can’t be explained simply by dopamine activation of reward responses, but is instead a complex subject.

    2. G. Schoenbaum, B. Setlow, Cereb. Cortex 15, 1162–1169 (2005).

      Schoenbaum and Setlow were interested in what drives continued drug use even if when it has negative consequences.

      The authors use reinforced devaluation to test whether drug exposed rats respond persistently after devaluation of a food reward.

    3. E. Dias-Ferreira et al., Science 325, 621–625 (2009).

      Dias-Ferreira et al. used rats as a model to study how chronic stress affects decision-making processes. His group was able to show that stress affects this process by causing changes in the physiology of neurons and brain regions associated with these functions.

    4. L. H. Corbit, B. C. Chieng, B. W. Balleine, Neuropsychopharmacology 39, 1893–1901 (2014).

      Corbit et al. were interested in how control can be reestablished after drug abuse.

      The authors assessed whether chronic drug use shifts behavior from a goal-oriented process to a habit learning process, and studied the physiological implications of those changes. In addition, they tested whether N-acetylcystine, a treatment previously shown to prevent relapse into cocaine use, could prevent the rapid formation of habits after drug exposure.

    5. B. W. Balleine, J. P. O’Doherty, Neuropsychopharmacology 35, 48–69 (2010).

      Balleine and O’Doherty review what is known about the decision-making process, looking at the relationship between action and outcome (goal-directed behavior) and the stimulus-response association (habitual behavior).

      The authors discuss the similarity between humans and rats in the decision-making process, showing that for both organisms the cortex and striatum areas are involved in goal-directed and habitual actions.

      It is this similarity that suggests that cooperation or competition between habitual and goal-directed actions mediates the integration of new information (learning).

    6. A. Dickinson, Philos. Trans. R. Soc. London Ser. B 308, 67–78 (1985).

      This article discusses whether a given behavior is an acquired habit to a stimulus or is a choice made due to an association between action and outcome (i.e., goal-oriented).

      For this study, the author used a food-reward experiment in rats and assessed their actions when the reward was gradually decreased. Extended training affected the relationship between stimulus and outcome, and limited training resulted in the rats being more likely to react to reward devaluation.

    7. B. J. Everitt, T. W. Robbins, Nat. Neurosci. 8, 1481–1489 (2005).

      This review by Everitt and Robbins discusses what is known about the transition from initial drug use to a habit.

      The article takes a physiological perspective by looking at the role of different areas of the brain in this transition, such as the amygdala and hippocampus.

    1. N. G. Jablonski, G. Chaplin, The evolution of human skin coloration. J. Hum. Evol. 39, 57–106 (2000). doi:10.1006/jhev.2000.0403pmid:10896812

      The work of Jablonski and Chaplin strongly supports the theory that melanin pigmentation in human skin is an adaptation to regulate the amount of UV radiation that gets into the epidermis, with different populations having different pressures based on their environments.

      They argue that protection against lysis of nutrients (such as folate) was the primary selective agent that led to darker pigmentation of people living near the equator, because folate is closely linked to reproductive success in humans.

      They also argue that skin pigmentation is so responsive to environmental conditions that skin pigmentation is not valuable when assess the genetic relatedness of human groups.

    1. K.D. Whitney, C.A. Gabler, Divers Distrib 14, 569–580 (2008).

      Whitney et al. analyzes the obstacle within risk assessment in calculating "invasive potential". Markers studied include predictors of "rapid microevolution such as extent of heterosis, adaptation to novel habitats, and hybridization impacts. They study 38 documented species known for their invasiveness and proceed to mark their generation times, growth rates, and populations in studied areas.