1,011 Matching Annotations
  1. Nov 2017
    1. D. L. Swofford, PAUP: Phylogenetic Analysis Using Parsimony, version 3.1; (Illinois Natural History Survey, Champaign, IL, 1993).

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

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

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

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

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

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

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

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

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

    1. (Bastian, 1986),

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

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

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

      -Kierra Hobdy

    2. Bullock and Heiligenberg, 1986

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

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

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

      Mikaela

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

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

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

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

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

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

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

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

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

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

    1. M. Nei, Genetics 89, 583 (1978)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      Harris reviews our current understanding of ticklishness in humans.

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

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

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

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

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

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

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

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

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

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

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

      Read more on eLife:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      See The Tragedy of the Commons.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    1. Entic's naval history

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      This classic book reviews six key sources of persuasion:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      All of this can be visualized in live mice!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      This line is from the Gospel of Mark.

    2. and the giver of Life

      This line is from the Chaldean Oracles.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      Bruce Alberts, Marc W. Kirschner, Shirley Tilghman and Harold Varmus describe the advances in scientific knowledge and human health that have accrued as a result of the long-standing public investment in biomedical research.

  12. Oct 2016
      • 5:48 Expert Political Judgment

        • Discusses the concept of Integrative Complexity
          • People with a lot of integrative complexity are more capable of reasoning about complex issues, distinguishing between facts and opinions, and seeing the world clearly as it is.
            • People who lack this quality tend to think in terms of black-and-white, and to have an arrogant and antagonistic attitude.
            • Fame is inversely correlated with integrative complexity
      • 11:29 The Big Sort by Bill Bishop

        • There is an ongoing trend, especially on the Internet, but also geographically, for people to cluster based on their own worldview, while they become less and less open to different ideas.
          • The content filtering mechanisms of Tumblr and other social media websites, where you can simply unfollow whoever you disagree with, are the reason why this phenomenon is so prevalent on the Internet.
      • 14:20 Pan's Labyrinth
        • Moral parable with "think for yourself; don't just blindly obey" as its message.
    1. - "Doing good (high quality work) matches with doing well (achieving wealth and professional advancement) in the field." -

      What's the source?

    2. a whole new field called positive psychology
    3. - "People are very bad at predicting what will bring them happiness." -

      What's the source?

    4. to quote Notorious B.I.G. - "Mo money mo problems"
    5. "The Happiness Hypothesis" by Jonathan Haidt
    6. http://en.wikipedia.org/wiki/Positive_psychology
    1. the demon scrupulously takes part in all these matters, sees all things, understands all things, and dwells in the most profound recesses of the mind, in the place of conscience.  He of whom I speak is entirely our guardian, our individual keeper, our watcher at home, our own proper regulator, a searcher Into our inmost fibres, our constant observer, our inseparable witness, a reprover of our evil actions, an approver of our good ones; if he is becomingly attended to, sedulously examined and devoutly worshipped, in the way in which he was worshipped by Socrates in justice and in innocence; he is our forewarner in uncertainty, our monitor in matters of doubt, our defender in danger, and our assistant in need. He is able also by dreams, and by tokens, and perhaps even openly, when necessity demands it, to avert from you evil, to increase your blessings, to aid you when depressed, to support you when falling, to lighten your darkness, to regulate your prosperity, and modify your adversity.

      This part is quoted in a talk on the Thelemic concept of Holy Guardian Angel here.

    1. the daemon who presides over you inquisitively participates of all that concerns you, sees all things, understands all things, and in the place of conscience dwells in the most profound recesses of the mind [see note 6]. For he of whom I speak is a perfect guardian, a singular prefect, a domestic speculator, a proper curator, an intimate inspector, an assiduous observer, an inseparable arbiter, a reprobater of what is evil, an approver of what is good; and if he is legitimately attended to, sedulously known, and religiously worshipped, in the way in which he was reverenced by Socrates with justice and innocence, will be a predictor in things uncertain, a premonitor in things dubious, a defender in things dangerous, and an assistant in want. He will also be able, by dreams, by tokens, and perhaps also manifestly, when the occasion demands it, to avert from you evil, increase your good, raise your depressed, support your falling, illuminate your obscure, govern your prosperous, and correct your adverse circumstances.

      This part is quoted in a talk on the Thelemic concept of Holy Guardian Angel here.

    1. Some references made in this video:

  13. Sep 2016
    1. J. J. Palop, J. Chin, L. Mucke, Nature 443, 768 (2006).

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

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

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

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

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

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

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

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

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

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

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

    1. G. D. Gilfillan et al., Am. J. Hum. Genet. 82, 1003 (2008)

      This study was about mutations in the SLC9A6 gene, which are related with neurological diseases, such as X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome.

      By using the experimental methods of linkage analysis and DNA sequencing they found out that a deletion in the SLC9A6 gene, encoding the Na(+)/H(+) exchanger NHE6, is basically responsible for these symptoms.

    2. M. L. Jacquemont et al., J. Med. Genet. 43, 843 (2006)

      M. L. Jacquemont worked on the genetic heterogeneity of syndromic autism, more easily revealed through array-CGH. The author suggested that this method should be prioritized in order to diagnose autism. This study also revealed that patients with locus duplications are less affected that those presenting deletions. Finally, the importance of the chromosomal imbalance has no direct relation with the severity of the mental retardation.

    3. J. Sebat et al., Science 316, 445 (2007).

      Sebat and colleagues worked on the involvment of de novo Copy Number Variations in autism.

      They showed that specific CNVs were mostly present in only one family among the tested group. They were also able to show the difference between simplex families, where autism is the result of spontaneous mutation and multiplex, where autism is most likely inherited.

    4. J. A. Vorstman et al., Mol. Psychiatry 11, 1 (2006).

      Vorstman provides a review of much of the recent cytogenetic studies on autism. In these studies, researchers were able to identify abnormalities by looking at the shapes and sizes of chromosomes. From these observations, they were able to deduce if there were large-scale deletions, repetitions, or inversions in the chromosomes. A small percentage (about 3%) of autistic patients had mutations like this. Vorstman gathers these findings into one article and proposes regions scientists should focus on in future research.

    5. P. Szatmari et al., Nat. Genet. 39, 319 (2007).

      P. Szatmari and colleagues have shown that copy number variants (CNV) were risk factors and causal events for autism. However, they are not the only parameters to be taken into account : oligogenic inheritance - inheritance of genes which, in a small quantity, code major changes - would be a prevalent factor of autism.

    6. R. Canitano, Eur. Child Adolesc. Psychiatry 16, 61 (2006)

      In this article, R. Canitano emphasizes the link between autism and epilepsy, showing that seizures are more frequent when mental retardation is associated with autism. The rate of comorbidity - cohabitation between two diseases, autism and epilepsy here - is estimated at 20-25%, meaning that this amount of autistic people is victim of seizures. This link has to be taken into account when considering therapy.

    7. E. Fombonne, J. Autism Dev. Disord. 33, 365 (2003).

      E. Fombonne has provided a review of epidemiological surveys on autism, in order to draw general conclusions. He concluded that autism is associated with mental retardation in about 70% of the cases and is overrepresented amongst males. He also showed that social class has no impact on the incidence of the disease. He also considered that available surveys did not allow to conclude that race or ethnicity influence the incidence of autism. Finally, no data could support the idea of secular evolution in the incidence of the disease.

    8. N. Risch et al., Am. J. Hum. Genet. 65, 493 (1999).

      Risch and colleagues studied the genetic makeup of subjects affected by autism.

      They showed that autism is most likely caused by multiple genes and identified several genes that could play a part in this disease in different individuals.

    9. A. E. West, E. C. Griffith, M. E. Greenberg, Nat. Rev. Neurosci. 3, 921 (2002).

      This study was about the regulation of specific transcription factors by neuronal activity. They found out, by using techniques as mass spectrometry and chromatin immunopreuritation, that synaptic activity determines the expression of a set of neural gene products.

      In this study also, a large nuclear protein, Cabin 1 (calcineurin-binding protein), was found out to be q cqlcium-regulated depressor of MEF2 activity.

    10. G. A. Cox et al., Cell 91, 139 (1997)

      This study was about a spontaneous mouse mutant, called slow-wave epilepsy (swe), which is related to several neurological syndromes, like ataxia, as well as about a unique epilepsy phenotype, that is characterized by 3/sec absence and tonic-clonic seizures.

      swe was fine-mapped on Chromosome 4 and identified as a null allele of Nhe1, which is the Na+/H+ exchanger, a ubiquitous, and acts as an integral membrane protein involved in pH regulation. It removes intracellular acid, exchanging a proton for an extracellular sodium ion.

    1. J. Celichowski, K. Grottel, Acta Neurobiol. Exp. (Warsz.) 58, 47–53 (1998).

      The aim of this study was to show the influence of two stimuli (produced in a short time sequence and called doublet) on the time where a tetanus was observed. By using single motor units of rats, it was shown that the doublet induced an increase of the tetanic tension and fusion. Also that slow motor units showed higher reaction to the doublet sensitivity than fast units.

    2. F. E. Zajac, J. L. Young, J. Neurophysiol. 43, 1206–1220 (1980).

      Researchers took muscle samples from cats and tried different tetanus on them. They seem to have found the efficient pulse and frequencies by the motor neuron to generate a optimum muscle tension.

    3. J. R. Gallant et al., Science 344, 1522–1525 (2014).

      They investigated the evolution of the electric organs of eels. They looked at the DNA of the electric eels and two other species with electric organs. They detected many different genes for the developement of electric organs. Their results show that despite big differences in the electric cells of the investigates species, they have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs.

    4. S. Hagiwara, T. Szabo, P. S. Enger, J. Neurophysiol. 28, 775–783 (1965).

      Some electrical fish produce not enough voltage to get an offensive or defensive meaning. In this study, authors try to understand in which this sorts of fish use this system. It will be demonstrate that it is used as direction and finding of the fish.

    5. K. K. Pedersen, O. B. Nielsen, K. Overgaard, Physiol. Rep. 1, e00026 (2013).

      Effects of high‐frequency stimulation and doublets on dynamic contractions in rat soleus muscle exposed to normal and high extracellular

    6. R. Hennig, T. Lømo, Nature 314, 164–166 (1985)

      By recording firing pattern in motor units of rats, authors demonstrates quantitatively that, contractile properties of the muscular system is improve by the tree different respond allowed (fast but easily fatigued, slow but fatigue resistant, both). Also this paper in studying and recording the normal value of muscular contraction of an healthy rats, will allow the searcher to notice if is somethings wrong or interact with the motor control system. Like in our articles where the Eels's electricity make the muscular system of the fish goes off. "Firing patterns of motor units in normal rats"

    7. G. M. Westby, Behav. Ecol. Sociobiol. 22, 341–354 (1988).

      The researchers investigated the behaviour of electric fish in french guiana. Notably, they describe in first the prey-capture behaviour of the electric eels.

    8. J. Keesey, J. Hist. Neurosci. 14, 149–164 (2005).

      Fish electric organs seams to be derived originally from muscle therefore a source of acetylcholine receptor. The Eels' anatomy was used many in different science domain such as Anatomy, embryology, and physiology. In previous research it was shown that the pathway between the nerve and electric organ used acetylcholine receptor. This is why this species, source of acetylcholine, conduct to very detailed studies by biochemist and neurologist.

    9. S. Finger, M. Piccolino, The Shocking History of Electric Fishes: From Ancient Epochs to the Birth of Modern Neurophysiology (Oxford Univ. Press, Oxford, 2011), p. 5.

      "The Shocking History of Electric Fishes: From Ancient Epochs to the Birth of Modern Neurophysiology" is a book written by Stanley Finger and Marco Piccolino. In this study they follow different types of animal (flat torpedo rays, the electric catfishes, and the "eel" of our article). All three are able to produce electricity shocks and explain how they helped to change the sciences and medicine.

    10. H. Grundfest, Prog. Biophys. Biop. Chem. 1957, 1–85 (1956)

      By studying the electroplaques of Torpedo-nobilian, the researcher try to understand how depolarising or hyperpolarizing changes in membrane potential occur. Furthermore they relief the latency time during stimulation of the nerve and the polarisation of the cells.

    1. W. R. Kerr, The ethnic composition of US inventors, Working Paper 08-006, Harvard Business School (2008)

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

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

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

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

      This paper explored the role of β-catenin (protein involved in growth and thought to be a morphogen) which is expressed in the placode.

      It was found that when this protein was mutated, the chickens would be scaleless(on the feet) and have abnormal feather growth.

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

      The development of skin cells that give rise to hairs is reviewed in this paper.

      A hair placode forms which allow for the expression of genes that determine skin cells and hair follicle development.

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

      This paper proposed the theory that mammal hairs evolved from glandular structures. Whereas reptiles and birds skin (including feathers and scales) evolved a different pathway where a thick protective covering which would become scales.

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

      This review deals with a model of how hair evolved, updating a model built in the 1972 (reference 3).

      This model supposes that the development of hair was caused by mutations in patterning genes. this development allowed hair to become useful insulation.

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

      This paper illustrates the way that crocodile head scales form. the process is different to the formation of other skin traits (such as feathers, hair and other scales).

      The crocodile face and jaw scales are formed through the force of the growing cells physically pushing and cracking about hard shell forming unique patterns.

    1. J. B. Silk, in The Oxford Handbook of Evolutionary Psychology, R. I. M. Dunbar, L. Barrett, Eds. (Oxford Univ. Press, Oxford, 2007), pp. 115–126.

      Chapter 10: Empathy, sympathy, and prosocial preferences in primates.

      There are several potential lines of evidence for the existence of empathy in nonhuman primates. Because of the subjectivity in interpretation of animals' intentions as well as no defined assay for empathy or sympathy, "we cannot be certain whether any given interpretation is right or wrong."

      "To transform singular observations of behavior into more robust findings we need to develop theoretically grounded hypotheses that we can subject to empirical testing."

      http://www.amazon.com/Oxford-Handbook-Evolutionary-Psychology-Handbooks/dp/0199561788

    2. although skeptics remain (27)

      "Current claims for the existence of empathy, sympathy, and moral sentiments and other-regarding preferences in other primates rest on an insecure empirical foundation.

      The anecdotal accounts have limited value because they rely on subjective interpretation of animals' intentions and motivations and they are not systematically collected or analysed.

      This means we cannot be certain whether any given interpretation is right or wrong and we have no means of discriminating against competing claims."

      The chapter covering this controversial view of whether nonhuman animals display empathy may be found here:

      http://www.amazon.com/Oxford-Handbook-Evolutionary-Psychology-Handbooks/dp/0199561788

      Type the word empathy into the "search inside this book" window.

    3. Initially, rats in the trapped condition opened the door in any of three ways: tipping the door over from the side or top or pushing it up with their heads

      From materials and methods: Measuring opening style: Each door opening was classified to indicate how the door was opened.

      Three types of opening were observed:

      1) Rats opened the door by nudging it up with their head from the front of the restrainer (“head”),

      2) rats opened the door by leaning on the heavy side of the door (“side”), or

      3) rats opened the door by standing on top of the door (“top”).

    4. D. Drai, I. Golani , SEE: A tool for the visualization and analysis of rodent exploratory behavior. Neurosci. Biobehav. Rev. 25, 409 (2001).

      This paper describes the patterns rodents take while exploring their environment using a computational method of analysis. SEE allows for the distinction between stopping and progressing, spatial spread, dynamics of space occupancy, number of stops per excursion, and the maximal speeds attained.

      [http://www.sciencedirect.com/science/article/pii/S0149763401000227]

    5. G. E. Rice, P. Gainer , “Altruism” in the albino rat. J. Comp. Physiol. Psychol. 55, 123 (1962)

      The authors tested whether albino rats could display altruistic characteristics. They defined altruism as "behavior of one animal that relieves another animal's 'distress.'"

      The distress-causing paradigm was using a harness to suspend one rat free from the floor. The second rat is free in a separate compartment and can see and hear the suspended rat.

      The second rat can bring the suspended rat down to the floor by pressing a lever, and did so significantly more than if there was a styrofoam block being suspended.

      These results do point toward rats being capable of altruistic behavior because the rats performed an action that was not beneficial to itself, but that benefits one of its species.

    6. D. J. Langford et al ., Social approach to pain in laboratory mice. Soc. Neurosci. 5, 163 (2010).

      These authors tested whether the purpose of pain expression is to attract comfort or receive aid from conspecifics.

      For this they assayed the likelihood of a free mouse to approach/contact a jailed mouse experiencing pain versus a jailed mouse unaffected by pain.

      This hypothesis was true in the case of female mice but not male mice. However the observer female mice only approached mice that were "known" (i.e., had previous contact with the observer mouse). Thus there is sex specificity to the social approach to pain in laboratory mice.

      The contact made by the free mouse with the mouse in pain resulted in less pain behavior.

    7. R. M. Church , Emotional reactions of rats to the pain of others. J. Comp. Physiol. Psychol. 52, 132 (1959).

      The authors of this paper measure the reaction one group of rats has to the outward show of pain of another rat receiving an electric shock.

      One group of rats had lever pushing for food associated with the electric shock of another rat and a shock to themselves (paired shock). A second group had lever pushing for food associated with only themselves receiving a shock (unpaired shock). The third group received no shock when they pushed the lever for food (no shock).

      The authors then measured the frequency of lever pushing by spectator rats from all three groups (paired shock, unpaired shock, and no shock) in response to shock delivery to the tester rat.

      Rats trained in the paired shock paradigm reacted by significantly less lever pushing compared with the no shock group.

      This suggests that the responses given by the paired shock group may be a result of conditioning rather than that action being a show of sympathy.

    8. J. Decety, P. L. Jackson , The functional architecture of human empathy. Behav. Cogn. Neurosci. Rev. 3, 71 (2004)

      In this review, the authors note that "Empathy involves not only any sentimentally commanded encounters with another person’s actual or inferred emotional state but also some minimal recognition and understanding of another’s emotional state."

      They also highlight the main components of empathy: shared neural representations, self-awareness, mental flexibility, and emotion regulation.

      These components are used together to form a model to predict empathy deficits in social and neurological disorders.

    9. (20–26)

      de Waal et al.

      The authors looked at consolation behavior in chimpanzees. Consolation is ranked under the same umbrella as empathy. In their paper it was defined as "an interaction in which an uninvolved bystander initiates friendly contact with a recent victim of aggression."

      Main finding: The empathy hypothesis that states that consolation is more likely to occur among animals that are socially close was supported.

    1. F. Soliman et al., Science 327, 863 (2010)

      This is a very interesting paper showing that a single-nucleotide polymorphism in the BDNF gene can impair the extinction of a conditioned fear response in both humans and mice. This polymorphism is also associated with anxiety-related behavior and atypical frontoamygdala activity in humans.

      This is important because it suggests that the variant allele may affect the efficacy of exposure therapy, which relies on the process of extinction.

    2. R. Garcia, G. Spennato, L. Nilsson-Todd, J. L. Moreau, O. Deschaux, Neurobiol. Learn. Mem. 89, 560 (2008).

      The goal of this study was to examine the effects of chronic mild stress on hippocampal and medial prefrontal cortex potentiation and extinction memory in rats.

      The authors found that chronic mild stress did not interfere with the extinction of fear, but did impair the recall of extinction.

      They found that chronic mild stress interfered with the development of extinction-related potentiation in the hippocampal/medial prefrontal cortex pathway.

    3. S. A. Heldt, L. Stanek, J. P. Chhatwal, K. J. Ressler, Mol. Psychiatry 12, 656 (2007).

      In this study, the BDNF gene was deleted from the hippocampi of mice. This impaired the animals' ability to recognize new objects, learn spatial orientation, and extinguish conditioned fear.

      These cognitive impairments are also found in anxiety disorders, suggesting that BDNF in the hippocampus may play a role in anxiety and depression.

    4. J. P. Chhatwal, L. Stanek-Rattiner, M. Davis, K. J. Ressler, Nat. Neurosci. 9, 870 (2006).

      This is a very interesting article showing that BDNF, acting through the tyrosine kinase B receptor, is required for the consolidation of stable extinction memories.

    5. W. A. Falls, M. J. Miserendino, M. Davis, J. Neurosci. 12, 854 (1992).

      This is an older paper that was one of the first to show that fear extinction may be an NMDA-dependent process by infusion an NMDA antagonist (AP5) into the amygdala and measuring fear potentiated startle.

    6. A. Burgos-Robles, I. Vidal-Gonzalez, E. Santini, G. J. Quirk, Neuron 53, 871 (2007).

      This paper shows that infusion of CPP, which is an NMDA receptor antagonist, into the ventromedial prefrontal cortex can impair extinction recall.

    7. C. R. Bramham, E. Messaoudi, Prog. Neurobiol. 76, 99 (2005).

      Here, the authors review current research describing the role of BDNF in long-term potentiation, and its known molecular mechanisms.

    8. T. W. Bredy et al., Learn. Mem. 14, 268 (2007).

      In this paper, the authors examine how epigentic gene expression regulation of BDNF enables fear extinction.

    9. F. Sotres-Bayon, L. Diaz-Mataix, D. E. Bush, J. E. LeDoux, Cereb. Cortex 19, 474 (2009).

      This paper investigates the role of NR2-containing N-methyl-D-aspartate receptors in the ventromedial prefrontal cortex and lateral amygdala in the consolidation of fear extinction memories.

    10. F. Sotres-Bayon, C. K. Cain, J. E. LeDoux, Biol. Psychiatry 60, 329 (2006).

      In this paper, the authors examine research that has led to the notion that the medial prefrontal cortex is a critical component in both emotional regulation and fear extinction.

  14. Aug 2016
    1. Given the 51 tons of ivory seized in 2013, the number of elephants killed that year could have exceeded 50,000, out of an estimated 434,000 elephants remaining (4)

      How does the author estimate the number of elephants killed based on the weight of seized ivory?

      It's known that only about 10% of all smuggled goods, such as ivory, drugs, or weapons, are caught by customs. So if 51 tons of seized ivory is only 10% of all poached ivory, the actual amount of all smuggled ivory should be 10 times as high, or about 510 tons (510,000 kilograms).

      510,000 kg of ivory corresponds to about 51,000 elephants.

    2. S. K. Wasser et al., Proc. Natl. Acad. Sci. U.S.A. 104, 4228–4233 (2007).

      In this study the authors used improved methods to identify the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. They showed that the ivory was from savanna elephants from a narrow east-to-west band of southern Africa, centered on Zambia.

      The findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes. They also led the Zambian government to improve antipoaching efforts.

    3. S. K. Wasser et al., Proc. Natl. Acad. Sci. U.S.A. 101, 14847–14852 (2004).

      This earlier paper by the first author describes in greater detail how the genetic reference map was constructed. It also explains the statistical smoothing method that the authors used to assign a geographic location to seized ivory.

    4. A. L. Roca, N. Georgiadis, J. Pecon-Slattery, S. J. O’Brien, Science 293, 1473–1477 (2001).

      This paper shows that African elephants that live in forests are actually a different species than African elephants that dwell in the savanna. Until this paper, all African elephants had been grouped together as a single species.

      The authors proposed two species names: Loxodonta africana for the savanna elephants and L. cyclotis for the forest elephants.

    5. United Nations, The Globalization of Crime (United Nations Office on Drugs and Crime, New York, 2010); http://unodc. org/unodc/en/data-and-analysis/tocta-2010.html.

      This document is produced by the United Nations Office on Drugs and Crime. It analyzes a range of key transnational crime threats and offers a view of its global dimensions.