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  1. Last 7 days
    1. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells

      negative results

  2. Nov 2019
    1. The He isotopic signatures released from the sparse fluid inclusions vary from 0.7 to 49.9 R/Ra (Figs. 1 and 2).

      This observation indicates that the R/Ra ratio measured from the sparse fluid inclusions cover a very wide range of values. Higher values indicate that the relative abundance of helium-3 to helium-4 to that in air is very high (almost 50 times). When the values are this high, there is a good chance of detection of elevated helium-3 isotope, thereby confirming the fact that these fluid inclusions are coming from a very ancient reservoir located deep inside the Earth.

    2. This observation requires that the high-3He/4He source has higher He abundances than reservoirs with low 3He/4He ratios and thus supports the presence of a primordial 3He plume.

      Any increase in the helium-3 isotope abundance provides strong evidence of the location and age of the chemical reservoirs explored in this study. Helium-3 isotope formation dates back to the beginning of Earth and any recent formation of the isotope on Earth's surface has been ruled out due to its tendency to get lost in the space. Thus the the authors are confident that this spike in helium-3 is coming from very ancient reservoir deep inside the Earth.

    3. The He isotopic data for fluid inclusions in superdeep diamonds presented here resolve this issue by showing direct evidence that the high-3He/4He source must be present in the deep mantle, beneath a depth of 410 km.

      This is the main conclusion of this research work. The authors have shown evidence that the diamond fluid inclusions analyzed originate from the deep mantle region of the Earth, which is at least 410 km underneath Earth's surface.

    4. Our diamonds have physical features and properties that are consistent with other diamonds from Earth’s transition zone (410 to 660 km depth), including dislocations or diffuse growth zones (database S1) and no detectable nitrogen (N) or fully aggregated N defects (database S2) (24).

      There has been an ongoing debate about the exact location of the chemical reservoirs that lie deep within the planet Earth. Timmerman and colleagues have successfully narrowed down this location to Earth's transition zone, i.e., 410 to 660 km underneath Earth's surface. These conclusions are based on not only the relative abundance of helium-3 to helium-4 isotopes, but also on the physical similarities between the studied diamonds with already identified ones.

    5. The highest R/Ra value for our diamonds was from the Juina-5 kimberlite, and it coincides with the R/Ra of 49.8 from Baffin Island picrites (4), the highest observed in basalts.

      In the diamond fluid inclusions richest in helium-3, the helium-3 to helium-4 ratio is about 50 times to that of air. This considerably high isotope ratio confirms the fact that the real age of these fluid inclusions date back to the early days of Earth's formation.

    6. We removed the outer rim of the diamond to eliminate any 4He implantation [up to 30 μm from the diamond surface

      The primordial diamonds excavated by the scientists contained fluid inclusions consisting both helium-4 and helium-3 isotopes. The helium-4 isotopes are formed from radioactive decay of trace-elements and hence take a long time to form. While, the helium-3 isotopes exist inside Earth from the early days of formation and there has been no new generation of helium-3 isotope since then. Hence, removing the outer rim consisting of helium-4 isotopes from the diamonds narrows the search to helium-3 isotopes located in very ancient chemical reservoirs.

  3. Sep 2019
    1. Results

      Results == Findings.

      I am aware that this section contains some statistical technique you did not learn in the course. Try to read the authors' descriptions, nonetheless, and see if you can make sense out of it. If the authors did their job, you should be able to understand their findings even if you might not appreciate the intricacies of their methodological choices.

      Please identify and highlight the key findings of this research.

  4. Apr 2019
  5. Mar 2019
    1. From this data, it can be concluded that cholesterol concentration in the diet group was statistically significantly higher than the exercise group (U = 110, p = .014). Depending on the size of your groups, SPSS Statistics will produce both exact and asymptotic statistical significance levels. Understanding which one to use is explained in our enhanced guide.

      Phrasing results for the Mann-Whitney U-test.

    1. This is one of many discussions of Kirkpatrick's four levels of evaluation. More of the page is taken up with decoration and graphics than needs to be the case but this page is included in this list because it offers a printable guide and because the hierarchy of the four levels is clearly shown. The text itself is printed in black on a white background and it is presented as a bulleted list (the bullets are not organized as well as they could be). Nonetheless it is a usable presentation of this model. rating 3/5

  6. Dec 2018
    1. larger fish have greater thermal inertia and increased cardiac capacity

      Thermal inertia is the ability of a body or object to maintain its temperature when ambient temperature changes. Larger objects have higher thermal inertia, so larger fish lose heat more slowly than smaller fish. Larger fish also have larger hearts, which can pump more blood.

    2. The largest size-based differences in energy intake were also observed in October (Fig. 6 and table S3), indicating that thermal niche expansion in this endothermic species results in high energetic reward.

      The increased temperature range allowed the tuna to forage and obtain energy more efficiently.

    3. Lower energy intake was observed during late summer (August and September), when bluefin tuna are moving up through the Southern California Bight (28° to 32°N).

      Lower energy intake during migrations.

  7. Nov 2018
    1. SurveyMonkey

      SurveyMonkey is a FREE survey platform that allows for the collection of responses from targeted individuals that can be easily collected and used to create reports and quantify results. SurveyMonkey can be delivered via email, mobile, chat, web and social media. The platform is easy to use and can be used as an add on for large CRMs such as Salesforce. There are over 100 templates and the ability to develop customized templates to suit your needs. www.surveymonkey.com

      RATING: 5/5 (rating based upon a score system 1 to 5, 1= lowest 5=highest in terms of content, veracity, easiness of use etc.)

  8. Aug 2018
    1. The patterns for Q. kelloggii are more complex.
      1. Still fewer teeth in warmer climates.
      2. Larger leaves in warmer climates.
      3. Correlations are stronger with elevation.
      4. No correlation of leaf traits to MAP
    2. There are many significant correlations in A. rubrum between MAT and leaf physiognomy
      1. Colder climates more teeth, larger teeth.
      2. Colder leaves are larger.
      3. MAP and leaf physiogony are weakly correlated.
    1. Weber notes that according to any economic theory that posited man as a rational profit-maximizer, raising the piece-work rate should increase labor productivity. But in fact, in many traditional peasant communities, raising the piece-work rate actually had the opposite effect of lowering labor productivity: at the higher rate, a peasant accustomed to earning two and one-half marks per day found he could earn the same amount by working less, and did so because he valued leisure more than income. The choices of leisure over income, or of the militaristic life of the Spartan hoplite over the wealth of the Athenian trader, or even the ascetic life of the early capitalist entrepreneur over that of a traditional leisured aristocrat, cannot possibly be explained by the impersonal working of material forces,

      Science could learn something from this. Science is too far focused on the idealized positive outcomes that it isn't paying attention to the negative outcomes and using that to better define its outline or overall shape. We need to define a scientific opportunity cost and apply it to the negative side of research to better understand and define what we're searching for.

      Of course, how can we define a new scientific method (or amend/extend it) to better take into account negative results--particularly in an age when so many results aren't even reproducible?

  9. Jun 2018
  10. Mar 2018
    1. Con-servative strategies (15) serve individual careerswell but are less effective for science as a whole.Such strategies are amplified by the file drawerproblem (16): Negative results, at odds withestablished hypotheses, are rarely published,leadingto a systemic bias in published researchand the canonization of weak and sometimesfalse facts (17). More risky hypotheses may havebeen tested by generations of scientists, but onlythose successful enough to result in publicationsare known to us.

      cc @Lepou

  11. Dec 2017
    1. Table 1

      mtDNA CO1 is a gene found within the mitochondria, it is used to measure the genetic difference between organisms. A higher mean indicates a larger difference between two organisms, which is indicative of being a different species. (JP)

    2. Fig. 2

      In general, this graph illustrates that as genetic distance between species increases (this is measured by Nei's D) then mtDNA divergence increases as well. Overall, compatibility between two different organisms will be less if they have high mtDNA divergence and a high Nei's D value. (JP)

    3. All the shrimps we studied are shallow water, fully marine forms with planktonic larvae.

      Main subjects studied. Planktonic larva is significant in this study because larva shrimp would migrate to different regions of the Isthmus of Panama which may be a significant contributor to speciation events ~J.D.A. (+ JP)

    4. 4.4 to 6.1 (P5-CS), 4.0 to 6.3 (P6-C6), and 6.8 to 9.1 (P7-C7) Ma

      mtDNA traced pairs back to million years ago. ~J.D.A.

    5. Even the least divergent pairs show substantial reproductive isolation

      Species so closely related showed two differ clutches. Isolation could've been geographical, though nothing that could completely cut them off from each other since they are similar. If anything, this could infer that they could've been selective in mating, or aggressive in behavior to even mate, thus preventing creation of offspring between them. ~J.D.A

    6. The null hypothesis, that isolation was simultaneous but rates of divergence are highly variable, is incompatible with the observed pattern because metabolic enzymes, mtDNA, and mate recognition share no mechanistic basis that would cause their divergence rates to be automatically associated.

      Basically, the null is rejected because it contradicts the observed data. The null states that isolation occurred around at the same time, but the observed data shows divergence indicators such as metabolic enzymes, mtDNA, and mate recognition, all of which are not associated at a single mechanistic basis required for concurrent divergence. ~S.Z.

    7. However, they do show some distributional differences that could affect sensitivity to changing conditions associated with gradual rise of the isthmus.

      The physical location of the shrimp could effect the divergence associated with the gradual rise of isthmus. ~S.Z

    8. Pacific members of the most divergent pairs are found deeper in the intertidal or are rare in habitats with heavy sedimentation (25) (Fig. 2). Thus, larval avoidance (26) of shoaling waters over the rising isthmus (6, 7) may have accelerated genetic isolation of these pairs.

      The shrimp located closer to the sea floor had a slimmer chance of being pushed over the isthmus; therefore had a higher chance of isolation and divergence. ~S.Z.

    9. Our data can also be used to estimate rates of divergence in reproductive compatibility. Even the least divergent pairs show substantial reproductive isolation

      The less compatible they are the more they have diverged. ~S.Z.

    10. Likewise, there is no evidence for differences among the pairs in historical effective population sizes or generation times that can be related to divergence (20).

      The generation types (ex. F1, F2, etc.) and population size were taken into account for each shrimp pair. These factors were found to not support the phenomenon of divergence among shrimp pairs because no differences were found. ~J.D.A.

    11. Geographic isolation is thought to permit divergence and speciation by disruption of gene flow

      The physical barrier created by the Isthmus of Panama prevented the exchange of genes; therefore, allowing the organism to develop differently on wither side of the barrier or diverge. (SZ)

    1. a phosphorylation-mimicking Thr205→Glu205 (T205E) tau variant coprecipitated significantly less with PSD-95 as compared with nonmutant and T205A (A, Ala) tau (Fig. 4C and fig. S21)

      Phosphorylation at T205 inhibits complex formation.

    2. T205 phosphorylation of tau is part of an Aβ toxicity–inhibiting response.

      Phosphorylation at T205 on tau limits Amyloid beta toxicity.

    3. p38γ regulated PSD-95/tau/Fyn complexes, likely at the level of PSD-95/tau interaction

      From Fig. 3 the authors conclude that p38y reduces PSD-95/tau/Fyn complex formation by affecting PSD-95/Fyn interactions.

    4. PTZ transiently increased PSD-95/tau/Fyn complex formation in p38γ+/+ animals; this effect was even more noticeable in p38γ−/− mice

      p38y was shown to inhibit the formation of complexes, but the addition of PTZ lowers the protective function of p38y.

    5. PSD-95/tau/Fyn interaction was reduced in transgenic mice with neuronal expression of p38γCA

      The interactions that are required to form the complexes are reduced in mice with an active form of p38y, demonstrating that p38y may prevent complex formation.

    6. PSD-95 copurified more tau and Fyn from p38γ−/− versus p38γ+/+ brains, and even more from APP23.p38γ−/− compared with APP23.p38γ+/+ and p38γ−/− brains

      An immunoprecipitation for PSD-95 was ran. The proteins that were associated with PSD-95 complexes also precipitated due being in a complex with PSD-95. The results show that tau and Fyn were contributing more to the PSD-95 complexes when p38y was not present.

    7. PSD-95/tau/Fyn interaction was enhanced in Alz17.p38γ−/− animals versus Alz17.p38γ+/+ mice

      Results show that more PSD-95/tau/Fyn complexes were in the brains of p38𝛾-/- vs. p38𝛾+/+. This shows that PSD-95/tau/Fyn complexes are associated Amyloid-beta induced excitotoxicity

    8. when compared to tau−/−.p38γ+/+mice, tau−/−.p38γ−/− animals showed similar protection from PTZ-induced seizures

      p38y only protects agianst PTZ-induce siezures only when tau is present. A difference between p38y being present and p38 being absent is only seen in mice that have tau.

    9. These data also showed that, compared with APP23 mice, APP23.p38γ−/− animals had aggravated memory deficits that persisted with aging

      APP23.p38y+/+ mice survived longer and had performed better in water maze than APP23.p38y-/- mice. Also shown in the results is that APP23.p38y+/+.tau-/- vs. APP23.p38y-/-tau-/- mice, are statistically the same, suggesting that the protective effect of p38 comes from phosphorylating tau.

    10. The exacerbating effects of p38γ loss on reduced survival, memory deficits, and neuronal network dysfunction of APP23 mice were virtually abolished in APP23.p38γ−/−.tau−/− mice

      The APP23 deficits improved when tau was not present in mice.

    11.  p38γ−/− mice showed no deficits and had normal motor function

      The lack of p38y kinase did not negatively affect the movement and motor function of the mice.

    12. Aβ pathology was comparable in the brains of APP23.p38γ−/− and APP23.p38γ+/+ mice (fig. S6), but p38γ deletion aggravated premature mortality and memory deficits of APP23 mice

      APP23 mice that had p38y and did not have p38y displayed similar traits, but the deficits in mice that did not possess p38y kinase were worse.

    13. Surprisingly, only p38γ depletion (p38γ−/−), but not systemic p38β, p38δ, or neuronal p38α (p38αΔneu) knockout, changed PTZ-induced seizures

      The only knockout mouse that displayed a change associated with PTZ-seizures was p38y. Because p38y was the only one that influenced the results, it is the focus of all the experiments.

    14. Finally, we found that tau-dependent Aβ toxicity was modulated by site-specific tau phosphorylation, which inhibited postsynaptic PSD-95/tau/Fyn complexes, revealing an Aβ toxicity–limiting role of p38γ in AD that is distinct and opposite to the effects of p38α and p38β (11, 13, 14).

      The authors state, contrary to popular belief, that tau can play a protective role in limiting amyloid beta toxicity by interacting with p38γ. By phosphorylating specific sites tau can increase neuron survival and improve memory loss.

    15. PTZ-induced seizures are reduced in tau−/− mice (8, 9). Adeno-associated virus (AAV)–mediated expression of WT and T205A neurons, but not T205E tau or green fluorescent protein (GFP), in the forebrains of tau−/− mice enhanced PTZ-induced seizures (Fig. 4D and fig. S25).

      The data shows that the tau-/-.AAV tauWT and tau-/-.AAV tauT205A were the most susceptible to seizures and had the most severe seizures out of the four genotypes.

    16. Hence, phosphorylation of tau at T205 should similarly mitigate neurotoxicity. Aβ caused cell death in WT and T205A neurons but significantly less in T205E tau-expressing neurons (fig. S23). Similarly, neurons expressing p38γ and, more so, p38γCA were significantly more resistant to Aβ-induced cell death than controls (fig. S24).

      The results from previous experiments showed that neurons survived at higher rates when they had T205E and p38γ.

    17. Pan-p38 inhibition stopped p38γ/p38γCA-induced disruption of PSD-95/tau/Fyn complexes

      If p38y is completely inhibited, the complexes are stable.

    18. Hence, p38γ regulated PSD-95/tau/Fyn complexes via phosphorylating tau at T205.

      The results of this experiment showed that p38γ helped to disrupt the PSD-95/tau/Fyn complexes through phosphorylation of T205.

    19. Increasing p38γ levels compromised PSD-95/tau/Fyn interaction in cells, and expression of a constitutively active p38γ variant (p38γCA) completely abolished this interaction

      p38y was shown to prevent the interactions required to form the complexes associated.

    20. Similarly, pT205 was markedly reduced in APP23.p38γ−/− animals compared with APP23.p38γ+/+ mice (Fig. 4B)

      The results of the previous experiment showed that APP23p38𝛾-/- mice had decreased T205 phosphorylation compared to the APP23p38𝛾+/+, which had T205 phosphorylation.

    21. no PSD-95/tau/Fyn complexes were isolated from tau−/− and tau−/−.p38γ−/− brains

      Demonstrates that the complexes will not form if unless tau is present.

    22. In summary, the levels of active p38γ kinase and tau phosphorylation at T205 determined susceptibility to excitotoxicity and Aβ toxicity.
    23. the effects of p38γ on excitotoxicity and Aβ toxicity were tau-dependent.

      The protective qualities of p38y are dependent on tau being present. If tau is not present, amyloid-beta toxicity effects the cells the same, even if p38y is present.

    24. increasing tau levels in p38γ−/− mice [brought about by crossing with nonmutant tau-expressing Alz17 mice (23)] significantly enhanced PTZ-induced seizures in Alz17.p38γ−/− mice

      Mice that had higher levels of tau were more susceptible to seizures.

    25. In summary, p38γ depletion exacerbated excitotoxicity, neuronal circuit synchronicity, mortality, and memory deficits in APP23 mice, without changes in Aβ pathology.

      Overall, every deficit associated with APP23 was made worse when p38y was not present.

    26. Electroencephalography showed enhanced spontaneous epileptiform activity and interictal hypersynchronous discharges in APP23.p38γ−/− compared with APP23.p38γ+/+ mice

      From the results, the researchers can infer that the presence of p38𝛾 kinase has a protective ability that lessens the amount of seizure trains that occur due to Aβ density bodies

    27. Compared with APP23.p38γ+/+ mice, APP23.p38γ−/− animals had increased sensitivity to PTZ-induced seizures

      From the results conducted in the experiment, specifically the Fig. 1 G-J, mice that did not possess p38y were more sensitive to seizures

    28. only p38γ localized to postsynapses and limited excitotoxicity.

      The only knockout mouse that was shown to cause a change in PTZ-induced seizures was p38𝛾. p38𝛾 was also the only kinase that was shown to localize in postsynapses between neurons.

    1. The data do not support the competing hypothesis that reef shark relative abundance was primarily driven by environmental variation between sites.

      The data did not support this particular hypothesis because there was very little variation between the sites to begin with. The BRUV's were positioned in locations that did not vary in high arrays therefore a correlation between the abundance and environmental variation as not conclusive. -Sindy

    2. The second prediction of our main hypothesis is that the relative abundance of Caribbean reef sharks is higher in reserves than similar fished reefs. The factor “marine reserve” was the most important predictor of shark presence or absence on BRUVs in the GLM, which is consistent with this prediction.

      This indicates that their second prediction was also correct and they again failed to reject the null hypothesis meaning that there was a correlation between population density of sharks and a marine reserve. -Sindy

    3. Sharks often exhibit an ontogenetic expansion of home range size [45] and we would expect a positive correlation between MLD and shark size if this is true for Caribbean reef sharks.

      MLD is mixed layer depth, they expect a correlation between MLD and shark size because shark size normally correlates to its age and thus its experience. So the older and more experience a shark is, the more likely to go into ocean parameters with a mix of density or temperature etc than a smaller or younger shark. -Sindy

    4. Transmitters are also more likely to be detected in the fore-reef because seafloor relief is low relative to water depth, whereas receivers in the lagoon are partially blocked by emergent patch reefs.

      The complication arises in the fact that the transmitters may have a hard time ensuring accuracy due to the enviroment in which they are in. For example, in the fore-reef, the see level is too shallow so it may be spotted and cause the shark to drift away from it. And in the lagoons, not many sharks may approach either simply for the reason that the transmitters are being blocked by the reef. It is a complication related to placement of the transmitters and its unforeseen consequences. -Sindy

    5. We tested the hypothesis that Caribbean reef sharks are to benefit from the local respite from fishing occurring within marine reserves by examining two of its key predictions. The first prediction is that Caribbean reef sharks exhibit high site-fidelity to reserve areas. Acoustic monitoring showed that most individuals exhibit a high degree of site-fidelity at GRMR.

      This shows that the authors predictions were correct and thus fail to reject his null hypothesis. -Sindy

    1. EGLN1 was identified by both,

      After running the XP-EHH and iHS testing EGLN1 was determined to be a gene that was undergoing local positive selection. Meaning that the gene was currently providing an adaptive advantage to the person who had it, and was increasing in occurrence in that population.

    2. It is plausible that the diminished Hb levels found in Tibetans offset complications associated with sustained high Hb levels (for instance, hyperviscosity) seen in non-Tibetans exposed to high-altitude conditions (10, 11). Alternatively, decreased Hb levels could be a side effect of other phenotypes that are the actual targets of natural selection.

      Overall, the decreased hemoglobin levels seen in the Tibetan highlanders may be the result of variants in PPARA and EGLN1 haplotypes. However, the decreased hemoglobin levels could a side effect of a currently unknown phenotype, which may be the actual target of natural selection.

  12. Nov 2017
    1. mimicking site-specific tau phosphorylation alleviated Aβ-induced neuronal death and offered protection from excitotoxicity.

      The site that is phosphorylated by p38y was found to be important for reducing effects of AD. Demonstrates that the function of p38y is important, and the mere presence of p38y in the cell is not protective, it has to be functional.

    2. depletion of p38γ exacerbated neuronal circuit aberrations, cognitive deficits, and premature lethality in a mouse model of AD, whereas increasing the activity of p38γ abolished these deficits

      The research found that the presence of p38y reduced the effects of AD in the mouse model.

    1. first, the sex-determining proteins studied in the present work evolve at constant rates, as suggested by global molecular clock tests (Table 1).

      From Table 1, the following sex-determining proteins display InL, InL(clock), and the p-value. These factors display the final calculations. From what the author first concluded, the InL(clock) values show that there is in fact a constant rate with which the proteins evolve. It is tested by the likelihood ratio tests based off the models of evolution defined. -Melanie

    1. The high levels of genetic differentiation detected within C. jimenezii raise questions whether these two populations can be treated as different varieties/subspecies within this taxon or if indeed they may represent two different species.

      In this study, the researchers found some questions as to whether the two species of C. jimenezii could be grouped with the same taxa.

      Upon meeting with the author, it was stated that the molecular tools used, found a large amount of differentiation. This was not what the authors hoped and in turn was concluded that they were to remain in separate taxa.

      RA

    2. Therefore we recommend not translocating material between these two populations for genetic conservation or ecological restoration programs until the taxonomy of this species within Coccothrinax is further studied.

      Genetic conservation of this population is important due to the few individuals left in Haiti and the Dominican Republic.

      Upon meeting with the author, the difficulty of finding the purebred species was discussed as were the methods.

      RA

    3. The taxonomic uncertainties between the two populations of C. jimenezii have important implications for reintroduction programs. These two sites of C. jimenezii represent two clear management units for conservation, and the population genetic data suggest that we cannot rule out that they are two distinct taxa.

      The authors concluded based off of the molecular data, that the two species of C. jimenezii could not be identified as two different taxa.

      RA

    4. We have not been able to find data regarding the environmental history in these two populations since the 15th century. However, there is agreement among conservation biologists that since the arrival of the Europeans to this island there has been habitat fragmentation and deforestation linked to rapid expansion of urban and rural activities (Sambrook et al., 1999; Alscher, 2011; Foxx, 2012). Palms have long-life cycles; therefore, the detrimental consequences of genetic drift on genetic diversity can take a long period of time to manifest because of their long generation time and the presence of overlapping cohorts (Duminil et al., 2009).

      Since the extinction of C. jimenezii is of primary concern, the authors grab resources from other works to help solidify this concept. It is clear that the conservation of this species is vital to this study.

      RA

    1. The answers to fundamental questions about the origins of animal life and the evolution of their diverse phenotypes may be held in the genomes of distinct invertebrate phyla.

      The conclusion explains why they investigated what standards an invertebrate must reach to be tested for a successful genome sequencing. The researchers also add that geneticists could choose another option than searching an organism that meets their criteria. This option is sequencing organisms and modeling them for another organism. This would allow the geneticist to understand the other organism by having an idea of how the genome functions.

      The researchers also state a challenge faced by the science community is understanding the data they collect from the genome sequence, apart from also gathering the sequences. They state the research they do will help advance knowledge about invertebrate genomes by providing the necessary tools to investigate the sequences. (NAJ)

    1. Likewise, there is no evidence for differences among the pairs in historical effective population sizes or generation times that can be related to divergence (20).

      The generation types (ex. F1, F2, etc.) and population size were taken into account for each shrimp pair. These factors were found to not support the phenomenon of divergence among shrimp pairs because no differences were found. ~J.D.A.

    2. Our data can also be used to estimate rates of divergence in reproductive compatibility.

      The less compatible they are the more they have diverged. ~S.Z.

    3. Pacific members of the most divergent pairs are found deeper in the intertidal or are rare in habitats with heavy sedimentation (25) (Fig. 2). Thus, larval avoidance (26) of shoaling waters over the rising isthmus (6, 7) may have accelerated genetic isolation of these pairs.

      The shrimp located closer to the sea floor had a slimmer chance of being pushed over the isthmus; therefore had a higher chance of isolation and divergence. ~S.Z.

    4. However, they do show some distributional differences that could affect sensitivity to changing conditions associated with gradual rise of the isthmus.

      The physical location of the shrimp could effect the divergence associated with the gradual rise of isthmus. ~S.Z

    5. The null hypothesis, that isolation was simultaneous but rates of divergence are highly variable, is incompatible with the observed pattern because metabolic enzymes, mtDNA, and mate recognition share no mechanistic basis that would cause their divergence rates to be automatically associated.

      Basically, the null is rejected because it contradicts the observed data. The null states that isolation occurred around at the same time, but the observed data shows divergence indicators such as metabolic enzymes, mtDNA, and mate recognition, all of which are not associated at a single mechanistic basis required for concurrent divergence. ~S.Z.

    6. Geographic isolation is thought to permit divergence and speciation by disruption of gene flow

      The physical barrier created by the Isthmus of Panama prevented the exchange of genes; therefore, allowing the organism to develop differently on wither side of the barrier or diverge. (SZ)

    7. Even the least divergent pairs show substantial reproductive isolation

      Species so closely related showed two differ clutches. Isolation could've been geographical, though nothing that could completely cut them off from each other since they are similar. If anything, this could infer that they could've been selective in mating, or aggressive in behavior to even mate, thus preventing creation of offspring between them. ~J.D.A

    8. 4.4 to 6.1 (P5-CS), 4.0 to 6.3 (P6-C6), and 6.8 to 9.1 (P7-C7) Ma

      mtDNA traced pairs back to million years ago. ~J.D.A.

    9. All the shrimps we studied are shallow water, fully marine forms with planktonic larvae.

      Main subjects studied. Planktonic larva is significant in this study because larva shrimp would migrate to different regions of the Isthmus of Panama which may be a significant contributor to speciation events ~J.D.A. (+ JP)

    10. Fig. 2

      In general, this graph illustrates that as genetic distance between species increases (this is measured by Nei's D) then mtDNA divergence increases as well. Overall, compatibility between two different organisms will be less if they have high mtDNA divergence and a high Nei's D value. (JP)

    11. Table 1

      mtDNA CO1 is a gene found within the mitochondria, it is used to measure the genetic difference between organisms. A higher mean indicates a larger difference between two organisms, which is indicative of being a different species. (JP)

    1. Energy intake and thermal excess were positively correlated with body size as measured by the curved fork length (CFL) of tagged tunas

      A big tuna (large body size) requires more energy which means it needs to feed from a higher amounts of prey or big preys. Consequently, the heat production is higher provoking a thermal excess. YS & WT

    2. Lower energy intake was observed during late summer (August and September), when bluefin tuna are moving up through the Southern California Bight (28° to 32°N).

      Lower energy intake during migrations - M.A.S

    3. The largest size-based differences in energy intake were also observed in October (Fig. 6 and table S3), indicating that thermal niche expansion in this endothermic species results in high energetic reward

      The increased temperature range allowed the tuna to forage and obtain energy more efficiently. -SES

    1. Management of nutrient effects on both of these pathways would positively affect riverine health.

      The purpose of these experiments were to test the effects of nutrients on terrestrial carbon loss that ultimately leads to a change in ecosystems.

      Learning the effects and ideal ratios of nitrogen to phosphorus for ecosystems will lead to better policies to protect them.

    2. Litter quantity in the streambed was predicted to be 2.8 times and 7.7 times higher in reference versus nutrient-enriched streams after 6 and 12 months,

      In the experiment, it was found that the addition of nutrients encouraged terrestrial organic carbon loss.

      This was tested by observing the litterbags of the experimental streams and comparing the data to the litterbags of the control stream.

      Since a large amount of mass was lost in the stream with nutrient additions, this gives some evidence that too many nutrients off-balances organic carbon levels.

    3. Reach-scale outputs of C increased as fine POC export, as well as respiration (15).

      Fine POC export represents the movement of broken down carbon along the stream. Finer particles move faster and further down a stream as biological factors such as microbes and fungi decomposing the terrestrial organic carbon.

    4. They may limit terrestrial C loss as CO2 and maintain downstream C export, but contribute to depletion of local C resources (22, 23).

      Detrivores have a different method of carbon depletion from streams. finer particulate organic carbon travels faster and further away from an area, deleting the area of carbon sources.

      Invertebrates may leave the system if there are no food sources and alter the food chain.

    5. However, roughly similar-sized effects of N and P on loss rates are strong evidence of co-limitation (Fig. 2 and table S3).

      Both nitrogen and phosphorus are contributing factors to changes in terrestrial carbon loss.

      Within the ecosystem, different organisms require different ratios of nutrients to react and convert terrestrial carbon to carbon dioxide.

    1. Another study in which mouse NC cultures were treated with Edn3, Edn1, or Kitl showed an increase in the number of melanocyte progenitors; however, Kitl alone was not sufficient to induce the differentiation of melanocyte progenitors into mature melanocytes. Mature melanocytes were however observed, when treatment with Kitl was followed by Edn3 or Edn1 (Reid et al., 1996). As previously noted, although in the absence of Edn3, Kit-positive and DOPA-positive cells arose in mouse NC cultures, Ednrb signaling was required for the generation of fully pigmented melanocytes (Ono et al., 1998). These findings hint to a specific requirement for Ednrb signaling, independent of Kit signaling, in melanocyte differentiation. This requirement for Ednrb in the final phase of melanocyte differentiation may occur cell-autonomously, as suggested by the inability of Ednrb null cells to generate pigment even in the presence of Kitl (Hou et al., 2004). Together these findings point at a cooperative interaction between Kit and Ednrb signaling in melanocyte development, with Ednrb signaling being specifically required in the final differentiation step

      This paragraph discusses how Ednrb is needed in order to further a melanocyte into melanoma, even if Kitl (another signaling pathway) is present. Therefore, this is the direct link to melanoma.

      (NB)

  13. Oct 2017
    1. Table 2

      By quantifying behavioral tolerance and intolerance of male-female transisthmian pairs, the researchers are able to compare interactions between closely related and distantly related species of snapping shrimp.

      For example, while keeping figure 1 and table 2 in mind, more closely related species have higher compatibility compared to more distantly related species. Although this is not an indicator of having viable offspring, this shows that closely related species may share similar behaviors or may have similar niches. (JP)

    2. Fig. 1 Single most parsimonious phylogenetic tree constructed on the basis of mtDNA sequences with PAUP (18). Transitions were given one-quarter the weight of transversions (based on the fourfold greater abundance of transitions than transversions in our data), and trees were rooted by the P7-P7'-C7 clade. Taxon codes are as in Table 1.

      Figure 1 is a visual representation of the relationship between differing species of snapping shrimps. This diagram was made using the mitochondria DNA sequences of the organisms and the PAUP program which calculates the level of relatedness between the sibling species of snapping shrimp.

      Comparing Table 1 with Figure 1, it is found that species more closely related, such as P2 and C2, had a lower mtDNA mean value (6.6). Meanwhile, species that were more distantly related, such as P7' and C7, had a higher mtDNA mean value (19.7). (JP)

    1. our findings suggest that the overexploitation of spawning aggregations can fundamentally alter the natural predator-prey equilibrium, limiting foraging options for reef sharks within aggregation sites.

      The inverted biomass pyramid is a good thing, but the fish spawning aggregations play an important role in whether or not this stays a good thing.

      • D.N.B.
    2. These observations confirmed that hundreds of sharks actively feed on a large variety of prey (at least 14 fish species; Figures 4 and S3). In particular, sharks feed aggressively on the large number of groupers present during spawning aggregations in June and July [13]. Shark abundance and residency times both increase when camouflage groupers (Epinephelus polyphekadion) arrive from the surrounding reef area to spawn

      there is an active correlation between the populations of prey and predators, when the camouflage groupers aggregate in order to spawn. This increase in prey is what attracts the sharks. MSARS , WT & YS

    3. Overall, sharks showed different degree of residency (mean ± SEM = 42.21% ± 7.75% of days present in the pass; range = 2.1%–95.9%; Table S3), with three transient (<20% residency), six semi-resident (20%–70% residency), and four highly resident (>70% residency) sharks (Figure S2).

      The study showed that overall, there was a higher number of sharks observed that spent most of their time in the pass than there were that spent less of their time in the pass. YS & WT

    1. Comparisons involving the static control law suggest three separate contributions to the success of this approach: discovering a good generic assistance pattern, customizing it to individual users, and facilitating motor learning.

      We can learn from static control law (constant torque) when compared to optimized assistance: it can identify similar patterns, it accommodates different individuals, and increase walking performance.

    2. Results from a prior experiment using the same hardware (17), comparing the zero-torque condition with walking in normal shoes (no exoskeleton) or with static assistance.

      Normal shoes mean no exoskeleton and static assistance mean exoskeleton and constant torque.

    3. Metabolic energy cost of walking for each condition, tested in validation trials. Optimized assistance resulted in the lowest metabolic rate and a large reduction compared to the zero-torque condition. Variability is primarily due to differences between participants. Bars are means, error bars are standard deviations, and asterisks denote statistical significance (P < 0.05)

      Three conditions were compared: zero torque (walking, no torque), optimized (walking, torque applied), and static (constant torque). In Figure 1A, the optimized method saved the most energy, with static coming in second, and zero torque last.

    4. The primary outcome was the energy cost of walking, defined as gross metabolic rate during walking minus the rate measured while standing still

      The goal of the optimization method, through the use of control laws governing the exoskeleton, is to reduce the amount of energy walking. The amount of energy lost during a walk is defined as the amount of energy measured walking subtracted by the amount of energy standing still (basal level).

    5. Static assistance resulted in a 19.3 ± 8.6% reduction in energy cost compared to zero torque (t test, P = 4 × 10−5, n= 11), a larger improvement than in our

      Compared with zero torque, static assistance out-performed zero torque (walking and no torque applied) with statistical difference.

    6. The static pattern, based on (17), is similar to the optimized patterns but resulted in higher metabolic rate. Torque was negligible in the zero-torque mode.

      Although static pattern and optimization both experience similar torque patterns, static condition had a higher metabolic rate, meaning it spent more energy.

    7. These tests hint at the potential for a new type of biomechanics study, in which human-in-the-loop optimization can be leveraged to compare the best possible outcomes for different devices or gait conditions or to test how various features of gait change with optimized performance.

      The authors suggest that human-in-the-loop technology will birth new biomechanic studies, where the proposed technology can be expanded to a large range of studies to improve performance.

    8. activity in the optimized condition was reduced by 41% compared to the zero-torque mode and 36% compared to walking in normal shoes

      With the optimization method, muscle performance was improved in addition to reducing metabolic energy compared to normal conditions without walking assistance.

    9. The evolutionary strategy that we used was more effective than other methods that we tried, but it seems likely that improved techniques could be developed.

      Compared to previous experiments, incorportating a mathematical model that integrates evolution strategies work best. However, the authors agree that there is room for improvement.

    10. These approaches have scope to improve mobility for people with a wide range of distinct physiological needs, from individuals with chronic stroke to athletes.

      The optimzation methods proposed in the paper can be used as a foundation to improve mobility for people with different illness backgrounds.

    1. A scaling argument predicts a maximum volume when the disk height reaches ZMaxVol/H ~ Fr* (16), in excellent agreement with observations

      The authors find that the height of the column at its maximal volume is proportional to Fr. A higher Fr means the inertial force drawing the column upwards is higher, this increases the heigh at which the volume is maximum.

    2. the domestic cat’s inertia- and gravity-controlled lapping mechanism is conserved among felines

      Inertia draws liquid upward into column (which reach the mouth). Faster lappings fails to maximize inertial entrainment. Slower lappings results in belated mouth closure that misses most of the fluid column.

    3. Gravity-driven drainage then reduces the rate of volume increase, and V is at a maximum when gravity and inertia balance (Fig. 4B).

      During lapping, the volume of the water column depends on its height and its radius. After the initial phase in which the volume is proportional to the height of the column, gravity starts pulling water back water inducing the a reduction in column diameter. As such, the height of the column increases but its thickness decreases.

    4. to defeat gravity and pull liquid into the mouth
    5. When the disk is close to the bath (Z << H), the column is cylindrical and V increases as V/R3 = πZ/R (Fig. 4B inset).

      In the first moments of a lap, while the water column height increases, the water has not yet started to collapse and its volume is proportional to its height. As such, the volume of the column increases linearly with Z, the height of the column.

    6. we find that Fr* is indeed of order unity (0.4), using the experimentally measured values UMAX =78 cm s−1 and H = 3 cm (Fig. 2B) and a tongue size of R ≈ 5 mm (Fig. 1G).

      Assuming that the cat closes its mouth at the highest point reached by the water column, the auhors related the lapping frequency of real cats to the parameters of their robotic disc dictacting the properties of the water column. They show that the lapping frequency of real cats is optimized to match the physical properties of the water column.

    7. For small disks (R = 2.5 and 5 mm), ZP/H increased linearly with Fr*, whereas large disks (R = 10 and 12.7 mm) reached the final height before pinch-off (ZP/H = 1). Theory also successfully predicts that pinch-off occurs close to the disk (Fig. 3).

      With a small disk, the height of the water column at pinch off is proportional to the speed of the disk. For a larger disk the height of the water column is higher at a given speed than for a smaller disk. Because of the big width of a large disk it needs to go slower for the water column to reach the same height.

    8. Estimation of the forces involved suggests that the fluid dynamics of lapping are governed by inertia and gravity, whereas viscous and capillary forces are negligible (16).

      The authors calculated the Reynold's number and Bond's number. The Reynold's number compares the opposing effects of motion and viscosity. The high velocity and low viscosity of the water column means that viscosity is negligible in cat lapping. Similarly, the Bond's number compares the effect of surface tension and gravity on a fluid. The high Bond number here shows that surface tension has little impact on the shape of the column.

    9. The tongue accelerates as it leaves the water surface, attains a remarkable maximum speed of UMAX = 78 ± 2 cm s−1, then decelerates as it enters the mouth. Recordings of 10 adult individuals (16) yielded a lapping frequency f = 3.5 ± 0.4 s−1 and an ingested volume per lap V = 0.14 ± 0.04 ml.

      The authors explains the characteristics of cat lapping that they observed by filming 10 cats. The lapping is characterised by the frequency, the maximal speed attained by the tongue during lapping, and the volume drunk by a cat for each lap.

    10. and yields a prediction for the dependence of frequency on animal mass

      In other words : the competition between inertia and gravity sets the lapping frequency and shows that there is a dependancy between frequency and animal mass. In general there is a balance.

    11. We find (16) that ZP/H ~ Fr* for Fr* < 1 and ZP/H ~ 1 otherwise.

      The authors were able to find a relationship between the height of the water column and its thickness and the size and speed of the robotic disk.

      As such, their relationship can be used to predict the height of the water column based on chosen parameters of the robotic disc.

  14. Sep 2017
    1. Sharks in the pass are using fish spawning aggregations as energetic subsidies to reduce the need for costly foraging excursions outside the pass boundaries, enabling this energy to be directed to other physiological functions.

      The sharks can afford to stay in a low-energy environment because it experiences spikes in energy input as multiple species spawn throughout the year. --CGG

    2. However, our results also suggest that when the spawning aggregation subsidies become scarcer during summer and metabolic rate increases due to warmer waters, sharks shift to investing in foraging excursions to escape low energy availability in the pass.

      Warmer water and lack of fish spawning sites cause reef sharks to invest more time in searching for higher energy food.-SES

    3. The consequence is sharks being forced to undertake energetically costly wider-range foraging as the only option to meet energy requirements

      Reef sharks spend more energy searching for food due to overexploitation of fish spawning sites.-SES

    1. alleles associated with high fitness within sites tend to be local alleles linked to particular climatic factors, providing evidence of local adaptation in A. thaliana at the scale of the European continent

      The main conclusions from this papers are: alleles associated with plant fitness have undergone local adaptation, they were correlated with climatic factors suggesting they are an adaptation to the local climate, they may be rare or common, they may be in different genetic locations and can code for multiple different molecular functions. Therefore, this paper has revealed multiple aspects about the genetic basis of local adaptation in the model plant Arabidopsis.

    2. the alleles associated with high fitness exhibited greater climate specificity

      Some of the alleles that were associated with high fitness were also associated with specific climates, as hypothesized by the authors. This suggests that these alleles are locally adapted due to unique climatic pressures.

    3. three most interesting candidate genes

      The analysis was able to identify three genes that are very likely to be the basis of local adaptation in some Arabidopsis populations. The three genes are LAC2, CHR8 and SAG21.

    4. no molecular function was significantly over- or underrepresented in all sets of candidate genes

      There was not one molecular function that was very common in all the locally adapted populations. Therefore, the authors conclude that a large variety of molecular functions are involved in local adaptations.

    5. Overall, among the 797 top SNPs, only 12 SNPs were associated with fitness in more than one environment; loci with major genetic effects were largely independent across sites

      It was rare to find the same allele associated with plant fitness in multiple populations. Alleles with large effects on fitness were mostly different in each population. Therefore, local adaptation acts on different genetic locations in different populations.

    6. no recent selective sweeps have occurred at these loci

      The authors found no evidence of selective sweeps in the alleles involved in local adaptation. This suggests that the genetic basis of local adaptation is in alleles that are already present in a population rather than on new alleles that rapidly spread through the population.

    7. alleles improving survival were high-frequency alleles

      In contrast to fecundity, alleles associated with increased survival were more common than control alleles. Therefore, for survival the genetic basis of local adaptation is the removal of locally deleterious genes. This result shows that the genetic basis for local adaptation can be different for different traits.

    8. Alleles associated with increased silique number were significantly rarer than genomic controls

      The authors found that alleles associated with increased numbers of siliques, and hence increased fecundity, were rarer than the control alleles. This suggests that for fecundity local adaptation’s genetic basis is the increase in a few beneficial genes.

    9. more often alleles associated with low fitness exhibited greater climate specialization

      This result was not predicted by the authors. Alleles that were deemed to be associated with low fitness in the common garden experiments may be less severe in certain climates and therefore have only been retained in populations within these climates.

    10. we found no evidence that the alleles conferring high fitness in Finland were locally abundant.

      Alleles linked to high survival and high fecundity in populations in Finland were not found to have geographic centroids significantly closer to Finland. Therefore, the authors cannot conclude that these alleles were the basis for local adaptation.

    11. associated with higher survival in England and Spain and silique number in Germany, England, and Spain were significantly closer to the planting sites in Germany, England, and Spain, respectively, relative to genomic controls

      The authors found that alleles that were linked to high survival in England and Spain, identified from the genome-wide association study, had a geographic centroid closer to these locations. The same result was found for silique number, a measure for fecundity, in Germany, England and Spain. Genomic controls on the other hand were not centered closer to these sites. This shows that these high survival and high fecundity alleles were the genetic basis for local adaptation.

    1. New candidate algorithms should tolerate high measurement noise, facilitate human adaptation, and require very few evaluations before converging.

      Now that an optimization method has been produced to reduce energy consumption when walking, future methods should be able to do the same job much faster.

    2. we found only small changes in optimized parameters (table S3) and no further reduction in metabolic rate (fig. S9).

      The convergence test was done to see if continuing the generations could lead to differences in the adaption. The small number of differences in the results indicates that the number of generations used at first was optimal.

    3. Successfully reducing both metabolic rate and muscle activity suggests that alternate objective functions with similar properties could be optimized—for example, related to speed (40), endurance (41), balance, or overall satisfaction

      The goal of the paper is to discuss control laws that can adapt to individual walking patterns, with the goal of improving walking and reducing energy consumption. Since the optimization method was successful, the authors suggest other properties that can be improved using similar optimization methods, such as endurance and balance.

    4. Optimizing a similar number of parameters in a feedback control structure, such as a neuromuscular model (38), or switching between optimized modes (39) could enhance performance under changing locomotor conditions.

      The optimization method is able to accomodate unique walking patterns.

    5. Optimized ankle exoskeleton torque pattern for each participant. Patterns varied widely and spanned a large portion of the allowable range. Lines are measured torque, normalized to stride time and body mass, averaged across strides.

      These are the torque patterns (amount of applied torque) that improve the walking performance for each participant. These curves have been normalized, meaning they have been numerically manipulated so that a generalization can be seen across participants.

    6. We also applied the approach to running with exoskeletons on both ankles (subject 2; table S1) and found a 27% improvement in energy cost compared to the zero-torque mode and 13% energy savings compared to normal running shoes (Fig. 4F).

      After putting a exoskeleton on both legs (two exoskeleton total) and having the participant run, the optimization method out-performed zero torque and normal shoes.

    7. At a slow walking speed (0.75 m s−1), the algorithm drove torque to its lower limit, resulting in a small reduction in energy cost compared to zero torque (Fig. 4A) and a 19% reduction compared to the initial control law (fig. S6).

      At a slow speed, the amount of torque reduced to its minumum, causing it to burn more energy than zero torque. This suggests limitations of the software after a specific level (or threshold).

    8. Optimized assistance reduced the metabolic cost of walking at a typical speed (1.25 m s−1; 33% reduction versus zero torque, 25% versus normal shoes; Fig. 4B)

      Optimized assistance out-performed walking in normal shoes, meaning that optimized assistance resulted in lower energy consumption.

    9. These wide-ranging control laws, some of which participants noted were initially uncomfortable, may have forced them to explore new motor control strategies, which has been shown to be a necessary part of skill acquisition in some interventions

      The participants experienced difficulty at first, which suggests that their mode of walking was not 'energy effecient'. Thus, the optimization method noted this mode of walking and attempted to improve stride patterns with the goal of reducing the amount of energy spent.

    10. Participants had a similar duration of exposure to the exoskeleton in both studies, but in the prior study, participants were trained with a narrow range of eight static control laws, whereas during optimization, they experienced 32 diverse control laws.

      Both experiments lasted the same duration, however, optimzation has many more control laws, the functions that accomodate unique exoskeleton behavior.

    11. The primary differences between these studies relate to the conditions during adaptation

      The major difference between the results for static assistance and zero torque are the method of exoskeleton adapting to human.

    12. Eight of 11 participants had a lower metabolic rate with optimized assistance, with the difference in rate ranging from a 3.3% increase to a 16.5% reduction

      Eight people experienced better performance with the optimied assistance (stride improved, energy reduced).

    13. Individually optimized assistance resulted in 5.8 ± 6.2% lower metabolic rate than with the static control law (t test, P = 0.01, n = 11)

      When compared to static condition, the optimized condition was better at reducing the amount of energy spent walking (improved stride).

    14. Static assistance (Fig. 3E) was similar to the average of the optimized control laws, and in our prior study (17), it delivered a 6% reduction in energy cost.

      In previous studies, the static performance was able to reduce the energy cost which displays how it can be beneficial. In addition, since the optimized assistance out-performed the static condition, which means optimization is a success.

    15. Human-in-the-loop optimization accommodates this complexity.

      Although their are large, biological differences between individuals, the optimization assistance can find similarities among the participants.

    16. Optimized torque patterns (Fig. 3D) did share some qualitative features with each other, such as a peak torque that occurred at about 50% of stride, suggesting qualities that may be beneficial for most people and useful initial parameters for future optimizations.

      Generally, participants share similar torque at 50% stride, this is the highest point in the curve displayed in Figure 3D. The authors believe parameters produced at 50% stride can be used for future experiments.

    17. For example, the timing of optimized torque onset ranged from onset at 17% to onset at 37% of the stride period (Fig. 3D), or about half the testable range in this and prior studies (3)

      The stride (heel up, see Figure 1C) begins at 17% and ends (toe firmly placed on treadmill, Figure 1C). Thus, image 3D represents a range of strides for the 11 participants.

    18. suggesting about a 14% net improvement with optimized assistance compared to normal shoes

      Although no torque is worst than wearing normal shoes, the overall effect of including the optimized assistance, torque applied to individual, is better (14% better) at reducing the amount of energy spent walking.

    19. Wearing the exoskeleton in zero-torque mode is about 10% more costly than walking in normal shoes without the exoskeleton (Fig. 3B)

      With the exoskeleton attached to a leg (see Figure 1C and 1D) and no torque applied, it cost an invidual more energy than not wearing the exoskeleton at all. This is not preferred, since the goal is to reduce the amount of energy.

    20. Optimized parameters were identified after four generations

      One generation, which is computed from covariance matrix adaptation evolution strategy (CMA-ES), is performed by the control law. Each generation is better than the previous generation, which is the evolutionary feature of the control law, see Figure 1A.

    21. Optimized assistance substantially improved energy economy for all participants, confirming the effectiveness of the method.

      Optimized assistance is the condition when torque is appled to improve stride, thus reducing the amount of energy spent. This method out-performed all other methods in reducing the amount of energy spent.

    22. Static assistance approximated the best hand-tuned torque pattern for this device, which had previously resulted in a 6% reduction in energy cost compared to zero torque (17)

      In previous experiments, the static condition performed better than having no torque applied to stride.

    23. (A) Slow walking (0.75 m s−1). (B) Normal walking (1.25 m s−1). (C) Fast walking (1.75 m s−1). (D) Uphill walking (10% grade). (E) Loaded walking (load equal to 20% of body mass).

      Under different walking conditions, the energy expenditure was measured for normal shoes, zero torque, and optimized.

    24. Optimized control law parameter values. Optimized values varied widely across participants. Values are normalized to their allowable range (26). Lines are medians, boxes cover the 25th to 75th percentiles, and whiskers show the range.

      Control parameters are a computed and customized for each individual participant, see Figure 1. The box-whisper plots for peak torque and peak time indicate that patients have similar optimal parameters (the boxes are much tighter), while rise time and fall time have larger ranges which displays the diversity between participants.

    25. Energy cost reductions ranged from 14.2 to 37.9% (fig. S4 and table S3), with an average reduction of 24.2 ± 7.4% (t test, P = 1 × 10−6, n = 11; Fig. 3A).

      The amount of energy saved with the effective control laws ranges between 14.2% to 37.9%. The average amount of energy saved with the new, optimized, stride (a result of the control laws, see Figure 1) is 24.2 +/- 7.4%. The reported values are statistically significant, meaning that there is a significant difference between having torque applied to stride and having no torque at all.

    26. Optimized assistance reduced the metabolic cost of walking to 2.16 ± 0.38 W kg−1, down from 2.84 ± 0.40 W kg−1 with zero torque (mean ± standard deviation).

      The amount of energy spent was reduced (2.16 +/- 0.40 W/kg ) when torque was applied as compared to energy spent with no torque (2.84+/- 0.40 W/kg). The "+/- 0.40" shows the range of energy values where the actual energy value must exist. For example, for no torque (2.84), the actual energy value is between 2.44 (minus portion) and 3.24.

    27. We optimized assistance for 11 participants (subjects 1 to 11; table S1) as they walked on a treadmill at a normal speed (1.25 m s−1).

      Eleven human volunteers were exposed to the flow chart and procedures in Figure 1 and the respective data was used to optimize the performance per patient. The treadmill speed at which they walked (and data was collected) was 1.25 meters per second (or approximately 4.1 feet per second).

    28. Ankle torque was determined by four parameters: peak torque, timing of peak torque, and rise and fall times (Fig. 2A) (26)

      As determined by the authors, four parameters were used to measure optimal torque applied to stride. These parameters use metabolic data from respiratory measurements and incorporate them into control laws to determine the best stride for each individual, with the goal of reducing energy expense.

    29. Ankle exoskeleton. Drive rope tension caused the device to push on the shank, heel, and toe contact, generating an ankle torque.

      Real experimental set up: tether is linked to controller, shank strap attaches to human calf, drive rope, heel rope, and load cell provide torque to leg. The joint encoder receives update from controller to provide optimal torque to human leg.

    30. Exoskeleton emulator system. Off-board motor and control hardware actuated a tethered exoskeleton worn on one ankle while participants walked on a treadmill.

      Figure C displays the experimental procedure to measure stride. Respirometry measures the metabolic rate, tether connects the device to the motor and eventually updates the control (optimizer algorithm is located here), control feeds back to exoskeleton and provides torque to test sample (human) to optimize posture. Finally, the treadmill is where human performance is measured.

    31. Examples of possible torque patterns.

      The figure displays various test subjects (human strides) that are displayed in different colors with respective strides. For example, the orange line displays small torque and long stride period. Green displays high torque and short stride period.

    32. Parameterization of ankle torque. Each control law determined applied torque as a function of time, normalized to stride period, as a cubic spline defined by peak time, rise time, fall time, and peak torque.

      The amount of torque (a type of force) as a function of time. The figure measures four parameters (peak time, rise time, fall time, and peak torque) that the authors believe to be important to determine the optimal stride posture, thus improving the amount of energy spent walking.

    33. A method for minimizing the energy cost of human walking, in which various control laws are applied, metabolic (met.) rate is quickly estimated (est.) for each, costs are compared, and an evolution strategy is used to generate a new set of control laws to be tested, all during walking.

      The goal of the optimizer is to reduce the amount of energy spent walking. This is accomplished by measuring respiratory data (metabolic data) and posture from the test subject (human) and updating the device to improve posture when walking.

    34. Measurements of human performance are used to update device control so as to improve performance in the human portion of the system.

      A human test is measured for metabolic rate, the minimal energy expenditure that mammals burn at rest, and the results are fed into the optimizing coder (exoskeleton). The optimizer chooses the best measurements and updates the device, which then feeds back into the human.

    1. The balance of inertia and gravity yields a prediction for the lapping frequency
    2. The tongue’s vertical position during upward motion is well described by an error-function

      An error function has an S-cure shape. The authors found that the motion of the tongue during its lifting (back in the mouth) resembles the S-shape of an error function.

    3. This competition between inertia and gravity sets the lapping frequency
    4. Consequently, the balance between inertia and gravity dictates the lapping frequency, f, by controlling the time of pinch-off

      The authors were able to see from the column dynamics that a higher inertia (upward force) to gravity (downward force) ratio influences the pinch-off time, which is time at which the water column loses contact with the disk after its elevation.

  15. Aug 2017
    1. Western assay of induced SX4 cells showed the presence of Venus only in the membrane fraction and not in the cytoplasmic fraction, suggesting efficient membrane localization of Tsr-Venus.

      The e coli strain engineered by the authors is behaving as they predicted.

  16. Mar 2017
    1. There are a number of possible explanations for this unanticipated result. First, union members may have a higher level of dissatisfaction with the organisation and management processes (Freeman and Medoff, 1984: 21; Bryson et al., 2004), including communications and participative arrangements, and therefore perceive less favourably their degree of influence within the organisation (Kleinman, 2000: 403–404) or the degree of managerial responsiveness (Bryson et al., 2006). Bryson (2004) found that union members had a higher level of job dissatisfaction than non-union workers but that after an extensive array of control variables were included, no significant negative relationship was found. This finding, they suggested, may well be due to a selection bias on the part of employees. Employees who had higher aspirations for their working life may be more likely to join a union. This proposition resonates well in the case of PSR, where some 63.8 per cent of unionised employees indicated that a major reason for joining the union was because they wanted to have a say in matters affecting their working life. Unions themselves may also contribute to this dissatisfaction by raising employee expectations that they are unable to meet (see also discussion on ‘consciousness raising’ in Guest and Conway, 2004: 115–116) and by providing their members with considerable information about problems within the organisation and the problems they are encountering with management. This is likely to be part of the explanation for the findings of this research as at the time of the survey, PSR management were keen to introduce a performance-related pay scheme which had led to an active campaign of opposition by the union.A second explanation is that union members may have higher expectations of voice. Employees join unions for a variety of reasons (Peetz, 1998), but overall, they expect unions to make a difference to their working lives. As Bryson and Freeman (2007: 84) found, ‘unionised workers reported more problems with management’ than non-union workers. In the case of PSR, the major reasons for employees joining the union were a belief in unions, wanting to have a say in things that affect their working life and a belief that unions generate better wages and conditions. Clearly, these union members had high expectations concerning voice. Yet, it was also the case that these expectations were not being met. Improved wages and working conditions were becoming harder to achieve as the enterprise bargaining system, with its emphasis on productivity improvements, had led to trade-offs involving redundancies, a decline in wage relativities with the private sector, and the possibility of a new performance-based pay scheme being introduced.A third explanation is that the overall focus within PSR at the time of the research had shifted from curiosity-led to commercially-driven research with an emphasis on productivity and efficiency. For employees of PSR, most of who were accustomed to the more protected working environment of the public sector, this meant that external factors were now driving research, and the scientific arguments used in the past for justifying research projects were becoming less important. In this environment, the value of union membership was becoming more marginal as union members had less protection than that of the past in the case of redundancies and adverse performance appraisals. In addition, other benefits of union membership such as access to grievance procedures were available to all employees regardless of their union status. It may also have been the case that management's approach to reform, for example the introduction of a performance-based pay scheme that ran counter to the wishes of union members and past practices, may have led many unionists to believe they were being targeted. In this context, the tense state of the relationship between management and the union may have created a negative perception of collective union voice (Freeman and Medoff, 1984).
  17. Aug 2016
    1. However, the specific benefit drongos gain from producing such a large array of mimetic alarm calls is unclear.

      Why do you think drongos can produce so many different alarm calls? What advantage may this give them?

  18. Jul 2016
    1. No significant effects were observed for the striatal volumes, with only a marginal effect observed for putamen (P = 0.062) when congruent reaction time was included as covariate.

      ID: 020
      Variable: Flanker performance, striatal vol
      Interpretation: no relationship found

      ID: 021 Variable: Flanker performance, putamen vol Model: ? (includes congruent RT) P: 0.062 Interpretation: slight cognitive control effect observed for putamen volume

  19. Mar 2016
    1. But there’s, I think there is a question of how you interpret the data, even ... ifthe experiments are very well designed. And, in terms of advice—not that I’mgoing to say that it’s shocking—but one of my mentors, whom I very muchrespect as a scientist—I think he’s extraordinarily good—advised me to alwaysput the most positive spin you can on your data. And if you try to present, like,present your data objectively, like in a job seminar, you’re guaranteed tonotgetthe job

      Importance of "spinning" data

  20. Aug 2015
    1. Quality (DRG) 1.2675 0.61

      It seems there is no statistically significant differences in the Quality measured between the two aggregation levels.

    Tags

    Annotators

  21. May 2015
    1. “Unfortunately, I couldn’t find the effect,” he said. “But the worst part was that when I submitted these null results I had difficulty getting them published.

      Important point to make again in the proposal as to why negative results are difficult to publish

  22. Apr 2015
    1. Why sully a CV with papers from the ‘Journal of Failed Experiments’? Don’t we want our colleagues (and especially our competitors) to believe that we succeed at every undertaking?

      Same reason pharma hates the term: Failed drugs

    2. Thus, although the arguments in favor of small-unit publishing all seem to revolve around benefits to the community, the costs of generating these small units would fall on individual authors. If the community is to reap the benefits, then the costs to the individual authors must be driven to zero – or associated with some reward.

      Will they do it?

    3. Time spent publishing small papers is time not spent developing big ones
    4. but because journal editors are obsessively vigilant about rejecting papers that fall below a threshold of ‘novelty’, these papers become unpublishable in practical terms

      The Inglefinger rule.

  23. Jan 2014
    1. Reasons for not making data electronically available. Regarding their attitudes towards data sharing, most of the respondents (85%) are interested in using other researchers' datasets, if those datasets are easily accessible. Of course, since only half of the respondents report that they make some of their data available to others and only about a third of them (36%) report their data is easily accessible, there is a major gap evident between desire and current possibility. Seventy-eight percent of the respondents said they are willing to place at least some their data into a central data repository with no restrictions. Data repositories need to make accommodations for varying levels of security or access restrictions. When asked whether they were willing to place all of their data into a central data repository with no restrictions, 41% of the respondents were not willing to place all of their data. Nearly two thirds of the respondents (65%) reported that they would be more likely to make their data available if they could place conditions on access. Less than half (45%) of the respondents are satisfied with their ability to integrate data from disparate sources to address research questions, yet 81% of them are willing to share data across a broad group of researchers who use data in different ways. Along with the ability to place some restrictions on sharing for some of their data, the most important condition for sharing their data is to receive proper citation credit when others use their data. For 92% of the respondents, it is important that their data are cited when used by other researchers. Eighty-six percent of survey respondents also noted that it is appropriate to create new datasets from shared data. Most likely, this response relates directly to the overwhelming response for citing other researchers' data. The breakdown of this section is presented in Table 13.

      Categories of data sharing considered:

      • I would use other researchers' datasets if their datasets were easily accessible.
      • I would be willing to place at least some of my data into a central data repository with no restrictions.
      • I would be willing to place all of my data into a central data repository with no restrictions.
      • I would be more likely to make my data available if I could place conditions on access.
      • I am satisfied with my ability to integrate data from disparate sources to address research questions.
      • I would be willing to share data across a broad group of researchers who use data in different ways.
      • It is important that my data are cited when used by other researchers.
      • It is appropriate to create new datasets from shared data.
    1. HR people can’t believe that a company the size of Netflix doesn’t hold annual reviews. “Are you making this up just to upset us?” they ask. I’m not. If you talk simply and honestly about performance on a regular basis, you can get good results—probably better ones than a company that grades everyone on a five-point scale.