1,180 Matching Annotations
  1. Nov 2018
    1. This paper described how to run dynamic languages efficiently byrecording hot traces and generating type-specialized native code.Our technique focuses on aggressively inlined loops, and for eachloop, it generates a tree of native code traces representing thepaths and value types through the loop observed at run time. Weexplained how to identify loop nesting relationships and generatenested traces in order to avoid excessive code duplication dueto the many paths through a loop nest. We described our typespecialization algorithm. We also described our trace compiler,which translates a trace from an intermediate representation tooptimized native code in two linear passes.

      First paragraph of 9. conclusions

    1. However, among the 92 microorganisms with MHETase homolog(s), 33 had homologs of both TPA and PCA dioxygenases. This suggests that a genomic basis to support the metabolism of MHET analogs was established much earlier than when ancestral PETase proteins were incorporated into the pathway. PET enrichment in the sampling site and the enrichment culture potentially promoted the selection of a bacterium that might have obtained the necessary

      The authors looked for other organisms that might have similar DNA coding for enzymes that can degrade PET. However, despite finding several organisms with the metabolism needed to degrade MHET, they were unable to find any with PETase enzymes.

      The authors concluded that the enzymes needed to degrade MHET predate PETase enzymes. They hypothesize that the PETase may have evolved from the similar enzyme family cutinase and then been passed from bacterium to bacterium in the PET-rich recycling site.

      Since the recycling site where the authors took their original samples had a lot of PET, bacteria with the ability to degrade PET may have been more able to survive and divide. This would have encouraged the spread of the PETase genes in the recycling site l. sakaiensis population.

    2. In the course of subculturing no. 46, we found a subconsortium that lost its PET degradation capability. This subconsortium lacked I. sakaiensis (fig. S3), indicating that I. sakaiensis is functionally involved in PET degradation.

      When the authors removed l. sakaiensis from sample no. 46, the plastic was not degraded. The authors therefore concluded that I. sakaiensis is responsible and necessary for the PET degradation activity in the sample.

    1. wolves we examined may not have been closely related to the population(s)/s that gave rise to dogs

      Wolves went through a sudden bottleneck—a big, sudden drop in population—right after dogs were domesticated. Three wolves were studied, and considering how different they were from each other and that none of them were more closely related to dogs than the others, it's a possibility that the wolf ancestor of dogs died off in the bottleneck.

    2. 60,000 to 20,000 years ago (fig. S17 and Fig. 2B). This date should not be interpreted as a time frame for domestication

      The wolves used in this study were modern wolves. We know that there was a bottleneck in the wolf population shortly after dogs were domesticated (see Freedman et al. in reference 6), so the wolves studied here may not be a close ancestor of the wolves that dogs came from. For this reason, 60,000-20,000 years is not an estimate of when dogs and wolves evolved from each other.

    3. Given the current lack of dog remains prior to 8000 years ago in Central Eurasia, a scenario involving a single origin followed by an early dispersal seems less likely.

      The lack of evidence for dogs in Central Eurasia over 12,500 years ago, and the presence of dogs on either side of the region suggests that dogs were domesticated twice.

      If dogs were domesticated just once in East Eurasia and transported west, there should be evidence for dogs in Central Eurasia and/or a gradual change in the dog genome as dogs moved East to West.

    4. Newgrange dog retained a degree of ancestry from an ancient canid population that falls outside of the variation of modern dogs, but that is also different from modern wolves.

      The Newgrange dog and East Asian dogs diverged earlier than East Asian and West Eurasian dogs. The best explanation for this, according to the data, is that the Newgrange dog retained some DNA from ancient wolves, wolves that are not closely related to modern wolves.

    1. persistently responded to stimuli previously associated with reward, irrespective of whether their behavior was actually rewarded or not

      CUD patients continued to respond to stimuli that were previously associated with a reward, even after the association with the reward was removed.

      Further, when the behavior became more habitual and less goal-oriented, they showed an increased response rate to the stimuli. This persisted even after the reward was removed.

    2. significantly short of that of control volunteers, irrespective of whether the goal was to make responses to obtain symbolic rewards or to avoid electrical shocks

      Cocaine use disorder (CUD) patients were not as successful as control volunteers in learning which animal pictures gained them points and which associated with electric shocks.

  2. Oct 2018
    1. Our findings are thus not only consistent with known functions of mammalian NPY and its mode of regulation, but also provide evidence for NPF functioning as a key molecular transducer between social experience and drug reward

      The researchers finally conclude that their findings are consistent with past research on NPY and NPF. Moreover, this research introduces a new dimension to our understanding of this molecule by demonstrating it to be a common substrate regulating both sex and alcohol consumption in complementary ways.

    2. Regardless of the exact mechanism, these data suggest that activity of the NPF system is regulated by at least two rewarding experiences, mating and ethanol intoxication.

      From this, the researchers conclude that the NPF system (circuit activity and amount of the molecule present) is affected by and reflective of rewarding experiences, including but not limited to mating and consumption of alcohol.

    3. NPF transcript levels increased 1 hour after exposure and returned to basal levels 24 hours later (Fig. 4F)

      The researchers found that shortly after exposure to alcohol, NPF levels were indeed elevated, but that these levels eventually returned back to normal by the next day. Exposure to air, on the other hand, had no impact whatsoever on the amount of NPF in the brain.

    4. Males displayed a strong preference for the mating-associated odor (Fig. 4A). We have separately shown that flies exhibit conditioned preference for an odor associated with ethanol intoxication in a similar assay (4).

      The researchers found that flies preferred the odor that was associated with mating, as well as with exposure to alcohol. This indicates that both of these things are "rewarding" experiences to the fly.

    5. There was no difference in ethanol preference between these two cohorts (fig. S3A). There was also no difference between males exposed individually to biologically relevant concentrations of cVA (13) and vehicle-exposed controls (fig. S3B) (11).

      The researchers found that both males exposed to mated females (and by extension cVA) as well as males exposed to decapitated virgin females (who lacked cVA) demonstrated a preference for alcohol. To confirm this finding, they also simply exposed a third group of males to the chemical by itself without a female present before testing their preference for alcohol. This third group too maintained a preference for alcohol. Based on this, they concluded that cVA could not be the driving cause for the observed alcohol preference, and that the effect was likely due to the actual sexual deprivation involved.

    6. These males, which experience neither rejection nor copulation, showed enhanced ethanol preference when compared to the mated-grouped cohort (Fig. 1C); the preference index was similar to that displayed by the rejected-isolated cohort

      The researchers found that even these males who did not experience the social aspect of rejection by a female maintained a preference for alcohol. From this, they concluded that social rejection was not the main cause for the observed alcohol preference amongst virgin male flies.

    1. Of those covariates, 26 had an analog in the LLDeep record

      26 of the 69 (37.6%) covariates found in the FGFP data had a comparable factor in the LLDeep cohort.

    2. revealed associations between genus abundances and hip circumference, uric acid concentrations, amoxicillin intake, and chocolate-type preference (namely, an increased abundance of unclassified Lachnospiraceae in participants with a preference for dark chocolate).

      Similar to how red blood cell counts were associated with differing abundances of Faecaelibacterium, the researchers also showed that there were associations between other genera and hip circumference (the distance around the largest part of your hips or the widest part of your buttocks), uric acid concentrations (a compound that is excreted in urine; high uric acid concentrations can indicate poor kidney function and low concentrations can indicate gout, a form of arthritis), amoxicillin (a type of antibiotic) intake, and chocolate preference.

    3. 24 matching covariates were found to be significantly associated with microbiome composition in the LLDeep cohort

      Of the 26 covariates that were comparable in both the FGFP and LLDeep data, 24 factors were found to be significantly associated with microbiome composition in the LLDeep cohort.

    4. Of the covariate interactions detected, 63% was driven by medication (Fig. 5B). This result highlights the versatility of drug-microbiome associations and stresses their importance as potentially confounding factors in clinical studies.

      They found that medication influenced 63% of the interactions between variables and may confuse or bias results in clinical studies.

    5. cumulative, nonredundant effect size of 7.63%. This suggests the influence of additional, currently unknown covariates as well as intrinsic microbial ecological processes

      Since their metadata could only explain less than 8% of the variation, the researchers suggest that there are other factors that were not accounted for in their study. This may be intrinsic properties to microbes, such as interactions between species.

    6. analyses revealed that effect size is small but significant (table S10). Notably, previously unidentified factors such as red blood cell (RBC) count and hemoglobin concentration indicated covariation of microbiome composition with blood oxygen uptake capacity

      They showed that there is a significant association between the microbiome composition and body mass index. They also found new correlations, like red blood cell count, with the microbiome composition.

    7. medication had the largest explanatory power on microbiome composition, including 10.04% of community variation

      Medication has an impact on the microbiome composition and accounted for 10.04% of the differences between samples.

    1. This proves that the fly’s circuit represents a previously unknown LSH family.

      One of the properties of an LSH algorithm is that it can organize input points into a new, smaller-dimensional matrix while preserving the distances between points. The authors proved that the fly algorithm also has this property but uses a different approach than other known LSH options. The different approach, in part, is to expand the dimension, as opposed to contracting the dimension.

      Therefore, the authors conclude that the fly's approach represents a completely new category of LSH algorithms.

    1. This definition has brought order to the field, but may also have constrained it by forcing untested assumptions about the true nature of the symbiosis. We suggest that the discovery of Cyphobasidium yeasts should change expectations about the potential diversity and ubiquity of organisms involved in one of the oldest known and most recognizable symbioses in science.

      The old definition of one fungus with one photobiont was helpful in guiding science's understanding of lichens. Yet, sometimes strict definitions can prevent us from asking good questions. This paper concludes that researchers should always push their investigations further. There might still be interactions we haven't identified in symbiotic relationships.

    2. These data suggested that a previously unrecognized basidiomycete was present in thalli of both species but was more abundant whenever vulpinic acid was present in large amounts

      After concluding that gene expression in the two symbionts could not account for lichen differences, the authors continued to investigate what might account for vulpinic acid production. The results of the transcriptome analysis indicated that gene expression from a basidiomycete was correlated with the presence of vulpinic acid.

    1. The catalytic preference of the ISF6_4831 protein for PET film over pNP-aliphatic esters was also substantially higher than that of TfH, LCC, and FsC (380, 48, and 400 times as high on average, respectively) (Fig. 2D). Thus, the ISF6_4831 protein prefers PET to aliphatic esters, compared with the other enzymes, leading to its designation as a PET hydrolase (termed PETase).

      The authors found that the enzyme (ISF6_4831 protein) they determined was responsible for degrading PET in l. sakaiensis was better at degrading PET than its ability to degrade other molecules, in this case paranitrophenol linked aliphatic esters also called pNP-aliphatic esters, that don't look like PET.

      Furthermore, the authors saw that other enzymes that are known to sometimes degrade PET degraded more pNP-aliphatic esters relative to PET than this new enzyme ISF6_4831. This led them to include that ISF6_4831 was specifically specialized at degrading PET.

      Thus, the authors begin referring to the ISF6_4831 protein as PETase.

    2. The activity ratios of PETase relative to the other enzymes decreased as the enzyme concentrations increased, indicating that PETase efficiently hydrolyzed PET with less enzyme diffusion into the aqueous phase and/or plastic vessels used for the reaction. PETase lacks apparent substrate-binding motifs such as the carbohydrate-binding modules generally observed in glycoside hydrolases.

      The authors added more protein to a sample of PET. The three previously discovered enzymes produced more product as the enzyme concentration increased. The new enzyme, PETase, did not increase the amount of product as more enzyme was added. The authors concluded that this was because PETase was attached to the film. So adding more enzyme once the film was already covered would not increase the rate.

    3. The catabolic genes for TPA and the metabolite protocatechuic acid (PCA) were up-regulated dramatically when cells were cultured on TPA-Na, BHET, or PET film. This contrasted with genes for the catabolism of maltose (Fig. 3A), which involves a pathway distinct from the degradation of TPA and EG, indicating efficient metabolism of TPA by I. sakaiensis. The transcript level of the PETase-encoding gene during growth on PET film was the highest among all analyzed coding sequences (table S4), and it was 15, 31, and 41 times as high as when bacteria were grown on maltose, TPA-Na, and BHET, respectively. This suggests that the expression of PETase is induced by PET film itself and/or some degradation products other than TPA, EG, MHET, and BHET.

      The authors measured which genes were being used when the l. sakaiensis cells were exposed to PET. They found that when PET film was present, the l. sakaiensis cells used the genes that make the PETase enzyme much more often then they used them when PET was not present.

      From this data, the authors concluded that either PET causes the cells to start making PETase or the enzyme production is induced by some degradation product of PET that they didn't test.

    4. For pNP-aliphatic esters, which are preferred by lipases and cutinases, the activity of the ISF6_4831 protein was lower than that of TfH, LCC, and FsC (Fig. 2D). The activity of the ISF6_4831 protein against the PET film, however, was 120, 5.5, and 88 times as high as that of TfH, LCC, and FsC, respectively.

      The authors exposed all of the enzymes to the different oligomers and measured the activity of each enzyme. The other enzymes did a better job of degrading substrates without aromatic groups, but ISF6_4831 did the best job degrading PET. From these results the authors concluded that ISF6_4831 had high specificity towards PET.

    5. a hydrolase from Thermobifida fusca (TfH) (fig. S4 and table S2) that exhibits PET-hydrolytic activity

      The authors found a part of I. sakaiensis's DNA that had 51% of the same patterns found in another protein known to degrade PET. They concluded that this stretch of DNA also made the protein that allowed l. sakaiensis to degrade PET.

    1. Adding emissions from VCPs (Fig. 3B) reduces the model bias in ambient air from –39% to +1%, and the R2 in the box model improves from 0.59 to 0.94.

      The model calculations don't agree well with the experimental data when the contribution from VCPs is ignored. When the contribution from VCPs is included in the model calculations, the model agrees well with the experimental data. This change in model agreement can be seen in the models bias and R-squared values.

      Model bias measures on average the percent error between the model calculations and the experimental measurements. Without the inclusion of VCPs the model was, on average, under predicting the concentrations of VOCs by 39% (Panel A of Figure 3). With the inclusion of VCPs the model was on average over predicting the concentration of VOCs by 1% (Panel B of Figure 3).

    2. A surprising result is that mobile-source emissions of ethanol account for less than 20% of ambient concentrations, even though gasoline blends now routinely include at least 10% ethanol. This suggests that other sources are contributing substantially to ambient ethanol concentrations, which we attribute to VCPs.

      Ethanol was measured in the air. Less than 20% of the ethanol comes from mobile sources (gasoline and other automobiles). The remaining 80% comes from other sources, such as volatile chemical products.

    3. transitioning away from transportation-related sources and toward VCPs.

      Hear the lead author, Brian McDonald, talk about the findings of this work in the podcast, Science Friday.

      https://www.sciencefriday.com/segments/theres-a-new-urban-air-polluter-on-the-block/

    1. To fully utilize the steep step in water uptake in the MOF-801 isotherm, a temperature difference of ~45°C between the condenser and the layer is necessary to achieve desorption at 10% RH

      The efficiency of the water-harvesting relies on the temperature difference between the MOF and the condenser, as well as the relative humidity, for the condenser to be able to collect all the water vapor desorbed from the MOF. The authors found that at 10% RH, a difference of 45°C is needed to reach the maximum water-harvesting capability.

    2. By saturating the MOF layer with ambient air at a solar flux less than 1 sun, ~0.3 liters kg–1 potentially can be harvested.

      The results of experiments and simulations show that the device can, at the maximum, collect 0.3 liters of water per kg of MOF material in normal outdoor usage.

    3. Continuously harvesting water in a cyclic manner for a 24-hour period with low-grade heat at 1 kW m–2 can yield ~2.8 liters kg–1 day–1 or ~0.9 liters m–2 day–1with a 1-mm-thick layer

      The result of the simulation shows that undergoing several cycles of adsoprtion-desoprtion can produce almost 3 liters of water per 24 hours with 1 kg of the MOF material. This is the case for a 1 mm-thick layer.

    4. However, at higher porosities, a thicker MOF-801 layer is required to harvest a sufficient amount of water, but the time scale and transport resistance for intercrystalline diffusion also scales with the MOF layer thickness as t ~ Lc2/Dv, where, t, Dv, and Lc are the time scale, intercrystalline diffusivity, and characteristic length scale (i.e., layer thickness), respectively.

      Porosity is a key parameter in the performance of the MOF material. If the porosity is too low, the adsoprtion process becomes slower because the molecules have to diffuse through the crystal. In contrast, if the porosity is too high, more MOF is required to harvest the same amount of water and the process is also slower.

    5. Each water-harvesting cycle, ~0.24 liters kg–1 were harvested (Fig. 2D), as determined by integrating the water-harvesting rate.

      The water harvesting rate measures liters per kilogram per second and varies during the experiment. To obtain the total amount of water harvested, the authors integrated the water harvesting rate over the whole duration of the experiment (100 minutes). In this time, the MOF water-harvesting device collected the equivalent of a small glass of water from the surrounding air.

    6. good performance driven by aggregation of water molecules into clusters within the pores of the MOF

      The authors found that a key parameter in the water uptake capacity of this MOF is the geometry that the water molecules adopt inside the cavities, forming multiple hydrogen bonds. This phenomenon is explained principally by the size of the pores of the MOF.

    1. Drawing on comprehensive range data, bumblebee species show opposite range responses across continents relative to most terrestrial assemblages (4): rapid losses from the south and lagging range expansions in the north

      As we can see from Figure 1, the northern/cold end of species' range limits are not shifting, whereas the southern end of the range have shifted northwards.

    2. In contrast to expectations and responses known from other taxa (4), there has been no change in the northern limits of bumblebee distributions in North America or Europe (Fig. 1A). Despite substantial warming (~ +2.5°C), bumblebee species have also failed to track warming along their cool thermal limits on both continents (Fig. 1B and Table 1).

      As we can see in Figure 1A, there was no shift in northern range limit for species (on average), in North America or Europe. As the authors point out, this is a surprising result because other marine and terrestrial ectotherms have been observed moving further north in recent years.

      This is also surprising because we can see in Figure 1B that species' cool range limits have warmed by about 2.5°C.

    1. selectively decreasing activity in excitatory local neurons of the STN appeared not to be sufficient by itself to affect motor symptoms.

      Selectively targeting eNpHR to the excitatory neurons of the STN showed to be insufficient at impacting the rotational behavior in the hemiparkinsonian rats. This alludes to the possibility of another mechanism of action being involved other than strict inhibition of excitatory neurons.

  3. Sep 2018
    1. Mean elevations among northern species in Europe and North America shifted lower.

      Interestingly, northern species shifted lower down the mountains—the opposite of southern species!

    2. Neither total pesticide nor neonicotinoid applications there relate to observed shifts in bumblebee species’ historical ranges or thermal limits (table S1).

      As we can see in Table S3, the land-use and pesticide variables were not useful in predicting range shifts.

      See the Supplementary Materials for more information.

    3. Species with southern geographical ranges retreated to higher elevations across Europe and North America (Table 1 and Fig. 2), consistent with observations of range losses from their southern range limits.

      As we can see from Figure 2, species with ranges further south moved to occupy higher elevation in recent years.

    1. cell type–targeted inhibition was temporally precise and reversible

      The authors were able to demonstrate the utility of selectively targeting specific excitatory neurons with an inhibitory opsin and then reversibly inhibit and record neural activity.

    1. The model-observation comparison of fossil-derived SOA improves substantially when we add VCP emissions to traditionally considered transportation emissions (fig. S6). Note that nonfossil contributions to SOA, such as from wood burning, cooking, and biogenic sources, are not considered here. If we consider emissions from mobile sources and upstream emission sources alone, then the amount of fossil SOA predicted by SOM is lower than measurements at the Pasadena ground site by a factor of 3.4 ± 1.7 (55, 56). The inclusion of VCP emissions is required to bring the modeled and measured SOA to agreement, within their respective uncertainties (fig. S6).

      The model calculations for formation of secondary organic aerosols (SOAs) do not agree with experimental data if the contribution from VCPs is ignored. The inclusion of VCP emissions in the model calculations allows the calculations to better agree with the experimental data.

    1. performance profile of CUD patients in the appetitive condition

      CUD patients may be at risk of developing habitual behavior due to their impairment in action-control behaviors.

      The fact that CUD patients respond equally to pictures associated with values and those without an association suggests that they can no longer control their actions.

      These reactions could indicate habitual behaviors, putting them at risk for compulsive behaviors.

    2. reduced performance accuracy during training (β = –0.410, P < 0.001) and higher numbers of stressful life events

      Stressful life events, decreased accuracy in responding to training, and cocaine addiction are factors that predict how likely someone is to develop habitual behaviors.

    3. Addiction to cocaine, but not to other drugs, explained ~13% of the variance of appetitive habits

      The authors found that cocaine explained 13% of the variance in performance in this study. This means that addiction to cocaine seems to play a significant role in developing habitual behaviors, but that there are also other things that play a greater role.

    4. CUD patients less sensitive to outcome devaluation

      CUD patients had more difficulty than controls in learning which pictures were no longer associated with a reward. They were also less able to change their responses based on new information, meaning that they continued to respond the same way even in the absence of a reward. Control participants, on the other hand, decreased their response when the reward was removed.

    1. These findings provide independent evidence for large body-size individuals among hominins as ancient as 3.66 Ma

      The authors concluded that Australopithecus afaransis males were generally of the same stature as early Homo individuals.

    2. In order to contextualise the australopithecine and early Homo stature estimates and range of variability obtained from the footprints within a broader picture (Figure 12), and to compare them with a larger sample, we extended our analysis to consistent data based on skeletal elements, namely femurs (see Materials and methods for details).

      Using an analysis of both the footprints and femurs to estimate stature makes the findings more accurate. It appears to the authors that Australopithecus afaransis males were generally of the same stature as early Homo individuals.

    3. the two individuals S1 and S2 were taller and had a larger body mass than the G individuals. The estimated about 165 cm stature of S1 is quite remarkable, exceeding G2 by more than 20 cm (Table 3).

      Based on their findings, the authors concluded that Australopithecines were larger in stature than previously thought.

    4. The depth distribution pattern indicates that the weight transfer of S1 was similar to that described for G1–3 (Robbins, 1987): starting from the heel, the weight was transferred along the lateral part of the foot (note the steep slope of the lateral wall of the tracks compared to that on the medial side) up

      How weight was distributed along the foot as the individual walked provides information that supports that all the Laetoli footprints were made by Australopithecus afarensis. The footprints also establish a morphology and gait pattern very different from that of non-hominins.

      Source: https://corewalking.com/chimpanzee-feet-vs-human-feet/

    5. The above-mentioned assemblage of terrestrial mammal and bird footprints suggests that the local palaeoenvironment was characterised by a mosaic of dry tropical bushland, woodland, open grassland and riverine forest similar to the extant one

      Identifying the species of animals that were present helped the authors to establish what the local environment was like during the time Australopithecus inhabited the region.

    6. Secondarily, stratigraphic relationships can be explored at higher detail, in order to assess whether the tracks of Site S were printed on exactly the same sublevel of the Footprint Tuff as those in Site G. This aspect would mostly concern the behavioural aspects of a hypothetical single group of hominins, but it must be pointed out that extra-fine correlation between outcrops, even in a depositional environment with moderate lateral variability like the Footprint Tuff deposition area, can be affected by major uncertainty.

      It is difficult to determine a relationship between a hypothetical group of hominins because external variables—such as geographic faults and fractures discussed earlier—make these extra-fine correlations generate uncertainty.

    7. Moreover, considering that Tuff 7 includes a sequence of several sublevels originated by distinct eruptions closely spaced in time, and that its overall deposition time was estimated in weeks (Hay and Leakey, 1982, p. 55; Hay, 1987, p. 36, it can be concluded that all the tracks belong to the same general population of hominins.

      Through an analysis of soil strata, the authors determined that the new set of footprints was left at the same time and in the same layer of volcanic tuff. This is important when using the data obtained from the analysis of the footprints to determine stature and the degree of dimorphism.

      It establishes that if the footprints in the original trackway were made by Australopithecus afaransis, the footprints in the newly discovered trackway were also made by A. afaransis.

    8. Nevertheless, there have always been disputes about the nature and degree of sexual dimorphism characterising this early bipedal hominin, with supporters of either pronounced (e.g., Johanson and White, 1979; Kimbel and White, 1988; McHenry, 1991; Richmond and Jungers, 1995; Lockwood et al., 1996; Plavcan et al., 2005; Harmon, 2006; Gordon et al., 2008) or moderate (Lovejoy et al., 1989) body-size dimorphism.

      The topic of body size and degree of sexual dimorphism present in Australopithecus afarensis continues to be hotly debated. The authors' analysis of the newly discovered footprints at Laetoli provides evidence that appears to support pronounced body-size dimorphism.

    1. The distribution of edits on transcripts was heavily skewed for REPAIRv1, with highly edited genes having more than 60 edits

      These transcripts are the most abundant in the cell and are therefore easily accessible for the deaminase. Multiple edits along the transcript may imply that the editing complex is able to stay bound to the mRNA long enough to modify not only the target A but also the surrounding adenosines.

    1. Breeding seabird densities were almost two orders of magnitude higher on fox-free than on fox-infested islands (Fig. 2B) (Mann-Whitney rank sum, T = 36, P < 0.001) (12). We estimate that this reduction in seabird abundance translates to a decline in annual guano input from 361.9 to 5.7 g m–2 (median values; T = 42, P = 0.005) (12). The resulting difference in marine nutrient input is reflected in soil fertility. Total soil phosphorus on fox-free islands was more than three times that on fox-infested islands (Fig. 2C) (F1,16 = 8.01, P = 0.012) (12). Although seabird colonies are often concentrated on the perimeter of islands, guano-derived nutrients can be broadly redistributed across islands and not solely concentrated within the colonies (17).

      The results show that there are much higher numbers of breeding seabirds on fox-free islands than on infested ones. This makes sense because foxes are predators of many types of birds which would lower the abundance of mating birds. This decrease in birds also had effects on the amount of guano being distributed across the land. This number decreased and in turn affected different nutrients that are derived in the soil from the bird guano such as phosphorous. Fox-free islands saw three times more soil phosphorus than fox infested islands. In this experiment, there is a chain effect of sorts going on where the presence or absence of foxes affects sea bird populations, which then affects guano inputs to the island and the soil nutrients derived from this are dependent again on sea bird populations that distribute the guano.

    2. Fox predation reduced seabird abundance and distribution, in turn reducing nutrient transport from sea to land. The more nutrient-impoverished ecosystem that resulted favored less productive forbs and shrubs over more productive grasses and sedges.

      Overall, the study found that the introduction of foxes turned the once-grassland into a tundra with less productive plants in its place because of the nutrient deprivation caused by fox predation on the birds, who are the main nutrient distributors on the archipelago.

      This shows the indirect effects that predation can have on ecosystems that rely so heavily on nutrient distribution from other living organisms, such as the seabirds. This also provides further evidence that trophic cascades do not only have to be top down; predators do effect herbivory, but there can be indirect effects from predators to plant communities through nutrient deprivation from predation on nutrient source organisms.

    1. Thus, locality-sensitive hashing may be a general principle of computation used in the brain

      The authors note that the specific process that the fly olfactory circuit uses to identify odors is similar to what other researchers have seen in other animals and other parts of the brain (see Table 1).

      From this observation, they conclude that the locality-sensitive hashing approach that they've identified in the fly olfactory circuit may not be limited to flies or even to odor recognition, but could be a standard processing technique that the brain uses for many different purposes.

    2. With further expansion of the dimensionality (from 20k to 10d KCs, closer to the actual fly’s circuitry), we obtained further gains relative to LSH in identifying nearest neighbors across all data sets and hash lengths

      For all three data sets (SIFT, MNIST, and GLOVE), the authors were able to improve the performance of the LSH algorithm by increasing the number of Kenyon cells that they used in the calculation. That is, using more KCs made it easier for the LSH algorithm to correctly identify the nearest neighbors (most similar images or words) in the data sets.

    3. sparsifying the tag using WTA resulted in better performance than using random tag selection

      The authors looked at how the LSH algorithm performed when using two different methods to create the tag:

      1. The tag is created from a random selection of Kenyon cells
      2. The tag is created from the Kenyon cells with the highest firing rates (this is the "winner takes all" or WTA approach)

      The result was that the LSH performed better with the WTA approach. Note that the authors measured performance using the mean average precision (see Fig. 2B)

  4. Aug 2018
    1. Fig. 3.

      Figure 3 shows the number of pollen grains adhering on the y axis and on the x axis is the fishing line difference. There showed to be no significant difference between the line thickness as you can see from the lines on the graph the largest size fishing line showed the greatest amount of pollen grains.

    1. The two known populations of C. jimenezii have a small number of individuals; however, it seems that stochastic events associated with drift and inbreeding have not been fully operating in these populations despite their very small size.

      Given how closely related and interbred they were, there was more genetic diversity in the Coccothrinax palms than expected.

    2. he mean number of alleles per locus ranged between 3.0 (Dominican Republic) and 3.1 (Haiti),

      The Palms from the Dominican Republic and Haiti were found to have similar average allele loci counts, but the Haitian ones have more on average.

    3. Distribution of Coccothrinax jimenezii showing the location of the only two known populations of this species in Haiti (Gonaïves) and Dominican Republic (Lago Enriquillo).

      Due to the small population of Coccothrinax jimenezii within Haiti and Dominican Republic, conservation efforts have been maximized to prevent extinction.

    1. Fig. 7 On this figure of electrosensory pathways in the gymnotiform fish (modified from Carr and Maler, 1986), we have labeled regions where the proposed computations for high-frequency electrolocation might be implemented.

      The author used results from video, electric images, and BEM simulations to depict the electrosensory pathways in the fish and where the fish has organs with receptors that are able to sense electric fields. By knowing the location of these electroreceptors, the author is able to determine where the organism is able to conduct electrolocation.

    1. Results of linear models examining the change in height, dispersal, competitive ability, and seed mass at the invasion front after six generations of evolution as a function of landscape patchiness (size of gaps between suitable habitat).

      Table 1 indicates that plant height, competitive ability, and seed mass had significant intercepts, meaning these traits changed from the original population, but only plant height showed a significant slope, meaning that the other traits did not have a significant rate of change.

    2. Fig. 2. Farthest distance colonized in each generation.

      As the distance between populations increased, the distance seeds were dispersed followed a similar increase for evolving populations, regardless of the distance between populations. Non-evolving populations dispersed seeds shorter distances based on how big the gap was between populations.

    1. VCPs have begun to contribute significantly to SOA formation outdoors. Given that global mortality from fine particles is significantly greater than for ambient O3 pollution (1), further study is needed on whether chemical products currently designed to mitigate O3 are also sufficient to protect humans from exposure to fine particles.

      VCPs are becoming more important for understanding air quality. Further research into these products and the potential health risks they pose is needed.

    2. In fig. S5, we show that half of measured OH reactivity (21 ± 7 s−1) can be explained by fossil fuel VOC emissions (3.9 ± 1.8 s−1) and other non-VCP sources of OH reactivity (7.3 ± 1.6 s−1). The emissions from use of VCPs contribute an additional 4.8 ± 3.4 s−1, bringing the summed OH reactivity to within ~25% of the observations (fig. S5). Although our inventory slightly underestimates OH reactivity, it is now within uncertainties of measurements. The inclusion of typically unmeasured or unreported oxygenated compounds from VCPs can help to resolve some of the missing OH reactivity observed over cities.

      Predicting reactivity of hydroxyl radical is important for understanding many atmospheric processes. The inclusion of VCPs into the model calculations is needed to get better agreement with experimental data.

      The agreement between experimental data and model calculations is still off by about 25%. The authors suggest that other VCPs that have not been included in the model could account for the difference.

    3. We attribute half of VOC reactivity (Fig. 4C) from petrochemical sources to VCPs and the other half to mobile and upstream sources. Because the VOC reactivity of VCPs is similar to that of transportation fuels (table S12), the distribution looks similar to that of VOC emissions (Fig. 4B).

      About half of the VOCs in air can be shown to come from VCPs, the other half comes from transportation sources (driving, etc.) and upstream sources (extracting oil, refining gasoline, making chemical products, etc.)

    4. The correspondence between our model predictions and indoor air quality measurements is high (Fig. 3D, R2 = 0.92). The model results are now consistent with typical indoor air concentrations for key markers (e.g., acetone, C9–C11 n-alkanes, ethanol, and dichloromethane) and important classes of SOA precursors, including terpenes (e.g., limonene) (41), glycols and glycol ethers (e.g., 2-butoxyethanol) (42), volatile methyl siloxanes (e.g., D5-siloxane) (43), aromatics (e.g., toluene, xylenes) (44), and heavier alkanes (e.g., C12–C13 n-alkanes) (45).

      If you just assume that VOCs in indoor air come from outdoor air sources, the model calculations and the experimental data have poor agreement.

      The model calculations agree well with experimental data if you account for VCPs that are directly emitted into indoor air.

    5. Except for formaldehyde, primary emissions of aldehydes do not appear to be good markers of fossil fuels (Fig. 3A) or VCPs (Fig. 3B) considered in this study, and are therefore excluded from our model bias and R2 calculations. One possible source of aldehydes is cooking emissions (39).

      The model calculations do not consider certain types of chemicals because they do not correlate well with emissions from fossil fuels or from VCPs. Other sources of VOCs, such as those that come from cooking, are not included in this study.

    1. This consortium degraded the PET film surface (fig. S1) at a rate of 0.13 mg cm–2 day–1 at 30°C (Fig. 1C), and 75% of the degraded PET film carbon was catabolized into CO2 at 28°C

      The data suggested that some organism that grows well in the soil around the PET recycling plant is responsible for degrading PET. The authors do not know at this point what organism is responsible or how the organism breaks down the PET fibers.

      Also note that the authors screened the different samples on low-crystallinity PET. PET is made with various degrees of crystallinity, or microscopic order, for different applications, and the authors cannot know from this data whether this same consortium would also be as effective at degrading higher-crystallinity film.

    2. Prominent pitting developed on the film surface

      Indeed, the isolated protein was found to degrade PET.

    3. appeared to be connected to each other by appendages

      The appendages allow the cells to remain close to the PET film that serves as their energy source and helps to degrade the PET more quickly.

    4. The strain represents a novel species of the genus Ideonella, for which we propose the name Ideonella sakaiensis 201-F6 (deposited in the National Center for Biotechnology Information taxonomy database under identifier 1547922).

      When the authors isolated different types of microbes, they discovered a new organism which they identified as belonging to a family of closely related organisms called ldeonella, and called it ldeonella sakaiensis or l. sakaiensis. This specific bacterium can degrade PET even in absence of all the other microbes in the consortium the authors tested earlier in the paper.

    1. In six species that historically provided 88% of floral resources for B. balteatus and B. sylvicola (18), the change in flower depth over time varied among species (F6,13 = 9.42, P = 0.0004). Species that now have shallower flowers received few (<10%) bumble bee visits historically (fig. S2A). On Pennsylvania Mountain and Niwot Ridge, short-tubed flowers show no systematic increase in abundance [coefficient of determination (R2) = 0.227, t1,4 = 1.21, P= 0.294; R2 = 0.0004, t1,9 = –0.62, P = 0.952, respectively) (fig. S2, B and C), suggesting that recent changes in floral trait distributions are insufficient to drive tongue length adaptation in bumble bees.

      Flowers typically pollinated by B. balteatus and B. sylvicola did not have a significant increase in pollinators during the recent history. This indicates that floral trait distribution are not what is causing the decrease in bee tongue lengths. This rejects the hypothesis that there is a direct correlation between flower depth and tongue length.

    2. With increasing competition from immigrant species, foraging breadth of resident bees should contract (19, 20). Yet alpine bumble bee host choice shows the opposite trend.

      For the native alpine bee species, access to food has not decreased. This rejects the hypothesis that competition between foreign and native bee species for resources decreases the native bee’s range of accessible food.

    1. We observed a statistically significant reduction in JHAMT transcript levels in the CA of starved adult female mosquitoes (Fig. 2B).

      The authors found that when mosquitoes had less sucrose to feed off of there were fewer enzymes to convert the JH acids into the juvenile hormones. These JHAMT (enzymes) are important for the final steps of JH biosynthetic pathway. If the mosquitoes drank water with 20% sucrose their JHAMT levels were significantly higher. Observations can be seen in Figure 2B.

    2. Our results reveal that starvation decreased JH synthesis via a decrease in insulin signaling in the CA. Starvation-induced up regulation of the insulin receptor increased CA insulin sensitivity and might “prime” the gland to respond rapidly to increases in insulin levels after feeding resumption. During this response to starvation the synthetic potential of the CA remained unaffected, and the gland rapidly and efficiently responded to insulin stimulation by increasing JH synthesis to rates similar to those of CA from non-starved females.

      The results of the experiment indicate that starving a mosquito ultimately decreases the production of JH due to a decrease in insulin signaling in the CA, which is located near an insect's brain. By being starved, the insulin receptor in the CA became more sensitive, so when a mosquito was fed, insulin levels rapidly increased due to this new sensitivity.

    1. Dorado showed relatively poor performance, both in absolute and size-corrected speeds,

      Dorado (also known as mahi mahi or dolphinfish) were overall the slowest, showing that they can't depend much on speed to catch their prey, rather more on their ability to maneuver to catch them.

    2. relatively high speed estimated for little tunny may partly be due to their higher muscle temperature

      Though the authors used statistical tests to determine that there was no statistically significant difference between the muscle temperatures of the fishes observed, so it shouldn't greatly affect the results, the fact still remains that it still has some effect.

      Perhaps the reason why the little tunny had the highest size-corrected maximum speed is due to muscles -which were warmed than the other fish. As a result, its muscles had a higher speed measured than if its temperature had been even closer the the other fishes' muscle temperatures.

    3. in bluefin tuna (Thunnus thynnus) the contraction time tends to increase towards the tail (see also Fig. 1A). This implies that at high speeds, muscles of opposite sides will progressively overlap their contractions towards the tail, stiffening the body.

      Unlike the other fish, the little tunny had muscle contraction times increasing from head to tail, implying that they used their head more than their tail for swimming fast. The authors compared this to another species of tuna, the bluefin tuna because it had a similar trend in muscle contraction. They analyzed this to mean that at high speeds, muscles from opposite sides of the fish (left and right) will contract so that the waves of contraction move towards each other and overlap, which makes the body stiff.

    4. Our data suggest that sailfish are not able to achieve the extremely high speeds claimed by earlier studies

      Here the author ties the goal of this study with the data collected. The goal of this study was to test whether earlier studies were correct in their estimations of maximum swimming speeds in sailfish. The author describes that the data collected disproves earlier studies and provides explanation as to why the data of the prior studies may have been skewed.

    5. sailfish appears to be the fastest

      Sailfish are the fastest of the four fish observed, but that's because they're the largest. When the variable of fish size is put aside (size-corrected performance), sailfish are actually the slowest and the smallest fish, little tunny is the fastest.

    6. on average 1.25 times faster swimming speed.

      Regardless from which part of the body the lowest contraction time (highest speed) was found, this time was used as the maximum swimming speed of that fish species. These higher measures for maximum swimming speed can be calculated about 1.25 times faster than the normal swimming speed of each fish.

    1. Given our results, we propose that the interaction between Piper and its natural enemies (mediated by secondary chemistry) is likely to play a major role in the community assembly and local coexistence of species in this genus.

      The chemical properties of Piper allow it to ensure its success. By doing this it influences other plants and animals in its community. This can include suppression of other plants, eliminating certain herbivores from the area, etc.

    2. It is important to note that, for our study system, there seem to be two distinct sets of traits that are influencing coexistence in opposite manners. While communities tend to be chemically overdispersed, the same communities are also phylogenetically underdispersed.

      The data suggest that the chemical products Pipers produce seems to be inversely proportional to their phylogenetic relatedness. So communities that tended to have a wider range of chemicals, were also the communities that were most closely related.

    3. Contrary to the effect of chemical similarity, Piper species that were closely related were more likely to coexist in a particular patch. This pattern is likely the result of other unmeasured traits that, unlike chemical similarity, are strongly conserved across the phylogenetic history of our target Piper species. One possibility could be a strong environmental niche conservatism in which closely related species are more likely to have similar habitat preferences

      Although the experiments showed that Piper species that were chemically similar were not likely to coexist, this was not the case for phylogenetically related species. The data suggest that the species who were most closely related, were actually more likely to coexist is a patch.

      There may be other traits of the Piper, other than chemical similarity, that may have an influence. The environment may push for the conservation of these traits.

    4. In our species-pair approach, we found that, independent of the measure of coexistence used, chemical similarity had a significant negative effect on species coexistence.

      The approach used in this study allowed the authors to conclude that the more similar plant metabolites are between Piper species, the least likely they are to be found next to each other.

    5. a significant positive relationship between species chemical distance and the likelihood of species co-occurrence for both species presence/absence data

      A positive relationship in this case means that the more different species are chemically, the more likely they are to coexist.

    6. The small value of K (K < 1) suggests that closely related species are less similar in their secondary chemistry than expected

      Through the presence or absence of chemicals within the leaves of the sampled species, the researchers conducted the K statistic for the phylogenetic signal of the secondary chemicals. Through this analysis, the authors found that related Piper species were less likely to share their secondary chemical characteristics.

    1. Significant implications about the social structure of this stem hominin species derive from these physical and behavioural characteristics, suggesting that reproductive strategies and social structure among at least some of the early bipedal hominins were closer to a gorilla-like model than to chimpanzees or modern humans.

      Based on the estimated sizes of the Laetoli trackway individuals at Sites S and G, the variability is most likely due to reproductive success. If the males had to compete for a chance to mate with females, larger stature would be a favorable adaptation leading to a high degree of sexual dimorphism.

    2. At the same time, these data contrast with the hypothesis of a temporal trend of body-size increase among Au. afarensis between the more ancient Laetoli and the more recent Hadar fossil samples (Lockwood et al., 2000).

      The authors concluded that hominids did not become larger in size between 3.66 and 3.2 million years ago. By combining data from the two Laetoli sites with those from the Hadar region, it was discovered that African Pliocene hominins varied in size from large-bodied to small. There was no evidence of an increase in overall body size between the older Laetoli and more recent Hadar fossil samples.

    3. The correlation between Site G and Site S cannot be absolutely undisputable, at least for the time being, because the original profile could not be examined directly. However, the geological and morphological setting of the area, as well as the characteristics of the newly exposed sequence, indicate with a very good margin of confidence that the newly discovered tracks belong to the Footprint Tuff.

      The authors are confident that the footprints at Sites G and S were made at the same time by the same hominin species.

    4. The Site S sequence does not fit the aforementioned descriptions perfectly, at least not within the observed area, which is rather narrow.

      There are some differences between the soil layers observed at Site S and the layers described for Site G. The authors attribute these differences to environmental factors. Deposition is affected by numerous factors such as the mass and size of particles and the wind.

    5. Even if the area of possible outcrop of the Footprint Tuff on gully sides close to Site S is covered by debris, the correlation between G and S is in general straightforward.

      The authors determined through an analysis of soil layers that the Footprint Tuff in Sites G and S were the same age.

    6. This may suggest a somewhat asymmetrical walking, in which the weight was sometimes loaded on the anterolateral part of the foot before the toe-off.

      The weight would be on the front side of the foot, away from the midline, before it is passed along to the toes. It is when the weight reaches the toes that the foot pushes off the ground.

    7. Numerous footprints were discovered in the new exposures (test-pits L8, M9, TP2 and M10) of the Footprint Tuff at Site S in Locality 8

      The presence of prints left by the same species of wildlife in Sites G and S helps to confirm that the Laetoli hominin prints in Sites G and S were made at the same time.

    1. In the generalized theory of relativity, the doctrine of space and time, kinematics, is no longer one of the absolute foundations of general physics. The geometrical states of bodies and the rates of clocks depend in the first place on their gravitational fields, which again are produced by the material systems concerned.

      General relativity theory expands special relativity theory to include any reference frame (not just inertial ones).

      With no constant frame of reference, general relativity theory cannot consider space and time as separable entities.

      Instead, general relativity theory describes something called "space-time" which is warped by massive bodies. Objects traveling through space-time that has been warped by these bodies will follow a warped path (even though it may appear "straight" to the object). We call this effect "gravity."

    2. Although it may be necessary for our descriptions of nature to employ systems of coordinates that we have selected arbitrarily, the choice should not be limited in any way so far as their state of motion is concerned.

      General relativity theory allows us to describe space and time regardless of a choice of coordinate systems or reference frames.

      Unlike special relativity, general relativity does not assume an inertial (i.e., static) frame of reference..

    3. It became evident that the inertia of such a system must depend on its energy content, so that we were driven to the conception that inert mass was nothing else than latent energy. The doctrine of the conservation of mass lost its independence and became merged in the doctrine of conservation of energy.

      Special relativity theory concludes a relationship between mass and energy (E=mc<sup>2</sup>).

      Therefore, the theory marries the conservation of mass and conservation of energy as one and the same law.

    4. It became evident that a statement of the coincidence of two events could have a meaning only in connection with a system of coordinates, that the mass of bodies and the rate of movement of clocks must depend on their state of motion with regard to the coordinates.

      Einstein states a major consequence of special relativity: We can only say two events occur simultaneously when those events share a system of coordinates.

      We can always put two events into the same coordinate system, but whether they are simultaneous depends on which coordinates we use.

      Einstein uses a famous thought experiment to describe this. Imagine a train traveling on railway tracks and equidistant between two trees (one ahead, one behind). If lightning strikes both trees at the same time, an observer on the train will see the lightning strike ahead before the lightning strike behind. However, an observer standing still next to the tracks (also equidistant between the trees) will see both at the same time. Thus, whether the lightning strikes are simultaneous depends on the observer's frame of reference.

    5. The second principle on which the special relativity theory rests is that of the constancy of the velocity of light in a vacuum. Light in a vacuum has a definite and constant velocity, independent of the velocity of its source.

      This is the second principle of special relativity:

      Light can be thought of as many particles (called photons) that move through space. These particles always travel at the same constant speed regardless of the inertial system in which light is observed. This has been well established by the work of many physicists.

      This means that it does not matter how fast you travel towards or away from a source of light—it will always travel at a constant velocity, the speed of light.

  5. Jul 2018
    1. the cumulative quantity of plastic waste available to enter the ocean from land is predicted to increase by an order of magnitude by 2025

      It is hoped that this number can be minimized through improved waste management techniques and infrastructure.

  6. Jun 2018
    1. The algorithm that swerved into one to save 10 always received many points, and the algorithm that swerved into one to save one always received few points

      Participants gave many points (of the 100 they were given) to the algorithm that sacrificed one pedestrian to save 10 other pedestrians, in each of the three categories listed in Figure 3B.

      Participants did not give many points to the algorithm that sacrificed one pedestrian to save one other pedestrian, in each of the three categories listed in Figure 3B.

    1. suggesting neither the SM tag nor the presence of Fab interfered with mRNA and KDM5B production and localization

      The two tags did not appear to affect the synthesis or location of the mRNA or the ribosomes.

    1. The limits of the Mediterranean vegetation types defined by biogeographers (19) broadly coincide with our simulated warm mixed forest biome

      Though this paper looks at all the plant ecosystems in the defined region, there are groups of plants that have been identified as characteristic of the Mediterranean climate, and biogeographers have identified regions where this mix of plants grow, generally distributed in the parts of the designated area that are closer to the Mediterranean Sea.

      This specific mix of plants is not one of the biome types that is defined in the BIOME4 model, but the "warm mixed forest biome" shows a similar distribution, with two main exceptions.

    2. Up to 2030, all four classes generate similar ecosystem distributions and generally remain within the bounds of Holocene fluctuations. By the end of the 21st century, RCP2.6L remains in the range of the 80th and 99th percentiles of the Holocene, whereas RCP2.6 simulates Mediterranean ecosystems as they were during the most extreme period of the Holocene (at 4700 yr B.P.), with a change of 12 to 15%.

      Starting in 2030, the simulations for all four pathways start to differ in their biome change ratios. By 2100, the 1.5°C pathway, RCP2.6L, stays within the higher end of range of variation seen during the Holocene. The 2.0°C pathway, RCP2.6, has a level of change that is only seen in the single most extreme Holocene timeslice.

      Both of the pathways with higher emissions have higher change ratios than those seen in any time in the Holocene.

    3. the projected warming in the Mediterranean basin exceeds the global trend for most simulations

      Most simulations show the Mediterranean Basin warming more than the global average.

    4. Only a 1.5°C warming scenario permits ecosystems to remain within the Holocene variability. At or above 2°C of warming, climatic change will generate Mediterranean land ecosystem changes that are unmatched in the Holocene, a period characterized by recurring precipitation deficits rather than temperature anomalies

      The modeling presented in this paper indicates that limiting warming to a global average of 1.5°C above the pre-industrial average will result in changes to ecosystems; but, those changes will be within the range of variation that was seen in the past ~10,000 years, which includes most of human history.

      However, at an average temperature increase at or above 2°C, the models indicate that the changes to the ecosystems will be far beyond what was seen in that time frame.

      In the past, ecosystem variation was largely due to reductions in rainfall and other precipitation, as opposed to the temperature-induced changes that are expected if the global average temperature increases.

  7. May 2018
    1. Two key biological traits, i.e. being epiphytic (so that its cultivation will not be at the expenses of native trees) and having renewable stem growth (enabling non-destructive, multiple-year harvesting) render Dendrobium orchids ideal for restoration-friendly cultivation.

      Based on the study where market demand of Dendrobium within TCM has diminished its population, restoration-friendly cultivation will be needed to restore this epiphytic plant species back into the environment. This form of conservation will not only help preserve the integral population of orchids in China, but also sustain the economy for its increasing demand.

    1. The special relativity theory is therefore the application of the following proposition to any natural process: "Every law of nature which holds good with respect to a coordinate system K must also hold good for any other system K' provided that K and K' are in uniform movement of translation."

      This is the first principle of Special Relativity:

      The laws of physics are the same for all observers in uniform motion relative to one another.

    1. we assumed they would interact with caterpillars more frequently than other predators

      Since the ants were found more in caterpillar at BNP authors assumed that the ants are the primary predators of caterpillars.

      Some other predators also influence caterpillar mortality, but ants are more abundant.

    2. early instar (small) caterpillars suffered higher mortality than late instar (bigger) caterpillars

      Authors ended up concluding that the smaller the caterpillars, the higher the rate of mortality.

    3. caterpillar absence assumed caterpillar mortality

      The authors conclude that since there is an absence of caterpillar it is assumed that there have been a sort of mortality for this species.

    4. that crawling predators such as ants, beetles, true bugs, spiders, and even lizards play a significant predator role

      This is a result where the authors implied that the crawling insects are the major predators of the species studied.

    5. Ants collected in pitfall traps in the canopies of Amyris elemifera and Zanthoxylum fagara: number of individuals of each species, and status

      The details of the ants captured by pitfall traps near the host plants of the Swallowtails. 5 of the 12 ant species captured were exotic and out of the total 243 individual ants caught, 144 were exotic

    1. Disease stabilization without unanticipated adverse effects, was observed in 6 of 35 patients at 12 weeks of treatment and in 5 of 35 patients at 24 weeks suggesting that Ednrb antagonists may prove useful in metastatic disease stabilization (Kefford et al., 2007) particularly when used in combination with other anticancer drugs (Berger et al., 2006; Kefford et al., 2007,).

      Disease stabilization is important in treating diseases because cancers can often become malignant, meaning they can spread to other parts of the body and cause other cancers. Therefore, this drug, together with other drugs, can prevent secondary cancers in other parts of the body (metastasis).

    2. Bosentan has also been tested in a phase II study as a single therapeutic agent for stage IV metastatic melanoma.

      Antagonist "Bosentan" was tested in a study and showed to stabilize the disease. This means that the disease is neither progressing nor regressing in development.

    3. This inhibitor was also capable of increasing cell death in culture and reducing human melanoma tumor growth in nude mice (Lahav et al., 1999). A subsequent study found that BQ788 is most effective at inducing apoptosis in metastatic melanoma cells (Lahav et al., 2004).

      The antagonist (inhibitor molecule that prevents the expression of Ednrb) also killed cells that were infected with the disease. This is another answer to the research question "If endothelin signaling were to be inhibited, would this serve as a new treatment for specific melanomas?".

    4. Ednrb small interfering RNA (siRNA) and the Ednrb antagonist BQ788 are able to block endothelin-induced effects that can lead to melanoma progression (Spinella et al., 2007). Other studies using the same antagonist have reported an inhibition of melanoma growth (Baganato et al., 2004; Lahav et al., 1999, 2004,)

      This result answers the question raised in the editors introduction: "If endothelin signaling were to be inhibited, would this serve as a new treatment for specific melanomas?". Yes, research showed that interfering RNAs (RNA molecules that prevent the expression of a gene) and a specific antagonist (another interfering molecule) can prevent endothelin signal pathways from leading to melanoma.

    5. Edn1 secretion from keratinocytes increases after exposure to UV radiation (Ahn et al., 1998; Imokawa et al., 1992, 1997; Jamal and Schneider, 2002) and it was found to have an antiapoptotic effect on melanocytes (Kadekaro et al., 2005).

      Exposure to UV radiation, such as from the sun, caused melanocytes to continue developing. This is because the programmed cell death (apoptosis) function was compromised in the presence of UV radiation. As a result, Edn1 (one type of endothelin peptide) had an increase in production and caused pigmentation to increase.

    6. Although Ednrb downregulation has been reported in some human melanoma cell lines (Eberle et al., 1999), other studies found Ednrb to be upregulated in most melanoma cell lines (Bittner et al., 2000; Ross et al., 2000). Ednrb expression was found to be enhanced in melanoma metastases compared to primary tumors and thus it has been proposed as a marker for melanoma progression (Demunter et al., 2001).

      Even though there are some contradictions to the research, generally, if there is more Ednrb activity (up-regulation) then there are more cancerous cells (melanomas). Because of this, observing the expression of the Ednrb gene can help researchers follow the progression of the disease.

    7. The placement of oncogenes under the control of melanocyte specific promoters has led to the development of melanoma in mice (Bradl et al., 1991; Broome-Powell et al., 1999; Chin et al., 1997; Kelsall and Mintz, 1998; Klein-Szanto et al., 1991, 1994; Powell et al., 1995; Wong and Chin, 2000; reviewed in Larue and Beermann, 2007), indicating that it is possible for melanoma to arise from a committed melanocyte precursor (reviewed in Grichnik, 2008). Recently, the finding that melanoma cell fractions transplanted into NOD/SCID IL2Rγnull mice are highly tumorigenic irrespective of whether or not they express the stem cell marker CD133, suggests that melanoma does not appear to follow the cancer stem cell model (Shackleton et al., 2009).

      This result contradicts the cancer cell model because the cell can be programmed to be cancerous by placing an oncogene (a mutated proto-oncogene that causes uncontrolled cell division) near a promoter (a region on DNA that allows for gene expression to occur via trascription/translation). Therefore, the cell does not have to follow the differentiation path to become cancerous.

    8. The stem cell marker-positive cells identified in melanomas were capable of self-renewal and of differentiating into various cell lineages. Furthermore, these cells were more tumorigenic when transplanted into immunocompromised NOD/SCID mice than their stem cell marker-negative counterparts.

      Because cells that contained this "marker-positive" were able to differentiate into many different types of cells, the original idea of linear progression of melanoma may not be useful in monitoring the disease. This is because the cancer can arise at different steps and differentiation points.

    9. Melanoblast numbers increased in the presence of either factor; however, treatment with both Edn3 and Kitl led to a significant increase in the number of melanoblasts compared to either factor alon

      The opposite of the previous statement is also true: If both of the signaling pathways are present, then there will be an increase of melanoblasts. This is because these pathways stimulate survival and cell division of melanoblasts.

    10. In mouse NC cultures, the lack of either Edn3 or Kitl resulted in nearly a complete loss of melanoblasts.

      This occurred because Edn3 works with Kitl (a signaling pathway) in order to stimulate the survival and cell division of melanoblasts (the cell stage that comes before the melanocyte). Therefore, the lack of these signaling pathways prevented melanoblats from forming.

    11. Ednrb signaling affects melanocyte development prior to or at E12.5.

      Mice with white coats (the piebald lethal phenotype) and mice with the inserted gene (lacZ) had a decreased amount of melanoblasts (cells that come before melanocytes) by day 12.5 in embryonic development. Therefore, Ednrb signaling must be occurring at or around this time in development.

    12. Edn1 and Edn3 have also been implicated in hyperpigmentation pathological conditions in mice

      Mice with dark, black coats were found to have hyper-pigmentation and a correlation with melanoma (tumor of the cells that produce pigment).

    13. Mutations or deletions of the mouse genes Ednrb and Edn3 result in the piebald lethal (sl) and lethal spotting (ls) phenotypes, respectively (Fig. 1). Mice carrying the piebald lethal mutation are mostly white, except for spotted regions in the head and rump. They die as juveniles

      Mice with white coats have a deadly mutation that kills the mice while they are very young. The phenotype (the physical expression from the gene) is called "piebald lethal". Mice with spotted coats have a similar outcome to mice with white coats and their phenotype is called "lethal spotting" or hypo-pigmentation (meaning lacking pigment).

    14. Edn3 was found to play a major role during the development of melanocytes from neural crest (NC) cell precursors.

      Researchers were able to determine that Edn3 plays a vital role in melanocyte development by studying the pigmentation of mice coats. The coats vary in pigment depending on the mutation on gene Ednrb.

    1. play an important role in its development

      Opiate-dependent patients might have impaired avoidance habits.

      Opiates are highly addictive drugs that are often used to treat chronic pain. Patients that are prescribed these medications sometimes experience withdrawal symptoms within hours of their last dose.

      Some patients will misuse the drug in trying to cope with chronic pain as well to avoid their withdrawal symptoms. In one study, the authors inferred that patients' avoidance response to punishment or aversive treatment would be higher compared to cocaine users, since these behaviors can make someone more susceptible to opiate addiction in the first place.

      To learn more about withdrawal management: https://www.ncbi.nlm.nih.gov/books/NBK310652/

    2. levels of impulsivity (β = 0.18, P = 0.047) and low avoidance accuracy during overtraining

      Due to impairment in brain function, CUD patients are unable to control impulses and avoid negative outcomes.

      Since CUD patients have an impairment in the brain regions that control responses to stimuli associated with both reward or punishment, it is likely that these impairments are what is giving rise to the high impulsive behaviors observed in CUD patients as compared to the control group.

    1. Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2 and HERC2 that are identical by descent from Africans.

      Crawford et al. find evidence that genetic variants associated with dark skin pigmentation have a single origin within Africa. Not only is this interesting from an evolutionary standpoint, it demonstrates that using only skin pigmentation to infer modern population structure is highly ineffective and erroneous.

      For example, if scientists wanted to explore the relationships between modern human populations, and used only the genetic variants associated with skin pigmentation to do so, they might end up lumping many of the African populations in with South Asian and Australo-Melanesian populations. Focusing solely on the genetic determinants of pigmentation would lead to inaccurate conclusions about relationships among modern human populations.

    1. We propose that appropriate plot methods, together with information from ad hoc sampling (Foster et al. 1998), will assist in the identification and monitoring of forest areas to meet conservation priorities.

      The results found from the experiment and those from ad hoc sampling can be used to enhance conservation of Neotropical forests.

      Ad hoc typically means a solution designed for a specific problem. Therefore, ad hoc sampling means a sampling method that would solve the conservation methods problem.

    2. Our analysis of the BCI dataset demonstrates how this choice of minimum diameter can influence interpretations. BCI has a relative ratio of overall richness between communities with minimum diameters of 10 cm vs. 2.5 cm that is only slightly higher than that of Yasuní

      This shows that there was higher species richness in species of 10 cm diameter versus 2.5 cm.

    3. we test a variety of plot methods to establish the most accurate and efficient way to reach this goal.

      Many different plot methods were used in order to see which method would provide better carbon and biodiversity information.

    4. A standardized rapid inventory method that provides information on both biodiversity and carbon stocks will thus represent an important tool to enhance our ability to maximize biodiversity conservation and to help quantify potential carbon emissions that result from deforestation and degradation (REDD).

      The purpose of the experiment is to find a proper method to measure biodiversity and carbon stocks of a community. Doing so will allow for better conservation methods and help quantify the amount of carbon emissions that result from deforestation and degradation of forests.

  8. Apr 2018
    1. Fig. 3 Heat storage (W m−2) for the North Atlantic for 1988–92 minus 1970–74.

      Areas where heat are being stored and the ocean warmed over the two decade period between 1970-74 and 1988-92 are colored in red with positive values. Ocean regions which are releasing heat and thus becoming colder over that period are colored in blue with negative values.

      Figure A focuses on the surface 300 m of the North Atlantic and suggest the higher latitudes, roughly 45°N to 70°N, were releasing heat while the regions below 45°N warmed over the two decades.

      Figure B looks at where heat is accumulating over the two decades from the surface down to 3000 m. From 1970-74 to 1988-92 the Labrador Sea (southwest of Greenland) and the subarctic region were cooling while the western mid-latitudes (20°N to 45°N) warmed.

      Most of the heat storage is occurring at depths below 300 m.

    2. Fig. 1 Time series for the period 1948 to 1998 of ocean heat content (1022 J) in the upper 300 m for the Atlantic, Indian, Pacific, and world oceans.

      This figure focuses on the annual anomalies in heat content of the surface 300 m of the ocean basins. Every year from 1948 to 1998 is plotted as a bar on these charts of temperature anomalies. Positive values indicate an above-average warm year, while negative values indicate a below-average cool year.

      Which ocean basins show a trend from cold, negative values to warm, positive values? Are the trends in one direction consistent over the full 50 year record or only for shorter periods of time?

      Levitus and coauthors found:

      • The Atlantic and Indian oceans overall show an increasing trend towards warming temperatures with time, a positive correlation.

      • Temperatures were cooler before the mid-1970s and warmer after that.

      • Of all the ocean basins, the North Atlantic ocean during the year 1998 saw the warmest temperatures of the last 50 years.

    3. Fig. 2 Temperature difference (°C) at 1750-m depth of the North Atlantic for (A) 1970–74 minus 1955–59 and (B) 1988–92 minus 1970–74.

      The areal extent of warming is colored in red, while the blue color represent areas that cooled between the time periods. The black contour lines are labeled with the exact extent of temperature change, where the thickest black line represents no change in temperature (0°) over the roughly 20 years between pentads.

      Figure A is presenting how temperatures have changed between the late 1950s and early 1970s in the North Atlantic at a depth of 1750 m. Much of the North Atlantic appears to be warming, excluding the Mediterranean Outflow area.

      Figure B presents the temperature change between the early 1970s and the 1990s. The Labrador Sea appears to have cooled substantially, with cooling also occurring in most of the rest of the North Atlantic.

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

      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.

    3. agricultural streams

      Poultry producer is fined by $1.4 million for polluting a local stream.

      Read more in WJCT: http://news.wjct.org/post/live-oak-poultry-producer-environmental-groups-reach-deal-over-suwannee-river-pollution

    4. Reach-scale outputs of C increased as fine POC export, as well as respiration

      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.

    5. 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.

    6. 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. In the squid light organ, the photoreceptive tissues also may function to perceive environmental light, providing the animal with a mechanism to compare this exogenous light with symbiont light emission.

      The finding that the light organ possesses the same proteins that are found in photoreceptors of the eye may mean that the light organ has the ability to sense light from both the environment and from the bacterial symbionts.

      The ability to compare the two light sources would potentially allow the squid to control the light produced by the bacteria in order to match the light in the environment.

    1. Selective logging is responsible for the conversion of at least 15 000 km2 of primary tropical forest in the Amazon each year (Asner et al. 2005; Asner, Loarie & Heyder 2010), and the resulting consequences for important ecosystem services including carbon storage and water and nutrient cycles remain unknown

      Global Changes influenced the expansion of selective logging, and brings questions about carbon emissions and the effects on recruitment and therefore diversity in forests.

    2. Our results further imply that communities may be altered by disturbance in ways significant to ecosystem processes, even when some measures of functional diversity do not change

      The authors suggest that losing or damaging communities would have considerably more negative effects on the ecosystem even if the sites are still diverse.

    3. gap edges discriminated slightly from gap centres, with a particular complement of heliophilic species (Table 2)

      Gap edges had more species that consumed higher amounts of sunlight (heliophiles).

    4. Some shade-tolerant species and some canopy taxa (Table 2) simply did not recruit into logged sites, even after 20 years

      Species that can grow in a closed forest canopy did not grow in sites that were logged after 20 years. These understory plants are important habitat and provide the forest with key services.

    5. we observed lower species evenness, as estimated by Pielou’s J, and much lower FEve, as estimated by Villéger’s FEve, in unlogged relative to logged habitats

      The authors did find that the relative number of species was lower in unlogged compared with logged habitats.

    6. We found no difference among logging habitats in taxonomic or FRic, with high richness in each of the three habitats (Fig. 2a, Table 1).

      There was no difference in the diversity of logged and unlogged habitat on either the types of species present or the functions they serve the community.

    1. These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years after human ancestors lost most of their protective body hair, though these ancestral hominins may have been moderately, rather than darkly, pigmented

      The authors conclude that darker skin pigmentation possibly appeared ~2 million years ago, in the genus Homo (which we, as Homo sapiens, are part of), and that this pigmentation may have arisen as our ancestors lost their protective body hair, which would have previously protected them from some of the harmful effects of the sun.

    2. 4.9 times lower expression in luciferase assays

      The authors explored if luciferase expression could be driven by different haplotypes; in other words, if the haplotypes had an effect on the expression of the luciferase reporter gene.

      If the expression from different haplotypes has the same distribution, the medians from the two groups would be equal, indicating that the different haplotypes have no impact on expression.

      In this case, the distribution of expression is not the same, indicating that the median expression is not equal, and the haplotypes do have an effect on on expression.

    3. These results indicate that mutation of Mfsd12 is responsible for the gray coat color of gr/gr mutant mice, and that loss of Mfsd12 reduces pheomelanin within the hairs of agouti mice.

      The authors conclude that the gr/gr "grizzled" mice are gray because of a mutation in Mfsd12, which they identified by sequencing DNA from these mice, and that losing expression of Mfsd12 leads to the same coat color phenotype in wild-type agouti mice

    4. Taken together, these results indicate that MFSD12 plays a conserved role in vertebrate pigmentation. Depletion of MFSD12 increases eumelanin content in a cell-autonomous manner in skin melanocytes, consistent with the lower levels of MFSD12 expression observed in melanocytes from individuals with African ancestry. Since MFSD12 localizes to lysosomes and not to eumelanosomes, this may reflect an indirect effect through modified lysosomal function. By contrast, loss of MFSD12 has the opposite effect on pheomelanin production, reflecting a more direct effect on function of pheomelanosomes, which have a distinct morphology (3), gene expression profile (36), and, like zebrafish pterinosomes, a potentially different intracellular origin from eumelanosomes (37). While disruption of MFSD12 alone accounts for changes in pigmentation, the role of neighboring loci such as HMG20B on pigmentation remains to be explored.

      The authors conclude that MFSD12 is important for skin pigmentation in vertebrates—they have data from humans, mice, and zebrafish, suggesting that this function is conserved in most animals.

      MFSD12 functions in a cell-autonomous manner in melanocytes, meaning the protein acts on the cell that it is in. As they saw MFSD12 localizing with lysosomes, not eumelanosomes, it doesn't seem to function by directly affecting the production of melanin; rather they suggest that it could be modifying lysosomal function leading to different levels of melanin in the cells.

      The authors note that while changes to MFSD12 have an effect on pigmentation, there are other nearby genes that might play a role as well.

    5. rs1426654 SNP between the West African Yoruba (YRI) and Ethiopian Amhara populations is 0.76

      An F<sub>ST</sub> of 0.76 here indicates that 76% of the variation in the people in these populations occurs between the two populations, whereas the remaining 24% of genetic variation occurs within the individual populations.

    6. We observe a signature consistent with positive selection at SLC24A5 in Europeans on the basis of extreme values of

      When looking at the variants in the gene SLC24A5 across different populations, the authors found that the pattern (or signature) of variants suggests that this gene is under directional, positive selection.

      Positive selection is a process leading to a particular trait being more common in the population than other traits. This leads to a higher number of low-frequency alleles than one would expect by chance, leading to an extreme, negative value of Tajima's D statistic.

      Finding a signature consistent with positive selection at this locus suggests that the particular variant that under selection may provide an advantage to the people with that variant.

    7. Additionally, most candidate causal variants are in non-coding regions, indicating the importance of regulatory variants influencing skin pigmentation phenotypes.

      The authors note that many of the variants they identified as causal are in noncoding regions, which indicates the importance of regulatory regions in controlling skin pigmentation (this means that the amount of specific proteins is important to skin pigmentation, not just having the functional proteins present).

    8. suggesting it is identical by descent.

      The authors conclude that this allele, rs4932620 (T), is identical by descent between Australo-Melanesians and Africans because the haplotype surrounding the allele is the same or similar. This suggests that they have a common ancestor.

    9. These data suggest that MFSD12 suppresses eumelanin content in melanocytes

      The authors conclude that MFSD12 normally acts to reduce eumelanin content in melanocytes, because when they reduce the amount of MFSD12 in cells they see more eumelanin. Eumelanin is brown/black pigment.

    10. MFSD12-HA localized to punctate structures throughout the cell. Surprisingly, these puncta, like those labeled by the endogenous lysosomal membrane protein LAMP2, but not the melanosomal enzyme TYRP1, overlapped only weakly with pigmented melanosomes (Fig. 6, E to G; quantified in Fig. 6H). Instead, MFSD12-HA co-localized with LAMP2 (Fig. 6E, quantified in Fig. 6H), indicating that MFSD12 protein localizes to late endosomes and/or lysosomes in melanocytes and not to eumelanosomes.

      The authors see the tagged MFSD12 protein in punctate structures, or small spots, throughout the cells. They were surprised to find that these puncta barely overlapped with pigmented melanosomes.

      They had expected to see MFSD12 localizing with (existing in the same spot as) TYRP1, an enzyme that is involved with melanin synthesis, but instead they found that MFSD12 was found in the same spots (co-localized) with LAMP2, a protein that functions in lysosomes.

    11. By studying ethnically, genetically, and phenotypically diverse Africans, we identify novel pigmentation loci that are not highly polymorphic in other populations. Interestingly, the loci identified in this study appear to affect multiple phenotypes.

      The authors have identified loci that are associated with pigmentation that were not known before, because they were the first to study such a diverse group of Africans. They note that the loci they identified have multiple effects in people, so the role for these loci in skin pigmentation may not be the only reason they are associated with particular populations.

    12. These results, combined with large FST values between Africans and Europeans at SNPs tagging the extended haplotype near DDB1 (e.g., FST = 0.98 between Nilo-Saharans and CEU at rs7948623, within the top 0.01% of values on chromosome 11, table S4) are consistent with differential selection of alleles associated with light and dark pigmentation in Africans and non-Africans at this locus.

      The authors conclude that at this particular locus, their data suggest that Africans and non-Africans have been subjected to different selective pressures that have led to different haplotypes in the two populations.

    13. Approximately 28.9% (S.E. 10.6%) of the pigmentation variance is attributable to these SNPs. Considering each locus in turn and all significantly associated variants (p-value < 5 × 10−8), the trait variation attributable to each locus is: SLC24A5 (12.8%, S.E. 3.5%), MFSD12 (4.5%, S.E. 2.1%), DDB1/TMEM138 (2.2%, S.E. 1.5%), and OCA2/HERC2 (3.9%, S.E. 2.9%). Thus ~29% of the additive heritability of skin pigmentation in Africans is due to variation at these four regions.

      The authors conclude that around 29% of the heritability (the amount of phenotype that can be attributed to a genotype) of skin pigmentation in Africans is due to changes in DNA in just four regions, which is fewer regions than they might have expected for a complex trait.

    14. Coalescent analysis indicates that the TMRCA of all lineages is 1.7 mya (95% CI: 1.5–2.0 mya) and the TMRCA of lineages containing the derived (T) allele is 629 kya (95% CI 426–848 kya) (Fig. 4). The deep coalescence of lineages, and the positive Tajima’s Dvalues in this region in both African and non-African populations (fig. S5), is consistent with balancing selection acting at this locus

      Using their mathematical models, the authors conclude that the TMRCA of the T allele, along with the positive Tajima's D value (which indicates an excess of intermediate alleles rather than rare alleles), suggest that there was balancing selection on this locus (selection to maintain multiple alleles at this locus).

    15. These results are consistent with selection for the rs1426654 (A) allele in African populations following introduction, although complex models of demographic history cannot be ruled out.

      The authors found that it is possible that the variation at the rs1426654 locus is due to selection for the A allele in African populations. However, there are other possible explanations for the variation observed that they can't rule out based on their data.

    1. The calculation of total fitness across the four life stages measured revealed that hybrid total fitness was more than 50% greater than either of their progenitors.

      This is a remarkably large increase in fitness due to hybrid. According to Dr. Geiger most plant hybrids that he's studied have shown a significant increase of 5-10% would already be impressive.

    2. The cumulative superiority of hybrids resulted in the establishment of nearly 45% more hybrid individuals than either parental type. In terms of seed germination, hybrids produced 20% more seedlings than eastern plants did. Hybrid seedlings had greater survival rates than western seedlings, with nearly 20% more living to the end of the experiment. The biomass of the resulting hybrid seedlings was also greater than that of the western seedlings; their average weight was 20% heavier.

      Hybrids had significantly better fitness in all categories tested. They germinated faster, produced more seeds, and grew to a larger size than the other types.

    3. Dry weight of harvested seedlings (i.e., biomass) was influenced by type (F ¼ 4:25, df ¼ 2, P ¼ 0:015), with hybrid seedlings obtaining greater dry weights than their western counterparts, 0:121 6 0:006 versus 0:100 6 0:005 g, respectively (fig. 6).

      Hybrid plants grew to the largest size of the three types.

    4. Mean proportion of fruit with exit hole

      Hybrids had the lowest rate of exit holes caused by predation due to the wasps, followed by eastern and western.

    5. Hybrid seeds germinated at higher rates (18:4% 6 0:009%) than eastern seeds (14:6% 6 0:008%); however, no differences were found in the germination rate of the western seeds (16:0% 6 0:007%) and the other types

      Hybrids had a significantly higher germination rate than the other two types. The other two types had no significant difference between each other. This may be a cause for hybrids higher fitness.

    1. a subset of seemingly heterogeneous autism-associated mutations

      There are many different mutations that can cause autism. The mutations described in this paper are just one type.

    2. Our finding that deletions of genes regulated by neuronal activity or regions potentially involved in regulation of gene expression in autism suggests that defects in activity-dependent gene expression may be a cause of cognitive deficits in patients with autism.

      In some patients with autism, the authors found deletions of genes involved in postnatal brain development, which are normally regulated by neural activity. They also saw deletions in regions that are important to gene expression.

      Taken together, these findings suggest that abnormalities in the expression of neural activity-dependent genes can lead to some of the symptoms associated with autism.

    3. The connection between experience-dependent neural activity and gene expression in the postnatal period forms the basis of learning and memory, and autism symptoms typically emerge during these later stages of development.

      The stages of brain development that occur after a child is born require input from the environment and regulation by neural activity. Some of this neural activity depends on a child's experiences. This is especially true during the later stages of development.

    4. The regulation of expression of some autism candidate genes by neuronal membrane depolarization suggests the appealing hypothesis that neural activity–dependent regulation of synapse development may be a mechanism common to several autism mutations.

      Several of the "candidate" genes (i.e., genes that may cause autism) the authors studied here are regulated by neural activity. Because of this, the authors suggest that disruptions in this regulation by neuron could be a potential cause of autism.

    5. Our data implicating noncoding elements in patients with shared ancestry, as well as the heterozygous nonsense changes in patients without shared ancestry, suggest that loss of proper regulation of gene dosage may be an important genetic mechanism in autism

      In addition to disease-causing autosomal and recessive mutations, the authors showed that in some cases regulatory elements and gene dosage can contribute to autism.

    6. The heterozygous changes, in particular the nonsense mutation, likely affect gene dosage and suggest that the study of consanguineous pedigrees may identify genes of importance in nonconsanguineous populations as well.

      Heterozygous mutations can be deleterious if two copies of the functional gene are required for a pathway. Even having one copy of the functional gene may not be enough.

      The authors suggest that looking at consanguineous families may help identify genes of interest in nonconsanguineous pedigrees, where there is more diversity.

    7. carried by two male siblings with autistic disorder as well as their mother

      The authors found the NHE9 nonsense mutation in two male siblings with autism, as well as their mother, who showed childhood signs of intellectual disability.

      In addition, one of the siblings had epilepsy and the other had symptoms of epilepsy (though no diagnosis).

      The authors did not find the mutation in any of the controls, even on resequencing.

    8. These transcriptional effects suggest that the homozygous deletions in autism patients may preferentially involve activity-regulated genes, either mutating their coding sequence (e.g., DIA1) or potentially affecting conserved DNA sequences (NHE9, PCDH10) that may be critical for proper transcriptional regulation.

      The different ways that homozygous deletions affect the transcription of the three genes here suggests that abnormalities in neural-activity regulated genes may play a large role in autism.

    9. Moreover, a separate screen using RNAi knock-down of NPAS4, a transcription factor activated in response to depolarization, showed that NHE9 was one of 292 out of 22,407 cDNAs (1.3%) whose transcription was significantly altered (in this case, increased) (Fig. 3D) (22), although NHE9 expression was not detectably altered by membrane depolarization alone

      Unlike c3orf58 and PCDH10, expression of NHE9 was not significantly altered by changes in neural activity alone. However, NHE9 is among a small number of genes whose transcription was altered when the neural-activity regulated transcription factor NPAS4 was inhibited.

    10. transcriptional target of MEF2

      MEF2 RNAi did not increase transcription of PCDH10 as much as it did c3orf58.

      However, a fusion protein that contains MEF2 greatly increased transcription. This suggests that, even though MEF2 alone did not increase transcription, PCDH10 is a target of MEF2.

    11. which suggests that c3orf58 may be a direct or indirect MEF2 target

      When the authors prevented MEF2 expression, they saw a corresponding inhibition of c3orf58 expression. This suggests that MEF2 either directly or indirectly mediates transcription of c3orf58.

    12. Neuronal activity induces a set of transcription factors (including MEF2, NPAS4, CREB, EGR, SRF, and others) with time courses of minutes to hours, and these transcription factors induce or repress specific target genes that mediate synaptic development and plasticity

      A significant number of the genes identified by the authors in this study were transcription factors that are involved in the growth and development of the brain.

    13. Smaller deletions (also unique to the individual family) (table S5) were closest to CNTN3, encoding BIG-1, an immunogloglobulin super-family protein that stimulates axon outgrowth (32); RNF8, encoding a RING finger protein that acts as a ubiquitin ligase and transcriptional co-activator (33); and SCN7A (amid a cluster of voltage-gated sodium channels that also includes SCN1A, SCN2A, SCN3A, and SCN9A) on 2q

      The authors found several smaller deletions in genes that are involved in the growth and development of the brain.

      The authors point out that further evidence is needed to say these genes are causative of autism. However, they suggest that several of them are likely to be (specifically the larger deletions).

    14. A second >300 kbp, linked, homozygous deletion (again not present in >2000 individuals other than this family) is closest to PCDH10 on 4q28 (Fig. 2 and table S5), which encodes a cadherin superfamily protein essential for normal forebrain axon outgrowth

      Another deletion the authors found in patient AU-3101 is in a gene that codes for a protein involved in the growth of neurons.

    15. The deletion completely removes c3orf58, which encodes an uncharacterized protein with a signal peptide that localizes to the Golgi (28). Moreover, the deletion is near the 5′ region of NHE9, such that only 60 to 85 kbp upstream

      The deletion in patient AU-3101 removes c3orf58, which codes for a protein in the Golgi apparatus.

      The deletion also removes part of the transcription initiation site for NHE9.

    1. A. berteroi is effectively pollinated by two native solitary bees

      The authors found that A. berteroi is best pollinated by bees.

      This is drawn from the fact that other visitors did not carry or deposit pollen well.

    2. The complex flower morphology of A. berteroi is similar to the morphology described for other Apocynaceae (Barrios and Koptur 2011). The flowers restrict access to only those visitors with mouthparts long enough to reach the nectar at the base of the floral tube. Furthermore, the sugar concentration of the nectar (30–67 %) is within the range of values reported for flowers pollinated by long-tongued bees (∼40 %; Proctor et al. 1996). Although Pascarella et al. (2001) stated that A. berteroi is visited exclusively by Lepidoptera, our field observations showed that long-tongued bees were common floral visitors, as well as skippers. Skippers were the most frequent and constant visitors, often visiting numerous flowers of the same species in a row.

      Apocynaceae flowers restrict visitors with mouthparts long enough to reach the base of the floral tube.

      Previous data states that the A. berteroi species is only visited by skipper butterflies. However, the authors found they are also visited by long-tongued bees to the same extent.

    3. appears that they were acting as nectar thieves.

      These butterflies were taking the reward meant for true pollinators without actually aiding the plant in reproduction.

    4. the width of the proboscis of the pollinators of A. berteroi is more important than the length in determining pollen transfer efficiency.

      This study found a correlation between the thickness and effectiveness of feeding parts used by pollinators.

      It is possible that a wide pollen receptacle results in a need to have thicker feeding parts.

    5. The final test of pollinator effectiveness, whether flowers visited by the different pollinators set fruit, provided clear results. Placing potted plants in the field, observing visits, bagging, tagging and following subsequent fruit set showed that only flowers visited by long-tongued bees set fruit following a single visit. Of the 44 flowers visited by long-tongued bees, 16 (36.4 %) set fruit. None of the flowers visited by the other pollinator groups (4 by non-skippers butterflies, 19 by skippers and 2 by short-tongued bees) produced any fruit. Fruit set differed significantly among pollinator groups (Kruskal–Wallis test, χ23=111.7, P = 0.009, n = 69). Though the sample sizes were small for non-skipper butterflies and short-tongued bees due to their lower rate of visitation (Table 2), we also found that these groups of visitors do not carry significant amounts of pollen on their proboscides; consequently, we conclude that these two groups of visitors are much less effective pollinators of A. berteroi than are long-tongued bees.

      The authors found that only flowers visited by long-tongued bees produced fruit after a single visit.

      The authors also determined that non-skipper butterflies and short-tongued bees are less effective pollinators in comparison.