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  1. Last 7 days
    1. Furthermore, partner sharing (how distinct species share resources) in SDNs on Oʻahu is structured in a complementary way among bird and plant species, giving rise to distinct modules in which certain birds and plants interact preferentially. The emergence of such structures indicates that these novel SDNs largely reproduce the well-known patterns exhibited in mutualistic networks (18) and that SDN structure is highly conserved, regardless of variation in plant and bird communities.

      The reason the introduced birds and plants integrate successfully into the ecosystem of O'ahu is because they follow the same strategies that the native plants and birds developed: creating beneficial relationships with specific species, and carefully sharing the resources of the island with other organisms.

    1. Axotomy of the petrosal neurons, separating the cell bodies from peripheral targets, resulted in a precipitous decline in TH catalytic activity and disappearance of TH immunoreactivity

      Cutting down the axons in the petrosal neurons causes a decrease in TH activity and immunoreactivity. However, there is a certain level of TH recovery after four weeks, which could be due to the regeneration or recovery of the severed axon.

    2. nicotinic receptor stimulation, with consequent depolarization or attendant transmembrane Na+ influx, or both, decrease substance P in mature sympathetic neurons, as in neonatal neurons

      With nicotinic receptor stimulation, the depolarization or the influx of sodium ions across the membrane causes a decrease in substance P in both mature and developing neurons.

    3. In culture, the (now denervated) adult ganglia exhibited a tenfold rise in substance P, mimicking the increase in neonatal ganglia

      Explants from superior cervical ganglia were obtained to address the question: is there transmitter plasticity in mature neurons? Explants were obtained from rats of age six months and one year. A ten-fold increase was observed in the activity of substance P.

    4. veratridine did not significantly alter TH-positive cell number, suggesting that depolarization increased TH per neuron rather than increasing the number of neurons.

      What could have been the cause of an increase in TH activity? The answers could be one of the two options: increase in the number of TH positive neurons in the sample or increase in the amount of TH per neuron. 

      In other words, is it an individual neuron's effect or a collective effort of all neurons in the sample? To address this, the authors decided to measure the number of TH positive cells in the control and veratridine-treated cultures. 

      The results show that the there is no difference in the number of neurons between both the group. Concluding that, there is an increase in the amount of TH per neuron individually but not in the total number of TH positive neurons.

    5. depolarizing concentrations of K+ reproduced the effect of veratridine, suggesting that depolarization per se increased TH activity

      Potassium(K+) is used as a depolarizing agent in this study. The depolarization using potassium is expected to behave similarly to the effects observed with veratridine as both the chemicals increase the influx of sodium channels.

      The authors show that, in the presence of potassium, there is approximately 35% increase in TH activity as compared to their controls.

    6. this effect was blocked by tetrodotoxin

      Tetrodotoxin is a sodium channel blocker while veratridine activates the influx of sodium. Since these two drugs act opposing to each other, we expect to have no net effect in the cultures. And that’s what was observed in the cultures exposed to veratridine in the presence of tetrodotoxin (see TTX+Ver in figure 4), there is no further effect in the TH activity as compared to their controls.

    7. These observations suggest that membrane depolarization and associated transmembrane Na+ influx decrease [Leu]enkephalin in adult medulla

      Decrease in [leu]enkephalin in adrenal medulla is dependent on two related factors: Membrane depolarization and the sodium influx through the membranes.

    8. In contrast, 4-day adult explants revealed a marked increase in proenkephalin mRNA, which paralleled the rise in [Leu]enkephalin

      At four days, mRNA of proenkephalin showed a greater increase similar to the increase observed in [leu]enkephalin in medullary explants.

    9. Our observations suggested, consequently, that opiate peptidergic and catecholaminergic traits may be differentially regulated in the adult medulla.

      The results described in the previous two sentences suggest that each class of transmitters are regulated differently in the adult medulla.

  2. Jun 2019
    1. among women with higher levels of stereotype endorsement, the end-of-semester FMCE scores were higher in the affirmation condition than in the control condition

      Values affirmation improved performance for women, especially those who endorsed the gender stereotype.

    2. men's exam scores were little affected by stereotype endorsement, regardless of condition

      Men's performance on exams was not affected by the degree to which they endorsed the gender stereotype.

    3. the values affirmation was particularly beneficial for women who tended to endorse the gender stereotype

      Values affirmation was more effective for women who believed more strongly that the gender stereotype (i.e., that men are better at physics than women) was true.

    4. suggesting that the reduced gender gap observed in this study is based more robustly on the affirmation’s positive impact on women than on its negative impact on men.

      Because women did better on all measures when they performed values affirmation, and men only performed worse according to one measure, it is likely that the reduction in the gender gap observed after the values affirmation intervention is due to women's scores improving rather than men's scores becoming worse. 

    5. affirmation negatively affected men’s exam scores

      Men who performed values affirmation did, on average, slightly worse on course exams than men who didn't perform values affirmation. However, this was not seen on all measures of success (for example, the effect was not seen on the FMCE score).

    6. The gender gap in the learning of physics concepts was substantial in the control condition (d = 0.46) (F1,304 = 6.23, P = 0.01), indicating that men improved their FMCE scores more than women over the semester. In the affirmation condition, however, this gender learning gap entirely disappeared (d = –0.12) (F1,304 = 0.96, P = 0.33), resulting in a significant gender × condition interaction [β = 0.12, t(296) = 2.13, P = 0.03].

      Values affirmation erased the gender gap in the Force and Motion Conceptual Evaluation.

      Women who did not affirm values did not increase their scores on the FMCE from the first test to the second test as much as men did. However, women who did values affirmations had score increases similar to men.

    7. more women earned B’s in the affirmation group than in the control group, whereas more women earned C’s in the control group than in the affirmation group

      Values affirmation resulted in a shift in the distribution of overall grades for women (but not men). In the values affirmation group, more women earned Bs (relative to Cs) than in the control group.

    8. The reduction in the gender gap remained evident on the final

      Values affirmation reduced the gender gap in final exam scores even though the intervention occurred several weeks before the final exam. This suggests that the effects may be relatively long-lasting.

    9. Course grades, based substantially (75%) on the exam scores, showed a similar pattern

      Values affirmation reduced the gender gap in overall course grades between men and women.

    10. the gender gap was significantly smaller in the affirmation condition than in the control condition

      The authors found that the values affirmation intervention reduced the gender gap between men and women on average exam score.

      In the control condition, men scored higher than women. However, in the values affirmation condition, there was no significant difference in scores between men and women.

    1. This high degree of similarity between novel and native-dominated networks suggests that the processes that structure interactions in such communities are largely independent of species identity and that ecological filtering occurs over relatively short (ecological) time, leading to functionally similar sets of players as compared with systems that have long evolutionary histories

      The authors concluded that novel species' interactions, developed over a relatively short period of time, still resemble much older interactions between native species.

    2. However, the lack of association between rewiring and examined factors indicates that birds and plants in the system are highly flexible and can switch partners, irrespective of abiotic conditions and the identity of species in the community.

      The authors found that neither abiotic (rainfall and elevation) nor biotic (invasive species) factors influenced the variations in plant and animal interactions measured from different sites with similar species populations.

    3. pecifically, interaction dissimilarity and the dissimilarity caused by species turnover were influenced by elevation and rainfall, but not by percent of introduced plant species (tables S6 to S9). This suggests that the environment indirectly influences interactions via effects on species distributions, including the distribution of introduced species.

      Results in the supplement section show that abiotic factors (rainfall and elevation) affected the composition of species found at a site, thereby creating different network interactions between sites.

    4. Thus, plant-animal networks appear to have distinct links (high interaction rewiring) even when the same species are present in both sites, irrespective of whether networks are dominated by native or introduced species

      The authors conclude that interactions between plant and animals in the develop their own unique structures, independent of a native of novel dominated populations.

    5. Surprisingly, only 53% of the interaction dissimilarity was due to differences in species composition among sites (βST = 0.30 ± 0.09), whereas 47% was because pairs of species that interacted in one site did not interact in another site where they co-occurred (βOS = 0.27 ± 0.07; fig. S4

      Referring to figure 3, the majority of dissimilarity across sites was due to linkage turnover, represented as the grey bars. This means that even though the sites shared similar species, the interactions were different.

    6. [interaction dissimilarity (βWN) = 0.57 ± 0.11, mean ± SE; n = 21 pairwise sites; Fig. 3 and table S5], indicating that, on average, only 43% of interactions were shared between sites despite the most common bird and plant species occurring at all sites (tables S2 and S3)

      The authors measured high levels of dissimilarity across various sites of the island, depicted as the black/gray bars in the graph of Figure 3

    7. We found that despite all interactions being novel and primarily involving introduced species, networks were structurally complex and notably similar between scales (local versus regional) and across sites.

      The authors concluded that overall, the complex network structures of island's ecosystem on both the local and regional scale remained the same, even though these networks were now infiltrated with invading plant and animal species.

    8. At the local scale, networks had low to intermediate connectance and, unlike the regional network, were not nested. Similar to the regional network, six of seven local networks were specialized and modular, presenting three or four modules (Fig. 2, fig. S3, and table S4)

      At individual sites, the authors again saw species mostly interact with only a subset of the total interactions available, with instances of specialized species interacting with birds/plants also found in networks of more generalized species.

    1. Similarly, the expression of FosB after cocaine administration was the same in mice exposed to nicotine 14 days earlier and in mice without previous nicotine exposure

      In contrast to the results we obtained with 7 days of nicotine treatment paired with cocaine, these animals did not show any change in the magnitude of LTP, no increase in locomotor activity of in FosB gene expression.

      This indicates that the priming effect of nicotine can occur only when the drugs are given in a close window and not otherwise.

    2. Theophylline-treated mice also showed a reduction in levels of acetylated histone H4

      A reduction in acetylated levels of histone H4 was observed

    3. The acetylated chromatin induced by nicotine exposure would then allow greater FosB gene expression in response to cocaine injection than FosB gene expression after cocaine alone.

      Figures 5 and 6 suggest that the nicotine inhibits HDAC activity, thereby causing global acetylation in the striatum and affecting gene expression.

      In response to cocaine, this acetylation is further enhanced, thus allowing a more significant response in gene expression.

    4. exhibited no increase in FosB mRNA expression in response to cocaine, although cocaine alone increased FosB expression by 176%

      FosB gene expression is also reduced in mice treated with theophylline and cocaine compared to theophylline alone.

    5. Both groups showed a comparable increase in LTP. However, the theophylline-treated mice exhibited an attenuated LTP reduction in response to cocaine treatment

      As expected, in LTP experiments, the mice treated with theophylline and cocaine injections showed a decrease in the magnitude of LTP compared to mice treated with theophylline alone.

    6. Similar to nicotine alone, SAHA alone did not cause a depression in LTP

      SAHA alone did not impair LTP just like nicotine did not impair LTP.

    7. SAHA pretreatment fully simulated nicotine pretreatment and induced a greater reduction in LTP in the core of the NAc than did cocaine alone

      Pretreatment with SAHA followed by cocaine caused a dramatic decrease in the magnitude of LTP response at 180 mins. These results suggest that nicotine does inhibit HDAC activity.

    8. we found that a single cocaine injection after local pretreatment with SAHA for 7 days resulted in 142% more FosB mRNA expression than without pretreatment with SAHA

      Further, when SAHA was infused into nuclear accumbens for 7 days followed by cocaine injection, the FosB expression levels and acetylation of histone residues in striatum increased than the pretreatment with SAHA.

    9. observed a 71% increase in FosB expression in the pretreated mice compared to mice treated with cocaine alone

      Similar to nicotine, SAHA increased the FosB expression levels by 71% and caused acetylation of histone residues in the striatum.

    10. there was a 28% reduction in HDAC of mice treated for 7 to 10 days with nicotine

      28% reduction in HDAC activity was measured in animals treated with nicotine, suggesting that the nicotine inhibits the HDAC activity, thereby decreasing deacetylase activity.

    11. 7 days of nicotine treatment (10 μg/ml) increased histone H3 and H4 acetylation by 32 and 61% in the whole striatum, compared with controls treated with water, much as it did at the FosB promoter

      Again, there was an increase in acetylation levels of H3 and H4 in the striatum.

      These results suggest that the nicotine increases the effect of cocaine on FosB expression by increasing the acetylated residues in FosB, thereby enhancing chromatin reorganization.

    12. We found that, after 7 days of nicotine treatment (10 μg/ml), acetylation of both histone H3 and histone H4 was increased by 34 and 39%, respectively

      Authors observed the acetylation of histone H3 and H4. It is shown that both H3 and H4 got acetylated after a single dose of cocaine injection and after nicotine pretreatment.

    13. The effects on FosB expression are unidirectional; nicotine primes the cocaine response, but cocaine does not prime the nicotine response

      This suggests that the nicotine precedes cocaine and not in the reverse order.

    14. We found that 7 days of cocaine treatment blunted rather than amplified the effect of nicotine on FosB expression in the striatum when compared to the response to nicotine alone.

      On the contrary, the increase in FosB expression we observed in nicotine pretreatment is entirely absent with the cocaine pretreated animals.

    15. Chronic nicotine administration produces changes in gene expression in the brain so that, after nicotine, the brain responds differently to cocaine with respect to long-term synaptic changes

      It could be that the nicotine causes a gene expression in animals. This primed response serves as a precursor for the brain to respond differently to cocaine to produce long term plasticity changes.

    16. As in the behavioral and physiological experiments, 24 hours of nicotine pretreatment produced quite different results from the 7-day treatment and did not lead to an increased FosB response to cocaine

      On the contrary, FosB expression was increased only in animals that received a cocaine injection after 7 days of nicotine treatment and not in 24 hours of treatment.

      This suggests that the long term nicotine effect is responsible for the changes in gene expression.

    17. we found that both 24 hours and 7 days of administration of nicotine (10 μg/mg) in the drinking water caused 50 and 61% increases in FosB expression

      Both 24 hours and 7 days of nicotine administration caused an increase in FosB expression by 50% and 61%.

    18. Treatment with cocaine alone for 7 days or cocaine treatment for 7 days followed by 24 hours of nicotine treatment did not alter LTP

      However, mice treated with cocaine show a 17% decrease in the observed LTP.

    19. The reduction started immediately after the high-frequency stimulation (HFS) and persisted for up to 180 min compared with cocaine alone

      In this experiment, the authors wanted to determine if the sequential drug use of cocaine can alter the cocaine-induced synaptic plasticity.

      After high-frequency stimulation (HFS), mice treated with nicotine alone or water exhibit LTP that lasts for 180 mins. Mice pretreated with nicotine combined with cocaine injection show a dramatic reduction (~40%) in the observed LTP.

      This suggests that the changes in LTP in nucleus accumbens is caused by pre-exposure of nicotine to the mouse.

    20. We found that the rate of cocaine dependence was the highest among cocaine users who initiated cocaine after having smoked cigarettes

      Similar to the results obtained from animals, the individuals who started using cocaine were also active smokers, i.e., they initiated cocaine after smoking.

    21. mice pretreated with nicotine showed a 78% further increase in preference for the cocaine-coupled chamber compared with mice treated only with cocaine, with no previous exposure to nicotine

      Mice pretreated with nicotine coupled with cocaine injections showed a further 78% increase in preference to cocaine-coupled chamber than cocaine-treated animals.

      This suggests that persistent treatment of nicotine for 7 days increases the locomotor activity and behavioral responses of the animals

    22. Cocaine alone increased place preference by 223% compared with saline control

      The experiment was performed to determine the behavioral response in the 4 groups of animals.

      Do these animals have a conditioned place preference or aversion to cocaine? If the place preference to cocaine exists, which group out of 4 show the most sensitization to the CPP?

      In the conditioned place preference test, mice pretreated with cocaine alone showed preference to the cocaine-coupled chamber by 223%.

    23. Mice treated with nicotine for 7 days followed by cocaine showed a significant enhancement of 98% in locomotor activity compared with mice treated with cocaine alone

      Mice treated with nicotine for 7 days, followed by cocaine for 4 days show a 98% increase in locomotor activity than the control mice

    24. Mice treated only with cocaine showed a 58% increase in locomotion (sensitization) compared with controls

      Mice treated with an injection of cocaine for 4 days show a 58% increase in locomotor activity than the control mice

    25. Mice treated with nicotine (50 μg/ml) showed the same levels of locomotion (that is, no increase in locomotion compared to day 1) as water controls.

      There is no difference in the distance traveled by the animals that were treated with nicotine in drinking water versus drinking water. (yellow vs. black bars, fig 1A).

    1. We propose that many of the ecological surprises that have confronted society over past centuries—pandemics, population collapses of species we value and eruptions of those we do not, major shifts in ecosystem states, and losses of diverse ecosystem services—were caused or facilitated by altered top-down forcing regimes associated with the loss of native apex consumers or the introduction of exotics.

      The disruption of many biological processes and natural ecosystem functions can be traced to the loss of predators shifting systems to a new state. Alternatively, introducing invasive exotic species that may outcompete native organisms, removing food sources of predators/herbivores, may cause ecosystem collapse via trophic cascade.

    2. Bottom-up forces are ubiquitous and fundamental, and they are necessary to account for the responses of ecosystems to perturbations, but they are not sufficient. Top-down forcing must be included in conceptual overviews if there is to be any real hope of understanding and managing the workings of nature

      Given the numerous instances of trophic cascades noted in the literature, and the critical impacts that top-down forcing can have as noted above, it is necessary for researchers to consider both bottom-up and top-down controls when looking at ecosystem function, change, and decline.

    3. Many practicing ecologists still view large animals in general, and apex consumers in particular, as ecological passengers riding atop the trophic pyramid but having little impact on the structure below.

      There has previously been lack of appreciation for the role that top-down forces can have within a system, often until those organisms are removed.

      The authors are calling for a change in the lens through which ecosystem ecologists view the role of these species. Specifically, that the working hypothesis of ecosystem ecologists should be that apex consumers play a fundamental role in any particular ecosystem's structure and stability until empirical research indicates otherwise.

    1. Based on retrograde rabies virus and anterograde AAV tracing, ZI axonal projections to the excitatory neurons of the PVT appear more robust than those from other known regions of the brain involved in food intake, suggesting the ZI is not a minor component

      More so than any region of the brain studied so far, ZI GABA neurons and their projections promote binge-like eating behavior.

    2. Bic attenuated photostimulation-evoked feeding (Fig. 2K). That Bic did not completely block photostimulation-evoked food intake could be a diffusion limitation of Bic after application, or ZI VGAT-Cre neurons may coexpress other neurotransmitters responsible for the remaining action.

      The authors found that blocking the function of the GABA receptor (GABA<sub>A</sub> receptor) in the PVT could blunt the increase in food intake mediated by stimulation of ZI terminals in the PVT. This suggests that GABA is an important neurotransmitter underlying this effect.

      The limitations of this approach include that the authors cannot control the spread of the GABA<sub>A</sub> receptor blocker or that other neurotransmitters might be involved.

  3. May 2019
    1. Stimulation of PSTh glutamatergic neuron terminals in the PVT inhibited food intake (Fig. 4L).

      PVT vGlut2 neurons decrease food intake. Therefore stimulation of excitatory neurons upstream of them, i.e. the vGlut2 PSTh neurons was also found to increase food intake.

    2. Brain slice electrophysiology confirmed that optogenetic activation of PSTh glutamatergic neuron terminals in the PVT evoked strong glutamate-mediated postsynaptic excitatory currents in PVT vGlut2-GFP neurons, suggesting a functional role for PSTh glutamate neurons in the synaptic excitation of PVT glutamate neurons

      The authors confirmed that stimulation of the PSTh terminals in the PVT was able to activate PVT neurons, i.e. induce excitatory activity in the PVT cells.

      This confirms the rabies tracing result and shows that the connection between the PSTh and the PVT is functional.

    3. In the absence of available food, optogenetic activation of the VGATZI-PVT pathway evoked a significant preference for the chamber associated with laser stimulation compared with the control chamber

      The mice preferred to spend more time in the compartment where they received stimulation of the ZI-PVT pathway. This suggests that stimulation of the neurons is pleasurable for the animal.

    4. This is almost 100 times faster than that reported for optogenetic stimulation of the AgRP neuron soma and 500 times faster than stimulation of AgRP-PVT axon terminals (19, 20). As soon as the laser was turned off, the mice stopped eating.

      The authors wanted to compare the latency of eating onset upon stimulation of ZI projections to the PVT versus that of agRP neurons, which are known to promote food intake in response to hunger.

      They found that mice start to each much faster than mice did in previous reports where AgRP neurons were stimulated or when agRP projections to the PVT were stimulated.

    5. ZI GABA neurons project to multiple brain regions, including the hypothalamus and midline thalamus (fig. S6). We therefore measured the relative contribution of stimulation of ZI somata with selective stimulation of ZI axons targeting the PVT. Stimulation of ZI VGAT cell bodies or VGATZI-PVT terminals in the PVT evoked similar levels of feeding

      This suggests that even though ZI GABA neurons project to other brain regions in addition to the PVT, the PVT projection appears to be the most important mediator of increased food intake.

      This is because ZI GABA cell body stimulation and stimulation of the projections to the PVT evoked similar degrees of food intake.

    6. In our monosynaptic retrograde tracing with Cre-dependent rabies virus, although less robust than the projection from the ZI, we found a substantial projection to PVT glutamate neurons from the parasubthalamic nucleus (PSTh) (Fig. 4I and fig. S11) (27, 28).

      Analysis of the inputs to PVH vGlut2 neurons showed that these neurons receive input from the parasubthalamic nucleus, a brain region with previously described roles in appetite.

    7. Food deprivation lasting 24 hours increased inhibitory synaptic neurotransmission to PVT glutamate neurons

      In food-deprived mice, PVT glutamate neurons receive more inhibitory inputs compared to fed mice. These may come from ZI inhibitory GABA neurons, which the authors demonstrated to have increased activity upon food deprivation.

    8. confirmed that PVT glutamate neurons receive strong and direct innervation from ZI neurons

      The authors confirm their anterograde tracing findings using retrograde tracing to show that ZI GABA neurons send projections to excitatory neurons in the PVT.

    9. Food deprivation lasting 24 hours increased ZI GABA neuron activity and excitatory neurotransmission to these neurons

      Recordings made in brain slices show that ZI GABA neurons fire more i.e. are more active in food deprived mice. Further, inputs from other neurons that excite/activate ZI GABA neurons are increased.

      See this video that explains how information is transmitted between neurons: Molecular mechanism of synapse function

      Therefore, increased ZI GABA neuron activity correlates with hunger.

    10. VGAT-Cre mice with ChIEF expression, bilateral laser stimulation (20 Hz) in the ZI increased food intake

      When ZI GABA neurons are activated by delivering blue light into the brains of the mice, the mice eat a large amount of food.

    11. ChIEF-tdTomato was selectively expressed in ZI GABA neurons

      The optogenetic tool ChIEF-tdTomato was found to be expressed only the ZI GABA neurons.

    12. Ghrelin, a hormone that signals a reduced gut energy state (12), excited ZI GABA neurons and increased excitatory synaptic input onto these neurons (Fig. 1, K to M, and fig. S2).

      Ghrelin is produced in the stomach. Its synthesis is increased by food deprivation.

      Application of Ghrelin to the brain slices containing ZI GABA neurons increases their activity similar to food deprivation.

    13. Satiety feedback signals can thus attenuate ZI-induced feeding.

      Signals from the body inform the brain that sufficient food has been eaten (satiety). These include release of hormones from the gut as well as stomach distention.

      The finding that ZI-stimulated mice will not eat indefinitely suggests that satiety feedback mechanisms are still intact.

    14. In control mice with tdTomato expression, consumption was only 4% of their 24-hour intake during the same period (Fig. 1E).

      Lack of food intake in a control animal that was injected with an AAV expressing only a fluorescent protein shows that the result seen in ChIEF expressing mice was not due to non-specific effects of AAV injection or protein expression in the neurons.

    15. Photostimulation of ZI-PVT inhibitory axons evoked gnawing, but not eating, of nonnutritional wood sticks (fig. S5, A and B); photostimulation leading to food intake eliminated subsequent evoked stick gnawing. A priori wood gnawing had no effect on photostimulation-evoked food intake (fig. S5, C and D).

      The authors conclude that the food intake seen with ZI stimulation is not because the manipulation increases gnawing behavior directed at any object, but directs behavior towards edible sources of food.

    16. Although mice prefer sweet and high-fat foods when stimulation is off,

      Mice will avidly consume high-fat and sweet foods even when not hungry. This is because these foods are palatable, meaning that they are pleasurable or rewarding to eat and so will be consumed even when nutrition requibments are met.

    17. After the days of photostimulation were completed, mice showed a significantly reduced food intake compared with that of controls (Fig. 3H).

      The authors measured daily food intake for 15 days during the stimulation protocol. They then continued measuring daily food intake in the absence of stimulation.

      The mice likely reduced their food consumption when the stimulation protocol ceased due to satiety signals that normally prevent overeating in the absence of the manipulation of the ZI to PVT pathway.

    18. Ablation of ZI GABA neurons decreased long-term food intake and reduced body weight gain by 53% over 8 weeks (Fig. 3, J and K).

      When the ZI GABA neurons were killed, the mice could no long maintain their normal body weight and ate less food than control mice that had their ZI GABA neurons intact.

      This suggests that these cells are required for normal food intake and body weight maintenance.

    19. Ablation of PVT vGluT2 neurons substantially increased both food intake and body weight gain for an extended period (16-week study) (fig. S10, G and H).

      The increase in food intake and body weight gain with PVT neuron ablation shows that these cells are important for body weight maintenance.

      This finding is opposite to what was found when ZI GABA neurons were ablated, suggesting that PVT neurons are downstream of ZI GABA neurons and have an opposing effect on food intake and body weight.

    20. photostimulation of ZI VGAT-ChIEF-tdTomato terminals in the PVT evoked GABA-mediated inhibitory currents in PVT vGlut2-GFP neurons (Fig. 2D).

      Stimulation of ZI GABA neuron projections (terminals) in the PVT with blue light led to inhibition of PVT excitatory neurons.

      This finding confirms the rabies tracing result and shows that the connection between ZI neurons and PVT neurons is inhibitory.

    21. In spite of the light aversion, photostimulation of VGATZI-PVTterminals significantly increased the time mice spent on the illuminated side to 61% when high-fat food was available (Fig. 3D). Photostimulation increased high-fat food intake in bright light (Fig. 3E).

      Mice that received stimulation of ZI GABA terminals in the PVT activated spent more time in the light compartment in the presence of high-fat food even though mice usually avoid places that are brightly lit.

      This means that the stimulation of the ZI to PVT projection was able to overcome the aversive nature of the light.

    1. The experimental proof of the colinearity of a gene and the polypeptide chain it produces may be confidently expected within the next year or so.

      Crick proposed that a gene was a linear sequence of nucleotides, where each gene encoded a single protein. However, this explanation is a bit too simplistic, especially for higher-level and multicellular organisms.

      In fact, we now know that colinearity is generally the exception, not the rule, in eukaryotic genomes.

      For more information, check out this piece in Nature Education: https://www.nature.com/scitable/topicpage/what-is-a-gene-colinearity-and-transcription-430

    2. That is, either (+ with + with +) or (- with - with -). Whereas a single + or a pair of them (+ with +) makes the gene completely inactive, a set of three, suitably chosen, has some activity.

      DNA with only one additional base generates a completely different protein than that of the original code. The same is true of DNA with two additional bases.

      However, when bases are added in triplets, the generated protein is identical to the native protein with one minor difference: an extra amino acid.

    3. The preliminary results presented so far disclose no clear difference, with respect to the code, between E. coli and mammals, and this is encouraging (10, 13).

      Since mammals and E. coli (a bacterium) are extremely different biological species, it is remarkable that their genes are comprised of identical genetic codes. Their similarity suggests the genetic code is not different per species, but universal across all living organisms.

    4. It is possible that some triplets may code more than one amino acid—that is, they may be ambiguous.

      While most amino acids are encoded by at least two codons (with the exception of methionine and tryptophan), the reverse is not true. Each codon specifies just one amino acid or stop signal. Thus, the genetic code is unambiguous.

    5. In general, more than one triplet codes each amino acid.

      In other words, the same amino acid is coded by more than one base triplet. For example, there are six different codon combinations to encode arginine. This property is now known as degeneracy.

    1. reduced contact area that slide against the DLC surface, achieving an incommensurate contact

      With a combination of materials (graphene, nanodiamond particles and DLC), the researchers where able to demonstrate the formation of nanoscrolls, which reduced the overall contact area between two sliding interfaces, leading to substantially decreased friction.

    1. One of these regions (~525 kb in size) showed the strongest differentiation in all three contrasts. The region included four genes: high mobility AT-hook 2 (HMGA2), methionine sulfoxide reductase B3 (MSRB3), LEM domain-containing protein 3 (LEMD3), and WNT inhibitory factor 1 (WIF1).

      This index scan allowed the researchers to narrow down the region that showed the strongest differences between the large, medium, and small ground and tree finches.

    2. The results suggest that the phenotypic effects of these loci are small relative to the effect of the HMGA2 locus.

      The investigators were able to rule out the six other loci that may have been associated with beak size, body size, or beak shape.

    3. This SNP showed a highly significant association with beak size, a significant association with body size, and no association with beak shape among medium ground finches (Fig. 2E).

      Investigations within the HMGA2 gene showed that it did, in fact, show a high relationship with beak size.

      This seems to confirm the fact that HMGA2 played an important role in the evolutionary shift in beak size during the drought.

    4. Our results provide evidence of two loci with major effects on beak morphology across Darwin’s finches. ALX1, a transcription factor gene, has been associated with beak shape (15), and here we find that HMGA2 is associated with beak size.

      Coupled with the team's previous study that showed the ALX1 gene controlled beak shape, this study shows evidence that HMGA2 is associated with beak size.

      These findings show how scientific researcher builds upon itself to continue to not only answer questions, but to continue to ask questions.

    5. We have shown that the HMGA2 locus played a critical role in this character shift. The selection coefficient at the HMGA2locus (s = 0.59 ± 0.14) is comparable in magnitude to the selection differential on the phenotype and is higher than other examples of strong selection, such as loci associated with coat color in mice (s < 0.42) (25). The main implication of our findings is that a single locus facilitates rapid diversification.

      This single HMGA2 locus seems to allow for diversity among finch beak size. However, the exact mechanism for how HMGA2 controls beak size in finches is unknown.

      Would the findings of this study provide enough justification for further studies that would attempt to better understand that function of HMGA2?

    6. Thus, we conclude that the relationship between HMGA2 and fitness was mediated entirely by the effect of this locus on beak size or associated craniofacial bones or muscles; developmental research will be necessary to reveal the underlying mechanism for the association. There is no evidence of pleiotropic effects of the gene on other, unmeasured, traits affecting fitness (table S5).

      The HMGA2 gene is strongly associated with beak size. Beak size is the main factor that allowed some medium ground and tree finches to survive after a drought.

      Thus, the researchers provided a direct link between this particular gene and the fitness of finches.

    7. Segregation is mainly observed in species with intermediate size (medium ground and tree finches).

      In contrast to haplotypes present in large and small finches, the medium-sized finches tended to inherit the particular genes from both parents.

      This is what we may call heterozygous condition.

    8. revealed two major haplotype groups associated with size; 98% of small birds (body weight <16 g) clustered into one group and 82% of the large birds (body weight >17 g) clustered into the other (Fig. 1D). The split between the two haplotypes occurred before the divergence of warbler and nonwarbler finches at the base of the phylogeny (Fig. 1D), about 1 million years ago (Fig. 1C).

      Why was it important to not only construct a phylogenetic tree based on the entire genome sequences (Fig. 1C), but also construct one based on the HMGA2 region (Fig. 1D)?

      What do these two trees reveal about the differing sizes of finches?

    9. Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59).

      After the drought, medium ground finches wither larger beaks were at a severe disadvantage because they could not compete for food with the large ground finch.

      When a genotype is shown to be disadvantaged, what happens to the genes in that gene pool? What happens to those disadvantaged individuals? What happens to the population as a whole?

    10. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin’s finch species with different beak sizes.

      For the first time, researchers have been able to find a gene that controls beak size in Darwin's finches. Why is this finding such an important part of the story of these birds and how they evolved?

    1. Thus, although introduced birds are critical for seed dispersal in the ecosystem, they are primarily dispersing introduced plants (only 6.7% of interactions involved native plants).

      The authors concluded that the majority of plants and animals involved in the seed dispersion networks were introduced species, and that it was primarily the introduced plant seeds being dispersed by the birds.

    2. Oʻahu’s SDN included 15 bird and 44 plant species connected by 112 distinct links (Fig. 1)

      The authors identified 44 different plant species and 25 different birds in O'ahu. Figure 1 depicts each bird (left column) and each plant (right column) as rectangles. The lines connecting a bird to a plant represents a seed dispersal event.

    1. in-class exam scores by approximately 61% and entirely eliminated the gap on the FCME

      Taking into account pre-existing differences in students' preparation for the class, values affirmation was highly effective in reducing or eliminating the gender gap.

    1. The transient nature of REPAIR-mediated edits will likely be useful for treating diseases caused by temporary changes in cell state, such as local inflammation, and could also be used to treat disease by modifying the function of proteins involved in disease-related signal transduction.

      Compared to DNA editing, RNA editing is temporary and can be reversed more easily. This means that RNA editing with REPAIR can be used not only to correct inherited mutations that cause disease, but disease-causing mutations that arise later in life. While DNA editing could treat a mutation that occurred later in life, the treatment would be permanent. RNA editing could treat something temporarily, so it could be used for temporary cell growth or inhibition of imflammation in response to an infection.

      The programmability of RNA and DNA editing by simple base pairing rules makes it much easier to develop than alternative therapies such as drug inhibitors that are targeted to specific enzymes. Finding an inhibitor that is specific enough without causing side effects is difficult. The REPAIR system is a potential solution to this precision problem.

    2. can target either the sense or antisense strand

      Cas9 (as the targeting unit of the DNA base editor) can be directed against the sense or antisense strand. The gRNA pairs with the strand, causing a short sequence of the opposite strand to be displaced. Then, the "free" fragment is accessible for the cytidine deaminase that acts on single-stranded DNA.

      This means that DNA base editors can be used to correct mutations in either strand. By contrast, RNA editors can only work with the mRNA which limits their editing ability two times.

      In contrast, REPAIR is not constrained by PAM, PFS, and other motifs, meaning it can act on a broader range of sequences (but can only act on transcripts).

    3. The lack of motif for ADAR editing, in contrast with previous literature, is likely due to the increased local concentration of REPAIR at the target site owing to dCas13b binding.

      Previously, it has been shown that the ADAR proteins prefer certain nucleotides at the 5' and 3' positions next to the target sequence (reference 21). However, this is not a strict preference, and some mutants are more strict than others.

      In addition, previous work has shown that when ADAR2 is site-specifically directed at a target, its local concentration is increased and less favorable reactions sometimes occur. 

    4. Deeper sequencing and novel inosine enrichment methods could further refine our understanding of REPAIR specificity in the future.

      In this work, the authors used next-generation sequencing to detect editing events. They compared the obtained sequences (reads) with the genomic sequence. If the genome contained A but the read had G at the same position, they considered that an editing event.

      However, this approach may overestimate the number of edits. First, the sequencing itself generates errors that can be mistakenly attributed to ADAR activity. Second, the gene may have many versions in a genome that differ at some positions, including A>G differences. This leads to some ambiguity in data interpretation.

      To make up for these problems, several approaches have been suggested to detect inosine modification directly, including chemical modification and antibody-based enrichment. Post publication of this paper, newer techniques have been introduced that could be used for chemical modification.

    5. it is unlikely to do so in this case because Cas13b does not bind DNA efficiently and because REPAIR is cytoplasmically localized.

      ADAR activity on DNA-RNA heteroduplexes might be a problem for precise RNA editing by REPAIR. Fortunately, Cas13b predominantly binds RNA and the REPAIR system is sequestered from the DNA in the cytoplasm as a result of the nuclear export sequence (NES) fused to Cas13b.

    6. The overlap in off-targets between the targeting and nontargeting conditions and between REPAIRv1 and BoxB conditions suggests that ADAR2DD drives off-targets independent of dCas13 targeting

      In summary, the authors found two pieces of evidence supporting the hypothesis that the ADAR2 deaminase domain is the main source of off-targets:

      First, they found overlap between the off-target effects of REPAIRv1 under different targeting conditions and ADAR2(DD).

      Second, they saw overlap in the off-target effects between REPAIR and ADAR2(DD) in a completely different targeting system. This offers strong support that ADAR2 drives off-target effects regardless of the targeting module.

    7. Given the high number of overlapping off-targets between the targeting and nontargeting guide conditions, we reasoned that the off-targets may arise from ADARDD.

      The authors found a lot of overlap between the off-target effects they saw in the targeting and non-targeting conditions, meaning that the REPAIRv1 complex was modifying adenosines even when the gRNA did not guide it. This suggests that ADAR is increasing off-target editing effects independent of dCas13b.

    8. These results indicate that Cas13a and Cas13b display similar sequence constraints and sensitivities against mismatches.

      The researchers found that Cas13a and Cas13b had the same sequence requirements for successful target recognition and cleavage. Neither nuclease was affected by changes to the PFS sequence, but both of them functioned less well when there were changes in the middle of the target sequence.

      Another consequence of these findings is that, because changes to PFS sequences (which are at the edge of target sequences) don't affect Cas13 activity, off-target mRNA molecules that differ from the target only in PFS sequences might be mistakenly destroyed by Cas13.

      Fortunately, because of its length (more than 30-nt), the spacer is highly specific and binds unique sequences.

    9. found that PspCas13b had consistently increased levels of knockdown relative to LwaCas13a (average of 92.3% for PspCas13b versus 40.1% knockdown for LwaCas13a)

      As you can see on the figures 1C and 1D, the blue line corresponding to the PspCas13b nuclease goes far beyond the red line which corresponds to the LwaCas13a nuclease.

      The signal of the Gluc luciferase that resulted from the PspCas13b knockdown was around 10% for all gRNA molecules along the transcript. This means that the average knockdown efficiency was 90%. The signal of Gluc in the case with LwaCas13a was not as consistent, but on average dropped by about 40%.

    10. We selected the top five Cas13b orthologs and the top two Cas13a orthologs for further engineering

      Several Cas13a and b orthologs decreased Gluc luciferase signal in up to 10-30% of the control cells. Some Cas13b nucleases demonstrated even greater effectiveness than the previously characterized Cas13a from Leptotrichia wadei.

    1. which enables maximum regeneration with minimal temperature increase

      This means that the water desorption process is highly efficient, not requiring a large amount of energy from heat.

    2. By considering both the adsorption and desorption dynamics, a porosity of 0.7 was predicted to yield the largest quantity of water.

      The results of the simulations show that if the porosity is too low, the adsoprtion process becomes slower. In contrast, if the porosity is too high, more MOF is required to harvest the same amount of water but the process is slower. The simulations showed that the ideal porosity was 0.7.

    3. We also report a device based on this MOF that can harvest and deliver water (2.8 liters of water per kilogram of MOF per day at 20% RH) under a nonconcentrated solar flux less than 1 sun (1 kW m–2), requiring no additional power input for producing water at ambient temperature outdoors.

      In this study, the authors demonstrate that a MOF-based device can harvest water from the atmosphere at humidity and temperature conditions similar to a desert, without requiring any more energy than natural sunlight. Since this paper was published, the authors published another paper with the results of a devise test in the Arizona desert. In the "Related Content" tab, see their 2018 Nature Communications paper.

  4. Apr 2019
    1. Our experimental studies confirm that the stable superlubricity regime occurs over a wide range of test conditions; when the load was changed from 0.5 to 3 N, velocity was varied from 0.6 to 25 cm/s, temperature increased from 20°C to 50°C (fig. S15), and the substrate was changed to nickel or bare silicon (fig. S16).

      Superlubricity experiments at any sliding interface should follow certain local load and sliding velocity conditions. Thermal effects are also dominant in frictional energy dissipation during sliding. Authors have tested a wide range of experimental conditions and shown that their system exhibits stable superlubricity under the tested conditions.

    2. nanodiamonds can activate, guide, and stabilize the scrolling

      The mechanism of superlubricity in the present system is explained. Authors found that nanodiamonds play a key role in the scroll formation and hence in facilitating the near zero friction state.

    3. The superlubricity is thus attributed to (i) reduction in the interfacial contact area (>65%) and (ii) incommensurability between DLC and graphene scrolls.

      The mismatching of the lattices at the sliding interfaces prevents interlocking of atoms, resulting in near zero friction. In the present case, a perfectly incommensurate surface along with reduced contact area benefited from the graphene scroll formation contributed to superlubricity.

    4. The tribological evolution of a single graphene patch at the nanoscale resembles that of a single asperity contact, whereas the mesoscopic behavior resembles a multiple asperity contact. The friction mechanism at the mesoscale for an ensemble of graphene patches is not different from nanoscale (single patch). The initial tribological state of the patches, as well as the configuration of the patches versus nanodiamonds, dictates the dynamics of scroll formation, which in turn affects the dynamical evolution of COF for the mesoscopic system

      The mechanism of friction reduction at the macroscale is found to be the same as that at the nanoscale. At the macroscale, nanoscrolls at different orientations are observed while an assembly of graphene patches at different initial configurations slide over the nanodiamonds. Over time, this reduced contact area leads to ultralow friction sliding at the large scale.

    5. We saw a dramatic reduction in friction, reaching the superlubric state

      The authors have designed and executed experiments to calculate the coefficient of friction. The combination of nanomaterials they used were found to be successful in achieving super low friction values in a dry environment.

    6. We found that the presence of defects greatly facilitates the adsorption of water from the ambient atmosphere (fig. S13). Water preferentially adsorbs and stabilizes defective sites, which further prevents the formation of scrolls

      There are some limitations for the present observed near zero friction sliding. A relatively poor tribological performance is found in humid test environments. The water molecules present at the interface is found to prevent the scrolling of graphene layers. Moreover, the defects present on graphene sheets acts as catalytic sites further hampering the near zero friction sliding in a humid environment.

    1. changes in sea surface temperature may remain relatively small in this region

      Has this hypothesis been proven true since this paper was published in 2000?

      Use the National Oceanic and Atmospheric Administration's (NOAA) website to investigate changes in ocean temperatures since this study was published: https://www.nodc.noaa.gov/OC5/3M_HEAT_CONTENT/

    2. changes we observe in global ocean heat content may be related to the hemispheric and/or global modal variability of the atmosphere

      The Earth is an interconnected system where conditions in the atmosphere also affect what happens in the oceans. While the authors cannot say for sure that specific climate oscillations are driving the changes in ocean heat content, it is possible to say that changing climates are likely impacting ocean heat content.

    3. increase in ocean heat content preceded the observed warming of sea surface temperature

      The heat content of the atmosphere contributes to the warming of the ocean, so it would seem logical for the surface ocean to warm more quickly than the deep ocean (because the deep ocean is farther from the atmosphere).

      However, data suggests that the heat content of the deep ocean is increasing more quickly than the surface ocean. This further suggests that deep ocean circulation is transporting warmth from the surface to greater depths.

    4. our results support the findings of Hansenet al.

      Levitus et al. found a ∼2 × 10<sup>23</sup> joules warming between the mid-1950s and mid-1990s, which corresponds to a warming rate of 0.3 watts per meter squared.

      Thus, the ocean appears to be absorbing nearly half of the total heat that results from the warming of the Earth.

    5. warming in the western midlatitudes is due to nearly equal contributions by the 0- to 500- and 500- to 1000-m layers

      The western midlatitudes in this case represent the area between 30° - 45°N and 80° - 40°W. In this area the surface 300 m of the ocean has warmed by 1-2°C from the 1970s to the 1990s (Fig. 3A). This increase is even more extreme in the deeper ocean which has warmed by as much as 8°C (Fig. 3B).

      After examining the data in 500 m increments, Levitus and coauthors determined that most of this warming is occurring in the top 1000 m.

    6. There is a consistent warming signal in each ocean basin, although the signals are not monotonic.

      In each ocean basin, there have been periods when the heat content has increased and periods when the heat has decreased. However, the overall trend shown by the data is that every ocean basin on the planet has been warming over the last 50 years.

      Most of that warming has occurred after the 1950s and 1960s.

    7. Only the Atlantic exhibits a substantial contribution to these basin integrals below 1000-m depth.

      It is only in the North Atlantic that the ocean is being warmed at deeper depths. In the Pacific and Indian oceans, warming appears to only occur in the surface 1000m. 

    8. The cooling of the Labrador Sea is composed of nearly equal contributions of about 1.0 W m−2 from each 500-m-thick ocean layer down to 2500-m depth.

      The Labrador Sea is the region between Greenland and Canada around 60°N, 50°W that shows some of the most extreme cooling throughout the water column (Fig. 3B).

      Levitus et al. found that the cooling of the Labrador Sea has consistently declined by 1W/m<sup>2</sup> for every 500m in depth, extending all the way down to 2500 m.

    9. maximum heat storage for this basin occurs at depths exceeding 300 m

      The North Atlantic ocean absorbs a lot of heat, but where is that heat being stored?

      The heat that the ocean absorbs does not remain in the surface ocean, but is instead carried to deeper depths by deep ocean convection currents. From the 1970s to the 1990s, the deep water of the North Atlantic has gained more heat than the surface ocean has over the same period.

    10. demonstrates the opposite picture.

      The deep ocean of the North Atlantic cooled between the period 1970-1974 and the period 1988-1992, two decades later. While higher latitudes show this cooling most strongly, the decline in deep water temperatures appears to have occurred through much of the North Atlantic.

    11. difference field for the two earlier periods shows that much of the North Atlantic was warming between these periods

      Overall, the deep water of the North Atlantic had higher temperatures during the period 1970-1974 than during a period two decades earlier, from 1955-1959.

    12. decadal variability of the upper ocean heat content in each basin is a significant percentage of the range of the annual cycle for each basin

      The change in heat content from one decade to the next is similar in scale to the shift in heat content that happens over the course of a year due to the change in seasons.

      That is, the range of temperature from the highs of summer to lows in winter is similar to the extent of change from one decade to the next.

    13. There is relatively little contribution to the climatological range of heat content from depths below 300 m.

      The deep ocean below 300m is disconnected from the atmosphere and appears to have little influence on climate.

    14. the two basins positively correlated

      While there are periods of increasing and decreasing heat content in the oceans, with swings happening roughly every two decades, the Pacific Ocean has seen an overall increase in temperature over time.

    15. temperature anomaly of 0.37°C

      In 1998, the North Atlantic ocean was 0.37°C (0.37°F) warmer than the 50-year average.

      Has this trend continued since Levitus et al. published this study in 2000?

      You can find the answer by examining ocean temperature data available from NASA: https://climate.nasa.gov/vital-signs/global-temperature/

    16. In each basin before the mid-1970s, temperatures were nearly all relatively cool, whereas after the mid-1970s these oceans are in a warm state.

      Levitus et al. found that, as time progresses, ocean temperatures increase. Thus, time and ocean temperature are positively correlated.

      Much of this ocean warming has occurred since the mid-1970s.

    1. Some early-life events that are generally thought to affect adult microbiota composition were not associated with microbiota composition variation in our study, including mode of birth [cesarean section (N = 36) or vaginal delivery (N = 1036)], place of birth [home (N = 207) or hospital (N = 899); increased diversity in home-born individuals, FDR>5% when controlling for age], and infant nutrition [breastfed (N = 537) or not breastfed (N = 359)]

      Their study suggests that early-life events, such as birth method or nutrition, do not have any significant correlations with the adult microbiome.

    2. the second bicluster, consisting of seven genera, including Bacteroides and Parabacteroides, comprised individuals with reduced microbiome diversity. Characterization of these individuals revealed a preference for white, low-fiber bread [bread being the major source of carbohydrates in an average Belgian diet (34)] and higher prevalence of recent amoxicillin treatment.

      The other subset of individuals was characterized by lower microbiome diversity, having only seven genera (compared to 15 genera in the first subset). These individuals showed a preference for white bread and were associated with recent antibiotic treatment.

    3. Moreover, correlations between RBC counts and Faecalibacterium abundances are in line with the known oxygen requirements of this genus

      They found that red blood cell counts were also associated with the relative abundance of Faecalibacterium. As oxygen transport is the most important function of red blood cells, this fits the oxygen requirements of this genus.

    4. 308 samples collected in Papua New Guinea (15), Peru (16), and Tanzania (17) reduced the size of the human core microbiota to 14 genera. Notably, Alistipes, Clostridium IV, Parabacteroides, and all Actinobacteria were excluded from the global core composition

      When data was collected from samples outside of Europe and the United States, the core microbiota (which is defined as a genus that is common to at least 95% of samples) decreased to 14 genera.

    5. core microbiota (i.e., the genera shared by 95% of samples) composed of 17 genera with a median core abundance (MA) of 72.20%

      They found that the core microbiota—defined by being shared by 95% of samples from the United Kingdom, United States, FGFP, and LLDeep data sets—was 17 genera. The median abundance of these genera was 72.20%.

    6. Combined, these data sets comprised a total richness of 664 genera (fig. S2A). Extrapolation estimated total western genus richness at 784 ± 40 (fig. S2B), suggesting that total western richness is still undersampled. Observing total richness would require sampling an estimated additional 40,739 individuals

      The overall microbiota richness of their samples accounted for 664 genera, but does not cover all 784 genera expected for the entire Western population. They calculate that in order to observe all 784 genera, they would need to sample over 40,000 more individuals.

    7. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate.

      The study found 69 dependent factors from clinical-based—that is, measurements taken by doctors—and questionnaire-based—that is, provided by the patients about their lifestyle—data. They found that for 92% of the factors that had a counterpart in an independent study (=LLDeep study), these factors were still significantly associated to variation in microbiome composition.

    1. having about equal amounts of uracil and cytosine in (presumably) random order, will increase the incorporation of the amino acids phenylalanine, serine,  leucine, and proline, and possibly threonine.

      As seen in the figure below, random triplet combinations of U and C are now known to encode for the amino acid residues Crick suspected.

  5. Mar 2019
    1. it can be established in only three generations

      The authors summarize all their evidence that homoploid hybrid speciation has occurred in the BigBird lineage. They note how unusual this example is because it occurs faster than expected.

    2. The key features of success of the new lineage are reproductive isolation based on learned song and morphology, transgressive segregation producing novel phenotypes, and the availability of underexploited food resources.

      Here, the authors list the main reasons that this hybrid lineage survived and reproduced rather than dying out or mating with members of the parental species.

    3. The low values probably represent low additive genetic variation because the traits are highly heritable in Geospizaspecies

      The authors conclude that their measurements, both genetic (inbreeding coefficient, admixture, average nucleotide diversity) and bill shape (length and depth) do show low levels of variation in the Big Bird population.

      They conclude that this is expected because the bill shape traits are highly determined by genes, and so low genetic diversity would lead to low physical diversity of certain traits, such as bill shape.

    4. the founder male (5110) was not a G. fortis x G. scandens hybrid as previously hypothesized (12), but a G. conirostris

      This conclusion of the authors is a reclassification of the founder male into a different species than previously thought, based on the genetic analysis.

    5. it is likely that the founder population has already become reproductively isolated from G. conirostris

      The authors suggest in this paragraph that the Big Bird lineage is likely to be reproductively isolated from both parental species, further providing support that the lineage is on its way to becoming a new species.

    6. larger mean bill size than five adults that died

      These data further support that natural selection is acting on bill size, as birds with smaller bills did not survive.

    7. all Big Birds were homozygous

      The constant frequency of L alleles for HGMA2 and B alleles for ALX1 indicate that at these loci, the allele frequencies have reached an equilibrium.

    1. Our data, in implicating deep layer V neurons as sufficient targets in primary motor cortex, may help address these issues by informing the design of cortical interventions with regard to subdural rather than superficial extradural stimulation.

      Based upon the investigators results, they can extrapolate how their findings will impact future treatment of Parkinson's disease—not by implementing an optogenetic approach, but by targeting a different area in the pathological neural circuit that could prove more effective.

    2. M1 stimulation of this kind potently influenced neural activity in the STN

      By doing a separated-optrode experiment where an optrode was placed over M1 and a recording electrode placed in STN, the researchers were able to see a frequency dependent resolution of parkinsonian motor deficits.

    3. indeed, as expected from our light-scattering measurements and tissue geometry, we found that at least 0.7 mm3 of STN is recruited by light stimulation, which closely matched the actual volume of the STN

      Measuring the area of c-fos activated neurons upon light stimulation provided the authors with support for using an optrode to stimulate the STN since the area activated closely matched the true volume of the STN.

    4. the direct activation of local glial cells appeared not to be sufficient to treat parkinsonian symptoms, pointing to consideration of other circuit mechanisms.

      When blue light passed through the optrode to the STN, neuronal firing was inhibited by activating ChR2-expressing astrocytes. ChR2 allowed for the influx of calcium into astrocytes causing a release of glutamate and adenosine into the cellular environment. Adenosine would then bind to adenosine A1 receptors and inhibit neuronal firing. Even though they were able to inhibit firing, motor pathology was still unaffected by this intervention alluding to other circuit mechanisms.

    1. Fig. 4 Time series of 5-year running composites of heat content (1022 J) in the upper 3000 m for each major ocean basin

      This figure shows how ocean temperatures have changed in each ocean basin from 0 to 3000m in depth. Due to gaps in temperature data (especially in the 1950s), Levitus et al. used 5-year averages (composites) instead of looking at annual data (as in Figure 1).

      The authors found that there is an overall increase in temperatures within each ocean basin. This warming is not consistent, but instead has periods of lower temperatures and periods of higher temperatures.

      How does this figure differ from Figure 1 that only looks at 0 to 300m depths?

    2. Atlantic and Pacific Oceans have undergone a net warming since the 1950s and the Indian Ocean has warmed since the mid-1960s

      All of the world's oceans have been warming since at least the 1970's according to measurements by ships and research vessels.

      From the data available, it appears the Atlantic and Pacific started warming before the Indian Ocean, but this result could be due to the fewer number of data points collected in the Indian Ocean.

    3. global volume mean temperature increase for the 0- to 300-meter layer was 0.31°C

      While the whole ocean warmed 0.06 C between the 1950s and 1990s, Levitus et al. found that the surface ocean (the top 300 meters or 984 feet) warmed by 0.31 C.

    4. volume mean warming of 0.06°C

      All of the world's oceans combined - the Atlantic, the Pacific, the Indian - have warmed by 0.06°C overall between 1948 and 1998.

      But have the oceans all warmed equally, or have some basins or depths warmed more than others?

    1. Depolarization with veratridine after 2 weeks in culture also significantly increased TH, suggesting that mature as well as developing locus ceruleus exhibits plastic responses to depolarization

      This experiment was focused on observing the changes in tyrosine hydroxylase (TH) activity in older cultures. Similar to developing cultures, the old cultures were also exposed to veratridine. 

    1. Focusing on the prevalent concern of BMI increase and suboptimal health, we assessed the sample size needed to evaluate microbiota compositional changes associated to obesity. To do so, we calculated the independent effect sizes of obesity status, gender, age, and BSS on microbiota variation (table S16). This allowed us to estimate that 865 lean (BMI <25) and 865 obese (BMI ≥30) volunteers would be necessary to study microbiota compositional shifts with P < 5% significance level and a power of 80%. When taking into account gender, age, and BSS score as covariates, the estimated sample size was reduced to 535

      Since there is recent concern regarding the association of BMI increase and poor health, the authors wanted to know how large a sample they would need to identify microbiota changes that could be associated with BMI. They did this by conducting a power analysis which allowed them to determine that the sample size needed to detect changes in microbiome composition associated with obesity (with a false positive score below 5% and 80% probability of detecting a real effect if it is present) is 535 samples when taking into account gender, age, and BSS score as covariates.

    2. Residence type [ranging from countryside (N = 77) over rural village (N = 500), small town (N = 272), suburb (N = 137), to city (N = 102)] during early childhood (up to 5 years old), one of the 69 FGFP microbiome covariates, was linked to adult microbial community composition, with a positive correlation between evenness and residence in more industrialized areas, though not statistically significant (FDR >5%) when correcting for age, gender, and BMI

      They found an association between the type of residence the participants lived in as a child (i.e. rural, urban) and their adult microbiota composition. Moreover, individuals that grew up in industrialized areas showed a more even microbial composition than those that grew up in rural areas—however these results were not statistically significant when correcting for age, gender, and BMI.

    3. Interindividual variation in microbiota composition mainly resulted from changes in relative abundance of core taxa

      Microbiome variation between individuals was largely a result of changes in relative abundance of the core taxa.

    4. these results by no means imply that early-life events do not affect microbiota assembly during infancy, nor do they question previous associations with disease or allergy (36, 37); our analyses only indicated that such events were not significantly associated with microbiome composition at adult age in the FGFP cohort

      The authors acknowledge that these early-life events may affect microbiota development during infancy, but did not observe an effect of these events on the microbiota composition at adult age in their cohort.

    5. The cluster was predominantly composed of women, individuals with a lower weight, and participants with a longer transit time, as reflected both by stool consistency and time since previous relief. Both microbiota richness and evenness were elevated in this cluster.

      When clustering the data based on taxonomic characteristics, one subset was predominantly female, having lower weight and low Bristol stool scale score and a longer time since last defecation. These individuals showed more equal and higher quantities of different microbial taxa.

    6. some of the medical conditions targeted by fecal microbiota research have much smaller microbiome effect sizes than commonly assumed. However, some of the covariates that we identified (such as BSS and medication) are currently largely ignored and should be taken into account in future clinical studies

      They conclude that some medical conditions do not have as great of an impact on gut microbiota as previously thought. However, other covariables are under accounted for in these types of clinical studies.

    7. We could detect a 9% difference between taxon proportions with 400 samples per group at a power above 95% and a 5% difference with 500 samples per group at a power of 80%

      The authors were able to show that with 800 samples, they could detect a 9% difference in taxon proportions at a power above 95% and a 5% difference in taxon proportions with 1000 samples at a power of 80%. The latter means: 80% probability of detecting 5% deviations in taxon proportion between samples.

    8. intake of several of these substances was associated with community composition variation (Fig. 5A and table S15). The only drugs significantly associated with the abundance of specific genera in phenotype-matched case-control analyses were β-lactam antibiotics (FDR <5%).

      While several medications were associated with variation in microbiota composition, the researchers found for only one drug significant associations with the abundance of specific genera (when comparing matched cases and controls), namely for beta-lactam antibiotics.

    9. The presence of Fusobacterium could not be linked to any of the nonredundant covariates identified in this study, which could indicate the specificity of its association with colorectal cancer

      The authors could not find any correlation between the presence of Fusobacterium and the set of 18 nonredundant covariates, suggesting that its presence is specifically associated with colorectal cancer.

    10. was also negatively associated with insulin resistance risk factors such as BMI and blood triglyceride concentrations

      They found that the abundance of Akkermansia was negatively associated with insulin resistance risk factors. This means that samples with higher amounts of Akkermansia belonged to subjects with lower risk of insulin resistance based on BMI and blood triglyceride values. Insulin resistance is a condition in which your cells cannot use insulin (a hormone) effectively, preventing them from absorbing glucose. This condition may result in diabetes, which is characterized by a buildup of glucose in the blood.

    11. features losing most explanatory power were time since previous relief (also indicative of passage rates), blood uric acid and hemoglobin levels, BMI, gender, and frequency of beer consumption

      Stool consistency correlated with other factors like the time since previous defecation, blood uric acid (a chemical produced by the breakdown of food) and hemoglobin (a protein responsible for transporting oxygen in blood) levels, BMI, gender, and frequency of beer consumption.

    12. 12 out of 20 of the FGFP 99% core genera covary with BSS scores, with overall core abundance increasing in looser stools

      In the FGFP cohort, the researchers observed that the overall abundance of core genera was higher in looser stools.

    13.  Faecalibacterium numbers were, as discussed, dependent on RBC counts, but our analysis did find a decreased abundance in ulcerative colitis patients

      They found that red blood cell counts were also associated with the relative abundance of Faecalibacterium. As oxygen transport is the most important function of red blood cells, this fits the oxygen requirements of this genus.

    14. set of 18 variables (Fig. 3B and table S10) with a cumulative (nonredundant) effect size on community variation of 7.63%. Here, we identified stool consistency as the top single, nonredundant microbiome covariate in the FGFP metadata

      When modelling the 69 covariates that had a significant impact on the gut microbiota composition (to see which combination of parameters could best explain the variation), a combination of 18 variables was found, that accounted for 7.63% of the variation. Stool consistency on its own accounted for most of the variation.

    15. Independently of gender, genus richness correlated positively with age, whereas total core abundance decreased

      Researchers found that as both males and females age, the number of genera increases. However, age was negatively correlated with abundance of core genera.

  6. Feb 2019
    1. Although manufacturers may engage in advertising and lobbying to influence consumer preferences and government regulations, a critical collective problem consists of deciding whether governments should regulate the moral algorithms that manufacturers offer to consumers

      Manufacturers may try to sway public opinion and laws regulating AVs, but that doesn't address the bigger issue: Should governments regulate the "moral" algorithms in autonomous vehicles—the algorithms that decide what to do in difficult situations like the ones in the study?

      The authors conclude that moral algorithms may be necessary, but that they create a social dilemma.

    2. As usual, the perceived morality of the sacrifice was high and about the same whether the sacrifice was performed by a human or by an algorithm (median = 70).

      Participants thought that a driver's sacrificing themselves to save other people was highly moral, whether the driver was a human or a computer algorithm.

    3. The algorithm that would kill its passenger to save 10 presented a hybrid profile.

      Unlike the other two algorithms in Figure 3B, which consistently received many points or few points in all of the categories listed, the algorithm that sacrificed its own passenger to save 10 others received high points in some categories and low points in others.

    4. they imagined future AVs as being less utilitarian than they should be.

      The ratings for "What will AVs do?" (whether people think AVs will actually be programmed to sacrifice one passenger over many) are lower than "What should AVs do?" (whether people think they should be programmed to do so.)

      Thus, people are less confident that AVs will actually be programmed to sacrifice their sole passenger to minimize casualties, even though people think that is the most moral approach.

    5. They overwhelmingly expressed a moral preference for utilitarian AVs programmed to minimize the number of casualties (median = 85)

      As shown in the bottom graph of Fig. 2A ("What should AVs do?"), many more people thought it was morally superior for AVs to minimize the number of casualties: There is a high number of responses on the right end of the graph.

      If you sort the responses that everyone gave from lowest to highest and take the middle, or median response, it is also very high, at 85. This indicates that people thought saving as many people as possible was the more moral choice.

    6. In study one (n = 182 participants), 76% of participants thought that it would be more moral for AVs to sacrifice one passenger rather than kill 10 pedestrians [with a 95% confidence interval (CI) of 69 to 82].

      The authors determined the percentage of people who thought it would be more moral to sacrifice one passenger for the good of the whole, or vice versa. In this study, 76% of the 182 participants said that one passenger should be sacrificed to save 10 pedestrians.

      A 95% confidence interval of 69 to 82 tells you that if you asked all people in a population (in this case, all U.S. citizens, since only U.S. citizens participated in the study) the same question, there is a 95% chance that between 69 and 82 percent of your respondents would say that the AV should sacrifice its passenger for the greater good.

      Thus, a confidence interval gives you a range of values that you are pretty sure contains the "true" one. A smaller confidence interval means you are more confident in the result.

    7. our results suggest that such regulation could substantially delay the adoption of AVs

      Based on the results in this paper, if governments regulate the "morality" of AVs, people would be less likely to buy them, even if they approve of them.

    8. Finally, participants were much less likely to consider purchasing an AV with such regulation than without (P < 0.001). The median expressed likelihood of purchasing an unregulated AV was 59, compared with 21 for purchasing a regulated AV.

      Overall, people did not approve of government regulation of utilitarian algorithms, and were much less likely to consider buying an AV if they were regulated by the government.

    9. This is a huge gap from a statistical perspective, but it must be understood as reflecting the state of public sentiment at the very beginning of a new public issue and is thus not guaranteed to persist

      The authors note that there is a large gap in their confidence interval, which indicates that there is not public consensus. They point out that this is because autonomous vehicles are a relatively new issue, so different people have thought about it more or less.

      As people get used to the idea and think about it more, the gap is expected to narrow.

    10. When we inquired whether participants would agree to see such moral sacrifices legally enforced, their agreement was higher for algorithms than for human drivers (P < 0.002), but the average agreement still remained below the midpoint of the 0 to 100 scale in each scenario.

      The authors asked the participants if there should be a law requiring self-driving cars and human drivers to sacrifice themselves to minimize casualties.

      Participants did not think that this type of moral situation should be regulated in general, as indicated by their lower approval ratings. However, participants were more likely to think that regulations on algorithms should be enforced, as opposed to human drivers.

    11. without actually wanting to buy one for themselves

      Again, the researchers found that participants thought self-sacrificing AVs are good for other people but would not want to buy one for themselves.

    12. Like the high-valued algorithm, it received high marks for morality (median budget share = 50) and was considered a good algorithm for other people to have (median budget share = 50). But in terms of purchase intention, it received significantly fewer points than the high-valued algorithm (P < 0.001) and was, in fact, closer to the low-valued algorithms (median budget share = 33).

      The high-valued algorithm is the one that sacrificed one pedestrian to save 10 others, which received many points for each of the three categories listed.

      The results showed that participants thought an algorithm that sacrificed one person to save 10 was more moral. The algorithm that sacrificed a passenger to save 10 pedestrians was slightly less preferred than the algorithm that sacrificed a pedestrian to save 10 other pedestrians.

      Participants also thought that other people should have a car programmed to sacrifice its passenger for the greater good, as shown by the high number of points in that category.

      However, like the "low-valued" algorithm that sacrificed one pedestrian to save one other pedestrian, participants were not very willing to buy a car that was programmed to sacrifice its own passenger, as shown by the lower number of points given to this category.

    13. Although the reported likelihood of buying an AV was low even for the self-protective option (median = 50), respondents indicated a significantly lower likelihood (P < 0.001) of buying the AV when they imagined the situation in which they and their family member would be sacrificed for the greater good (median = 19). In other words, even though participants still agreed that utilitarian AVs were the most moral, they preferred the self-protective model for themselves.

      Even though participants reported that self-driving cars should sacrifice passengers for the greater good, they reported that they were not very likely to buy such a car. Further, they were much less likely to buy an AV that would sacrifice its passengers if it included family members.

      Taken together with previous results, this shows that even though participants thought that the most moral choice was to sacrifice the passengers for the greater good, when thinking about their own lives, the participants still preferred a car that would not do so.

    14. Imagining that a family member was in the AV negatively affected the morality of the sacrifice, as compared with imagining oneself alone in the AV (P = 0.003). But even in that strongly aversive situation, the morality of the sacrifice was still rated above the midpoint of the scale, with a 95% CI of 54 to 66

      Participants thought that having a family member in the car made the decision of sacrificing the car's passengers less moral.

      Even so, participants thought that sacrificing the car's passengers, including a family member, for the greater good was still overall more moral.

    15. robust to treatments in which they had to imagine themselves and another person, particularly a family member, in the AV

      Even in scenarios when a family member was in the car with them, participants thought that sacrificing the passengers in a self-driving car for the greater good was a more moral decision.

    16. their moral approval increased with the number of lives that could be saved (P < 0.001)

      Participants thought that the more people you could save, the more moral the choice was.

      The very low P value (P < 0.001) means that this conclusion has a very low probability (less than one thousandth) of being due to chance. This provides strong evidence supporting the authors' findings.

    17. However, participants were less certain that AVs would be programmed in a utilitarian manner (67% thought so, with a median rating of 70).

      When the participants in Study 1 were asked whether AVs would actually be programmed to save as many people as possible and sacrifice one passenger for the greater good, they had a more varied response.

      67% percent of the 182 participants thought that AVs would actually be programmed this way.

      This viewpoint is also reflected in the participants' ratings of how moral each choice was. The upper graph of Fig. 2A ("What will AVs do?") shows what people thought AVs would do, and is more evenly distributed than the graph of what AVs should do.

      The median or midpoint value of the participants' responses for the upper graph was 70, which is lower than the median of 85 given for the bottom graph. This suggests that people were less sure that AVs would actually be programmed to minimize casualties, even though most people thought that this is how AVs should be programmed.

    18. Overall, participants strongly agreed that it would be more moral for AVs to sacrifice their own passengers when this sacrifice would save a greater number of lives overall.

      The authors found that, overall, participants thought it was better for a car to sacrifice its own passenger to save a group of pedestrians (because this sacrifice would save a greater number of lives overall).

    19. The study participants disapprove of enforcing utilitarian regulations for AVs and would be less willing to buy such an AV. Accordingly, regulating for utilitarian algorithms may paradoxically increase casualties by postponing the adoption of a safer technology.

      People who took part in the study do not want the government to regulate the morality of self-driving cars, particularly if they will sacrifice their passengers for the greater good. They are also less likely to buy a car subject to those regulations.

      This may cause more deaths in the long run. Even though AVs are a safer technology, people would not want to buy these vehicles, which would inhibit the widespread adoption of AVs. If fewer people adopt AVs, then the technology (and increases in safety) will improve more slowly.

    1. they are consistent with the hypothesis

      The different effects of the B alleles, and the fact that they segregate, supports the idea that at the ALX1 gene locus, there are more than two alleles, all of which affect bill size differently. However, more data are needed to further support this hypothesis.

    2. possibly caused by natural selection

      Based on their detailed analysis of the body and bill shape of these Big Birds, the authors conclude that a change in the characteristics of the population is occurring such that it is becoming different than the parent populations. They suggest that it is possible that natural selection is the method by which this change is occurring, which supports their argument that a new species is forming.

    3. transgressive segregation produced genotype combinations

      Because the bill depth trait changed without changes of body size or bill length, the authors suggest that the unique combinations produced by transgressive segregation were an adaptation that allowed these birds to survive and reproduce.

    4. evolutionary importance of rare and chance events

      The authors conclude that chance events were important in this speciation event: these include the founder male's unusual song, unusual migration, his immature age, and the selection event mentioned in the next sentence.

    5. more indicative of selection than of drift.

      The authors combine the knowledge of genotype frequencies with the changes in bill shape, and conclude that the likely reason for this is natural selection, further support for their argument that speciation is occurring.

    1. It appears that the number of nonsense triplets is rather low, since we only occasionally come across them.

      Crick has evidence from his frameshift experiments that some triplets do not code for any amino acids, but these triplets are rare.

    2. Detailed examination of these results shows that they' are exactly what we should expect if the message were read in triplets, starting from one end.

      By adding and subtracting bases from the genetic code, certain patterns arose. These patterns were consistent with three bases coding for one amino acid.

    3. If, for example, all the codons are triplets, then in addition to the correct reading of the message there are two incorrect readings which we shall obtain if we do not start the grouping into sets of three at the right place.

      For example, if a DNA sequence contains ...CCGGAUC...

      Then an individual codon might be (1) CCG (2) CGG or (3) GGA. One of these would be correct and the other two incorrect.