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.

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

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.

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?

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.

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?

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?

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

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.

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).

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. 

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.

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.

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.

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.

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.

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%.

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.

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

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.

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.

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.

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.

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/

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.

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.

Levitus et al. found a ∼2 × 10²³ 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.

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.

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.

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. 

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/m² for every 500m in depth, extending all the way down to 2500 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.

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.

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.

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.

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

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.

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/

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.

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

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.

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.

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.

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%.

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.

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.

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.

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.

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

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

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.

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?

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.

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.

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?

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. 

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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).

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.

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

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

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.

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.

Overall, the researchers showed that when they artificially decreased NPF activity, flies preferred alcohol more, and when they artificially increased NPF activity, flies preferred alcohol less. Thus, they were able to establish a causal relationship between NPF and alcohol. Since the amount of NPF in a fly's brain is dependent on sexual history, this would explain their initial finding that sexually deprived flies prefer alcohol more than mated flies do.

Consistent with earlier results, the researchers found that the rejected subgroup maintained their preference for alcohol. On the other hand, the initially rejected but then mated subgroup demonstrated no alcohol preference. From this, the researchers concluded that it was the experience of sexual deprivation that was causing the rejected males to develop a preference for alcohol.

The researchers found that when given a choice between normal food and alcohol-mixed food, male flies who had mated with female flies did not prefer the alcohol, whereas male flies who had been rejected by the female flies did prefer the alcohol.

REPAIRv2 showed a moderate decrease in on-target activity, but at the same time it had substantially lower off-target editing.

There is a trade-off between on-target activity and off-target numbers. Depending on how an editor is being used, it may be more useful to have high activity and low specificity or lower activity and high specificity.

There is a middle ground where an editor is less active (but still useful) but more accurate.

The authors demonstrated that the constructs with mutated ADAR had enhanced editing activity at both on-target and off-target sites. They also observed that the construct with the full-length ADAR protein was less efficient at editing and had fewer off-target effects.

This conclusion was drawn from the observation that ADAR deaminase domain alone could produce a substantial number of off-targets found under the condition when the full REPAIRv1 system was applied.

Nevertheless, figure S8C shows that ADAR activity cannot account for all off-targets and there are likely other sources of off-target effects. Comparing the off-target numbers for four different conditions shows that the REPAIRv1 construct has a greater level of irrelevant editing than the ADAR domain alone.

The REPAIR construct with the largest C-terminal truncation (removal of the end) of dCas13b demonstrated the same level of RNA editing as the original REPAIRv1. This meant that the researchers were able to shorten dCas13b enough to fit into an AAV, but not destroy its ability to bind RNA.

The longer, 50-nt spacers showed higher rates of editing but also more off-target effects. This suggests a tradeoff between the efficiency of editing and the specificity.

The authors found that the the length of the guide RNA affects how efficiently the RNA-editing protein complex finds the target sequence.

In order to find the best construct, it is important to test different targeting conditions, testing as many target sequences as possible while also considering the resources required to test each one.

If ancient European dogs were the ancestors of modern European dogs, we expect that they would mostly belong to the same haplogroups. This is not the case, however, which tells us that these ancient dogs were replaced by another population of dogs.

We know that there were indigenous dogs in Europe 15,000 years ago. It's estimated that East Asian and Western Eurasian dogs had common ancestors 14,000-6400 years ago, and probably sooner than that (Western Eurasian dogs kept some of their ancestral wolf DNA, which is throwing off the estimated divergence time). The authors suggest that the dogs present 15,000 years ago were replaced by dogs that arrived from East Eurasia.

According to radiocarbon dating, the Newgrange dog is 4800 years old. By using three different ancestry analysis tools, there was no doubt that the Newgrange dog is most similar to the modern European dogs, which tells us that the East Asian dogs and Western Eurasian dogs had evolved from each other before 4800 years ago.

For Ice Age temperatures to occur, Arrhenius calculated that atmospheric CO2 levels must decrease to 0.62 to 0.55 times the current levels.

This calculation required him to extrapolate from the data in Table VII because the lowest case he modeled was CO2 at 0.67 times current level.

The ultimate summary of the whole paper. It explains why there needed to be side experiment analyzing different variables that would then clarify the conclusion that supports the given hypothesis.

The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.

This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.

The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.

Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.

The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.

This is explaining how the variation of herbivore species is closely related to the variation of plants in the location. The study explains how certain insects prefer to ingest other substances that can be identified, allowing the experimenter to see how the insects lived in accordance to where the plants where, instead of plants appearing around certain species of insects.

The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.

Main goal for the paper.

These express results for another question posed that clarifies variables that pertain to the specialization of the main topic. What is important is to grasp that this variable was accounted for in the process of understanding how specialization works in P. subserratum.

This information clarifies a question posed in the introduction. This knowledge fills the gaps of different variables that could affect the main goal of specialization.

This database will only be able to be completed with the participation and commitment from the scientific community around the world.

Overall, 0.5 hectare gentry plots were the best method.

Figure 1 shows how the coefficient of variability changed for the different types of plots used. The use of smaller plots had a smaller CV meaning that the results had low variance and did not stray much from the standard deviation compared to the larger plots.

It was found that the plots that were smaller than 1 hectare had better results than the plots that were larger (1 hectare).

The author further determined that due to the cause of the toxins released by the bacteria from the Red Tide it can influence methylation patterns of DNA. By influencing methylation , there exists a relationship in environmental stress and epigenetics. As the amount of time increases with the concentration of toxins remaining stable within the sample, the less there are accounts of genome wide DNA methylation.

Ultimately, the authors have observed a positive correlation between H2A.X and Oxidative DNA damage, in such that H2A.X increases in the presence of Oxidative DNA damage (due to the presence of brevotoxins). Based on these results, they have concluded that H2A.X is a good indicator of oxidative stress.

The authors found that the histone varaints that were derived from the major histones such as H2A.X, were also passed down as an evolutionary trait. The authors also determined that the antibodies could detect the histones in the oysters, and is signified as a possible method to detect further damage done by the toxic.

The phosphorylation of H2A.X appeared to be positively correlated to the exposure of K. brevis to the Easter Oysters.

Because of lack of change over the course in the experiment, it is concluded that there is no response from the oyster in K. brevis in terms of gene modification in H2A.X, H2A.Z, and macroH2A transcription.

The results showed that the simulation was an accurate representation of what happens during HAB.

The application of Land Surface Phenology may become increasingly important as technology advances. As scientists continue to better understand the drivers of phenological changes in the past, it can help us to plan for future changes within complex ecosystems such as tropical ecosystems.

The authors analyzed how phenology can aid in conservation science. With understanding the importance of this knowledge, scientists have laid out goals for future phenology studies, which includes creating a global model for monitoring changes in phenology to improve biodiversity. The key finding of this paper is understanding the importance of phenology and how it can help in future management discussions.

Although there is a lot of focus on what an ecosystem can offer us within society, in terms of a tropical ecosystem, managers of the specific services need to take into account the relative abundance of the various resources within the ecosystem. This is important in order to healthily sustain the diversity within the ecosystem while at the same time maximizing the productivity within the ecosystem for human use.

The causes for latent reproductive phenology in plants have yet to be determined. However, scientists can now use digital technologies (like digital cameras and remote sensing) to capture phenological events as they occur. This gives them the opportunity to examine changes without having to worry about the amount of time they have to analyze those changes.

Authors found out in the field that the sheer caterpillar size was a mechanism of defense to against predators.

Based on species abundance, the Pseudomyremx gracilis received the highest score.

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

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

Lower energy intake during migrations.

In order to confirm that NPF was causally related to the observed changes in alcohol preference, the researchers manually reduced the amount of NPF receptor the flies could produce in all neurons. They did this by using an RNAi, which can specifically prevent the formation of molecules coded by genes. Since the researchers had previously shown that mated flies have higher levels of NPF than virgin flies, and that this was correlated with a reduced preference for alcohol, they hypothesized that if they manually inhibited NPF's ability to affect the fly, then mated flies would show an increase in their preference for alcohol.

The researchers found that genetically reducing the number of NPF receptors in the brain for mated flies (who would have had elevated levels of the NPF molecule) caused these flies to develop a preference for alcohol. On the other hand, virgin flies (who would have had average levels of NPF molecules in their brains) were unaffected by this. This points to a causal relationship between the function of NPF and its receptor, and preference for alcohol.

The researchers found that the flies who had learned to associate an odor with activation of the NPF circuit preferred that odor in the Y maze, relative to the unpaired/neutral odor.

Other control flies who underwent partial genetic manipulations but did not experience NPF activity-odor pairings had no odor preference in the maze.

The researchers found that when they manually activated NPF-related neurons (recall that when using dTRPA1, this occurs at a higher temperature), preference for alcohol was significantly diminished, even amongst virgin flies.

The researchers found that flies that had experienced sexual rejection had significantly reduced levels of NPF in their brain, and flies that had undergone mating had significantly increased levels of NPF. This supports the hypothesis that sexual history can affect the amount of NPF that gets made in the brain, which can in turn change how much alcohol an organism might consume.

The researchers found that even when the male virgin flies were housed in large groups, their preference for alcohol persisted, and that mated flies with similar housing conditions did not prefer alcohol. This indicates that social isolation is not the reason for the observed alcohol preference in virgin flies.

When NPF cells are activated in tandem with the ethanol vapour and odor exposure, the preference for the ethanol paired odor (that develops for controls) is completely absent. This indicates that the activity of the NPF cells, which the previous experiment showed was inherently rewarding, interferes with the experience of the ethanol.

The ability to digest starch was important to look at, because it gives an idea of when dogs were domesticated, and who domesticated them—hunter-gatherers (meat-based diet) or farmers (starch-based diet).

The data presented in this paper mean that it can’t be ruled out that the newly identified basidiomycete is involved in vulpinic acid formation. Questions to be tested in the future include whether basidiomycetes produce the acid directly, or whether their presence causes the other fungal players to produce the acid themselves.

These Cyphobasidium cells were found throughout the lichen, and show evidence of living their whole life cycle within the lichen. Therefore, at this point, it cannot be ruled out that these basidiomycetes might be integral to the structure, phenotype, and formation of some lichen species.

The results of imaging showed that more basidiomycete cells were present in the lichen that produce vulpinic acid (B. tortuosa). This result supported the gene expression analysis results.

The researchers demonstrated, using rRNA analyses, that the new basidiomycete probably evolved with the lichen species. They showed that different lichens carried different basidiomycete strains. They concluded that basidiomycete symbionts are present in many lichens, and many lichen carry a specific strain.

The scientists found that genes in Ascomycota (the mycobiont in both lichens) and Viridiplantae (both lichen's photobiont) were expressed similarly in both lichens. Therefore, they concluded it was unlikely that a common gene was causing the production of vulpinic acid in one lichen but not the other. Therefore, the phenotypic differences between two lichen species could not be explained simply by looking at gene expression in the symbionts.

When the DNA sequences of 605 dogs were examined, two different groups were identified—the East Asian and Western Eurasian core groups. A dog may fall into either group, or between groups, with elements of both groups in its DNA (admixed).

The 605 dogs were from different parts of the world, and when represented on a map (as in Figure 1A) it was clear that dogs are mostly of the East Asian core group (in red dots) in East Asia, and mostly of the Western Eurasian core group (in yellow) in Western Eurasia.

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

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

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

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

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

In this paper, the authors were able to use their knowledge of the fly olfactory circuit to improve the performance of a standard LSH algorithm. This suggests that the brain uses computational strategies for similarity searches that are better than what are currently used in data science.

By studying the way the brain computes information, scientists can create faster and more efficient algorithms for solving the nearest-neighbor search problems that arise in everyday life (e.g. databases and search engines).

Computational savings refers to the efficiency of an algorithm—that is, how much time and space on the computer it requires to run. Especially when working with very large data sets, computational savings is an extremely important factor to consider since analyzing the data can take a very long time (imagine if you had to wait more than a fraction of a second every time you entered search terms into Google).

Here, the authors note that by modifying their experimental algorithm to include sparse, binary random projections instead of dense, Gaussian random projections, they were able to make the algorithm 20 times more efficient. That's big!

A typical LSH algorithm uses a dense Gaussian random projection, while the fly algorithm uses a sparse binary random projection. To test whether this made any difference in the performance of the two algorithms, the authors modified their LSH algorithm to use sparse binary random projections instead.

The result was that this made no noticeable difference in the performance of the two algorithms (see Figure 2A).

If codons do not overlap, then a single base change would alter the code for only a single amino acid. If codons do overlap, then a single base change may alter the code for multiple amino acids.

Since the complement base to A is U, the complementary code hypothesis would suspect AAA to code the same amino acid as UUU. Instead, AAA codes for a different amino acid (lysine) than UUU (phenylalanine), ruling out the complementary code hypothesis.

Since a strand of RNA lacking uracil encoded for various amino acids, uracil is not necessary to encode for an amino acid.

Since the only base found on the synthetic RNA was uracil (U), Crick concludes that triplets of uracil must encode phenylalanine residues.

The authors identified a genetic culprit, which they call Yob, which explains the factors that initiate the genetic pathway to maleness in Anopheles gambiae mosquito embryos.

In many of the genetically-modified mosquito-control efforts, it is necessary to only release males into the environment. Male mosquitoes do not bite and may or may not pass their genetic modifications to the next generation (depending on the design of the intervention). The authors propose that by over-expressing Yob in laboratory raised mosquitoes, scientists will be able to produce male-only populations without the labor-intensive process of sexing of pupae.

Conversely to the previous experiment where the authors added more Yob and saw evidence of female death, the authors reduced Yob expression in this experiment and saw evidence of male death as survivors had XX genotypes, likely due to under-expression of genes on the male's single X chromosome.

All embryos that underwent successful injection of Yob (as indicated by expression of the fluorescent marker) had the appearance of male larvae and had an XY genotype. The authors think that expression of Yob in XX embryos may have killed them.<br> Embryos that were not successfully injected had approximately 50/50 male to female ratios, as expected.

The Yob transcripts with changes in them, did not change the splicing pattern of dsx like the normal transcript does. Since the changes they made in the transcripts render the transcript non-function, they can assume that the normal Yob transcript is translated into a protein.

In one portion of the Yob region, the authors found evidence of evolutionary selection through the amount, types and patterns of changes in sequence. Other areas of the gene likely had changes between species as well, but they may appear more random in their pattern.

There is less female-form dsx in cells that were transfected with Yob than in cells not transfected, or those transfected with non-functional Yob. They found the same results whether the transfection was done in cell culture or done in live mosquito larvae. The authors still can not tell if Yob is directly interacting with dsx, but they now know that Yob does have an upstream impact dsx splicing.

Simply by evaluating timing of expression, the authors conclude that Yob must be upstream of dsx. However, this statement is also a hypothesis, as they have not found a direct connection between the two genes. This statement will serve as motivation for their next experiments.

They find from an mRNA gel that both males and females express a female form of a downstream sex determination gene (dsx) at 1 hour after fertilization. From the previous experiment, the authors know that Yob expression begins at about 2.5 hours after fertilization. In this experiment, the authors see that at 4 hours post fertilization, the female form of dsx begins to disappear in males but not females. By 8 hours, males start expressing the male form of dsx and the female form is completely absent. In order for the male to start becoming a genetic male, female form transcripts from the mother must be removed before male specific expression can begin.

Of the ~500,000 mRNA sequences returned, a very small portion of them (only 21) were found to derive from the Y chromosome. While the authors didn't explicitly say this, it is assumed that these sequences were not found in the female embryos.

The fact that cocaine use accounts for only 9% of the observed variance in avoidance response learning indicates that there are other variables (not taken into consideration) that could influence why CUD patients respond to stimuli that they should be avoiding.

Cocaine causes physiological changes that lead to impairment of brain regions involved in control functions.

Cocaine blocks dopamine re-uptake, leading to overstimulation. Overstimulation affects the way individuals assimilate and learn new information. A lack of control over actions after cocaine dependence makes individuals respond based on habit rather than a structured plan.

The author's findings might have implications for the future treatment of CUD patients.

Cultivating desirable habits or replacing bad ones could be effective treatments for cocaine use disorder patients. Introducing these types of interventions could be essential to reducing one of the major public health problems that we currently face.

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

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

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

First paragraph of 9. conclusions

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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