This shows that having more or less voltage wouldn't affect the peak muscle contraction time, so having different fish be stimulated at different voltages wouldn't have affected the minimum contraction time that the authors were looking for during their experiment.

A small amount of voltage was used at first (10V), and this was then increased by doubling the initial voltage, until contraction occurred. However, a voltage above 100V was never used. To put this amount into perspective, the standard voltage for electrical outlets in the United States is 120V.

A statistical test used to confirm where the differences between groups occurred when it's known that there is a statistically significant difference between the means/averages of the groups.

A statistical method used to measure the variance in data between different groups.

They also measured the muscle temperatures of each fish at the 5 different areas (along the length of the fish from head to tail) where they measured muscle contraction times. The temperature of the muscle would affect whether it contracts faster or slower (warmer is faster).

The temperature at which fish live in also affects their swimming speed because warmer water generally enables them to propel through water more efficiently. That's why is it was especially important to record the temperatures of the waters from where the fish were collected.

Measuring the muscle contraction times of the fish after taking them out of the water enabled the researchers to know what the highest potential speed a fish can reach is without real-life factors of the fish's environment, like water current, affecting their data. Representative of data as if they had observed the fish in action with high-speed cameras.

It's too difficult to observe maximum speed as it's happening in the wild so the best method would be to observe the physiology of the fish. The faster the muscle of an organism contracts, the faster it can move. As a result, the lower the time it takes for fish muscle to make one contraction, the faster the fish.

Using calculations, it should not be possible for sailfish and marlin to swim as fast as previously thought because swimming that fast would cause cavitation bubbles in the fish leading to death.

In most scientific journals the Materials and Methods are part of the main text, but in Science they are part of the references and Supplementary Materials. For details on how the researchers developed their pathways and models, and information on the different ecosystem groupings, check out that link.

The authors of this experiment used the SPSS statistical software system to create the graphs presented in the article, showing the descriptive statistic analysis.

Author used descriptive statistics (mean, median, mode, etc) to compare data collected on the oocyte Wobalchia titer and those collected on oocyte size.

Using the AmScope digital camera, the authors were able to improve the visualization of the ovaries by having the field of view appear on a computer screen and analyze from there.

In this experiment, the authors used the Fiji Image J processing software in order to calculate the size and area of the oocytes, providing more insight into how the oocytes were affected.

The authors involved compared the oocyte titer raw data for each experimental replicate using the ANOVA analysis system by testing the differences of the means present.

The authors used photoshop, an image editing software, in order to remove and unnecessary signaling outside the oocyte, making it easier to analyze and interpret the data.

Full tutorial and introduction to processing scientific images in photoshop: https://www.youtube.com/watch?v=SbsDtPouggs

The authors collected confocal images though confocal laser scanning microscopy which is an optical imaging technique to increase the optical resolution and contrast of a micrograph by using a spatial pinhole to block out-of-focus light during image formation.

Laser scanning was used to magnify the cells and staining enhanced the detail of the structures, shown in black and white for differentiation purposes as well as measurement.

The authors of this experiment used flies this young in order to ensure the flies had not developed any Wolbachia yet, meaning it would be easier to extract the oocytes without shredding the tissue.

Specific genotypes allowed for less error or genetic disruption of results.

The authors placed the vials in an ice bath (placed in bucket of ice) in order to ensure a homogenous suspension, meaning that the substances in the vials were equally suspended from each other.

The recipes for the substance-enriched foods given to the flies.

The researcher's reasoning for executing this experiment was to uncover the frontier that is the mechanism that act in Wolbachia concentration, as there is very little information on it.

The paper attempts to find the mechanism responsible for Wolbachia concentration increase in germ line cells through tests of natural/artificial sugars and yeast.

Gene partitioning involves looking at the make up of complex traits. It involves computing heritability contributions from subsets of predictors to try and narrow down the search for causal variants.The reason why gene partitioning is so important is because if it is not done correctly the sister genomes results in aneuploidy. The consequences of these errors range from loss of normal cellular function to cell death. Stationary partitioning is superior to non-stationary because better results are given when trying to find these casual variants that are important for hereditary information.

The main goal of this paper is to revise the previous work made on the construction of phylogenetic trees because according to previous studies by Rokas and Gee, those trees that have been created are fairly inaccurate. This research is being made to demonstrate how these phylogenetic trees are in fact accurate and correct the conclusions made by previous scientists.

In this experiment, the authors had to find out the lowest possible amount of data they needed to come up with a correct species tree. In other words, they want to discover the most efficient way possible to create an accurate phylogenetic tree.

It is hypothesized that no matter what, the accuracy of a tree is directly related to the number of genes used to create that tree. This means that the greater number of genes studied, the more accurate the tree, so with an infinite number of genes one can achieve an infinite amount of accuracy.

The second part of the hypothesis states that the above statement should be true due to the fact that there is no set evidence that can "rank" a gene's ability to contribute to a phylogenetic tree. This is hypothesizing that all genes contribute an equal amount to a phylogenetic tree, with no gene being able to contribute any more or less than another gene.

Partitioned Bremer support is a method for assessing the similarity in joined data collections, although, there are some point of views that require some insight. When more than one similar parsimonious tree is found in the middle of varied ones, averaging Partitioned Bremen support for each set of data over these trees can avoid trouble, and it should ideally be analyzed for each unnatural tree. When numerous most parsimonious trees are examined due to joint data collection, Partitioned Bremen support is generally computed on the common tree. Be that as it may, extra information can be acquired on the off chance that Partitioned Bremen support is computed on each of the most parsimonious trees or less quality trees.

"Bootstrapping" is a technology based practice for determining the accuracy or precision of many statistical results. For phylogenetic  trees, the bootstrap helps by exampling "confidence" in related organisms (common ancestor) in proportion with organisms from the same "family".

During this procedure, the authors essentially performed an analysis to determine how divergent, or dissimilar, the genes had come to be.

On a daily basis, experts looked for specific hashtags and keywords that indicated activities related to ISIS or to civil unrest. Then, at the same time each day, these experts logged into VK.com--an equivalent of Facebook that is popular in Europe--and searched for newly created aggregates, which were then inserted into a database.

The author of this paper is currently doing research on the olfactory receptors that mediate the mosquito’s human and plant host-seeking behavior and the genes that regulate their appetitive drives. This includes research on Ir40a.

These are some of the main general biomes found in the Mediterranean region. The BIOME4 model uses a longer list of specific biome types, and more than 20 were found in the Mediterranean region. For the analysis, this larger list was grouped into ten “aggregated biome types” which are presented in Figure 3. To see how the aggregated biomes were grouped, check out Table S1 in the Supplementary Materials.

Each of the colored lines is generated from using multiple climate models as input to the BIOME4 model. The solid line indicates the average change ratio predicted from multiple runs of the model.The variation within each model is indicated by the shaded region, which encompasses the 25% of results above and below the average. As you can see, some models had higher variability than others, and the predicted changes within the first 50 years overlap between models.

Though the BIOME4 methods have limitations, there are two major advantages.

First, the model is based on the underlying processes that connect climate and ecosystems, so it avoids the assumptions made by models that are based on correlating current ecosystem distributions and climate values. For example, these models often assume that the current ecosystem distributions are stable and at equilibrium, rather than in flux.

Second, the researchers are able to use the same model for both the past reconstructions and for the future projections. This allows for more direct comparison between the two groups.

To reconstruct Holocene climate variables and biome types, the researchers "inverted" the BIOME4 model, flipping the input and output data. Rather than using climate data as the input, it uses plant data.

The researchers started by converting the pollen core data for a given time and location into "plant functional type" scores, which BIOME4 uses to rank and select biome types based on the "best match." "Plant functional type" groups species together based on similar characteristics such as respiration rate, response to climate variation, and genetic makeup.

The researchers then ran the BIOME4 model in "inverse" mode, testing a large number of randomized climate inputs for each time and location. The set of climate inputs that resulted in the best match to the pollen core data is used for the reconstruction.

In many scientific journals, the Materials and Methods are part of the main text, but in Science they are part of the references and Supplementary Materials. For details on how the researchers developed their pathways and models, and information on the different ecosystem groupings, check out the supplementary information.

These boxes show a range of results from many model runs for each scenario. The dot indicates the 50th percentile (median) result for all runs. The box shows the range containing the middle 50% of the results.

WMISH is a common technique for visualizing the location of expressed RNAs in embryos.

In this study, the authors used WMISH to show that Shh was expressed in the placode.

Individual lizards with different physical traits were bred together in order to observe how those traits were passed on to the offspring.

The authors of this study expand on the findings of previous studies by showing that the elevations that result in scales correspond to the anatomical placode in mammals and birds, which gives rise to hair and feathers.

The authors took successive microscopic images of different body parts in both lizards and snakes, specifically focusing on the places that scales form.

The authors use population density data and waste accumulation rates to predict how much plastic might enter the ocean as marine debris.

Compared to other reptiles, snakes' scale development is unique.

PCNA is a protein involved in cell division, so it is used as a marker to locate cells that are actively dividing.

This analysis showed that the cells of the placode were reproducing very slowly.

The authors of this study provide evidence for the theory that hair, feathers, and scales are homologous structures.

Luciferase RNA was transfected into human embryonic kidney cells with increasing amounts of MSI1 to test the translation regulation abilities of MSI1. The result is an increase in luciferase translation due to MSI1 regulation (meaning MSI1 may stabilize the genome of RNA).

The viral binding affinity was tested using the viral binding assay along with the a pseudotyped particle infectivity assay to test the ability of the virus to infect a cell. The results for the assays did not show a significant change in binding affinity.

Numbers of viral dsRNA, flavivirus E protein, and infectious particles were determined using confocal microscopy. Copies of viral RNA were measured after introducing the MR766 strain. The authors use this method to understand the replication processes that can increase or, in this article, decrease due to the inactivatoin of MSI1. The results observed showed a decrease in the amounts of viral particles and MR766 replication.

MSI1 knockout cells (KO) were created using CRISPR/Cas9. KO1 and KO2 were then probed with N and C termini MSI1 and MSI2 antibodies. The results showed a decrease in viral load after 24 and 48 hours.

Cells were observed after being infected with PE243, a control siRNA (small interfering RNA used to silence protein coding genes), and MSI1 siRNA. Western blots were run on the proteins from the cells. The results of the observations showed a decrease in viral RNA levels.

UV radiation was used to run a CLIP (cross-linking immunoprecipitation used to bind proteins together using UV radiation) analysis on infected cells. A western blot was run on the results, which allowed scientists to find the strong bond between MSI1 and PE243 ZIKV RNA.

BRUV's were placed in sites different to the determined video sites in order to serve as a control for the experiment. The author expected to see distinct measures of site fidelity and examine these results in order to prevent false positives and ensure that the results gathered from the no take marine reserves were higher or more accurate than results measuring site fidelity in open waters. -Sindy

BRUV is a system used in marine biology research. By attracting shark into the field of view of a remotely controlled camera, the technique records sharks diversity, abundance and behavior of species. -Sindy

As the shark gets further away from the initial location of tagging, its prevalence of location indicating site fidelity decreases because it is getting further and further away from its initial site. -Sindy

This research is centered around this idea of uncovering information on the abundance of sharks in zones that are monitored but reserved for marine animals It tests the efficiency of no-take marine reserves and its correlation to the site fidelity of reef sharks. -Sindy

This question sheds light on a topic regarding the suitability of marine reserves not only as a permanent safety harbor for recovery and expansion of the species but also the temporary inhibition of the space by species that are mobile, whether they would use the space to breed for protection or for a stable source of food and shelter. -Sindy

A signaling pathway allows an activation process to occur for a cell to have a specific function. So a communication takes place between these two different hormones, juvenile and insulin. These hormones work with energy to develop an insect. -Nicole Jones

BIOEDIT is a computer program that is capable of editing and aligning sequences rapidly and effectively. It is meant to be easy to use and is intended to allow researchers to easily create and analyze basic sequences. It is incredibly useful in this case as it allows the researcher to analyze sequences of multiple insect species rapidly and quickly. Learn more at http://www.mbio.ncsu.edu/BioEdit/page2.html -Eri-Ray

The conserved relationship among all dipterans suggests that this form of relationship evolved to be long ago. Part A of Figure 1 explains the cascade of how sex is determined among drosophila. This serves an example of a mechanism that works efficiently in determining sex. Through evolution and natural selection, the mechanisms that would perform most efficiently would be passed on (as can be expressed in Part A of Figure 1), while the other inefficient mechanisms would be removed from the population. -Elder

Different positions of the fish led to more or less efficient muscle contraction times. So, the authors used the positions that would best decrease contraction time to find the maximum speed of a fish.

Parafilm was used to make sure the needles didn't slip while measuring muscle contraction time, because that would lead to a source of error.

The scientists injected a fluorescent tracer, FITC, into a large reservoir of CSF called the cisterna magna.

This enabled the scientists to detect CSF as it circulated through the brain and diffused into the interstitial space between neurons.

The scientists observe that the CSF in sleeping mice flows robustly along arteries and diffuses into the surface of the brain (the parenchyma).

The scientists awaken sleeping mice and inject a second tracer (also small) into their CSF.

The scientists observe far less CSF flow along arteries and into the brain. This suggests that wakefulness exerts a powerful and rapid effect on CSF circulation.

This experiment compares two arousal states within the same mouse, rather than comparing the two states in two different mice. This kind of experimental design minimizes the impact of genetic and environmental variability between mice and makes this study extremely powerful.

The scientists have already demonstrated that CSF circulation is reduced when they wake a sleeping mouse.

However, it is possible that this is only true when a mouse is awakened in the middle of its sleep cycle, or that it is a short-lived effect that only matters during the first several minutes of wakefulness.

The scientists expanded their finding by injecting tracer into awake mice and then anesthetizing them.

An Analysis of Variance (ANOVA) is a statistical method for determining whether multiple groups being studied are truly different from each other.

"n = 6 mice" means that six mice were compared in total; this is a small sample, but because of the powerful design of their study (comparing arousal states within the same mouse), the scientists are able to detect significant differences between groups.

In order to test whether their findings may be relevant for understanding Alzheimer's disease (AD), the scientists wanted to determine if the clearance (removal) of beta amyloid, Aβ, a protein that accumulates during AD, was more or less efficient during sleep.

The scientists injected small amounts of a slightly radioactive form of Aβ, then waited for between 10 minutes and 4 hours, giving the brain an opportunity to remove the Aβ.

The radioactive label is believed to not impact the clearance of Aβ, and allowed the authors to determine how much of the Aβ protein remained in the brain using a gamma counter.

HRM v. DGGE with videos

HRM: https://www.youtube.com/watch?v=mrGXyfU3DsA

DGGE: https://www.youtube.com/watch?v=9ufRMr5ZKX8 SM

The authors compared GeCKO screening to a similar screen performed with shRNA.

The authors used an algorithm to rank the genes enriched in their screen by how likely it is these genes contribute to PLX resistance.

After 14 days, the authors saw a change in the distribution of sgRNAs in drug-resistant cells. From the new distribution of sgRNAs, they were able to identify genes that may contribute to PLX resistance.

PLX exposure stops growth in cells with a specific BRAF mutation. Treating a group of cells with PLX will halt the growth of cells without resistance, but cells that are resistant to PLX will continue to grow. This allowed the researchers to isolate drug-resistant cells.

To test the GeCKO library's effectiveness for positive selection (genetic variation that is beneficial to the cell), the authors tried to use it to identify which genes result in resistance to PLX.

PLX is a BRAF enzyme inhibitor. BRAF is involved in the uncontrolled (cancerous) cell growth in melanoma.

To determine how effective the GeCKO library is at knocking out targeted genes, the authors first used a negative selection screen (which tests for deleterious effects).

They infected cells with the library of sgRNAs. At the end of 14 days, they observed a reduction in the diversity of sgRNAs, as those sgRNAs that targeted genes necessary for survival were lost when cells died.

The authors produced a wide variety of sgRNAs that were used to find the 5’ end of constitutive exons, sequences that are constantly turned on and being used to create proteins.

As noted above, genome-wide screening has been successfully performed with RNAi. Here, the authors wanted to know if CRISPR could offer a more accurate and precise way to screen genomes.

The authors are looking to see if CSF influx (part of the convective exchange) is different between:

awake mice sleeping mice anesthetized mice

This illustrates how scientists ask questions.

The authors take an observed phenomenon (sleep) and carefully form testable hypotheses about its function.

They combine their observation that sleep is restorative and dysregulated sleep is associated with mental illness, with their knowledge of the glymphatic system.

They hypothesize a connection between the two, which they carefully test in well-designed experiments.

They choose powerful methods for data collection and analysis, making comparisons within individuals to minimize variability, and systematically recording data at a variety of time points and conditions to increase their probability of answering their questions.

Finally, they connect their findings into a general model for how sleep, arousal, and glymphatic function could interplay in normally functioning as well as diseased brains.

The scientists are asking two questions in this study:

"why do we need sleep?"

"why do we feel bad if we do not get enough sleep?"

The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.

-Luisa Bermeo

Polyester rope is used because it has extreme resistance to abrasion and sunlight. -Sindy

The presence of reef sharks with external transmitters as well as internal transmitters further validates the results obtained. Despite the turbulence of weather conditions, all sharks were accounted for, providing an accurately measured population pool. -Sindy

The author expects the well being and population of reef sharks living in no-take marine reserves to be beneficial and higher respectively than those living elsewhere. No-take marine reserves are protected areas of a marine habitat that prohibit human activity. This makes sense because the disastrous effects that human actions have on marine environments is common knowledge. Reef sharks would thrive in a location where adequate amounts of supply are met due to natural resources and the fact that a no-take reserve are essentially a no-fishing area. This prevents sharks from being hunted for their fins, meat etc. In a fiji no-take marine reserve, there was observed to be four times as many sharks than in an areas where fishing was allowed.

https://www.youtube.com/watch?v=mYZ6AIgFMQg

-Sindy

HyPhy stands for hypothesis testing using phylogenies. Hyphy is a software package that serves many purposes as well as multiple audiences. It is used primarily for the analysis of genetic sequences using techniques in phylogenetics (studies of evolutionary history). Though it is also commonly used in molecular evolution, and to study rates and patterns of sequence evolution. It can also be compiled as a shared library and called upon by other programming environments, thus making HyPhy great for group work. To learn more, click here https://academic.oup.com/bioinformatics/article/21/5/676/220389/HyPhy-hypothesis-testing-using-phylogenies -Jake Barbee

The author’s goal for this article is to find high rates of evolution at the basal components of the cascade. The author does this by examining the displayed variations of five sex-determining proteins in a sample of fifty-nine insect species. To see a simple example of what the author is trying to determine click here. https://www.youtube.com/watch?v=7usaaiggDgw -Jake Barbee

Splicing refers to the process of joining or inserting genes or fragments of genes. This excerpt refers to the phenotypic and genotypic relationship between Sxl and other sex determinants that contain a hierarchy and produce a "suppressor" that controls the transcription of the gene downstream. Where downstream refers to the final level of the cascade. -Elder

The "Sex lethal" gene is the sex determining gene of the sexually reproducing Drosophilia Melanogaster, During embryonic development, an XX embryo would have the Sxl gene expressed or active, while the XY embryo would have the Sxl gene suppressed or dormant to ensure the development of a male Drosophilia. -Elder

The author is using the chart to display sex-determining proteins of the Drosophila species. He does this to better describe how proteins play an important role in sex determination. The author also displays how Drosophila evolved bottom-up to create a higher divergence towards the top of the cascade. This would thus explain why genes evolved earlier would be more restricted than those evolved later down the cascade. To better explain sex-determination please watch this video. https://www.youtube.com/watch?v=NQ4Mh_CU15E -Jake Barbee

The hypotheses is saying the mosquitoes nutrition has an effect on "insulin sensitivity" and "juvenile hormone synthesis."Insulin is a hormone that works with the amount of glucose (sugar) in blood. A juvenile hormone is a hormone in insects that work with maturation and reproduction. So the researchers are saying that the amount of nutrition (food) the mosquitoes eat will determine the amount of these two hormones in the insect body, insulin and juvenile.

Since the researchers hypothesize that how much the mosquitoes eat determines how much insulin and juvenile hormones work, this means how much insects reproduce is also affected. So the researchers are saying if the insects eat enough, they will reproduce with better conditions than not eating enough. This is because the hormones that control reproduction are controlled by the insects nutrition.

-Nicole Jones

In this sentence, the authors are hypothesizing that the EOD pattern incorporated into electrosensory nervous system of the electric fish uses the information of size, shape, and distance of the objects in an algorithm used to process and relay information to the electric fish brain.

-Kierra Hobdy

Electric fish are able to receive signals and information from their environment though the emission of electroreceptors thorough their skin. After the contact of the electroreceptors and the external stimuli, information is relayed in a pattern to the electro-receptory organs of the fish. Since this is an essential part of their way of life , the authors know a large amount of neurons and brain matter are involved in this process. Therefore, they hypothesized, that in order to insure this sensory information is relayed efficiently and quickly to the brain of the electric fish, there must be an algorithm used by the neural networks in the fish in order for this process to occur.

-Kierra Hobdy

Here, the authors describe a problem of judging the replication success by evaluating the replication effect against the original effect size. When the replication effects size is near zero, it could be possible that the data shows no effect, and therefore we would find an unsuccessful replication attempt.

However, the estimation of the effect size could be imprecise. This means that there could be a lot of “noise” in the data, from random or systematic errors in the measurement. If there was a lot of noise in the data, it could distort our impression of whether the effect is really zero or not.

We might conclude that a replication with an effect size close to zero was sufficiently different from zero and thus successful, although the effect was really just produced by noise in the data, and the true effect is zero, meaning that the replication could be falsely taken as a success.

Here, the authors describe a problem of judging the replication success by evaluating the replication effect against the original effect size. When the replication effect size is near zero, it could be possible that the data shows no effect, and therefore we would find an unsuccessful replication attempt. However, the estimation of the effect size could be imprecise. This means that there could be a lot of “noise” in the data, from random or systematic errors in the measurement. If there was a lot of noise in the data, it could distort our impression of whether the effect is really zero or not. We might conclude that a replication with an effect size close to zero was sufficiently different from zero and thus successful, although the effect was really just produced by noise in the data, and the true effect is zero, meaning that the replication could be falsely taken as a success.

Last, the authors wanted to know if successfully reproducible studies differed from studies that could not be replicated in a systematic way.

For this, they checked if a number of differences in the original studies, such as the size of the effect originally reported, was systematically related to successfully replicated studies.

They also checked if a number of differences in the replication studies themselves, such as the size of the effect of the replication study, related systematically to successful replications.

The authors combined the results of each original and replication study to determine if the cumulative joint effect size was significantly different from zero. If the overall effect was significantly different from zero, this could be treated as an indication that the effect exists in reality, and that the original or replication did not erroneously pick up on an effect that did not actually exist.

The authors hypothesized that in half the replication studies, the effect would be stronger in the original than the replication.

The reason for choosing this null hypothesis here is that this is the expectation we would have if chance alone determined the effect sizes. There are two likely outcomes for each replication study: (1) that its effect size is bigger than that of the original study, and (2) that its effect size is smaller than that of the original study.

If chance alone determined the effect size of the replication, we would see each possible outcome realized in 50% of the cases. If the proportion of replication effects that are bigger than the effect of the original study was significantly different from 50%, it could be concluded that this difference was not random.

After completing their replication attempt, independent reviewers checked that each team's procedure was well documented, that it followed the initial replication protocol, and that the statistical analysis on the effects selected for replication were correct.

Then, all the data were compiled to conduct analyses not only on the individual studies, but about all replication attempts made. The authors wanted to know if studies that replicated and those that did not replicate would be different.

For instance, they investigated if studies that replicated would be more likely to come from one journal than another, or if studies that did not replicate would be more likely to have a level of statistical significance than studies which could be replicated.

To determine whether multiple polysomes can interact with one another to translate multiple mRNAs, the authors transfected two KDM5B genes into the cell, one containing the HA SM tag and one containing the FLAG SM tag. These two tags can be detected by different antibodies bound to different color fluorochromes.

Photobleaching or FRAP uses laser light to quench the fluorescence being emitted by the fluorescent tag. The fluorescence can be recovered by Fab antibodies leaving the translated proteins and being replaced by new antibodies. Thus, this experiment can determine how length of time that the Fab antibodies can bind to the newly translated proteins. These experiments were used to gather baseline data to determine the rate of transcriptional elongation.

This experiment measured how quickly the Fab antibodies bound to the polysomes by injecting the antibodies into cells containing the KDM5B gene and the MCP fluorescent marker.

Using the FLAG tag described above, the authors measured how quickly the ribosomes translated the proteins by determining when the ribosomes left the mRNA after translation.

To determine how many proteins are being translated at any one time from a single molecule of mRNA, beta actin was labelled with only one FLAG tag (rather than 10). Multiple proteins can be translated from one mRNA using polysomes.

Using a system to track mRNA during translation, scientists were able to visualize the size of translation sites, the mobility of the molecules, and how bright each molecule appeared after being tagged with fluorescence.

Procedure used to identify proteins by separating the proteins by length

To further test the abilities of identifying translation dynamics using the previously identified system, experiments were conducted using smaller proteins, beta-actin and H2B, rather than KDM5B.

A fourth experiment was conducted in order to positively identify that the co-located protein-mRNA spots were sites of translation, 4 micrograms of cycloheximide were added. The addition of the cycloheximide caused translation to slow down while also allowing for more ribosomes to attach to a single transcript.

To test the co-moving protein-mRNA spots (areas/spots in the images taken, Fig. 1, C and D, where a red and green dots were co-located) were locations of translation, 50 micrograms of puro-mycin was added to U2OS cells containing the transiently transferred plasmid. The puromycin leads to the inhibition of translation while mRNAs are still present.

The authors do not include changes that occur in the RCP2.6L scenario in the Figure 3H map. Why might they have left that out?

The four maps for the future pathways, 3D to 3G, are based on putting the climate data for year 2100 for each pathway into the BIOME4 model, running in "forward" mode.

The first map, 3A, comes from putting pollen core data from the past century into the BIOME4 inversion model, the same method as is used for the past biome map (3B).

None of the existing RCPs resulted in a projection of 1.5°C, so the researchers created a new model so that they could evaluate the scenario.

By examining older hAPP mice with and without tau, the authors could test how tau causes Alzheimer’s disease to progress as an animal ages.

After the researchers trained all mice to swim to a platform hidden under the water surface, the authors removed the platform to see how much time they spent in the area where the platform used to be. This way the researchers were able to test the memory of the mice.

Alzheimer’s mice (with hAPP) that had normal amounts of tau (Tau+/+) took longer to learn to swim to a visible platform than the other five types of mice.

The authors used mice that were genetically engineered to express a human copy of the amyloid precursor protein (called hAPP mice). hAPP mice are a common animal model of Alzheimer’s disease. They develop amyloid plaques and severe memory and cognitive problems later in life, just like humans with the disease.

The authors bred these hAPP mice with other mice that were missing both their genes for the tau protein (called Tau-/- mice). From this breeding plan, the authors produced hAPP mice with normal amounts of tau (hAPP/Tau+/+), with half the normal amount of tau (hAPP/Tau+/-), and with no tau (hAPP/Tau-/-).

They also produced mice without the human APP gene that had normal, half, and no tau.

The authors saw an increase in total tau protein in blast-exposed mice. To confirm that this increase was also true for phosphorylated tau, they computed the ratio of phosphorylated tau to total tau.

The authors used western blotting to detect abnormal phosphorylated tau and confirm their electron microscopy observations. They confirmed that levels of phosphorylated tau were elevated in the brains of blast-exposed mice as compared to the control group.

For more on western blotting, see the Journal of Visualized Experiments:

http://www.jove.com/science-education/5065/the-western-blot

This is an important "negative" finding that is reported in almost all cases of blast exposure. There is a lack of gross (visible to the naked eye) brain injury in the brains of people that have been exposed to a nonpenetrating blast.

The fact that this finding is replicated in this study encouraged the authors to explore whether there were "invisible injuries" in the brains of blast-exposed mice.

To test the water hammer effect, the authors compared the pressure resulting from a blast wave both inside and outside the head of a living mouse. They then compared these measurements to similar measurements performed on a decapitated mouse head.

Because the disembodied mouse head had no vascular system or thorax, the water hammer could not contribute to the shock wave pressure inside the head. However, the authors observed similar shock wave pressures in both the live mouse and the mouse head, showing that the water hammer effect cannot be the primary source of brain damage.

Explosion simulation software based on a large data base of experimentally obtained blast data. ConWep enables comparative analysis of blasts. The authors used the software to verify that their simulated blasts closely matched explosions that would happen in the field.

In animal studies (especially those using mice) it is important for the researchers to identify the genotype of the species they're studying. This helps other researchers either replicate the findings or identify errors in the authors' reasoning due to the genetic makeup of the model organism.

C57BL/6 mice are the most commonly used nontransgenic mouse in biomedical research. They are called "wild-type" because their genetics have not been changed by humans.

Mouse colonies like this are inbred to make sure the mice are as genetically identical as possible. This helps eliminate extra, unexpected variables in an experiment that could affect the results in unknown ways.

The authors designed a "shock tube" to create controlled blasts. A shock tube is basically a wind tunnel: Pressure is built up on one side and suddenly released, creating a shock wave that travels down the tube.

Source: Fraunhofer CMI

After finding identical CTE-linked problems in the brains of military veterans with blast exposure and athletes who suffered head injuries, the authors investigated how blast exposure might cause brain injury using a mouse model.

Mice are commonly used to model human diseases.

In this figure, the authors look at the CTE neuropathology (neurological abnormalities) in blast-exposed military veterans and young American football athletes.

Through postmortem analysis (still the only way to identify CTE), they found the same disease in both groups.

From these findings, the authors were motivated to investigate whether blast injury would cause the same disease as sport-related head injuries.

Immunohistochemistry (IHC) is a technique used to identify the biochemical and cellular cause of disease in a tissue.

First, a tissue is treated with a primary antibody. This antibody binds to the target protein in the tissue.

Next, the sample is treated with a second antibody that will bind to and detect the primary antibody. This second antibody has a colored or fluorescent tagged [is there a word missing here?] so that it can be detected with a microscope or other tool.

Question: Why do scientists use a second, additional antibody instead of just tagging the primary antibody and using that for analysis?

Tau-46 is a "pan-tau" stain, meaning it detects all (or many) forms of tau protein, both normal and abnormal.

In normal control cases, nonphosphorylated tau immunostaining would be diffuse and light. In pathologic cases, phosphorylated tau immunostaining would be present in neurons and glia.

The authors used these to measure the mean annual exposure of species to pesticides. See the Supplementary Materials for more information.

Here the authors outline one of their main hypotheses (species will expand their northern range limits to track climate change), and the subsequent prediction.

If you're interested in downloading the data and reproducing the experiments the authors did, visit here! The authors provide a script of code so by downloading the statistical tool R, you can easily repeat their experiments and reproduce their figures yourself. Try it out!

The main hypothesis tested was whether rats would voluntarily act to free a trapped cagemate because of feeling sympathy for the trapped rat.

The authors ask whether the free rat, upon seeing and hearing its trapped cagemate, will act to release the cagemate.

Neuropathological analyses consisted of staining thin sections of postmortem brain tissue from autopsy donors and examining these specimens under a microscope for evidence of disease.

The presence, distribution, and phosphorylation state (whether or not the protein has a phosphoryl group attached to it) is used to confirm CTE diagnosis after death.

In this model, the authors try to control for the fact that an application could be selected because the applicant writes well, rather than based on the quality of the application.

The algorithm in question was developed by William Kerr to estimate the contribution of Chinese and Indian scientists to the U.S. Patent and Trademark Office.

What the authors mean here is that they made statistical computations that allow them to remove the effect that the position of a name in the authors row can have in a publication.

Previous work has shown that receiving a grant increases scientific productivity. However, the paper authors want to know if NIH is awarding grants to projects that will make the best use of the money.

The authors used a small electrical current to trigger neurons in the somatosensory cortex to fire in the absence of tickling. They then determined whether this neural stimulation caused the production of USVs.

The authors implanted a microelectrode into the somatosensory cortex of the rat's brain and recorded neural activity (rate of neuron firing) in this region during tickling, touch, breaks, and play.

Finally, the authors included a last measure for replication success: a subjective rating. All researchers who conducted a replication were asked if they thought their results replicated the original effect successfully. Based on their yes or no answers, the authors calculated subjective replication success.

The authors compared the size of the original study effects with their replication study's effects to determine if the original study results fell within the confidence interval (CI) of the replication.

If the original study's effect size was within the CI of the replication study, the effect size can be assumed to be similar.

The third indicator of replication success was the effect sizes of original and replication studies. The authors calculated correlation coefficients to indicate effect sizes.

In a single study, when the means of two groups are similar, the correlation coefficient will be close to 1, and when the means of two groups are very different, the correlation coefficient will be close to 0.

The effect size of original studies was always coded as positive (values between 0 and 1). When the effect in the relevant replication study went in the same direction, the effect size was also coded as positive (values between 0 and 1), but when the effect in the replication went in the other direction, the effect size was coded as negative (values between -1 and 0).

In addition to comparing the proportion of studies yielding signficant results, the authors compared the p-values of these studies to find out how similar they were to each other.

Next, the authors conducted another test to find out if the proportion of original studies that produced significant results was equal to or different from the proportion of replication studies that produced significant results.

The first analysis that the authors ran on the data assessed all replication studies that yielded non-significant results.

The authors used Fisher's method to determine whether these studies actually had effects or if the original study authors were interpreting nonsignificant results as significant.

Here, the authors explain how they deal with the problem that some of the original studies reported results as significant when they were, in fact, not significant.

In each case, the threshold that is customarily set to determine statistical significance (p<0.05) was not met, but all reported p-values fell very close to this threshold (0.06>p>0.05). Since the original authors treated these effects as significant, the current analysis did so as well.

Because the large-scale comparison of original and replication studies is a new development in the field of psychology, the authors had to formulate a plan for their analysis that did not rely much on previous research.

They decided to use 5 key indicators for evaluating the success of the replications. They compared the original and the replicated studies in terms of the number of significant outcomes, p-values, and effect sizes. They also assessed how many studies were subjectively judged to replicate the original effect. Finally, they ran a meta-analysis of the effect sizes.

One of the indicators for whether a study was replicated successfully or not was a subjective rating: each team of replicators was asked if their study replicated the original effect (yes or no).

The authors wanted to make sure that the studies that were selected for replication would be representative of psychological research. Representativeness was important because it would mean that the conclusions that would be drawn from the replication outcomes could be cautiously extended to assumptions about the state of the field overall.

At the same time, they had to make sure that the studies selected could also be conducted (that is, that one of the coauthors had the necessary skill or equipment to collect the data).

To achieve this goal, a step-wise procedure was used: starting from the first issue of 2008 from three important psychology journals, 20 studies were selected and matched with a team of replicators who would conduct the replication attempt. If articles were left over because no-one could conduct the replication, but more replication teams were willing to conduct a study, another 10 articles were made available. In the end, out of 488 studies drawn from the population of studies, the authors attempted to replicate 100.

Before collecting data for the replication studies, the authors produced a detailed protocol that described how they were going to select the studies that were available for replication, how they would decide which effect they would attempt to replicate, and which principles would guide all replication attempts.

Importantly, this protocol was made public, and all individual replication attempts had to adhere to it.

The authors observed injured corals and sponges for several months after Hurricane Allen to see if they survived, noting the initial degree of injury.

The authors measured the degree of damage to certain species of corals, taking care to note the growth form and size. This allowed them to look at how shape and size influenced patterns of damage.

The authors observed a variety of sites with different profiles both before and after the hurricane. They describe the variation within and between sites here.

The authors noted damage to corals after the hurricane and tracked their subsequent recovery (or death).

Because these reefs had been well-surveyed before Hurricane Allen, the authors conducted surveys using the same methods after the hurricane to examine the impacts of the storm.

Neurospheres are useful for modeling very early (embryonic) development, while organoids are used to study later stages of development.

The authors also compared ZIKV infection to dengue virus 2 (DENV2) infection. DENV2 is similar to ZIKV.

Both infected and uninfected organoids were immersed in a fixative solution to "freeze" them and allow them to be visualized.

It was then possible to use an electron microscope to compare the infrastructure of infected cells and uninfected cells.

Neurospheres that contained cells infected with Zika virus were oddly shaped, and some cells broke away.

Mock NSCs were not infected with Zika.

In order to obtain neural stem cells from human iPS, researchers cultured iPS in a special medium.

To create neurospheres and organoids, neural stem cells were divided and again cultured in a special medium.

Finally, ZIKV was diluted and added to the different types of culture for 2 hours.

Because the authors only looked at projects that received grant funding, their analysis does not take into account how many high-potential projects were rejected by peer review.

The authors acknowledge that there is sometimes a long delay between a grant award and patenting, so their analysis may not be a good indicator of how relevant research is to commercial applications.

The patents like the grants are checked according to certain indicators: institutional quality, gender, and ethnicity of applicants.

Finally, the authors wanted to figure out if peer reviewers are good at choosing applicants for their innovation, their practicality, or if they are simply good at weeding out low-quality research.

The authors removed the influence of the grant applicant's background, demographics, and writing skill in order to look at what effect a reviewer's expertise has.

The authors control for yet another potential variable, an applicant's research background (they use the PI's publication history to do this).

The authors try to remove the effect of an article's field on its impact. For example, a biochemistry article may appear to have a smaller impact because of the high rate of publication and citation in that field, whereas a physics article's impact may be inflated due to a lower publication and citation rate.

Several factors can lead to the trends in Figure 1 being misinterpreted, like the age of the grant and the field of study. The authors address these concerns by adjusting their model to account for these effects.

Here, the authors estimated how much a decrease of one standard deviation on the percentile score affected the number of publications and citations of a grant recipient.

The authors studied some characteristics such as the grant history or the institutional affiliation to see if the previous work of the applicant has an impact on the result of the grant application.

The last measure is the number of patents that cite those publications from (i), or acknowledge support from the grant.

The second measure is the total number of citations the publications from (i) received through 2013.

The first measure of success is the number of papers a team published during the 5 years after they received the grant.

The authors considered grants which were already funded and competing for renewal. This makes it easier to attribute differences in research productivity to the peer review process, rather than the amount of funding the project has.

The percentile score is assigned by the peer review committee. It ranks all authors to determine which was the most favored by the committee. A lower score means the committee liked the application more.

If the evaluation by the peer review committee is correlated with the quality of work put out by the research group, then peer review has high value-added (meaning, it is useful for choosing research groups with the highest potential).

The outcome of this study could have important implications for how the NIH evaluates and chooses who it gives money to.

Although the wild-type mouse model has limitations (as do all experimental models), using laboratory animals allows researchers to test things that can't be directly tested in humans.

For example, mouse models are useful tools to study the effects of different genes. Biological research has generated thousands of genetically modified mouse strains that allow researchers to test hypotheses regarding specific genes and how these genes influence human diseases.

It was important to assess locomotion (movement) because the behavioral cognition test used relies on locomotion for its results.

If locomotion were impaired, then the results of the behavioral test could not be linked to cognition alone.

The authors did not detect any abnormalities in locomotion in either the control or experimental group, meaning that any cognitive abnormalities they observed were not due to locomotor defects. This strengthens the argument that any of the abnormalities they saw were due to blast-related interference with brain functions affecting learning and memory.

As above, the authors found impairments in a neuronal process thought to be involved in memory storage.

Following blast exposure, the authors observed a slowing of axonal conduction in structures of the hippocampus that are important for long-term potentiation (LTP).

In this section, the authors sought to find out if their mouse model of blast neurotrauma caused similar brain abnormalities as those observed in human CTE cases.

If so, it would mean there is a causal linkage between blast exposure and development of CTE later in life.

The authors used high-speed video cameras (which capture 100,000 frames per second) to record mouse head movements during blast exposure.

The videos showed violent winds pushing and pulling on the head during the blast, which the authors measured as the kinematics (motions over time) of the head.

These pushing and pulling forces during blast exposure were similar to sport-related impacts leading to injury.

After investigating the effects of blast waves on the skull and brain, the authors turned their attention to the effects of blast wind.

See the following video for a look at the destructive nature of these blast winds during a 1955 atomic weapons test:

https://www.youtube.com/watch?v=ztJXZjIp8OA

The first potential injury source the authors investigated was the interaction of the blast wave with the brain. The authors tested whether this interaction was destructive to the brain. To do this, they measured the pressure of the brain in living mice using a small needle hydrophone (a microphone used to detect sound waves underwater).

In areas of the cortex where the authors saw irregular tau proteins, they saw damage to the axons in the white matter beneath.

Although not shown in the figure below, the authors also examined the brains of healthy controls that matched the age and sex of the experimental subjects. They used the same IHC technique.

No abnormalities were observed in the control cases.

The abnormalities seen in the brains of head-injured athletes and blast-exposed military veterans were similar, so the authors hypothesized that the cause of CTE in these two groups must also be similar. However, it is currently not possible to diagnose CTE until after a patient has died and their brain can be autopsied.

The authors identified a correlation between neurotrauma and CTE, but in order to test their hypothesis and prove a causal connection, they had to perform controlled experiments. They used a mouse model for this.

Monoclonal antibodies are used in immunohistochemical staining to detect abnormal phosphorylated tau proteins. In this study, several different antibodies were used to detect various forms of tau proteins in different places in the brain.

If the specific set of abnormalities is detected in the postmortem brain of someone who had a history of neurotrauma, the diagnosis is CTE.

The authors used neuropathological analysis to compare the brains of military veterans who were exposed to blasts with young American football players, a professional wrestler, and normal controls.

If a mouse's head was prevented from moving when it was exposed to a blast, the learning and memory deficits described above did not occur.

A common format of experimental design in medical research is to formulate a hypothesis based on findings in human patients and test the hypothesis in an animal model.

The authors measured the degree of damage to certain species of corals, taking care to note the growth form and size. This allowed them to look at how shape and size influenced patterns of damage.

The authors observed injured corals and sponges for several months after Hurricane Allen to see if they survived, noting the initial degree of injury.

The Mann-Whitney U test is a statistical test used when values are not normally distributed. Here it is used to compare live tissue coverage before and after the hurricane. The P-value of less than 0.001 indicates that there was a statistically significant difference between the two groups.

The authors observed a variety of sites with different profiles both before and after the hurricane. They describe the variation within and between sites here.

Because these reefs had been well-surveyed before Hurricane Allen, the authors conducted surveys using the same methods after the hurricane to examine the impacts of the storm.

Moreover, the authors planned to combine the results of each original and replication study, to show if the cumulative effect size was significantly different from zero. If the overall effect was significantly different from zero, this could be treated as an indication that the effect exists in reality, and that the original or replication did not erroneously pick up on an effect that did not actually exist.

In this case, testing against the null hypothesis that the half of the replication effects are stronger than the original study effects means assuming that there is only a chance difference between the effect sizes. The alternative hypothesis is that the replication effects are on average stronger, or weaker, than the original study effects.

One of the indicators for whether a study was replicated successfully or not was a subjective rating: each team of replicators was asked if their study replicated the original effect (yes or no).

The authors wanted to make sure that the studies that were selected for replication would be representative of psychological research, that means they would give a good picture of which kinds of studies psychologists typically run. Representativeness was important because it would mean that the conclusions that would be drawn from the replication outcomes could be cautiously extended to assumptions about the state of the field overall.

At the same time, they had to make sure that the studies selected could also be conducted (that is, that one of the coauthors had the necessary skill or equipment to collect the data).

To achieve this goal, a step-wise procedure was used: starting from the first issue of 2008 from three important psychology journals, 20 studies were selected and matched with a team of replicators who would conduct the replication attempt. If articles were left over because no-one could conduct the replication, but more replication teams were willing to conduct a study, another 10 articles were made available. In the end, out of 488 studies drawn from the population of studies, 100 studies were attempted to be replicated.