In fig. S1, countries that have lost forests without gain are high on the y axis (Paraguay, Mongolia, and Zambia). Countries with a large fraction of forest area disturbed and/or reforested/afforested are high on the x axis (Swaziland, South Africa, and Uruguay).
On page 7 of the supplemental material s Figure S2. On the x-axis are the countries with forestry programs, whereas countries on the y-axis have deforestation caused by factors other than forestry.
tree canopy densities
Tree canopy density is an important concept in this study, because it determines whether an area of land is a "forest" or not a "forest."
To explain, Hansen and colleagues could analyze the satellite images of Earth at a resolution of 30 m by 30 m. For each of these 30 m by 30 m sections, they then calculated the proportion of that section that was covered in a tree canopy.
Using this map, forests can be defined as a user prefers by applying a threshold of tree cover density; for example, tree cover greater than 50% can be labeled as forest.
Landsat data
Landsat is a a joint program between the U.S. Geological Service (USGS) and the National Aeronautics and Space Administration (NASA).
In this program, satellites orbit around Earth and take photos of Earth's surface.
The photos taken from the satellites are not the type of photos you would take with a typical smartphone. Instead, these images can show the energy that is both reflected and emitted from Earth in many different wavelengths, including blue, green, red, near-infrared, midinfrared, and thermal-infrared light.
For a look at energy wavelengths click here.
To distinguish forests from other land types (e.g., grasslands, water, etc.), one can look at a combination of different wavelengths in the Landsat data. For instance, looking at a combination of the red, near-infrared, and shortwave infrared wavelengths helps identify forests. Our eyes are similar to a satellite sensor, except we only see in the visible wavelengths, namely red, green, and blue. Forests, to our eyes, appear dark green, meaning low blue and red reflectance and brighter green reflectance. By using remote sensing technology, we can improve our identification of forest extent and change by adding other wavelengths of reflected and emitted energy not visible to the naked eye.
Find out more about how the different wavelengths can help identify different features, here.
You can view some Landsat photos here. Be sure to check out the photos of deforestation in Bolivia, which is particularly relevant to this study!
Also check out this Landsat image video.
Landsat images are online and available to the public. You can find data here.
preprocessing of geometric and radiometric corrections of satellite imagery
Before Hansen and colleagues could analyze the Landsat images, they had to preprocess them. This preprocessing included making corrections for clouds and shadows, assessing the quality of the images, and normalizing the images so that they can all be directly compared.
sample sizes
The total number of samples taken from a sample population.
SEM
Standard error of the mean = standard deviation/number of samples (Reference)
fig. S5
Figure 5 in Supplementary Materials shows differences in the cost of treatment in two cases: Average HRT and T=20C, Long HRT and T=25C (As mentioned before HRT describes the time necessary for particles to travel the system from the entrance till the outlet.)
Figure S5 shows the cost of treatment per m3 of water treated in the y-axis. The x-axis presents the two different scenarios: baseline (average HRT and T=20C) and long HRT and T=25C.
They looked at the effect of these two scenarios in two samples:
Source water sulfate with 15 mgS/L and Source water with no sulfate. In both scenarios, source water with sulfate had higher expenses compared with the condition with no sulfate in source water.
The long HRT condition is investigated to account for the conditions that could favor sulfide formation and corrosion in the sewer, in other words it is a representation of the worst-case scenario.
Fourth, the estimated duration should be consistent both with the available evidence of increased risk of mortality after MV, compared with uninfected children, and with the time required to build a protective immune repertoire in early life (Fig. 1D, fig. S2, and SM 5 and 6).
Author's Hypothesis: 4
The estimated duration of immune suppression in hypothesis 3 must be biologically relevant. We have years of data from other scientists who have measured the amount of mortality following measles infections. Thus, to strengthen the reliability of this paper's findings, then the duration of immune-amnesia that this paper determines should agree with the time frame during which previous studies have found children to be at increased risk of mortality following measles.
Additionally, a basic hypothesis underlying this paper is that children recover from immune-amnesia by rebuilding their immune response through re-exposure to pathogens. This process is similar to how children first build up their immune response after birth - through exposure to pathogens. Thus, if the hypothesis put forth in this paper is correct, then the time it takes to recover from measles induced immune-amnesia (i.e. the duration of immune-amnesia) should be similar to the amount of time it takes children to build an immune response in the first place.
As a further test of the immunosuppressive impact of measles, we carried out a similar analysis on pertussis.
This is a control experiment preformed by the authors.
To test that their analysis doesn't result in falsely positive results another childhood disease, Pertussis, which is preventable by vaccination but does not cause immunomodulation was also analyzed. It was found that data did not demonstrate immunomodulation like measles disease.
These y– F1♂ were considered candidates for carrying the y-MCR construct and were crossed to y+ females
The authors also crossed the yellow F1 males to wildtype females to generate F2 offspring. A diagram of this cross is shown in Figure 2A.
Six such yMCR F1♀ were crossed individually to y+♂
After they had determined which of the F1 progeny expressed the mutagenic chain reaction allele (yMCR), they crossed the yMCR F1 females back to wildtype males to obtain the F2 progeny.
Wild-type (y+) embryos were injected with the y-MCR element (see supplementary materials), and emerging F0 flies were crossed to a y+ stock
The authors injected their construct into fly embryos so that the germline cells in the embryo would incorporate the construct into their nuclei. Once these flies (called the F0 generation) were adults, they crossed them back to wildtype flies to obtain the F1 progeny.
This study tests whether summer jobs, which shift focus from remediation to prevention, can reduce crime.
This paper uses a new approach to look at an old problem--the problem of youth violence. The new approach involves testing whether summer jobs programs result in reduced youth violence.
intravital microscopy (IVM)
Intravital microscopy is a technique used to image live animals. It is a live video of processes occurring in the animal while it is still alive. It gives information on different cellular interactions and activities in real time.
In this experiment, the authors inject tumor necrosis factor-α, an inflammatory cytokine within the scrotum of mice, and, via IVM, study local inflammatory response in the cremaster (that covers the testis and speramtic cord) muscles.
we searched for the receptor(s) mediating these contacts
They next determined the receptor on the cell surface that allows these cells to interact with each other during these collisions.
However, the theory on summer jobs is not entirely clear-cut
There are also reasons why summer jobs might not have any effect or have the opposite effect by actually increasing violent activity. This is why this study is important to do.
The left and right y-MCR PCR junction fragments were sequenced from y– F1 progeny from five independent F0 parents.
In addition to the PCR genotyping, the authors performed DNA sequencing using DNA from F1 flies that were yellow (y-). DNA sequencing is a tool that allows you to determine the exact nucleotide sequence of a region of DNA. The goal of the sequencing was to confirm that the expected MCR construct had been inserted into the y locus.
mean biodegradation rates and mean apparent quantum yields for photoreactions
This is information from Table 1.
measured and modeled UV radiation in the atmosphere
In other words, measured or calculated sunlight intensities.
135 different lakes and 73 rivers
These are the sites marked on the map in figure S1 (see Figure 1 annotations).
We scaled these measures of DOC processing to the open-water period in three water types—small streams, larger rivers, and lakes
As briefly discussed earlier in the paper, the authors used their calculated daily areal rated of dissolved organic carbon (DOC) processing to calculate the total amount of each type of DOC processing that occurs in their entire study area.
They calculated separate rates for three different types of water bodies.
Carbon processing at the scale of the Kuparuk River basin (~8000 km2) was estimated by summing areal rates over time (Fig. 2) for the period 2011–2013 and multiplying by the surface area of each water type (Table 2).
The authors were able to use their dissolved organic carbon (DOC) degradation rates for the different types of water bodies to calculate the relative importance of sunlight- and microbial-driven DOC degradation in the whole study area (row labeled "sum" in Table 2).
We quantified the importance of photodegradation in DOC processing by directly measuring dark bacterial respiration and each of the DOC photoproducts listed above.
The authors determined how important sunlight is for breaking down organic carbon by comparing how much microbes can degrade in the dark and how much all the sunlight-driven processes can degrade.
photostimulated bacterial respiration
Measurement methods are summarized here and provided in detail in Reference 11.
Photostimulated bacterial respiration was measured by exposing some sterile water samples to sunlight and keeping some in the dark, then adding bacteria and measuring the difference in how much carbon dioxide was produced in the bacteria in the sunlight-exposed samples versus the bacteria in samples that were kept in the dark.
We mapped global tree cover extent, loss, and gain for the period from 2000 to 2012 at a spatial resolution of 30 m, with loss allocated annually.
Hansen and colleagues looked at satellite images of Earth (see "Landsat data") for every year from 2000 to 2012 and determined how much of Earth is covered in forest, and whether forests increased or decreased in size from year to year.
This method involves a lot of computer processing, because the raw satellite images need to be screened and assessed before they can be used.
Hansen and colleagues performed the computational processing in Google's Earth Engine.
being derived through an internally consistent approach that is exempt from the vagaries of different definitions, methods, and data inputs
This sentence is referring to how Hansen and colleagues used Landsat data (e.g., the satellite images of Earth), which is all collected in exactly the same way each time. Thus, there are no inconsistencies between one sampling event (e.g., photo) and another sampling event.
The proportion of total aggregate forest change emphasizes countries with likely forestry practices by including both loss and gain in its calculation, whereas the proportion of loss to gain measure differentiates countries experiencing deforestation or another loss dynamic without a corresponding forest recovery signal.
By looking at the forest loss with or without subsequent forest gain, Hansen and colleagues can determine whether a country may have forestry programs or some other type of deforestation.
To explain, forestry programs treat forests as a crop in that the trees are harvested and subsequently replanted/regrown until the next harvest, and so on. Thus, countries that experience forest loss and subsequent gain likely have forestry programs.
Countries that have forest loss without much forest gain probably do not have forestry programs, and thus the deforestation is caused by some other factor. What could be some other causes of deforestation?
efficiently process and characterize global-scale time-series data sets in quantifying land change
Hansen and colleagues are illustrating how the work they conducted in this study can be applied and used by governments around the globe to monitor changes in land cover over time.
Also, to clarify, "time-series data sets" refers to how their data (forest cover measurements) were collected, i.e., in this case in a series of collections through time (one collection of satellite images of Earth for each year from 2000 to 2012).
Logistic regressions predicting the presence or absence of emotion words/emoticons at the tweet level were conducted, with political party followed as the independent variable
The researchers examined whether or not an individual's usage of positive/negative words and emoticons in tweets could be statistically predicted based on that individual's assumed political party affiliation (either Democrat or Republican).
In study 4, we analyzed 457 publicly available photographs of individuals from LinkedIn, a business-oriented social networking Web site.
This study is essentially the same as the one that examined photographs of members of Congress (Study 2), but this one uses photographs from a business setting, rather than a political one.
whether conservatives’ reports of greater subjective well-being, relative to liberals, could be attributed to self-enhancing tendencies
This is the main hypothesis for Study 1. The authors predict that the reason why conservatives report higher levels of well-being is that, compared with liberals, conservatives are more likely to self-enhance.
Stimulation was discontinued at any sign of arousal from sleep
This procedure is necessary in order to ensure that any effect the authors find is specific to sleep (as opposed to hearing the sound consciously while awake).
we administered another task wherein the same two sounds prompted participants to form a corresponding face-word pairing
The purpose of this task is to make the association between the sound and the training stronger.
On each trial participants were presented with a female face, a Black face, a science word and a good word.
If they they heard the gender-associated sound they had to match the female face with the science word. If they heard the race-associated sound they had to match the Black face with the good word.
Two unusual frequency-modulated sounds were presented during training
The sounds were played immediately after a correct response. One sound was played for counter-gender bias responses, the other for counter-race bias responses.
For some participants Sound A was played with the gender items and Sound B with the race items, and for other participants Sound B was played with the gender items and Sound A with the race items.
Participants viewed several types of face-word pairing but were required to attend and respond only to pairings that countered the typical bias
Participants were asked to press the spacebar as quickly as possible after seeing a face-word pair that countered the typical bias (e.g. a female face with the word 'science').
Half the pairs countered the typical bias and half were filler trials that participants were not supposed to respond to (female + art, male + science, male + art).
could be expanded through the use of homologs with different PAM requirements (9) or by directed evolution
This is another area for potential future research
directed evolution of these nucleases toward higher specificity
This is another area for potential future research.
off-target nuclease activity
This is a problem that will definitely need to be resolved before these technologies can be deployed in human beings
it is likely that the target locus's underlying chromatin structure and epigenetic state will also affect the efficiency of genome editing in eukaryotic cells (13), although we suspect that Cas9's helicase activity may render it more robust to these factors, but this remains to be evaluated
This is another area for possible future research.
8 to 12 bases is less well understood and may depend on the binding strength of the matching gRNAs or on the inherent tolerance of Cas9 itself
This could be an area of future research
puromycin selection
Puromycin is an antibiotic that can be used to select cells which have developed resistance to it by killing off all the cells which have not. It is used here to purify a cell strain by eliminating all the cells which did not develop resistance. http://agscientific.com/blog/index.php/2012/10/10/puromycin-faqs/
endogenous locus
That is, the AAVS1 locus in the PPP1R12C gene of chromosome 19 as mentioned above.
next-generation sequencing of the targeted locus
The authors checked the DNA sequence of daughter cells after they did the editing
which demonstrates that CRISPR-mediated genome editing is sequence-specific
This supports the authors' interpretation of what is happening.
HR but lower nonhomologous end joining (NHEJ) rates
By increasing the proportion of homologous recombination the researchers have better control over the process. Nonhomologous end joining is a less exact process and leads to more spontaneous errors.
GFP+ cells appearing ~20 hours post transfection compared with ~40 hours for the AAVS1 TALENs.
The results of the editing process appeared sooner in the case of the authors' engineered guide RNAs as compared with the earlier method using TALENs
gene correction rates using the T1 and T2 gRNAs approaching 3% and 8%
In other words, 3-8% of the cells returned to being fluorescent.
two gRNAs
The authors constructed two different guide RNAs
the intervening AAVS1 fragment
This is the 68-bp fragment mentioned toward the end of the last paragraph. When it is expressed, it makes the protein non-fluorescent.
flow-activated cell sorting (FACS)
This method uses a laser to identify which cells are of interest and thus sort them out. http://www.bio.davidson.edu/courses/genomics/method/facs.html
renders the expressed protein fragment nonfluorescent
By introducing the green fluorescent protein sequence and then disrupting it the authors were able to measure how well their genetic editing worked. They could measure this by determining how many of the daughter cells were fluorescent.
guide RNAs
In the natural CRISPR system guide RNAs take fragments of the viral or plasmid DNA and guide them to specific locations in the CRISPR locus. The idea here is that these artificial guide RNAs can similarly guide a short strand of nucleic acids into a specific place in the target genome.
crRNA-tracrRNA fusion transcripts
The authors combined two proteins which are needed for correct functioning of the CRISPR type II system.
a mammalian expression system
Genes code for proteins, but characteristics of the cells that the genes are in may either help or hinder the genes from actually producing the desired protein.
For example, there are differences between insect protein and the protein of mammals. Cells can be engineered to produce the desired type of protein. For more about expression systems, see this link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848218/
C-terminal SV40 nuclear localization signal
Nuclear localization signals are amino acid sequences that mark a protein to be transported to a specific place in the nucleus.
human codon–optimized version
A codon is a sequence of DNA "letters" that corresponds to a specific amino acid. By using a sequence of codons, specific proteins can be constructed.
Taking into consideration the role of sleep in memory consolidation, we adapted procedures for (i) reducing implicit social biases and (ii) reactivating this training during sleep.
To design their study, the authors combined counterbias training (discussed in the previous paragraph) with memory reactivation during sleep (discussed in this paragraph) in order to reduce racial and gender biases.
We reactivated counterbias information during sleep using subtle auditory cues that had been associated with counterbias training
While participants were asleep, the experimenters played one of two sounds - either the sound associated with the gender counterbias training or the sound associated with the racial counterbias training. The sounds were played softly so that the participants did not wake up.
implicit association test (IAT)
The IAT is a test that measures your implicit (unconscious) biases. You initially practice classifying items based on one set of two categories (e.g. good words respond with the left hand and bad words respond with your right hand). After a number of trials you then classify another set of two categories (e.g. White faces with the left hand and Black faces with the right hand). Then the categories are paired together (e.g. if you see a good word or a White face respond with the left hand and if you see a bad word or a Black face respond with your right hand). Finally the pairings are switched (e.g. if you see a good word or a Black face respond with the left hand and if you see a bad word or a White face respond with your right hand).
Your score is calculated based on your reaction times for responding to White faces when the same key is used to classify good words than your reaction time for responding to Black faces when the same key is used to classify good words.
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