5,190 Matching Annotations
  1. Nov 2018
    1. fear conditioning

      Training that is performed to teach individuals to predict a negative outcome following a stimulus. This is done by repeatedly presenting an individual with a negative outcome following stimulation.

    1. p-nitrophenol–linked aliphatic esters (pNP-aliphatic esters)

      Aliphatic means that there is no aromatic group on the ester part of this molecule. A p-nitrophenol group is an aromatic ring with an oxygen linked to one carbon and a nitrogen attached to two oxygens linked to the opposite carbon.

    2. maltose

      Maltose is a disaccharide sugar that is closely related to sucrose (table sugar). Sucrose is made of two simple sugars—glucose and fructose—whereas maltose is made of two glucose molecules.

    3. GenBank or Protein Data Bank

      GenBank is a database that is publicly available where scientists can record genetic sequences and the proteins they code for so that future researchers can use the information. Protein Data Bank focuses on recording and storing information on the shape of 3D molecules, particularly proteins.

    4. buffer

      A solution that prevents the pH from changing very much. A buffer is made of a weak acid and a weak base together in solution. If you add acid, it just reacts with the base. If you add base it reacts with the acid, preventing the pH from changing.

    5. polyesters

      A type of polymer that is used in many types of plastics. A polymer is a chemical made of one or more simple molecules, called monomers, bonded to itself many times in a repeating pattern. You may recognize polyester as the fabric that makes up some types of athletic wear.

    6. catabolic enzymes

      Catabolic reactions are those that break molecules into pieces, often giving off energy in the process. Enzymes are a type of protein that help speed up reactions. Therefore, catabolic enzymes help speed up reactions that turn large and complex molecules into smaller and more simple ones.

    1. haplotype

      A set of single DNA bases that tend to be inherited together from a single parent, and often vary between individuals. Variation in single bases gives us information about evolution.

      Check out this video from the University of Utah to learn more about how halotypes can be used to understand genetic relationships between humans, and dogs too!

    2. drift

      This is one way that evolution can occur. It is an entirely random process, in which some individuals, by chance, contribute more of their genes to the future population that other individuals.

    3. mitochondrial DNA

      Genetic material that exists in the cell's mitochondrion. It is very important for studying ancestry since it is inherited from the mother only, and it allows researchers to trace the maternal lineage.

  2. Oct 2018
    1. NPF-NPFR pathway

      In neuroscience, a pathway or a circuit refers to a set of neurons that function together to accomplish the same function. Often, these neurons all release the same molecules. Here, the researchers draw our attention to sets of neurons releasing NPF, referring to this as the NPF-NPFR pathway.

    2. NPF transcript levels

      There are a number of steps that must occur in order for neuropeptide F to be made in the brain. The first step is for the gene for NPF to be read by the neuron. As the neuron reads this gene, it makes a local copy of it known as a transcript. These transcripts are then recruited by other processes in the cell that use the transcript as an instruction manual about how to build the NPF molecule. Each time a new NPF molecule is made, a new NPF transcript must be created first. For this reason, it is possible to measure the amount of NPF transcripts in the brain in order to determine how much NPF was being produced.

    3. early maternal separation

      Another experimental method for causing rodents to experience stress in which newly born offspring are taken away from their mothers and raised separately. The lack of a mother present to raise the babies causes them to experience intense stress.

    4. chemosensory cues

      Flies do not have language, but they do communicate with one another in other ways. One such way a fly may communicate is by releasing chemical compounds that other flies can sense, and accordingly respond to. These are known as chemosensory cues. In this case, the authors are referring to chemicals released by the mated female that signal to the male that she is no longer receptive to mating.

    1. knockdown

      A process when expression of a particular protein is suppressed at the level of RNA.

      This is similar to knockout, where the expression of a protein is blocked at the DNA level. Unlike knockout, knockdown can be reversed.

      The most widely used method for knockdown is RNA interference.

    2. prokaryotic

      Prokaryotes are a class of single-celled organisms with no membrane-bound nucleus, mitochondria, or other membrane-bound organelles.

      Examples include bacteria and archaea.

    1. biotic

      Describes systems consisting of living organisms. Here, the authors believe that interactions between different microbiota communities may contribute to some variation in genera abundance they could not account for.

    2. collinear variables

      Two variables are collinear if they can be predicted from each other accurately, suggesting that they are highly correlated. It is often redundant to have both variables if they are collinear because they can be used as proxies for each other and may hamper interpretation of results.

    3. stochastic

      Refers to anything that has a random probability distribution that can be analyzed statistically, but not precisely predicted. Here, the researchers suggest that some variation in genera abundance might be due to random, uncontrollable factors.

    4. phylogenetic profiling

      Refers to a bioinformatics technique in which the presence or absence of traits across a large number of species can be used to infer biological connections.

    5. cold chain monitoring

      A practice in which the storage, shipping, and distribution of samples are continuously kept in a temperature controlled environment. This prevents samples that may be sensitive to temperature fluctuations from degrading.

    1. exponential

      An exponential distribution is a type of probability distribution, In general, a probability distribution shows the probability that an event (such as a neuron firing) will occur over a given time interval. Specifically, an exponential distribution describes a situation where the probability that the event will occur is proportional to the length of the time interval.

      Note: In the image, the x-axis is time, the y-axis is the probability, 1/λ is the mean (average) of the distribution. Each lamda(λ) curve represents an exponential distribution with a different mean.

    2. sparse

      Thinly populated. Here, it means that each tag consists of only a small percentage of the neurons present in the olfactory circuit. That is, only a small percentage of neurons fire action potentials in response to the odor.

    3. approximate similarity (or nearest-neighbors) search

      A type of algorithm that takes a point in a data set and then seeks to find other points in the set that are most similar to it.

    1. cloud condensation nuclei, CCN

      Cloud condensation nuclei (CCN) are small particle that facilitate cloud growth by serving as location of water vapor condensation in the atmosphere. Aerosols often act as surfaced for cloud droplet growth.

    2. δ≅0.05

      The \(\delta\) is a Greek symbol used to represent instantaneous change. Here, the authors are providing a numerical value of the change of aerosol optical depth in the Southern Hemisphere (SH), compared to natural background.

    3. aerosol optical depth

      Particles, or aerosols, in the atmosphere, such as dust or smoke, scatter or absorb sunlight. Aerosol optical depth (AOD) tells us how much sunlight was prevented from reaching the surface due to these particles. It is a unitless values that corresponds to the amount of aerosols in the atmosphere over the location where is was measured, often using a satellite.

    4. sulfate aerosol

      Sulfate aerosols are formed from the condensation of oxidized sulfur dioxide (SO\(_2\)) emitted from fossil fuels combustion or volcanoes. Because humans are the main source of sulfate aerosols, the concentration of this particle is higher over land in the Northern Hemisphere, which the majority of industrial processes take place. The remainder of this paper provides more details on the different impacts these aerosols have on the Earth system.

    5. planetary albedo

      Planetary albedo is a measurement of the amount of light reflected from the surface of a planet, in this case, the Earth. Aerosols that reflect more light, such as sulfate aerosols, will enhance the planetary albedo so more incoming solar radiation is reflected back to space. Scientists estimate that Earth's average albedo is 0.3.

    6. relative humidities

      Relative humidity (RH) is the ratio of the amount of water vapor in the air (actual vapor density) relative to the amount of water the air could hold (saturation vapor density)

      It is given by: \(Relative Humidity\) = \((\dfrac{actual vapor density}{saturation vapor density})\)\(*100%\)

      The relative humidity is simply a way for meteorologists and scientists to describe how much moisture is in the air at a give temperature. You and I might feel this on a warm day, where is feels much hotter outside when the humidity is higher.

    7. in situ

      Measurements of temperature or other weather conditions, such as relative humidity, are called in situ if they are taken in the original location. It is a latin phrase used to differentiate observations taken from satellites, called remote observations.

    8. climate models

      Climate models are numerical representations of the Earth system. Some models are very complex and can take months to run on a supercomputer, others can be run on a laptop in a matter of seconds. More complex models include representations of the atmosphere, oceans, and change in ice dynamics. Simple climate models often represent on the most fundamental physics of the climate system, such as a carbon cycle.

    9. greenhouse warming

      Greenhouse gases (GHGs) absorb outgoing infrared radiation and trap the energy in the atmosphere, causing an increase in temperature over time called greenhouse warming.

    10. greenhouse gases

      Greenhouse gases (GHGs) are atmospheric species that absorb outgoing infrared radiation, such as carbon dioxide (CO\(_2\)) and chlorofluerocarbons (HFCs). GHG have long atmospheric lifetimes ranging from hundreds to thousands of year depending on their chemical and radiative properties. These differences also impacts their radiative forcing abilities.

    11. tropospheric aerosol

      The troposphere is the area of the atmosphere where you and I live and breathe. It is between 5 - 9 miles thick, depending on your location on Earth. Its name derives from "Tropos”, meaning change, because weather and clouds form in this region of the atmosphere.

      Aerosols are small particles suspended in the atmosphere. Sunlight can be absorbed or reflected from the surface of aerosols depending on the size and type of aerosols. These factor determine the atmospheric properties of the aerosol. Aerosols generally have short atmospheric lifetimes compared to greenhouse gases, such as carbon dioxide. For example, black carbon, a type of aerosol emitted from incomplete combustion and biomass burning, have an atmospheric lifetime between 3-5 days.

      Tropospheric aerosols are very important to understand because they impact the climate, but also can impact the quality of human health. For example, very fine particles, called Particulate Matter (PM) 2.5, a reference to the diameter of the aerosols in micrometers, are dangerous from humans and leads to increased cardiovascular problems and even death.

    12. 1850

      Climate scientists generally use the Industrial Revolution as a benchmark in time. Though there is debate in some spheres about the exact date that should be chose, these authors use 1850 to indicate the shift toward industrialization, including use of fossil fuels. Time periods before 1850 are termed "pre-industrial."

    13. radiative forcing

      The Earth's surface temperature is determined by the balance between incoming solar radiation (sunlight) and outgoing infrared radiation. Radiative forcing (RF) is a measure of the ability of a gas or particle, for example, to effect that energy balance. The units of RF are watt per meter squared (W/m\(^2\)), which translate to the rate of energy change per unit area on the globe as measured from the top of the atmosphere.

    14. global climate change

      Climate change refers to changes in the Earth system from both natural and human factors. Global warming is often use synonymously with climate change, but global warming specifically refers to the rise in global average temperature. More generally, climate change includes the melting of polar ice, increase in ocean acidity, and measured global mean temperature increases.

    15. anthropogenic

      Anthropogenic means resulting from human activity. Scientists often speak about anthropogenic climate change to specifically discuss the changes resulting from the burning of fossil fuels or land use change, for example.

    1. secondary metabolites

      Any organic substance that is not directly involved in the growth, development, or reproduction of an organism. Vulpinic acid is an example of a secondary metabolite.

    2. ribosomal RNA (rRNA)

      This is a gene that helps stabilize the ribosome. It is found in all living organisms, so this gene is often used in phylogenetic comparisons of different species.

    3. metatranscriptomics

      A transcriptome sample that is taken from a collection of organisms. mRNAs must be mapped onto each of the genomes from the organisms in the sample in order to figure out which gene came from which organism. In some cases, there is not a genome available for mapping and instead mRNA is mapped against a large database in order to find a close relative and guess where the mRNA could have come from.

    4. axenic

      Denotes a laboratory culture that is free from living organisms other than the species required. In this case, lichens could not be formed in a laboratory using only the two known species.

    1. esterases, lipases, or cutinases

      These are types of enzymes that are capable of breaking apart certain types of cell compounds. Esterases break down a wide range of compounds called esters. Lipases break down fats and cutinase hydrolyzes cutin, part of the waxy substance you find on leaves.

    2. environmental remediation

      A process of repairing human-caused damage to the natural environment. For example, environmental remediation might involve removing harmful chemicals from water sources, or removing dangerous radioactive elements from soil. This work is looking at using biological organisms to remove PET film from the environment.

    3. reaction intermediate

      Sometimes a reaction occurs in more than one step. The original material reacts to form what we call a reaction intermediate, which may exist briefly or for a longer period of time, but is later turned into a final product.

      In this case, in simplified terms, PET is converted into reaction intermediate MHET (mono(2-hydroxyethyl) terephthalic acid), which is then converted to TPA (terephthalic acid) and EG (ethylene glycol).

    4. culture fluid

      The growing material, which contains water, inorganic minerals, and small organic molecules. Most of the microbes in the test tube attached to the PET film, making the liquid culture appear clear.

    5. ethylene glycol

      A chain of two carbon atoms between two oxygen atoms. When two ethylene glycol groups bond to either end of TPA, you get the MHET, the basic monomer of PET. You may have encountered ethylene glycol in the form of anti-freeze.

    1. Volatile methyl siloxanes

      Silicone is a polymer that is made up of siloxanes. Silicone is used in many household products including baby bottles, adhesives, and skin and hair care products. The smaller the polymer is, the more volatile it will be. Many skin and hair care products use smaller siloxanes which are volatile.

    2. mobile sources

      Produced from transportation-related activities; for example, driving.

      Mobile sources also include off-road engine sources (e.g. construction equipment, lawn mowers, and recreational vehicles), not necessarily related to transportation per se.

    3. tropospheric

      Refers to the lowest portion of the atmosphere, from the surface of Earth out to about 5 miles above the surface.

      The troposphere contains all the breathable oxygen in the atmosphere sustaining all life on Earth.

    1. diffusion

      Spontaneous movement of a substance due to the difference in its concentration between different areas. For example, if you put a tea bag in water, the tea leaves will spread by diffusion, giving the water its color.

    2. isotherm

      A curve joining points measured at the same temperature. In this case, the water uptake capacity of the MOF is measured by varying either the humidity or the vapor pressure but keeping the temperature constant (isotherm) during the measurement.

    3. passive heat sink

      Heat sinks are devices that are used to transfer heat, usually to keep a hot component cool. Although active heat sinks like fans require an input of energy, passive heat sinks are usually made of aluminum fins and rely on their surface area to dissipate heat and do not require energy.

    4. UiO-66

      A different metal-organic-framework. The name UiO is used for the MOFs developed at the University of Oslo. This MOF is constituted of the same metal clusters as MOF-801 but with different linkers between them.

    5. metal-organic framework

      Structure composed of metal ions linked together by small molecules. This structure repeats itself to form a network that is often porous and can be used to trap chemicals in their cavities like a sponge.

    6. low-grade energy

      An energy that cannot be fully converted into another type of energy. Heat is considered a low-grade energy. Low-grade energies are naturally less expensive than high-grade energies such as electricity.

    1. climatic refugia

      Regions where the speed and variability of climate change are lower than in the surrounding area. These climate refugia have the potential to act as "safe havens" where species can retreat to and persist as the climate changes.

      A similar concept is the glacial refugia used by many species during the last ice age. Visit the Encyclopedia of Earth for more information on refugia.

    2. behavioral thermoregulation

      Thermoregulation is the process through which animals increase or decrease their body temperature. Thermoregulation can be done physiologically (e.g. by sweating to cool down during a hot day), or can be done behaviorally (e.g. by taking shelter in the shade during the hottest parts of the day).

      Common examples of behavioral thermoregulation are lizards or butterflies basking in the sun. (Photo courtesy Discover Wildlife)

    3. Palearctic

      One of eight "realms" that divide Earth's surface. It comprises Europe, North Africa, Asia (north of the Himalayas), and the northern and central Arabian Peninsula. The Palearctic is primarily boreal/subarctic and temperate in climate.

    4. sampling intensity

      Refers to the thoroughness of people having surveyed a region for species observations. Certain regions and times are more surveyed than others for often mundane reasons, such as accessibility. For example: If a flood washes out the road to a popular park, the park will likely not be searched as often until the road is rebuilt.

      These differences in sampling effort between regions and time periods can create trends within the data that are not real. For instance, in the aforementioned example, after the road is washed out and sampling effort decreases, it would appear as if there are less organisms in the park, when in reality there could be the same number of organisms and just fewer people to record them.

      In this study, the authors account for differences in sampling intensity by only including species in their study if they had over 100 observations in a baseline time period, and over 30 observations in each other time period.

    5. phylogenetic tree

      Describes the evolutionary relationships among organisms (i.e. how related is one organism to another), based off of similarities and differences in physical or genetic characteristics.

      Visit here for more information on what phylogenetic trees are and how scientists build them, by Khan Academy.

    6. phylogenetic generalized least-squares models

      Tests for a relationship between two or more variables, while accounting for phylogeny (i.e. the fact that some species, or lineages, are more closely related than others).

      "Regular" models, such as Generalized least-squares models, or Ordinary least-squares models, also test for a relationship between two or more variables, but these tests assume that variables and species are independent (i.e. are all equally related). When this assumption is violated, the test results can be biased.

    7. full extents of their latitudinal and thermal limits

      Latitudinal range limits are the northernmost and southernmost edges of where a species can be found.

      Thermal range limits are the hottest and coldest places of where a species live.

    8. georeferenced observations

      "Georeferenced" means that we know where a species observation was made. This means that we have the latitudinal and longitudinal coordinates for the location where someone found a particular species. It's not just a description of the place, like "third mountain from the left, in Colorado," because that doesn't help us know where a species was found very reliably. These days, it's a lot easier to figure out those coordinates, because most smartphones include GPS that records exactly where something is found. This is the same feature that lets a user track where they are on a map, use Pokémon Go to find an elusive Pokémon, and so on. But instead of finding virtual animals, we can record where the real ones are found. But records from a hundred years ago (obviously) didn't get stored using smartphones, so there's a lot of manual work needed to figure out where those records came from.

    9. land-use intensification

      Common land-uses include: agriculture, urban space, or wilderness. An intensification of a land-use means that the human influence on the land has increased, but without changing the type of land-use. Typically this includes an increased output of pollutants.

      For example, while a pesticide-heavy, monocultured farm field has the same land-use as a pesticide-free organic farm, the intensity of land-use at the monocultured farm would be greater, even if the farms were the same size.

    1. DNA

      Deoxyribonucleic acid, or DNA for short, is one class of genetic material. It is an example of a nucleic acid molecule.

      DNA is composed of three chemical building blocks: a sugar (called deoxyribose), a phosphate group, and a nitrogenous base.

  3. Sep 2018
    1. d-dimensional

      When a vector is d-dimensional, d refers to a placeholder value that could stand for any integer, depending on how many feature values are associated with each image.

    2. hash function

      Hashing is used in computer science to reorganize large data sets (regardless of their size) into tables of fixed size. During this process, multiple data points will typically be stored in the same bin (or hash) based on how similar they are. The hash is then represented with a shortened name, or key, that takes up less storage space in the computer.

      In other words, this process helps compress the data so that a computer can use it more efficiently. It also makes it easier and faster to look up data in the table.

      ![] (https://upload.wikimedia.org/wikipedia/commons/5/58/Hash_table_4_1_1_0_0_1_0_LL.svg)

    1. bumblebee

      Not all bees are honeybees! There are actually about 25,000 different species of bees, and the European Honeybee is just one. Bumblebees (genus Bombus) can be distinguished by their fuzzy abdomens and generally larger size.

      Check out this infographic from Gould (2015) showing the different families of bees, and "bee hotspots" around the world.

      (c) Gould 2015

    2. Experimental relocation

      Also known as assisted colonization or facilitated colonization, is the act of deliberately moving a species to a different habitat, that the species would have eventually occupied given enough time or the removal of another barrier to its natural dispersal. This is in contrast to other types of assisted migrations or species introductions, where species are moved to completely new regions that they would likely never see without human intervention (e.g. the introduction of Cane Toads to Australia, or mongoose in Hawaii).

      In this instance, the authors suggest that controlled and carefully managed relocations of bumblebee colonies further north could help these species to track climate change and avoid range compressions.

    3. range shifts

      Indicates a change in where species are found. There are two ways this can happen. First, a species can move into a new place where it never used to be found. Second, a species can disappear (or go locally extinct) from a place where it used to be found.

    1. dopaminergic (DA) neurons

      Cells that synthesize and release a compound called dopamine, commonly referred to as a neurotransmitter. Neurotransmitters are released at distant structures of a neuron that come into contact with close or distant cells, called synapses.

    1. Variant Description ModelThis model type is used to describe the set of features of a single productin the product line. Taking the Input Models of a Configuration Space andmaking choices where there is variability in the Input Models creates thesemodels
    2. Family ModelThis model type is used to describe how the products in a product line willbe assembled or generated from pre-specified components. Each compo-nent in a Family Model represents one or more functional elements of theproducts in the product line, for example software (in the form of classes,objects, functions or variables) or documentation. Family models are de-scribed in more detail in Section 5.4, “Family Models”.
    3. Feature ModelThis model type is used to describe the products of a product line in termsof the features that are common to those products and the features that varybetween those products. Each feature in a Feature Model represents a prop-erty of a product that will be visible to the user of that product. These mod-els also specify relationships between features, for example, choices be-tween alternative features. Feature Models are described in more detail inSection 5.3, “Feature Models”.
    1. oxidation

      In Earth's atmosphere, oxidation generally involves the reaction of a chemical species (such as a VOC) with an oxygen-containing molecule (such as ozone) or a radical (such as OH). The oxidized molecule will generally be less volatile and more water soluble than the starting material. The oxidized product may condense more easily (due to lowered vapor pressure) and form SOA in the atmosphere.

    2. three-way catalytic converters

      An emission control device that simultaneously removes three air pollutants from tailpipe exhaust by oxidizing carbon monoxide and VOCs, and reducing nitrogen oxides.

    3. secondary organic aerosols

      Small particles that are formed in the atmosphere from the oxidation (a type of chemical reaction) of carbon-containing gases such as VOCs. Later referred to as SOAs in this paper.

    1. aircraft penetrations

      As part of weather missions, certain aircraft literally penetrate to a storm's center in order to drop sensors that can transmit information about the storm back to the National Hurricane Center.

      This supplies data on environmental conditions of different storms in order to directly compare against satellite images.

      For more information, check out the "Hurricane Hunters" tab on NOAA"s website: https://www.noaa.gov/explainers/hurricane-forecasting

    2. aircraft reconnaissance

      The Department of Defense in conjunction with the National Oceanic and Atmospheric Administration (NOAA) have access to a fleet of aircraft to conduct hurricane/tropical cyclone reconnaissance, general surveillance, and research missions.

      The aircraft take measurements of geographic position, pressure height and altitude, wind direction and speeds, temperature and dew point temperature among others. These data are collected anywhere from every 30 seconds to every half hour while in flight. Up to five reconnaissance missions may go out in a day.

      This image shows some of the types of aircraft used by the U.S. to study hurricanes: Image from NOAA's Hurricane Hunters