5,090 Matching Annotations
  1. May 2016
    1. CA2 region

      Not much is known about the CA2 region of the hippocampus, but it has been shown to be instrumental for certain forms of learning, memory, and social behavior.

    2. Kenyon cells (KCs) in mushroom bodies of the insect brain are similar in function to hippocampal neurons

      Kenyon cells are a type of Mushroom Body neuron that are responsible for learning and memory. The authors highlight similarities between Kenyon cells and mammalian hippocampal neurons, as both are involved in learning and long- and short-term memory.

      During Alzheimer's disease in humans, early symptoms like memory loss and disorientation are due to damage to the hippocampus.

      See here to learn more!

    3. associative learning

      Associative learning is the process by which one learns to associate one stimulus with another, or with a stimulus and a behavior.

      For example, Pavlov's dogs learning to associate the ringing of a bell with receiving a treat is an example of associative learning.

      Watch this video to learn more about learning.

    4. sensory input

      i.e. information acquired using the senses: sight, smell, touch, taste, hearing.

    5. nicotinic acetylcholine receptor (nAChR)

      Nicotinic aceylcholine receptors (nAChR) are a type of ligand-gated ion channel - ion channels that open in response to binding its specific signal molecule, or ligand.

      nAChR can be activated by two possible ligands — acetylcholine, a neurotransmitter, and nicotine.

    6. genera

      The plural of "genus," a group of organisms ranking above "species" and below "family" in modern taxonomy.

    7. action potential firing threshold

      When a cell is not firing, it is "at rest." The resting potential of a cell is the difference in charge between the inside of the cell and the environment outside it. For the average human neuron, the resting membrane potential is approximately -70 millivolts, meaning the inside of the cell has a charge that is 70 millivolts lower than the outside.

      While a resting potential occurs when a neuron is at rest, an action potential occurs when a neuron is firing.

      Neurons send signals down their axons, long arms that conduct electrical impulses down the neuron (typically away from the neuron's cell body.) An action potential occurs when neurons send these signals down their axons, causing a short, fast increase in electrical activity. Scientists therefore often refer to action potentials as nerve "spikes" or "impulses."

      Action potentials are caused by the passage of ions through a membrane; the electrical current that results from this passage is how neurons send signals.

      Image Description

      When a neuron receives a stimulus, a sodium channel opens first. As the inside of the cell is negative (remember the -70 mV resting potential!), positively-charged sodium ions waiting outside the cell move into the cell through this open channel.

      As the positively-charged ions enter the cell, the charge inside the cell increases slowly at first. If the potential inside the cell doesn't increase to a certain firing threshold (in human neurons, -55 mV), the result is a small, localized increase in potential called a graded potential. The neuron doesn't fire in response, and the signal is not sent down the neuron's axon.

      If, however, the firing threshold is achieved, voltage-gated sodium channels open and the resulting rapid influx of sodium ions causes the spike in electrical activity that we call an action potential. The charge inside the cell rapidly approaches 0 mV, then crosses it to reach a maximum potential of about +40 mV. This rapid increase in the cell's potential is called depolarization.

      In response to the increasingly positive charge inside the cell, the voltage-gated sodium channels close and potassium channels slowly begin to open. As the cell is now positively charged relative to the environment outside it, positively-charged potassium ions inside the cell exit through the channels.

      The action potential then decreases back down to -70 mV, a process called repolarization, and actually passes a little bit below it (hyperpolarization), as the potassium channels stay open slightly longer than necessary.

      Ion levels within the cell gradually balance out to resting levels with the help of Sodium-Potassium ion pumps, and the cell returns to its -70 mV resting potential.

      All action potentials for neurons of the same size will always have the same magnitude. So in the case of human neurons, the action potential will always reach +40 mV, no more, no less. So how do our nerves convey signals of different intensities?

      While the magnitudes of these action potentials don't vary, their frequencies can. The more action potentials occurring in a given time frame, the more intense a signal the neuron is sending.

      For a great visual explanation of these concepts, watch the Crash Course video here.

    8. classical conditioning of feeding responses (proboscis extension reflex)

      Classical conditioning is a form of learning in which a subject learns to associate a neutral stimulus (in this case, the floral odor), with a stimulus of biological significance (in this case, receiving sugar), which elicits an innate, often reflexive, response (the extension of the honeybee's proboscis, or mouthpart).

      As a result of this association, the first stimulus (the floral odor) is able to elicit the conditioned response (proboscis extension), even though it previously elicited no response at all.

      See here for a great review of the history of classical conditioning of honeybees, as well as a detailed description of the methods involved.

    9. Mann-Whitney

      The Mann-Whitney U Test is a statistical test used to test the null hypothesis that two populations (in this case, the caffeine concentrations from C. canephora and C. arabica) are the same, against an alternative hypothesis (in this case, that the mean caffeine concentration in one genus is greater than that of the other).

      Put simply, this test allowed the scientists to determine whether or not the caffeine concentrations were significantly different.

      This particular test is necessary when you are comparing two groups (in this case, the mean caffeine concentration of Citrus and Coffea) whose data is not distributed across a bell-curve, or in other words is not normally distributed (see here).

      See here for a more detailed explanation of nonparametric statistics and the Mann-Whitney U Test.

    10. spike-timing–dependent plasticity

      Spike-timing-dependent plasticity adjusts the strength of connections between neurons in the brain based on the relative timing of a particular neuron's output and input spikes (or action potentials).

    11. memory trace

      A memory is the thing remembered (a scent, a sound, an event, etc.), but the "memory trace" is the structural alteration of brain cells that occurs after learning that, in a way, serves as a physical representation of that memory.

    1. defensive self-evaluation

      Defensive self-evaluation is a form of self-evaluation that is affected by external sources, such as the evaluations of other people.

      Defensive self-evaluation is less stable than "secure" self-evaluation, which is driven by internal sources.

    2. Positive and Negative Affect Schedule: Expanded Form (PANAS-X)

      The Positive and Negative Affect Schedule scale is a very common way of measuring an individual's mood.

      The scale involves the presentation of a list of different emotions (e.g., cheerful, sad, relaxed, distressed), and participants are asked to rate to what extent they currently feel each emotion.

      The expanded form of the scale involves emotions that can be split into a number of different dimensions: general positive affect, general negative affect, basic positive emotions, basic negative emotions, and "other" affective states (shyness, fatigue, serenity, and surprise).

    3. Conservatism

      In a footnote, the authors explain that "conservatism" is a complex concept, involving many different factors. So in this research, they restrict their research to U.S. samples and use multiple different ways of defining conservatism.

      They use participants' self-reported political ideology (Study 1), party affiliation (i.e., Republican versus Democrat) (Study 2), congressional voting records (Study 2), social media use (Study 3), and involvement with liberal and conservative organizations (Study 4).

    4. meta-analytic review

      A "meta-analysis" is a kind of statistical technique for analyzing results across many different studies that all examine the same thing.

      So, this meta-analytic review of the topic (done by Onraet, Van Hiel, and Dhont, 2013) looked at data from close to 70,000 participants, across 97 studies, all of which examined the relationship between political ideology and happiness in some way.

    5. personal agency

      "Agency" refers to the extent that people feel like they have personal control over their lives.

      The more agentic someone feels, the more he or she feels like they are free to make personal choices.

    6. “ideological happiness gap”

      The "ideological happiness gap" is a way of referring to this self-reported difference in happiness between conservatives and liberals.

      That is, there is a "gap" in levels of happiness, based on political ideology.

    7. “big data”

      "Big data" is a relatively new term, and it refers to collecting information from an exceptionally large data set.

      Studies that use "big data" do not involve running an experiment in a laboratory; instead, they involve analyzing data that are already out there in the world.

      Social media platforms, such as Facebook or Twitter, are common sources of "big data."

    8. self-enhancing

      "Self-enhancement" is the act of making yourself seem better (or, in this case, happier) than you really are.

      It's the idea of putting your best foot forward, and it helps people feel good about themselves and maintain self-esteem.

    9. mediated

      "Mediation" is a statistical term, which tries to answer the question of 'why' a relationship between two variables occurs.

      If X causes Y because of Z, then Z mediates (or explains) the relationship between X and Y.

    10. subjective well-being

      "Subjective well-being" (SWB) refers to an individual's perception of personal happiness and quality of life.

      SWB is often meant to include mood/emotions, general happiness, and overall life satisfaction.

    1. underwater light absorption

      This is what aCDOM,λ and Kd,λ measure—see the next sentence/annotation.

    2. low pH

      pH is a measurement of how acidic a liquid is.

      Low pH means very acidic.

    3. ~2 Pg C year−1; 1 Pg = 1015 g

      This is more than 2 billion tons (!!) of carbon transferred from lakes, streams, and rivers to the atmosphere.

    4. dissolved organic carbon (DOC)

      Organic carbon is found in all soils and water on Earth and is produced by the decay of living things (plants, animals, etc.).

      Organic carbon compounds are made of carbon atoms attached to at least one hydrogen atom.

      Organic molecules can be large and contain hundreds of carbon atoms, have only one or two carbon atoms, or anything in between.

    5. permafrost soils

      Permafrost is a layer of soil that stays frozen all year—even in the summer ("permanently frosted" soil).

      Global warming is causing some permafrost in the arctic to thaw.

    1. carbon stocks

      "Carbon stocks" refers to the amount of carbon that is stored in forests. Trees, other plants, and even forest soils store organic carbon (e.g., think of photosynthesis).

    2. normalize

      To normalize data in statistics refers to adjusting the values in a way that gets rid of confounding factors, in this case these factors are the large variation in sizes of different countries and sizes of forests that are being changed in each country.

      By normalizing these data, Hansen and colleagues can directly compare the forest change in different countries.

      Normalization is akin to the saying "comparing apples to oranges," and taking the apples and oranges and making them more similar to each other so that they can be directly compared, like comparing star fruit with star fruit. (Star fruits taste like the cross between an apple and an orange.)

    1. (a proxy for family poverty),

      A proxy is a substitute. In the analysis of research, sometimes certain measurements or indicators are wanted but missing from the data set. If that is the case, a proxy measurement can be the solution.

      In this case the researcher wants to have an indication of family poverty because poverty is an important piece for understanding the background of the students involved in the study. Because free or reduced price lunches are based on household income levels, they can serve as a proxy measurement.

    2. Despite some promising observational studies (21), there is little convincing causal evidence on the effects of these short-term, low-cost programs and, to my knowledge, no experimental evidence

      Observational studies are those based only on the observation of interactions. There is no experimental intervention.

      Because the previous observational studies do not prove that summer jobs cause a reduction in violence, the author proposes an experimental research design.

    1. fibrosis

      Covered with fibrotic tissue.

      A scar on human skin is an example of fibrosis. Instead of skin cells replacing the injury, fibrotic connective tissue takes it place.

    2. growth factor

      A hormone that acts as a signal for growth in an organism. Can either be a sterol or protein.

      At the cellular level, growth factors often promote synthesis of new DNA and cell division.

    3. Schwann cell

      A type of cell that is closely affiliated with cells making up the peripheral nervous system. Briefly, these cells provide support for the nerve cells.

      They are also thought to be important in promoting the regeneration of peripheral nerves after transection

    4. wrist level blastema is grafted onto a shoulder stump

      A wrist level stump is made by transecting the "hand" of the salamander off.

      That blastema is then grafted on the shoulder stump of another salamander. The shoulder stump of that salamander is made by amputating the whole limb.

    5. A textbook/reference book that provides readers a basic foundation of regenerative biology.

    6. proliferation

      An increase in how often the cells divide.

    7. low power

      Another way of saying low magnification, zoomed far out.

    8. urokinase-type plasminogen activator receptor

      A GPI-anchored protein important in tissue reorganization events.

    9. secreted protein

      A protein that has gone through the secretory pathway and been released into the outside environment.

      For a video on protein trafficking and secretion please see: https://www.youtube.com/watch?v=rvfvRgk0MfA

    10. cutting the spinal nerves at the brachial plexus of the right limb

      The nerves that extend into the limb were cut at the brachial plexus. This is essentially the region where the limb meets body. In humans, roughly around the shoulder area.

      For an image see here

    11. atrophic

      Deformed, wasted, smaller in size.

    12. glandular

      A gland or glands or related to them.

    13. XAG2

      The authors rename the homolog of this protein as nAG in their studies. The "n" stands for newt.

    14. early bud stage

      This is a stage in early limb regeneration where the blastema is still present, but you are starting to see growth of the new limb.

    15. dissociated

      Breaking tissue or a clump of cells down into single, individual cells.

    16. rescue

      Save or reverse. To put another way, "can nAG restore limb regeneration in denervated animals?"

    17. metastasis

      The movement of cancer from one location to another.

      For example, lung cancer can metastasize and spread to the lymph nodes.

    18. pulse labeling

      BrdU was added to medium for a period of time and then removed.

      Pulse labeling, in general, is the addition of substance and then its subsequent removal.

      This is much like the pulse button of a blender where you press it for a few seconds to blend and then release it shortly after to stop.

    19. HNK1

      Stands for Human Natural Killer-1. Based on this naming what organism was originally discovered in?

    20. Xenopus

      African clawed frogs (scientific name Xenopus laevis or shortened to Xenopus) is a common model organism in biology.

    21. patterning

      Development of a pattern.

      In the case of biology, this usually refers to how a structure such as the limb becomes patterned. That is, how muscle cells are specified, how the digits are made, how the cells know to become skin cells, etc.

    22. digit stage

      The regeneration stage where digits (fingers) are clearly visible and present.

    23. contralateral limb

      The limb on the other side of the body. For example, your left arm is contralateral to your right arm.

    24. acetylated tubulin

      Tubulin is a major protein of the cytoskeleton and makes up microtubules.

      Acetylated tubulin is very similar, but has an acetyl group (COCH\(_3\)) added to it.

    25. AG proteins

      Proteins that are part of the same family as nAG.

    26. nerve dependence of limb regeneration.

      That is, for a limb to regenerate it depends on, or needs the nerve.

      Without the nerve supply to the limb, it fails to regenerate.

    1. sewage pumping stations

      Sewage Pumping Stations

      Real world image:

      Sewer pumping station

    2. gravity sewer sections

      Gravity sewer systems are used to transport wastewater by means of gravity.

      Gravity Sewer

    3. reverse osmosis

      Mostly used in seawater desalination, which means removing salt from seawater to produce drinkable water. A more detailed explanation on how reverse-osmosis works can be found here.

    4. equitable

      Fair

    5. anaerobic conditions

      Conditions in absence of oxygen.

      Another common term in this context is anoxic conditions. It refers to the conditions without oxygen but with the presence of nitrate.

    6. infrastructure

      Infrastructure (e.g. roads, bridges, pipe lines, etc.): basic equipment and structures for proper functioning of a region or organization (Reference).

    7. coagulants

      Coagulants are chemicals used to remove particulates by forming flocs and therefore increasing the weight and facilitating the gravity settling (Reference).

    8. sewage-borne diseases

      Diseases could be bacterial, viral, or parasitic. Examples: diarrhoea, hepatitis A, and giardiasis (Reference).

    9. mitigation

      Mitigation can be defined as actions to prevent damage to the property (Reference).

    10. Coagulation

      Here is an informative and funny (close to the end) video describing coagulation/flocculation process.

    11. colloidal

      Particles ranging between 1 and 1000 nanometers in diameter (Reference)

    12. hydraulic retention time

      The time needed for a component to exit the system.

    13. median

      A statistical term. When you order the numbers in a sample from lowest to highest the number in the middle gives the median value.

    14. domestic

      Domestic watewaters are produced in our homes, whereas industrial wastewaters, as the name implies, are produced as a result of an industrial activity.

    15. Sulfide

      Inorganic anion (a negatively charged ion) of sulfur

    16. drinking water treatment

      Here is a fun video showing drinking water treatment.

  2. Apr 2016
    1. sequelae

      Sequelae simply means a negative after-effect.

      In this case, it is the long-term negative impact on the bodies defense system (immune system) following a measles infection. This negative impact is also known as immunosuppression.

    2. typified

      Typified means "characteristic of", as in basically all measles virus infections will behave this way.

    3. vaccination targets remain unmet

      Unmet vaccination targets mean that countries are failing to vaccinate enough of their populations to achieve herd immunity and provide adequate protection to prevent the spread of the measles disease.

    4. polymicrobial

      Polymicrobial

      Poly = many, like how a polyhedron is a shape with many sides

      Microbial = having to do with microorganisms, or living things that are too small to see with the naked eye. Like viruses, bacteria and fungi, some of which can make you sick, and some which can be beneficial (like yogurt!)

    5. all-cause infectious disease

      All-cause infectious disease in this paper aims to describes infectious diseases other than measles. In other words, diseases caused by all infectious agents.

    6. B and T lymphocytes

      B and T lymphocytes are important cell types that make up the long-term response of your immune system.

      When the body fights off disease it uses some generic, built-in responses to be able to start controlling an infection right away, but this innate response is rarely able to cure you. After about a week, your body learns the specific pathogen that is making you sick and makes B and T lymphocytes to effectively fight off that specific pathogen, and importantly, to remember it in case you get sick with the same thing again. Using this learning response (called an adaptive immune response because it adapts to the infection you have) is how vaccines work.

      If the B and T lymphocytes you made against a specific pathogen are killed then you loose that specific response, the "memory" you built to defend yourself.

      If the number of B and T lymphocytes you have is reduced, this can also impair your ability to fight off a pathogen no matter if you have done so before.

      To learn more about how the immune system works to fight off infection you can read this free Chapter from the textbook "Molecular Biology of the Cell"

    7. interannual fluctuations in nonmeasles deaths

      Interannual fluctuations in nonmeasles deaths is another way to say "the yearly change in the numbers of nonmeasles deaths." In other words, the number of children who die from diseases other than measles changes from year to year.

      The authors in this paper will use these changes in the number of deaths, correlated to the number of measles cases, to demonstrate the long-term effect of measles caused immunosuppression.

    8. pre- and post-vaccine eras

      The pre-vaccine era is before the measles vaccine became available for the public for use in the 1960's.

      The post-vaccine era continues today, when the measles vaccine (MMR) is available to those who wish to receive it.

    9. disease mortality

      Disease mortality is the scientific term used for the amount of death a disease causes. The flu, which kills many people every year, has a HIGHER mortality than the common cold.

    10. more prolonged effect

      A more prolonged effect simply means a change which lasts longer. In this case it is a longer effect on host resistance (see next annotation).

    11. predispose

      Predispose means to make something easier to happen, in this case easier to get sick. For example, if you do not exercise and eat right you are predisposed to (or more likely to become) obese.

    12. population-level data

      Population-level data is a term that is used in statistics to describe including the entire population in your analysis. This is in contrast to using a smaller sample population to infer (make an educated guess) things about the whole population.

      For example, imagine that your entire school is the population you wish to study. If you want to collect population-level data you will need to ask everyone if they like chocolate ice cream. Sometimes this isn't possible so scientists collect the data from a smaller sample, like just your class. They learn that 75% of your class likes chocolate ice cream and so they infer that 75% of the entire school likes chocolate ice cream. This approach is easier, but it is still more accurate to survey the entire class.

      In this study, the use of full population-level data, not inferences from sample data, makes their conclusions stronger.

      A sample is part of a who population

      Food for thought: What is the population that is really important to study in this research? In other worlds, the population of a single country is really a sample of what even larger population?

    1. Facial Action Coding System (FACS)

      The Facial Action Coding System (FACS) is a system for identifying and categorizing changes in facial expression.

      Even minute anatomical changes in facial muscles (i.e., contraction or relaxation of specific muscles in the face) can be coded as distinct "action units," and there is extensive training involved in being able to identify and code these facial movements.

      The head scientist involved in designing the FACS system, Paul Ekman, is known for using FACS to detect microexpressions—brief, involuntary facial movements that can be used, among other things, in the detection of deception.

      The television show Lie To Me was loosely based on Ekman and his work.

    2. Duchenne smiling

      Named after 19th century French physician Guillaume Duchenne, a "Duchenne smile" is one that involves both the mouth and the eyes; it is considered to be a more "genuine" display of happiness, compared with a smile that only involves the mouth.

      Here's an example, modeled by psychologist Paul Ekman, who is an expert on facial expressions and emotion.

      .

      Can you tell which one is which?

      Test yourself with this short video!

    3. Linguistic Inquiry Word Count software (LIWC)

      The Linguistic Inquiry Word Count (LIWC, pronounced "Luke") software is text analysis software that can analyze linguistic content for specific words and/or categories of words.

    4. orbicularis oculi (AU6)

      This is the muscle that circles around the eye. It controls blinking, squinting, and the movement at the corners of the eyes that relates to Duchenne smiles.

      Image Description

    5. hedonic

      Hedonic well-being is characterized by the achievement/fulfillment of pleasure. It is often considered to be a relatively short-term form of happiness.

    6. zygomatic major (AU12)

      This is the muscle that controls the corners of the mouth.

      Image Description

    7. ego defensiveness

      "Ego defensiveness" is very similar to self-protection. The idea is that people have psychological mechanisms that are commonly used to protect/defend the "ego," or the self.

    8. political ideology

      "Political ideology" refers to how people identify themselves on the spectrum between liberalism and conservatism.

    9. self-report measures

      "Self-report measures" involve responses to basic survey questions. For example, asking participants how happy they are, on a scale from 1 to 10, would be a self-report measure.

    1. leukocytes

      Leukocytes are also called white blood cells. The vast majority of immune cells are leukocytes, neutrophils being one of them.

    2. integrins

      Integrins are another class of cell adhesion molecules. These receptors are known to interact with the extracellular matrix or surface proteins on endothelial cells, and help in the process of leukocyte extravasation, a process that involves the movement of leukocytes (white blood cells) through the walls of the blood vessels into the site of infection.

    3. chemokine

      Chemokines are proteins released by cells that can recruit other cells by forming a chemical gradient (similar to a trail of scent).

      Chemokines and selectins become alert/activated during an infection and, in turn, activate/trigger the integrins to initiate cellular recruitment.

      In case of cellular responses, activation involves biochemical changes in the structure of molecules, which now allow it to bind/release from certain other molecules.

      A series of such activation events is what induces a signaling cascade in cells.

    4. endothelial selectins

      Selectins are carbohydrate-binding molecules present on cell surfaces. Endothelial cells line the the walls of blood vessels.

      E-selectins are produced by endothelial cells. During an infection, selectins serve to recruit immune cells to the site of inflammation.

    5. inflammatory injury

      Inflammation, meaning swelling with redness and pain, is one of the major consequences of an immune response. However, sometimes excessive inflammation can be harmful to the host, hence referred to as inflammatory injury (injury inflicted upon the host by the body's immune system).

    6. immune response

      In general, when the mammalian body encounters a foreign object, be it a pathogen causing disease or an allergic nonpathogenic molecule, the immune cells in the system are triggered and begin a cascade of reactions in an attempt to contain and eventually eliminate the foreign entity.

    7. leukocytes

      White blood cells

  3. Mar 2016
    1. somatic

      Somatic refers to all the cells of the body that are not germline cells (eggs or sperm).

    2. germline

      Germline cells are the sex cells in the body (sperm in males and eggs in females).

    3. Drosophila

      A genus of flies that are often used as model organisms in research. They are commonly called "fruit flies."

    4. chimeric

      A chimeric fly has two distinct cell populations. In this case, a mutagenic event occurred early in the development of the female chimera, causing it to have one genotype on one half of its body, and a different genotype on the other half.

    5. wild-type

      Refers to the phenotype of an organism as it was found in nature. In contrast to a mutant allele, the wildtype phenotype is the product of the "normal" allele for a particular gene.

    6. autocatalytic

      A genetic element is autocatalytic if it converts the companion chromosome to its own state.

    7. homology arms

      Homology arms are DNA sequences in a plasmid that are identical to a specific genomic DNA sequence. The homology arms are used to direct homologous recombination of a plasmid into the genome.

    8. mosaics

      Mosaic organisms have multiple cells populations with different genotypes. In this case, the mosaic flies had small patches of brown color but were mostly yellow.

    1. inland waters

      Lakes, rivers, streams, etc. (NOT the ocean)

    2. surface waters

      Lakes, rivers, streams

    3. labile

      susceptible

    4. residence time

      Amount of time a molecule exists before it is broken down

    5. wavelength

      Light travels from place to place in the form of a wave. All types of light have a characteristic wavelength. In the visible spectrum, red light has the longest wavelengths and purple has the shortest. UV light has shorter wavelengths than visible light.

    6. shallow-headwater stream

      Headwater streams are small, shallow streams that carry water from the surrounding land area into a main river.

    7. glacial-fed

      Indicates that the water in this river came from melting glaciers

    8. residence times

      The amount of time that water stays in a lake before evaporating or flowing into another body of water.

    9. benthic

      Benthic is a word used to describe things that take place in the sediments at the bottom of a body of water.

    10. bacterial respiration

      Bacterial respiration is when microbes “eat” organic carbon, causing it to break down into smaller molecules. In most cases, bacteria require oxygen to break down organic carbon.

    11. photochemical oxidation

      Photochemical oxidation is when sunlight and oxygen react with organic carbon, causing it to break down into smaller molecules

    12. ultraviolet (UV) light

      The invisible component for sunlight that is responsible for sunburn and breaks down organic compounds. UV light has a shorter wavelength than visible light. See this link for more information.

    13. photochemical degradation

      This video, made by people who work with primary author Rose Cory, explains what photodegradation is.

    14. At the basin scale

      In other words, over the area where rain water flows into the river and lake system we studied.

    15. mineralization

      Mineralization refers to the break down of organic molecules to inorganic molecules. For the purposes of this paper, it means conversion of organic carbon to carbon dioxide.

    16. N

      N represents the number of samples tested.

    17. quantum yields

      Quantum yield is a measurement of how much of a chemical reacts when exposed to light. For example, in this study it would be the amount of carbon dioxide produced divided by the amount of UV sunlight absorbed by dissolved organic carbon.

    18. ice-out

      The day in the spring when all of the ice in a lake has melted.

    19. Areal rates

      Areal rate refers to the amount of something that happens over an amount of surface area. For example the rate of bacterial respiration is measured as the amount of oxygen released per day, but the areal rate would be measured as the amount of oxygen released per square meter per day.

    1. attribution bias

      This refers to how we interpret our own behavior as well as the behaviors of the people we interact with.

    2. remediation

      Remediation means trying to resolve a problem once it has already occurred. In this case, the author is referring to remediating violence.

    3. About 20% had been arrested at baseline, and just over 20% had been victimized

      Baseline measurements are measurements that report on the sample population prior to the experiment. In this case, prior to the start of the jobs summer jobs program, 20% of the youth in the study had been arrested and 20% had been victims of violent activity.

    4. operative mechanism

      By operative mechanism, the author is referring to the thing or factor that helps us understand why this summer jobs program helps reduce violent crime.

    5. The empirical literature

      Empirical literature refers to articles that are based on data that has been collected in a field (real-world) or laboratory setting. Because science is a process that builds upon itself, scientists are always looking to see what the existing empirical literature establishes so that a study that presents something new can be designed.

    6. outcome measures

      In this experimental study, outcome measures refer to violent activity as well as other types of crime and schooling outcomes. This paper reports specifically on whether summer jobs have any affect on violent activity.

    1. disturbance

      What is a disturbance, in this context? In ecology, a disturbance is anything that changes the ecosystem. For example, a forest fire, tornado, human activity (building more houses in an area that used to be a grassland), etc.

    2. moratorium

      Not being allowed to do a particular activity (in this case, cut down forests) for a set amount of time

    3. aggregate dynamic

      Aggregate dynamic refers to the combination of forest loss and gain.

    4. slower regrowth dynamics

      Why do boreal forests grow slower than other forest types? For starters, boreal forests have shorter growing seasons. Also, boreal forests have only conifer tree species that do not grow as quickly as deciduous trees.

    5. carbon storage

      Why is carbon storage important? Find out by following this link to explore carbon "sequestration" (just a fancy term for "storage") and how this process can help curb global warming.

    6. importance of forest ecosystem services

      What are important ecosystem services that forests provide?

      First, let's break this down into what an ecosystem service is. These services include any benefit that an ecosystem can provide to people.

      So, what can forests provide that benefit people? Here are some examples: Forests provide timber, store carbon, purify air and water, and provide space for recreation (e.g., hiking in the woods!).

    7. biodiversity richness

      Richness is simply the number of different species.

      Biodiversity refers to the diversity of biology (a.k.a. the number of different species).

      Putting this all together, we can determine that forests, compared with other types of ecosystems (e.g., deserts), have a lot of different species of plants, animals, bacteria, etc. (this is especially the case in tropical forests).

    8. spatially explicit

      Describes where things are in relation to each other. In this case, the satellite images of Earth provide a clear picture of where forests are located and distributed.

      Imagine having spatially explicit data of Earth's surface, all collected at the same time. This is what satellite-based imaging systems do. By examining these pictures over time, we are able to map forest loss and gain. Imagine trying to do this task from the ground. It would be very hard indeed.

    9. tropical, subtropical, temperate, and boreal

      Tropical: Areas near Earth's equator that are warm/hot year-round with consistent or seasonal rainfall.

      Subtropical: Areas with hot and humid summers and mild winters.

      Temperate: Areas with four seasons (summer, fall/autumn, winter, and spring) divided mainly by differences in temperature.

      Boreal: Subarctic areas with long, cold winters and short, cool summers.

      Check out where these climate domains/zones are around the world on this map.

    10. deforestation dynamics

      "Deforestation dynamics" refers to changes (i.e., dynamics) in forests due to cutting down trees and replacing them with nonforest land uses, such as agriculture or development (houses, buildings, etc.).

    11. statistically significant trend

      This wording implies that Hansen and colleagues ran a statistical model to determine whether the loss or gain in forest cover over time was more or less than what you would expect if forest cover did not change.

      The tropics experienced a clear increasing rate of forest loss, expressed in units of forest area loss per year, whereas other climate domains (e.g., temperate, boreal, subtropical) all lost and gained forest cover

      However, when you add all of the subtropical regions of Earth together, for instance, there isn't a clear net loss or gain in forest cover. This is because of the fact that most forest change in the subtropics is due to forestry land uses where trees are grown as a crop. In forestry land uses, trees are continuously grown and cut down to make products such as lumber and paper.

    12. short-cycle tree planting and harvesting

      This statement refers to "short rotation forestry," which is a type of forestry that densely plants fast-growing tree species (e.g., poplar trees).

      Once these trees reach a certain size (e.g., stems that are 10–20 cm in diameter at breast height), they are then cut down and harvested for lumber, pulp, and paper products, or energy.

      The trees then regrow from the stumps, sending up new trunks. This process of cutting down a tree to stimulate regrowth is called "coppice."

    13. systematic global image acquisitions

      In this context, the authors are describing the satellite images—these images are widespread (e.g., systemic) in that they photograph the entire surface of Earth.

    14. Google cloud

      The authors used Google Earth Engine to process the Landsat images.

      The Google Earth Engine is a cloud platform, meaning that a network of thousands of computers works together to perform a task that a single computer would take years to do.

      Similarly, Google Cloud provides the same features. Google Cloud allows you to store, manage, and process information on computer servers that are accessed through the Google Cloud website.

      Cloud computing is especially helpful for processing large amounts of data/information.

      Hansen and colleagues processed 700,000 images of Earth. Processing this information through the Google Earth Engine with 10,000 computers took approximately 15 days. If the authors only had one computer to work with, these calculations would have taken a few years!

  4. Nov 2015
    1. cortical networks

      Connections in the brain between brain cells (neurons) in the cortex (the surface level, grey-matter of the brain).

      Click here to see a picture of the cerebral cortex

    2. catastrophizing

      The belief that something is much worse than it actually is.

    3. interpersonal interactions

      interactions between people, for example when you have a conversation with someone or work with other people to solve a problem.

    4. olfactory

      Smells

    5. auditory

      Sounds

    6. SWS × REM sleep duration

      A measure that reflects the amount of time participants spent in slow-wave sleep and rapid-eye-movement sleep.

      It is calculated by multiplying the number of minutes of SWS by the number of minutes of REM sleep.

    7. declarative

      Declarative memories are memories of facts (e.g. the U.S. Declaration of Independence was signed in 1776) and personal life events (e.g. your 10th birthday).

      Declarative memories are generally able to be consciously recalled.

      Click here for more information

  5. Oct 2015
    1. DNA binding protein

      DNA binding proteins recognize and bind with specific DNA sequences. They are useful not only in genomic editing but also in regulation. http://www.wiley.com/college/pratt/0471393878/student/structure/dna_binding_proteins/index.html

    2. homologs

      Other genes derived from a common ancestor

    3. ZFNs and TALENs

      These are the two existing commonly used genetic editing strategies.

    4. Sanger sequencing

      Sanger sequencing is a method of reading DNA codes which relies on normal and modified deoxynucleosidetriphosphates (dNTPs). The modified dNTPs terminate the sequence prematurely, and the sequence is then assayed https://www.thermofisher.com/us/en/home/life-science/sequencing/sanger-sequencing/sanger_sequencing_method.html

    5. polymerase chain reaction (PCR)

      This is a method for rapidly increasing the amount of a sample of DNA by artificially replicating the DNA using a polymerase.

    6. oligo donor

      A DNA sequence derived from self.

    7. multiplexed editing

      Editing using more than one targeting strategy.

    8. NHEJ events

      In non-homologous end joining splices in DNA are repaired by splicing rather than by referring to an intact complementary strand of DNA. This method of repair is less accurate than homologous recombination.

    9. GFP reporter assay

      This is the integrated reporter mentioned earlier in the paragraph.

    10. PGP1 human induced pluripotent stem (iPS) cells

      Induced pluripotent stem cells come from adult cells which have been artificially changed to exhibit stem cell properties. These properties are immortality and the ability to develop into various different cell types. These cells are thus unspecialized. https://www.thermofisher.com/us/en/home/references/protocols/cell-culture/stem-cell-protocols/ipsc-protocols/generation-human-induced-pluripotent-stem-cells-fibroblasts.html

    11. K562 cells

      This cell line is derived from myelogenous leukemia cells and is considered an excellent target to test the function of natural killer cells. http://www.atcc.org/products/all/CCL-243.aspx

    12. 293Ts

      These cells are the human embryonic kidney cells mentioned above.

    13. ubiquitously expressed

      These are genes which are expressed in almost all the cells or an organism.

    14. chromosome 19

      Chromosome 19 includes about 1500 genes and 59 million base pairs. For a brief summary of chromosome 19 see http://ghr.nlm.nih.gov/chromosome/19

    15. PPP1R12C gene

      This is a gene concerned with protein phosphatase regulation http://www.genecards.org/cgi-bin/carddisp.pl?gene=PPP1R12C

    16. AAVS1 locus

      This is a site on human chromosome 19 which the adeno associated virus type 1 targets.

    17. native locus

      The researchers now turned to modifying a natural DNA sequence.

    18. integrated reporter

      The integrated reporter was the green fluorescent DNA sequence which was integrated into the target DNA. The green fluorescent sequence could then be manipulated, and the results could be measured.

    19. DNA methyl transferase 3a (DNMT3a
    20. 3′ end

      DNA strands have 2 ends, a 3' end and a 5' end. The 3' end is joined to the 5' end of the complementary strand.

    21. Cas9D10A

      This is an enzyme which nicks specific sites in the genome without damaging unintended sites.

    22. heterodimer

      Heterodimers are molecules composed of two different macromolecular chains.

    23. TAL effector nuclease

      A transcription activator-like effector nuclease is an artificial restriction enzyme (enzyme that cuts DNA at a specific spot). Talens are created by fusing DNA binders to DNA cleavers. They are modeled from proteins secreted by Xanthomonas bacteria. http://bfg.oxfordjournals.org/content/early/2014/06/06/bfgp.elu013.full

    24. multiplex editing

      Multiplex editing aims either to make several different changes at once or changes in several different locations of the genome at once.

    25. exons

      Exons are parts of genes that code for proteins.

    26. Homologous recombination

      Homologous recombination is a naturally occurring method of repairing breaks to DNA. This method relies on the unbroken strand of DNA to correct errors on the broken strand. https://www.qiagen.com/us/shop/genes-and-pathways/pathway-details/?pwid=143

    27. AAVS1 locus

      This is a site on human chromosome 19 which the adeno associated virus type 1 targets.

    28. 68-bp

      Since DNA consists of a double strand, the bases form into pairs such that cytosine always pairs with guanine and adenine always pairs with thymine. A 68 bp sequence would contain 68 of these pairs.

    29. genomically integrated GFP coding sequence

      This means that the green fluorescent protein is integrated into the host's DNA

    30. stable cell line

      A stable cell line is one in which there is little variation from one cell to another. Another desirable characteristic of stable cell lines is that most of the cells are not actively dividing unless they are stimulated to do so by the researcher. https://www.mirusbio.com/tech-resources/tips/generate-stable-cell-lines

    31. human embryonic kidney HEK 293T cells

      These cells were developed from the kidney of a human embryo. They are easy to grow, and it is easy to introduce foreign nucleic acids (RNA and DNA fragments) into them. http://www.atcc.org/products/all/CRL-3216.aspx#documentation

    32. GN20GG

      The system can target sequences between one guanine (G) followed by 20 nucleotides (pairs of amino acides) and ending with two guanines in a row (GG).

    33. U6

      The U6 gene is commonly found throughout the human genome. It is also a well studied gene

    34. PAM (protospacer-adjacent motif)

      The PAM is a short DNA sequence close to the targeted DNA sequence of the invading organism. The PAM is crucial for the system to recognize whether or not the DNA sequence is self or not self. If the PAM is missing the system will not be activated

    35. human U6 polymerase III promoter

      An enzyme important in the production of short RNA

    36. Cas9 protein

      The Cas9 protein is the hallmark protein of type II CRISPR systems

    37. genome engineering

      Genome engineering is targeted change in the DNA sequence.

    38. RNA

      In contrast to DNA, which is a double strand of linked amino acids, RNA is a single strand. The four "letters" in the DNA alphabet are adenine, thymine, cytosine, and guanine. RNA is made up of adenine, thymine, and cytosine, but in place of guanine it has uracil.

    39. cleaving

      Breaking

    40. eukaryotic

      Eukaryotic cells have a membrane around their nucleus, in contrast to prokaryotic cells such as bacteria or archaea.

    1. cognitive

      Having to do with mental processes for example memory, language, problem solving, and creativity.

    2. affective

      Having to do with emotions

    3. memory consolidation

      The process by which memories become more stable (less likely to be forgotten). The authors' work is based on previous findings that sleep is particularly important for memory consolidation.