4,406 Matching Annotations
  1. Jun 2016
    1. neurogenesis

      Generation of neurons from neural stem cells and neural progenitor cells.

    2. neural stem cell

      Neural stem cells are cells that are able to self-renew, and are capable of differentiating into any cell type in the central nervous system.

    3. neurogenic niche

      A specialized microenvironment favorable to the regulation of stem cells in the nervous system.

    4. central nervous system

      The central nervous system is a complex network of nerve tissues that control functions of the body. It consists of the brain and spinal cord.

  2. May 2016
    1. cellular materials

      Cellular materials (materials with a significant amount of porosity) present a number of properties (namely low weight, high sound absorption, crashworthiness, high permeability, thermal properties) that make them suitable for a large range of applications.

    2. “mechanical metamaterials”

      Metamaterials are a class of objects whose properties are related to the geometrical properties of the constituting structure and not to the mechanical properties of the constituting material.

      These metamaterials present properties not obtained with regular materials.

    3. buckling-dominated failure

      Buckling is a phenomenon of instability: A slender structure submitted to a compressive load can bend and deform in the direction perpendicular to the compression axis.

      The structure will then be submitted to a bending load rather than a compression load.

    4. “ductile”

      Ductile is the opposite of brittle. A ductile material can deform plastically without breaking when subjected to a load.

    5. brittle

      A brittle material submitted to a stress breaks without significant deformation.

    6. tetrakaidecahedron

      A tetrakaidecahedron, also called tetradecahedron (from the Greek words tetra, four, and deca, 10) is a polyhedron with 14 faces.

    7. hysteresis

      A material is said to present hysteresis if its behavior depends on the current loads applied and on the history of the past loads.

      For example, a material that presents hysteresis will not sustain the same stresses if the strains are increasing or decreasing: The stress-strain curve will present a loop.

    8. Uniaxial compression studies

      This parameter characterizes the ability of a material to withstand loads tending to reduce its size in one dimension.

      It is defined as the maximum force per unit area of a material to withstand loadings before it fails plastically (i.e., in a permanent and irreversible way) or fractures.

    9. their Young’s modulus E

      Young's modulus is a parameter used to characterize the stiffness of a material.

      It is defined as the ratio between the stress (force per unit area) and the strain (displacement normalized by the initial length) and it is expressed in Pa.

    10. sintering

      Sintering is the process of forming a solid mass of material by heating or pressuring particles of this material without reaching the melting point.

    11. atomic layer deposition (ALD)

      Atomic Layer Deposition is a method to deposit a thin film on a substrate. It consists of exposing the surface of the substrate to gaseous species.

    12. electroless nickel plating

      Electroless nickel plating is a chemical technique to deposit a layer of nickel alloy on a solid piece made of another metal or of plastic.

    13. Scanning electron microscopy

      Scanning electron microscopy is a technique used to image the surface of a sample with a high resolution. (The resolution is in the nanometer scale.)

    14. three-dimensional CAD model

      The first step to manufacture a piece with 3D printing techniques consists of designing a numerical or analytical model of it.

      Software called computer-aided design software can help create a 3D model of the desired piece.

    15. photomask

      A photomask defines the area that will be illuminated. For the stereolithography technique, this area corresponds to a 2D cross section of the object.

      To get the complete 3D object, different photomasks must be generated for each slice, each 2D cross-section.

    16. spatial light modulator

      A spatial light modulator is a device that allows one to modify the characteristics (phase, intensity, or polarization) of a light beam.

      In this article, the spatial light modulator is used to define the mask, the area that will be illuminated.

    17. photosensitive

      The photosensitivity is the ability of some materials to react to the light. In this example, when the liquid polymer resin is exposed to light, it cures and becomes solid.

    18. rapid prototyping methods

      Rapid prototyping is a family of techniques used to quickly create models and prototypes, using 3D computer-aided design data. The most "famous" technique is 3D printing.

    19. tessellation

      The tessellation of a surface consists of tiling this surface using one or more geometric patterns (called tiles) without overlaps or gaps.

    20. uniaxial compressive loading

      Loading a piece of material with an uniaxial compressive load means that the load applied tends to reduce the size of the sample in one specific direction.

    21. fcc structure

      FCC structure means a face-centered cubic structure. A structure is said to have an FCC architecture if its joints are located on the eight corners of a cube and in the center of each of the eight faces of the cube.

    22. aspect ratios

      The aspect ratio is a parameter used to define the shape of a structure. For example, the aspect ratio of an image is the ratio of the width to the height.

      Here, for the struts, the aspect ratio refers to the ratio of the length of the strut to its diameter.

    23. Maxwell’s criterion

      Maxwell suggested a rule to set out the condition of rigidity for a cell structure with b struts and j frictionless joints.

    24. frictionless joints

      A joint designates the connection between two struts. This connection is supposed to be frictionless, which means that there is no force resisting the relative motions of the two connected parts.

    25. struts

      A strut is a structural component designed to resist longitudinal compression. Struts are the rod parts Fig1 A, B, C.

    26. critical features

      The critical features, in this case, refer to the dimensions of the smallest controllable feature size of the structure (for example, the length or the diameter of a strut).

    27. face-centered cubic

      A structure is said to have a face-centered cubic face if its joints are located on the eight corners of a cube and in the center of each of the eight faces of the cube.

    28. stretch-dominated

      Cellular materials can be classified in two categories: the bend-dominated structures and the stretch-dominated structures.

      If a compressive loading is applied to a bend-dominated cellular structure, the cell's edges bend. If a tensile loading is applied to a stretch-dominated cellular structure, the material responds by an elastic stretching of its struts.

      If a compressive loading is applied to a stretch-dominated cellular structure, no bending deformation exists in structural members. The material responds by an elastic stretching of its struts.

    29. fracture toughness

      The fracture toughness is a property of a material that describes the ability of this material to resist fracture.

    30. loading directions

      Generally, an object does not behave the same way when a load is applied to it along a direction or when the load is applied along another direction. Thus it is important to know what the loading direction is.

      This is especially true among previous works, such as structural honeycombs and sandwich panels.

    31. bending

      Bending = flexure. It describes the way a slender structure behaves when a load is applied perpendicularly to its longitudinal axis.

    32. stochastic

      Stochastic means random, unorganized.

    33. bulk value of the solid constituent material property

      The material properties (Young's modulus, yield strength) of a solid with a high porosity are not the same as those of a solid bar of the same material but with no porosity.

      The properties of the material with no porosity, the intrinsic properties of the material, are called bulk properties.

    34. yield strength

      The yield strength is the stress at which a material begins to deform plastically.

      Below this value, the deformation of the material is elastic: once the applied stress is removed, the material returns to its initial shape. Above this value, the deformation becomes permanent and irreversible.

    35. Young’s modulus

      Young's modulus is a parameter used to characterize the stiffness of a material. It is defined as the ratio between the stress (force per unit area) and the strain (displacement normalized by the initial length) and it is expressed in Pa.

    36. stiffness

      Stiffness is a parameter describing the rigidity of a given piece of material, i.e., the way this piece resists deformation when a force is applied to it.

      An object with low stiffness (such as a piece of rubber) will exhibit large deformation in response to an applied force. On the other hand, a material with high stiffness (like a metallic piece) will deform less if the same force is applied.

      Stiffness-to-weight ratio means the stiffness per unit mass density. This parameter characterizes the mechanical efficiency of a material.

    37. cellular materials

      Assembly of basic cells (either open or closed) with solid edges and faces packed together to form a material with specific properties.

    38. microstereolithography

      Stereolithography is a method of 3D printing. Objects are printed one layer at a time by curing a photosensitive resin with a UV source.

      Microstereolithography is the same technique applied to fabricate structures with microscale feature resolutions.

    39. microlattices

      A microlattice is a connected network of struts of microscopic size.

    40. connectivity

      The connectivity characterizes the degree by which each individual structural element is connected to others.

      For example, a connectivity of eight means each node inside the unit cell is connected with eight structural filaments.

    41. isotropic

      An isotropic object is an object whose properties are the same whatever the considered direction.

    42. microarchitected materials

      Microarchitected materials are composed of elements of microscopic size organized in a designed topology.

    43. mechanical properties

      The mechanical properties of a material are indices used to describe the way this material behaves when submitted to a load.

    1. against invading pathogens

      Check out ImmiFlex's video on Neutrophil Phagocytosis


    2. rapid shift from a symmetric morphology into a polarized form

      A rapid process that involves change in the distribution of cell surface receptors on leukocytes. This aids in the process of extravasation into the tissue from blood vessels.

    3. infarcted hemisphere

      Death of tissue when blood and oxygen supply gets blocked is an infarction. In this case, the authors observed that tissue death/infarction in the brain was decreased when neutrophils were depleted.

    4. permanent occlusion of the middle cerebral artery

      The middle cerebral artery is one of the major blood vessels that supplies blood to the brain, occlusion of this would create loss of blood to the brain and thus mimic stroke. This is a method to induce stroke experimentally.

    5. ischemic injury

      Injury when blood supply to tissues being restricted leads to shortage of oxygen in the tissue, such as during a stroke, where blood supply to brain is restricted.

    6. pulmonary microcirculation

      Lung blood flow.

    7. vascular inflammation

      Inflammation of the blood vessels.

    8. pathogenic inflammation

      Inflammatory response to a pathogen or an insult. In this paper's context, it also refers to injury-induced inflammation.

    9. mislocalization

      The original distribution of these receptors was disturbed in the PSGL-1–deficient mice.

    10. chemokine receptor CXCR2

      CXCR-2 is a receptor that binds to interleukin 8 (called KC in mice; secreted signaling proteins molecule). This activates neutrophils. Chemokines are secreted signaling molecules that attract cells to an area because of its gradient (mimicking chemoattraction).

    11. cannot propagate outside-in signals because of the absence of the cytoplasmic domain

      Cytoplasmic domain is the part of the receptor that is present inside the surface of cells. On stimulation at the surface, the transduction of signal occurs through the cytoplasmic domain/tail that further instructs the cell.

    12. Rho-GTPase

      Guanine nucleotide exchange factor belonging to the family with Rac GTPases that functions in a similar manner to Rac GTPases, described earlier.

    13. intravascular behavior

      The behavior of the neutrophils in the vasculature. In this study, this includes the mobility of the neutrophils.

    14. vessel lumen

      Inside space of a blood vessel.

    15. a guanine nucleotide exchange factor of Rac GTPases

      Rac GTPases are a class of G proteins that respond to a stimulus and transmit a signal from outside of a cell to its inside. They are usually in an "off" or inactive state when bound to a molecule called GDP (two phosphate groups).

      Dock-2 helps Rac GTPasq2es in the exchange of GDP to GTP (three phosphate groups) so that the GTPase is now in the "on" or active state to transmit signal.

    16. CD62L-enriched uropod

      CD62L is a type of selectin found on lymphocytes. It is required for lymphocytes to move from circulation through the endothelial cell lining into tissue. CD62L on lymphocytes bind to ligands on endothelial cells, particularly those present in lymph nodes, to facilitate this movement.

    17. glycosylated

      Glycosylation is the process of adding a sugar molecule to a protein or lipid.

    18. uropod

      The uropod is defined as the tail end of a cell.

    19. lamellipodia

      Motile cells develop a leading front that is made of actin filaments. Actin is a protein that is crucial for cell motility. Lamellipodia behaves like the engine of a motile cell pulling it forward.

    20. Neutrophils

      Neutrophils are also called white blood cells. These are the first cells that respond to an infection.

      They are normally found in the blood vessels, but on chemical induction owing to an infection, they migrate out of the blood vessels and into the site of infection.

    21. PSGL-1

      Interaction between neutrophils protruding into the blood vessel and platelets inside the blood vessel via PSGL-1 initiated a signaling cascade that allowed neutrophils to redistribute their cell surface receptors, polarize, and eventually migrate.

    22. polarized morphology

      For mobility of cells, polarization is a process that marks a cell with a front and tail end. The two ends usually differ in the arrangement of proteins (receptors) on the cell surface.

      Thus, polarization of cells usually results in the redistribution of receptors.

    1. arrested


    2. transecting

      Cutting in the transverse plane, or across.

    3. 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.

    4. 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.

    5. 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

    6. 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.

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

    8. proliferation

      An increase in how often the cells divide.

    9. low power

      Another way of saying low magnification, zoomed far out.

    10. urokinase-type plasminogen activator receptor

      A GPI-anchored protein important in tissue reorganization events.

    11. 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

    12. 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

    13. atrophic

      Deformed, wasted, smaller in size.

    14. glandular

      A gland or glands or related to them.

    15. XAG2

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

    16. 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.

    17. dissociated

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

    18. rescue

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

    19. metastasis

      The movement of cancer from one location to another.

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

    20. 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.

    21. HNK1

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

    22. Xenopus

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

    23. 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.

    24. digit stage

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

    25. contralateral limb

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

    26. 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.

    27. AG proteins

      Proteins that are part of the same family as nAG.

    28. 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. hippocampal networks

      Connections between brain cells (neurons) in the hippocampus.

      The hippocampus is a seahorse-shaped structure that is associated with the formation of new memories. Damage to the hippocampus results in an inability to form new memories (like in the movie Memento).

      Click here to learn more about the hippocampus

    2. sleep neurophysiology

      Brain activity during sleep - for example, sleep spindles.

    3. rapid-eye-movement (REM) duration

      The length of time spent in rapid-eye-movement (REM) sleep (the stage of sleep often associated with dreaming).

    4. slow waves

      A pattern of brainwave activity represented by slower, rhythmic activity.

      Slow waves occur most often during deep sleep and are thought to play a role in consolidation.

    5. sleep spindles

      A pattern of brainwave activity represented by bursts of fast rhythmic activity.

      Sleep spindles are not well understood but are thought to help coordinate information transfer between different areas of the brain. They may play a role in transforming memories into more permanent, long-term storage.

    6. systems-level consolidation

      Systems-level consolidation specifically refers to the process of memory stabilization that involves multiple brain regions, takes a longer time, and results in more permanent long-term memory (as opposed to synaptic consolidation which occurs more immediately after learning).

      Click here for more information on the neurological processes of memory stabilization

    7. procedural

      Procedural memories are memories for skills (e.g. riding a bike or hitting a baseball).

      When you have learned a skill, you are generally unable to consciously describe the specific knowledge that you've gained.

      Click here for more information

    8. out-group members

      People who are not part of the group being preferred (the in-group). If in one context, the group of individuals being preferred is a group of White individuals, then out-group members would be all other individuals.

    9. counterstereotype information

      Information that goes against the stereotype - in this case information that pairs Black with positive items and women with math and science.

    10. social biases

      A tendency to generalize about members of a group or to attribute certain characteristics to one group over another. These preferences and attributions can be conscious or unconscious.

      Click here to learn more about how biases have become more subtle in the last century.

    1. emotional contagion

      The tendency to feel and express emotions similar to and influenced by those of others.

    2. Pro-social behavior

      Voluntary behavior designed to help others.

    3. conspecific

      Of the same species.

    4. cagemate

      An animal that shares the same cage as another.

    5. Control conditions

      Experiments in which the variables are controlled so that the effects of varying one factor at a time may be observed.

    6. non–food-deprived

      These rats had regular access to food before the experiment

    7. empathic

      Communication of feelings, thoughts, or attitudes between individuals.

    1. Abstract

      An abstract is a short overview of the experiments and results found in a paper. In this case, the abstract outlines Hansen and colleagues' work on mapping forest cover changes across the globe through time.

      Science is interdisciplinary. Take a look at the authors who worked together on this project. Some of them are from remote sensing fields at various universities, whereas others are computer scientists and engineers at Google.


      Matthew C. Hansen (remote sensing scientist at University of Maryland, and associate team member of NASA's MODIS Land Science Team)

      Peter V. Potapov (remote sensing scientist at University of Maryland)

      R. Moore (Google)

      M. Hancher (Google)

      S. A. Turudanova (University of Maryland)

      A. Tyukavina (University of Maryland)

      D. Thau (Google)

      S.V. Stehman (Syracuse University)

      S. J. Goetz (Woods Hole Research Center)

      T. R. Loveland (U.S. Geological Survey)

      A. Kommareddy (South Dakota University)

      A. Egorov (South Dakota University)

      L. Chini (University of Maryland)

      C. O. Justice (University of Maryland)

      J.R.G. Townshend (University of Maryland)

      Also, if you are interested in taking a closer look at the results, the data from this paper are featured here.

    2. 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).

    3. 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. ecological

      Ecology is the scientific study of interactions between organisms and their environment. It considers the relationships between organisms of the same species, organisms of different species, and the nonliving, chemical and physical components of their environment.

    2. pharmacologically

      Through the use of a drug, or a molecule that has a biological effect on the cells, tissues, or organs of an organism.

    3. Coffea

      A genus of flowering plants whose seeds (coffee beans) are used to make coffee.

    4. Citrus

      A genus of flowering plants including oranges, lemons and limes.

    5. sucrose

      A naturally occurring carbohydrate commonly known as table sugar.

    6. potentiated

      To increase the power or effect of something. Often used in reference to the effect of a drug.

    7. mushroom body neurons

      A pair of structures in the brain of insects known to play a role in learning and developing memories of smells.

      Picture: Drosophila Mushroom Bodies

    8. caffeine

      A drug that acts as a stimulant of the Central Nervous System found in common beverages like coffee, tea, and some sodas.

      Picture: 3D Structure of Caffeine_3D_ball.png)

    9. olfactory

      Relating to the sense of smell.

    10. antagonist

      A substance that interferes with the activity of another. In this case, it blocks the activation of adenosine receptors.

    11. bitter taste threshold

      The amount of a substance at which the taste buds are able to detect its bitter taste.

    12. cognitive performance

      The ability to acquire and then use knowledge.

    13. floral nectar and pollen

      Though both are commonly associated with honey bees, the nectar and pollen are two very different things.

      Nectar is a sugar-rich liquid produced by flowering plants in order to attract pollinators like honey bees. The more pollinators visit a flower, the more nectar it produces. Nectar is most commonly known as the sugar source for the honey produced by bees.

      Pollen is the reason why flowering plants produce nectar in the first place. Pollen is a powder that carries the male sperm cells of a seed plant to the stigma of another flower. There, it can make its way to the female reproductive organ of the flower, where fertilization will occur. This is the process by which flowering plants reproduce.

      However, pollen can't move on its own; that's where pollinators like honey bees come in. When a pollinator comes to a flower to drink its nectar, the flower's pollen gets stuck on the pollinator, which then carries it to another flower.

    14. significantly

      When scientists use the word "significant," they don't necessarily mean to say that something is particularly important or noteworthy.

      "Significant" used this way is a specific statistical term that indicates that something is unlikely to have arisen simply by chance.

      Since in this context the authors found that the concentration was NOT significantly different, that means that the concentrations were the same between genera, and any differences seen were most likely due to chance rather than due to some systematic process.

    15. If caffeine confers a selective advantage

      That is, if caffeine makes these plants more "fit," or more likely to survive and reproduce, thereby successfully passing on their genes to the next generation of plants.

    16. concentrations

      In chemistry, a measure of the amount of dissolved substance per unit of volume.

    17. mM.

      Millimolar, or millimoles per liter - a unit of concentration.

    18. logistic regression

      In statistics, a regression analysis is a method for estimating relationships among variables.

      It helps you understand how one variable (the dependent variable) changes when another variable (the independent variable) is changed, while all other variables remain constant.

      This type of analysis is often used for prediction or forecasting.

      Logistic regression is a regression analysis where the dependent variable is categorical. This means that it does not have a numerical value, for example a study participant's eye color or blood type.

      See this video for more information on how logistic regression works.

    19. Z = –1.09

      A Z-Score is a statistical measurement of the number of standard deviations an observation is above the mean. (To learn more about standard deviations, see here)

      Thus, Z-score of 0 means the observation is the same as the mean, a positive Z-score tells you the observation fell that many standard deviations above the mean, and a negative score tells it fell that many standard deviations below the mean.

      So in this case, a Z score of -1.09 tells us that the observation fell 1.09 standard deviations below the mean.

      See here to learn more about how Z-scores are calculated.

    20. P = 0.272

      When you perform a statistical test, a p-value helps you determine whether or not your results are significant. A p-value can be calculated by several different statistical tests.

      A very small p-value (usually less than or equal to 0.05, though this varies depending on the field of study) indicates that there is strong evidence that the results were not due to chance. Therefore, the results are significant.

      A large p-value (usually larger than 0.05) indicates that there is weak evidence that the results were not due to chance, and therefore the results are not considered significant.

      In this case, the p-value is 0.272. As this is much greater than 0.05, the median caffeine concentrations in both genera are not considered significantly different.

    21. adenosine receptor

      Adenosine receptors are proteins that, when they come into contact with the molecule adenosine, play an important role in cellular signaling.

      Adenosine receptors in the brain regulate the release of neurotransmitters, chemicals that send messages from neurons to other cells.

    22. sensilla

      Sensilla are little hair-like sensory organs that help insects detect a number of different chemical and mechanical stimuli, like smells or touch.

    23. concomitantly

      Concurrently; existing or occurring at the same time.

    24. foraging

      i.e., while looking for food.

    25. action as an adenosine receptor antagonist

      When adenosine binds to its receptors in the brain, neural activity slows down. This has a number of effects, including dilating the blood vessels in your brain and making you fall asleep.

      When caffeine binds to these same receptors, it takes the place that adenosine would normally fill, but it doesn't slow neural activity. This makes it harder for you to fall asleep.

      Any substance that blocks the normal activity of another, like caffeine blocks the activity of adenosine in this case, is called an "antagonist."

    26. hippocampal

      The hippocampus is the region of the human brain (also present in many other vertebrates) that is important for spatial navigation and for processing information from short-term to long-term memory.

      Fun fact: the name "hippocampus" come from the Greek "hippos" (horse) and "kampos" (sea monster) - the scientists who first named the hippocampus thought its shape very closely resembled a seahorse!

    27. long-term potentiation

      Long-term potentiation is thought to be one of the key cellular processes behind learning and memory.

      "Synaptic plasticity" is a term used in neurobiology to refer to the ability of synapses, the structure that allows neurons to send signals to each other, to change their strength. That is to say that they can change how strong or weak the signals being passed between neurons are. Memories are thought to be encoded by these changes in synaptic strength.

      Long-term potentiation is the persistent, long-lasting strengthening of these synapses. It's one of the processes underlying synaptic plasticity and has been shown to be required for the formation of memories, though scientists are still not completely clear on how that happens.

      See here to learn more about long-term potentiation and synaptic plasticity.

    28. 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.

    29. 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!

    30. 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.

    31. sensory input

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

    32. 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.

    33. genera

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

    34. 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.

    35. 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.

    36. 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.

    37. 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).

    38. 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. (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. 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


    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.

  3. 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


      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?