4,435 Matching Annotations
  1. Aug 2019
    1. Fourier

      Joseph Fourier (1768-1830) was a French scientist and mathematician who studied heat transfer. He theorized that Earth's atmosphere could act as a thermal insulator by absorbing heat (radiation) emitted by Earth's surface.

    2. Professor Högbom

      Arvid Hogbom (1857-1940), a Swedish geologist, was a colleague of Arrhenius, a professor at Stockholm University and a member of the Physical Society.

    3. transparency of the atmosphere

      De Marchi seems to refer to the ability of the atmosphere to let through all wavelengths of radiation. He probably focused on the ability of water vapor in clouds to reflect incoming solar radiation, reducing how much solar energy reaches Earth's surface.

      When Arrhenius discusses transparency in relation to his model, he focuses on the ability of water vapor to absorb infrared radiation and re-emit it back toward Earth's surface.

    4. L. De Marchi

      Luigi De Marchi was an Italian meteorologist. The work quoted here is from his prize-winning essay for a competition on the causes of the Ice Age.

    5. eccentricity

      A measure of the shape of an ellipse, how far it is flattened from a circular shape. An orbit with low eccentricity is almost circular, whereas an orbit with high eccentricity is highly elliptical.

      Items 3, 5 and 9 in De Marchi's list make up the Milankovitch Cycles, which affect how much energy Earth receives from the Sun and how that energy is distributed over the globe.

      For more information, see this resource from Climatica: http://climatica.org.uk/climate-science-information/long-term-climate-change-milankovitch-cycles

    6. The position of the equinoxes.

      Also called "precession", this refers to the orientation of Earth's rotational axis relative to its position in its orbit around the Sun.

      Items 3, 5 and 9 in De Marchi's list make up the Milankovitch Cycles, which affect how much energy Earth receives from the Sun and how that energy is distributed over the globe.

      For more information, see this resource from Climatica: http://climatica.org.uk/climate-science-information/long-term-climate-change-milankovitch-cycles

    7. The obliquity of the earth's axis to the ecliptic.

      The tilt of Earth's rotational axis relative to the plane of its orbit around the Sun.

      Items 3, 5 and 9 in De Marchi's list make up the Milankovitch Cycles, which affect how much energy Earth receives from the Sun and how that energy is distributed over the globe.

      For more information, see this resource from Climatica: http://climatica.org.uk/climate-science-information/long-term-climate-change-milankovitch-cycles

    8. diminution


    9. A fortiori

      even more

      This is a Latin phrase which translates as "from the stronger". Here, Arrhenius uses it to indicate that the remainder of the sentence presents an even stronger argument than the previous sentence.

    10. untenable


    11. viz.

      namely; in other words

  2. Jul 2019
    1. differentially expressed genes (DEGs)

      Differentially expressed genes are ones that have higher expression in one condition versus another.

    2. bulk sequencing

      In this context, bulk sequencing refers to the analysis of whole tissue, as opposed to single cells or nuclei.

    3. protoplasmic astrocytes

      Protoplasmic astrocytes are a subset of astrocytes that are located in the gray matter (which consists mostly of cell bodies) in the brain. They have many complex processes that can contact blood vessels and neurons.

    4. unbiased clustering

      Unbiased clustering is a statistical approach to make sense of large sets of data. It allows scientists to group together ("cluster") genes that are similar to one another.

    5. astrocytes

      Astrocytes, like microglia, are cells that facilitate neuronal functions. They mediate neuronal signaling, support the blood brain barrier, and help respond to sites of trauma.

    6. interneurons

      Interneurons are neurons that act as an intermediate between two other neurons.

    7. upper-layer excitatory neurons

      Upper-layer refers to where in the cortex these neurons are located.

      Excitatory neurons are neurons which increases the activity of the cells it's connected to.

    8. RNA integrity number

      The RNA integrity number, or RIN, is an index of RNA quality. RNA can sometimes be degraded when it is isolated, so this is a useful way to see if the RNA is still reliable.

    9. postmortem interval

      The postmortem interval is the time between when an individual died and when the tissue was prepared.

    10. anterior cingulate cortex

      The anterior cingulate cortex is the part of the brain associated with higher level functions such as emotion, empathy, and decision making.

    11. prefrontal cortex

      The prefrontal cortex is an area at the front of the brain. It is associated with social behavior, decision making, and personality.

    12. cortico-cortical projection neurons

      Cortico-cortical projection neurons are cortical neurons which project (or connect to) other cortical neurons.

    13. microglia

      Microglia are "helper cells" in the brain. They help mediate neuron responses, clear out dead cells, and control immune responses.

    14. synaptic signaling

      Synaptic signaling refers to how neurons communicate with one another.

      A projection called an axon from the pre-synaptic neuron touches or "synapses on" the dendritic projections of the post-synaptic neuron. Chemicals called neurotransmitters are released from the pre-synaptic neuron and mediate responses in the post-synaptic neuron.

    15. transcriptomic

      The transcriptome refers to the total set of RNA transcribed from DNA.

    16. single-nucleus RNA sequencing

      In single-nucleus RNA sequencing, the nucleus (which contains DNA and nascently transcribed RNA) is isolated from a single cell. The isolated RNA undergoes RNA-sequencing, in which the RNA is broken up into fragments. Using a database, these fragments are then aligned to specific transcripts.

    17. neocortex

      The neocortex is the part of the brain that in humans is associated with higher level functions such as cognition and language.

    18. genetic heterogeneity of autism

      Genetic heterogeneity refers to the ability of a phenotype (in this case, autism) to manifest via genetic mutations in multiple different loci. This means that there isn't one single genetic mutation that's associated with autism.

    1. downstream processing

      Refers to the process of separating desired products from biosynthetic pathways

    2. chiral reagents

      Any reagent that exhibits chirality (or asymmetry) in its molecular structure

    3. carbene insertion

      carbene is a neutral reactive intermediate; a carbene insertion reaction is the insertion of carbene in a carbon-hydrogen bond.

    4. directed evolution

      Is a method of engineering proteins towards a defined goal or purpose. Directed evolution mimics 'real' evolution and is accelerated in the laboratory by focusing on individual genes expressed in fast‐growing microorganisms such as E.Coli. Enzyme chosen (known as wild type) must show at least a minimal desired reactivity. Mutations are introduced at strategic locations in the wild type protein. Then, the library of mutant proteins is screened for the mutated enzymes with enhanced reactivity. The improved enzymes are used as parents for the next round of mutation and screening. Additional beneficial mutations are introduced if needed. This can continue for several cycles until a desired and beneficial evolution of the enzyme is attained.

    5. physiological

      conditions that occur in nature for an organism in contrast to laboratory conditions

    6. bioorthogonal chemistry

      A new approach of conducting chemical reactions where reactants must react rapidly and selectively with each other under physiological conditions. Two key and relevant features of bioorthogonal reactions is high selectivity and compatibility with naturally occurring functional groups.

    7. metabolic engineering

      Metabolic engineering is the production of specific target chemicals in high yield and stereoselectivity by altering the metabolic pathways. Metabolic pathway is changed via recombinant DNA technology.

    8. heteroarenes

      aromatic compounds where one or more ring carbon atoms are replaced by a heteroatom such as nitrogen, sulfur or oxygen.

    9. naphthalenes

      compounds that contain two fused benzene rings; also referred to as polycyclic aromatic hydrocarbon

    10. amides

      organic compounds that contain -CONH2 structural feature

    11. esters

      organic compounds that contain -COOR functional group

    12. alkyl halides

      organic compounds that contain a halogen connected to an alkyl group such as methyl ethyl etc.

    13. aryl halides

      organic compounds that contain a halogen connected to a benzene ring

    14. ethers

      organic compounds that contains C-O-C structural feature

    15. anaerobic

      oxygen free conditions

    16. recombinantly expressed in Escherichia coli.

      At the theoretical level, the steps needed for obtaining a recombinant protein are straightforward. Take your gene of interest, clone it, transform it into the host of choice (here it is E.Coli), induce and then, the protein is ready for purification and characterization.

    17. adventitious “active site”

      an active site created by chance rather than by design

    18. Met

      The amnio acid, methionine

    19. distal

      located at a further distance

    20. His

      The amino acid, histadine

    21. proximal

      located at a closer distance

    22. hydrophobic

      repels or has no affinity towards water

    23. eukaryotic

      cells with membrane bound organelles

    24. functionally conserved

      relatively unchanged when one goes back in genealogical time

    25. thermohalophilic

      An organism that thrives in extreme high temperature and high salt concentrations

    26. enantioinduction

      Enantioinduction is also popularly known as asymmetric induction. This process is the preferential formation of one enantiomer over the other as a result of the influence of a chiral feature present in reactants or the catalyst.

    27. molecular biology

      branch of biology that deals with structure and function of nucleic acids and proteins

    28. genetically encoded

      Is the order of nucleotides that make up the genetic codes that is translated into proteins

    29. isostere

      elements that have the same number of electrons in the outermost shell (also known as valence shell) and have similar electronic properties

    30. biocompatible

      not harmful to living cells

    31. organosilicon

      Compounds that contain carbon-silicon bonds

    32. enantiopure

      A compound available in one enantiomeric form

    33. turnover

      The number of moles of substrata that a catalyst can convert into the desired product before becoming inactive

    34. chemo- and enantioselectivity

      Chemoselectivity is the preferential reaction of a reagent with a specific functional group over others. Enantioselectivity is the extent to which one enantiomer is formed over the other in a chemical reaction.

    35. heme proteins

      is a type of metalloprotein and contains a heme group which is required for the functionality of the protein

    36. catalyze

      speed up a reaction with the use of external agent, typically a chemical compound

  3. Jun 2019
    1. We decomposed this metric into two components: species turnover (βST—the proportion of interactions that are not shared owing to differences in species composition between two networks) and linkage turnover [βOS, also called rewiring—the proportion of interactions unique to a single network despite the occurrence of both partners in both networks (30)

      The authors measured the overall dissimilarity between different locations by two factors:

      species turnover- when two locations do not share similar networks because they are inhabited by different species,

      and linkage turnover- when species found in both locations develop different interactions specific to their site

    2. The wider variety of partners used at the larger scale (regional network) corresponds to the “fundamental niche,” whereas the subset of partners found at local scales indicates that local populations have much more restricted “realized niches” (27, 28).

      A species' fundamental niche encompasses all of the possible roles it has in its environment, whereas the realized niche are the actual roles that a species plays in its environment, taking into account competition, predation, and other interactions with neighboring species.

      The video below further explains this.

    3. niche broadening

      A niche is an organism's role in its ecosystem, describing how it utilizes the resources and interacts with living and nonliving factors of its environment.

      Niche broadening is when a species expands its roles in its habitat, as a tool for survival.

    4. interaction release

      In response to lack of food and increased populations, animals broaden the scope of species they interact with beyond their original interactions.

    5. frugivores

      An animal that eats primarily fruit

    6. interaction dissimilarity

      When the behavior between species in one area differs from the behaviors between species in another location.

    7. introduced species

      Plants or animals not originally from that area

    8. novel interactions

      A new relationship or pattern of behavior between plants and animals.

    9. seed dispersal

      The distribution or spreading of seeds throughout an area

    10. binary

      Binary calculations are a straightforward form of measurement that states the presence or absence of an interaction.

    11. weighted

      Weighted networks assign some form of quantitative value, in this case frequency, as a measure of the interaction in a network.

    12. biotic factors

      Living parts of an ecosystem, in this case, invasive species on the island

    13. Abiotic factors

      Non-living parts of an ecosystem, such as elevation of rainfall

    1. dimorphic

      Dimorphic indicates differences in characteristics between males and females of the same species other than the sex cells.

    2. gonad

      Gonad refers the organ that produces an organism's reproductive cells.

      For mammals, this is the testis in males and ovary in females.

    3. transcription

      The creation of an RNA transcript from DNA.

    4. aromatase

      An enzyme that produces estrogen, the main female sex hormone.

    5. intron retention

      A transcription event in which introns, which are frequently excluded from mRNA, are instead maintained in the mRNA transcript.

      Intron retention allows for more diversity of mRNA transcripts from the same DNA.

    1. recitation

      A meeting of a subset of students from a larger lecture course in which students can ask questions, get clarification on lecture topics, and may solve additional problems or take quizzes (typically required with very large college courses).

    2. effect size

      Statistical measure of the strength of the relationship between two variables.

    3. gender gap

      Another term for the "gender achievement gap" in which men outperform women in the same field.

    4. lucrative


    5. conceptual mastery

      Understanding the main ideas that make up the field.

    6. interactive techniques

      Activities in which the student participates (as opposed to passively listening to a lecture).

    7. curricular materials

      Educational resources that can be incorporated into a teacher's lessons.

    8. context-rich problems

      Short scenarios that give the student a real-world situation in which to apply their knowledge.

    9. fear of being devalued based on a group identity

      Stereotype threat or identity threat.

    10. evaluative stress

      Fear and anxiety caused by the thought of having to take an exam.

    11. pedagogical

      Related to teaching.

    12. control group

      The subjects that do not receive treatment.

    13. self-relevant

      Related to an individual's sense of identity.

    14. cumulative exam

      Test on all material covered during the course.

    15. distribution

      The frequency of occurrence of some measure (for example: how many students got As, Bs, Cs, Ds, and Fs).

    16. SOM

      Supporting Online Materials (typically located at the end of the article).

    17. significant

      The result deviates from that expected to arise by chance (from random variation or errors in sampling).

    18. psychological intervention

      Any activity used to modify behavior, emotional state, or feelings.

    19. gender achievement gap

      The difference in test scores, course performance, and job prospects between people of different genders.

    20. instructional methods

      How course material is taught, such as through context-rich problems or curricular materials.

    21. cognitive

      Perception, attention, learning, memory, and problem solving.

    22. theoretically motivated

      Based on a hypothesis that may have been supported in laboratory experiments, but has not yet been shown to work in practice.

    23. replicated

      Repeating a scientific experiment and finding the same results.

    24. resulting in a significant gender × condition interaction

      Interaction effects occur when the effect of one variable depends on another variable.

      In this case, the effect of the intervention (values affirmation or control) depended on the student gender (male or female).

    25. discipline

      A specific branch of knowledge, such as physics or biology.

    26. z scores

      A z-score is a measure of the number of standard deviations above or below the average score a raw, individual score is. The higher the z-score, the more different a data point is from the average.

    27. continuous

      Continuous variables have an infinite number of possible values. This is in contrast to categorical variables, which have a discrete number of defined values (for example, in this study "man" or "woman" for gender).

    28. SD

      Standard deviation, a measure of the amount of variation in data.

      It can be used to quantify how far an individual's data is from the average of a data set.

    29. negative relation

      A condition in which when the value of one variable goes up (endorsement of the gender stereotype), the value of the other variable goes down (exam scores).

    30. as a function of

      A function defines one variable in terms of another. Here, the more strongly a woman in the control group endorsed the gender stereotype, the lower her exam scores were.

      Defining y "as a function of" x means that y varies based on the level of x.

    31. χ2

      Chi-squared, a test which tells whether there is a statistically significant difference between the distribution of two categorical variables (for example, gender).

    32. SE

      Refers to standard error, which is a measure of how far away the mean of your data is likely to be from the true mean of the population.

    33. P

      The P value is a measure of how likely it is that your null hypothesis (that values affirmation has no effect) is true.

    34. outcome measure

      Tools used to assess a subject's performance.

    35. condition

      Assigned group, either the intervention group or the control group. In this case, the control group contained students who did not participate in the values affirmation intervention.

    36. social-psychological

      Effects that result from interactions within groups, and between both groups and individuals.

    37. randomized

      Participants are randomly assigned to different test conditions.

      In this case, participants are equally likely to end up in the control group and the values affirmation test group.

    1. chlorisondamine

      A drug that blocks the binding of acetylcholine to its nicotinic receptors.

    2. neurogenesis

      Formation of new neurons.

    3. autoreceptors

      Referring to a case where the neurotransmitter and the receptors are present on the same cell. The released neurotransmitter binds to the receptor on the same cell.

    4. morphometric analysis

      A quantitative measurement of a neuron size, shape, or density.

    5. petrosal and nodose neurons

      Brain cells in a group of nerves found at the base of the skull. The nodose and petrosal neurons are part of the vagus and glossopharyngeal nerves, respectively.

    6. unmanipulated

      No change; unaltered.

    7. nicotinic receptors

      These are receptors that respond to the neurotransmitter, acetylcholine.

    8. methylates

      Introduces a methyl (CH<sub>3</sub>) group. Here, PNMT adds a CH<sub>3</sub> group onto norepinephrine creating epinephrine (also known as adrenaline).

    9. pituitary-adrenal axis

      Refers to the connections and interactions between the pituitary gland and adrenal glands. 

    10. caudal thoracic

      Situated in the tail part of the body.

    11. progenitors


    12. tetrodotoxin

      Sodium channel blocker. It blocks the influx of sodium into the cell.

    13. influx

      Act of flowing in.

      Example: An influx of tourists was observed over the holidays.

    14. catecholaminergic

      Refers to the cell group that releases one of the neurotransmitters, dopamine or norepinephrine.

    15. tyrosine hydroxylase

      An enzyme responsible for the conversion of tyrosine (an amino acid) to dopamine, a neurotransmitter.

    16. quantitative

      Refers to the measurement of quantities, a countable amount of something. For example: A baby weighs 7 pounds and 4 ounces.

    17. qualitative

      Refers to the measurement of qualities, a describable trait of something. For example: The girl has brown eyes.

    18. phenotype

      Here, referring to the physical characteristics of the neurons.

    19. peptide putative transmitters

      Widely accepted class of neurotransmitters.

      Read more about the different neurotransmitters here.

    20. Neurotransmitters

      A chemical that is released by brain cells called neurons. These chemicals aid in communication or passing messages between neurons.

    21. veratridine

      Drug that increases the influx of sodium into the cell.

    22. mutability

      The ability to change.

      For example, think of a caterpillar, which has the ability to change to butterfly.

    23. thermoregulation

      Maintaining the body’s temperature within the normal limits.

    24. basal

      Normal or minimum level.

    1. translational

      Research that can be useful to prevent or treat disease

    2. developmental

      Relating to the growth of the individual.

    3. subsequent


    4. cocaine-induced

      The response prompted by cocaine.

    5. nicotine-induced

      Response prompted by nicotine.

    6. risk

      Prone to; susceptible.

    7. pretreatment

      Treatment received prior to something in advance

    8. assessed

      Evaluate; measure.

    9. administered


    10. prompted

      Pushed; urged; required.

    11. diminished


    12. endpoints


    13. long-term synaptic potentiation

      Strengthening of synapses between neurons

    14. prenatal

      before birth; during pregnancy

    15. phenocopied

      mimicked; acted similarly

    16. transient

      only for a short time

    17. baseline


    18. facilitation

      help; make the process easy

    19. variant


    20. ERK/MAPK

      signaling pathways that help in gene regulation

    21. phosphorylates

      adding phosphate residues

    22. concurrent

      happening at the same time

    23. Hypoacetylated

      not enough acetylation

    24. deacetylase

      removal of acetyl groups

    25. hyperacetylation

      increase or excessive acetylation

    26. promoter

      DNA sequences that define where the transcription should start in a gene

    27. disinhibits


    28. simulate

      prompt or trigger

    29. psychostimulants

      drugs that cause an increased behavioral or motor response

    30. robust

      widely used

    31. behavioral paradigm

      a model designed to perform behavioral experiments

    32. acetylation

      Process by which acetyl groups are added to preferred residues in a protein.

      For instance, acetyl groups are added to lysine residues in a protein structure

    33. histone

      components of chromatin that helps in gene regulation

    34. chromatin

      DNA + histone

    35. FosB

      it is one of the transcription factors that help in gene expression

    36. transcription

      the process by which a copy of genetic information is made from DNA to RNA

    37. synaptic

      A synapse is a space between the neurons that allows passage of electric or chemical signals between the neurons.

      Anything that occurs between synapses is referred to as synaptic

    38. plasticity

      the ability of the neurons (brain cells) to change and learn new things by changing their synaptic strength

    39. spiny neurons

      Medium sized neurons that have dendritic branches

    40. inhibitory

      slowing down, hold back, restrain, negatively affecting a response

    41. GABAergic

      neurons that contain inhibitory neurotransmitter, GABA

    42. prefrontal cortex

      Part of the frontal cortex in the brain. Its function includes planning, organization, and decision making

    43. amygdala

      A brain region present in the temporal lobe. It is almond In shape. It plays an important role in emotions.

      Eg. When we see a lion, we immediately run due to fear. The fear response is due to the amygdala.

    44. ventral tegmental area

      A brain region in the midbrain. Serves as a center for the origin of dopaminergic neurons

    45. glutamatergic

      neurons that can modulate (or alter or modify) the neurotransmitter, glutamate. Glutamate is an excitatory neurotransmitter

    46. dopaminergic

      neurons that contain neurotransmitter, dopamine. Dopamine plays a vital role in the reward pathway

    47. integration

      to combine the similarities together

    48. convergence

      bringing together two different concepts that share similarities

    49. reward

      recognition of one’s work or effort

    50. ventral striatum

      contains the brain region, nucleus accumbens

    51. nucleus accumbens

      A brain region in the forebrain. It has two parts: core and shell

    52. addictive

      causing someone to become dependent

    53. cocaine

      Recreational drug. Referred as coke.

    54. nicotine

      primary chemical present in tobacco

    55. addiction

      dependency, craving