5,090 Matching Annotations
  1. Oct 2017
    1. RT-PCR

      Reverse transcriptase polymerase chain reaction is a variation of polymerase chain reaction (PCR). RT-PCR begins with an "extra" step in which RNA is reverse transcribed into its DNA complement and then amplified using traditional PCR.

      It is commonly used to analyze the expression patterns of infections and diseases.

    1. benchmarking problems

      Benchmark problem is a way to compare several algorithms to check wich one is the more efficient to solve a problem.

    2. parametric interactions

      parametric interaction is the way parameters interact or influence each other.

    3. time-varying dynamics

      The dynamic of a system is how this system will evolve with time. Time-varying means here that the system will have different patterns according to the time it was recorded.

    4. human locomotor performance

      Locomotor performances are the variety of movements a human can do related to the energy needed for such a movement.

    5. torque patterns

      Torque represents a rotational force. It can be seen as the twist of an object.

    6. nervous systems

      The nervous system is responsible for the coordination of body by sending signals to the other organ systems.

    7. Soleus

      A major muscle in the calf.

    1. domestic cat

      An indoor feline that doesn't need to be distinguished from other felids.

    2. inertia

      Inertia is a Newtonian law of motion that describes the tendency of matter to be in an unchanging state of motion when not acted upon by external forces. This could either be an object moving along a trajectory or stationary.

    3. conserved

      Conservation in evolution refers to a trait of a species that remains unchanged over generations. It is maintained and passed down to the next generation because it is usually essential and helps the organism to survive.

    4. hydrophilic

      Hydro refers to water. Phylic refers to member of the same group.

      Hydrophylic is a substance that is attracted and mixes well with water.

    1. ellipsoids

      A 3D geometric figure whose planes or sections consist of ellipses or circles. -Kierra Hobdy

    2. impedance

      The resistance of an electric circuit to an opposing or alternating current. -Kierra Hobdy

    3. propagating caudally

      This means to spread toward the tail or posterior section of the body-Kierra Hobdy

    4. oscillating dipole

      Dipoles are equal magnetic positive and negative charges separated by a distance. In this case oscillate means to cause the electric current to move in a way that influences the dipoles to change and fluctuate. Picture strings vertically tied to a rope in the middle, movement to the rope cause the strings to ripple in the direction they are facing outward. -Kierra Hobdy

    5. neural substrates

      Functional units of the Central Nervous System that are organized systematically based on function and vary in their anatomical location in the body; they all work together to carry out complex body functions, in this case the process of electrolocation. -Kierra Hobdy

    6. interpolating

      The act of inserting one object or substance into another. so for this study , the slices from the EOD records taken through time are put into the slices from EOD records taken through space to create a map that shows the potential and amplitude of the EOD. - Michelle Gomez-Guevara

    7. neurocomputational

      "neuro" refers to the organism's nerves and nervous system and "computional" refers to any act that the organisms does. The study , is measuring the work that the nervous system is conducting in order to use electrolocation. - Michelle Gomez-Guevara

    1. splicing regulation

      join or insert (a gene or gene fragment). -Melanie

    2. basal

      forming or belonging to a bottom layer or base -Melanie

    3. TRA

      represents the fastest evolving protein in the sex determination cascade -Melanie

    4. epistatic

      the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another -Melanie

    5. phylogeny

      is the branch of biology that deals with phylogenesis; the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism -Melanie

  2. Sep 2017
    1. electromotor

      This usually term refers to a machine that is able to produce electricity in order to produce motion. For electric fish and similar organisms , it means their organs have the ability to produce electricity , that is used to produce movement.- Michelle Gomez-Guevara

    2. electrosensory

      The ability of the nervous system if certain organisms to sense electrical impulses in their environment . It's similar to when a person uses their nose to smell a certain scent or odor in the proximity ; in this case the electric fish are able to use their organs to sense electrical pulses nearby. - Michelle Gomez-Guevara

    1. Calliphoridae

      Calliphoridae is the scientific name for "blow flies". -Jake Barbee

    2. truncated

      To truncate something means to cut off a piece of in order to shorten it. In this case the SXL and TRA proteins have been cut short. - Jake Barbee

    3. Drosophila melanogaster

      Drosophila melanogaster is the scientific name for the common fruit fly. -Jake Barbee

    4. cascade

      Cascade is a series of events that occur subsequently to one another. -Jake Barbee

    5. deleterious pleiotropic effects

      You can break this down into two main parts: deleterious, and pleiotropic. "Deleterious" meaning something that is harmful or causes damage, while "pleiotropic" means one gene is adversely affecting other phenotypic traits . In this way we can conclude that a "deleterious pleiotropic effect" is when one gene causes harm or damage to phenotypic traits. -Jake Barbee

    1. pristine

      It is a paleontological term which describes earliest period or states of life before human impact. YS

    2. inverted biomass pyramid

      A biomass pyramid where there is a larger biomass of larger predator species and a smaller biomass of smaller, prey species. - M.A.S.

    3. bioenergetics

      Is the study of the energy conversion within an organism's metabolism. -MSars

    4. subsidies

      a contribution from an outside source -M.A.S.

    5. biosphere reserve

      a UNESCO label given to an ecosystem with plants and animals of unusual scientific and natural interest to help protect the site UNESCO- United Nations Educational, Scientific, and Cultural Organization -M.A.S.

    6. bathymetry map

      Map of underwater features-SES

    7. bathymetry map

      A topographical map of the sea floor showing depth and structure through use of different colors. - WT & YS

    8. acoustic telemetry

      a way of remotely tracking the movement of a fish using tags that communicate with sound. -RKL

    9. baseline

      a point used to compare things against -RKL

    10. acoustic telemetry

      Tagging method that consists on getting information about the tagged fish through underwater sound signals.

      Acoustic waves are converted into electrical signals that can be tracked to follow the position of the species. YS & WT

    1. cryptic

      Camouflaged or otherwise hidden (e.g. in a crevice).

    2. hydrocoral Millepora spp.

      A hydrocoral looks like a coral, but is actually in the class Hydrozoa rather than the class Anthozoa, like true corals. Millepora hydrocorals are also known as fire corals due to their painful sting.

    3. The advantage of flexibility was evident among gorgonian branches encrusted

      Millepora hydrocorals can detect nearby gorgonians and attack them by growing on top of them.

    4. significant at P < .001, Mann-Whitney U test

      The Mann-Whitney U test is a statistical test used when values are not normally distributed. Here, it is used to compare live tissue coverage before and after the hurricane. The P-value of less than 0.001 indicates that there was a statistically significant difference between the two groups (a P-value of less than 0.05 is commonly accepted as statistically significant under convention).

    5. Fore Reef

      The fore reef is the ocean-facing section of a reef, seaward of the reef flat.

    6. reef flat

      The flat, shallowest part of a coral reef.

    7. natural experiment

      When natural events (i.e. fires, hurricanes, or other disturbances) happen to only some areas, scientists can study the effects by comparing affected and unaffected sites.

      This is a natural experiment.

    8. community composition

      A community is a group of interacting organisms that live in the same location. Community composition is the makeup of a community.

    9. Coral reefs

      Corals are a group of colonial marine animals that form hard calcium skeletons. They have stinging cells that can be used to catch and kill small prey, but they also often carry symbiotic algae inside that they can use to convert sunlight into cellular energy.

      When corals live together in large groups, they can form a buildup of sediment and minerals in the ocean called a reef. The complex structures of reefs create habitats for many other ocean animals.

    1. geographic centroids of the alleles

      In this study the geographic centroid of an allele is the average location calculated from every location where the allele is present. Such that if an allele is most abundant in Portugal than its geographic centroid will be in Portugal.

    2. fecundity

      A measurement of the reproductive rate of an organism. In this research it is measured as the number of siliques.

    3. ecotypes

      A term for plants derived from a geographically distinct population.

    4. latitude

      A geographic coordinate that specifies the north-south position of a location.

    5. continental

      A location far from the coast, such as the site in Germany.

    6. Mediterranean

      In southern Europe, Mediterranean environments are characterized by rainy winters and hot summers.

    7. Nordic

      Northern Europe where the climate is generally much colder and sees more snow than southern Europe.

    8. transcription factor

      A protein that can bind to DNA to alter the expression of genes.

    9. genetic architecture

      The set of genes that create characteristics in the organism. In this case the genes that are involved in local adaptation.

    10. viability

      A measurement of how many seeds are able to develop into adult plants that are capable of reproduction

    11. heritable variation

      Heritability is a measurement of how much variation in a trait is caused by genetic factors, rather than environmental factors. Heritable variation occurs in a population when the influence of genetic factors on a trait differs between individuals.

    12. silique

      The fruit of the Arabidopsis plant where the seed is stored

    13. selection

      Environmental pressures result in individuals with certain characteristics reproducing more than others. This results in these individuals genes becoming more common in the population. This is the process of evolution.

    14. molecular functions

      The actions of cellular components such as DNA and proteins.

    15. climate spaces

      An area of the environment that is suitable for a particular population to survive.

    16. alleles

      A variation of a gene. Most multi-cellular organisms, including Arabidopsis, have duplicated chromosomes meaning that every gene is present twice in the genome and hence may have two variations of a gene.

    17. fitness

      This evolutionary term describes how successful an organism is at reproducing and passing its genes through the next generations. Factors such as lifespan and percentage of offspring that survive contribute to this.

    18. genome-wide association study

      This method searches for small variations in the genomes of a large population and investigates whether these variations are associated with certain characteristics. This helps researchers identify which genes might control traits in an organism. The method is used in a large variety of research including human and plant science.

    19. candidate loci

      Locations in the genome that contain genes with functions of interest, in this case this is genes that been involved in local adaptation.

    20. Arabidopsis thaliana

      Commonly called thale cress, this plant is a small flower that is a weed in the wild but is a very popular model organism used in plant science research.

    21. genetic basis

      The genes that become locally adapted.

    22. Local adaptation

      Local adaptation occurs when a population that is spatially separate from others of its species faces selective pressures unique to its environment. Therefore, the population evolves to be best suited to its local environment.

    1. interspecific scalings

      Comparison of elative sizes of anatomical structures in different species.

    2. Inertial entrainment

      Inertial entrainment, (see inertia, already referenced) describes the physical dynamics of motion caught in stasis.

      Entrainment uses the law of inertia as a method of synchronising two events. In this case, the water travelling in constant motion with the tongue.

    3. Froude number

      Froude number, a quantity without dimensions, describes water flowing in an open channel. It is calculated as a ratio of flow of inertia (the ease in which water flows) and gravity (water moving down a surface).

    4. growth dynamics

      Describes the growth and evolution of a particular phenomena.

    5. marginally positive allomety

      Allometry is the key word here. It studies not proportional body growth.

    6. Gaussian profile

      The Gaussian profile, commonly referred to as ‘the normal distribution’, is characterised by a graph representing a bell shaped curve. The ‘bell’ of the curve represents a probability distribution, giving the approximation of an event. In this case, the graph characterises the vertical velocity, where the highest point of the curve shows the likeliest vertical velocity of the cats tongue.

    7. kinematics

      A branch of physics that studies motion of objects.

    8. Isometry

      It's the study of proportional body growth.

    9. lapping

      The intake of a liquid by an animal by way of the tongue.

    10. environmental

      Environmental refers to anything exterior to the skin of an organism. Environmental constraints are limits to the ability of an organism because of the environment they inhabit.

    11. order unity

      Order unity refers to the fact that these numbers are similar and close to the value of 1.

    12. palate’s rugae

      The palate's rugae refers to the roughness caused by wrinkles or skin folds on the upper palette of the cats mouth.

    13. nonreturn device

      In mechanics, a nonreturn device refers to a valve that only allows flow in one direction.

    14. line of best fit

      A line of best fit is a line sumperimposed on a scatter plot that best represents the trend of the data.

    15. caudally

      Caudally refers to the back end of the organism.

    16. physiological

      Physiology refers to the area of biology studying the function of living organism and their constituent parts.

      Physiological constraits are limits of the ability of the organism based on the function of the organism.

    17. adhesion

      Adhesion refers to the attraction of the molecular properties of a liquid to a surface wall. This will define the particular adhesion between the liquid and the surface of the tongue.

      Antonym: cohesion (water molecules attraction and hydrogen bond to other molecules of water).

    18. temporal derivative

      Derivative refers to the rate of the change of a function. Temporal refers to the time component of the function.

      A temporal derivative is the rate of change of the function with respect to time.

    19. Vertebrates

      An animal in a large evolutionary group characterized by the possesion of a backbone/spinal column. Classes in this group include birds, reptiles, mammals, and fish.

    20. dorsal

      Dorsal refers to "back." Antonyms include: ventral, belly.

    1. musculoskeletal

      Musculoskeletal system (or locomotal system) is the system that allow a body to move. It is mainly composed of skeleton and muscles.

    2. gradient descent

      Gradient descent is an optimization strategy to find the minimum of a function.

    3. line search

      Line search is an optimization strategy to find the minimum of a function.

    4. metabolic energy cost,

      Metabolism is how the body will use "fuel", such as sugar, for the cell activity. Metabolic energy cost referes to the amount of energy needed for a specific metabolic task in an organism.

    5. humanoid robots

      Humanoid robot is a robot with a body shaped like the human body.

    1. SunTag

      System of tagging RNA so the movement of mRNA in the cell can be seen.

    2. HA

      A protein used by influenza virus to enter cells and infect them. Here it is used to as a tag to label proteins as they are translated so that translation and protein movement can be seen.

    3. cycloheximide

      An organic compound that interferes with protein synthesis

      https://upload.wikimedia.org/wikipedia/commons/4/48/Cycloheximide.png

    4. photobleaching

      Fading of the fluorophore to stop the fluorescence of the protein

    5. fluorescence correlation spectroscopy (FCS)

      Procedure that compares the fluorescent intensity between different molecules

    6. Gaussian fitting

      A statistical method used to show the normal distribution of data

    7. diffraction limited spots

      A restricted area that is seen through the lens of a microscope

    8. 3′ UTR

      Untranslated region of the mRNA at the 3’ end

    9. core histone H2B

      Histone protein that is part of the core, or the part of the histone the DNA wraps around

    10. beta-actin

      Nonmuscular cytoskeleton protein involved in movement and structure of the cell

  3. Aug 2017
    1. montane

      Mountain ecosystems.

    2. sclerophyllous vegetation

      Plants with hard leaves that are close together on the stem, adapted to hot and dry conditions.

    3. steppe

      Plains or grasslands, generally without trees except in areas around water like lakes or rivers.

    4. 2°C

      A 2°C change is about the same as a 3.6°F change.

    5. the past 10,000 years

      The past 10,000 years of the Holocene includes all of recorded human history, and is a common timeframe for examining the recent (geologically speaking) past. The geological epoch of the Holocene began about 11,700 years ago with the end of the last major ice age.

    6. RCP8.5

      This RCP assumes that greenhouse gas emissions continue to rise from now through 2100. The Materials and Methods section calls this the "business as usual" scenario, and indicates this would result in an average global temperature increase of 4°C by 2100.

    7. RCP4.5

      In this RCP, the greenhouse gas emissions increase until 2040, and then decrease. This results in the total concentration leveling out after approximately 2060.

    1. Plaques

      Plaques are buildups of calcium or whatever.

    2. excitotoxicity

      A process in which neurons are damaged or die as a result of too much stimulation (or excitation, hence "excito-toxicity").

      For example, excitotoxicity can occur from a seizure.

    3. endogenous

      Originating from within the body. In this case, "endogenous" refers to the tau proteins that occur naturally in the body of the mice.

    4. tau

      Tau proteins are primarily found in neurons of the central nervous system.

      They stabilize the neuron's microtubules, which are components of the cell's cytoskeleton, the inner stabilizing network of filaments and tubules.

    5. microtubule-associated protein

      A protein that is bound to microtubules.

      Microtubules are part of a neuron’s inner cytoskeleton that maintains the structure and stability of the cell.

    6. peptides

      A small protein.

    7. hAPP-nontransgenic mice

      Mice that do not have the hAPP gene (normal mice).

    8. aberrant

      Wrong or deviating from the norm.

    9. neurites

      Any extension of a neuron, like an axon or a dendrite.

    10. dystrophic

      Wasting away.

    11. punctae

      Dots or points.

    12. proteolysis

      The breakdown of a protein by enzymes.

    13. hippocampal homogenates

      Ground up or processed tissue.

    14. effectors

      A molecule that binds to a protein and changes its function.

    15. etiology

      Cause or origin.

    16. spatial learning

      Learning (and remembering) where something is in 3D space.

      In this case, the mouse cannot see the platform hidden under the surface of the water. It has to remember from previous trials where it's located.

    17. Morris water maze

      A maze in which mice learn the location of a platform. The platform is visible at first and then hidden under the water surface once the mice learn its location.

      This type of maze requires the hippocampus, one of the first parts of the brain to become damaged in Alzheimer’s disease.

      See a video about the Morris Water maze here:

      http://www.jove.com/video/897/morris-water-maze-experiment

      https://youtu.be/leHLL4vcbCc

    18. familial AD mutations

      Specific genetic mutations that cause Alzheimer’s disease.

      These mutations are very rare and only account for about 2% of all cases of Alzheimer’s disease. If an individual has one of these rare mutations s/he is destined to get Alzheimer’s disease (100% chance of developing Alzheimer's).

    19. transgenic mice expressing human amyloid precursor protein

      Mice that have been genetically engineered to produce the amyloid precursor protein, which is thought to give rise to amyloid-β.

    20. haplotypes

      A set of genes inherited together.

      In this case, the authors discuss the idea that several genes related to the tau protein seem to affect the probability that a person will develop Alzheimer’s disease later in life.

    21. posttranslationally

      This means that molecular changes are made to tau proteins after they are being made.

      Some types of abnormal tau appear in cases of Alzheimer’s disease.

    22. Alzheimer's disease

      Alzheimer's disease is the most common type of dementia. It's a disease of aging in which the proteins amyloid-β and tau build up or aggregate in the brain, causing neurons to die.

      Amyloid-β proteins build up into clumps called plaques, and abnormal tau proteins fall off of their microtubules, which kills the neurons. These tau proteins later aggregate into clumps called tangles.

      Symptoms of Alzheimer’s disease include memory and cognitive problems, and patients eventually die from the disorder.

    23. amyloid-β peptide

      This peptide consists of a strand of up to about 40 amino acids that are the main component of the amyloid plaques found in the brains of Alzheimer's patients.

    1. Schaffer collateral

      A specific type of branch given off by axons that is important to learning and memory.

    2. hippocampal neurophysiology

      The hippocampus is a part of the brain that is critical to learning and memory. Because of this, it is one of the most often studied and well-understood structures and there are established experimental methods to study it.

      The authors investigated the hippocampus because their results indicated that damage occurs to it during blast exposure.

    3. enzyme-linked immunosorbent assay (ELISA)

      ELISA is a common test used to identify and quantify a protein in a sample. It is similar to immunoblotting in tissues, but is performed in a solution.

      To learn about ELISA, see the Journal of Visualized Experiments:

      https://www.jove.com/science-education/5061/the-elisa-method

    4. Increased astrocytic GFAP immunoreactivity

      Glial fibrillary acid protein (GFAP) is a naturally ocurring protein expressed in the astrocytes of the brain.

      After blast TBI or other forms of brain injury, GFAP expression is increased, indicating astrocytic activation. This increase in GFAP expression can be seen in the figure by comparing Panel G with Panel H, or by comparing the right side of the blast-exposed brain with the left side (Panel H).

    5. “dark neurons”

      Neurons that stain darker than surrounding neurons.

      Dark neurons are controversial in neuropathology because there is evidence that rough handling of tissue samples can cause them. However, the dark neurons that the authors observed are not uniform [AND THEREFORE?] could not be the result of improper handling. The presence of dark neurons in blast-exposed mice suggests dead or dying neurons.

    6. lipofuscin granules

      Pigment granules associated with wear and tear on a cell. Abnormal accumulation can be a sign of disease.

    7. hydropic perivascular astrocytic end-feet

      Perivascular astrocytes have feetlike structures that interact with blood vessels in the brain. Hydropic means that these "feet" are filled with fluid.

    8. cerebral cortex, hippocampus, brainstem, internal capsule, cerebellum, and corticospinal tract

      To explore these regions of the brain, see the Allen Brain Atlas.

    9. air-skull impedance mismatch

      When transmitting a signal (using light, sound, electricity, etc), transmission is most efficient when the two objects have similar impedance (like resistance). If the impedance values between the objects is different, the signal is both transmitted and at least partially reflected.

      A blast pressure wave traveling through air behaves similarly to a signal transmission. In this case, the difference in impedance led to a back reflection of part of the shock wave.

    10. executive function

      Executive function refers to specific cognitive functions carried out in the frontal lobes. They include things such as making decisions, setting and planning for multistep goals, controlling our emotions, moral reasoning, and our working memory (part of our short-term memory).

      Activities like writing a paper use many cognitive tasks that depend on executive function. Damage to the prefrontal cortex can impair executive function and interfere with tasks that rely on it.

    11. myelinated axonopathy, microvasculopathy

      "-pathy" comes from the Greek pathos and means disease. Words that end in -pathy indicate disease.

      For example, myelinated axonopathy refers to disease of the myelinated axons.

    12. sequelae

      A medical condition that is the result of a previous disorder or disease.

      Pronounced "seh kweh lay."

    13. traumatic brain injury (TBI)

      Damage to the brain caused by a strong outside force, such as a football tackle or an explosion.

    14. cognitive

      Related to thinking, understanding, learning, and memory.

    15. postmortem brains

      Brains that came from people who had already died.

    16. chronic traumatic encephalopathy (CTE)

      A brain disease often found in athletes with a history of repeated head injuries and military veterans with a history of blast exposure.

    17. recapitulated

      Replicated.

    18. traumatic brain injury (TBI)

      Damage to the brain caused by a strong outside force, such as a football tackle or an explosion.

    19. precipitant

      Cause.

    20. tau protein

      A protein found in the brain that is important to the structure of neurons. Functional tau protein is important to proper intracellular communication and healthy neurons.

      Diseases caused by defective tau protein are called tauopathies. Examples of tauopathies include chronic traumatic encephalopathy (CTE) and Alzheimer's disease.

    1. Warming-related extreme events

      Extreme (weather) events such as hurricanes, tornadoes, and floods, and particularly warming-related extreme weather events, such as droughts and heatwaves, are expected to become more frequent as a result of climate change.

      Visit here for more information on extreme weather events and their relation to climate change, courtesy of the 2014 U.S. Global Change Research Program.

    2. Global Biodiversity Information Facility

      The Global Biodiversity Information Facility (GBIF), is a free, open-access platform for collecting and sharing data on species observations.

      Visit GBIF here.

    3. Bumblebees of North America

      Bumblebees of North America is a comprehensive guide to North American bumblebees.

      See here to preview the guide yourself.

    1. exogenous

      Exogenous refers to something originating outside the organism.

    2. endogenous

      Endogenous refers to something originating within the organism.

    3. chimeric

      Chimeric refers to something composed of two different elements

    4. methylation-dependent chemotaxis receptor protein (MCP)

      The receptor protein tsr undergoes post-translation modifications in the form of methylation of some of its glutamine residues to attain the active form. It's called a chemotactic protein since it controls swimming behavior of E.Coli by generating signals by sensing ribose and galactose that influence the direction of flagellar rotation.

    5. cellular autofluorescence

      Autofluorescence is the fluorescence emitted by cellular structures when they have absorbed light. This often obscures signals from proteins of interests in microscopy especially when signal is week.

    6. copy numbers

      Copy number here refers to the number of protein molecules existing in the cell at any instant of time.

    7. temporal

      A Temporal change refers to change as a function of time.

    8. lac operon

      Lac Operon is a collection of adjacent bacterial genes responsible for the entry and metabolism of lactose. It contains the genes coding for three enzymes and is flanked by a repressor and a promoter region to control expression.

    9. central dogma of molecular biology

      The central dogma of molecular biology states that biological information flows in only one direction, from DNA to RNA to proteins.

      Exceptions have since been found, however: for example, reverse transcriptase is an enzyme that uses RNA as a template to form DNA --- so information, as known now, can flow in the wrong direction too (from RNA to DNA).

    10. low-level gene expression

      Not all genes in the cell are expressed in equal amount; some are expressed much lesser than others. Studying such genes requires methods to probe one or very few molecules at a time.

    11. stochastically

      A stochastic process is one involving a random variable. It used as a counterpart of the word "deterministic".

    12. yellow fluorescent protein (YFP)

      Yellow fluorescent protein (GFP) and homologous fluorescent proteins must undergo chemical reactions after translation in order to become fluorescent.

      Going from the translated polypeptide to the fluorescent form of the protein is called "maturation. The variant of YFP used here (Venus) has a short maturation time.

    1. gene duplication events

      Errors during DNA replication or the invasion by viral DNA can lead to the duplication of a gene. Over time, the two copies of the genes differentiate. Three scenarios are known: Neofunctionalization: One gene develops a new function

      Subfunctionalization: The two copies of the gene split the functionality between them

      Loss: One gene loses its functionality.

    2. dynamic rewiring

      In this context, dynamic rewiring refers to the change of interactions over time after a gene duplication event.

    3. interactome network

      The representation of all interactions in an organism (molecular interactome network). The molecules are mostly visualized as nodes and the interactions as edges.

    4. interaction map

      A representation of interactions between different entities. The interactions are often visualized as lines or arrows.

    5. Arabidopsis thaliana

      A small plant that occurs in many different parts. It's genome is small compared to other plants, therefore it is widely used as a model organism for plants.

    6. proteome

      The proteome is all proteins of an organism at a given time point and under clearly specified conditions. The proteome differs with time and condition.

    1. cumulative process

      The term “cumulative process” here refers to taking an approach to research in which we try to gain insight not by interpreting strongly the results of one individual study at a time, but by integrating the results of several studies and broader research programs to gain an overview of the overall evidence.

    2. validity

      Validity refers to the degree to which a certain result or conclusion in research corresponds with reality. There are different aspects of a study which can improve or decrease its validity.

      For example, a study has high ecological validity if its results can be directly applied to real-life situations outside of the lab.

    3. innovation versus verification

      Innovation refers to coming up with new ideas for research, in other words to generating new hypotheses.

      Verification refers to checking if a certain idea holds up in subsequent research, in other words to confirming hypotheses.

    4. broad-and-shallow evidence

      This refers to results of studies that cover a wide range of different topics, without going into detail on a specific area.

    5. preregistration

      A preregistration is a document in which researchers compile information on how their study will be run and analyzed before it is conducted.

      The document often contains information on which research question will be pursued, which hypothesis will be tested, how the data is collected and how the sample is generated, which data is excluded, and how the data will be prepared for analysis and ultimately analyzed.

      Documenting in advance helps separate confirmatory hypothesis testing from exploratory research.

    6. upwardly biased effect sizes

      Here, upwardly biased means that the effect sizes reported in the literature are distorted to appear bigger than they really are.

    7. consistently

      When results of several analyses point in the same direction, we say the results are consistent.

      For example, if we run three correlation analyses and find that enjoyment of hiking, self-assessed nature-lovingness, and number of times previously hiked all correlate positively with the probability that someone enjoys hiking holidays, we would say that the results are consistent.

      If we found that the number of times previously hiked was negatively correlated with the probability that someone enjoys hiking holidays, the results would be less consistent.

    8. repeated measurement designs

      A repeated measurement design assesses the same outcome variable at several points in time.

      For example, let’s say we want to find out whether jogging before class improves students’ ability to follow a class. We might ask 20 students to jog before class and 20 students not to jog before class, and then after class ask them how easy it was for them to follow the class.

      However, we might be unlucky and conduct our experiment on a day where a particularly difficult topic was covered in class. No-one, neither the joggers nor the non-joggers, could understand the lecture, so all our subjects report they absolutely couldn’t follow the class.

      This problem could be ameliorated if we used a repeated measurement design instead. We would ask our 20 joggers and 20 non-joggers to either jog nor not-jog before class on 5 days in a row, and then ask them for their ability to follow the class each time. Now, we would have not only one point of measurement form each student, but 5 points of measurement of their ability to follow the class at several points in time.

    9. within-subjects manipulations

      Within-subjects manipulations refer to situations in experiments where the same person is assigned to multiple experimental conditions.

      For example, let’s say we want to find out which of two different learning techniques (A and B) is more effective in helping students prepare for a vocabulary test. If we conducted a within-subjects manipulation, each student would apply both learning techniques.

      Let’s say every student must first apply learning technique A, then take a vocabulary test, and then a week later for the next test apply learning technique B. We could now compare following which learning technique the students perform better.

      In contrast, if we conducted a between-subjects manipulation, each student would only apply one learning technique. We would split the group of students, so that half of them use learning technique A and then take the vocabulary test, while the other students use learning technique B and then take the vocabulary test. Again, we could compare following which learning technique the students perform better.

    10. pre-analysis plans

      A pre-analysis plan is a document that specifies which analyses will be run on the data, before these analyses are performed.

      This plan can specify which variables and analyses will be used, how data will be prepared for analyses, and in which cases data will be excluded from analyses. This tool helps researchers specify and commit to the way they want to run the analyses in their study.

    11. confirmatory tests

      A confirmatory test is a statistical analysis of a certain relationship which had previously been hypothesized to hold. The test tries to find out if the hypothesis is supported by the data.

    12. publication bias

      Publication bias is a type of distortion that can occur in making academic research public. When findings which show that a certain effect of interest was found to be statistically significant are more likely to be published than findings which show no evidence or even evidence against this effect, publication bias is present.

      In this case, if you only read the published papers, you would find a lot of papers showing support for an effect, while studies which do not show support for the same effect are not published, giving you the impression that the effect was less disputed and more consistently found than it actually is.

    13. fixed-effect model

      A fixed effects model is a statistical model which accounts for individual differences in the data which cannot be measured by treating them as non-random, or “fixed” at the individual level.

      As an example, let’s say we wanted to study if drinking coffee makes people are more likely to cross the street despite a red light. Our outcome variable of interest is how often each subject crosses a street despite a red light on a walk with 10 red traffic lights. The explanatory variable we manipulate for each participants is if they had a cup of coffee before the experiment or a glass of water (our control condition), and we would use this variable to try to explain ignoring red lights.

      However, there are several other influences on ignoring red lights which we have not accounted for. Next to random and systematic error, we have also not accounted for individual characteristics of the person such as their previous experience with ignoring red lights. For instance, have the participants received a fine for this offense? If so, they might be less likely to walk across a red light in our experiment.

      Using a fixed effects model makes it possible to account for these types of characteristics that rest within each individual participant. This, in turn, gives us a better estimate of the relationship between coffee drinking and crossing red lights, cleaned from other individual-level influences.

    14. Spearman’s rank-order correlations

      Spearman’s rank-order correlation is a specific type of correlation analysis, which assess the relationship between two variables with regard to its strength and direction.

    15. multivariate interaction effects

      A multivariate interaction effect is an effect that is the product of several variables working together and influencing each other.

      For example, we might be interested in finding out how water temperature (warm: 38°C; cold: 15°C) affects the body temperature of humans and sea lions. We might find that humans, on average, have a higher body temperature than sea lions, and that body temperature is higher when the body is immersed into warm compared to cold water.

      However, we might find that a human’s body temperature shows bigger differences between the warm and cold water conditions than the sea lion’s body temperature. Because sea lions have a substantive layer of protective fat, they body temperature does not change as much when water temperature changes, compared to humans.

      Here, species and water temperature show an interaction effect on body temperature.

    16. sample size

      The sample size refers to the number of people from whom data is collected in a study.

    17. accumulated evidence

      Accumulated evidence refers to the results of several studies taken together.