5,190 Matching Annotations
  1. Dec 2016
    1. 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.

  2. Nov 2016
    1. caspase 3/7

      Caspases are endoproteases (a type of enzyme that breaks down proteins) that play a critical role in both inflammation and cell death.

      The presence of caspase 3 and 7 can be used as a sign that cells are preparing to die.

    2. Zika virus (ZIKV)

      An RNA virus transmitted by mosquitos and sexual interaction with a carrier.

      It was first isolated from the Zika Forest of Uganda in 1947. It was previously only known to occur in a narrow range in Africa and Asia. However, in 2015 there was a Zika outbreak in Brazil.

    1. covariates

      A covariate is a variable that used in a regression analysis. It is a variable that might be responsible for the outcome of a study, or that might be interfering.

      Here, all of the additional variables added in each model were covariates (writing ability, gender, ethnicity, etc.)

    2. Matthew effect

      The Matthew Effect can be summarized as "the rich get richer and the poor get poorer." It describes the idea that benefits are distributed unevenly, and that those who already have the benefits will continue to accumulate them while those without will not have the chance.

      In scientific publication, the Matthew Effect refers to the phenomenon where researchers who are established publish more often simply because they are established (and regardless of the quality of their work).

    3. principal investigator (PI),

      A principal investigator (PI) is the holder of an independent grant administered by a university and the lead researcher for the grant project, usually in the sciences.

      The phrase is also often used as a synonym for "head of the laboratory" or "research group leader."

    4. U.S. Patent and Trademark Office (USPTO)

      The United States Patent and Trademark Office (USPTO or Office) is an agency of the U.S. Department of Commerce which stores, classifies, and disseminates information on patents and gives grant patents for the protection of inventions and to register trademarks.

    5. U.S. National Institutes of Health

      The National Institutes of Health (NIH) is an agency of the Department of Health and Human Services and the main agency of the U.S. government responsible for biomedical research and healthcare-related research.

  3. Oct 2016
    1. z, F, t, and χ2

      z, F, t and X2 test statistics are parameters that are calculated from a sample and compared with what is expected given the null hypothesis (that there is no effect in reality). The test statistic allows inferences on whether the data allows us to reject the null hypothesis and assume an effect is present.

    2. Cohen’s d

      Cohen's d is a measure for the size of an effect, used to report the standardized difference between two means. It is used to make a judgment if an effect is small (d>0.20), medium (d>0.50) or large (d>0.80).

    3. Wilcoxon signed-rank test

      The Wilcoxon signed-rank test is a statistical procedure that is used on paired data. The test compares the differences between paired data points, ranks the differences by size and considers the direction of the difference by retaining its sign (+ or -), to then allow an inference on whether the mean ranks differ or are the same.

    4. central tendency

      The central tendency of a distribution is captured by its central, or typical values. Central tendency is usually assessed with means, medians ("middle" value in the data) and modes (most frequent value in the data).

    5. nominal data

      Nominal data is the simplest form of data, since it implies no natural ordering between values. For instance, consider subject gender (male and female), which is a nominal variable: neither male nor female comes first, and neither male nor female is larger than the other.

    6. McNemar test

      McNemar's test is a statistical procedure for analyzing data that is measured on a nominal scale and where pairs of data points exist. In this example, we have pairs of data points when we consider that each original study and its replication belong together. The test assesses if the outcomes (proportion of significant vs. non-significant results) are the same in the original and the replication studies.

    7. confidence interval

      A confidence interval is the range of values in which the true value of the variable of interest would fall, if the experiment were to be repeated again and again. In the case of the 95% confidence interval, the true value would fall in this range in 95% of all cases. Confidence intervals are often referred to with the abbreviation "CI".

    8. two-tailed test

      A two-tailed test looks for a hypothesized relationship in two directions, not just one. For example, if we compare the means of two groups, the null hypothesis would be that the means are not different from each other. The alternative hypothesis for a two-tailed test would be that the means are different, regardless if the one is bigger or smaller than the other. For a one-tailed test, one would formulate a more specific alternative hypothesis, for instance that the mean of the first group is bigger than the mean of the second group.

    9. within-subjects designs

      Within-subjects designs vary the predictor in question within each subject: each participant will complete all experimental procedures, in all different conditions. In contrast, between-subjects designs vary the predictor in question between the subjects: each participant completes only one experimental condition.

      For example, if a study wanted to test how eating an apple or eating a banana impacts the performance in a subsequent math test, a within-subjects design would have all participants first eat one fruit and complete a test, and then eat the other fruit and complete an equivalent test. A between-subjects design would have half of the participants eat an apple and complete the test, and the other half of the participants eat a banana and complete the test. Some questions are better suited to be studied with a within-subjects design, others are better studied with a between-subjects design.

    10. citation impact

      Citation impact refers to the importance of an effect deduced from how much of the subsequent body of literature refers to and builds on it by including a reference to the original paper.

    11. selection biases

      Selection bias here refers to systematic error in the way studies are included or excluded in the sample of studies which would be replicated. An unbiased selection would be truly random, such that the sample of studies used for replication would be representative of the population of studies available.

    12. statistically significant results

      Results are referred to as statistically significant when we find the result convincing because it is extremely unlikely to find this data if the effect did not really exist.

  4. Sep 2016
    1. 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.

    2. 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).

    3. 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.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    1. pithed

      pithing is a method used while preparing specimen for experimental procedures and dissection. It is done by inserting a metal rod into the brain or spinal chord of a living specimen as to kill or immobilise in the least painful way. This method is useful in that it allows for the testing and examination of the physiology of the organs of the prey because they still work, but the animal feels no pain and has no control over their muscles.

    2. tetanus

      Tetanus could refer to the disease caused by a bacterial infection or to rapid/continuous muscle contraction. In this context it is referring to the latter definition;muscle contraction. Each contraction produces an involuntary twitch. Because the electric shocks produced by the electric eel are very frequent the fish ends up constantly twitching with no breaks and no control over its movement .

      for more information about muscle contraction; Mann MD (2011). "Chapter 14: Muscle Contraction: Twitch and tetanic contractions". The Nervous System In Action. Michael D. Mann

    3. Plexiglas

      Is a sturdy alternative to glass. made out of acrylic it is shatter proof as well as sound proof. this is ideal in this experiment because it is clear enough for the eel to se through but does not allow noise or movement of prey to go through, or electric shocks of eel.

    4. neuromuscular junction

      The connection point between the motor neuron (carrying signal from the spinal chord) and a muscle fibre. This is the communication channel between the two where messages are transmitted using calcium ions. This is necessary to control muscles.

    5. latency

      Latency refers to the time thats elapses between an action and a reaction in a system. In this context it refers to the time it takes for the activation of the motor neurone efferents of the prey after the release of the eel electric discharge.

    6. Electrophorus electricus

      While they are referred to as Eels, Electric Eels actually belong to the nocturnal family of knifefish which consists of electric fish that have organs that generate electric current. Eels are the largest Gymnotiformes and use electric current to defend and hunt.

    7. efferent

      when a neutron is described as being efferent it means that it carries orders away from the central nervous system, which acts like a control centre, towards organs, mainly muscles and glands

    8. providing a combined discharge of up to 600 V

      This is almost five times more voltage than what you would get out of an Electrical outlet in a US household (120V) and more than twice the voltage of an outlet in Europe (220-240 V)

    9. mechanosensory

      mechano referes to mechanical stimulus, which is a physical change such as direct contact, change in pressure or vibration. This change can be sensed by special sensory cells that are found all over the body. These cells allow us to sense vibrations from and contact with other objects.

    1. homozygous

      Humans have chromosomes by pairs. An individual receives one chromosome from each parent. Therefore, he receives two copies of each gene. One says that an individual is homozygous for a certain gene when both of its chromosomes carry the same version of the gene.

    2.  PCDH10

      Generally PCDH10 belongs to a proto cadherin protein family and it acts as a potential tumor suppressor protein, as the dysregulation of PCDH10 gene frequently existed in multiple human tumors.

      PCDH10 is a transcriptional target of p53 and exhibits inhibitory roles in cancer cell motility and cell migration.

    3.  MEF2 transcription factor

      The myocyte enhancer factor 2 (MEF2) transcription factor holds together the transcriptional circuits and controls cell differentiation and organogenesis. In adult tissues, Mef2 proteins are also reported to regulate the stress-response during cardiac hypertrophy and tissue remodeling in cardiac and skeletal muscle.

    4. transcription

      At the beginning of the transcription process, the genetic information of a strand of DNA is copied onto a new molecule, called messenger RNA (mRNA). The mRNA can then exit the nucleus of the cell to be translated into a protein.

    5. single-nucleotide polymorphism

      A variation of a single nucleotide in a DNA sequence. When less than 1% of a population carries the nucleotide at this position, this variation is classified as a SNP. Some SNPs are associated with certain diseases.

    6. Identifying Autism

      DNA is a macromolecule forming a long double helical shape and containing the “blueprint” of an organism. It gives the instructions for the production of all the proteins of the organism. Each long portion of DNA is called a chromosome.

    7. Endosomal trafficking and protein turnover

      Other genes the authors identified are involved in how cells move proteins around. Cells usually do this by packing proteins into endosomes (small spheres made out of membrane) to send proteins to specific places.

    8. stop codon

      A stop codon (or termination codon) is a nucleotide triplet, which stops the synthesis of a protein molecule. It's placed within messenger RNA and signals a termination of translation into proteins.

      This termination is taking place due to binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.

    1. in-frame deletion

      As you know from molecular biology, protein-coding region of DNA transcribe into mRNAs and then, mRNAs, in their turn, translate into proteins on ribosomes. Basically three nucleotides are required to code for any aminoacid, so the part of mRNA that translates into proteins has a "frame" which is divisible by three; if a deletion cause removal of three or a multiplicate of three then the frame will stop at the previous stop codon and other aminoiacs remain untouched, otherwise the deletion may turn the protein to anything at all.

      https://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/RNA-codons-aminoacids.svg/2000px-RNA-codons-aminoacids.svg.png

    2. PCNA

      A protein of DNA polymerase delta. it is involved in the control of eukaryotic DNA replication. PCNA is important for replication and participates in cell division. so it's present in cell shows that the cell is proliferating.

    3. molecular markers

      Basically, in biology each cellular function achieves by corporation of protein complexes; for example in mammals, DNA replication happens by DNA polymerase and a dozen of other molecules( for example PCNA); so if we recognise any of these molecules that make DNA replication happens; it shows that the cell is proliferating;

    4. fossil intermediate

      A transitional fossile that gives us information about a transition from one species to another. Actually is one that falls between "before transition forms" and "after transition forms"

    5. cDNA

      DNA (which stores genetic information) makes RNA (which transports genetic information) which is then read to make a protein which is functional

      cDNA is a copy of the RNA which is tells us what protein will be created.

    1. National Science Foundation

      The National Science Foundation (NSF) is an independent agency of the U.S. government that is responsible for the development of science and technology. The Foundation carries out it's mission by providing, in general, temporary grants.

    1. bat-detector

      A piece of equipment used to record and identify high frequency calls beyond the range of human hearing.

      These detectors have a frequency dial. Once a frequency is chosen, the detector only detects sounds at that frequency. Because the dial was set at 23 kHz, sounds far above or below that frequency would not be detected.

      http://www.batbox.com

    2. empathic concern

      Empathic concern (identifying with the emotions of another person) in humans is thought to be hard-wired into our brains. It becomes evident as early as age 2 and is dependent on our social interactions.

      There are several contributors to empathy including:

      (A) Shared neural representations (activity in the brain in response to an experience in your environment). For example, the neural networks that are active when you feel sad would also be active when you see someone else expressing sadness and feel empathy for them.

      (B) Self-awareness (conscious knowledge of one's own character, feelings, motives, and desires).

      (C) Mental flexibility, or the ability to shift a course of thought or action according to the changing demands of a situation. It allows an individual to abandon a previous response set or pattern in order to generate an alternative that is better suited to the requirements of the situation at hand.

      (D) Emotion regulation, or the ability to respond to the ongoing demands of an emotional experience in a manner that is socially tolerable and sufficiently flexible to permit spontaneous reactions.

    1. single-nucleotide polymorphism

      A single-nucleotide polymorphism is a variation in a single nucleotide at a particular location in the genome.

      The authors are referring to a position in the human BDNF gene. Variation in the DNA sequence at this position is associated with a reduced ability to recall extinction.

    2. putative

      Based on previous research (see references 14–16), the authors chose to test the amygdala and hippocampus because they were the most likely contributors of BDNF to the IL mPFC.

    3. in vitro

      When something is said to occur "in vitro," it means that it has been tested or observed in parts of an organism that have been removed from their original biological surroundings.

      Examples include most studies done in test tubes or petri dishes, where some tissues or cells are isolated so they can be studied more carefully.

    4. habituation

      A type of learning where repeated presentation of a stimulus leads to a decrease in response. If you put an animal into a new environment for behavioral testing, the animal may become agitated or fearful.

      However, if you expose the animal to that environment a few times before the experiment begins, the animal will not be as nervous because it has been “habituated” to the testing environment.

    5. latent inhibition

      Pre-exposure to a stimulus can make it difficult to form new associations with that stimulus. In other words, it takes longer for a familiar stimulus to acquire meaning than a new stimulus.

      In this case, the authors wanted to see whether BDNF was changing freezing behavior by enhancing the effects of habituation trials.