4,705 Matching Annotations
  1. Nov 2021
  2. Oct 2021
    1. intron retention

      RNA transcripts have two major components - exons and introns. Exons stay in the transcript that gets made into a protein, whereas introns are cut out, and this is known as splicing.

      Intron retention refers to a transcription event where an intron is kept in the RNA instead of being removed. This process can allow for more diversity of transcripts from the same gene.

      You can visualize the splicing process here: https://www.biointeractive.org/classroom-resources/rna-splicing

    2. lentivirus

      Lentivirus is a type of virus that contains reverse transcriptase - a molecule that transcribes RNA into DNA to integrate into the genome and infect host cells.

      Lentivirus can be used to deliver desired DNA into cells. This lentiviral transduction allows for gene expression of desired sequences in organisms of interest.

      You can watch more about cloning to make the DNA for transduction here: https://www.biointeractive.org/classroom-resources/dna-cloning-plasmids, and you visualize the workflow of lentiviral transduction here: https://www.mirusbio.com/applications/high-titer-virus-production/lentivirus-production#figure1303

    3. RNA interference (RNAi)

      RNAi describes the process in which small RNA molecules target and degrade RNA molecules to block protein expression.

      shRNAs are one type of RNA that is used for RNAi.

      This tutorial provides further exploration of RNAi: https://www.biointeractive.org/classroom-resources/rna-interference

    4. transcription

      The creation of an RNA molecule from DNA.

      The RNA that is transcribed from DNA is commonly referred to as a "transcript".

      Canonically, this RNA is later translated to make protein, as described by gene "expression".

      You can visualize and learn more about transcription here: https://www.biointeractive.org/classroom-resources/dna-transcription-advanced-detail

    5. histone

      Histones are a family of proteins that help organize and compact DNA in the eukaryotic genome. DNA wraps around histones to fit inside the nucleus, like yarn around a spool.

      Here is an illustration of this organization: https://www.genome.gov/sites/default/files/tg/en/illustration/histones.jpg and a video that walks through DNA compaction: https://www.biointeractive.org/classroom-resources/how-dna-packaged

    6. H3 lysine 27 (H3K27) demethylase KDM6B

      The histone proteins have exposed "tails" of peptides that can be modified with additional chemical groups, such as methyl or acetyl molecules. These molecules can alter how the histone interacts with its associated DNA.

      These chemical modifications can be added or removed by specific proteins, such as KDM6B, which removes histone subunit 3 lysine residue 27 methylations.

      You can learn more about histone modifications here: https://www.youtube.com/watch?v=OqRt723t33o

    7. meiotic

      Meiotic is the adjective for meiosis, which is the cell division that gives rise to sex cells.

      You can learn more about meiosis here: https://www.biointeractive.org/classroom-resources/meiosis

    8. RNA sequencing analysis

      RNA sequencing (RNA-seq) is a high performance technique that measures which and how many transcript sequences are present in a given biological sample.

      You can learn more about the technique and its analysis here: https://www.youtube.com/watch?v=tlf6wYJrwKY

    9. chromatin immunoprecipitation (ChIP)

      Chromatin immunoprecipitation, or ChIP, identifies the DNA regions were a protein binds across the genome.

      First, an antibody recognizes and binds a protein of interest in the nucleus. Then the antibody holding onto the protein is isolated and any DNA bound the protein is captured for analyses.

      This article describes ChIP and it's application, with some example data analysis, here: https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/genomics/gene-expression-and-silencing/chromatin-immunoprecipitation-chip

    10. in situ hybridization

      A common technique to visualize nucleotide (DNA or RNA) in cells.

      A chemical or radioactive label is added to a nucleotide sequence that is complimentary to the sequence of interest. When added to the cells, this complimentary nucleotide sequence will bind to and tag the sequence of interest, allowing scientists to visualize the DNA or RNA of interest within the cell.

      You can read more about in situ hybridization methods here: https://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327/

    11. reverse transcription quantitative real-time fluorescence polymerase chain reaction (qRT-PCR)

      Reverse transcription quantitative real-time fluorescence polymerase chain reaction, or qRT-PCR, is a widely used molecular technique to measure RNA levels.

      RNA is first reverse transcribed into complimentary DNA. This complimentary DNA is then used as a template for a fluorescence-tagged amplification reaction to calculate the relative amount of a specific starting transcript.

      Thermo Fisher provides an extensive introduction to gene expression measuring technologies here: https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-learning-center/gene-expression-analysis-real-time-pcr-information/introduction-gene-expression.html

    12. quantitative PCR (qPCR)

      Quantitative polymerase chain reaction (qPCR) measures RNA or DNA levels for comparison among samples.

      This technique is very similar to qRT-PCR (described in above annotations), but does not always require reverse transcription.

    13. molecular basis

      The authors are hoping to reveal the molecular biology underlying Kdm6b-depletion sex reversal. They will test for the genes that KDM6B can directly bind and activate expression for in developing T.scripta gonads.

    14. ectopic

      Ectopic describes events occurring in locations that do not naturally have such events.

      For example, expression of a brain-specific gene in a toenail would be considered ectopic gene expression.

      Here ectopic describes the presence of aromatase in Kdm6b-depleted gonads at MPT, which produces female sex hormones.

    15. loss-of-function mutants

      A mutation is a change to the structure or sequence of a gene compared to a reference.

      Loss of function mutations cause a gene not to make functional amounts or forms of its protein.

      Here, the shRNA is blocking Kdm6b expression, meaning that there is not enough KDM6B to function normally in the Kdm6b-RNAi embryos.

    16. master regulator

      A master regulator often refers to a protein that initiates the cascade of expression for all genes involved in a specific pathway, such as cell fate and development pathways.

    17. germ cells

      Germ cells are an organism's reproductive cells, or the cells that go on to make gametes, like sperm and eggs.

      Every organism is comprised of somatic cells and germ cells.

    18. seminiferous cords

      Seminiferous cords are one of the earliest male-specific tissues formed as the gonad develops. These cords ultimately develop into tubules which hold sperm.

    19. expression

      Expression refers to the active process of making a protein from a gene.

    20. epigenetic

      Epigenetic describes heritable changes in gene expression, or transcription, that do not alter an organism's DNA sequence.

    21. promoter

      The region of DNA that is required for transcription initiation.

    22. gonad

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

      The gonad is the testis in males and is the ovary in females.

    23. phenotypic plasticity

      A phenotype describes the physical properties of an organism that can be observed.

      A genotype defines the genetic composition of an organism, including chromosomes and DNA sequences.

      Together, phenotypic plasticity is the ability of one genotype to produce multiple different phenotypes in an organism.

    24. molecular mechanism

      Now that authors have seen that Kdm6b regulates Dmrt1 activation, they are interested in how the molecules interact in the male sex development pathway.

    25. overexpress

      The opposite of knock-down or RNAi, overexpression describes a technique were an RNA transcript for a particular gene is increased above it's normal biological level.

    1. public health (non-pharmaceutical) interventions

      Public health interventions are everyday actions that the public can take to stop the spread of an infectious disease. As indicated by the word in the parentheses, taking medication or vaccination is not considered a public health intervention.

    1. Hydrometallurgy, a process that uses chemicals such as acids or cyanide to leach metals, generates toxic effluent.
    2. Pyrometallurgy involves heating e-waste to more than 1,000 °C, requiring a lot of energy and releasing toxic gases.
    3. bioleaching

      Using bacteria to leach metals from electronics.

    4. e-waste

      Electronic waste: discarded or no longer used electronic devices.

    1. congenital

      Present from birth

    2. etiology

      Cause of a disease

    3. cortical progenitor cells

      Specialized cells in the outermost regions of the brain that give rise to most of the cells in the central nervous system

    4. proliferative defects

      Limited cell growth and division

  3. Sep 2021
    1. Sham

      placebo

    2. sulpiride

      The dopamine receptor antagonist sulpiride functions by binding to the D2 dopamine receptor to block dopamine from binding.

    3. dopamine receptor antagonists SCH23390

      SCH23390 functions by binding to the D1 dopamine receptor to block dopamine from binding.

    4. 6-hydroxydopamine (6-OHDA)

      a neurotoxic synthetic organic compound used by researchers to selectively destroy the brain's dopaminergic as well as noradrenergic neurons. In this paper, it was used to ablate dopaminergic neurons, so as to stop dopamine synthesis.

    5. sham control

      a control treatment that is similar to the experimental treatment, but omits the key therapeutic element being tested.

    6. single-molecule fluorescence in situ hybridization

      this technique enables measurement of gene expression in single cells by detecting and counting individual RNA molecules.

    7. en passant terminals

      places along the length of an axon, other than the axon terminal, that join with other neurons.

    8. reserve pool of cells

      In a review article on reserve pool neuron transmitter respecification, Dulcis et al. provide a helpful analogy for understanding reserve pools. In this analogy, the role of reserve pools is compared to having two jobs, and following certain physiological stimuli, one of those jobs is relinquished. Dulcis et al. defines reserve pool neurons as "cells that share inputs and outputs with adjacent core pools of neurons but express different neurotransmitters." In one situation, the neurons from both pools could be expressing the same transmitters, but the core neurons also express a secondary transmitter; following the change in circuit activity, the neurons of the reserve pool will stop expressing the transmitter that it has in common with the core pool of neurons. In an alternative scenario, these two pools of neurons could be expressing different neurotransmitters, and the change in circuit activity results in the neurons of the reserve pool acquiring the expression of the transmitter that is already expressed by the core neurons (23).

    9. diurnal

      active during the day; opposite of nocturnal.

    10. BrdU

      BrdU is an analog of the nucleoside thymidine, and would be incorporated into newly synthesized DNA. Since the fundamental requirement for cell proliferation is DNA synthesis, quantifying the incorporation of BrdU following application of anti-BrdU antibodies will therefore enable measurements of cell proliferation.

    11. PeVN

      The periventricular nucleus is a thin sheet of neurons located in the hypothalamus.

    12. PaVN

      The paraventricular nucleus is a region of the hypothalamus, considered to be the body's most important autonomic control center. The neurons of the PaVN are involved in controlling stress, metabolism, growth, reproduction, immune, gastrointestinal, renal, and cardiovascular functions.

    13. A13

      The A13 group or A13 dopaminergic cell group consists of dopaminergic neurons residing in a region of the brain called the subthalamic nucleus.

    14. circadian rhythm

      our body's "internal clock" that regulates the sleep–wake cycle and repeats every 24 hours.

    15. vesicular monoamine transporter 2 (VMAT2)

      VMAT2 is the CNS vesicular transporter that packages monoamines, such as dopamine, from the cytosol into synaptic vesicles for their release from the neuron.

    16. anxiogenic

      anxious

    17. neuroplastic changes

      Neuroplastic changes refers to the adjustments that neurons make in response to changes in their environment.

    18. dopaminergic neurons

      Neurons that produce the neurotransmitter dopamine. For mammals, this is the main source of dopamine in the CNS.

    1. nested topology—specialist species tend to interact with subsets of partners of the most generalist species

      Metaphorically, nestedness can be compared to a Russian doll, where the diet of specialist species (smaller dolls) fits within the diet of the more generalist species (larger dolls).

    2. playback

      A recording of a bird's native calls is played to lure the species into an area.

    3. weighted

      A weighted network assigns some form of quantitative value to each connection between two partners (an example is shown below in figure 4). In this case, the value assigned was the frequency of interaction.

    4. Abiotic factors

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

    5. 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 interaction patterns because they are inhabited by different species,

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

    6. 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 niches 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: https://www.youtube.com/watch?v=-6COob_bymw

    7. supergeneralist

      A species that interacts with a wide number of species in ecological network. 

    8. well integrated into novel networks,

      ability to establish new interactions with partner species present in the ecosystem

    1. replacement rate

      The replacement rate of 1 means that one case in a completely susceptible population can lead to one secondary case. Assuming that the initial case can be cured and reach full recovery — which is what all of us hope — a rate equal to 1 means that one is infected when another gets well, leading to an unchanged number of cases.

    2. U = 8197, z = –3.4, P < 0.01

      The Mann-Whitney U statistic can be seen as the cumulative result of comparing the randomly drawn values from two populations. z is the standardized value and is dependent on the sizes of the two populations. P is the probability for a null hypothesis to be true.

    3. Mann-Whitney

      The Mann-Whitney U test is a test for a null hypothesis that it is equally possible for a value drawn from a population to be greater or smaller than another from a different population. This test is useful when the distributions of values are unspecified. In this study, one population comprises cities that took action earlier, and the other is for cities that responded later.

    4. P < 0.01

      P is the probability that the null hypothesis is true. The null hypothesis, in this case, is that the total number of cases reported from each province shows no significant linear correlation with the total number of travelers from Wuhan.

    5. r = 0.98

      r is the correlation coefficient for an association between two factors. It can take values between -1 and 1. A correlation coefficient equal to -1 indicates a perfectly inverse linear correlation, meaning that one variable decreases in its value in response to the increase of the other linearly. In contrast, an r equal to 1 indicates a perfect linear positive correlation. An r of zero signifies the nonexistence of an association.

    6. cordon sanitaire

      A cordon sanitaire is a movement restriction of people into or out of a specific region. This measure is taken to stop the rapid spread of an infectious disease.

    7. pathogen

      A pathogen is any tiny organism that causes disease.

    8. (13.0; 7.1-18.8)

      The first number in the parentheses is the mean for the number of reported cases, and the range after the semicolon is the 95%CI.

    9. agent

      Agents are the causes of diseases and injuries, but they are not the sole determinant for the occurrence of a disease. The other two factors are the host (the human who can get the disease) and the environment that brings the agents and the host together.

    1. modal

      Modal refers to the mode, or most frequently occurring value in a distribution.

      Here, modal describes the distribution of particle sizes.

    2. overturning circulation

      Stratospheric overturning circulation refers to the atmospheric "conveyor belt" that moves air from the Earth's equator toward the poles.

      This system carries chemicals and ozone throughout the Earth's atmosphere.

      Read more here: https://news.mit.edu/2017/strength-global-stratospheric-circulation-measured-first-time-0828

    3. greenhouse gases

      Greenhouse gases are gases which trap heat in the atmosphere and are responsible for human-caused global warming.

    4. Montreal Protocol

      The Montreal Protocol is an international agreement to phase out the use and production of substances that deplete the ozone layer. The agreement was finalized in 1987.

      Read more here: https://www.epa.gov/ozone-layer-protection/international-actions-montreal-protocol-substances-deplete-ozone-layer

    5. inline

      Inline refers to the insertion of a smaller computer program into a larger, main code.

      The inline code performs a specific function.

      Here, the inline code generates the aerosol properties needed for the ozone calculation.

    6. suborbital

      Suborbital refers to a path that is less than one full revolution around a body.

      Here, it refers to data that was not obtained by satellite.

    7. austral

      Austral means southern. Here, it relates to the Southern Hemisphere of the Earth.

  4. Aug 2021
    1. Some bacteria produce chemicals that leach metals from electronic scrap

      bioleaching is a term used.

    2. precious metals

      Metallic chemicals of high economic value.

    3. Chromobacterium violaceum

      Batista and Silver Neto describe Chromobacterium violaceum as a soil and water organism with the ability to produce industrially important small molecules and be used as a model of an environmental opportunistic pathogen.

    4. violacein

      Violacein is a pigment that occurs naturally and has antibiotic properties.

    1. His

      The amino acid, histidine

    2. wild-type Rma cyt c

      Natural variant of cytochrome c protein from the natural variant Rhodothermus marinus.

    3. genetically encoded

      The sequence of nucleotides that is translated into proteins

    4. isostere

      Elements that have the same number of electrons in the outermost shell (also known as valence shell) and have similar electronic properties. For example, carbon and silicon are isosteres as they both have four valence electrons.

    5. turnover

      The turnover number of an enzyme, is the number of substrate molecules converted into product by an enzyme molecule in a unit time when the enzyme is fully saturated with substrate.

    6. directed evolution

      IA method of engineering proteins towards a defined property. Process of directed evolution: 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 randomly or site specifically introduced to the gene of the wild type protein. Then, the library of protein variants is screened for the ones 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 new property of the enzyme is attained.

    7. carbene insertion

      Carbene is a neutral reactive intermediate; a carbene insertion reaction is the insertion of a carbene into a chemical bond.

    8. physiological

      conditions that occur in the natural host organism in contrast to laboratory conditions

    1. phenocopying

      exhibiting a phenotype (a set of features/behaviors) that does not correspond to one's own genotype, but rather is environmentally induced.

    2. photoperiods

      A photoperiod is the daily duration that an organism receives light exposure, i.e., length of day.

    3. interneurons

      Interneurons connect sensory neurons, the nerve cells that convert environmental stimuli into internal electrical impulses, and motor neurons, which transmit signals from the brain to control muscle movements. Therefore, interneurons act as a "middle-man", passing signals from sensory neurons to motor neurons.

    4. dopamine

      Commonly called the "feel-good" chemical because of its role in the brain's reward system, dopamine is a neurotransmitter associated with feelings of pleasure, learning, memory, and motor system functions.

    5. somatostatin

      Also known as growth hormone-inhibiting hormone, somatostatin is a peptide hormone that primarily functions to prevent the unnatural rapid proliferation of cells, the hallmark of tumors. Somatostatin also plays a role in the gastrointestinal system.

    6. Neurotransmitters

      Neurotransmitters are signaling molecules used by the nervous system to transmit messages between neurons.

    1. multiple spatial scales

      Local scales (specific sites) and regional scales (entire regions, like an island or an archipelago)

    2. restoration of native ecosystems

      process of assisting the recovery of an ecosystem that has been degraded, damaged or destroyed

    1. the (basic) case reproduction number (R0)

      The basic reproduction number is the average number of secondary cases that can be produced by one case in a completely susceptible population. \(R_0\) higher than 1 indicates that an epidemic will continue, and \(R_0\) lower than 1 is a sign for the epidemic to end.

    2. epidemiology

      Epidemiology investigates the distribution and determinants of health-related states or events concerning specific populations. The study guides the control of health problems.

    3. etiological agent

      Etiology is the medical study of the causes of disease. An etiological agent refers to the origin identified.

    4. 95%CI

      The confidence interval is a range that is likely to contain the true population parameter with a confidence level specified by the percentage.

      In this case, there is a 95% probability that the confidence interval of 2.54-3.29 contains the average delay of arrival of COVID-19.

    5. coronavirus

      Coronaviruses are a family of viruses. This name comes from the solar corona-like characteristic appearance of these viruses under the electron microscope.

    6. outbreak

      Outbreaks are the occurrence of a more-than-expected number of cases.

    1. aromatase

      Aromatase is an enzyme that produces estrogen, the main female sex hormone.

    2. dimorphic

      Differences in characteristics between males and females of the same species other than the sex cells.

    3. medullary cords

      Medullary describes the inside, and cords refer to the early structures that will become an organism's gonads.

      A critical step in sex development of males is when medullary cord cells differentiate into Sertoli cells. If the cords degenerate, the sex cords will instead develop into an ovary - the female gonad.

    4. morphology

      Morphology is the study of the structure of an organism. This often includes observations about the size or shape of an organism.

      Here the authors describe the Kdm6b-deficient embryo gonads as having a structure that looks like a developing female.

    1. Cause AreasProblems people work on, and concepts related to those problems.Global health and developmentAid and paternalismBurden of diseaseDewormingEconomic growthEducationFamily planningForeign aidForeign aid skepticismGlobal povertyImmigration reformMalariaMass distribution of long-lasting insecticide-treated netsMicronutrient programsResearch into neglected tropical diseasesSmallpox Eradication ProgrammeTobacco controlUniversal basic incomeGlobal Catastrophic Risk (other)AsteroidsBiosecurityCivilizational collapseCuban Missile CrisisClimate changeClimate engineeringConservationDystopiaExistential risks from fundamental physics researchGeomagnetic stormsGreat power conflictHuman extinctionManhattan ProjectNuclear warfareNuclear winterNuclear disarmament movementPandemic preparednessRussell–Einstein ManifestoTerrorismTrinitySupervolcanoWeapon of mass destructionAnimal welfareAnimal product alternativesCorporate cage-free campaignsCultured meatDietary changeFarmed animal welfareFish welfareInvertebrate welfareLogic of the larderMeat-eater problemSpeciesismWelfare biologyWild animal welfareBuilding effective altruismAltruistic motivationBuilding effective altruismCommunityCompetitive debatingConsultancyEffective altruism educationEffective altruism groupsEffective altruism in the mediaEffective altruism messagingEffective altruism outreach in schoolsEvent strategyField buildingFundraisingGlobal outreachMoral advocacyMovement collapseNetwork buildingPublic givingRequest for proposalScalably using labourValue driftValue of movement growthOther causesAnti-aging researchArmed conflictAutonomous weaponCause candidatesCause XCluster headachesCognitive enhancementCOVID-19 pandemicCriminal justice reformElectoral reformGlobal priorities researchInstitutional decision-makingLand use reformLess-discussed causesLife extensionLife sciences researchLocal priorities researchMental healthMeta-scienceMoral circle expansionNear-term AI ethicsResearchRisks from malevolent actorsSpace colonizationGlobal Catastrophic Risk (AI)AI alignmentAI boxingAI ethicsAI forecastingAI governanceAI risksAI safetyAI skepticismAI takeoffAI winterAnthropic captureArtificial intelligenceArtificial sentienceBasic AI driveCapability control methodCollective superintelligenceComprehensive AI ServicesComputation hazardHuman-level artificial intelligenceIndirect normativityInfrastructure profusionInstrumental convergenceIntelligence explosionMalignant AI failure modeMind crimeMotivation selection methodOracle AIOrthogonality thesisPerverse instantiationQuality superintelligenceSovereign AISpeed superintelligenceSuperintelligenceTool AIWhole brain emulation
    2. Other ConceptsConcepts that apply to multiple causes, or the entire project of trying to do more good.Moral PhilosophyAnimal cognitionAnimal sentienceApplied ethicsAstronomical wasteAxiologyClassical utilitarianismCluelessnessConsciousness researchConsequentialismCosmopolitanismDemandingness of moralityDeontologyEthics of existential riskEthics of personal consumptionExcited vs. obligatory altruismFuture of humanityHedonismHedoniumInfinite ethicsIntrinsic value vs. instrumental valueIntrospective hedonismIntuition of neutralityLongtermismMetaethicsMoral offsettingMoral patienthoodMoral uncertaintyMoral weightNaive vs. sophisticated consequentialismNegative utilitarianismNon-wellbeing sources of valueNormative ethicsNormative uncertaintyOther moral theoriesPain and sufferingPatient altruismPerson-affecting viewsPersonal identityPhilosophy of mindPopulation ethicsPrioritarianismSentienceSubjective wellbeingSuffering-focused ethicsUniverse's resourcesUtilitarianismValenceVirtue ethicsWelfarismWellbeingLong-Term Risks and FlourishingAlternative foodAnthropogenic existential riskAnthropic shadowBroad vs. narrow interventionsCompound existential riskDecisive strategic advantageDefense in depthDifferential progressEstimation of existential riskExistential catastropheExistential riskExistential risk factorExistential securityFermi paradoxFlourishing futuresGlobal catastrophic riskGlobal catastrophic biological riskHellish existential catastropheHinge of historyIndirect long-term effectsInstitutions for future generationsLong reflectionLong-term futureNatural existential riskNon-humans and the long-term futureS-riskSingletonSpeeding up developmentState vs. step riskTechnological completion conjectureTime of perils hypothesisTiming of existential risk mitigationTotal existential riskTrajectory changesTransformative developmentTranshumanismUnknown existential riskUnprecedented risksValue lock-inVulnerable world hypothesisWarning shotDecision Theory and RationalityAcausal tradeAlternatives to expected value theoryAltruistic coordinationAltruistic wagerAnthropicsBayesian epistemologyBounded rationalityCause neutralityCause prioritizationCognitive biasCounterfactual reasoningCredal resilienceCrucial considerationDebunking argumentDecision theoryDecision-theoretic uncertaintyDefinition of effective altruismDisentanglement researchDoomsday argumentEpistemic deferenceEpistemologyEvolution heuristicExpected valueFanaticismFermi estimationForecastingGame theoryIdeological Turing testInformation hazardInside vs. outside viewInstrumental vs. epistemic rationalityIntervention evaluationLong-range forecastingMarginal charityMeasuring and comparing valueModel uncertaintyModelsMoral cooperationMoral psychologyMoral tradePrediction marketsPrinciple of epistemic deferencePsychology researchRandomized controlled trialsResearch methodsReversal testRisk aversionScope neglectSimulation argumentStatistical methodsStatus quo biasThinking at the marginUnilateralist's curseValue of informationEconomics and FinanceAdjusted life yearBlockchainCost-benefit analysisDivestmentImpact investingInternational tradeMacroeconomic policyMechanism designMicrofinanceWelfare economicsPolitics, Policy, and CultureBallot initiativeConflict theory vs. mistake theoryCultural evolutionCultural lagCultural persistenceDemocracyElectoral politicsGlobal governanceInternational organizationInternational relationsLawLeadershipMisinformationPeace and conflict studiesPolarityPolicyPolitical polarizationProgress studiesSafeguarding liberal democracySocial and intellectual movementsSpace governanceSystemic changeSurveillanceTotalitarianismEffective GivingCash transfersCertificate of impactCharity evaluationConstraints on effective altruismCost-effectivenessCost-effectiveness analysisDiminishing returnsDonation choiceDonation matchingDonation pledgeDonation writeupDonor lotteriesEffective altruism fundingFunding high-impact for-profitsGiving and happinessImpact assessmentImportanceInterpersonal comparisons of wellbeingInvestingITN frameworkMarket efficiency of philanthropyMarkets for altruismNeglectednessOrg strategyPhilanthropic coordinationPhilanthropic diversificationProblem frameworkRoom for more fundingSocially responsible investingTemporal discountingTiming of philanthropyTractabilityVolunteeringWorkplace activismCareer choiceAcademiaCareer capitalCareer choiceCareer frameworkEarning to giveEffective altruism hiringEntrepreneurshipExpertiseFellowships & internshipsIndependent researchJob satisfactionOperationsPersonal fitPublic interest technologyReplaceabilityResearch careersResearch training programsRole impactSoftware engineeringSupportive conditionsWorking at EA vs. non-EA orgsOtherAtomically precise manufacturingChinaComputational power of the human brainComputroniumCryonicsEuropean UnionExtraterrestrial intelligenceFabianismGene drivesHistoryHistory of philanthropyIndiaInformation securityIterated embryo selectionKidney donationRationality communityPhilippinesPhilosophic RadicalsQueen's Lane Coffee HouseReligionRussiaScientific progressSemiconductorsUnited States politicsUtilitarian SocietyTransparency
    1. Open collaboration is collaboration that is egalitarian (everyone can join, no principled or artificial barriers to participation exist), meritocratic (decisions and status are merit-based rather than imposed) and self-organizing (processes adapt to people rather than people adapt to pre-defined processes).
    1. molecular clock

      The average speed that a genome accumulates changes to the nucleotide sequence also known as mutations.

    2. sequenced

      DNA and RNA are molecules that provide the code for cells to carry out their functions. They are composed of a small number nucleotides and the order of these nucleotides determines function. Sequencing allows us to determine what the order of nucleotides within a DNA or RNA molecule.

    3. genome

      The full set of genes or heritable genetic material like DNA or RNA present in an organism.

    4. Neolithic revolution

      When humans transitioned from small migrating groups of hunter gatherers to more stationary settlements that focused on farming and raising animals. This led to a significant growth in population sizes.

    5. divergence time

      The point where rinderpest and measles virus became different species. Virus species are distinguished by a variety of criteria including structural factors, host range, the disease they cause, and genetic similarities.

    6. Retrospective diagnosis

      When the identification of an illness is carried out after a patients death.

    7. Galen

      A Greek physician and surgeon who influenced the development of several medical disciplines.

    8. Hippocratic corpus

      A collection of medical texts from ancient Greece that are attributed to various physicians from the Alexandrian era (4th century BC).

    9. Peste des petits ruminants virus

      A virus that causes fever, ulcers of the mouth, pneumonia, stomach problems, and sometimes death in goats and sheep.

    10. Paramyxoviridae

      A family of viruses that infect vertebrates or animals with a spine. They cause a variety of diseases including measles, mumps, and various respiratory tract infections.

    11. bronchopneumonia

      Pneumonia is a type of infection causes by a variety of organisms that inflames the lungs. Bronchopneumonia is a type of pneumonia that causes inflammation of a part of the lungs called the alveoli. This inflammation makes it difficult for the lungs to get enough air.

    12. substitution saturation

      This occurs when a nucleotide is switched at the same spot in a gene sequence multiple times. It makes it seem like the rate of sequence divergence is lower than what it actually is.

    13. purifying selection

      Selection refers to natural selection the process by which organisms that are better adapted for their environment survive and produce more offspring. Natural selection causes the evolution of species. Purifying selection removes harmful variations from the population by ensuring those individuals produce fewer offspring.

    14. heterochronous

      Chronous refers to time while hetero means different meaning that the measles genomes analyzed were from different timepoints.

  5. Jul 2021
    1. bioorthogonal chemistry

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

    2. metabolic engineering

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

    3. heteroarenes

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

    4. amides

      organic compounds that contain a -CONH2 structural feature

    5. esters

      organic compounds that contain a -COOR functional group

    6. alkyl halides

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

    7. ethers

      organic compounds that contain a C-O-C structural feature

    8. anaerobic

      oxygen-free conditions

    9. 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.

    10. distal

      located at a farther distance

    11. eukaryotic

      cells with membrane-bound organelles

    12. molecular biology

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

    13. selectivity

      The preference shown by an enzyme when exposed to a competitive attack on two or more substrates or two or more positions in the same substrate.

    14. specificity

      The ability of a protein's binding site to bind to only specific ligands. The fewer ligands a protein can bind to, the greater its specificity.

    15. halogenated solvents

      Solvents that contain halogens such as fluorine, chlorine, bromine and iodine. For example, methylene chloride, CH2Cl2, is a halogenated solvent.

    16. Rhodothermus marinus

      gram-negative, rod-shaped bacterium

    17. cytochrome

      Cytochromes are proteins that contain heme as the prosthetic group.

    18. heme proteins

      A type of metalloprotein that contains a heme group, which is required for the functionality of the protein

    1. El Niño

      El Niño refers to a climate pattern that pushes warm water into the Pacific Ocean.

      This warming of the Pacific Ocean impacts global weather patterns.

      Read more here: https://oceanservice.noaa.gov/facts/ninonina.html

    2. geophysical

      The prefix "geo" means Earth.

      Thus, geophysical refers to physics occurring on and near the Earth.

    3. troposphere

      The troposphere is one of the five major layers of the Earth's atmosphere.

      It is the layer closest to the surface of the Earth.

    4. ozonesonde

      A sonde is an instrument that measures and transmits information about a remote location.

      An ozonesonde is a device that is carried by a balloon into the atmosphere. As it travels, it transmits ozone concentration information back to a station on the ground.

    5. balloon ozone trends

      Balloon ozone data is measured by instruments carried into the atmosphere by balloons.

    6. forcings

      Forcings refers to factors that drive changes in the climate.

    7. absorption of sunlight

      Light absorption occurs when light transfers energy to an object.

      Here, the sunlight's energy is transferred to ozone in the form of heat.

    8. radiatively

      Radiation refers to energy that travels at the speed of light.

      Here, it refers to a form of heat transfer that causes atmospheric temperature changes.

    9. polar cap

      The polar cap is the region of the poles that is covered in ice.

    10. anomalous

      Something that is anomalous differs from what is normal or typical.

    11. climatologies

      Climatology is the study of climate science.

    12. high-latitude

      High latitudes are approximately 60 degrees of the equator and higher. This includes the polar regions.

    13. OCS

      OCS is carbonyl sulfide with a molecular structure consisting of an oxygen (O), carbon (C), and sulfur (S) atom.

    14. Chemistry and Climate Model Intercomparison (CCMI)

      The CCMI project develops models that describe how atmospheric chemistry and climate interact with each other.

      The primary focus of the project is understanding atmospheric ozone.

    15. meteorological fields

      A field is a property of a physical system that can be measured.

      Here, it refers to properties of the atmosphere.

    16. Total Ozone Mapping Spectrometer/Ozone Monitoring Instrument (TOMS/OMI)

      TOMS and OMI are instruments used to measure the total ozone in the atmosphere.

      The TOMS data set has provided a record of total atmospheric ozone since 1978. OMI was launched in 2004 to continue the collection of ozone data.

      Both data sets are merged to obtain a more complete record of the ozone layer over time.

    17. Solar Backscatter Ultra-Violet satellite

      The SBUV is an instrument that measures the amount of ozone in the atmosphere.

      The instrument, mounted on a weather satellite, measures the sunlight reflected back from the Earth.

      Since ozone is known to reflect light at a particular wavelength, the amount of light reflected at this wavelength indicates how much ozone is present in the atmosphere.

    18. aerosol particles

      Aerosols are solid particles or liquid droplets that are suspended in a gas.

      Here, the particles are suspended in air.

    19. meteorological variability

      Meteorological variability refers to changes in atmospheric weather conditions.

    20. heterogeneous chlorine and bromine chemistry

      Heterogeneous chemistry is a chemical process that involves different phases of matter.

      Here, it refers to gaseous chlorine and bromine reacting on the surface of condensed phase cloud particles.

    21. polar stratospheric cloud (PSC) particles

      Polar stratospheric clouds form under extremely cold winter conditions in the Arctic and Antarctic.

      They support the destructive halogen chemistry responsible for ozone depletion.

    22. confounding factors

      A confounding factor impacts both variables of interest and makes it more difficult to determine the cause and effect relationship between them.

    23. monotonic

      A monotonic quantity is either always increasing or always decreasing.

    24. Polar ozone

      Polar ozone refers to the ozone layer over the Arctic and Antarctic regions.

    25. lidar

      Lidar stands for "light detection and ranging" and is a technique for measuring the distance to an object. It involves shining a laser on the object and measuring the time it takes for the light to be reflected back.

    26. dynamical variability

      Dynamical variability refers to naturally occurring changes in the climate from year-to-year.

      Halogen-induced changes become more apparent when naturally occurring changes are removed from the analysis.

    27. anthropogenic

      Anthropogenic means it was caused by human activity.

      In this context, humans released chemicals into the atmosphere, and these chemicals produced the hole in the ozone layer.

    28. interannual variability

      Interannual events take place in different years.

      Here, it refers to variations that occur from year-to-year.

    29. low latitudes

      The low-latitudes are approximately between 0 degrees (equator) and 30 degrees.

    30. stratosphere

      The stratosphere is one of the five major layers of the Earth's atmosphere.

      It is the second closest to the surface of the Earth, and it contains the ozone layer.

    31. ozone

      Ozone is a gaseous molecule composed of 3 oxygen atoms with the chemical formula, O3.

      Here, the authors are referring to the layer of ozone in the Earth's atmosphere that filters harmful ultraviolet radiation from the sun.

    32. halogens

      Halogens are a group of elements that includes fluorine, chlorine, bromine, iodine, astatine, and tennessine.

    33. halocarbons

      Halocarbons are chemicals that contain bonds between carbon and halogen atoms.

      Halogens are a group of elements that includes fluorine, chlorine, bromine, iodine, astatine, and tennessine.

      Halocarbons are highly reactive in the Earth's atmoshpere and lead to ozone depletion.

    34. mid-latitudes

      Latitude is the coordinate that specifies the north-south location on the surface of the Earth and ranges from 0 degrees at the equator to 90 degrees at the North and South Poles.

      Mid(or middle)-latitudes are approximately between 30 degrees to 60 degrees.

    35. total integrated column amount

      The integrated column is a way to quantify how much of a particular gas is found in the Earth's atmosphere.

      For a vertical path, or column, that extends through the atmoshpere, the number of gas molecules is measured at each point along the path. Then, the sum total is calculated for the entire path.

      In this case, it is used to measure the amount of ozone in the atmoshpere.

    36. depletion

      To deplete is to reduce the amount of something.

      Here, the amount of ozone in the Earth's atmosphere has been reduced.

    1. epidemic

      An epidemic is the appearance of a disease in a large number of people within a short period of time.

    2. geocoded repository

      Geocoding is a process to transform commonly text-based descriptions of locations (e.g., addresses) to coordinates on the Earth's surface. Geocoding allows further mapping and spatial analysis using various software. In a geocoded repository, all data are attributes to spatial coordinates.

    1. substitution rates

      The speed at which mutations occur to a genome.

    2. Bayesian

      Refers to a branch of statistics based on Bayes' theorem. This theorem is used to update the probability or likelihood of a hypothesis or proposed explanation as more information is available. This method allows for inference or the ability to draw conclusions about a larger group based on a smaller sample.

    3. endemic

      A disease is endemic when it is found regularly in a population.

    4. live-attenuated vaccine

      A vaccine is a substance that causes the body to recognize and stop a disease-causing agent via a type of protein called antibodies. Antibodies combine with proteins on the surface of invading pathogens and alert the immune system. A live-attenuated vaccine uses a weakened for of a virus to cause this immune response.

    1. Components let you split the UI into independent, reusable pieces, and think about each piece in isolation.

      I like this definition of 'components'.

  6. Jun 2021
    1. 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 to enhance its chances of survival.

    1. order of magnitude

      An order of magnitude is a comparison of size used when the item being compared is 10 times larger or smaller than the item it is being compared to. The difference between 1 and 10 is an order of magnitude, as is the difference between 10 and 100. The difference between 1 and 100 is 2 orders of magnitude, and the difference between 1 and 1000 is 3 orders of magnitude.

    2. MT

      A MT (metric ton) is a unit of weight equal to 1000 kilograms (2205 pounds).