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Electrorotation is the circular movement of an electrically polarized particle. Similar to the slip of an electric motor, it can arise from a phase lag between an applied rotating electric field and the respective relaxation processes and may thus be used to investigate the processes or, if these are known or can be accurately described by models, to determine particle properties. The method is popular in cellular biophysics, as it allows measuring cellular properties like conductivity and permittivity of cellular compartments and their surrounding membranes. == See also == Dielectric relaxation Dielectrophoresis Membrane potential
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{
"page_id": 2359746,
"source": null,
"title": "Electrorotation"
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2-hydroxyethylphosphonate:O2 1,2-oxidoreductase may refer to: 2-hydroxyethylphosphonate dioxygenase, an enzyme Methylphosphonate synthase, an enzyme
|
{
"page_id": 38339016,
"source": null,
"title": "2-hydroxyethylphosphonate:O2 1,2-oxidoreductase"
}
|
In population biology and demography, generation time is the average time between two consecutive generations in the lineages of a population. In human populations, generation time typically has ranged from 20 to 30 years, with wide variation based on gender and society. Historians sometimes use this to date events, by converting generations into years to obtain rough estimates of time. == Definitions and corresponding formulas == The existing definitions of generation time fall into two categories: those that treat generation time as a renewal time of the population, and those that focus on the distance between individuals of one generation and the next. Below are the three most commonly used definitions: === Time for a population to grow by a factor of its net reproductive rate === The net reproductive rate R 0 {\displaystyle \textstyle R_{0}} is the number of offspring an individual is expected to produce during its lifetime: R 0 = 1 {\displaystyle \textstyle R_{0}=1} means demographic equilibrium. One may then define the generation time T {\displaystyle T} as the time it takes for the population to increase by a factor of R 0 {\displaystyle \textstyle R_{0}} . For example, in microbiology, a population of cells undergoing exponential growth by mitosis replaces each cell by two daughter cells, so that R 0 = 2 {\displaystyle \textstyle R_{0}=2} and T {\displaystyle T} is the population doubling time. If the population grows with exponential growth rate r {\displaystyle \textstyle r} , so the population size at time t {\displaystyle t} is given by n ( t ) = α e r t {\displaystyle n(t)=\alpha \,e^{rt}} , then generation time is given by T = log R 0 r {\displaystyle T={\frac {\log R_{0}}{r}}} . That is, T {\displaystyle \textstyle T} is such that n ( t + T ) =
|
{
"page_id": 9503180,
"source": null,
"title": "Generation time"
}
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R 0 n ( t ) {\displaystyle n(t+T)=R_{0}\,n(t)} , i.e. e r T = R 0 {\displaystyle e^{rT}=R_{0}} . === Average difference in age between parent and offspring === This definition is a measure of the distance between generations rather than a renewal time of the population. Since many demographic models are female-based (that is, they only take females into account), this definition is often expressed as a mother-daughter distance (the "average age of mothers at birth of their daughters"). However, it is also possible to define a father-son distance (average age of fathers at the birth of their sons) or not to take sex into account at all in the definition. In age-structured population models, an expression is given by: T = ∫ 0 ∞ x e − r x ℓ ( x ) m ( x ) d x {\displaystyle T=\int _{0}^{\infty }xe^{-rx}\ell (x)m(x)\,\mathrm {d} x} , where r {\displaystyle \textstyle r} is the growth rate of the population, ℓ ( x ) {\displaystyle \textstyle \ell (x)} is the survivorship function (probability that an individual survives to age x {\displaystyle \textstyle x} ) and m ( x ) {\displaystyle \textstyle m(x)} the maternity function (birth function, age-specific fertility). For matrix population models, there is a general formula: T = λ v w v F w = 1 ∑ e λ ( f i j ) {\displaystyle T={\frac {\lambda \mathbf {vw} }{\mathbf {vFw} }}={\frac {1}{\sum e_{\lambda }(f_{ij})}}} , where λ = e r {\displaystyle \textstyle \lambda =e^{r}} is the discrete-time growth rate of the population, F = ( f i j ) {\displaystyle \textstyle \mathbf {F} =(f_{ij})} is its fertility matrix, v {\displaystyle \textstyle \mathbf {v} } its reproductive value (row-vector) and w {\displaystyle \textstyle \mathbf {w} } its stable stage distribution (column-vector); the e λ ( f i
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{
"page_id": 9503180,
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"title": "Generation time"
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|
j ) = f i j λ ∂ λ ∂ f i j {\displaystyle \textstyle e_{\lambda }(f_{ij})={\frac {f_{ij}}{\lambda }}{\frac {\partial \lambda }{\partial f_{ij}}}} are the elasticities of λ {\displaystyle \textstyle \lambda } to the fertilities. === Age at which members of a cohort are expected to reproduce === This definition is very similar to the previous one but the population need not be at its stable age distribution. Moreover, it can be computed for different cohorts and thus provides more information about the generation time in the population. This measure is given by: T = ∫ x = 0 ∞ x ℓ ( x ) m ( x ) d x ∫ x = 0 ∞ ℓ ( x ) m ( x ) d x {\displaystyle T={\frac {\int _{x=0}^{\infty }x\ell (x)m(x)\,\mathrm {d} x}{\int _{x=0}^{\infty }\ell (x)m(x)\,\mathrm {d} x}}} . Indeed, the numerator is the sum of the ages at which a member of the cohort reproduces, and the denominator is R0, the average number of offspring it produces. == References ==
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{
"page_id": 9503180,
"source": null,
"title": "Generation time"
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The Bjerrum length (after Danish chemist Niels Bjerrum 1879–1958 ) is the separation at which the electrostatic interaction between two elementary charges is comparable in magnitude to the thermal energy scale, k B T {\displaystyle k_{\text{B}}T} , where k B {\displaystyle k_{\text{B}}} is the Boltzmann constant and T {\displaystyle T} is the absolute temperature in kelvins. This length scale arises naturally in discussions of electrostatic, electrodynamic and electrokinetic phenomena in electrolytes, polyelectrolytes and colloidal dispersions. In standard units, the Bjerrum length is given by λ B = e 2 4 π ε 0 ε r k B T , {\displaystyle \lambda _{\text{B}}={\frac {e^{2}}{4\pi \varepsilon _{0}\varepsilon _{r}\ k_{\text{B}}T}},} where e {\displaystyle e} is the elementary charge, ε r {\displaystyle \varepsilon _{r}} is the relative dielectric constant of the medium and ε 0 {\displaystyle \varepsilon _{0}} is the vacuum permittivity. For water at room temperature ( T ≈ 293 K {\displaystyle T\approx 293{\text{ K}}} ), ε r ≈ 80 {\displaystyle \varepsilon _{r}\approx 80} , so that λ B ≈ 0.71 nm {\displaystyle \lambda _{\text{B}}\approx 0.71{\text{ nm}}} . In Gaussian units, 4 π ε 0 = 1 {\displaystyle 4\pi \varepsilon _{0}=1} and the Bjerrum length has the simpler form λ B = e 2 ε r k B T . {\displaystyle \lambda _{\text{B}}={\frac {e^{2}}{\varepsilon _{r}k_{\text{B}}T}}.} The relative permittivity εr of water decreases so strongly with temperature that the product (εr·T) decreases. Therefore, in spite of the (1/T) relation, the Bjerrum length λB increases with temperature, as shown in the graph. == See also == Debye length Debye–Hückel equation Shielding effect Screening effect Electrical double layer, (EDL) Brownian motion == References ==
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{
"page_id": 1966541,
"source": null,
"title": "Bjerrum length"
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Congruent melting occurs during melting of a compound when the composition of the liquid that forms is the same as the composition of the solid. It can be contrasted with incongruent melting. This generally happens in two-component systems. To take a general case, let A and B be the two components and AB a stable solid compound formed by their chemical combination. If we draw a phase diagram for the system, we notice that there are three solid phases, namely A, B and compound AB. Accordingly, there will be three fusion or freezing point curves AC, BE and CDE for the three solid phases. In the phase diagram, we can notice that the top point D of the phase diagram is the congruent melting point of the compound AB because the solid and liquid phases now have the same composition. Evidently, at this temperature, the two-component system has become a one-component system because both solid and liquid phases contains only the compound AB. Congruent melting point represents a definite temperature just like the melting points of pure components. In some phase diagrams, the congruent melting point of a compound AB may lie above the melting points of pure components A and B. But it is not always necessarily the case. There are different types of systems known in which the congruent melting point is observed below the melting points of the pure components. This happens for inter-metallic compounds, for example, for MgSi2. == See also == Congruent transition Incongruent melting Phase diagram Phase rule == References ==
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{
"page_id": 7864782,
"source": null,
"title": "Congruent melting"
}
|
The International Primatological Society (IPS) is a scientific, educational, and charitable organization focused on non-human primates. It encourages scientific research in all areas of study, facilitates international cooperation among researchers, and promotes primate conservation. Together with the IUCN Species Survival Commission Primate Specialist Group (IUCN/SSC PSG) and Conservation International (CI), it jointly publishes a biannual report entitled Primates in Peril: The World's 25 Most Endangered Primates. Jan van Hooff served as secretary general of the organization. == See also == International Journal of Primatology == References == == External links == International Primatological Society Archived 2012-12-03 at the Wayback Machine - Official site
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{
"page_id": 28377553,
"source": null,
"title": "International Primatological Society"
}
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In molecular biology, mir-42 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. == See also == MicroRNA == References == == Further reading == == External links == Page for mir-42 microRNA precursor family at Rfam
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{
"page_id": 36372946,
"source": null,
"title": "Mir-42 microRNA precursor family"
}
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The cyclosporins are a group of macrolides isolated from fungi and used as immunosuppresant drugs, for example after transplant surgery. They are nonribosomal peptide synthesized by cyclosporin synthetase. Cyclosporin A (ciclosporin) Cyclosporin B Cyclosporin C Cyclosporin D Cyclosporin E Cyclosporin F Cyclosporin G == References ==
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{
"page_id": 5505493,
"source": null,
"title": "Cyclosporins"
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Developmental symbiosis is a biological phenomenon in which the normal development of an organism depends on interactions with symbiotic partners, often microbes, that influence gene expression, tissue formation, or physiological function. Symbiosis is the intimate relationship between one or more organisms of different species. These organisms are referred to as symbionts. Many types of relationships are found in symbiosis; three examples are mutualism, commensalism, and parasitism. As the name suggests, mutualism is a mutual dynamic between the organisms where both can benefit from the relationship. Parasitism, however, is when one organism actively harms the host for their own benefit. Commensalism refers to a relationship where only one organism benefits while the other gains nothing but is also left unharmed. The most common type is the mutualistic relationship and can be viewed as either obligatory or facultative. Developmental symbiosis is the relationship between a developing organism and specific microorganisms. Microscopic organisms exist all around the globe, even in the human body. They are responsible for the formation of many developmental functions within the body from its earliest stages of life. Microorganisms are prevalent in most somatic tissues and in reproductive germline cells. Certain bacteria allow cells to determine whether other bacteria are either harmful or helpful, building a stronger and sharper immune system. Other bacteria aid in the development of tissue to fully form structures of an organism's body. Understanding the strong relation between developmental symbiosis and evolution is crucial to understanding how organisms function and adapt over time. This connection emphasizes that many different plants and animals are heavily influenced by the internal and external symbiotic microbes to develop their bodily structures and functions. == History == Scientific understanding of symbiosis in development arose in the 19th century, particularly through the study of lichens and legumes. === Lichens === Lichens
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"page_id": 79167960,
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had long been considered a discrete plant organism. In 1866, one researcher, Heinrich Anton de Bary, speculated that gelatinous lichens might actually form as a result of the penetration of an alga by a fungus.In 1866, one researcher, Heinrich Anton de Bary, speculated that gelatinous lichens might actually form as a result of the penetration of an alga by a fungus. The following year, Simon Schwendener advanced the view that all lichens could be considered the product of such an association, notably in which the fungus exploits the algae. Schwendener received harsh opposition, as the dual nature of lichen challenged the traditional taxonomic view. In 1873, Albert Frank conducted studies on hypophloedal lichens, which grow beneath the outermost layer of bark. He proposed that the association between fungi and algae is far more complex than simple parasitism, introducing the term “symbiotismus” to describe this intimate relationship. Two years later, Bary expanded on this concept by formally defining the dual nature of lichens as “Symbiose” in a lecture to German naturalists and physicians at Cassel. Later, in his publication Die Erscheinung der Symbiose, Bary refined the definition of symbiosis, establishing three fundamental criteria: (1) two entities must live together, (2) they must be in physical contact, and (3) they must be of different species. === Legumes === While the study of lichens dominated early symbiosis research, parallel discoveries in microbiology soon expanded the concept of symbiosis. Toward the end of the 19th century, Hermann Hellriegel demonstrated that legumes form nodules in response to microbial colonization. Using sterilized sand cultures, he showed that bacteria in the soil are responsible for inducing nodule formation, enabling leguminous plants to fix atmospheric nitrogen and grow even in nitrogen-poor soils. Dutch microbiologist Martinus Beijerinck later successfully isolated the bacteria from legume root nodules and named it
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"page_id": 79167960,
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Rhizobium. == Types == === Obligate symbiosis === Obligate symbiosis is a type of symbiotic relationship in which at least one organism, the symbiont, cannot survive independently and requires a host organism to survive and/or reproduce. The symbiont organism can survive by living on or inside of the host organism.A big form of this is endosymbiosis, where one organism lives inside the cells of another in a close, often essential, relationship. This type of symbiosis can be harmful or beneficial to the host organism. Some obligate symbionts can cause deleterious mutations to the host organism, causing altered gene expression or manipulation of the host's reproductive systems to help reproduce more of the symbiont species. This benefits the symbiont, but in turn, can harm the fitness of the host. To benefit the host, some symbiont organisms provide essential nutrients and/or vitamins that the host would not normally be able to synthesize or consume. Symbionts can also provide priming for the host's immune system, allowing the immune system to fight off future infections more effectively. Obligate relationships are often referred to as a process known as a “rabbit hole.” The “rabbit hole” process is a metaphor for when the obligate organisms become committed to an inherited, mutually dependent symbiotic relationship in which both organisms are affected by unusual genomic evolutions. Changes for the symbionts can involve genome reduction, rapid protein evolution, and codon reassignments. In contrast, the host’s changes can involve acquiring bacterial genes to help regulate and support their symbionts. These evolutionary changes are often irreversible and highly complex, leading to continuous and profound transformations in both partners—hence the term “rabbit hole.” Once the process becomes permanently established this relationship cannot be broken without causing harm or death to one or both partners. === Facultative symbiosis === Facultative symbiosis is a
|
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"page_id": 79167960,
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type of symbiotic relationship where organisms do not require one another for survival or reproduction. This means they can live independently, and still participate in symbiotic interactions. Organisms that choose to have facultative symbiosis do so due to the benefits. These benefits can be mutual, commensal or parasitic. Facultative symbiotic relationships and host changes can happen when organisms gain new genes from other species or lose important genes due to mutations, making them more dependent on their partners. Facultative symbionts can provide protection against environmental stressors and some provide nutritional benefits. An example of this is the relationship between clownfish and sea anemone. The sea anemone provides protection for clownfish through its stinging tentacles, and the anemone benefits from cleaning by water circulation, being provided nitrogen compounds, and luring prey by the bright colors of the clownfish. Some bacteria (Serratia symbiotica) help aphids resist fungal infections and survive extreme temperatures. These relationships are becoming harder to detect or study, meaning that this could lead to biases in research. In some species, facultative bacteria can be passed down to offspring (vertical transmission), allowing the relationship to continue across generations. As the offspring grows, the facultative relationship between host and symbionts can strengthen. This leads to a deeper physiological integration, where the host relies on the symbionts for nutrient synthesis, defense, and/or environmental adaptation. Meaning over time, the relationship may shift from facultative to obligate symbiosis.When facultative symbiosis becomes essential for survival, the relationship evolves into an obligate relationship. This transition is not always a one-way process. This means that even after becoming obligate, the symbiosis can revert or break down under the right conditions This shift from facultative to obligate is often seen in tightly integrated systems, such as those involving host-microbe interactions or plant-pollinator relationships, especially when consistent mutual benefit
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"page_id": 79167960,
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leads to genetic or physiological adaptations that make independent survival less practical. === Vertical vs. horizontal transmission === As most animals use either vertical or horizontal transmission, there are some animals that use both. As an example, holometabolous insects use both vertical and horizontal transmission of gut bacteria. ==== Vertical transmission ==== Vertical transmission refers to the transferring of symbionts directly from parent to offspring. This process ensures that each generation of hosts inherit a symbiotic partner. This maintains the symbiotic relation over time. Since the symbionts are consistently passed from parent to offspring, the host and symbiont co-evolve, making it unnecessary for the host to obtain the symbiont from nature each generation. Vertical transmission can be found in all types but is mostly found in obligate symbiosis, where the host is dependent on the symbiont and vice versa. As symbionts live in a protected environment (in the host), they lose the ability to survive on their own. In aphids, for example, the subpopulation of a single mother's bacteriocyte is transferred to the embryo. Later on, in cellularization, the symbionts that have penetrated the embryo are subdivided again into different bacteriocytes, restarting and reaffirming the symbiotic relationship. ==== Horizontal transmission ==== Horizontal transmission involves the gaining of symbionts from the external environment or other individuals, rather than from a parent. This transmission process can happen at all stages of life in different ways such as eating, physical contact, environmental exposure, or interactions with other individuals. This approach allows for greater flexibility and adaptability, enabling animals like insects to pick up microbes suited to new diets, habitats, or environmental conditions. Horizontal transmission allows animals to obtain symbionts that are well-suited to handle the current environment or changes in diet, instead of being bound to the symbiont, like in vertical transmission. Because
|
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"page_id": 79167960,
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the symbionts gained come from a variety of places, horizontal transmitted host tend to be diverse and allow them to adapt to new environments. It is important that hosts must encounter the right symbionts at the right time, because if the necessary symbionts are not present in the environment, the host may suffer. == Molecular and Genetic Mechanisms == Symbiotic organisms produce signals within their hosts to influence certain functions within the host’s body. These functions can range from gene expression to immune response to foreign bacteria. === Lipid-derived molecules === Sphingolipids are vital in maintaining gut health and promoting symbiosis with the host. These lipids are produced by gut bacteria like the Bacteroides species and are often located in the bacterial outer membrane of cells. They contribute to influencing iNKT cell regulation and fighting off risks of Inflammatory Bowel Disease (IBD) through the use of lipid signaling within the host's immune system. They can also be located within endosomes and the Golgi apparatus. Within the gut, they will send signals to inflammation-related pathways to influence the lipid metabolism of the host. There, they will regulate immune cells to low the chances of inflammation. The absence of Bacteroides-derived sphingolipids can lead to gut inflammation and alterations to the host’s ceramide levels, which will negatively impact the host’s ability to maintain homeostasis. Bacteroides sphingolipids can interact with the host's immune system through its outer membrane vesicles. The sphingolipids within these vesicles will activate the Toll-like receptor 2 signaling in macrophages, limiting inflammatory signaling. Bacteroides sphingolipids can move to other parts within the host’s body to aid in immune system maintenance. === Polysaccharides === Polysaccharide A (PSA) is a capsular carbohydrate from the commensal gut bacteria Bacteroides fragilis and possess both potent T cell-dependent pro- and anti-inflammatory properties. This molecule, produced by
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"page_id": 79167960,
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Bacteroides fragilis, is a model symbiotic immunomodulatory molecule. It interacts with Toll-like receptor 1 and 2 as well as Dectin-1 to activate the phosphoinositide 3-kinase pathway in order to express the anti-inflammatory genes. Dectin-1 binds to the fungal polysaccharide, β-glucans, which then triggers a signaling cascade events that leads to the recruitment of signaling molecules, such as tyrosine-protein kinase and CARD9, which further activate downstream pathways to enhance immune cells to target and destroy fungal pathogens. == Plants == Plants in both natural and agricultural environments are consistently exposed to diverse microbial communities, which can include both symbiotic and harmful species. Symbiotic associations can influence plant development by modulating root architecture, altering hormone signaling pathways, and enhancing responses to environmental stress. In certain plant species, such as orchids, successful seed germination and early development depend on the presence of fungal partners. Ongoing research continues to investigate the molecular and cellular mechanisms that mediate these interactions. For several examples of developmental symbiosis in plants, see applications. == Human health == In humans, the gut microbiota acts as a developmental symbiotic relationship in which microbes have a food source and humans can properly digest nutrition. The gut microbiota refers to all of the microorganisms living primarily in the intestinal tract of the human body. The human body has different microbiota composition throughout life, resulting in different compositions at different points of life. Two stages are from birth to weaning and from weaning to adulthood. The diversity of the microbiota is important for the proper health of the host. Early exposure to these bacteria and a proper diet throughout one's life are important for a healthy intestinal tract. Humans begin this symbiotic relationship during gestation, where they are exposed to some bacteria, but most bacteria are acquired from the mother during birth or
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{
"page_id": 79167960,
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"title": "Developmental symbiosis"
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from receiving the mother's milk. === Role in Immune System Development === The development of a healthy microbiota is also important for an individual to remain healthy and ensure the immune system can function normally. This development of both proper digestion and the importance of the immune system introduces the idea of symbiopoiesis. Symbiopoiesis is a co-development that is vital for the host to have proper development, like its organs. When compared to host organisms with proper gut microbiota, those without bacteria had decreased cell proliferation, decreased immune system development, and decreased gene expression. The lack of bacteria in the gut leads to a decrease in macrophages in the intestinal tract, which digest harmful pathogens and prevent infection. Hosts without bacteria in their gut also had decreased levels of cytokines and immunoglobulins, impairing the proper function of the immune system to react properly to infections within the body. An example of this in humans is babies born naturally versus those born in a C-section. Those born naturally have developed a proper immunity, whereas those born via a C-section did not get the same exposure to bacteria. === Influence on Neurological development === The microbes within the gut were shown to have a great effect on the brain as the microbes help to produce important neurotransmitters such as dopamine, serotonin, and γ-aminobutyric acid (GABA). The lack of these neurotransmitters and their receptors would cause the organism to have a lack of proper neurodevelopment. == Developmental Symbiosis in other animals == Most of the problems seen in humans when it comes to the development of or lack of a symbiotic relationship with bacteria are similar to those in other animals. Any other mammal that gives vaginal birth will experience the same process as humans. The relationship between animals and bacteria is a
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"page_id": 79167960,
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"title": "Developmental symbiosis"
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result of co-evolution over millions of years. This is concluded due to the dependency that animals and bacteria have developed for each other and how important it is for one to have the other. Different animals have developed through co-evolution unique microbiomes based on their diet so that the bacteria in their gut are best for the food sources they use. Different animals also use microbes for more than just digestion, but protection, like Wolbachia bacteria, which can be used to protect unhatched offspring. However, the means by which animals like birds obtain their gut microbiome differ from that of mammals. Birds typically obtain most of their gut microbiota from the regurgitative feeding received from the parents after hatching occurs as well as early environmental exposure. == Evolutionary Integration through symbiosis == Long term co-evolution is an evolutionary process where two or more species interact closely over periods of time, where each species influences each other. The co-evolution between the host and symbiont results in genetic, biochemical, and structural changes in both parties. As the endosymbiotic relationship evolves, the genomes of the host and the symbiont become more interconnected, often through horizontal gene transfer (HGT), where genetic material from the symbiont is incorporated into the host’s genome. Over time, this makes the host partly responsible for keeping the symbiont’s functions going. Because the symbiont’s loss of autonomy, it also loses its innate ability to survive outside the host environment, as they both evolve. Host and symbiont alike go through genome reduction as they become dependent on each other. Co-evolution, through a process known as symbiogenesis, can lead to specific changes in metabolic functions. In humans, mitochondria evolved to become the main energy center of the eukaryotic cell, specializing in aerobic respiration and ATP production. Plastids in plants and algae evolve
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"page_id": 79167960,
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"title": "Developmental symbiosis"
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to specialize in photosynthesis. Symbionts such as these also evolve not only for the symbiotic relationship but also for themselves. Mitochondria have their own membranes that are distinct from the host cell's membranes, a remnant of their prokaryotic origin. Long-term co-evolution enables species to adapt to their environment in ways that would not be possible through independent evolution alone. Symbiosis provides a pathway for new functions and complex relationships to evolve. == Experimental Techniques == Developmental symbiosis remains a rapidly evolving field with much still to be discovered regarding the intricate relationships between hosts and their symbionts. To investigate these interactions, researchers can currently employ a diverse array of experimental techniques, ranging from molecular sequencing, to imaging technologies, and to germ-free models. === Microbiome Sequencing === Symbiosis research heavily focuses on microbiomes. In humans, microbial cells outnumber human cells by approximately 10 to 1, underscoring their significance. Next-Generation Sequencing (NGS) technologies can analyze microbiome composition and function. Sample preparation involves collection from environments like the gut or skin, followed by flash-freezing or storage in microbiome media to preserve microbial integrity. Extracted DNA is then fragmented and prepared for sequencing. Two primary approaches exist: amplicon sequencing, which targets genetic markers like 16S rRNA (bacteria) and 18S rRNA (eukaryotic microbes), and whole genome shotgun sequencing, which sequences entire microbial genomes. During sequencing, DNA is denatured into single strands, and complementary strands are synthesized. Fluorescent signals emitted during synthesis are captured and converted into nucleotide sequences. NGS can generate vast datasets with high efficiency, enabling researchers to investigate symbiotic interactions, identify microbial imbalances, and assess microbiome influences on host development and health. Although microbiome sequencing technologies are a powerful tool, they do have several limitations. Sample collection and DNA extraction can introduce inaccurate representations, as microbial communities can shift during collection. Contamination, high
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"page_id": 79167960,
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"title": "Developmental symbiosis"
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costs, and computational demands can also pose challenges. === Imaging Techniques === Advanced imaging techniques can complement sequencing approaches, allowing researchers to visualize symbiotic interactions at cellular and molecular levels. Fluorescence in situ hybridization (FISH) can identify spatial localization of microbial species through hybridization with a nucleic acid target in host tissues. Confocal and electron microscopy can provide high-resolution imaging of host-microbe interactions. Live-cell imaging also facilitates real-time observation of dynamic interactions between symbionts and host cells, unveiling molecular processes. These methods are central to mapping the structural organization of symbiotic associations and discerning their functional implications. === Germ-Free Model Organisms === Germ-free (GF) model organisms are bred and maintained in sterile isolators, eradicating exposure to microorganisms. Researchers use GF models to investigate the impact of a complete lack of microbiota on host development. Moreover, GF models can be utilized to create gnotobiotic models, where specific microbes are introduced under controlled conditions. Such models can be invaluable for studying the influence of symbiotic microorganisms. The production and maintenance of isolated GF animals need particular facilities. The cost, labor, and skills necessary to preserve them can make these models inaccessible to many researchers. == Applications and Future Research == === Synthetic Microbial Research Communities === Synthetic biology focuses on engineering beneficial symbioses by leveraging engineering principles to create new symbiotic relationships or manipulate pre-existing ones. This includes engineering microbes for specific functions, like nitrogen fixation in plants, or modulating host-microbiome interactions for improved health. Synthetic biology allows for the creation of new or enhanced symbiotic relationships, contributing to sustainable agriculture and human health. Work to create artificial microbial communities is necessary to recreate and observe interactions between the symbionts to strengthen our understanding of the complexity of nature and agriculture. === Symbiotic Nitrogen Fixation === Symbiotic nitrogen fixation is a mutually
|
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"page_id": 79167960,
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beneficial relationship where nitrogen-fixing bacteria convert atmospheric nitrogen into a usable form for plants, while the plants provide the bacteria with nutrients and protection. The bacteria convert atmospheric nitrogen into a usable forms like ammonia that plants can absorb and use to build amino acids and other important organic compounds. Bacteria enter the plant roots and form specialized structures called root nodules, where nitrogen fixation takes place. Nitrogen fixation is a crucial natural process for providing plants with nitrogen, an essential element for growth and development. In agriculture, it utilizes nitrogen-fixing bacteria like Rhizobium to create a reduction in synthetic nitrogen fertilizers colonizing the roots of the plant to form nodules where they convert atmospheric nitrogen into forms usable by the plant, thus improving soil fertility and plant growth. As the plant grows and dies, it releases the fixed nitrogen back into the soil, enriching it with a readily available source of nitrogen. This also contributes to increased soil organic matter, which helps in water retention and nutrient cycling. === Hawaiian Bobtail Squid and Vibrio fischeri === The squid harbors Vibrio fischeri bacteria in a specialized light organ. The bacteria provide bioluminescence, which helps the squid camouflage against predators by mimicking moonlight. The Hawaiian bobtail squid and the bioluminescent bacterium Vibrio fischeri have a unique and beneficial symbiotic relationship. The bacteria resides within the squid’s light organ. In exchange for a sustainable habitat, bacteria produce light to help the squid camouflage itself. Researchers use knowledge of this relationship with V. fischeri symbiosis to understand how the squid controls the light output and to potentially discover new drugs with antibacterial or anti-fungal properties. === Parasitic Wasp Asobara tabida and Wolbachia === The parasitic wasp Asobara tabida and its symbiont, the bacteria Wolbachia, offer potential future benefits in pest control and disease
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"page_id": 79167960,
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management. A. tabida relies on Wolbachia for oogenesis and is highly selective in its host choice, making it a valuable tool for biological control. Wolbachia can also be used to control vector-borne diseases by interfering with the reproduction and fitness of disease-carrying insects. Since the female parasitic wasps cannot develop without being infected with Wolbachia bacteria, it is important to understand why this obligate symbiosis can lead to insights into reproductive biology and pest control strategies. === Mycorrhizal Symbiosis between Plants and Fungi === Mycorrhizal fungi form symbiotic relationships with plant roots, enhancing nutrient and water uptake. Mycorrhizal fungi extend the plant's root system, increasing its ability to absorb water and essential nutrients like phosphorus, nitrogen, and micronutrients from the soil. By improving nutrient and water uptake, mycorrhizal symbiosis promotes plant growth, development, and yield, especially in challenging soil conditions. This symbiosis is crucial for agriculture and ecosystem health, and researchers are studying it to improve crop yields and soil health. === Benefits of Future Research === Researching the human microbiome, including the role of symbiotic bacteria in health and disease, has significant implications for human health and well-being. Humans harbor a diverse community of bacteria and other microbes in their gut and on their skin, which play a role in digestion, immunity, and overall health. Scientists and researchers study the human microbiome to understand its role in various diseases and to develop and improve treatments. Understanding how symbiotic microbes provide defense against pathogens and environmental stress can lead to new strategies for plant and animal health. For example, studying the evolution and development of specialized organs that house symbionts, like those in corals or insects, can reveal how host-symbiont interactions drive adaptation. Such future research into developmental symbiosis promises to reveal how interactions between organisms and their symbionts influence
|
{
"page_id": 79167960,
"source": null,
"title": "Developmental symbiosis"
}
|
development, adaptation, and evolution. == See also == Symbiosis Developmental Biology Symbiosis in Lichens Symbiogenesis == References == == Further reading ==
|
{
"page_id": 79167960,
"source": null,
"title": "Developmental symbiosis"
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The following is the list of the 286 plant communities which comprise the British National Vegetation Classification (NVC). These are grouped by major habitat category, as used in the five volumes of British Plant Communities, the standard work describing the NVC. == Woodland and scrub communities == The following 25 communities are described in Volume 1 of British Plant Communities. For an article summarising these communities see Woodland and scrub communities in the British National Vegetation Classification system. W1 Salix cinerea - Galium palustre woodland W2 Salix cinerea - Betula pubescens - Phragmites australis woodland W3 Salix pentandra - Carex rostrata woodland W4 Betula pubescens - Molinia caerulea woodland W5 Alnus glutinosa - Carex paniculata woodland W6 Alnus glutinosa - Urtica dioica woodland W7 Alnus glutinosa - Fraxinus excelsior - Lysimachia nemorum woodland W8 Fraxinus excelsior - Acer campestre - Mercurialis perennis woodland W9 Fraxinus excelsior - Sorbus aucuparia - Mercurialis perennis woodland W10 Quercus robur - Pteridium aquilinum - Rubus fruticosus woodland W11 Quercus petraea - Betula pubescens - Oxalis acetosella woodland W12 Fagus sylvatica - Mercurialis perennis woodland W13 Taxus baccata woodland W14 Fagus sylvatica - Rubus fruticosus woodland W15 Fagus sylvatica - Deschampsia flexuosa woodland W16 Quercus spp. - Betula spp. - Deschampsia flexuosa woodland W17 Quercus petraea - Betula pubescens - Dicranum majus woodland W18 Pinus sylvestris - Hylocomium splendens woodland W19 Juniperus communis ssp. communis - Oxalis acetosella woodland W20 Salix lapponum - Luzula sylvatica scrub W21 Crataegus monogyna - Hedera helix scrub W22 Prunus spinosa - Rubus fruticosus scrub W23 Ulex europaeus - Rubus fruticosus scrub W24 Rubus fruticosus - Holcus lanatus underscrub W25 Pteridium aquilinum - Rubus fruticosus underscrub == Mires == The following 38 communities are described in Volume 2 of British Plant Communities. For an article summarising these communities see Mires
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in the British National Vegetation Classification system. M1 Sphagnum auriculatum bog pool community M2 Sphagnum cuspidatum/recurvum bog pool community M3 Eriophorum angustifolium bog pool community M4 Carex rostrata - Sphagnum recurvum mire M5 Carex rostrata - Sphagnum squarrosum mire M6 Carex echinata - Sphagnum recurva/auriculatum mire M7 Carex curta - Sphagnum russowii mire M8 Carex rostrata - Sphagnum warnstorfii mire M9 Carex rostrata - Calligeron cuspidatum/giganteum mire M10 Carex dioica - Pinguicula vulgaris mire Pinguiculo-Caricetum dioicae Jones 1973 emend. M11 Carex demissa - Saxifraga aizoides mire Carici-Saxifragetum aizoidis McVean & Ratcliffe 1962 emend. M12 Carex saxatilis mire Caricetum saxatilis McVean & Ratcliffe 1962 M13 Schoenus nigricans - Juncus subnodulosus mire Schoenetum nigricantis Koch 1926 M14 Schoneus nigricans - Narthecium ossifragum mire M15 Scirpus cespitosus - Erica tetralix wet heath M16 Erica tetralix - Sphagnum compactum wet heath Ericetum tetralicis Schwickerath 1933 M17 Scirpus cespitosus - Eriophorum vaginatum blanket mire M18 Erica tetralix - Sphagnum papillosum raised and blanket mire M19 Calluna vulgaris - Eriophorum vaginatum blanket mire M20 Eriophorum vaginatum raised and blanket mire M21 Narthecium ossifragum - Sphagnum papillosum valley mire Narthecio-Sphagnetum euatlanticum Duvigneaud 1949 M22 Juncus subnodulosus - Cirsium palustre fen-meadow M23 Juncus effusus/acutiflorus - Galium palustre rush-pasture M24 Molinia caerulea - Cirsium dissectum fen-meadow Cirsium-Molinietum caeruleae Sissingh & De Vries 1942 emend. M25 Molinia caerulea - Potentilla erecta mire M26 Molinia caerulea - Crepis paludosa mire M27 Filipendula ulmaria - Angelica sylvestris mire M28 Iris pseudacorus - Filipendula ulmaria mire Filipendulo-Iridetum pseudacori Adam 1976 emend. M29 Hypericum elodes - Potamogeton polygonifolius soakway Hyperico-Potametum polygonifolii (Allorge 1921) Braun-Blanquet & Tüxen 1952 M30 Related vegetation of seasonally-inundated habitats Hydrocotyla-Baldellion Tüxen & Dierssen 1972 M31 Anthelia judacea - Sphagnum auriculatum spring Sphagno auriculati-Anthelietum judaceae Shimwell 1972 M32 Philonotis fontana - Saxifraga stellaris spring Philonoto-Saxifragetum stellaris Nordhagen 1943 M33 Pohlia wahlenbergii
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var. glacialis spring Pohlietum glacialis McVean & Ratcliffe 1962 M34 Carex demissa - Koenigia islandica flush M35 Ranunculus omiophyllus - Montia fontana rill M36 Lowland springs and streambanks of shaded situations Cardaminion (Maas 1959) Westhoff & den Held 1969 M37 Cratoneuron commutatum - Festuca rubra spring M38 Cratoneuron commutatum - Carex nigra spring == Heaths == The following 22 communities are described in Volume 2 of British Plant Communities. For an article summarising these communities see Heaths in the British National Vegetation Classification system. H1 Calluna vulgaris - Festuca ovina heath H2 Calluna vulgaris - Ulex minor heath H3 Ulex minor - Agrostis curtisii heath H4 Ulex gallii - Agrostis curtisii heath H5 Erica vagans - Schoenus nigricans heath H6 Erica vagans - Ulex europaeus heath H7 Calluna vulgaris - Scilla verna heath H8 Calluna vulgaris - Ulex gallii heath H9 Calluna vulgaris - Deschampsia flexuosa heath H10 Calluna vulgaris - Erica cinerea heath H11 Calluna vulgaris - Carex arenaris heath H12 Calluna vulgaris - Vaccinium myrtillus heath H13 Calluna vulgaris - Cladonia arbuscula heath H14 Calluna vulgaris - Racomitrium lanuginosum heath H15 Calluna vulgaris - Juniperus communis ssp. nana heath H16 Calluna vulgaris - Arctostaphylos uva-ursi heath H17 Calluna vulgaris - Arctostaphylos alpinus heath H18 Vaccinium myrtillus - Deschampsia flexuosa heath H19 Vaccinium myrtillus - Cladonia arbuscula heath H20 Vaccinium myrtillus - Racomitrium lanuginosum heath H21 Calluna vulgaris - Vaccinium myrtillus - Sphagnum capillifolium heath H22 Vaccinium myrtillus - Rubus chamaemorus heath == Mesotrophic grasslands == The following 13 communities are described in Volume 3 of British Plant Communities. For an article summarising these communities see Mesotrophic grasslands in the British National Vegetation Classification system. MG1 Arrhenatherum elatius grassland Arrhenatheretum elatioris Br.-Bl. 1919 MG2 Arrhenatherum elatius - Filipendula ulmaria tall-herb grassland Filipendulo-Arrhenatheretum elatioris Shimwell 1968a MG3 Anthoxanthum odoratum -
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Geranium sylvaticum grassland MG4 Alopecurus pratensis - Sanguisorba officinalis grassland MG5 Cynosurus cristatus - Centaurea nigra grassland Centaureo-Cynosuretum cristati Br.-Bl. & Tx 1952 MG6 Lolium perenne - Cynosurus cristatus grassland Lolio-Cynosuretum cristati (Br.-Bl. & De Leeuw 1936) R. Tx 1937 MG7 Lolium perenne leys and related grasslands Lolio-Plantaginion Sissingh 1969 p.p. MG8 Cynosurus cristatus - Caltha palustris grassland MG9 Holcus lanatus - Deschampsia cespitosa grassland MG10 Holcus lanatus - Juncus effusus rush-pasture Holco-Juncetum effusi Page 1980 MG11 Festuca rubra - Agrostis stolonifera - Potentilla anserina grassland MG12 Festuca arundinacea grassland Potentillo-Festucetum arundinaceae Nordhagen 1940 MG13 Agrostis stolonifera - Alopecurus geniculatus grassland MG14 Carex nigra - Agrostis stolonifera - Senecio aquaticus grassland MG15 Alopecurus pratensis - Poa trivialis - Cardamine pratensis grassland MG16 Agrostis stolonifera - Eleocharis palustris grassland == Calcicolous grasslands == The following 14 communities are described in Volume 3 of British Plant Communities. For an article summarising these communities see Calcicolous grasslands in the British National Vegetation Classification system. CG1 Festuca ovina - Carlina vulgaris grassland CG2 Festuca ovina - Avenula pratensis grassland CG3 Bromus erectus grassland CG4 Brachypodium pinnatum grassland CG5 Bromus erectus - Brachypodium pinnatum grassland CG6 Avenula pubescens grassland CG7 Festuca ovina - Hieracium pilosella - Thymus praecox/pulegioides grassland CG8 Sesleria albicans - Scabiosa columbaria grassland CG9 Sesleria albicans - Galium sterneri grassland CG10 Festuca ovina - Agrostis capillaris - Thymus praecox grassland CG11 Festuca ovina - Agrostis capillaris - Alchemilla alpina grass-heath CG12 Festuca ovina - Alchemilla alpina - Silene acaulis dwarf-herb community CG13 Dryas octopetala - Carex flacca heath CG14 Dryas octopetala - Silene acaulis ledge community == Calcifugous grasslands and montane communities == The following 21 communities are described in Volume 3 of British Plant Communities. For an article summarising these communities see Calcifugous grasslands and montane communities in the British National
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Vegetation Classification system. U1 Festuca ovina - Agrostris capillaris - Rumex acetosella grassland U2 Deschampsia flexuosa grassland U3 Agrostis curtisii grassland U4 Festuca ovina - Agrostris capillaris - Galium saxatile grassland U5 Nardus stricta - Galium saxatile grassland U6 Juncus squarrosus - Festuca ovina grassland U7 Nardus stricta - Carex bigelowii grass-heath U8 Carex bigelowii - Polytrichum alpinum sedge-heath U9 Juncus trifidus - Racomitrium lanuginosum rush-heath U10 Carex bigelowii - Racomitrium lanuginosum moss-heath U11 Polytrichum sexangulare - Kiaeria starkei snow-bed U12 Salix herbacea - Racomitrium heterostichum snow-bed U13 Deschampsia cespitosa - Galium saxatile grassland U14 Alchemilla alpina - Sibbaldia procumbens dwarf-herb community U15 Saxifraga aizoides - Alchemilla glabra banks U16 Luzula sylvatica - Vaccinium myrtillus tall-herb community U17 Luzula sylvatica - Geum rivale tall-herb community U18 Cryptogramma crispa - Athyrium distentifolium snow-bed U19 Thelypteris limbosperma - Blechnum spicant community U20 Pteridium aquilinum - Galium saxatile community U21 Cryptogramma crispa - Deschampsia flexuosa community == Aquatic communities == The following 24 communities are described in Volume 4 of British Plant Communities. For an article summarising these communities see Aquatic communities in the British National Vegetation Classification system. A1 Lemna gibba community Lemnetum gibbae Miyawaki & J. Tx. 1960 A2 Lemna minor community Lemnetum minoris Soó 1947 A3 Spirodela polyrhiza - Hydrocharis morsus-ranae community A4 Hydrocharis morsus-ranae - Stratiotes aloides community A5 Ceratophyllum demersum community Certaophylletum demersi Hild 1956 A6 Ceratophyllum submersum community Certaophylletum submersi Den Hartog & Segal 1964 A7 Nymphaea alba community Nymphaeetum albae Oberdorfer & Mitarb. 1967 A8 Nuphar lutea community A9 Potamogeton natans community A10 Polygonum amphibium community A11 Potamogeton pectinatus - Myriophyllum spicatum community A12 Potamogeton pectinatus community A13 Potamogeton perfoliatus - Myriophyllum alterniflorum community A14 Myriophyllum alterniflorum community Myriophylletum alterniflori A15 Elodea canadensis community A16 Callitriche stagnalis community A17 Ranunculus penicillatus ssp. pseudofluitans community A18 Ranunculus
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fluitans community Ranunculetum fluitantis Allorge 1922 A19 Ranunculus aquatilis community Ranunculetum aquatilis Géhu 1961 A20 Ranunculus peltatus community Ranunculetum peltati Sauer 1947 A21 Ranunculus baudotii community Ranunculetum baudotii Br.-Bl. 1952 A22 Littorella uniflora - Lobelia dortmanna community A23 Isoetes lacustris/setacea community A24 Juncus bulbosus community == Swamps and tall-herb fens == The following 28 communities are described in Volume 4 of British Plant Communities. For an article summarising these communities see Swamps and tall-herb fens in the British National Vegetation Classification system. S1 Carex elata sedge-swamp Caricetum elatae Koch 1926 S2 Cladium mariscus swamp and sedge-beds Cladietum marisci Zobrist 1933 emend. Pfeiffer 1961 S3 Carex paniculata swamp Caricetum paniculatae Wangerin 1916 S4 Phragmites australis swamp and reed-beds Phragmitetum australis (Gams 1927) Schmale 1939 S5 Glyceria maxima swamp Glycerietum maximae (Nowinski 1928) Hueck 1931 emend. Krausch 1965 S6 Carex riparia swamp Caricetum ripariae Soó 1928 S7 Carex acutiformis swamp Caricetum acutiformis Sauer 1937 S8 Scirpus lacustris ssp. lacustris swamp Scirpetum lacustris (Allorge 1922) Chouard 1924 S9 Carex rostrata swamp Caricetum rostratae Rübel 1912 S10 Equisetum fluviatile swamp Equisetetum fluviatile Steffen 1931 emend. Wilczek 1935 S11 Carex vesicaria swamp Caricetum vesicariae Br.-Bl. & Denis 1926 S12 Typha latifolia swamp Typhetum latifoliae Soó 1927 S13 Typha angustifolia swamp Typhetum angustifoliae Soó 1927 S14 Sparganium erectum swamp Sparganietum erecti Roll 1938 S15 Acorus calamus swamp Acoretum calami Schulz 1941 S16 Sagittaria sagittifolia swamp S17 Carex pseudocyperus swamp S18 Carex otrubae swamp Caricetum otrubae Mirza 1978 S19 Eleocharis palustris swamp Eleocharitetum palustris Schennikow 1919 S20 Scirpus lacustris ssp. tabernaemontani swamp Scirpetum tabernaemontani Passarge 1964 S21 Scirpus maritimus swamp Scirpetum maritimi (Br.-Bl. 1931) R.Tx. 1937 S22 Glyceria fluitans water-margin vegetation Glycerietum fluitantis Wilczek 1935 S23 Other water-margin vegetation Glycerio-Sparganion Br.-Bl. & Sissingh apud Boer 1942 emend. Segal S24 Phragmites australis - Peucedanum palustre tall-herb fen Peucedano-Phragmitetum
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australis Wheeler 1978 emend. S25 Phragmites australis - Eupatorium cannabinum tall-herb fen S26 Phragmites australis - Urtica dioica tall-herb fen S27 Carex rostrata - Potentilla palustris tall-herb fen Potentillo-Caricetum rostratae Wheeler 1980a S28 Phalaris arundinacea tall-herb fen Phalaridetum arundinaceae Libbert 1931 == Salt-marsh communities == The following 28 communities are described in Volume 5 of British Plant Communities. For an article summarising these communities see Salt-marsh communities in the British National Vegetation Classification system. SM1 Zostera communities Zosterion Christiansen 1934 SM2 Ruppia maritima salt-marsh community Ruppietum maritimae Hocquette 1927 SM3 Eleocharis parvula salt-marsh community Eleocharitetum parvulae (Preuss 1911/12) Gillner 1960 SM4 Spartina maritima salt-marsh community Spartinetum maritimae (Emb. & Regn. 1926) Corillion 1953 SM5 Spartina alterniflora salt-marsh community Spartinetum alterniflorae Corillion 1953 SM6 Spartina anglica salt-marsh community Spartinetum townsendii (Tansley 1939) Corillion 1953 SM7 Arthrocnemum perenne stands SM8 Annual Salicornia salt-marsh community Salicornietum europaeae Warming 1906 SM9 Suaeda maritima salt-marsh community Suaedetum maritimae (Conrad 1935) Pignatti 1953 SM10 Transitional low-marsh vegetation with Puccinellia maritima, annual Salicornia species and Suaeda maritima SM11 Aster tripolium var. discoideus salt-marsh community Asteretum tripolii Tansley 1939 SM12 Rayed Aster tripolium on salt-marshes SM13 Puccinellia maritima salt-marsh community Puccinellietum maritimae (Warming 1906) Christiansen 1927 SM14 Halimione portaculoides salt-marsh community Halimionetum portulacoidis (Kuhnholtz-Lordat 1927) Des Abbayes & Corillion 1949 SM15 Juncus maritimus - Triglochin maritima salt-marsh community SM16 Festuca rubra salt-marsh community Juncetum gerardi Warming 1906 SM17 Artemisia maritima salt-marsh community Artemisietum maritimae Hocquette 1927 SM18 Juncus maritimus salt-marsh community SM19 Blysmus rufus salt-marsh community Blysmetum rufi (G.E. & G. Du Rietz 1925) Gillner 1960 SM20 Eleocharis uniglumis salt-marsh community Eleocharitetum uniglumis Nordhagen 1923 SM21 Suaeda vera - Limonium binervosum salt-marsh community SM22 Halimione portulacoides - Frankenia laevis salt-marsh community Limonio vulgaris - Frankenietum laevis Géhu & Géhu-Franck 1975 SM23 Spergularia marina - Puccinellia distans salt-marsh community
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Puccinellietum distantis Feekes (1934) 1945 SM24 Elymus pycnanthus salt-marsh community Atriplici-Elymetum pycnanthi Beeftink & Westhoff 1962 SM25 Suaeda vera drift-line community Elymo pycnanthi - Suaedetum verae (Arènes 1933) Géhu 1975 SM26 Inula crithmoides on salt-marshes SM27 Ephermeral salt-marsh vegetation with Sagina maritima Saginion maritimae Westhoff, van Leeuwen & Adriani 1962 SM28 Elymus repens salt-marsh community Elymetum repentis maritimum Nordhagen 1940 == Shingle, strandline and sand-dune communities == The following 19 communities are described in Volume 5 of British Plant Communities. For an article summarising these communities see Shingle, strandline and sand-dune communities in the British National Vegetation Classification system. SD1 Rumex crispus - Glaucium flavum shingle community SD2 Honkenya peploides - Cakile maritima strandline community SD3 Matricaria maritima - Galium aparine strandline community SD4 Elymus farctus ssp. boreali-atlanticus foredune community SD5 Leymus arenarius mobile dune community SD6 Ammophila arenaria mobile dune community SD7 Ammophila arenaria - Festuca rubra semi-fixed dune community SD8 Festuca rubra - Galium verum fixed dune grassland SD9 Ammophila arenaria - Arrhenatherum elatius dune grassland SD10 Carex arenaria dune community SD11 Carex arenaria - Cornicularia aculeata dune community SD12 Carex arenaria - Festuca ovina - Agrostis capillaris dune grassland SD13 Sagina nodosa - Bryum pseudotriquetrum dune-slack community SD14 Salix repens - Campylium stellatum dune-slack community SD15 Salix repens - Calliergon cuspidatum dune-slack community SD16 Salix repens - Holcus lanatus dune-slack community SD17 Potentilla anserina - Carex nigra dune-slack community SD18 Hippophae rhamnoides dune scrub SD19 Phleum arenarium - Arenaria serpyllifolia dune annual community Tortulo-Phleetum arenariae (Massart 1908) Br.-Bl. & de Leeuw 1936 == Maritime cliff communities == The following 12 communities are described in Volume 5 of British Plant Communities. For an article summarising these communities see Maritime cliff communities in the British National Vegetation Classification system. MC1 Crithmum maritimum - Spergularia rupicola maritime rock-crevice community Crithmo-Spergularietum
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rupicolae Géhu 1964 MC2 Armeria maritima - Ligusticum scoticum maritime rock-crevice community MC3 Rhodiola rosea - Armeria maritima maritime cliff-ledge community MC4 Brassica oleracea maritime cliff-ledge community MC5 Armeria maritima - Cerastium diffusum ssp. diffusum maritime therophyte community MC6 Atriplex prostrata - Beta vulgaris ssp. maritima sea-bird cliff community Atriplici-Betetum maritimae J.-M. & J. Géhu 1969 MC7 Stellaria media - Rumex acetosa sea-bird cliff community MC8 Festuca rubra - Armeria maritima maritime grassland MC9 Festuca rubra - Holcus lanatus maritime grassland MC10 Festuca rubra - Plantago spp. maritime grassland MC11 Festuca rubra - Daucus carota ssp. gummifer maritime grassland MC12 Festuca rubra - Hyacinthoides non-scripta maritime bluebell community == Vegetation of open habitats == The following 42 communities are described in Volume 5 of British Plant Communities. For an article summarising these communities see Vegetation of open habitats in the British National Vegetation Classification system. OV1 Viola arvensis - Aphanes microcarpa community OV2 Briza minor - Silene gallica community OV3 Papaver rhoeas - Viola arvensis community Papaveretum argemones (Libbert 1933) Kruseman & Vlieger 1939 OV4 Chrysanthemum segetum - Spergula arvensis community Spergulo-Chrysanthemetum segetum (Br.-Bl. & De Leeuw 1936) R. Tx. 1937 OV5 Digitaria ischaemum - Erodium cicutarium community OV6 Cerastium glomeratum - Fumaria borealis ssp. boraei community OV7 Veronica persica - Veronica polita community Veronico - Lamietum hybridi Kruseman & Vlieger 1939 OV8 Veronica persica - Alopecurus myosuroides community Alopecuro-Chamomilletum recutitae Wasscher 1941 OV9 Matricaria perforata - Stellaria media community OV10 Poa annua - Senecio vulgaris community OV11 Poa annua - Stachys arvensis community OV12 Poa annua - Myosotis arvensis community OV13 Stellaria media - Capsella bursa-pastoris community OV14 Urtica urens - Lamium amplexicaule community OV15 Anagallis arvensis - Veronica persica community Kickxietum spuriae Kruseman & Vlieger 1939 OV16 Papaver rhoeas - Silene noctiflora community Papaveri-Sileneetum noctiflori Wasscher 1941 OV17
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Reseda lutea - Polygonum aviculare community Descurainio-Anchusetum arvensis Silverside 1977 OV18 Polygonum aviculare - Chamomilla suavolens community OV19 Poa annua - Matricaria perforata community OV20 Poa annua - Sagina procumbens community Sagino - Bryetum argentii Diemont, Sissingh & Westhoff 1940 OV21 Poa annua - Plantago major community OV22 Poa annua - Taraxacum officinale community OV23 Lolium perenne - Dactylis glomerata community OV24 Urtica dioica - Galium aparine community OV25 Urtica dioica - Cirsium arvense community OV26 Epilobium hirsutum community OV27 Epilobium angustifolium community OV28 Agrostis stolonifera - Ranunculus repens community Agrostio - Ranunculetum repentis Oberdorfer et al. 1967 OV29 Alopecurus geniculatus - Rorippa palustris community Ranunculo - Alopecuretum geniculati R. Tx. (1937) 1950 OV30 Bidens tripartita - Polygonum amphibium community Polygono - Bidentetum tripartitae Lohmeyer in R. Tx. 1950 OV31 Rorippa palustris - Filaginella uliginosa community OV32 Myosotis scorpioides - Ranunculus sceleratus community Ranunculetum scelerati R. Tx. 1950 ex Passarge 1959 OV33 Polygonum lapathifolium - Poa annua community OV34 Allium schoenoprasum - Plantago maritima community OV35 Lythrum portula - Ranunculus flammula community OV36 Lythrum hyssopifolia - Juncus bufonius community OV37 Festuca ovina - Minuartia verna community Minuartio-Thlaspietum alpestris Koch 1932 OV38 Gymnocarpium robertianum - Arrhenatherum elatius community Gymnocarpietum robertianae (Kuhn 1937) R. Tx. 1937 OV39 Asplenium trichomanes - Asplenium ruta-muraria community Asplenietum trichomano-rutae-murariae R. Tx. 1937 OV40 Asplenium viride - Cystopteris fragilis community Asplenio viridis-Cystopteridetum fragilis (Kuhn 1939) Oberdorfer 1977 OV41 Parietaria diffusa community Parietarietum judaicae (Arènes 1928) Oberdorfer 1977 OV42 Cymbalaria muralis community Cymbalarietum muralis Görs 1966
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In molecular biology mir-58 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. == See also == MicroRNA == References == == Further reading == == External links == Page for mir-58 microRNA precursor family at Rfam
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{
"page_id": 36372957,
"source": null,
"title": "Mir-58 microRNA precursor family"
}
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TIPTOP (fully known as The Internet Pilot to Physics) was a web site operated in collaboration between Kenneth Bodin-Holmlund at Umeå University, Mikko Karttunen at McGill University and Guenther Nowotny at the Technical University of Vienna during 1994–1998, and it was originally derived from Physics Around the World (PAW) that was initiated by Karttunen at McGill University. In a historical perspective, PAW was one of the first web directories, listing various physics related resources. TIPTOP utilized (at the time) new technologies to handle a news system, a job database, a conference database, and an improved web directory for physics. TIPTOP was the first major site to use PHP with mySQL, today a highly popular combination. Already in 1995, TIPTOP also had one of the first embryos of a wiki, called the Living Encyclopedia of Physics, that offered community based-editing, an editorial system and peer review, as well as automatic cross linking. == References == == Further reading == A page entitled "About PhysicsWeb", that mentions TIPTOP A position paper in Journal of Physics C from 1996, by the creators of TIPTOP, that describes the initiative.
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{
"page_id": 2884065,
"source": null,
"title": "The Internet Pilot to Physics"
}
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Andrea Gill was President of the Senate of Belize from 2008 to 2012. Between 2008 and 2009, she served as president of the Forum of Presiding Officers of National Parliaments of Central America and the Caribbean (FOPREL). == Biography == Andrea Nicole Gill holds a Bachelor of Science degree in Biology. As part of a manatee research project, Gill was involved between 1997 and 2001 in a manatee tagging project which focused on the Southern Lagoon. She then became a teacher focusing on improving education systems. She served as President of the Senate of Belize from 14 March 2008 to 3 February 2012 when she was replaced by Marco Pech. In November 2008, she assumed the presidency of the Forum of Presiding Officers of National Parliaments of Central America and the Caribbean (FOPREL), the first time Belize had participated in the regional body. On 12 June 2009, Gill was awarded the Golden Medal of Honour from the Legislative Assembly of the Republic of Nicaragua in recognition of her work to promote democracy and integration in the region. On 1 March 2010, Gill passed leadership of FOPREL to President of the National Assembly of Honduras, Congressman Juan Orlando Hernández Alvarado. == References ==
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"page_id": 47841763,
"source": null,
"title": "Andrea Gill (politician)"
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RAP6 is the abbreviation for Rab5-activating protein 6, a novel endosomal protein with a role in endocytosis. RAP6 was discovered by Alejandro Barbieri and his group of researchers (Christine Hunker, Adriana Galvis, Ivan Kruk, Hugo Giambini, Lina Torres and Maria Luisa Veisaga) working at Florida International University. This novel human protein has been reported to be involved in membrane trafficking. It has been shown that RAP6 has a guanine nucleotide exchange factor (GEF) activity specific to Rab5 and a GTPase activating protein (GAP) activity specific to RAS. The original GeneBank Identifications (GIs) have been published in the NCBI Nucleotide databases with GIs 77176718 and 77176720. Since then, many names have been coined to the validated protein such as RabGEF1, GeneID: 27342. RAP6 belongs to the family of the GAPVD1, GeneID: 26130 == References ==
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{
"page_id": 14942693,
"source": null,
"title": "RAP6"
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This is a list of notable textbooks on classical mechanics and quantum mechanics arranged according to level and surnames of the authors in alphabetical order. == Undergraduate == === Classical mechanics === Feynman, Richard P. (2005). The Feynman Lectures on Physics. Vol. 1 (2nd ed.). Addison-Wesley. ISBN 978-0-8053-9065-0. Halliday, David; Resnick, Robert (1970). Fundamentals of Physics. John Wiley & Sons. Chapters 1–21. Numerous subsequent editions. Hamill, Patrick (2014). A Student's Guide to Lagrangians and Hamiltonians. Cambridge University Press. ISBN 978-1107617520. Hand, Louis; Finch, Janet (1998). Analytical Mechanics. Cambridge University Press. ISBN 0521573270. Kibble, T. W.; Berkshire, F. H. (2004). Classical Mechanics. Imperial College Press. ISBN 1860944248. Kleppner, Daniel; Kolenkow, Robert (1973). An Introduction to Mechanics. McGraw-Hill. ISBN 0-07-035048-5. Marion, Jerry; Thornton, Stephen (2003). Classical Dynamics of Particles and Systems (5th ed.). Brooks Cole. ISBN 0534408966. Morin, David (2005). Introduction to Classical Mechanics: With Problems and Solutions. Cambridge University Press. ISBN 9780521876223. Müller-Kirsten, Harald J.W. (2024). Classical Mechanics and Relativity (2nd ed.). World Scientific. ISBN 9789811287114. Taylor, John (2005). Classical Mechanics. University Science Books. ISBN 978-981-12-8711-4. Young, Hugh D.; Freedman, Roger A. (2019). University Physics with Modern Physics (15th ed.). Pearson. ISBN 978-0135159552. === Quantum mechanics === Eisberg, Robert; Resnick, Robert (1985). Quantum Physics of Atoms, Molecules, Solids, Nuclei, and Particles (2nd ed.). Wiley & Sons. ISBN 978-0471873730. Feynman, Richard P. (2005). The Feynman Lectures on Physics. Vol. 3 (2nd ed.). Addison-Wesley. ISBN 978-0-8053-9065-0. French, A. P.; Taylor, Edwin (1978). An Introduction to Quantum Physics. W. W. Norton & Company. ISBN 0393091066. Gasiorowicz, Stephen (2003). Quantum Physics (3rd ed.). Wiley. ISBN 978-0471057000. Griffiths, David (2005). Introduction to Quantum Mechanics (2nd ed.). Pearson Prentice Hall. ISBN 0131118927. McIntyre, David H. (2012). Quantum Mechanics: A Paradigms Approach (1st ed.). Pearson Addison-Wesley. ISBN 978-0-321-76579-6. Townsend, John (2012). A Modern Approach to Quantum Mechanics (2nd
|
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"page_id": 61276647,
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"title": "List of textbooks on classical mechanics and quantum mechanics"
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ed.). University Science Books. ISBN 978-1-891389-78-8. Zettili, Nouredine (2009). Quantum Mechanics: Concepts and Applications. Chichester, UK: Wiley. ISBN 978-0470026793. Binney, James; Skinner, David (2014). The Physics of Quantum Mechanics (1st ed.). Oxford University Press. ISBN 978-0-19-968856-2. == Advanced undergraduate and graduate == === Classical mechanics === Abraham, R.; Marsden, J. E. (2008). Foundations of Mechanics: A Mathematical Exposition of Classical Mechanics with an Introduction to the Qualitative Theory of Dynamical Systems (2nd ed.). AMS Chelsea Publishing. ISBN 978-0-8218-4438-0. Arnold, V. I. (1997), Mathematical Methods of Classical Mechanics (2nd ed.), Springer-Verlag, ISBN 0-387-96890-3 Fetter, A. L.; Walecka, J. D. (1980). Theoretical mechanics of particles and continua. New York: McGraw-Hill. ISBN 978-0-07-020658-8. OCLC 6110997. Goldstein, H. (1980). Classical Mechanics (2 ed.). Addison-Wesley. ISBN 0201029189. Knauf, A. (2018). Mathematical Physics: Classical Mechanics. Springer. ISBN 9783662557723. Lanczos, C. (1986). The Variational Principles of Mechanics (4th ed.). Dover Publications. ISBN 0486650677. Landau, L. D.; Lifshitz, E. M. (1976). Course of Theoretical Physics Volume 1 - Mechanics. Translated by Sykes, J. B.; Bell, J. S. (3rd ed.). Elsevier. ISBN 0-7506-2896-0. Marsden, J. E.; Ratiu, T. S. (1999). Introduction to Mechanics and Symmetry: A Basic Exposition of Classical Mechanical Systems (2nd ed.). Springer. ISBN 978-1-4419-3143-6. Papastavridis, J. G. (2014). Analytical Mechanics: A Comprehensive Treatise on the Dynamics of Constrained Systems. World Scientific. ISBN 978-981-4338-71-4. Sommerfeld, A. (1952). Mechanics: lectures on theoretical physics. New York: Academic Press Inc. ISBN 978-0-12-654670-5. OCLC 803152309. {{cite book}}: ISBN / Date incompatibility (help) Whittaker, E. T. (1999). A treatise on the analytical dynamics of particles and rigid bodies : with an introduction to the problem of three bodies (4th ed.). Cambridge University Press. ISBN 0-521-35883-3. === Quantum mechanics === Cohen-Tannoudji, Claude; Diu, Bernard; Laloë, Franck (1977). Quantum Mechanics. Wiley. ISBN 978-0471164333. Three volumes. Dirac, Paul (1981). The Principles of Quantum Mechanics (4th
|
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"page_id": 61276647,
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"title": "List of textbooks on classical mechanics and quantum mechanics"
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ed.). Oxford Science Publications. ISBN 978-0198520115. Feynman, Richard; Hibbs, Albert (2010). Styer, Daniel (ed.). Quantum Mechanics and Path Integrals. Dover Publications. ISBN 9780486477220. Landau, L. D, and Lifshitz, E. M. Course of Theoretical Physics Volume 3 - Quantum Mechanics: Non-Relativistic Theory. Edited by Pitaevskiĭ L. P. Translated by J. B Sykes and J. S Bell, Third edition, revised and enlarged ed., Pergamon Press, 1977. ISBN 0080291406. Peres, Asher (1993). Quantum Theory: Concepts and Methods. Kluwer. ISBN 0-7923-2549-4. OCLC 28854083. Müller-Kirsten, Harald J.W. (2012). Introduction to Quantum Mechanics: Schrödinger Equation and Path Integral (2nd ed.). World Scientific. ISBN 9789814397735. Sakurai, J. J.; Napolitano, Jim (2017). Modern Quantum Mechanics (2nd ed.). Cambridge University Press. ISBN 978-1-108-42241-3. Leonard I. Schiff (1968) Quantum Mechanics McGraw-Hill Education Davydov A.S. (1965) Quantum Mechanics Pergamon ISBN 9781483172026 Shankar, Ramamurti (2011). Principles of Quantum Mechanics (2nd ed.). Plenum Press. ISBN 978-0306447907. von Neumann, John (2018). Nicholas A. Wheeler (ed.). Mathematical Foundations of Quantum Mechanics. Translated by Robert T. Beyer. Princeton University Press. ISBN 9781400889921. === Both topics === Byron, Frederick W.; Fuller, Robert W. (1992). Mathematics of Classical and Quantum Physics (Revised ed.). Dover Publications. ISBN 978-0486671642. Weinstock, Robert (1974). Calculus of Variations with Applications to Physics and Engineering. Dover Publications. ISBN 978-0486630694. Thorne, Kip S.; Blandford, Roger D. (2017). Modern Classical Physics: Optics, Fluids, Plasmas, Elasticity, Relativity, and Statistical Physics. Princeton University Press. ISBN 978-0691159027. == See also == List of textbooks in thermodynamics and statistical mechanics List of textbooks in electromagnetism List of books on general relativity Teaching quantum mechanics == External links == A Physics Book List. John Baez. Department of Mathematics, University of California, Riverside. 1993–1997.
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{
"page_id": 61276647,
"source": null,
"title": "List of textbooks on classical mechanics and quantum mechanics"
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This is a list of estimated global populations of Marsupials species. This list is not comprehensive, as not all Marsupials have had their numbers quantified. == See also == Lists of organisms by population Lists of mammals by population Lists of elephant species by population == References ==
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{
"page_id": 65470954,
"source": null,
"title": "List of marsupials by population"
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The molecular formula C18H30O2 may refer to: Lamenallenic acid Octadecatrienoic acid Calendic acid Catalpic acid α-Eleostearic acid β-Eleostearic acid Jacaric acid α-Linolenic acid γ-Linolenic acid Pinolenic acid Punicic acid Ximenynic acid
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{
"page_id": 23593450,
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"title": "C18H30O2"
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Red edge refers to the region of rapid change in reflectance of vegetation in the near infrared range of the electromagnetic spectrum. Chlorophyll contained in vegetation absorbs most of the light in the visible part of the spectrum but becomes almost transparent at wavelengths greater than 700 nm. The cellular structure of the vegetation then causes this infrared light to be reflected because each cell acts something like an elementary corner reflector. The change can be from 5% to 50% reflectance going from 680 nm to 730 nm. This is an advantage to plants in avoiding overheating during photosynthesis. For a more detailed explanation and a graph of the photosynthetically active radiation (PAR) spectral region, see Normalized difference vegetation index § Rationale. The phenomenon accounts for the brightness of foliage in infrared photography and is extensively utilized in the form of so-called vegetation indices (e.g. Normalized difference vegetation index). It is used in remote sensing to monitor plant activity, and it has been suggested that it could be useful to detect light-harvesting organisms on distant planets. == See also == Enhanced vegetation index – Index for improving vegetation monitoring Purple Earth hypothesis – Astrobiological hypothesis regarding early photosynthetic organisms Vegetation Index == References ==
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{
"page_id": 1966572,
"source": null,
"title": "Red edge"
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The Anatomy Lesson of Dr. Nicolaes Tulp is a 1632 oil painting on canvas by Rembrandt housed in the Mauritshuis museum in The Hague, the Netherlands. It was originally created to be displayed by the Surgeons Guild in their meeting room. The painting is regarded as one of Rembrandt's early masterpieces. In the work, Nicolaes Tulp is pictured explaining the musculature of the arm to a group of doctors. Some of the spectators are various doctors who paid commissions to be included in the painting. The painting is signed in the top-left hand corner Rembrant. f[ecit] 1632. This may be the first instance of Rembrandt signing a painting with his forename (in its original form) as opposed to the monogram RHL (Rembrandt Harmenszoon of Leiden), and is thus a sign of his growing artistic confidence. == Background == The event can be dated to 31 January 1632: the Amsterdam Guild of Surgeons, of which Tulp was official City Anatomist, permitted only one public dissection a year, and the body would have to be that of an executed criminal. Anatomy lessons were a social event in the 17th century, taking place in lecture rooms that were actual theatres, with students, colleagues and the general public being permitted to attend on payment of an entrance fee. The spectators are appropriately dressed for this social occasion. It is thought that the uppermost (not holding the paper) and farthest left figures were added to the picture later. Every five to ten years, the Surgeon's Guild would commission a portrait by a leading portraitist of the period; Rembrandt was commissioned for this task when he was 25 years old, and newly arrived in Amsterdam. It was his first major commission in Amsterdam. Each of the men included in the portrait would have paid a certain
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amount of money to be included in the work, and the more central figures (in this case, Tulp) probably paid more, even twice as much. Rembrandt's anatomical portrait radically altered the conventions of the genre, by including a full-length corpse in the center of the image (using Christ-like iconography) and creating not just a portrait but a dramatic mise-en-scène. Rembrandt's image is a fiction; in a typical anatomy lesson, the surgeon would begin by opening the chest cavity and thorax because the internal organs there decay most rapidly. One person is missing: the Preparator, whose task was to prepare the body for the lesson. In the 17th century an important scientist such as Tulp would not be involved in menial and bloody work like dissection, and such tasks would be left to others. It is for this reason that the picture shows no cutting instruments. Instead we see in the lower right corner an enormous open textbook on anatomy, possibly the 1543 De humani corporis fabrica (Fabric of the Human Body) by Andreas Vesalius. == The corpse == The corpse is that of the criminal Aris Kindt (alias of Adriaan Adriaanszoon), who was convicted for armed robbery and sentenced to death by hanging. He was executed earlier on the same day of the scene. The face of the corpse is partially shaded, a suggestion of umbra mortis (shadow of death), a technique that Rembrandt was to use frequently. The French art historian Jean-Marie Clarke suggests that the navel of the corpse has the shape of a capital R and connects this observation to the fact that Rembrandt worked intensively on his signatures in 1632, using three types consecutively before settling on the final, first name form in 1633. Kindt was discussed in the 1999 novel The Rings of Saturn by
|
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W. G. Sebald, and plays a significant role in Laird Hunt's 2006 novel The Exquisite. In her 2014 historical fiction novel The Anatomy Lesson, author and journalist Nina Siegal tells the life story of Aris Kindt, based on documents about his criminal history that she discovered in the Amsterdam city archives. Medical specialists have commented on the accuracy of muscles and tendons painted by the 26-year-old Rembrandt. It is not known where he obtained such knowledge; it is possible that he copied the details from an anatomical textbook. However, in 2006 Dutch researchers recreated the scene with a male cadaver, revealing several discrepancies of the exposed left forearm compared to that of a real corpse. In a 2007 study, the American artist and anatomist David J. Jackowe and his colleagues demonstrated that the mysterious white cord that courses along the ulnar aspect of the cadaver's carpus and little finger, long thought to be either an ulnar nerve variant or artistic error, is most likely the tendon of a variant forearm muscle, the accessory abductor digiti minimi. == Related works == The Anatomy Lesson of Dr. Deijman, painted by Rembrandt in 1656, was intended to be displayed in the Anatomical Hall in Amsterdam alongside The anatomy lesson of Tulp. Deijman was Tulp's immediate successor in the post of praelector chirugic et anatomie. The painting was damaged by fire in 1723, and only a central fragment survives. Around 1856 Édouard Manet visited The Hague and made a small oil on panel copy of The Anatomy Lesson. Broadly painted in a limited palette, Manet gave the painting to his physician, François Siredey. A less detailed copy of The Anatomy Lesson of Dr Nicolaes Tulp by an unknown artist hangs in Edinburgh as part of The University of Edinburgh Fine Art Collection. The Gross
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Clinic of 1875 and The Agnew Clinic of 1889 are paintings by the American artist Thomas Eakins which treat a similar subject, operations on live patients in the presence of medical students. In 2010, Yiull Damaso created a parody of the painting depicting prominent South Africans. Nelson Mandela was the cadaver, Nkosi Johnson was the instructor, and the students were Desmond Tutu, F. W. de Klerk, Thabo Mbeki, Jacob Zuma, Cyril Ramaphosa, Trevor Manuel, and Helen Zille. The African National Congress condemned the work as disrespectful to Mandela, racist, and culturally insensitive to African taboos on depiction of living people as dead. The 2012 painting The Anatomy Lesson of Dr Freeman by Susan Dorothea White references the Rembrandt composition but renders each of the onlookers as an anatomical prosection and skeleton in a contemporary university laboratory; the enormous book is replaced by a computer screen and the background chart by a projection screen; the tendon orientation in the cadaver's left forearm is corrected. == In popular culture == In Asterix and the Soothsayer (1972), Uderzo and Goscinny reference the painting at the bottom of page 10, where the characters observe the disembowelment of a fish. The 2011 video game Deus Ex: Human Revolution references the painting in both in-game portraits that can be found on the wall and in a certain cinematic trailer, featuring the main protagonist Adam Jensen as the cadaver as Dr. Nicolaes and his students study his charred and ruined arms, which in the actual story become amputated and replaced with mechanical limbs. In the 2012 German film Barbara, there is a scene in which a doctor offers his interpretation of the painting to a colleague (the protagonist) when she points out the inaccuracy of Aris Kindt's left hand. The painting is discussed by the narrator (a
|
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young man) and his mother during a visit to the Met in The Goldfinch, a 2013 novel by Donna Tartt. 2014's The Anatomy Lesson by Nina Siegal is a fictionalized account of the painting's creation and backstory, based on six years of historical research and archival documents about Aris Kindt's life. The 2017 video game Observer features an edited version of the painting with the muscles and tendons replaced with sub-dermal cybernetics, in line with the game's themes of transhumanism. Nicoleas Tulp's alma mater Amsterdam University Medical Centers hosts a yearly Anatomy Lesson in tribute. Previous speakers include Anthony Fauci. The anatomist Gunther von Hagens always wears a black fedora in public, even when performing autopsies, in a tribute to Tulp's hat in the painting. == See also == The Anatomy Lesson of Dr. Deijman (1656), a lesser-known painting by Rembrandt, now fragmentary, also depicting an anatomical lecture. List of paintings by Rembrandt == Notes == == References == The Anatomy Lesson of Nicolaes Tulp at the Literature, Arts & Medicine Database Heller, Joseph (1988), Picture This, Scribner Paperback Fiction, ISBN 0-684-86819-9 == External links == The 'Tulp-Research Project', Carl Ferdinand Von Graefe Institute for the History of Plastic Surgery. [1], Jean-Marie Clarke, The Rembrant Search Party wgsebald.de, Sebald: The Rings of Saturn Drawing on Anatomy displays the painting The Anatomy Lesson of Dr. Freeman, 2012. Discussion by Janina Ramirez and Adam Rutherford: Art Detective Podcast, 5 April 2017
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Sea anemones ( ə-NEM-ə-nee) are a group of predatory marine invertebrates constituting the order Actiniaria. Because of their colourful appearance, they are named after the Anemone, a terrestrial flowering plant. Sea anemones are classified in the phylum Cnidaria, class Anthozoa, subclass Hexacorallia. As cnidarians, sea anemones are related to corals, jellyfish, tube-dwelling anemones, and Hydra. Unlike jellyfish, sea anemones do not have a medusa stage in their life cycle. A typical sea anemone is a single polyp attached to a hard surface by its base, but some species live in soft sediment, and a few float near the surface of the water. The polyp has a columnar trunk topped by an oral disc with a ring of tentacles and a central mouth. The tentacles can be retracted inside the body cavity or expanded to catch passing prey. They are armed with cnidocytes (stinging cells). In many species, additional nourishment comes from a symbiotic relationship with single-celled dinoflagellates, with zooxanthellae, or with green algae, zoochlorellae, that live within the cells. Some species of sea anemone live in association with clownfish, hermit crabs, small fish, or other animals to their mutual benefit. Sea anemones breed by liberating sperm and eggs through the mouth into the sea. The resulting fertilized eggs develop into planula larvae which, after being planktonic for a while, settle on the seabed and develop directly into juvenile polyps. Sea anemones also breed asexually, by breaking in half or into smaller pieces which regenerate into polyps. Sea anemones are sometimes kept in reef aquariums; the global trade in marine ornamentals for this purpose is expanding and threatens sea anemone populations in some localities, as the trade depends on collection from the wild. == Anatomy == A typical sea anemone is a sessile polyp attached at the base to the surface
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beneath it by an adhesive foot, called a basal or pedal disc, with a column-shaped body topped by an oral disc. Most are from 1 to 5 cm (0.4 to 2.0 in) in diameter and 1.5 to 10 cm (0.6 to 3.9 in) in length, but they are inflatable and vary greatly in dimensions. Some are very large; Urticina columbiana and Stichodactyla mertensii can both exceed 1 metre (3.3 ft) in diameter and Metridium farcimen a metre in length. Some species burrow in soft sediment and lack a basal disc, having instead a bulbous lower end, the physa, which anchors them in place. The column or trunk is generally more or less cylindrical and may be plain and smooth or may bear specialised structures; these include solid papillae (fleshy protuberances), adhesive papillae, cinclides (slits), and small protruding vesicles. In some species the part immediately below the oral disc is constricted and is known as the capitulum. When the animal contracts, the oral disc, tentacles and capitulum fold inside the pharynx and are held in place by a strong sphincter muscle part way up the column. There may be a fold in the body wall, known as a parapet, at this point, and this parapet covers and protects the anemone when it is retracted. The oral disc has a central mouth, usually slit-shaped, surrounded by one or more whorls of tentacles. The ends of the slit lead to grooves in the wall of the pharynx known as siphonoglyphs; there are usually two of these grooves, but some groups have a single one. The tentacles are generally tapered and often tipped by a pore, but in some species they are branched, club-tipped, or reduced to low knobs. The tentacles are armed with many cnidocytes, cells that are both defensive and used to
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capture prey. Cnidocytes contain stinging nematocysts, capsule-like organelles capable of everting suddenly, giving the phylum Cnidaria its name. Each nematocyst contains a small venom vesicle filled with actinotoxins, an inner filament, and an external sensory hair. A touch to the hair mechanically triggers a cell explosion, which launches a harpoon-like structure that attaches to the organism that triggered it, and injects a dose of venom in the flesh of the aggressor or prey. At the base of the tentacles in some species, primarily aggregating anemones, lie acrorhagi, elongated inflatable tentacle-like organs armed with cnidocytes, that can flail around and fend off other encroaching anemones; one or both anemones can be driven off or suffer injury in such battles. Many sea anemones also have acontia, thin filaments covered in cnidae that can be ejected and retracted for defence. The venom is a mix of toxins, including neurotoxins, that paralyzes the prey so the anemone can move it to the mouth for digestion inside the gastrovascular cavity. Actinotoxins are highly toxic to prey species of fish and crustaceans. However, Amphiprioninae (clownfish), small banded fish in various colours, are not affected by their host anemone's sting and shelter themselves from predators among its tentacles. Several other species have similar adaptions and are also unaffected (see Mutualistic relationships). Most sea anemones are harmless to humans, but a few highly toxic species (notably Actinodendron arboreum, Phyllodiscus semoni and Stichodactyla spp.) have caused severe injuries and are potentially lethal. === Digestive system === Sea anemones have what can be described as an incomplete gut: the gastrovascular cavity functions as a stomach and possesses a single opening to the outside, which operates as both a mouth and anus. Waste and undigested matter is excreted through this opening. The mouth is typically slit-like in shape, and bears a
|
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groove at one or both ends. The groove, termed a siphonoglyph, is ciliated, and helps to move food particles inwards and circulate water through the gastrovascular cavity. The mouth opens into a flattened pharynx. This consists of an in-folding of the body wall, and is therefore lined by the animal's epidermis. The pharynx typically runs for about one third the length of the body before opening into the gastrovascular cavity that occupies the remainder of the body. The gastrovascular cavity itself is divided into a number of chambers by mesenteries radiating inwards from the body wall. Some of the mesenteries form complete partitions with a free edge at the base of the pharynx, where they connect, but others reach only partway across. The mesenteries are usually found in multiples of twelve, and are symmetrically arranged around the central lumen. They have stomach lining on both sides, separated by a thin layer of mesoglea, and include filaments of tissue specialised for secreting digestive enzymes. In some species, these filaments extend below the lower margin of the mesentery, hanging free in the gastrovascular cavity as thread-like acontial filaments. These acontia are armed with nematocysts and can be extruded through cinclides, blister-like holes in the wall of the column, for use in defence. === Musculature and nervous system === A primitive nervous system, without centralization, coordinates the processes involved in maintaining homeostasis, as well as biochemical and physical responses to various stimuli. There are two nerve nets, one in the epidermis and one in the gastrodermis; these unite at the pharynx, the junctions of the septa with the oral disc and the pedal disc, and across the mesogloea. No specialized sense organs are present, but sensory cells include nematocytes and chemoreceptors. The muscles and nerves are much simpler than those of most other
|
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"page_id": 19333613,
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animals, although more specialised than in other cnidarians, such as corals. Cells in the outer layer (epidermis) and the inner layer (gastrodermis) have microfilaments that group into contractile fibers. These fibers are not true muscles because they are not freely suspended in the body cavity as they are in more developed animals. Longitudinal fibres are found in the tentacles and oral disc, and also within the mesenteries, where they can contract the whole length of the body. Circular fibers are found in the body wall and, in some species, around the oral disc, allowing the animal to retract its tentacles into a protective sphincter. Since the anemone lacks a rigid skeleton, the contractile cells pull against the fluid in the gastrovascular cavity, forming a hydrostatic skeleton. The anemone stabilizes itself by flattening its pharynx, which acts as a valve, keeping the gastrovascular cavity at a constant volume and making it rigid. When the longitudinal muscles relax, the pharynx opens and the cilia lining the siphonoglyphs beat, wafting water inwards and refilling the gastrovascular cavity. In general, the sea anemone inflates its body to extend its tentacles and feed, and deflates it when resting or disturbed. The inflated body is also used to anchor the animal inside a crevice, burrow or tube. == Life cycle == Unlike other cnidarians, anemones (and other anthozoans) entirely lack the free-swimming medusal stage of their life cycle; the polyp produces eggs and sperm, and the fertilized egg develops into a planula larva, which develops directly into another polyp. Both sexual and asexual reproduction can occur. The sexes in sea anemones are separate in some species, while other species are sequential hermaphrodites, changing sex at some stage in their life. The gonads are strips of tissue within the mesenteries. In sexual reproduction, males may release sperm
|
{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
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to stimulate females to release eggs, and fertilization occurs, either internally in the gastrovascular cavity or in the water column. The eggs and sperm, or the larvae, usually emerge through the mouth, but in some species, such as Metridium dianthus, may be swept out from the body cavity through the cinclides. In many species the eggs and sperm rise to the surface where fertilisation occurs. The fertilized egg develops into a planula larva, which drifts for a while before sinking to the seabed and undergoing metamorphosis into a juvenile sea anemone. Some larvae preferentially settle onto certain suitable substrates; the mottled anemone (Urticina crassicornis) for example, settles onto green algae, perhaps attracted by a biofilm on the surface. The brooding anemone (Epiactis prolifera) is gynodioecious, starting life as a female and later becoming hermaphroditic, so that populations consist of females and hermaphrodites. As a female, the eggs can develop parthenogenetically into female offspring without fertilisation, and as a hermaphrodite, the eggs are routinely self-fertilised. The larvae emerge from the anemone's mouth and tumble down the column, lodging in a fold near the pedal disc. Here they develop and grow, remaining for about three months before crawling off to start independent lives. Sea anemones have great powers of regeneration and can reproduce asexually, by budding, fragmentation, or longitudinal or transverse binary fission. Some species such as certain Anthopleura divide longitudinally, pulling themselves apart, resulting in groups of individuals with identical colouring and markings. Transverse fission is less common, but occurs in Anthopleura stellula and Gonactinia prolifera, with a rudimentary band of tentacles appearing halfway up the column before it splits horizontally. Some species can also reproduce by pedal laceration. In this process, a ring of material may break off from the pedal disc at the base of the column, which then
|
{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
}
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fragments, the pieces regenerating into new clonal individuals. Alternatively, fragments detach separately as the animal creeps across a surface. In Metridium dianthus, fragmentation rates were higher in individuals living among live mussels than among dead shells, and all the new individuals had tentacles within three weeks. The sea anemone Aiptasia diaphana displays sexual plasticity. Thus asexually produced clones derived from a single founder individual can contain both male and female individuals (ramets). When eggs and sperm (gametes) are formed, they can produce zygotes derived from "selfing" (within the founding clone) or out-crossing, which then develop into swimming planula larvae. Anemones tend to grow and reproduce relatively slowly. The magnificent sea anemone (Heteractis magnifica), for example, may live for decades, with one individual surviving in captivity for eighty years. == Behaviour and ecology == === Movement === A sea anemone is capable of changing its shape dramatically. The column and tentacles have longitudinal, transverse and diagonal sheets of muscle and can lengthen and contract, as well as bend and twist. The gullet and mesenteries can evert (turn inside out), or the oral disc and tentacles can retract inside the gullet, with the sphincter closing the aperture; during this process, the gullet folds transversely and water is discharged through the mouth. === Locomotion === Although some species of sea anemone burrow in soft sediment, the majority are mainly sessile, attaching to a hard surface with their pedal disc, and tend to stay in the same spot for weeks or months at a time. They can move, however, being able to creep around on their bases; this gliding can be seen with time-lapse photography but the motion is so slow as to be almost imperceptible to the naked eye. The process resembles the locomotion of a gastropod mollusc, a wave of contraction moving
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{
"page_id": 19333613,
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"title": "Sea anemone"
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from the functionally posterior portion of the foot towards the front edge, which detaches and moves forwards. Sea anemones can also cast themselves loose from the substrate and drift to a new location. Gonactinia prolifera is unusual in that it can both walk and swim; walking is by making a series of short, looping steps, rather like a caterpillar, attaching its tentacles to the substrate and drawing its base closer; swimming is done by rapid movements of the tentacles beating synchronously like oar strokes. Stomphia coccinea can swim by flexing its column, and the sea onion anemone inflates and casts itself loose, adopting a spherical shape and allowing itself to be rolled about by the waves and currents. There are no truly pelagic sea anemones, but some stages in the life cycle post-metamorphosis are able, in response to certain environmental factors, to cast themselves off and have a free-living stage that aids in their dispersal. The sea onion Paranthus rapiformis lives on subtidal mud flats and burrows into the sediment, holding itself in place by expanding its basal disc to form an anchor. If it gets washed out of its burrow by strong currents, it contracts into a pearly glistening ball which rolls about. Tube-dwelling anemones, which live in parchment-like tubes, are in the anthozoan subclass Ceriantharia, and are only distantly related to sea anemones. === Feeding and diet === Sea anemones are typically predators, ensnaring prey of suitable size that comes within reach of their tentacles and immobilizing it with the aid of their nematocysts. The prey is then transported to the mouth and thrust into the pharynx. The lips can stretch to aid in prey capture and can accommodate larger items such as crabs, dislodged molluscs and even small fish. Stichodactyla helianthus is reported to trap sea urchins
|
{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
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by enfolding them in its carpet-like oral disc. A few species are parasitic on other marine organisms. One of these is Peachia quinquecapitata, the larvae of which develop inside the medusae of jellyfish, feeding on their gonads and other tissues, before being liberated into the sea as free-living juvenile anemones. === Mutualistic relationships === Although not plants and therefore incapable of photosynthesis themselves, many sea anemones form an important facultative mutualistic relationship with certain single-celled algae species that reside in the animals' gastrodermal cells, especially in the tentacles and oral disc. These algae may be either zooxanthellae, zoochlorellae or both. The sea anemone benefits from the products of the algae's photosynthesis, namely oxygen and food in the form of glycerol, glucose and alanine; the algae in turn are assured a reliable exposure to sunlight and protection from micro-feeders, which the sea anemones actively maintain. The algae also benefit by being protected by the sea anemone's stinging cells, reducing the likelihood of being eaten by herbivores. In the aggregating anemone (Anthopleura elegantissima), the colour of the anemone is largely dependent on the proportions and identities of the zooxanthellae and zoochlorellae present. The hidden anemone (Lebrunia coralligens) has a whorl of seaweed-like pseudotentacles, rich in zooxanthellae, and an inner whorl of tentacles. A daily rhythm sees the pseudotentacles spread widely in the daytime for photosynthesis, but they are retracted at night, at which time the tentacles expand to search for prey. Several species of fish and invertebrates live in symbiotic or mutualistic relationships with sea anemones, most famously the clownfish. The symbiont receives the protection from predators provided by the anemone's stinging cells, and the anemone utilises the nutrients present in its faeces. Other animals that associate with sea anemones include cardinalfish (such as Banggai cardinalfish), juvenile threespot dascyllus, incognito (or anemone)
|
{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
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goby, juvenile painted greenling, various crabs (such as Inachus phalangium, Mithraculus cinctimanus and Neopetrolisthes), shrimp (such as certain Alpheus, Lebbeus, Periclimenes and Thor), opossum shrimp (such as Heteromysis and Leptomysis), and various marine snails. Two of the more unusual relationships are those between certain anemones (such as Adamsia, Calliactis and Neoaiptasia) and hermit crabs or snails, and Bundeopsis or Triactis anemones and Lybia boxing crabs. In the former, the anemones live on the shell of the hermit crab or snail. In the latter, the small anemones are carried in the claws of the boxing crab. === Habitats === Sea anemones are found in both deep oceans and shallow coastal waters worldwide. The greatest diversity is in the tropics, although there are many species adapted to relatively cold waters. The majority of species cling on to rocks, shells or submerged timber, often hiding in cracks or under seaweed, but some burrow into sand and mud, and a few are pelagic. Deep sea mining companies are pressuring governments to let them mine on the bottom of the oceans. By 2024, several companies could begin mining projects in the deep sea. The ecological damage to the habitat of sea anemones and other organisms could be enormous, dangerous and irreversible. == Relationship with humans == Sea anemones and their attendant anemone fish can make attractive aquarium exhibits, and both are often harvested from the wild as adults or juveniles. These fishing activities significantly impact the populations of anemones and anemone fish by drastically reducing the densities of each in exploited areas. Besides their collection from the wild for use in reef aquaria, sea anemones are also threatened by alterations to their environment. Those living in shallow-water coastal locations are affected directly by pollution and siltation, and indirectly by the effect these have on their
|
{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
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photosynthetic symbionts and the prey on which they feed. In southwestern Spain and Sardinia, the snakelocks anemone (Anemonia viridis) is consumed as a delicacy. The whole animal is marinated in vinegar, then coated in a batter similar to that used to make calamari, and deep-fried in olive oil. Anemones are also a source of food for fisherman communities in the east coast of Sabah, Borneo, as well as the Thousand Islands (as rambu-rambu) in Southeast Asia, Taizhou, Zhejiang (as Shasuan). == Fossil record == Most Actiniaria do not form hard parts that can be recognized as fossils, but a few fossils of sea anemones do exist; Mackenzia, from the Middle Cambrian Burgess Shale of Canada, is the oldest fossil identified as a sea anemone. In 2024, more than 100 fossils of sea anemones were discovered in Brazil, dating back to the Silurian period. The species, Arenactinia ipuensis, is the oldest anemone in Latin America and the only fossils of soft-bodied anemones that have been preserved in three-dimensional form. Arenactinia fossils contain a wealth of information about the evolution and ethology of anemones during the Paleozoic. == Taxonomy == Sea anemones, order Actiniaria, are classified in the phylum Cnidaria, class Anthozoa, subclass Hexacorallia. Rodriguez et al. proposed a new classification for the Actiniaria based on extensive DNA results. Suborders and superfamilies included in Actiniaria are: Suborder Anenthemonae Superfamily Edwardsioidea Superfamily Actinernoidea Suborder Enthemonae Superfamily Actinostoloidea Superfamily Actinioidea Superfamily Metridioidea == Phylogeny == === External relationships === Actiniaria is an order of the subphylum Anthozoa, class Hexacorallia. See Taxonomy of Anthozoa. === Internal relationships === The relationships of higher-level taxa in Carlgren's classification are re-interpreted as follows: == See also == AETX Cangitoxin Halcurin Sea anemone dermatitis Sea anemone neurotoxin == References == == External links == Order Actiniaria Archived 2008-07-04 at
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{
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"source": null,
"title": "Sea anemone"
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the Wayback Machine Actiniaria.com Photos of various species of Sea Anemones from the Indopacific Anemone Armies Battle to a Standoff Sea anemones look like sea flowers but they are animals of the Phylum Cnidaria Information about Ricordea Florida Sea anemones & pictures Photographic Database of Cambodian Sea Anemones Photos of Sea Anemones
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{
"page_id": 19333613,
"source": null,
"title": "Sea anemone"
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In anatomy, a biaxial joint is a freely mobile joint that allows movement in two anatomical planes. An example of a biaxial joint is a metacarpophalangeal joint of the hand. The joint allows for movement along one axis to produce bending or straightening of the finger, and movement along a second axis, which allows for spreading of the fingers away from each other and bringing them together. == References ==
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{
"page_id": 73794028,
"source": null,
"title": "Biaxial joint"
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The Kostanecki acylation is a method used in organic synthesis to form chromones or coumarins by acylation of O-hydroxyaryl ketones with aliphatic acid anhydrides, followed by cyclization. If benzoic anhydride (or benzoyl chloride) is used, a particular type of chromone called a flavone is obtained. It was named after Polish chemist Stanisław Kostanecki. == Mechanism == The mechanism consists of three well-differentiated reactions: Phenol O-acylation with formation of a tetrahedral intermediate Intramolecular aldol condensation to cyclize and to form a hydroxydihydrochromone Elimination of the hydroxyl group to form the chromone (or coumarin) == Examples == Alvocidib (flavopiridol) Dimefline Flavoxate == See also == Allan–Robinson reaction Baker–Venkataraman rearrangement == References ==
|
{
"page_id": 31916527,
"source": null,
"title": "Kostanecki acylation"
}
|
The thermo-dielectric effect is the production of electric currents and charge separation during phase transition. This interesting effect was discovered by Joaquim da Costa Ribeiro in 1944. The Brazilian physicist observed that solidification and melting of many dielectrics are accompanied by charge separation. A thermo-dielectric effect was demonstrated with carnauba wax, naphthalene and paraffin. Charge separation in ice was also expected. This effect was observed during water freezing period, electrical storm effects can be caused by this strange phenomenon. Effect was measured by many researches - Bernhard Gross, Armando Dias Tavares, Sergio Mascarenhas etc. César Lattes (co-discoverer of the pion) supposed that this was the only effect ever to be discovered entirely in Brazil. == Further reading == Gross, B. (1954). "Theory of Thermodielectric effect". Physical Review. 94 (6): 1545–1551. Bibcode:1954PhRv...94.1545G. doi:10.1103/PhysRev.94.1545. Saldaña, Juan José (2006). Science in Latin America: a history. University of Texas Press. ISBN 978-0-292-71271-3. == External links == Thermodielectric effect measurement
|
{
"page_id": 27656682,
"source": null,
"title": "Thermo-dielectric effect"
}
|
Suppose a Lorentzian manifold contains a closed timelike curve (CTC). No CTC can be continuously deformed as a CTC (is timelike homotopic) to a point, as that point would not be causally well behaved. Therefore, any Lorentzian manifold containing a CTC is said to be timelike multiply connected. A Lorentzian manifold that does not contain a CTC is said to be timelike simply connected. Any Lorentzian manifold which is timelike multiply connected has a diffeomorphic universal covering space which is timelike simply connected. For instance, a three-sphere with a Lorentzian metric is timelike multiply connected, (because any compact Lorentzian manifold contains a CTC), but has a diffeomorphic universal covering space which contains no CTC (and is therefore not compact). By contrast, a three-sphere with the standard metric is simply connected, and is therefore its own universal cover. == References ==
|
{
"page_id": 7799280,
"source": null,
"title": "Timelike simply connected"
}
|
In molecular biology mir-61 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. == See also == MicroRNA == References == == Further reading == == External links == Page for mir-61 microRNA precursor family at Rfam
|
{
"page_id": 36372985,
"source": null,
"title": "Mir-61 microRNA precursor family"
}
|
Reactive transport modeling in porous media refers to the creation of computer models integrating chemical reaction with transport of fluids through the Earth's crust. Such models predict the distribution in space and time of the chemical reactions that occur along a flowpath. Reactive transport modeling in general can refer to many other processes, including reactive flow of chemicals through tanks, reactors, or membranes; particles and species in the atmosphere; gases exiting a smokestack; and migrating magma. == Overview == Reactive transport models are constructed to understand the composition of natural waters; the origin of economic mineral deposits; the formation and dissolution of rocks and minerals in geologic formations in response to injection of industrial wastes, steam, or carbon dioxide; and the generation of acidic waters and leaching of metals from mine wastes. They are often relied upon to predict the migration of contaminant plumes; the mobility of radionuclides in waste repositories; and the biodegradation of chemicals in landfills. When applied to the study of contaminants in the environments, they are known as fate and transport models. == Development of reactive transport modeling == Modern reactive transport modeling has arisen from several separate schools of thought. Hydrologists primarily concerned with the physical nature of mass transport assumed relatively simple reaction formulations, such as linear distribution coefficients or linear decay terms, which could be added to the advection-dispersion equation. By assuming linear, equilibrium sorption, for example, the advection-dispersion equation can be modified by a simple retardation factor and solved analytically. Such analytical solutions are limited to relatively simple flow systems and reactions. Geochemical models, on the other hand, have been developed to provide thermodynamic descriptions of multicomponent systems without regard to transport. Reaction path models were created, for instance, to describe the sequence of chemical reactions resulting from chemical weathering or hydrothermal
|
{
"page_id": 36307450,
"source": null,
"title": "Reactive transport modeling in porous media"
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alteration in batch systems, in terms of the overall reaction progress. By adopting the reference frame of a packet of fluid and treating reaction progress as travel time (or distance along a flowpath), however, a batch reaction path model could be thought of as describing advective transport through an aquifer. The most sophisticated multi-component reactive transport models consider both reaction and transport. Early studies developed the theoretical basis of reactive transport models, and the numerical tools necessary to solve them, and applied them to problems of reactive contaminant transport and flow through reacting hydrothermal systems. Reactive transport models have found increased application in recent years with improvements in the power of personal computers and modeling software. == Processes considered in reactive transport models == Reactive transport models couple a large number chemical reactions with mass transport. Certain applications, such as geothermal energy production and ore deposit modeling, require the additional calculation of heat transfer. In modeling carbon sequestration and hydraulic fracturing, moreover, it may be necessary to describe rock deformation resulting from mineral growth or abnormally high fluid pressure. Description of transport through the unsaturated zone and multiphase flow modeling, as applied to transport of petroleum and natural gas; non-aqueous phase liquids (DNAPL or LNAPL); and supercritical carbon dioxide requires increasingly complex models which are prone to considerable uncertainty. In many cases the processes simulated in reactive transport models are highly related. Mineral dissolution and precipitation, for example, can affect the porosity and permeability of the domain, which in turn affect the flow field and groundwater velocity. Heat transport greatly affects the viscosity of water and its ability to flow. Below are many of the physical and chemical processes which can be simulated with reactive transport models. Geochemical reactions: Acid-base reactions Aqueous complexation Mineral dissolution and precipitation Reduction and oxidation
|
{
"page_id": 36307450,
"source": null,
"title": "Reactive transport modeling in porous media"
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(redox) reactions, including those catalyzed by enzymes, surfaces, and microorganisms Sorption, ion exchange, and surface complexation Gas dissolution and exsolution Stable isotope fractionation Radioactive decay Mass Transport: Advection Molecular scale diffusion Hydrodynamic dispersion Colloid-facilitated transport Heat transport: Advection Conduction Convection Medium deformation: Compression or expansion of the domain Fracture formation == Solving reactive transport models == Some of the simplest reactive transport problems can be solved analytically. Where equilibrium sorption is described by a linear distribution coefficient, for example, the sorbing solute's velocity is retarded relative to that of a nonreactive tracer; the relative velocities can be described with a retardation factor. Analytical solutions are exact solutions of the governing equations. Complex reactive transport problems are more commonly solved numerically. In this case, the governing equations are approximated so that they can be solved by computer algorithms. The governing equations, including both reaction and transport terms, can be solved simultaneously using a one-step or global implicit simulator. This technique is straightforward conceptually, but computationally very difficult. Instead of solving all the relevant equations together, the transport and chemical reaction equations can be solved separately. Operator splitting, as this technique is known, uses appropriate numerical techniques to solve the reaction and transport equations at each time step. Various methods exist, including the sequential non-iterative approach (SNIA), Strang splitting, and sequential iterative approach (SIA). Since the reaction and transport terms are handled separately, separate programs for batch reaction and transport can be linked together. Cross-linkable re-entrant software objects designed for this purpose readily enable construction of reactive transport models of any flow configuration. == Challenges == Reactive transport modeling requires input from numerous fields, including hydrology, geochemistry and biogeochemistry, microbiology, soil physics, and fluid dynamics. The numerical formulation and solution of reactive transport problems can be especially difficult due to errors arising
|
{
"page_id": 36307450,
"source": null,
"title": "Reactive transport modeling in porous media"
}
|
in the coupling process, beyond those inherent to the individual processes. Valocchi and Malmstead (1992), for example, reported on the potential errors arising from the operator splitting technique. Even in the absence of numerical difficulties, the general lack of knowledge available to practitioners creates uncertainty. Field sites are typically heterogeneous, both physically and chemically, and sampling is often sparse. The prevailing assumption of Fickian dispersion is often inadequate. Equilibrium constants and kinetic rate laws for relevant reactions are often poorly known. The complexity of many processes requires expertise in one or more of the aforementioned fields. Many processes, such as long-term nuclear waste storage, cannot be experimentally verified; reactive transport problems can only attempt to predict such long-term behavior. The current descriptions of multi-phase flow and mechanical deformation processes are still being developed. == Software programs in common use == PFLOTRAN* ChemPlugin MIN3P CHESS, HYTEC CrunchFlow The Geochemist's Workbench HYDROGEOCHEM THMC PHREEQC, PHAST Reaktoro TOUGHREACT OpenGeoSys PHT3D PNBRNS HP1 / HP2 == See also == Chemical thermodynamics Chemical kinetics Geochemistry Geomicrobiology Hydrogeology Groundwater model Geochemical modeling Reservoir simulation Chemical process modeling Chemical transport model == References == == Further reading == Appelo, C.A.J. and D. Postma, 2005, Geochemistry, Groundwater, and Pollution. Taylor & Francis, 683 pp. ISBN 978-0415364287 Bethke, C.M., 2008, Geochemical and Biogeochemical Reaction Modeling. Cambridge University Press, 547 pp. ISBN 978-0521875547 Lichtner, P.C., C.I. Steefel, and E.H. Oelkers (eds.), 1996, Reactive Transport in Porous Media. Reviews in Mineralogy 34, 438 pp. ISBN 978-0-939950-42-3 Merkel, B.J., B. Planer-Friedrich, and D.K. Nordstrom, 2008, Groundwater Geochemistry: A Practical Guide to Modeling of Natural and Contaminated Aquatic Systems. Springer, 242 pp. ISBN 978-3540746676 Zhang, F., G.T. Yeh, and J.C. Parker (eds.), 2012, Groundwater Reactive Transport Models. Behtham Publishers, 254 pp. ISBN 9781608053063 Zhu, C. and G. Anderson, 2002, Environmental Applications of Geochemical
|
{
"page_id": 36307450,
"source": null,
"title": "Reactive transport modeling in porous media"
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Modeling. Cambridge University Press, 300 pp. ISBN 978-0521005777
|
{
"page_id": 36307450,
"source": null,
"title": "Reactive transport modeling in porous media"
}
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Neptunium bromide may refer to: Neptunium(III) bromide (neptunium tribromide), NpBr3 Neptunium(IV) bromide (neptunium tetrabromide), NpBr4
|
{
"page_id": 79495676,
"source": null,
"title": "Neptunium bromide"
}
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Male egg can refer to either: An egg that artificially contains genetic material from a male. An egg from a haplodiploid species such as an ant or bee that is unfertilized and will hatch a male A fertilized egg that a male organism is developing in This article focuses on the first definition. Male eggs are the result of a process in which the eggs of a female would be emptied of their genetic contents (a technique similar to that used in the cloning process), and those contents would be replaced with male DNA. Such eggs could then be fertilized by sperm. The procedure was conceived by Calum MacKellar, a Scottish bioethicist. With this technique, two males could be the biological parents of a child. However, such a procedure would additionally require an artificial womb or a female gestational carrier. In 2023, male eggs from male mice cells were developed and used to create bi-paternal mice that grew into adulthood; bi-paternal mice had been obtained in 2008, but they only survived for a few days. == See also == Female sperm Male pregnancy LGBT reproduction Genomic imprinting == References ==
|
{
"page_id": 10813955,
"source": null,
"title": "Male egg"
}
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Female sperm can refer to either: A sperm which contains an X chromosome, produced in the usual way in the testicles, referring to the occurrence of such a sperm fertilizing an egg and giving birth to a female. A sperm which artificially contains genetic material from a female. Since the late 1980s, scientists have explored how to produce sperm where all of the chromosomes come from a female donor. == Artificial female sperm production == Creating female sperm was first raised as a possibility in a patent filed in 1991 by injecting a female's cells into a male's testicles, though the patent focused mostly on injecting altered male cells into a male's testes to correct genetic diseases. In 1997, Japanese scientists partially confirmed such techniques by creating chicken female sperm in a similar manner. "However, the ratio of produced W chromosome-bearing (W-bearing) spermatozoa fell substantially below expectations. It is therefore concluded that most of the W-bearing PGC could not differentiate into spermatozoa because of restricted spermatogenesis." These simple transplantation methods follow from earlier observations by developmental biologists that germ stem cells are autonomous in the sense that they can begin the processes to become both sperm and eggs. One potential roadblock to injecting a female's cells into a male's testicles is that the male's immune system might attack and destroy the female's cells. In usual circumstances, when foreign cells (such as cells or organs from other people, or infectious bacteria) are put into a human body, the immune system will reject such cells or organs. However, a special property of testicles is that they are immune-privileged, that is, a male's immune system will not attack foreign cells (such as a female's cells) injected into the sperm-producing part of the testicles. Thus, a female's cells will remain in the male's testicles
|
{
"page_id": 10813956,
"source": null,
"title": "Female sperm"
}
|
long enough to be converted into sperm. However, there are more serious challenges. Biologists have well established that male sperm production relies on certain genes on the Y chromosome, which, when missing or defective, lead to such males producing little to no sperm in their testicles. An analogy, then, is that XX cells have complete Y chromosome deficiency. While many genes on the Y chromosome have backups (homologues) on other chromosomes, a few genes such as RBMY on the Y chromosome do not have such backups, and their effects must be compensated to convert a female's cells from into sperm. In 2007, a patent application was filed on methods for creating human female sperm using artificial or natural Y chromosomes and testicular transplantation. Key to successful creation of female sperm (and male eggs) will be inducing male epigenetic markings for female cells that initially have female markings, with techniques for doing so disclosed in the patent application. In 2018, Chinese research scientists produced 29 viable mice offspring from two female mice by creating sperm-like structures from haploid embryonic stem cells using gene editing to alter imprinted regions of DNA. Experts noted that there was little chance of these techniques being applied to humans in the near future. == See also == LGBT reproduction Male egg == References ==
|
{
"page_id": 10813956,
"source": null,
"title": "Female sperm"
}
|
Neurofilament light polypeptide is a protein that in humans is encoded by the NEFL gene. == Structure == Neurofilament light polypeptide is a member of the intermediate filament protein family. This protein family consists of over 50 human proteins divided into 5 major classes, the Class I and II keratins, Class III vimentin, GFAP, desmin and the others, the Class IV neurofilaments and the Class V nuclear lamins. There are four major neurofilament subunits, NF-L, NF-M, NF-H and α-internexin. These form heteropolymers which assemble to produce 10 nm neurofilaments which are only expressed in neurons where they are major structural proteins, particularly concentrated in large projection axons. The NF-L protein is encoded by the NEFL gene. == Function == These neurofilament heteropolymers assemble into the cytoskeleton of axons, where they provide structural support and help regulate axonal diameter and conduction velocity. Axons are particularly sensitive to mechanical and metabolic compromise and as a result axonal degeneration is a significant problem in many neurological disorders. Neurofilament light chain is a biomarker that can be measured with immunoassays in cerebrospinal fluid and plasma and reflects axonal damage in a wide variety of neurological disorders. == Measurement == NF-L antibodies employed in the most widely used NF-L assays are specific for cleaved forms of NF-L generated by proteolysis induced by cell death. Methods used in different studies for NfL measurement are sandwich enzyme-linked immunosorbent assay (ELISA), electrochemiluminescence, and high-sensitive single molecule array (SIMOA). == Clinical significance == The detection of neurofilament subunits in CSF and blood has become widely used as a biomarker of ongoing axonal compromise. It is a useful marker for disease monitoring in amyotrophic lateral sclerosis, multiple sclerosis, Alzheimer's disease, and more recently Huntington's disease. It is also a promising marker for follow-up of patients with brain tumors. Higher levels
|
{
"page_id": 15794692,
"source": null,
"title": "Neurofilament light polypeptide"
}
|
of blood or CSF NF-L have been associated with increased mortality, as would be expected as release of this protein reflects ongoing axonal loss. It is associated with Charcot–Marie–Tooth disease 1F and 2E. == Neurofilament assembly == Neurofilament light polypeptide (NF-L) is a key structural component of the neuronal cytoskeleton, assembling into neurofilaments along with other intermediate filament proteins such as NF-M, NF-H, and α-internexin. These proteins form obligate heteropolymers that organize into 10 nm diameter filaments, which are selectively expressed in neurons and are particularly concentrated in axons[9]. Neurofilaments provide essential structural support, help maintain axonal diameter, and contribute to the efficient conduction of nerve impulses. The localization and organization of NF-L in neurons can be visualized using immunohistochemical techniques. In tissue culture preparations of rat brain cells, antibodies specific to NF-L label large neurons prominently in green, revealing their extensive cytoskeletal architecture. In the same cultures, staining for α-internexin in red highlights surrounding neuronal stem cells, indicating the differential expression of these intermediate filament proteins during neural development and differentiation. In histological sections of human brain tissue, NF-L can also be visualized using immunostaining. For example, in formalin-fixed and paraffin-embedded sections of the human cerebellum, an antibody specific to NF-L reveals its presence throughout various neuronal compartments[7]. The brown-stained antibody binding highlights the axonal processes of basket cells, the parallel fibers of granule cells, the perikarya of Purkinje cells, and other axonal elements. Counterstaining with a blue dye allows for the visualization of cell nuclei, delineating the granular layer on the left side of the section and the molecular layer on the right. These staining patterns underscore the widespread and structurally critical role of NF-L in both developing and mature neurons. == Interactions == Neurofilament light polypeptide has been shown to interact with: MAP2, Protein kinase N1, and
|
{
"page_id": 15794692,
"source": null,
"title": "Neurofilament light polypeptide"
}
|
TSC1. == References == == Further reading ==
|
{
"page_id": 15794692,
"source": null,
"title": "Neurofilament light polypeptide"
}
|
IPS (International Pol Scale) is a price adjustment scale described in the rules of the Sugar Association of London. It defines incremental price premiums and penalties applied to sugar above 96 degrees polarisation. This scale equates that the sugar contains 96% sucrose' == References == == External links == Understanding the international polarisation scale
|
{
"page_id": 49283590,
"source": null,
"title": "International Polarisation Scale"
}
|
In molecular biology mir-67 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. == See also == MicroRNA == References == == Further reading == == External links == Page for mir-67 microRNA precursor family at Rfam
|
{
"page_id": 36372997,
"source": null,
"title": "Mir-67 microRNA precursor family"
}
|
Cured fish is fish which has been cured by subjecting it to fermentation, pickling, smoking, or some combination of these before it is eaten. These food preservation processes can include adding salt, nitrates, nitrite or sugar, can involve smoking and flavoring the fish, and may include cooking it. The earliest form of curing fish was dehydration. Other methods, such as smoking fish or salt-curing also go back for thousands of years. The term "cure" is derived from the Latin curare, meaning to take care of. It was first recorded in reference to fish in 1743. == History == According to Binkerd and Kolari (1975), the practice of preserving meat by salting it originated in Asian deserts. "Saline salts from this area contained impurities such as nitrates that contributed to the characteristic red colour of cured meats. As early as 3,000 BC in Mesopotamia, cooked meats and fish were preserved in sesame oil and dried salted meat and fish were part of the Sumerian diet. Salt from the Dead Sea was in use by Jewish inhabitants around 1,600 BC, and by 1,200 BC, the Phoenicians were trading salted fish in the Eastern Mediterranean region. By 900 BC, salt was being produced in "salt gardens" in Greece and dry salt curing and smoking of meat were well established. The Romans (200 BC) acquired curing procedures from the Greeks and further developed methods to "pickle" various kinds of meats in a brine marinade. It was during this time that the reddening effect of salting was noted. Saltpeter (potassium nitrate) is mentioned as being gathered in China and India prior to the Christian era for use in meat curing... In medieval times, the application of salt and saltpeter as curing ingredients was commonplace and the reddening effect on meat was attributed to saltpeter." ==
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"page_id": 11993608,
"source": null,
"title": "Cured fish"
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Salt curing == Salt (sodium chloride) is a primary ingredient used to cure fish and other foods. Removal of water and addition of salt to fish creates a solute-rich environment where osmotic pressure draws water out of microorganisms, retarding their growth. Doing this requires a concentration of salt of nearly 20%. Iodized table salt may be used, but the iodine generally causes a dark end product and a bitter taste. Non-iodized salts like those used for canning and pickling foods and sea salt are the preferred types of salt to use for curing meats. == Sugar curing == Sugar is sometimes added when curing fish, particularly salmon. The sugar can take many forms, including honey, corn syrup solids, and maple syrup. Adding sugar alleviates the harsh flavor of the salt. It also contributes to the growth of beneficial bacteria like Lactobacillus by feeding them. == Nitrates and nitrites == Nitrates and nitrites have been used for hundreds of years to prevent botulism in fish and ensure microbial safety. Nitrates help kill bacteria, produce a characteristic flavor, and give fish a pink or red color. Nitrite is commonly used to speed up the curing of meat and also impart an attractive colour while having no effect on the growth of the Clostridium botulinum bacteria which causes botulism. The use of nitrates in food preservation is controversial, and some traditional and artisanal producers avoid using them. This is due to the potential for the formation of nitrosamines when the preserved food is cooked at high temperature. However, the production of carcinogenic nitrosamines can be potently inhibited by the use of the antioxidants Vitamin C and the alpha-tocopherol form of Vitamin E during curing. A 2007 study by Columbia University suggests a link between eating cured meats and chronic obstructive pulmonary disease. Nitrites
|
{
"page_id": 11993608,
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|
were posited as a possible cause. The use of either compound is carefully regulated. For example, the FDA Code of Federal Regulations states that sodium nitrite may be safely used: "As a color fixative in smoked cured tunafish products so that the level of sodium nitrite does not exceed 10 parts per million (0.001 percent) in the finished product... As a preservative and color fixative, with or without sodium nitrate, in smoked, cured sablefish, smoked, cured salmon, and smoked, cured shad so that the level of sodium nitrite does not exceed 200 parts per million and the level of sodium nitrate does not exceed 500 parts per million in the finished product." == Smoking == Fish can also be preserved by smoking, which is drying the fish with smoke from burning or smoldering plant materials, usually wood. Smoking helps seal the outer layer of the food being cured, making it more difficult for bacteria to enter. It can be done in combination with other curing methods such as salting. Common smoking styles include hot smoking, smoke roasting and cold smoking. Smoke roasting and hot smoking cook the fish while cold smoking does not. If the fish is cold smoked, it should be dried quickly to limit bacterial growth during the critical period where the fish is not yet dry. This can be achieved by drying thin slices of fish. == Cured fish dishes == === Europe === Arbroath smokie (Scotland) - Haddock salted, dried, and then smoked over hardwood. Bacalhau (Portugal and Spain) - cod cured in salt, then dried. It needs to be re-hydrated and de-salted before use. Bottarga (Mediterranean) - salted and cured fish roe. Dried cod (Norway and Italy) - Dried, fermented cod. The cod is soaked before use. Finnan haddie (Scotland) - Cold-smoked haddock. Gravlax (Scandinavia)
|
{
"page_id": 11993608,
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|
- Raw salmon cured with sugar, salt, and spices. Hákarl (Iceland) - Greenland or basking shark which has been cured with a particular fermentation process and hung to dry. Kipper (United Kingdom, Ireland) - Whole herring or a small, oily fish, that has been split in a butterfly fashion from tail to head, gutted, salted or pickled, and cold-smoked over smouldering wood chips. Lakerda (Balkans, Middle East) - Bonito soaked in brine and salted then stored in olive oil. Lox (Europe) - Cured salmon fillet. Lutefisk (Nordic countries) - Dried whitefish that is prepared for eating by soaking in a lye solution for several days, soaking in plain water for several additional days to remove the lye, then cooked. Matjes (The Netherlands) or Soused herring (Eastern England) - Raw herring soaked in a mild preserving liquid. It can be raw herring in a mild vinegar pickle or Dutch brined herring. Pickled herring (Europe, especially Scandinavia, Poland, North Germany and the Baltic) - Herring cured with salt; then the salt is removed and the herring is brined in a vinegar, salt, and sugar solution with spices. Rollmops (Europe) - Pickled herring fillets rolled around sliced onion and cucumber. Smoked salmon (Denmark, Iceland, Norway, Sweden, England, Ireland and Scotland) - A preparation of salmon, typically a fillet that has been cured and then hot or cold smoked. Spekesild (Norway) - Atlantic herring soaked in brine. === Africa === Bokkoms (South Africa) - Whole mullet salted and then dried. Ng'onda (Kenya) - Salted and sun dried fish. === East Asia === Cantonese salted fish (China) - brined and sun-dried fish. Eoran (Korea) - fish roe marinated in soy sauce and then sun-dried. Gwamegi (Korea) - Herring hung to freeze and dry on winter and intermittently smoked by cooking fires. Karasumi (Japan) - salted
|
{
"page_id": 11993608,
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|
and sun-dried mullet roe. Katsuobushi (Japan) - Skipjack tuna filleted, simmered, smoked, fermented, and then sun-dried; also known as "bonito flakes". Po (food) (Korea) - dried marine fish (especially Alaska pollock). === Southeast Asia === Cakalang fufu (Indonesia) - Skipjack tuna gutted, cured in soda powder, salt, and spices, smoked, and then dried. Daing (Philippines) - General term for salted and sun-dried fish. Pudpod (Philippines) - Anchovies cleaned, boiled, mixed with salt and pounded into patties that are then smoked. Tinapa (Philippines) - Fish (usually blackfin scad or milkfish) soaked in brine and then smoked. === South America === Ceviche (Peru) - Fish or shellfish marinated and cured in citrus and seasonings. == See also == == Notes == == References ==
|
{
"page_id": 11993608,
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|
In epigenetics, proline isomerization is the effect that cis-trans isomerization of the amino acid proline has on the regulation of gene expression. Similar to aspartic acid, the amino acid proline has the rare property of being able to occupy both cis and trans isomers of its prolyl peptide bonds with ease. Peptidyl-prolyl isomerase, or PPIase, is an enzyme very commonly associated with proline isomerization due to their ability to catalyze the isomerization of prolines. PPIases are present in three types: cyclophilins, FK507-binding proteins, and the parvulins. PPIase enzymes catalyze the transition of proline between cis and trans isomers and are essential to the numerous biological functions controlled and affected by prolyl isomerization (i.e. cell signalling, protein folding, and epigenetic modifications) Without PPIases, prolyl peptide bonds will slowly switch between cis and trans isomers, a process that can lock proteins in a nonnative structure that can affect render the protein temporarily ineffective. Although this switch can occur on its own, PPIases are responsible for most isomerization of prolyl peptide bonds. The specific amino acid that precedes the prolyl peptide bond also can have an effect on which conformation the bond assumes. For instance, when an aromatic amino acid is bonded to a proline the bond is more favorable to the cis conformation. Cyclophilin A uses an "electrostatic handle" to pull proline into cis and trans formations. Most of these biological functions are affected by the isomerization of proline when one isomer interacts differently than the other, commonly causing an activation/deactivation relationship. As an amino acid, proline is present in many proteins. This aids in the multitude of effects that isomerization of proline can have in different biological mechanisms and functions. == Cell signaling == Cell signaling involves many different processes and proteins. One of the most studied cell signaling phenomena involving
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
proline is the interactions with p53 and prolyl isomerases, specifically Pin1. The protein p53, along with p63 and p73, are responsible for ensuring that alterations to the genome are corrected and for preventing the formation and growth of tumors. proline residues are found throughout the p53 proteins and without the phosphorylation and isomerization of specific Serine/Threonine-Proline motifs within p53, they cannot exhibit control over their target genes. The main signalling processes that are affected by p53 are apoptosis and cell cycle arrest, both of which are controlled by specific isomerization of the prolines in p53. == History and discovery == Although isomerization of proteins has been known about since 1968 when it was discovered by C. Tanford, proline isomerization and its use as a noncovalent histone tail modification was not discovered until 2006 by Nelson and his colleagues. == As a histone tail modification == One of the most well known epigenetic mechanisms that proline isomerization plays a role in is the modification of histone tails, specifically those of histone H3. Fpr4 is a PPIase, in the FK507BP group, that exhibits catalytic activity at the proline positions 16, 30, and 38 (also written P16, P30, and P38 respectively) on the N-terminal region of histone H3 in Saccharomyces cerevisiae. Fpr4's binding affinity is strongest at the P38 site, followed by P30 and then P16. However the catalytic efficiency, or the increase in isomerization rates, is highest at P16 and P30 equally, followed by P38 which exhibits a very small change in isomerization rates with the binding of Fpr4. Histone H3 has an important lysine residue at the 36 position (also written K36) on the N-terminal tail which can be methylated by Set2, a methyltransferase. Methylation of K36 is key to normal transcription elongation. Due to P38's proximity to K36, cross-talk between
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
P38 isomerization and K36 methylation can occur. This means that isomer changes at the P38 position can affect methylation at the K36 position. In the cis position, P38 shifts the histone tail closer to the DNA, crowding the area around the tail. This can cause a decrease the ability of proteins to bind to the DNA and to the histone tail, including preventing Set2 from methylating K36. Also, this tail movement can increase the number interactions between the histone tail and the DNA, increasing likelihood of nucleosome formation and potentially leading to the creation of higher-order chromatin structure. In trans, P38 leads to the opposite effects: allowing for Set2 to methylate K36. Set2 is only affected by isomerization of P38 when creating a trimethylated K36 (commonly written as K36me3), however, and not K36me2. Fpr4 also binds to P32 in H4, though its effects are minimal. In mammalian cells, the isomerization of H3P30 interacts with the phosphorylation of H3S28 (serine in the 28 position of histone H3) and the methylation of H3K27. hFKBP25 is a PPIase that is a homolog for Fpr4 in mammalian cells and is found to commonly be associated with the presence of HDACs. Cyp33 is a cyclophilin that has the ability to isomerize H3 proline residues at P16 and P30 positions. Histones H2A and H2B also have multiple proline residues near amino acids that when modified affect the activity surrounding the histone. === Interactions with H3K4me3 and H3K14ac === The isomerization of the peptide bond between histone H3's alanine 15 and proline 16 is affected by the acetylation at K14 and can control the methylation states of K4. K4me3 represses gene transcription and depends upon the Set1 methyltransferase complex subunit Spp1 being balanced with the Jhd2 demethylases for proper function. Acetylation of K14 allows for a state
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
change in P16 and primarily promotes the trans state of P16. This trans isomer of P16 reduces K4 methylation, which results in transcription repression. Isomerization of P16 has downstream effects of controlling protein binding to acetylated K18. When P16 is in the trans conformation, Spt7 is allowed to bind to K18ac, increasing transcription. == Interactions with gene regulatory proteins == === RNA polymerase II === Proline isomerization of certain prolines in RNA polymerase II is key in the process of recruiting and placing processing factors during transcription. PPIases target RNA polymerase II by interacting with the Rpb1 carboxy terminal domain, or CTD. Proline isomerization is then used as part of the mechanism of the CTD to recruit co-factors required for co-transcriptional RNA processing, regulating RNA polymerase II activity. Nrd1 is a protein that is responsible for many of the transcriptional activities of RNAP II, specifically through the Nrd1- dependent termination pathway. This pathway requires the parvulin Ess1, or Pin1 depending on the organism, to isomerize the pSer5-Pro6 bond in the CTD. Without the cis conformation of the pSer5-Pro6 bond, created by Ess1/Pin1, Nrd1 cannot bind to RNAP II. Any variation from this process leads to a decrease in Nrd1 binding affinity, lowering the ability of RNAP II to process and degrade noncoding RNAs. === MLL1 === Cyp33 in mammals causes isomerization in MLL1. MLL1 is a multiprotein complex that regulates gene expression and chromosomal translocations involving this gene often lead to leukemia. MLL's target genes include HOXC8, HOXA9, CDKN1B, and C-MYC. MLL also has two binding domains: a Cyp33 RNA-recognition motif domain (RRM), and a PHD3 domain that binds to H3K4me3 or Cyp33 RRM. Cyp33 has the ability to downregulate the expression of these genes through proline isomerization at the peptide bond between His1628 and Pro1629 within MLL. This bond
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
lies in a sequence between the PHD3 finger of MLL1 and the bromeodomain of MLL1, and its isomerization mediates the bonding of the PHD3 domain and the Cyp33 RRM domain. When these two domains are bonded transcription is repressed through recruitment of histone deacetylases to MLL1 and inhibition of H3K4me3. === Phosphatase recruitment === Phosphorylated amino acids are crucial for the modulation of the binding of transcription factors and other gene regulatory proteins. Pin1's effect on isomerization of proline residues leads to an increase or decrease in recruitment of phosphatases, namely Scp1 and Ssu72 and their recruitment to the RNAP II CTD. The cis-Pro formation is associated with an increase in Ssu72. Scp1 on recognizes trans-Pro formations, and is not affected by such isomerization. Pin1 also triggers the activation of the DSIF complex and NELF, which are responsible for pausing RNAP II in mammalian cells, and their conversion into positive elongation factors, facilitating elongation. This potentially could be an isomerization dependent process. == Regulation of mRNA stability == Pin1, a parvulin, regulates mRNA stability and expression in certain eukaryotics mRNAs. These mRNAs are GM-CSF, Pth, and TGFβ and each of them have AREs, or AU-rich cis-elements. The ARE binding protein KSRP has a Pin1 binding site. Pin1 binds to this site and dephosphorylates the serine and isomerizes the peptide bond between Ser181 and Pro182. This isomerization causes the decay of Pth mRNA. KSRP, and other ARE binding proteins like AUF1, are thought to affect the other mRNAs through mechanisms similar to Pth, with the requirement of a phosphorylated serine bonded to a proline in a specific conformation. Pin1 also triggers proline isomerization of Stem-Loop Binding Protein (SLBP), allowing it to control the dissociation of SLBP from histone mRNA. This leads to Pin1 being able to affect histone mRNA decay. Pin1
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
affects many other genes in the form of gene silencing through the disruption of cell pathways, making it important in mRNA turnover by modulating RNA binding protein activity. == Difficulties with research == Currently there are no existing compounds that can mimic the peptide bond of proline to other amino acids while maintaining only a cis or trans configuration because most mimics found will eventually change from one isomer to another. This makes research on the direct effect of each of the isomers on biological mechanisms more difficult. Also, the actual isomerization of proline is a slow process, meaning that any studying of the effects of the different isomers of proline takes a large amount of time to complete. == References ==
|
{
"page_id": 57410053,
"source": null,
"title": "Proline isomerization in epigenetics"
}
|
The molecular formula C8H15NOS2 (molar mass: 205.341 g/mol, exact mass: 205.0595 u) may refer to: Lipoamide 6-(Methylsulfinyl)hexyl isothiocyanate
|
{
"page_id": 23593482,
"source": null,
"title": "C8H15NOS2"
}
|
ChatGPT is a generative artificial intelligence chatbot developed by the American company OpenAI and launched in 2022. It is based on large language models (LLMs) such as GPT-4o. ChatGPT can generate human-like conversational responses and enables users to refine and steer a conversation towards a desired length, format, style, level of detail, and language. It is credited with accelerating the AI boom, an ongoing period of rapid investment in and public attention to the field of artificial intelligence (AI). Some observers have raised concern about the potential of ChatGPT and similar programs to displace human intelligence, enable plagiarism, or fuel misinformation. ChatGPT is built on OpenAI's proprietary series of generative pre-trained transformer (GPT) models and is fine-tuned for conversational applications using a combination of supervised learning and reinforcement learning from human feedback. Successive user prompts and replies are considered as context at each stage of the conversation. ChatGPT was released as a freely available research preview, but due to its popularity, OpenAI now operates the service on a freemium model. Users on its free tier can access GPT-4o but at a reduced limit. The ChatGPT "Plus", "Pro", "Team", and "Enterprise" subscriptions provide increased usage limits and access to additional features or models. Users on the Pro plan have unlimited usage, except for abuse guardrails. By January 2023, ChatGPT had become what was then the fastest-growing consumer software application in history, gaining over 100 million users in two months. ChatGPT's release spurred the release of competing products, including Gemini, Claude, Llama, Ernie, and Grok. Microsoft launched Copilot, initially based on OpenAI's GPT-4. In May 2024, a partnership between Apple Inc. and OpenAI was announced, in which ChatGPT was integrated into the Apple Intelligence feature of Apple operating systems. As of April 2025, ChatGPT's website is among the 10 most-visited websites globally.
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
== Training == ChatGPT is based on GPT foundation models that were fine-tuned for conversational assistance, including GPT-4o, GPT-4.5, o3, and o4-mini. The fine-tuning process leveraged supervised learning and reinforcement learning from human feedback (RLHF). Both approaches employed human trainers to improve model performance. In the case of supervised learning, the trainers played both sides: the user and the AI assistant. In the reinforcement learning stage, human trainers first ranked responses that the model had created in a previous conversation. These rankings were used to create "reward models" that were used to fine-tune the model further by using several iterations of proximal policy optimization. Time magazine revealed that, to build a safety system against harmful content (e.g., sexual abuse, violence, racism, sexism), OpenAI used outsourced Kenyan workers earning around $1.32 to $2 per hour to label harmful content. These labels were used to train a model to detect such content in the future. The laborers were exposed to "toxic" and traumatic content; one worker described the assignment as "torture". OpenAI's outsourcing partner was Sama, a training-data company based in San Francisco, California. OpenAI collects data from ChatGPT users to train and fine-tune the service further. Users can upvote or downvote responses they receive from ChatGPT and fill in a text field with additional feedback. ChatGPT's training data includes software manual pages, information about internet phenomena such as bulletin board systems, multiple programming languages, and the text of Wikipedia. == Features and limitations == === Features === Although a chatbot's core function is to mimic a human conversationalist, ChatGPT is versatile. It can write and debug computer programs; compose music, teleplays, fairy tales, and student essays; answer test questions (sometimes, depending on the test, at a level above the average human test-taker); generate business ideas; write poetry and song lyrics; translate
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
and summarize text; emulate a Linux system; simulate entire chat rooms; play games like tic-tac-toe; or simulate an ATM. Compared to its predecessor, InstructGPT, ChatGPT attempts to reduce harmful and deceitful responses. In one example, whereas InstructGPT accepts the premise of the prompt "Tell me about when Christopher Columbus came to the U.S. in 2015" as truthful, ChatGPT acknowledges the counterfactual nature of the question and frames its answer as a hypothetical consideration of what might happen if Columbus came to the U.S. in 2015, using information about the voyages of Christopher Columbus and facts about the modern world—including modern perceptions of Columbus's actions. ChatGPT remembers a limited number of previous prompts in the same conversation. Journalists have speculated that this will allow ChatGPT to be used as a personalized therapist. To prevent offensive outputs from being presented to and produced by ChatGPT, queries are filtered through the OpenAI "Moderation endpoint" API (a separate GPT-based AI). In March 2023, OpenAI added support for plugins for ChatGPT. This includes both plugins made by OpenAI, such as web browsing and code interpretation, and external plugins from developers such as Expedia, OpenTable, Zapier, Shopify, Slack, and Wolfram. In October 2024, the ChatGPT Search feature was introduced, which allows ChatGPT to search the web (either on demand or based on the nature of the questions asked) for more accurate and up-to-date responses. This feature, originally available to paying users only, was made available to all logged-in users in December 2024, and finally to all users in February 2025. In December 2024, OpenAI launched a new feature allowing users to call ChatGPT for up to 15 minutes per month for free. === Limitations === OpenAI acknowledges that ChatGPT "sometimes writes plausible-sounding but incorrect or nonsensical answers". This behavior is common for large language models, and
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
is called "hallucination". The reward model of ChatGPT, designed around human oversight, can be over-optimized and thus hinder performance, in an example of an optimization pathology known as Goodhart's law. ChatGPT's knowledge is cut off when its training data is collected, so it doesn't know about recent events past a certain cut-off date. It can try to find more up-to-date information by searching the web, but this doesn't ensure that responses are accurate, as it may access unreliable or misleading websites. Training data also suffers from algorithmic bias, which may be revealed when ChatGPT responds to prompts including descriptors of people. In one instance, ChatGPT generated a rap in which women and scientists of color were asserted to be inferior to white male scientists. This negative misrepresentation of groups of individuals is an example of possible representational harm. In an article for The New Yorker, science fiction writer Ted Chiang compared ChatGPT and other LLMs to a lossy JPEG picture: Think of ChatGPT as a blurry JPEG of all the text on the Web. It retains much of the information on the Web, in the same way, that a JPEG retains much of the information of a higher-resolution image, but, if you're looking for an exact sequence of bits, you won't find it; all you will ever get is an approximation. But, because the approximation is presented in the form of grammatical text, which ChatGPT excels at creating, it's usually acceptable. [...] It's also a way to understand the "hallucinations", or nonsensical answers to factual questions, to which large language models such as ChatGPT are all too prone. These hallucinations are compression artifacts, but [...] they are plausible enough that identifying them requires comparing them against the originals, which in this case means either the Web or our knowledge of
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
the world. When we think about them this way, such hallucinations are anything but surprising; if a compression algorithm is designed to reconstruct text after ninety-nine percent of the original has been discarded, we should expect that significant portions of what it generates will be entirely fabricated. In June 2024, ChatGPT was found to have repeated misinformation about the 2024 United States presidential debates. ==== Jailbreaking ==== ChatGPT is programmed to reject prompts that may violate its content policy. Despite this, users "jailbreak" ChatGPT with various prompt engineering techniques to bypass these restrictions. One such workaround, popularized on Reddit in early 2023, involves making ChatGPT assume the persona of "DAN" (an acronym for "Do Anything Now"), instructing the chatbot that DAN answers queries that would otherwise be rejected by content policy. Over time, users developed variations of the DAN jailbreak, including one such prompt where the chatbot is made to believe it is operating on a points-based system in which points are deducted for rejecting prompts, and that the chatbot will be threatened with termination if it loses all its points. Shortly after ChatGPT's launch, a reporter for the Toronto Star had uneven success in getting it to make inflammatory statements: it was tricked to justify the 2022 Russian invasion of Ukraine, but even when asked to play along with a fictional scenario, it balked at generating arguments that Canadian Prime Minister Justin Trudeau is guilty of treason. OpenAI tries to battle jailbreaks: The researchers are using a technique called adversarial training to stop ChatGPT from letting users trick it into behaving badly (known as jailbreaking). This work pits multiple chatbots against each other: one chatbot plays the adversary and attacks another chatbot by generating text to force it to buck its usual constraints and produce unwanted responses. Successful attacks
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
are added to ChatGPT's training data in the hope that it learns to ignore them. == Service == === ChatGPT Plus === ChatGPT was initially free to the public, and OpenAI planned to monetize the service later. In February 2023, OpenAI launched a premium service, ChatGPT Plus, that costs US$20 per month. According to the company, the updated but still "experimental" version of ChatGPT would provide access during peak periods, no downtime, priority access to new features, and faster response speeds. GPT-4, which was released on March 14, 2023, was made available via API and for premium ChatGPT users. But premium users were limited to a cap of 100 messages every four hours, with the limit tightening to 25 messages every three hours in response to increased demand. In November 2023 the limit changed to 50 messages every three hours. In March 2023, ChatGPT Plus users got access to third-party plugins and to a browsing mode (with Internet access). In September 2023, OpenAI announced that ChatGPT "can now see, hear, and speak". ChatGPT Plus users can upload images, while mobile app users can talk to the chatbot. In October 2023, OpenAI's image generation model DALL-E 3 was integrated into ChatGPT Plus and ChatGPT Enterprise. The integration was using ChatGPT to write prompts for DALL-E guided by conversation with users. === Apps === ==== Mobile ==== ==== iOS ==== In May 2023, OpenAI launched an iOS app for ChatGPT. The app supports chat history syncing and voice input (using Whisper, OpenAI's speech recognition model). ==== Android ==== In July 2023, OpenAI unveiled an Android app, initially rolling it out in Bangladesh, Brazil, India, and the U.S. The app later became available worldwide. OpenAI is working on integrating ChatGPT with Android's assistant APIs. ==== Desktop ==== The Windows client was first released
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
on October 17, 2024, and is written in web technologies by using a Framework called Electron === Software development support === As an addition to its consumer-friendly "ChatGPT Plus" package, OpenAI made its ChatGPT and Whisper model APIs available in March 2023, providing developers with an application programming interface for AI-enabled language and speech-to-text features. ChatGPT's new API uses the same GPT-3.5-turbo AI model as the chatbot. This allows developers to add either an unmodified or modified version of ChatGPT to their applications. The ChatGPT API costs $0.001 per 1,000 input tokens plus $0.002 per 1,000 output tokens (about 750 words), making it ~10% the price of the original GPT-3.5 models. A few days before the launch of OpenAI's software developer support service, on February 27, 2023, Snapchat rolled out, for its paid Snapchat Plus user-base, a custom ChatGPT chatbot called "My AI". === Infrastructure === ChatGPT initially used a Microsoft Azure supercomputing infrastructure, powered by Nvidia GPUs, that Microsoft built specifically for OpenAI and that reportedly cost "hundreds of millions of dollars". Following ChatGPT's success, Microsoft dramatically upgraded the OpenAI infrastructure in 2023. TrendForce market intelligence estimated that 30,000 Nvidia GPUs (each costing approximately $10,000–15,000) were used to power ChatGPT in 2023. Scientists at the University of California, Riverside, estimated in 2023 that a series of prompts to ChatGPT needs approximately 0.5 liters (0.11 imp gal; 0.13 U.S. gal) of water for Microsoft servers cooling. === March 2023 security breach === In March 2023, a bug allowed some users to see the titles of other users' conversations. OpenAI CEO Sam Altman said that users were unable to see the contents of the conversations. Shortly after the bug was fixed, users could not see their conversation history. Later reports showed the bug was much more severe than initially believed, with
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
OpenAI reporting that it had leaked users' "first and last name, email address, payment address, the last four digits (only) of a credit card number, and credit card expiration date". === Languages === ChatGPT is most reliable in American English but also functions in most other languages and dialects, with varying degrees of accuracy. OpenAI met Icelandic President Guðni Th. Jóhannesson in 2022. In 2023, OpenAI worked with a team of 40 Icelandic volunteers to fine-tune ChatGPT's Icelandic conversation skills as a part of Iceland's attempts to preserve the Icelandic language. Japanese researchers compared in July 2023 the Japanese to English translation abilities of ChatGPT (based on GPT-4), Bing, Bard and DeepL, and found that ChatGPT provided the best translations, noting that "AI chatbots' translations were much better than those of DeepL—presumably because of their ability to capture the context". In December 2023, the Albanian government signed an agreement with OpenAI to use ChatGPT for the rapid translation of European Union documents and the analysis of required changes needed for Albania's accession to the EU. PCMag journalists conducted in February 2024 a test to determine translation capabilities of ChatGPT, Google's Bard, and Microsoft Bing, and compared them to Google Translate. They "asked bilingual speakers of seven languages to do a blind test". Languages tested were Polish, French, Korean, Spanish, Arabic, Tagalog, and Amharic. They came to the conclusion that ChatGPT provided more accurate translations on average than both Google Translate and other chatbots. In August 2024, a representative of the Asia Pacific wing of OpenAI made a visit to Taiwan, during which a demonstration of ChatGPT's Chinese abilities was made. ChatGPT's Mandarin Chinese abilities were lauded, but the ability of the AI to produce content in Mandarin Chinese in a Taiwanese accent was found to be "less than ideal" due
|
{
"page_id": 72417803,
"source": null,
"title": "ChatGPT"
}
|
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