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solving problems, for example Ant colony optimization and Ant robotics. This area of biomimetics has led to studies of ant locomotion, search engines that make use of "foraging trails", fault-tolerant storage, and networking algorithms. === As pets === From the late 1950s through the late 1970s, ant farms were popular educational children's toys in the United States. Some later commercial versions use transparent gel instead of soil, allowing greater visibility at the cost of stressing the ants with unnatural light. === In culture === Anthropomorphised ants have often been used in fables, children's stories, and religious texts to represent industriousness and cooperative effort, such as in the Aesop fable The Ant and the Grasshopper. In the Quran, Sulayman is said to have heard and understood an ant warning other ants to return home to avoid being accidentally crushed by Sulayman and his marching army.[Quran 27:18], In parts of Africa, ants are considered to be the messengers of the deities. Some Native American mythology, such as the Hopi mythology, considers ants as the first animals. Ant bites are often said to have curative properties. The sting of some species of Pseudomyrmex is claimed to give fever relief. Ant bites are used in the initiation ceremonies of some Amazon Indian cultures as a test of endurance. In Greek mythology, the goddess Athena turned the maiden Myrmex into an ant when the latter claimed to have invented the plough, when in fact it was Athena's own invention. Ant society has always fascinated humans and has been written about both humorously and seriously. Mark Twain wrote about ants in his 1880 book A Tramp Abroad. Some modern authors have used the example of the ants to comment on the relationship between society and the individual. Examples are Robert Frost in his poem "Departmental" and
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T. H. White in his fantasy novel The Once and Future King. The plot in French entomologist and writer Bernard Werber's Les Fourmis science-fiction trilogy is divided between the worlds of ants and humans; ants and their behaviour are described using contemporary scientific knowledge. H. G. Wells wrote about intelligent ants destroying human settlements in Brazil and threatening human civilization in his 1905 science-fiction short story, The Empire of the Ants. A similar German story involving army ants, Leiningen Versus the Ants, was written in 1937 and recreated in movie form as The Naked Jungle in 1954. In more recent times, animated cartoons and 3-D animated films featuring ants have been produced including Antz, A Bug's Life, The Ant Bully, The Ant and the Aardvark, Ferdy the Ant and Atom Ant. Renowned myrmecologist E. O. Wilson wrote a short story, "Trailhead" in 2010 for The New Yorker magazine, which describes the life and death of an ant-queen and the rise and fall of her colony, from an ants' point of view. Ants also are quite popular inspiration for many science-fiction insectoids, such as the Formics of Ender's Game, the Bugs of Starship Troopers, the giant ants in the films Them! and Empire of the Ants, Marvel Comics' super hero Ant-Man, and ants mutated into super-intelligence in Phase IV. In computer strategy games, ant-based species often benefit from increased production rates due to their single-minded focus, such as the Klackons in the Master of Orion series of games or the ChCht in Deadlock II. These characters are often credited with a hive mind, a common misconception about ant colonies. In the early 1990s, the video game SimAnt, which simulated an ant colony, won the 1992 Codie award for "Best Simulation Program". == See also == Glossary of ant terms International Union
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for the Study of Social Insects Myrmecological News (journal) Task allocation and partitioning in social insects == References == === Cited texts === Borror DJ, Triplehorn CA, Delong DM (1989). Introduction to the Study of Insects (6th ed.). Saunders College Publishing. ISBN 978-0-03-025397-3. Hölldobler B, Wilson EO (1990). The Ants. Harvard University Press. ISBN 978-0-674-04075-5. == Further reading == == External links == AntWiki – Bringing Ants to the World Wilson, Andrew (1878). "Ant" . Encyclopædia Britannica. Vol. II (9th ed.). pp. 94–100. AntWeb from The California Academy of Sciences Ant Species Fact Sheets from the National Pest Management Association on Argentine, Carpenter, Pharaoh, Odorous, and other ant species Ant Genera of the World – distribution maps The super-nettles. A dermatologist's guide to ants-in-the-plants
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Various tetradecadienyl acetate compounds serve as insect mating pheromones especially among the Pyralidae. These include: (Z,E)-3,5-tetradecadienyl acetate — Prionoxystus robiniaea mating attractant: 41 (E,E)-3,5-tetradecadienyl acetate — Accosus centerensis mating attractant: 41 (Z,E)-4,8-tetradecadienyl acetate — Borkhausenia schefferella mating attractant: 41 (Z,Z)-7,11-tetradecadienyl acetate — Conistra vaccinii mating attractant: 41 (Z,E)-9,11-tetradecadienyl acetate (abbr. Z9,E11-14:Ac) — Spodoptera littoralis: 41 and S. litura: 41 mating attractant and mating inhibitor.: 41 Female pheromone, lures males. Used by McVeigh and Bettany 1986 and Downham et al., 1995 over the course of three years in a 99:1 with (E,E)-10,12-tetradecadienyl acetate. Although they achieved good mating disruption this did not result in lower egg mass or population. The results of Campion et al., 1980 suggest that may be due to the need for other, minor female volatiles. Martinez et al., 1993 study control of its synthesis in S. littoralis by hormones, finding that the reduction step may be controlled by pheromone biosynthesis activating neuropeptide. (Z,Z)-9,12-tetradecadienyl acetate — Plodia interpunctella mating inhibitor: 41 (Z,E)-9,12-tetradecadienyl acetate (abbr. Z9,E12-14:Ac) — In 2006 the United States Environmental Protection Agency granted an exemption to permit use without regard to the residue on resulting food. This is thought to be the first registration for indoor use in the United States of any sex pheromone to disrupt mating. Produced by species: Adoxophyes fasciata synergistic attractant: 41 Anagasta kuehniella mating attractant produced by both male and female: 41 Cadra cautella female-produced mating attractant and mating inhibitor: 41 (found by Kuwahara et al., 1971) C. figulilella female-produced mating attractant Elasmopalpus lignosellus mating disruptor Ephestia elutella mating attractant Plodia interpunctella (also by Kuwahara 1971) == References ==
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"page_id": 70584868,
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"title": "Tetradecadienyl acetates"
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In chemistry, isomerization or isomerisation is the process in which a molecule, polyatomic ion or molecular fragment is transformed into an isomer with a different chemical structure. Enolization is an example of isomerization, as is tautomerization. When the activation energy for the isomerization reaction is sufficiently small, both isomers can often be observed and the equilibrium ratio will shift in a temperature-dependent equilibrium with each other. Many values of the standard free energy difference, Δ G ∘ {\displaystyle \Delta G^{\circ }} , have been calculated, with good agreement between observed and calculated data. == Examples and applications == === Alkanes === Skeletal isomerization occurs in the cracking process, used in the petrochemical industry to convert straight chain alkanes to isoparaffins as exemplified in the conversion of normal octane to 2,5-dimethylhexane (an "isoparaffin"): Fuels containing branched hydrocarbons are favored for internal combustion engines for their higher octane rating. Diesel engines however operate better with straight-chain hydrocarbons. === Alkenes === ==== Cis vs trans ==== Trans-alkenes are about 1 kcal/mol more stable than cis-alkenes. An example of this effect is cis- vs trans-2-butene. The difference is attributed to unfavorable non-bonded interactions in the cis isomer. This effects helps to explain the formation of trans-fats in food processing. In some cases, the isomerization can be reversed using UV-light. The trans isomer of resveratrol converts to the cis isomer in a photochemical reaction. ==== Terminal vs internal ==== Terminal alkenes prefer to isomerize to internal alkenes: H2C=CHCH2CH3 → CH3CH=CHCH3 The conversion essentially does not occur in the absence of metal catalysts. This process is employed in the Shell higher olefin process to convert alpha-olefins to internal olefins, which are subjected to olefin metathesis. === Other organic examples === Isomerism is a major topic in sugar chemistry. Glucose, the most common sugar, exists in four
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forms. Aldose-ketose isomerism, also known as Lobry de Bruyn–van Ekenstein transformation, provides an example in saccharide chemistry. === Inorganic and organometallic chemistry === The compound with the formula (C5H5)2Fe2(CO)4 exists as three isomers in solution. In one isomer the CO ligands are terminal. When a pair of CO are bridging, cis and trans isomers are possible depending on the location of the C5H5 groups. Another example in organometallic chemistry is the linkage isomerization of decaphenylferrocene, [(η5-C5Ph5)2Fe]. == Kinetic classification == From the kinetic viewpoint, isomerizations can be classified into two categories. Cases in the first category involve transformations between equivalent structures. Most chemical species are in principle susceptible to such processes. Many such cases involve fluxional molecules, such as the cyclohexane ring flip (chair inversion), the pyramidal inversion of ammonia, the Berry pseudorotation in pentacoordinate compounds (e.g. PF5, Fe(CO)5), the Cope rearrangements of bullvalene or the Ray-Dutt/Bailar twists for the racemization of octahedral complexes with three bidentate chelate rings (helical chirality). In the second broad category of isomerizations, the isomers are nonequivalent. Examples include tautomerizations (keto-enol, lactam-lactim, amide-imidic, enamine-imine, nitroso-oxime, ketene-ynol, etc) in which one isomer is more stable than the other. This scheme leads to the following system of differential rate equations: == See also == Base-promoted epoxide isomerization Epimerization Racemization Tautomerization Linkage isomerism == References ==
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{
"page_id": 264740,
"source": null,
"title": "Isomerization"
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Trifluoroethane may refer to either of two isomeric fluorocarbons which differ by the location of attachment of the fluorine atoms: 1,1,2-Trifluoroethane (R-143) 1,1,1-Trifluoroethane (R-143a) Both are used as refrigerant and propellant gases.
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"page_id": 1968677,
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William Howard Stein (June 25, 1911 – February 2, 1980) was an American biochemist who collaborated in the determination of the ribonuclease sequence, as well as how its structure relates to catalytic activity, earning a Nobel Prize in Chemistry in 1972 for his work. Stein was also involved in the invention of the automatic amino acid analyzer, an advancement in chromatography that opened the door to modern methods of chromatography, such as liquid chromatography and gas chromatography. == Life and education == === Early life and education === William H. Stein was born on June 25, 1911 in New York City into a Jewish family. His father, Fred M. Stein, was a businessman who retired early to support local New York health organizations. His mother, Beatrice Borg Stein, was a children's rights activist who developed afterschool activities. Staunch advocates for the welfare of society, Stein's parents fostered his interests in the life sciences from a young age. As a child, Stein attended the recently established "progressive" Lincoln School which was sponsored by the Teachers College of Columbia University; there, he was able to explore the natural sciences through field trips and science projects. At the age of sixteen, Stein was transferred to the Phillips Exeter Academy in New England to prepare for higher education. In 1936, during his graduate studies at Columbia University, William H. Stein married Phoebe Hockstader. They had three sons together: William H. Stein, Jr., David F. Stein, and Robert J. Stein. Stein lived with his family in New York the rest of his life—mainly in Manhattan and briefly in Scarsdale, New York. === Academic career === William H. Stein began his higher education as a chemistry major at Harvard University in 1929. He spent one year as a graduate student at Harvard University before transferring to
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the Department of Biological Chemistry at the College of Physicians and Surgeons, Columbia University, in 1934 to focus on biochemistry. Hans Thatcher Clarke, the chairman of the department at the time, was collecting many talented graduate students who would become the distinguished biochemists of the early twentieth century. In 1937, Stein completed his thesis on the amino acid composition of elastin, earning his Ph.D. Stein was introduced to potassium trioxalatochromate and ammonium rhodanilate by Max Bergmann, a Jewish-German biochemist who fled to the United States in 1934 under threat of Nazi occupation and worked in a laboratory at the Rockefeller Institute. He used these two precipitating agents to isolate the amino acids glycine and proline, respectively, for his research on elastin. With the conclusion of his academic career, Stein went on to work under Bergmann. === Later life and death === William H. Stein and his wife traveled around the world and hosted many prominent scientists in their own home in New York City throughout his scientific career. In addition to Stein's long-term professorship at Rockefeller Institute, he served as a visiting professor to the University of Chicago in 1961 and Harvard University in 1964. Stein also lectured at the Washington University in St. Louis and Haverford College. In 1969, Stein experienced sudden paralysis, diagnosed as Guillain–Barré syndrome, after developing a fever several days prior during a symposium in Copenhagen. Despite remaining quadriplegic the rest of his life, Stein's colleagues alleged that his spirit and sense of humor endured. He continued to be a guiding presence at the Rockefeller Institute to his younger colleagues and their work on the study of RNase. At the age of sixty-eight, Stein experienced unexpected heart failure. William H. Stein died February 2, 1980 in New York City. == Scientific career == === Early work
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=== Following the completion of his formal education, Stein became a researcher under Bergmann at Rockefeller Institute, where much of his most important work was done. Stanford Moore joined Bergmann's lab in 1939, where he and Stein began research focusing on amino acids. According to Moore, "During the early years of our cooperation, Stein and I worked out a system of collaboration that lasted for a lifetime." Their work in this area was disrupted with the beginning of World War II, and they temporarily parted ways to aid the war efforts, Stein staying with Bergmann to research the molecular scale effect of blister agents on the human body. They began collaborating again, however, after Bergmann died in 1944 and they were given an opportunity by the Director of the Rockefeller Institute, Herbert S. Gasser, to continue Bergmann's work in amino acids. === Chromatography === Stein and Moore developed a method to quantify and separate amino acids with column chromatography, using potato starch as the stationary phase. The fractions, originally collected manually, were collected in their newly developed automated fraction collector, and the amount of each amino acid was determined by an adjusted color reaction with ninhydrin. They began testing other methods of separation, such as ion exchange chromatography, to reduce the analysis time, as it took two weeks to analyze one protein using the starch columns. Ion exchange chromatography reduced the time to 5 days during initial experiments, and eventually Stein and Moore whittled the process down even further with the help of Daryl Spackman, which resulted in the first automatic amino acid analyzer. Along with their well-known work in protein sequences, this automatic amino acid analyzer was also utilized in Stein's study of amino acids in human urine and blood plasma. === Determination of protein sequences === With their
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success in improving the analysis time for amino acids, Stein and Moore began to determine the structure of an entire protein molecule, specifically bovine ribonuclease, in the early 1950s. They determined the entire sequence of ribonuclease by 1960. This sequence combined with X-ray analysis of the crystallized ribonuclease lead to the determination of the nuclease's active site. Stein won a Nobel Prize in Chemistry in 1972 with Moore and Christian Boehmer Anfinsen, for their work on ribonuclease and "for their contribution to the understanding of the connection between chemical structure and catalytic activity of the ribonuclease molecule." == Awards and honors == === Awards === William H. Stein received a number of awards for his contributions to the biochemical field, including: American Chemical Society Award in Chromatography and Electrophoresis (1964) with Stanford Moore Richards Medal of the American Chemical Society (1972) with Stanford Moore Kaj Linderstrøm-Lang Award, Copenhagen (1972) with Stanford Moore The Nobel Prize in Chemistry (1972) with Stanford Moore and Christian B. Anfinsen === Honors === William H. Stein received numerous honors from Columbia University and the Albert Einstein College of Medicine of Yeshiva University, including: D.Sc. honoris causa, Columbia University (1973), D.Sc. honoris causa, Albert Einstein College of Medicine of Yeshiva University (1973), and the Award of Excellence Medal, Columbia University Graduate Faculty and Alumni Association (1973). === Scientific societies === William H. Stein was a member of several scientific societies, including the: National Academy of Sciences (elected to membership in 1960), American Academy of Arts and Sciences (elected to membership in 1960), American Society of Biological Chemists, Biochemical Society of London, American Chemical Society, American Association for the Advancement of Science, and Harvey Society of New York. == See also == List of Jewish Nobel laureates == References == == Further reading == Moore, Stanford (October
|
{
"page_id": 789033,
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"title": "William Howard Stein"
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1980). "William H. Stein". The Journal of Biological Chemistry. 255 (20): 9517–9518. doi:10.1016/S0021-9258(18)43417-5. PMID 7000757. == External links == "Form and Function: The First Sequence of an Enzyme, Ribonuclease". The Rockefeller University. William Howard Stein on Nobelprize.org with the Nobel Lecture, December 11, 1972 The Chemical Structures of Pancreatic Ribonuclease and Deoxyribonuclease
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"page_id": 789033,
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Arabinosyl nucleosides are derivatives of the nucleosides. They contain β-D-arabinofuranose, in contrast to most nucleosides which contain β-D-ribofuranose. They are used as cytostatics or virostatics. == Examples == == References ==
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"page_id": 40897065,
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"title": "Arabinosyl nucleoside"
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An unsaturated fat is a fat or fatty acid in which there is at least one double bond within the fatty acid chain. A fatty acid chain is monounsaturated if it contains one double bond, and polyunsaturated if it contains more than one double bond. A saturated fat has no carbon-to-carbon double bonds, so the maximum possible number of hydrogen is bonded to carbon, and thus, is considered to be "saturated" with hydrogen atoms. To form carbon-to-carbon double bonds, hydrogen atoms are removed from the carbon chain. In cellular metabolism, unsaturated fat molecules contain less energy (i.e., fewer calories) than an equivalent amount of saturated fat. The greater the degree of unsaturation in a fatty acid (i.e., the more double bonds in the fatty acid) the more susceptible it becomes to lipid peroxidation (rancidity). Antioxidants can protect unsaturated fat from lipid peroxidation. == Composition of common fats == In chemical analysis, fats are broken down to their constituent fatty acids, which can be analyzed in various ways. In one approach, fats undergo transesterification to give fatty acid methyl esters (FAMEs), which are amenable to separation and quantitation using gas chromatography. Classically, unsaturated isomers were separated and identified by argentation thin-layer chromatography. The saturated fatty acid components are almost exclusively stearic (C18) and palmitic acids (C16). Monounsaturated fats are almost exclusively oleic acid. Linolenic acid comprises most of the triunsaturated fatty acid component. == Chemistry and nutrition == Although polyunsaturated fats are protective against cardiac arrhythmias, a study of post-menopausal women with a relatively low fat intake showed that polyunsaturated fat is positively associated with progression of coronary atherosclerosis, whereas monounsaturated fat is not. This probably is an indication of the greater vulnerability of polyunsaturated fats to lipid peroxidation, against which vitamin E has been shown to be protective. Examples of
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unsaturated fatty acids are palmitoleic acid, oleic acid, myristoleic acid, linoleic acid, and arachidonic acid. Foods containing unsaturated fats include avocado, nuts, olive oils, and vegetable oils such as canola. Meat products contain both saturated and unsaturated fats. Although unsaturated fats are conventionally regarded as 'healthier' than saturated fats, the United States Food and Drug Administration (FDA) recommendation stated that the amount of unsaturated fat consumed should not exceed 30% of one's daily caloric intake. Most foods contain both unsaturated and saturated fats. Marketers advertise only one or the other, depending on which one makes up the majority. Thus, various unsaturated fat vegetable oils, such as olive oils, also contain saturated fat. == Membrane composition as a metabolic pacemaker == Studies on the cell membranes of mammals and reptiles discovered that mammalian cell membranes are composed of a higher proportion of polyunsaturated fatty acids (DHA, omega-3 fatty acid) than reptiles. Studies on bird fatty acid composition have noted similar proportions to mammals but with 1/3rd less omega-3 fatty acids as compared to omega-6 for a given body size. This fatty acid composition results in a more fluid cell membrane but also one that is permeable to various ions (H+ & Na+), resulting in cell membranes that are more costly to maintain. This maintenance cost has been argued to be one of the key causes for the high metabolic rates and concomitant warm-bloodedness of mammals and birds. However polyunsaturation of cell membranes may also occur in response to chronic cold temperatures as well. In fish increasingly cold environments lead to increasingly high cell membrane content of both monounsaturated and polyunsaturated fatty acids, to maintain greater membrane fluidity (and functionality) at the lower temperatures. == See also == Iodine value – a chemical analysis method to determine the proportion of unsaturated fat.
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List of unsaturated fatty acids == References ==
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{
"page_id": 264748,
"source": null,
"title": "Unsaturated fat"
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This list of life sciences comprises the branches of science that involve the scientific study of life – such as microorganisms, plants, and animals including human beings. This science is one of the two major branches of natural science, the other being physical science, which is concerned with non-living matter. Biology is the overall natural science that studies life, with the other life sciences as its sub-disciplines. Some life sciences focus on a specific type of organism. For example, zoology is the study of animals, while botany is the study of plants. Other life sciences focus on aspects common to all or many life forms, such as anatomy and genetics. Some focus on the micro-scale (e.g. molecular biology, biochemistry) other on larger scales (e.g. cytology, immunology, ethology, pharmacy, ecology). Another major branch of life sciences involves understanding the mind – neuroscience. Life sciences discoveries are helpful in improving the quality and standard of life and have applications in health, agriculture, medicine, and the pharmaceutical and food science industries. For example, it has provided information on certain diseases which has overall aided in the understanding of human health. == Basic life science branches == Biology – scientific study of life Anatomy – study of form and function, in plants, animals, and other organisms Histology – the study of tissues Neuroscience – the study of the nervous system Astrobiology – the study of the formation and presence of life in the universe Biotechnology – study of combination of both the living organism and technology Biochemistry – the study of the chemical reactions required for life to exist and function, usually focused on the cellular level Quantum biology – the study of quantum phenomena in organisms Bioinformatics – developing of methods or software tools for storing, retrieving, organizing and analyzing biological data to
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generate useful biological knowledge Biophysics – study of biological processes by applying the theories and methods that have been traditionally used in the physical sciences Biomechanics – the study of the mechanics of living beings Botany – study of plants Agrostology – the study of grasses and grass-like species Phycology – the study of algae Cell biology (cytology) – study of the cell as a complete unit, and the molecular and chemical interactions that occur within a living cell Developmental biology – the study of the processes through which an organism forms, from zygote to full structure Ecology – study of the interactions of living organisms with one another and with the non-living elements of their environment Enzymology – study of enzymes Evolutionary biology – study of the origin and descent of species over time Evolutionary developmental biology – the study of the evolution of development including its molecular control Genetics – the study of genes and heredity Immunology – the study of the immune system Marine biology – the study of ocean organisms Biological oceanography – the study of life in the oceans and their interaction with the environment Microbiology – the study of microscopic organisms (microorganisms) and their interactions with other living organisms Aerobiology – study of the movement and transportation of microorganisms in the air Bacteriology – study of bacteria Virology – study of viruses and virus-like agents Molecular biology – the study of biology and biological functions at the molecular level, some cross over with biochemistry, genetics, and microbiology Structural biology – a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macro-molecules Mycology – the study of fungi Paleontology – the study of prehistoric organisms Parasitology – the study of parasites, their hosts, and the relationship between them Pathology –
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study of the causes and effects of disease or injury Human biology – the biological study of human beings Pharmacology – study of drug action Biological (or physical) anthropology – the study of humans, non-human primates, and hominids Biolinguistics – the study of the biology and evolution of language Physiology – the study of the functioning of living organisms and the organs and parts of living organisms Population biology – the study of groups of conspecific organisms Population dynamics – the study of short-term and long-term changes in the size and age composition of populations, and the biological and environmental processes influencing those changes. Population dynamics deals with the way populations are affected by birth and death rates, and by immigration and emigration, and studies topics such as ageing populations or population decline. Synthetic biology – the design and construction of new biological entities such as enzymes, genetic circuits and cells, or the redesign of existing biological systems Systems biology – the study of the integration and dependencies of various components within a biological system, with particular focus upon the role of metabolic pathways and cell-signaling strategies in physiology Theoretical biology – use of abstractions and mathematical models to study biological phenomena Toxicology – the study of poisons Zoology – the study of (generally non-human) animals Ethology – the study of animal behavior == Applied life science branches and derived concepts == Agriculture – science and practice of cultivating plants and livestock Agronomy – science of cultivating plants for resources Biocomputers – systems of biologically derived molecules, such as DNA and proteins, are used to perform computational calculations involving storing, retrieving, and processing data. The development of biological computing has been made possible by the expanding new science of nanobiotechnology. Biocontrol – bioeffector-method of controlling pests (including insects, mites, weeds
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and plant diseases) using other living organisms. Bioengineering – study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology Bioelectronics – field at the convergence of electronics and biological sciences. The electrical state of biological matter significantly affects its structure and function, compare for instance the membrane potential, the signal transduction by neurons, the isoelectric point (IEP) and so on. Micro- and nano-electronic components and devices have increasingly been combined with biological systems like medical implants, biosensors, lab-on-a-chip devices etc. causing the emergence of this new scientific field. Biomaterials – any matter, surface, or construct that interacts with biological systems. As a science, biomaterials is about fifty years old. The study of biomaterials is called biomaterials science. It has experienced steady and strong growth over its history, with many companies investing large amounts of money into the development of new products. Biomaterials science encompasses elements of medicine, biology, chemistry, tissue engineering and materials science. Biomedical science – healthcare science, also known as biomedical science, is a set of applied sciences applying portions of natural science or formal science, or both, to develop knowledge, interventions, or technology of use in healthcare or public health. Such disciplines as medical microbiology, clinical virology, clinical epidemiology, genetic epidemiology and pathophysiology are medical sciences. Biomonitoring – measurement of the body burden of toxic chemical compounds, elements, or their metabolites, in biological substances. Often, these measurements are done in blood and urine. Biopolymer – polymers produced by living organisms; in other words, they are polymeric biomolecules. Since they are polymers, biopolymers contain monomeric units that are covalently bonded to form larger structures. There are three main classes of biopolymers, classified according to the monomeric units used and the structure of the biopolymer formed: polynucleotides (RNA and DNA),
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which are long polymers composed of 13 or more nucleotide monomers; polypeptides, which are short polymers of amino acids; and polysaccharides, which are often linear bonded polymeric carbohydrate structures. Biotechnology – manipulation of living matter, including genetic modification and synthetic biology Conservation biology – the management of nature and of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions. It is an interdisciplinary subject drawing on natural and social sciences, and the practice of natural resource management. Environmental health – multidisciplinary field concerned with environmental epidemiology, toxicology, and exposure science. Fermentation technology – study of use of microorganisms for industrial manufacturing of various products like vitamins, amino acids, antibiotics, beer, wine, etc. Food science – applied science devoted to the study of food. Activities of food scientists include the development of new food products, design of processes to produce and conserve these foods, choice of packaging materials, shelf-life studies, study of the effects of food on the human body, sensory evaluation of products using panels or potential consumers, as well as microbiological, physical (texture and rheology) and chemical testing. Genomics – application of recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism). The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of
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single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks. Health sciences – sciences which focus on health, or health care, as core parts of their subject matter. These two subject matters relate to multiple academic disciplines, both STEM disciplines, as well as emerging patient safety disciplines (such as social care research), and are both relevant to current health science knowledge. Medical devices – A medical device is an instrument, apparatus, implant, in vitro reagent, or similar or related article that is used to diagnose, prevent, or treat disease or other conditions, and does not achieve its purposes through chemical action within or on the body (which would make it a drug). Whereas medicinal products (also called pharmaceuticals) achieve their principal action by pharmacological, metabolic or immunological means, medical devices act by other means like physical, mechanical, or thermal means. Medical imaging – the technique and process used to create images of the human body (or parts and function thereof) for clinical or physiological research purposes Immunotherapy – the "treatment of disease by inducing, enhancing, or suppressing an immune response". Immunotherapies designed to elicit or amplify an immune response are classified as activation immunotherapies, while immunotherapies that reduce or suppress are classified as suppression immunotherapies. Kinesiology – scientific study of human movement. Kinesiology, also known as human kinetics, addresses physiological, mechanical, and psychological mechanisms. Applications of kinesiology to human health include: biomechanics and orthopedics; strength and conditioning; sport psychology; methods of rehabilitation, such as physical and occupational therapy; and sport and exercise. Individuals who have earned degrees in kinesiology can work in research, the fitness industry, clinical settings, and in industrial environments. Studies of
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}
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human and animal motion include measures from motion tracking systems, electrophysiology of muscle and brain activity, various methods for monitoring physiological function, and other behavioral and cognitive research techniques. Optogenetics – a neuromodulation technique employed in neuroscience that uses a combination of techniques from optics and genetics to control and monitor the activities of individual neurons in living tissue—even within freely-moving animals—and to precisely measure the effects of those manipulations in real-time. The key reagents used in optogenetics are light-sensitive proteins. Spatially-precise neuronal control is achieved using optogenetic actuators like channelrhodopsin, halorhodopsin, and archaerhodopsin, while temporally-precise recordings can be made with the help of optogenetic sensors like Clomeleon, Mermaid, and SuperClomeleon. Pharmacogenomics – field of science and technology that analyses how genetic makeup affects an individual's response to drugs. Pharmacogenomics (a portmanteau of pharmacology and genomics) deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. Pharmacology – branch of medicine and biology concerned with the study of drug action, where a drug can be broadly defined as any human-made, natural, or endogenous (within the body) molecule which exerts a biochemical and/or physiological effect on the cell, tissue, organ, or organism. More specifically, it is the study of the interactions that occur between a living organism and chemicals that affect normal or abnormal biochemical function. If substances have medicinal properties, they are considered pharmaceuticals. Proteomics – the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The proteome is the entire set of proteins, produced or modified by an organism or system. This varies with time and distinct requirements, or stresses, that a cell or
|
{
"page_id": 68140,
"source": null,
"title": "List of life sciences"
}
|
organism undergoes. == See also == Outline of biology Divisions of pharmacology Control theory == References == == Further reading == Magner, Lois N. (2002). A history of the life sciences (Rev. and expanded 3rd ed.). New York: M. Dekker. ISBN 0824708245.
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{
"page_id": 68140,
"source": null,
"title": "List of life sciences"
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TIGR-Tas (Tandem Interspaced Guide RNA-associated proteins) is a family of RNA-guided DNA-targeting systems discovered in prokaryotes and their viruses. These systems represent a novel class of programmable molecular tools that utilize a unique dual-spacer targeting mechanism, distinct from CRISPR-Cas systems. TIGR-Tas systems were reported in February 2025 by researchers at the Broad Institute of MIT and Harvard and MIT's McGovern Institute for Brain Research, a collaborative effort led by Guilhem Faure under the direction of Feng Zhang, with contributions from renowned evolutionary biologist Eugene Koonin. == Discovery == TIGR-Tas systems were discovered through computational mining approaches that began with structural analysis of the RNA-binding domain of SpCas9. Through iterative structural and sequence homology-based searches, Faure, Zhang, and colleagues identified proteins containing Nop domains—hallmarks of eukaryotic box C/D snoRNA ribonucleoproteins (RNPs)—that were associated with distinctive tandem interspaced guide RNA arrays. The discovery was first presented at the Systems and Synthetic Biology conference at Institut Pasteur in 2025. The discovery process employed advanced computational methods, including protein large language models, to cluster related proteins based on their likely evolutionary relationships. "When you are doing iterative, deep mining, the resulting hits can be so diverse that they are difficult to analyze using standard phylogenetic methods, which rely on conserved sequence," explained Guilhem Faure, a senior group leader in Zhang's lab. This approach identified more than 20,000 different Tas proteins, predominantly from bacteriophages and parasitic bacteria. == System components == === TIGR arrays === TIGR arrays consist of repetitive sequences organized into dual-repeat units or stem-loop structures. Each unit contains: Edge repeats and loop repeats (8-12 nucleotides each) Spacer A and Spacer B (typically 9 nucleotides each) Conserved box C and box D motifs similar to those found in snoRNAs === Tas proteins === TIGR-associated (Tas) proteins are classified into three main types: TasA:
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"page_id": 80022060,
"source": null,
"title": "TIGR-Tas"
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Contains only the Nop domain TasH: Nop domain fused with an HNH nuclease domain TasR: Nop domain fused with a RuvC nuclease domain == Mechanism of action == === RNA processing === TIGR arrays are transcribed and processed into 36-nucleotide guide RNAs called tigRNAs. Processing occurs at precise sites within edge repeats and requires the presence of Tas proteins, though the proteins themselves do not directly catalyze the cleavage. === DNA targeting === Unlike CRISPR systems that use a single guide RNA to target one DNA strand, TIGR systems employ a tandem-spacer targeting mechanism: Spacer A pairs with one DNA strand Spacer B pairs with the complementary DNA strand Both spacers must be correctly paired for efficient cleavage No protospacer-adjacent motif (PAM) is required === Cleavage pattern === TasR nucleases create double-strand breaks with 8-nucleotide 3' overhangs, cleaving 3' to the nucleotide complementary to the 5th base of each spacer (following a "C - 5 rule"). == Structural features == Cryo-electron microscopy studies revealed that TasR forms a C2-symmetric dimer that binds target DNA and tigRNA. The structure shows: Dramatic 180° DNA bending upon complex formation Nop domains that recognize box C/D motifs in tigRNAs RuvC domains positioned for coordinated cleavage of both DNA strands Faure and colleagues demonstrated that this dual-guide mechanism could make TIGR systems a more reliable tool for genetic modifications, potentially minimizing the off-target effects that have hampered some CRISPR applications. == Distribution and diversity == TIGR systems are found primarily in: Bacteriophages and archaeal viruses Parasitic bacteria of the Candidate Phyla Radiation Various prokaryotic genomes Two main architectural variants exist: Dual-repeat arrays: Traditional TIGR organization Stem-loop arrays: Alternative organization lacking separating repeats == Evolutionary relationships == TIGR systems show evolutionary connections to: IS110 transposases: Share structural domains and RNA-binding mechanisms Box C/D snoRNPs: Common Nop
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"page_id": 80022060,
"source": null,
"title": "TIGR-Tas"
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domain architecture and box C/D motifs These relationships suggest TIGR systems may represent an ancestral form of RNA-guided systems. == Applications and potential == === Genome editing === Faure, Zhang, and their team demonstrated that TIGR-TasR systems can be successfully adapted for: Programmable DNA cleavage in human cells Genome editing with unique targeting properties === Advantages over CRISPR === TIGR-Tas systems offer several potential advantages over CRISPR technology: No PAM requirement: Can theoretically target any genomic site Compact size: Tas proteins are approximately one-quarter the size of Cas9, potentially facilitating cellular delivery for therapeutic applications Dual-guide system: May enhance specificity by requiring correct recognition of both DNA strands Modularity: Distinct functional domains that could be engineered for various applications === Therapeutic potential === The small size and modularity of TIGR-Tas systems make them promising candidates for therapeutic gene editing applications, potentially overcoming delivery challenges associated with larger CRISPR proteins. == Biological functions == While the exact biological roles remain unclear, proposed functions include: Mobile genetic element (MGE) interference Gene regulation Plasmid maintenance and inheritance Inter-MGE competition The researchers are now investigating TIGR's natural role in viruses to better understand the system and how it can be further adapted for research and therapeutic uses. "I think there's more there to study in terms of what some of those relationships may be, and it may help us better understand how these systems are used in humans," Zhang said. == See also == CRISPR-Cas systems RNA-guided systems Box C/D snoRNPs IS110 transposases Feng Zhang Eugene Koonin == References == == External links == The New TIGR-Tas Gene Editing System by Steven Novella Move Over, CRISPR. Smaller, Smarter Gene-Editing System Found New RNA-guided system TIGR-Tas could challenge CRISPR’s stronghold
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{
"page_id": 80022060,
"source": null,
"title": "TIGR-Tas"
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Androstenediol may refer to: 5-Androstenediol (androst-5-ene-3β,17β-diol) – an endogenous weak androgen and estrogen and intermediate to/prohormone of testosterone 4-Androstenediol (androst-4-ene-3β,17β-diol) – a weak androgen and prohormone of testosterone and hence an anabolic-androgenic steroid 1-Androstenediol (5α-androst-1-ene-3β,17β-diol) – a prohormone of 1-testosterone (Δ1-DHT) and hence an anabolic-androgenic steroid == See also == Androstanediol Androstenedione Dehydroepiandrosterone Androstenolone Androstanedione Androstanolone
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{
"page_id": 6031916,
"source": null,
"title": "Androstenediol (disambiguation)"
}
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In physics, a pair potential is a function that describes the potential energy of two interacting objects solely as a function of the distance between them. Some interactions, like Coulomb's law in electrodynamics or Newton's law of universal gravitation in mechanics naturally have this form for simple spherical objects. For other types of more complex interactions or objects it is useful and common to approximate the interaction by a pair potential, for example interatomic potentials in physics and computational chemistry that use approximations like the Lennard-Jones and Morse potentials. == Functional form == The total energy of a system of N {\displaystyle N} objects at positions R → i {\displaystyle {\vec {R}}_{i}} , that interact through pair potential v {\displaystyle v} is given by E = 1 2 ∑ i = 1 N ∑ j ≠ i N v ( | R → i − R → j | ) . {\displaystyle E={\frac {1}{2}}\sum _{i=1}^{N}\sum _{j\neq i}^{N}v\left(\left|{\vec {R}}_{i}-{\vec {R}}_{j}\right|\right)\ .} Equivalently, this can be expressed as E = ∑ i = 1 N ∑ j = i + 1 N v ( | R → i − R → j | ) . {\displaystyle E=\sum _{i=1}^{N}\sum _{j=i+1}^{N}v\left(\left|{\vec {R}}_{i}-{\vec {R}}_{j}\right|\right)\ .} This expression uses the fact that interaction is symmetric between particles i {\displaystyle i} and j {\displaystyle j} . It also avoids self-interaction by not including the case where i = j {\displaystyle i=j} . == Potential range == A fundamental property of a pair potential is its range. It is expected that pair potentials go to zero for infinite distance as particles that are too far apart do not interact. In some cases the potential goes quickly to zero and the interaction for particles that are beyond a certain distance can be assumed to be zero, these are said
|
{
"page_id": 10422831,
"source": null,
"title": "Pair potential"
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|
to be short-range potentials. Other potentials, like the Coulomb or gravitational potential, are long range: they go slowly to zero and the contribution of particles at long distances still contributes to the total energy. == Computational cost == The total energy expression for pair potentials is quite simple to use for analytical and computational work. It has some limitations however, as the computational cost is proportional to the square of number of particles. This might be prohibitively expensive when the interaction between large groups of objects needs to be calculated. For short-range potentials the sum can be restricted only to include particles that are close, reducing the cost to linearly proportional to the number of particles. == Infinitely periodic systems == In some cases it is necessary to calculate the interaction between an infinite number of particles arranged in a periodic pattern. == Beyond pair potentials == Pair potentials are very common in physics and computational chemistry and biology; exceptions are very rare. An example of a potential energy function that is not a pair potential is the three-body Axilrod-Teller potential. Another example is the Stillinger-Weber potential for silicon, which includes the angle in a triangle of silicon atoms as an input parameter. == Common pair potentials == Some commonly used pair potentials are listed below. Hard Sphere potential Sutherland potential Buckingham (or exp-6) potential Mie potential Lennard-Jones (12-6) potential Stockmayer potential Coloumb potential Yukawa potential Morse potential == References ==
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"page_id": 10422831,
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"title": "Pair potential"
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In physics, a pseudopotential or effective potential is used as an approximation for the simplified description of complex systems. Applications include atomic physics and neutron scattering. The pseudopotential approximation was first introduced by Hans Hellmann in 1934. == Atomic physics == The pseudopotential is an attempt to replace the complicated effects of the motion of the core (i.e. non-valence) electrons of an atom and its nucleus with an effective potential, or pseudopotential, so that the Schrödinger equation contains a modified effective potential term instead of the Coulombic potential term for core electrons normally found in the Schrödinger equation. The pseudopotential is an effective potential constructed to replace the atomic all-electron potential (full-potential) such that core states are eliminated and the valence electrons are described by pseudo-wavefunctions with significantly fewer nodes. This allows the pseudo-wavefunctions to be described with far fewer Fourier modes, thus making plane-wave basis sets practical to use. In this approach usually only the chemically active valence electrons are dealt with explicitly, while the core electrons are 'frozen', being considered together with the nuclei as rigid non-polarizable ion cores. It is possible to self-consistently update the pseudopotential with the chemical environment that it is embedded in, having the effect of relaxing the frozen core approximation, although this is rarely done. In codes using local basis functions, like Gaussian, often effective core potentials are used that only freeze the core electrons. First-principles pseudopotentials are derived from an atomic reference state, requiring that the pseudo- and all-electron valence eigenstates have the same energies and amplitude (and thus density) outside a chosen core cut-off radius r c {\displaystyle r_{c}} . Pseudopotentials with larger cut-off radius are said to be softer, that is more rapidly convergent, but at the same time less transferable, that is less accurate to reproduce realistic features in
|
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different environments. Motivation: Reduction of basis set size Reduction of number of electrons Inclusion of relativistic and other effects Approximations: One-electron picture. The small-core approximation assumes that there is no significant overlap between core and valence wave-function. Nonlinear core corrections or "semicore" electron inclusion deal with situations where overlap is non-negligible. Early applications of pseudopotentials to atoms and solids based on attempts to fit atomic spectra achieved only limited success. Solid-state pseudopotentials achieved their present popularity largely because of the successful fits by Walter Harrison to the nearly free electron Fermi surface of aluminum (1958) and by James C. Phillips to the covalent energy gaps of silicon and germanium (1958). Phillips and coworkers (notably Marvin L. Cohen and coworkers) later extended this work to many other semiconductors, in what they called "semiempirical pseudopotentials". === Norm-conserving pseudopotential === Norm-conserving and ultrasoft are the two most common forms of pseudopotential used in modern plane-wave electronic structure codes. They allow a basis-set with a significantly lower cut-off (the frequency of the highest Fourier mode) to be used to describe the electron wavefunctions and so allow proper numerical convergence with reasonable computing resources. An alternative would be to augment the basis set around nuclei with atomic-like functions, as is done in LAPW. Norm-conserving pseudopotential was first proposed by Hamann, Schlüter, and Chiang (HSC) in 1979. The original HSC norm-conserving pseudopotential takes the following form: V ^ ps ( r ) = ∑ l ∑ m | Y l m ⟩ V l m ( r ) ⟨ Y l m | {\displaystyle {\hat {V}}_{\textit {ps}}(r)=\sum _{l}\sum _{m}|Y_{lm}\rangle V_{lm}(r)\langle Y_{lm}|} where | Y l m ⟩ {\displaystyle |Y_{lm}\rangle } projects a one-particle wavefunction, such as one Kohn-Sham orbital, to the angular momentum labeled by { l , m } {\displaystyle \{l,m\}} . V l m
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( r ) {\displaystyle V_{lm}(r)} is the pseudopotential that acts on the projected component. Different angular momentum states then feel different potentials, thus the HSC norm-conserving pseudopotential is non-local, in contrast to local pseudopotential which acts on all one-particle wave-functions in the same way. Norm-conserving pseudopotentials are constructed to enforce two conditions. 1. Inside the cut-off radius r c {\displaystyle r_{c}} , the norm of each pseudo-wavefunction be identical to its corresponding all-electron wavefunction: ∫ r < r c d r 3 ϕ R , i ( r → ) ϕ R , j ( r → ) = ∫ r < r c d r 3 ϕ ~ R , i ( r → ) ϕ ~ R , j ( r → ) {\displaystyle \int _{r<r_{c}}dr^{3}\phi _{\mathbf {R} ,i}({\vec {r}})\phi _{\mathbf {R} ,j}({\vec {r}})=\int _{r<r_{c}}dr^{3}{\tilde {\phi }}_{\mathbf {R} ,i}({\vec {r}}){\tilde {\phi }}_{\mathbf {R} ,j}({\vec {r}})} , where ϕ R , i {\displaystyle \phi _{\mathbf {R} ,i}} and ϕ ~ R , i {\displaystyle {\tilde {\phi }}_{\mathbf {R} ,i}} are the all-electron and pseudo reference states for the pseudopotential on atom R {\displaystyle \mathbf {R} } . 2. All-electron and pseudo wavefunctions are identical outside cut-off radius r c {\displaystyle r_{c}} . === Ultrasoft pseudopotentials === Ultrasoft pseudopotentials relax the norm-conserving constraint to reduce the necessary basis-set size further at the expense of introducing a generalized eigenvalue problem. With a non-zero difference in norms we can now define: q R , i j = ⟨ ϕ R , i | ϕ R , j ⟩ − ⟨ ϕ ~ R , i | ϕ ~ R , j ⟩ {\displaystyle q_{\mathbf {R} ,ij}=\langle \phi _{\mathbf {R} ,i}|\phi _{\mathbf {R} ,j}\rangle -\langle {\tilde {\phi }}_{\mathbf {R} ,i}|{\tilde {\phi }}_{\mathbf {R} ,j}\rangle } , and so a normalised eigenstate of the
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"page_id": 2099759,
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pseudo Hamiltonian now obeys the generalized equation H ^ | Ψ i ⟩ = ϵ i S ^ | Ψ i ⟩ {\displaystyle {\hat {H}}|\Psi _{i}\rangle =\epsilon _{i}{\hat {S}}|\Psi _{i}\rangle } , where the operator S ^ {\displaystyle {\hat {S}}} is defined as S ^ = 1 + ∑ R , i , j | p R , i ⟩ q R , i j ⟨ p R , j | {\displaystyle {\hat {S}}=1+\sum _{\mathbf {R} ,i,j}|p_{\mathbf {R} ,i}\rangle q_{\mathbf {R} ,ij}\langle p_{\mathbf {R} ,j}|} , where p R , i {\displaystyle p_{\mathbf {R} ,i}} are projectors that form a dual basis with the pseudo reference states inside the cut-off radius, and are zero outside: ⟨ p R , i | ϕ ~ R , j ⟩ r < r c = δ i , j {\displaystyle \langle p_{\mathbf {R} ,i}|{\tilde {\phi }}_{\mathbf {R} ,j}\rangle _{r<r_{c}}=\delta _{i,j}} . A related technique is the projector augmented wave (PAW) method. == Fermi pseudopotential == Enrico Fermi introduced a pseudopotential, V {\displaystyle V} , to describe the scattering of a free neutron by a nucleus. The scattering is assumed to be s-wave scattering, and therefore spherically symmetric. Therefore, the potential is given as a function of radius, r {\displaystyle r} : V ( r ) = 2 π ℏ 2 m b δ ( r ) {\displaystyle V(r)={\frac {2\pi \hbar ^{2}}{m}}b\,\delta (r)} , where ℏ {\displaystyle \hbar } is the Planck constant divided by 2 π {\displaystyle 2\pi } , m {\displaystyle m} is the mass, δ ( r ) {\displaystyle \delta (r)} is the Dirac delta function, b {\displaystyle b} is the bound coherent neutron scattering length, and r = 0 {\displaystyle r=0} the center of mass of the nucleus. The Fourier transform of this δ {\displaystyle \delta } -function leads to
|
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the constant neutron form factor. == Phillips pseudopotential == James Charles Phillips developed a simplified pseudopotential while at Bell Labs useful for describing silicon and germanium. == See also == Density functional theory Projector augmented wave method Marvin L. Cohen Alex Zunger == References == == Pseudopotential libraries == Pseudopotential Library : A community website for pseudopotentials/effective core potentials developed for high accuracy correlated many-body methods such as quantum Monte Carlo and quantum chemistry NNIN Virtual Vault for Pseudopotentials : This webpage maintained by the NNIN/C provides a searchable database of pseudopotentials for density functional codes as well as links to pseudopotential generators, converters, and other online databases. Vanderbilt Ultra-Soft Pseudopotential Site : Website of David Vanderbilt with links to codes that implement ultrasoft pseudopotentials and libraries of generated pseudopotentials. GBRV pseudopotential site : This site hosts the GBRV pseudopotential library PseudoDojo : This site collates tested pseudo potentials sorted by type, accuracy, and efficiency, shows information on convergence of various tested properties and provides download options. SSSP : Standard Solid State Pseudopotentials == Further reading == Hellmann, Hans (1935), "A New Approximation Method in the Problem of Many Electrons", Journal of Chemical Physics, vol. 3, no. 1, Karpow-Institute for Physical Chemistry, Moscow, p. 61, Bibcode:1935JChPh...3...61H, doi:10.1063/1.1749559, ISSN 0021-9606, archived from the original on 2013-02-23 Hellmann, H.; Kassatotschkin, W. (1936), "Metallic Binding According to the Combined Approximation Procedure", Journal of Chemical Physics, vol. 4, no. 5, Karpow-Institute for Physical Chemistry, Moscow, p. 324, Bibcode:1936JChPh...4..324H, doi:10.1063/1.1749851, ISSN 0021-9606, archived from the original on 2013-02-23 Harrison, Walter Ashley (1966), Pseudopotentials in the theory of metals, Frontiers in Physics, University of Virginia Brust, David (1968), Alder, Berni (ed.), "The Pseudopotential Method and the Single-Particle Electronic Excitation Spectra of Crystals", Methods in Computational Physics, vol. 8, New York: Academic Press, pp. 33–61, ISSN 0076-6860
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{
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Heine, Volker (1970), "The Pseudopotential Concept", Solid State Physics, Solid State Physics, vol. 24, Academic Press, pp. 1–36, doi:10.1016/S0081-1947(08)60069-7, ISBN 9780126077247 Pickett, Warren E. (April 1989), "Pseudopotential methods in condensed matter applications", Computer Physics Reports, vol. 9, no. 3, pp. 115–197, Bibcode:1989CoPhR...9..115P, doi:10.1016/0167-7977(89)90002-6 Hamann, D. R. (2013), "Optimized norm-conserving Vanderbilt pseudopotentials", Physical Review B, vol. 88, no. 8, p. 085117, arXiv:1306.4707, Bibcode:2013PhRvB..88h5117H, doi:10.1103/PhysRevB.88.085117, S2CID 119232272 Lejaeghere, K.; Bihlmayer, G.; Bjorkman, T.; Blaha, P.; Blugel, S.; Blum, V.; Caliste, D.; Castelli, I. E.; Clark, S. J.; Dal Corso, A.; de Gironcoli, S.; Deutsch, T.; Dewhurst, J. K.; Di Marco, I.; Draxl, C.; Du ak, M.; Eriksson, O.; Flores-Livas, J. A.; Garrity, K. F.; Genovese, L.; Giannozzi, P.; Giantomassi, M.; Goedecker, S.; Gonze, X.; Granas, O.; Gross, E. K. U.; Gulans, A.; Gygi, F.; Hamann, D. R.; Hasnip, P. J.; Holzwarth, N. A. W.; Iu an, D.; Jochym, D. B.; Jollet, F.; Jones, D.; Kresse, G.; Koepernik, K.; Kucukbenli, E.; Kvashnin, Y. O.; Locht, I. L. M.; Lubeck, S.; Marsman, M.; Marzari, N.; Nitzsche, U.; Nordstrom, L.; Ozaki, T.; Paulatto, L.; Pickard, C. J.; Poelmans, W.; Probert, M. I. J.; Refson, K.; Richter, M.; Rignanese, G.-M.; Saha, S.; Scheffler, M.; Schlipf, M.; Schwarz, K.; Sharma, S.; Tavazza, F.; Thunstrom, P.; Tkatchenko, A.; Torrent, M.; Vanderbilt, D.; van Setten, M. J.; Van Speybroeck, V.; Wills, J. M.; Yates, J. R.; Zhang, G.-X.; Cottenier, S. (2016), "Reproducibility in density functional theory calculations of solids", Science, 351 (6280): aad3000, Bibcode:2016Sci...351.....L, doi:10.1126/science.aad3000, hdl:1854/LU-7191263, ISSN 0036-8075, PMID 27013736 Bosoni, Emanuele; Beal, Louis; Bercx, Marnik; Blaha, Peter; Blügel, Stefan; Bröder, Jens; Callsen, Martin; Cottenier, Stefaan; Degomme, Augustin; Dikan, Vladimir; Eimre, Kristjan; Flage-Larsen, Espen; Fornari, Marco; Garcia, Alberto; Genovese, Luigi; Giantomassi, Matteo; Huber, Sebastiaan P.; Janssen, Henning; Kastlunger, Georg; Krack, Matthias; Kresse, Georg; Kühne, Thomas D.; Lejaeghere, Kurt; Madsen,
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Georg K. H.; Marsman, Martijn; Marzari, Nicola; Michalicek, Gregor; Mirhosseini, Hossein; Müller, Tiziano M. A.; Petretto, Guido; Pickard, Chris J.; Poncé, Samuel; Rignanese, Gian-Marco; Rubel, Oleg; Ruh, Thomas; Sluydts, Michael; Vanpoucke, Danny E. P.; Vijay, Sudarshan; Wolloch, Michael; Wortmann, Daniel; Yakutovich, Aliaksandr V.; Yu, Jusong; Zadoks, Austin; Zhu, Bonan; Pizzi, Giovanni (January 2024). "How to verify the precision of density-functional-theory implementations via reproducible and universal workflows". Nature Reviews Physics. 6 (1): 45–58. arXiv:2305.17274. Bibcode:2024NatRP...6...45B. doi:10.1038/s42254-023-00655-3.
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What Darwin Didn't Know is a documentary show on BBC Four presented by Armand Marie Leroi which charts the progress in the field of evolutionary theory since the original publication of Charles Darwin's On the Origin of Species in 1859. The theory of evolution by natural selection is now orthodoxy, but when it was unveiled it caused a storm of controversy, from fellow scientists as well as religious people. They criticised it for being short on evidence and long on assertion and Darwin, being the honest scientist that he was, agreed with them. He knew that his theory was riddled with "difficulties", but he entrusted future generations to complete his work and prove the essential truth of his vision, which is what scientists have been doing for the past 150 years. The evolutionary biologist Professor Armand Marie Leroi charts the scientific endeavour that brought about the triumphant renaissance of Darwin's theory. He argues that, with the new science of evolutionary developmental biology (evo devo), it may be possible to take that theory to a new level – to do more than explain what has evolved in the past, and start to predict what might evolve in the future. == Notes == == External links == What Darwin Didn't Know at BBC Online
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"page_id": 17959476,
"source": null,
"title": "What Darwin Didn't Know"
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Australasian Palaeontologists was formerly known as The Association of Australasian Palaeontologists, which was a specialist group of the Geological Society of Australia for palaeontologists in Australia. In 2015 members elected to shorten the name from The Association of Australasian Palaeontologists to Australasian Palaeontologists. == Publications == Alcheringa - quarterly publication of the AAP (published through Taylor & Francis) Memoirs of the AAP - occasional publication covering large paleontological articles Nomen Nudum - newsletter of the AAP == References == == External links == aap.gsa.org.au - official website of the Association of Australasian Palaeontologists gsa.org.au - official website of the Geological Society of Australia
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{
"page_id": 19335737,
"source": null,
"title": "Association of Australasian Palaeontologists"
}
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The term zygoma generally refers to the zygomatic bone, a bone of the human skull that is commonly referred to as the cheekbone or malar bone, but it may also refer to: The zygomatic arch, a structure in the human skull formed primarily by parts of the zygomatic bone and the temporal bone The zygomatic process, a bony protrusion of the human skull, mostly composed of the zygomatic bone but also contributed to by the frontal bone, temporal bone, and maxilla == See also == Zygoma implant Zygoma reduction plasty
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"page_id": 330303,
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"title": "Zygoma"
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A trichocyst is an organelle found in certain ciliates and dinoflagellates. A trichocyst can be found in tetrahymena and along cila pathways of several metabolic systems. It is also a structure in the cortex of certain ciliate and flagellate protozoans consisting of a cavity and long, thin threads that can be ejected in response to certain stimuli. Trichocysts may be widely distributed over an organism or restricted to certain areas (e.g., tentacles, papillae, around the mouth). There are several types. Mucoid trichocysts are elongated inclusions that may be ejected as visible bodies after artificial stimulation. Filamentous trichocysts in Paramecium and other ciliates are discharged as filaments composed of a cross-striated shaft and a tip. Toxicysts (in Dileptus and certain other carnivorous protozoans) tend to be localized around the mouth. When discharged, a toxicyst expels a long, nonstriated filament with a rodlike tip, which paralyzes or kills other microorganisms; this filament is used to capture food and, presumably, in defense. The functional significance of other trichocysts is uncertain, although those of Paramecium apparently can be extruded for anchorage during feeding. == References == == External links == Picture of a Trichocyst
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{
"page_id": 7735873,
"source": null,
"title": "Trichocyst"
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Bioactive agents are substances that can influence an organism, tissue or cell. Examples include enzymes, drugs, vitamins, phytochemicals, and bioactive compounds. Bioactive agents can be incorporated into polymers, which has applications in drug delivery and commercial production of household goods and biomedical devices. In drug delivery systems, bioactive agents are loaded into enzyme-responsive polymers which can then be cleaved by target enzymes. Activation of the bioactive agents leads to the release of therapeutic cargos. == References ==
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"page_id": 69339714,
"source": null,
"title": "Bioactive agents"
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Artbreeder, formerly known as Ganbreeder, is a collaborative, machine learning-based art website. Using the models StyleGAN and BigGAN, the website allows users to generate and modify images of faces, landscapes, and paintings, among other categories. == Overview == On Artbreeder, users mainly interact through the remixing - referred to as 'breeding' - of other users' images found in the publicly accessible database of images. The creation of new variations can be done by tweaking sliders on an image's page, known as "genes", which in the "Portraits" model can range from color balance to gender, facial hair, and glasses. Additionally, any image can be "crossbred" with other publicly viewable images from the database, using a slider to control how much of each image should influence the resulting "child". The site also allows for uploading new images, which the model will attempt to convert into the latent space of the network. == Notable usages == The similarly AI-driven text adventure game AI Dungeon uses Artbreeder to generate profile pictures for its users, and The Static Age's Andrew Paley has used Artbreeder to create the visuals for his music videos. Artbreeder has been used to create portraits of characters from popular novels such as Harry Potter and Twilight. They have also been used to add realistic features to ancient portraits. Artbreeder was used to create characters in the sequel to Ben Drowned with the titular villain, an AI-construct itself, created entirely using the website. == Changes to Artbreeder == ArtBreeder underwent an overhaul, introducing several features to enhance the user experience. Among these updates is the integration SD-XL, developed by stability.ai. Additionally, ArtBreeder also added a functionality known as ControlNet, which enables users to create images based on specific poses. With ControlNet, users can incorporate various poses into their AI Artworks. More features
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"page_id": 66980419,
"source": null,
"title": "Artbreeder"
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that were introduced into Artbreeder, are Pattern, which creates AI Pattern Images, Outpainting or Uncropping was also an added feature to Artbreeder, that allows the user to expand the image beyond the normal dimensions of the image. == Reception == The artwork generated by users of the website has been described as "beautiful" and "surreal," drawing comparisons to "weird, incomprehensible dreams" that "somehow touch the deep, unconscious parts of [the] mind". However, the generated faces were noted as "creepy and 'off'", and still nowhere near the quality attained by actual digital artists. Additionally, the site faced criticism for perceived confusing aspects of the AI's behavior. Jonathan Bartlett of Mind Matters News noted that "As is always the case with AI, sometimes the [gene] knobs don't work as expected and sometimes the results are... strange," while conceding that Artbreeder was still "probably the start of a new future of made-to-order stock images." Writers from Hyperallergic also took issue with perceived racial biases in the Portraits model, citing a comment from a user who faced difficulty from the neural network while attempting to darken the skin of a portrait to match a source image. == See also == This Person Does Not Exist DALL-E Stable Diffusion Text-to-image model == References == == Bibliography == George, Binto; Carmichael, Gail (2021). Mathai, Susan (ed.). Artificial Intelligence Simplified: Understanding Basic Concepts (2nd ed.). CSTrends LLP. ISBN 9781944708047.
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{
"page_id": 66980419,
"source": null,
"title": "Artbreeder"
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The characteristic energy length scale χ {\displaystyle \chi } describes the size of the region from which energy flows to a rapidly moving crack. If material properties change within the characteristic energy length scale, local wave speeds can dominate crack dynamics. This can lead to supersonic fracture. == References ==
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"page_id": 2230854,
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"title": "Characteristic energy length scale"
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The Okinawa diet describes the traditional dietary practices of indigenous people of the Ryukyu Islands (belonging to Japan), which were claimed to have contributed to their relative longevity over a period of study in the 20th century. == Relative longevity == As assessed over 1949 to 1998, people from the Ryukyu Islands (of which Okinawa is the largest) had a life expectancy among the highest in the world (83.8 years vs. 78.9 years in the United States), although the male life expectancy rank among Japanese prefectures plummeted in the 21st century. Okinawa had the longest life expectancy in all prefectures of Japan for almost 30 years prior to 2000. The relative life expectancy of Okinawans has since declined, due to many factors including Westernization. In 2000, Okinawa dropped in its ranking for longevity advantage for men to 26th out of 47 within the prefectures of Japan. In 2015, Japan had the highest life expectancy of any country: 90 years for women and for men, 84 years. Although there are myriad factors that could account for differences in life expectancy, calorie restriction and regular physical activity could be factors. People have promoted the "Okinawa diet", despite the fact that the diet alone is unlikely to solely explain high life expectancy among seniors on Okinawa in the 20th century. == Indigenous islanders' diet == The traditional diet of the islanders contained sweet potato, green-leafy or root vegetables, and soy foods, such as miso soup, tofu or other soy preparations, occasionally served with small amounts of fish, noodles, or lean meats, all cooked with herbs, spices, and oil. Although the traditional Japanese diet usually includes large quantities of rice, the traditional Okinawa diet consisted of smaller quantities of rice; instead the staple was sweet potato. The Okinawa diet had only 30% of the
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"page_id": 461383,
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sugar and 15% of the grains of the average Japanese dietary intake. Okinawan cuisine consists of smaller meal portions of green and yellow vegetables, soy and other legumes, relatively small amounts of rice compared to mainland Japan, as well as occasional fish and pork. The center of the Okinawan cuisine is the sweet potato. Not only is the sweet potato tuber used but so are the leaves from the plant. The leaves are used often in miso soup. In Okinawa, the bitter melon is called goya and is served in the national dish, gōyā chanpurū. === Food proportions === The dietary intake of Okinawans compared to other Japanese circa 1950 shows that Okinawans consumed: fewer total calories (1785 vs. 2068), less polyunsaturated fat (4.8% of calories vs. 8%), less rice (154g vs. 328g), significantly less wheat, barley and other grains (38g vs. 153g), less sugars (3g vs. 8g), more legumes (71g vs. 55g), significantly less fish (15g vs. 62g), significantly less meat and poultry (3g vs. 11g), less eggs (1g vs. 7g), less dairy (<1g vs. 8g), much more sweet potatoes (849g vs. 66g), less other potatoes (2g vs. 47g), less fruit (<1g vs. 44g), and no pickled vegetables (0g vs. 42g). As proportions of total caloric intake, foods in the traditional Okinawa diet included sweet potato (69%), rice (12%), other grains (7%), legumes including soy (6%), green and yellow vegetables (3%), refined oils (2%), fish (1%) and seaweed, meat (mostly pork), refined sugars, potato, egg, nuts and seeds, dairy and fruit (all <1%). Specifically, the Okinawans circa 1950 ate sweet potatoes for 849 grams of the total 1262 grams of food that they consumed, which constituted 69% of their total daily calories. The traditional Okinawan diet as described above was widely practiced on the islands until about the 1960s.
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"page_id": 461383,
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Since then, dietary practices shifted towards Western and mainland Japanese patterns, with fat intake rising from about 6% to 27% of total caloric intake and the sweet potato being supplanted with rice and bread. Another low-calorie staple in Okinawa was seaweed, particularly, konbu or kombu. This plant, like much of the greenery from the island, is rich in protein, amino acids and minerals such as iodine. Another seaweed commonly eaten was wakame, which is rich in minerals like iodine, magnesium and calcium. Seaweed and tofu in one form or other were eaten on a daily basis. Okinawans ate three grams total of meat – including pork and poultry – per day, substantially less than the 11-gram average of Japanese as a whole in 1950. The pig's feet, ears, and stomach were considered as everyday foodstuffs. In 1979 after many years of Westernization, the quantity of pork consumption per person a year in Okinawa was 7.9 kg (17 lb), exceeding by about 50% that of the Japanese national average. === Okinawan health === In addition to their relative longevity identified in the mid-20th century, islanders were noted for their low mortality from cardiovascular disease and certain types of cancers. One study compared age-adjusted mortality of Okinawans versus Americans and found that, during 1995, an average Okinawan was 8 times less likely to die from coronary artery disease, 7 times less likely to die from prostate cancer, 6.5 times less likely to die from breast cancer, and 2.5 times less likely to die from colon cancer than an average American of the same age, though more than 10% of the Okinawans suffered from cheilosis from a low consumption of vitamin B2. Delayed menstruation and deficient lactation were also relatively frequent at 9% and almost 18% due to low caloric intake and/or low
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"page_id": 461383,
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"title": "Okinawa diet"
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body fat levels in women. In the 21st century, the shifting dietary trend coincided with a decrease in longevity, where Okinawans actually developed a lower life expectancy than the Japanese average. Overall, the traditional Okinawa diet led to little weight gain with age, low body mass index throughout life, and low risk from age-related disease. No ingredients or foods of any kind have been scientifically shown to possess antiaging properties. == Research == In the 1972 Japan National Nutrition Survey, it was determined that Okinawan adults consumed 83% of what Japanese adults did and that Okinawan children consumed 62% of what Japanese children consumed. Since the early 2000s, the difference in life expectancy between Okinawan and mainland Japanese decreased, possibly due to Westernization and erosion of the traditional diet. The spread of primarily American fast-food chains was linked with an increase in cardiovascular diseases, much like the ones noted in Japanese migrants to the United States. == Culture and customs == Okinawa and Japan have food-centered cultures. Festivities often include food or are food-based. Moreover, the food tends to be seasonal, fresh and raw. Portion sizes are small and meals are brought out in stages that starts with appetizers, many main courses including sashimi (raw fish) and suimono (soup), sweets and tea. The food culture and presentation is preserved, passing low-calorie food from generation to generation. == See also == Calorie restriction Hara hachi bun me List of diets Okinawan cuisine Mediterranean diet == References == == Bibliography == Albala, Ken, ed. (2011). Food cultures of the world encyclopedia. Santa Barbara, Calif.: Greenwood. ISBN 9780313376276.
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In chemistry, an onium ion is a cation formally obtained by the protonation of mononuclear parent hydride of a pnictogen (group 15 of the periodic table), chalcogen (group 16), or halogen (group 17). The oldest-known onium ion, and the namesake for the class, is ammonium, NH+4, the protonated derivative of ammonia, NH3. The name onium is also used for cations that would result from the substitution of hydrogen atoms in those ions by other groups, such as organic groups, or halogens; such as tetraphenylphosphonium, (C6H5)4P+. The substituent groups may be divalent or trivalent, yielding ions such as iminium and nitrilium. A simple onium ion has a charge of +1. A larger ion that has two onium ion subgroups is called a double onium ion, and has a charge of +2. A triple onium ion has a charge of +3, and so on. Compounds of an onium cation and some other anion are known as onium compounds or onium salts. Onium ions and onium compounds are inversely analogous to -ate ions and ate complexes: Lewis bases form onium ions when the central atom gains one more bond and becomes a positive cation. Lewis acids form -ate ions when the central atom gains one more bond and becomes a negative anion. == Simple onium cations (hydrides with no substitutions) == === Group 13 (boron group) onium cations === boronium cation, BH+4 (protonated borane) further boronium cations, BxH+y (protonated boranes) === Group 14 (carbon group) onium cations === carbonium ions (protonated hydrocarbons) have a pentacoordinated carbon atom with a +1 charge. alkanium cations, CnH+2n+3 (protonated alkanes) methanium, CH+5 (protonated methane) (Sometimes called carbonium, because it is the simplest member of that class, but that use is deprecated because of multiple definitions. Sometimes called methonium, but methonium also has multiple definitions. Abundant in outer
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space.) ethanium, C2H+7 (protonated ethane) propanium, C3H+9 (propane protonated on an unspecified carbon) propylium, or propan-1-ylium (propane protonated on an end carbon) propan-2-ylium (propane protonated on the middle carbon) butanium, C4H+11 (butane protonated on an unspecified carbon) n-butanium (n-butane protonated on an unspecified carbon) n-butylium, or n-butan-1-ylium (n-butane protonated on an end carbon) n-butan-2-ylium (n-butane protonated on a middle carbon) isobutanium (isobutane protonated on an unspecified carbon) isobutylium, or isobutan-1-ylium (isobutane protonated on an end carbon) isobutan-2-ylium (isobutane protonated on the middle carbon) octonium or octanium, C8H+19 (protonated octane) silanium (sometimes silonium), SiH+5 (protonated silane) (should not be called siliconium disilanium, Si2H+7 (protonated disilane) further silanium cations, SinH+2n+3 (protonated silanes) germonium, GeH+5 (protonated germane) stannonium, SnH+3 (protonated SnH2) (not protonated stannane SnH4) plumbonium, PbH+3 (protonated PbH2) (not protonated plumbane PbH4) flerovonium, FlH+3 (protonated FlH2) (not protonated flerovane FlH4) === Group 15 (pnictogen) onium cations === ammonium (IUPAC name azanium), NH+4 (protonated ammonia (IUPAC name azane)) phosphonium, PH+4 (protonated phosphine) arsonium, AsH+4 (protonated arsine) stibonium, SbH+4 (protonated stibine) bismuthonium, BiH+4 (protonated bismuthine) moscovonium, McH+4 (protonated moscovine) === Group 16 (chalcogen) onium cations === oxonium, H3O+ (protonated water (IUPAC name oxidane). Oxonium is better known as hydronium, though hydronium implies a solvated or hydrated proton. It may also be called hydroxonium.) sulfonium, H3S+ (protonated hydrogen sulfide) selenonium, H3Se+ (protonated hydrogen selenide) telluronium, H3Te+ (protonated hydrogen telluride) polononium, H3Po+ (protonated hydrogen polonide) livermoronium, H3Lv+ (protonated hydrogen livermoride) === Hydrogen onium cation === hydrogenonium, better known as trihydrogen cation, H+3 (protonated molecular or diatomic hydrogen), found in ionized hydrogen and interstellar space === Group 17 (halogen) onium cations, halonium ions, H2X+ (protonated hydrogen halides) === fluoronium, H2F+ (protonated hydrogen fluoride) chloronium, H2Cl+ (protonated hydrogen chloride) bromonium, H2Br+ (protonated hydrogen bromide) iodonium, H2I+ (protonated hydrogen iodide) astatonium, H2At+ (protonated hydrogen astatide) tennessonium, H2Ts+ (protonated hydrogen
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tennesside) ==== Pseudohalogen onium cations ==== aminodiazonium, [H2N=N=N]+ ⇌ [H2N−N≡N]+ (protonated hydrogen azide) methylidyneammonium and hydrocyanonium, H2CN+, isomers HC≡NH+ ⇌ N≡CH+2 (protonated hydrogen cyanide) === Group 18 (noble gas) onium cations === hydrohelium or helonium, better known as helium hydride ion, HeH+ (protonated helium) neonium, NeH+ (protonated neon) argonium, ArH+ (protonated argon) kryptonium, KrH+ (protonated krypton) xenonium, XeH+ (protonated xenon) radonium, RnH+ (protonated radon) oganessonium OgH+ (protonated oganesson) == Onium cations with monovalent substitutions == primary ammonium cations, RH3N+ or R−NH+3 (protonated primary amines) hydroxylammonium, H3N+−OH (protonated hydroxylamine) methylammonium, CH3NH+3 (protonated methylamine) ethylammonium, CH3CH2NH+3 (protonated ethylamine) hydrazinium, or diazanium, H2N−NH+3 (protonated hydrazine, a.k.a. diazane) anilinium (a.k.a. phenylammonium), C6H5−NH+3 (protonated aniline, a.k.a. phenylamine, aminobenzene) secondary ammonium cations, R2NH+2 (protonated secondary amines) dimethylammonium (sometimes dimethylaminium), (CH3)2NH+2 (protonated dimethylamine) diethylammonium (sometimes diethylaminium), (CH3CH2)2NH+2 (protonated diethylamine) ethylmethylammonium, (CH3CH2)(CH3)NH+2 (protonated ethylmethylamine) diethanolammonium (sometimes diethanolaminium), (OHCH2CH2)2NH+2 (protonated diethanolamine) tertiary ammonium cations, R3NH+ (protonated tertiary amines) trimethylammonium (CH3)3NH+ (protonated trimethylamine) triethylammonium (CH3CH2)3NH+ (protonated triethylamine) quaternary ammonium cations, R4N+ or NR+4 tetrafluoroammonium, NF+4 tetramethylammonium, (CH3)4N+ tetraethylammonium, (CH3CH2)4N+ tetrapropylammonium, (CH3(CH2)2)4N+ tetrabutylammonium, (CH3(CH2)3)4N+ or abbreviated Bu4N+ trimethyl ammonium compounds, (CH3)3RN+ didecyldimethylammonium, (CH3(CH2)9)2(CH3)2N+ pentamethylhydrazinium, (CH3)2N−N(CH3)+3 quaternary phosphonium cations, R4P+ or PR+4 tetraphenylphosphonium, (C6H5)4P+ quaternary arsonium cations, R4As+ or AsR+4 tetraphenylarsonium, (C6H5)4As+ quaternary stibonium cations, R4Sb+ or SbR+4 tetraphenylstibonium, (C6H5)4Sb+ primary oxonium cations, ROH+2 (protonated alcohols R−O−H) alkyloxonium cations ROH+2 (protonated alcohols) methyloxonium, CH3OH+2 (protonated methanol) ethyloxonium, CH3CH2OH+2 (protonated ethanol) dioxidanonium (hydroxylhydronium), HO−OH+2 (protonated hydrogen peroxide) secondary oxonium cations, R2OH+ (protonated ethers R−O−R) dialkyloxonium cations (protonated ethers) dimethyloxonium, (CH3)2OH+ (protonated dimethyl ether) tertiary oxonium cations, R3O+ trifluorooxonium, OF+3 (hypothetical) trimethyloxonium, (CH3)3O+ triethyloxonium, (CH3CH2)3O+ oxatriquinacene, C9H9O+ (cyclic oxonium ion) oxatriquinane, C9H15O+ (cyclic oxonium ion) primary sulfonium cations, RSH+2 (protonated thiols R−S−H) secondary sulfonium cations, R2SH+ (protonated thioethers R−S−R) dimethylsulfonium, (CH3)2SH+ (protonated dimethyl sulfide) tertiary sulfonium cations, R3S+ trimethylsulfonium, (CH3)3S+ tertiary selenonium cations, R3Se+
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"title": "Onium ion"
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triphenylselenonium, (C6H5)3Se+ tertiary telluronium cations, R3Te+ triphenyltelluronium, (C6H5)3Te+ primary fluoronium cations, RFH+ (protonated fluorides RF) secondary fluoronium cations, R2F+ dichlorofluoronium, Cl2F+ secondary iodonium cations, R2I+ diphenyliodonium, (C6H5)2I+ == Onium cations with polyvalent substitutions == secondary ammonium cations having one double-bonded substitution, R=NH+2 diazenium, HN=NH+2 (protonated diazene) guanidinium, C(NH2)+3 (protonated guanidine) (has a resonance structure and a planar molecular geometry) tertiary ammonium cations having one triple-bonded substitution, R≡NH+ nitrilium, R−C≡NH+ (protonated nitrile) diazonium or diazynium, N≡NH+ (protonated nitrogen, in other words, protonated diazyne) cyclic tertiary ammonium cations where nitrogen is a member of a ring, RNH+R (the ring may be aromatic) pyridinium, C5H5NH+ (protonated pyridine) quaternary ammonium cations having one double-bonded substitution and two single-bonded substitutions, R=NR+2 iminium, R2C=NR+2 (substituted protonated imine) diazenium, RN=NR+2 (substituted protonated diazene) thiazolium, [C3NSR4]+(substituted protonated thiazole) quaternary ammonium cations having two double-bonded substitutions, R=N+=R nitronium, [NO2]+ bis(triphenylphosphine)iminium, ((C6H5)3P=)2N+ quaternary ammonium cations having one triple-bonded substitution and one single-bonded substitution, R≡NR+ diazonium, N≡NR+ (substituted protonated nitrogen, in other words, substituted protonated diazyne) nitrilium, RC≡NR+ (substituted protonated nitrile) tertiary oxonium cations having one triple-bonded substitution, R≡O+ acylium ions, R−C≡O+ ↔ R−C+=O nitrosonium, N≡O+ cyclic tertiary oxonium cations where oxygen is a member of a ring, RO+R (the ring may be aromatic) pyrylium, C5H5O+ tertiary sulfonium cations having one triple-bonded substitution, R≡S+ thionitrosyl, N≡S+ dihydroxyoxoammonium, [H2NO3]+ (protonated nitric acid) trihydroxyoxosulfonium, [H3SO4]+ (protonated sulfuric acid) == Double onium dications == hydrazinediium or hydrazinium(2+) dication, H3N+−+NH3 (doubly protonated hydrazine, in other words, doubly protonated diazane) diazenediium cation, H2N+=+NH2 (doubly protonated diazene) diazynediium cation, HN+≡+NH (doubly protonated dinitrogen, in other words, doubly protonated diazyne) == Enium cations == The extra bond is added to a less-common parent hydride, a carbene analog, typically named -ene or -ylene, which is neutral with 2 fewer bonds than the more-common hydride, typically named -ane or -ine.
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borenium cations, R2B+ (protonated borylenes a.k.a. boranylidenes) carbenium cations, R3C+ (protonated carbenes) have a tricoordinated carbon atom with a +1 charge. alkenium cations, CnH+2n+1 (n ≥ 2) (protonated alkenes) methenium cation, H3C+ (protonated methylene) ethenium, C2H+5 (protonated ethene) benzenium, C6H+7 (protonated benzene) tropylium, C7H+7 (protonated tropylidene) silylium cations, R3Si+ (protonated silylenes) nitrenium cations, R2N+ (protonated nitrenes) phosphinidenium cations, R2P+ (protonated phosphinidene) mercurinium cations, R3Hg+ (protonated organomercury compounds; formed as intermediates in oxymercuration reactions) === Substituted eniums === diphenylcarbenium, (C6H5)2CH+ (di-substituted methenium) triphenylcarbenium, (C6H5)3C+ (tri-substituted methenium) == Ynium cations == carbynium ions (protonated carbynes) have a carbon atom with a +1 charge. alkynium cations, CnH+2n-1 (n ≥ 2) (protonated alkynes) methynium cation, H2C+ (protonated methylidyne radical) ethynium, C2H+3 (protonated ethyne) == See also == Carbonium ion Lyonium ion, a protonated solvent molecule Lyate ion, a deprotonated solvent molecule == References == == External links == Ions and Radicals, Queen Mary University of London Onium compounds at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
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An Ellingham diagram is a graph showing the temperature dependence of the stability of compounds. This analysis is usually used to evaluate the ease of reduction of metal oxides and sulfides. These diagrams were first constructed by Harold Ellingham in 1944. In metallurgy, the Ellingham diagram is used to predict the equilibrium temperature between a metal, its oxide, and oxygen — and by extension, reactions of a metal with sulfur, nitrogen, and other non-metals. The diagrams are useful in predicting the conditions under which an ore will be reduced to its metal. The analysis is thermodynamic in nature and ignores reaction kinetics. Thus, processes that are predicted to be favourable by the Ellingham diagram can still be slow. == Thermodynamics == Ellingham diagrams are a particular graphical form of the principle that the thermodynamic feasibility of a reaction depends on the sign of ΔG, the Gibbs free energy change, which is equal to ΔH − TΔS, where ΔH is the enthalpy change and ΔS is the entropy change. The Ellingham diagram plots the Gibbs free energy change (ΔG) for each oxidation reaction as a function of temperature. For comparison of different reactions, all values of ΔG refer to the reaction of the same quantity of oxygen, chosen as one mole O (1⁄2 mol O2) by some authors and one mole O2 by others. The diagram shown refers to 1 mole O2, so that e.g. the line for the oxidation of chromium shows ΔG for the reaction 4⁄3 Cr(s) + O2(g) → 2⁄3 Cr2O3(s), which is 2⁄3 of the molar Gibbs energy of formation ΔGf°(Cr2O3, s). In the temperature ranges commonly used, the metal and the oxide are in a condensed state (solid or liquid), and oxygen is a gas with a much larger molar entropy. For the oxidation of each
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"page_id": 3738185,
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metal, the dominant contribution to the entropy change (ΔS) is the removal of 1⁄2 mol O2, so that ΔS is negative and roughly equal for all metals. The slope of the plots d Δ G / d T = − Δ S {\displaystyle d\Delta G/dT=-\Delta S} is therefore positive for all metals, with ΔG always becoming more negative with lower temperature, and the lines for all the metal oxides are approximately parallel. Since these reactions are exothermic, they always become feasible at lower temperatures. At a sufficiently high temperature, the sign of ΔG may invert (becoming positive) and the oxide can spontaneously reduce to the metal, as shown for Ag and Cu. For oxidation of carbon, the red line is for the formation of CO: C(s) + 1⁄2 O2(g) → CO(g) with an increase in the number of moles of gas, leading to a positive ΔS and a negative slope. The blue line for the formation of CO2 is approximately horizontal, since the reaction C(s) + O2(g) → CO2(g) leaves the number of moles of gas unchanged so that ΔS is small. As with any chemical reaction prediction based on purely thermodynamic grounds, a spontaneous reaction may be very slow if one or more stages in the reaction pathway have very high activation energies EA. If two metals are present, two equilibria have to be considered. The oxide with the more negative ΔG will be formed and the other oxide will be reduced. == Diagram features == Curves in the Ellingham diagrams for the formation of metallic oxides are basically straight lines with a positive slope. The slope is proportional to ΔS, which is approximately constant with temperature. The lower the position of a metal's line in the Ellingham diagram, the greater is the stability of its oxide.
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For example, the line for Al (oxidation of aluminium) is found to be below that for Fe (formation of Fe2O3) meaning that aluminium oxide is more stable than iron(III) oxide. Stability of metallic oxides decreases with increase in temperature. Highly unstable oxides like Ag2O and HgO easily undergo thermal decomposition. The formation free energy of carbon dioxide (CO2) is almost independent of temperature, while that of carbon monoxide (CO) has negative slope and crosses the CO2 line near 700 °C. According to the Boudouard reaction, carbon monoxide is the dominant oxide of carbon at higher temperatures (above about 700 °C), and the higher the temperature (above 700 °C) the more effective a reductant (reducing agent) carbon is. If the curves for two metals at a given temperature are compared, the metal with the lower Gibbs free energy of oxidation on the diagram will reduce the oxide with the higher Gibbs free energy of formation. For example, metallic aluminium can reduce iron oxide to metallic iron, the aluminium itself being oxidized to aluminium oxide. (This reaction is employed in thermite.) The greater the gap between any two lines, the greater the effectiveness of the reducing agent corresponding to the lower line. The intersection of two lines implies an oxidation-reduction equilibrium. Reduction using a given reductant is possible at temperatures above the intersection point where the ΔG line of that reductant is lower on the diagram than that of the metallic oxide to be reduced. At the point of intersection the free energy change for the reaction is zero, below this temperature it is positive and the metallic oxide is stable in the presence of the reductant, while above the point of intersection the Gibbs energy is negative and the oxide can be reduced. === Reducing agents === In industrial processes, the
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reduction of metal oxides is often effected by a carbothermic reaction, using carbon as a reducing agent. Carbon is available cheaply as coal, which can be rendered to coke. When carbon reacts with oxygen it forms the gaseous oxides carbon monoxide and carbon dioxide, so the thermodynamics of its oxidation is different from that for metals: its oxidation has a more negative ΔG with the higher temperatures (above 700 °C). Carbon can thus serve as reducing agent. Using this property, reduction of metals may be performed as a double redox reaction at relatively low temperature. For example the minimum temperature for which ZnO can be reduced by C is 1000°C. The reaction is as follows ZnO+C→Zn+CO == Use of Ellingham diagrams == The main application of Ellingham diagrams is in the extractive metallurgy industry, where it helps to select the best reducing agent for various ores in the extraction process, purification and grade setting for steel manufacturing. It also helps to guide the purification of metals, especially the removal of trace elements. The direct reduction process for making iron rests firmly on the guidance of Ellingham diagrams, which show that hydrogen by itself can reduce iron oxides to the metal. === Reducing agent for haematite === In iron ore smelting, haematite gets reduced at the top of the furnace, where temperature is in the range 600 – 700 °C. The Ellingham diagram indicates that in this range carbon monoxide acts as a stronger reducing agent than carbon since the process 2 CO + O2 → 2 CO2 has a more-negative free energy change than the process: 2 C + O2 → 2 CO. In the upper part of the blast furnace, haematite is reduced by CO (produced by oxidation of coke lower down at the bottom of blast furnace, at
|
{
"page_id": 3738185,
"source": null,
"title": "Ellingham diagram"
}
|
higher temperature) even in the presence of carbon – though this is mainly because the kinetics for gaseous CO reacting with the ore are better. === Reducing agent for chromic oxide—carbon cannot be used === The Ellingham curve for the reaction 2C(s) + O2(g) → 2CO(g) slopes down and falls below the curves for all the metals. Hence, carbon can normally act as a reducing agent for all metal oxides at very high temperatures. But chromium formed at these temperatures reacts with carbon to form its carbide, which gives undesirable properties to the chromium metal obtained. Hence, for high temperature reduction of chromic oxide, carbon cannot be used. === Aluminothermic process === The Ellingham curve for aluminium lies below the curves of most metals such as chromium, iron, etc. This fact indicates that aluminium can be used as the reducing agent for oxides of all these metals. This result is illustrated as follows: The free energies of formation of chromium(III) oxide and aluminium oxide per mole of oxygen consumed are -541 kJ and -827 kJ respectively. The processes are: The second equation minus the first equation gives: Δ G 0 = − 287 kJ {\displaystyle {\ce {\Delta G^0 = -287 kJ}}} So aluminium oxide is more stable than chromium oxide (at least at normal temperatures, and in fact all the way up to the decomposition temperatures of the oxides). Since the Gibbs free energy change is negative, aluminium can reduce chromium oxide. In pyrometallurgy, aluminium is used as a reducing agent in the aluminothermic process, also known as the thermite reaction, to extract chromium and manganese by reduction of their oxides. == Extensions to other gas-phase reactions == The concept of plotting the free energies of reaction of various elements with a given gas-phase reactant may be extended beyond oxidation
|
{
"page_id": 3738185,
"source": null,
"title": "Ellingham diagram"
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|
reactions. The original paper by Ellingham explicitly to the reduction of both oxygen and sulfur by metallurgical processes, and anticipated the use of such diagrams for other compounds, including chlorides, carbides, and sulfates. The concept is generally useful for studying the comparative stability of compounds across a range of partial pressures and temperatures. The construction of an Ellingham diagram is especially useful when studying the stability of compounds in the presence of a reductant. Ellingham diagrams are now available for bromides, chlorides, fluorides, hydrides, iodides, nitrides, oxides, sulfides, selenides, and tellurides. == References == == External links == Interactive Ellingham diagrams Archived 2007-10-24 at the Wayback Machine at San José State University Ellingham diagram tutorial and interactive diagram (University of Cambridge)
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{
"page_id": 3738185,
"source": null,
"title": "Ellingham diagram"
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Myzocytosis (from Greek: myzein, (μυζεῖν) meaning "to suck" and kytos (κύτος) meaning "container", hence referring to "cell") is a method of feeding found in some heterotrophic organisms. It is also called "cellular vampirism" as the predatory cell pierces the cell wall and/or cell membrane of the prey cell with a feeding tube, the conoid, sucks out the cellular content and digests it. Myzocytosis is found in Myzozoa and also in some species of Ciliophora (both comprise the alveolates). A classic example of myzocytosis is the feeding method of the infamous predatory ciliate, Didinium, where it is often depicted devouring a hapless Paramecium. The suctorian ciliates were originally thought to have fed exclusively through myzocytosis, sucking out the cytoplasm of prey via superficially drinking straw-like pseudopodia. It is now understood that suctorians do not feed through myzocytosis, but actually, instead, manipulate and envenomate captured prey with their tentacle-like pseudopodia. == References == == Further reading == Eva C. M. Nowack and Michael Melkonian (2010) Endosymbiotic associations within protists Phil. Trans. R. Soc. B 12 March 2010 vol. 365 no. 1541 699-712
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{
"page_id": 2755147,
"source": null,
"title": "Myzocytosis"
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A direct acoustic cochlear implant - also DACI - is an acoustic implant which converts sound in mechanical vibrations that stimulate directly the perilymph inside the cochlea. The hearing function of the external and middle ear is being taken over by a little motor of a cochlear implant, directly stimulating the cochlea. With a DACI, people with no or almost no residual hearing but with a still functioning inner ear, can again perceive speech, sounds and music. DACI is an official product category, as indicated by the nomenclature of GMDN. A DACI tries to provide an answer for people with hearing problems for which no solution exists today. People with some problems at the level of the cochlea can be helped with a hearing aid. A hearing aid will absorb the incoming sound from a microphone, and offer enhanced through the natural way. For larger reinforcements, this may cause problems with feedback and distortion. A hearing aid also simply provides more loudness, no more resolution. Users will view this often as, "all sounds louder, but I understand nothing more than before." Once a hearing aid offers no solution anymore, one can switch to a cochlear implant. A Cochlear implant captures the sound and sends it electrically, through the cochlea, to the auditory nerve. In this way, completely deaf patients can perceive sounds again. However, As soon as there are problems not only at the level of the cochlea, but also in the middle ear (the so-called conductive losses), then there are more efficient ways to get sound to the partially functioning cochlea. The most obvious solution is a BAHA, which brings the sound to the cochlea via bone conduction. However, patients who have both problems with the cochlea, as with the middle ear (i.e. patients with mixed losses), none of
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{
"page_id": 39914061,
"source": null,
"title": "Direct acoustic cochlear implant"
}
|
the above solutions is ideal. To this end, the direct acoustic cochlear implant was developed. A DACI brings the sound directly to the cochlea, and provides the most natural way of sound amplification. == History == The first DACI was implanted in Hannover. In Belgium, the first DACI was implanted at the Catholic University Hospital of Leuven. In the Netherlands, the Radboud clinic in Nijmegen was the first while in Poland it was first implanted at the Institute of Physiology and Pathology of Hearing in Warsaw. == See also == BAHA Hearing Cochlear implant == References == == External links == DACI in the Netherlands DACI in Belgium DACI in Poland
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{
"page_id": 39914061,
"source": null,
"title": "Direct acoustic cochlear implant"
}
|
TK is an experimental cell therapy which may be used to treat high-risk leukemia. It is currently undergoing a Phase III clinical trial to determine efficacy and clinical usefulness. TK is currently being investigated in patients with acute leukemia in first or subsequent complete remission and at high risk of relapse or in patients with relapsed disease who are candidates for haploidentical transplantation of hemopoietic stem cells (taken from a partially HLA-compatible family donor). == Research == TK is a cellular therapy based on the genetical engineering of donor T lymphocytes in order to express a suicide gene (thymidine kinase of the Herpes simplex virus, namely TK). Once the lymphocytes donated by partially compatible family donors (haplo-transplant) have been genetically modified, they can be infused in patients in need of hematopoietic cell transplantation. The infusion of lymphocytes expressing the TK suicide gene, has the aim to prevent or treat leukemic relapse and promote immune reconstitution, necessary to protect patients from infections that often limit transplant efficacy. The presence of TK allows for retention of immune protection and anti-leukaemic effects of donor T lymphocytes and at the same time to control and annul possible harmful reactions between these lymphocytes and healthy tissues of the patient, reaction known as graft-versus-host disease. Activation of the cell suicide system is obtained by the administration of ganciglovir, an antiviral drug, which only leads to the death of cells expressing TK in patients with graft-versus-host disease. TK has been granted Orphan Drug designation both in the EU and the United States. == References == == External links == Official website http://www.molmed.com/node/1866?language=en
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{
"page_id": 39782989,
"source": null,
"title": "TK cell therapy"
}
|
Atomic absorption spectroscopy (AAS) is a spectro-analytical procedure for the quantitative measurement of chemical elements. AAS is based on the absorption of light by free metallic ions that have been atomized from a sample. An alternative technique is atomic emission spectroscopy (AES). In analytical chemistry, the technique is used for determining the concentration of a particular element (the analyte) in a sample to be analyzed. AAS can be used to determine over 70 different elements in solution, or directly in solid samples via electrothermal vaporization, and is used in pharmacology, biophysics, archaeology and toxicology research. Atomic emission spectroscopy (AAS) was first used as an analytical technique, and the underlying principles were established in the second half of the 19th century by Robert Wilhelm Bunsen and Gustav Robert Kirchhoff, both professors at the University of Heidelberg, Germany. The modern form of AAS was largely developed during the 1950s by a team of Australian chemists. They were led by Sir Alan Walsh at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Chemical Physics, in Melbourne, Australia. == Instrumentation == In order to analyze a sample for its atomic constituents, it has to be atomized. The atomizers most commonly used nowadays are flames and electrothermal (graphite tube) atomizers. The atoms should then be irradiated by optical radiation, and the radiation source could be an element-specific line radiation source or a continuum radiation source. The radiation then passes through a monochromator in order to separate the element-specific radiation from any other radiation emitted by the radiation source, which is finally measured by a detector. === Atomizers === The atomizers most commonly used nowadays are spectroscopic flames and electrothermal atomizers. Other atomizers, such as glow-discharge atomization, hydride atomization, or cold-vapor atomization, might be used for special purposes. ==== Flame atomizers ==== The oldest
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{
"page_id": 2637,
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"title": "Atomic absorption spectroscopy"
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and most commonly used atomizers in AAS are flames, principally the air-acetylene flame with a temperature of about 2300 °C and the nitrous oxide system (N2O)-acetylene flame with a temperature of about 2700 °C. The latter flame, in addition, offers a more reducing environment, being ideally suited for analytes with a high affinity to oxygen. Liquid or dissolved samples are typically used with flame atomizers. The sample solution is aspirated by a pneumatic analytical nebulizer, transformed into an aerosol, which is introduced into a spray chamber, where it is mixed with the flame gases and conditioned in a way that only the finest aerosol droplets (< 10 μm) enter the flame. This conditioning process reduces interference, but only about 5% of the aerosolized solution reaches the flame because of it. On top of the spray chamber is a burner head that produces a flame that is laterally long (usually 5–10 cm) and only a few mm deep. The radiation beam passes through this flame at its longest axis, and the flame gas flow-rates may be adjusted to produce the highest concentration of free atoms. The burner height may also be adjusted so that the radiation beam passes through the zone of highest atom cloud density in the flame, resulting in the highest sensitivity. The processes in a flame include the stages of desolvation (drying) in which the solvent is evaporated and the dry sample nano-particles remain, vaporization (transfer to the gaseous phase) in which the solid particles are converted into gaseous molecule, atomization in which the molecules are dissociated into free atoms, and ionization where (depending on the ionization potential of the analyte atoms and the energy available in a particular flame) atoms may be in part converted to gaseous ions. Each of these stages includes the risk of interference
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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in case the degree of phase transfer is different for the analyte in the calibration standard and in the sample. Ionization is generally undesirable, as it reduces the number of atoms that are available for measurement, i.e., the sensitivity. In flame AAS, a steady-state signal is generated during the time period when the sample is aspirated. This technique is typically used for determinations in the mg L−1 range and may be extended down to a few μg L−1 for some elements. ==== Electrothermal atomizers ==== Electrothermal AAS (ET AAS) using graphite tube atomizers was pioneered by Boris V. L'vov at the Saint Petersburg Polytechnical Institute, Russia, since the late 1950s, and investigated in parallel by Hans Massmann at the Institute of Spectrochemistry and Applied Spectroscopy (ISAS) in Dortmund, Germany. Although a wide variety of graphite tube designs have been used over the years, the dimensions nowadays are typically 20–25 mm in length and 5–6 mm inner diameter. With this technique liquid/dissolved, solid, and gaseous samples may be analyzed directly. A measured volume (typically 10–50 μL) or a weighed mass (typically around 1 mg) of a solid sample are introduced into the graphite tube and subject to a temperature program. This typically consists of stages, such as drying – the solvent is evaporated; pyrolysis – the majority of the matrix constituents are removed; atomization – the analyte element is released to the gaseous phase; and cleaning – eventual residues in the graphite tube are removed at high temperature. The graphite tubes are heated via their ohmic resistance using a low-voltage high-current power supply; the temperature in the individual stages can be controlled very closely, and temperature ramps between the individual stages facilitate the separation of sample components. Tubes may be heated transversely or longitudinally, where the former ones have the advantage
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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of a more homogeneous temperature distribution over their length. The so-called stabilized temperature platform furnace (STPF) concept, proposed by Walter Slavin, based on research of Boris L'vov, makes ET AAS essentially free from interference. The major components of this concept are atomization of the sample from a graphite platform inserted into the graphite tube (L'vov platform) instead of from the tube wall in order to delay atomization until the gas phase in the atomizer has reached a stable temperature; use of a chemical modifier in order to stabilize the analyte to a pyrolysis temperature that is sufficient to remove the majority of the matrix components; and integration of the absorbance over the time of the transient absorption signal instead of using peak height absorbance for quantification. In ET AAS, a transient signal is generated, the area of which is directly proportional to the mass of analyte (not its concentration) introduced into the graphite tube. This technique has the advantage that any kind of sample, solid, liquid, or gaseous, can be analyzed directly. Its sensitivity is 2–3 orders of magnitude higher than that of flame AAS, so that determinations in the low μg L−1 range (for a typical sample volume of 20 μL) and ng g−1 range (for a typical sample mass of 1 mg) can be carried out. It shows a very high degree of freedom from interferences, so that ET AAS might be considered the most robust technique available nowadays for the determination of trace elements in complex matrices. ==== Specialized atomization techniques ==== While flame and electrothermal vaporizers are the most common atomization techniques, several other atomization methods are utilized for specialized use. ===== Glow-discharge atomization ===== A glow-discharge device (GD) serves as a versatile source, as it can simultaneously introduce and atomize the sample. The glow discharge
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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|
occurs in a low-pressure argon gas atmosphere between 1 and 10 torr. In this atmosphere lies a pair of electrodes applying a DC voltage of 250 to 1000 V to break down the argon gas into positively charged ions and electrons. These ions, under the influence of the electric field, are accelerated into the cathode surface containing the sample, bombarding the sample and causing neutral sample atom ejection through the process known as sputtering. The atomic vapor produced by this discharge is composed of ions, ground state atoms, and a fraction of excited atoms. When the excited atoms relax back into their ground state, a low-intensity glow is emitted, giving the technique its name. The requirement for samples of glow discharge atomizers is that they are electrical conductors. Consequently, atomizers are most commonly used in the analysis of metals and other conducting samples. However, with proper modifications, it can be utilized to analyze liquid samples as well as nonconducting materials by mixing them with a conductor (e.g. graphite). ===== Hydride atomization ===== Hydride generation techniques are specialized in solutions of specific elements. The technique provides a means of introducing samples containing arsenic, antimony, selenium, bismuth, and lead into an atomizer in the gas phase. With these elements, hydride atomization enhances detection limits by a factor of 10 to 100 compared to alternative methods. Hydride generation occurs by adding an acidified aqueous solution of the sample to a 1% aqueous solution of sodium borohydride, all of which is contained in a glass vessel. The volatile hydride generated by the reaction that occurs is swept into the atomization chamber by an inert gas, where it undergoes decomposition. This process forms an atomized form of the analyte, which can then be measured by absorption or emission spectrometry. ===== Cold-vapor atomization ===== The cold-vapor
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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|
technique is an atomization method limited only for the determination of mercury due to it being the only metallic element to have a large vapor pressure at ambient temperature. Because of this, it has an important use in determining organic mercury compounds in samples and their distribution in the environment. The method initiates by converting mercury into Hg2+ by oxidation from nitric and sulfuric acids, followed by a reduction of Hg2+ with tin(II) chloride. The mercury is then swept into a long-pass absorption tube by bubbling a stream of inert gas through the reaction mixture. The concentration is determined by measuring the absorbance of this gas at 253.7 nm. Detection limits for this technique are in the parts-per-billion range, making it an excellent mercury detection atomization method. === Radiation sources === We have to distinguish between line source AAS (LS AAS) and continuum source AAS (CS AAS). In classical LS AAS, as it has been proposed by Alan Walsh, the high spectral resolution required for AAS measurements is provided by the radiation source itself that emits the spectrum of the analyte in the form of lines that are narrower than the absorption lines. Continuum sources, such as deuterium lamps, are only used for background correction purposes. The advantage of this technique is that only a medium-resolution monochromator is necessary for measuring AAS; however, it has the disadvantage that usually a separate lamp is required for each element that has to be determined. In CS AAS, in contrast, a single lamp, emitting a continuum spectrum over the entire spectral range of interest is used for all elements. Obviously, a high-resolution monochromator is required for this technique, as will be discussed later. ==== Hollow cathode lamps ==== Hollow cathode lamps (HCL) are the most common radiation source in LS AAS. Inside the
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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sealed lamp, filled with argon or neon gas at low pressure, is a cylindrical metal cathode containing the element of interest and an anode. A high voltage is applied across the anode and cathode, resulting in an ionization of the fill gas. The gas ions are accelerated towards the cathode and, upon impact on the cathode, sputter cathode material that is excited in the glow discharge to emit the radiation of the sputtered material, i.e., the element of interest. In the majority of cases single element lamps are used, where the cathode is pressed out of predominantly compounds of the target element. Multi-element lamps are available with combinations of compounds of the target elements pressed in the cathode. Multi element lamps produce slightly less sensitivity than single element lamps and the combinations of elements have to be selected carefully to avoid spectral interferences. Most multi-element lamps combine a handful of elements, e.g.: 2 - 8. Atomic Absorption Spectrometers can feature as few as 1-2 hollow cathode lamp positions or in automated multi-element spectrometers, a 8-12 lamp positions may be typically available. ==== Electrodeless discharge lamps ==== Electrodeless discharge lamps (EDL) contain a small quantity of the analyte as a metal or a salt in a quartz bulb together with an inert gas, typically argon gas, at low pressure. The bulb is inserted into a coil that is generating an electromagnetic radio frequency field, resulting in a low-pressure inductively coupled discharge in the lamp. The emission from an EDL is higher than that from an HCL, and the line width is generally narrower, but EDLs need a separate power supply and might need a longer time to stabilize. ==== Deuterium lamps ==== Deuterium HCL or even hydrogen HCL and deuterium discharge lamps are used in LS AAS for background correction purposes.
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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The radiation intensity emitted by these lamps decreases significantly with increasing wavelength, so that they can be only used in the wavelength range between 190 and about 320 nm. ==== Continuum sources ==== When a continuum radiation source is used for AAS, it is necessary to use a high-resolution monochromator, as will be discussed later. In addition, it is necessary that the lamp emits radiation of intensity at least an order of magnitude above that of a typical HCL over the entire wavelength range from 190 nm to 900 nm. A special high-pressure xenon short arc lamp, operating in a hot-spot mode has been developed to fulfill these requirements. === Spectrometer === As already pointed out above, there is a difference between medium-resolution spectrometers that are used for LS AAS and high-resolution spectrometers that are designed for CS AAS. The spectrometer includes the spectral sorting device (monochromator) and the detector. ==== Spectrometers for LS AAS ==== In LS AAS, the high resolution that is required for the measurement of atomic absorption is provided by the narrow line emission of the radiation source, and the monochromator simply has to resolve the analytical line from other radiation emitted by the lamp. This can usually be accomplished with a band pass between 0.2 and 2 nm, i.e., a medium-resolution monochromator. Another feature to make LS AAS element-specific is modulation of the primary radiation and the use of a selective amplifier that is tuned to the same modulation frequency, as already postulated by Alan Walsh. This way any (unmodulated) radiation emitted for example by the atomizer can be excluded, which is imperative for LS AAS. Simple monochromators of the Littrow or (better) the Czerny-Turner design are typically used for LS AAS. Photomultiplier tubes are the most frequently used detectors in LS AAS, although solid
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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|
state detectors might be preferred because of their better signal-to-noise ratio. ==== Spectrometers for CS AAS ==== When a continuum radiation source is used for AAS measurement it is indispensable to work with a high-resolution monochromator. The resolution has to be equal to or better than the half-width of an atomic absorption line (about 2 pm) in order to avoid losses of sensitivity and linearity of the calibration graph. The research with high-resolution (HR) CS AAS was pioneered by the groups of O'Haver and Harnly in the US, who also developed the (up until now) only simultaneous multi-element spectrometer for this technique. The breakthrough, however, came when the group of Becker-Ross in Berlin, Germany, built a spectrometer entirely designed for HR-CS AAS. The first commercial equipment for HR-CS AAS was introduced by Analytik Jena (Jena, Germany) at the beginning of the 21st century, based on the design proposed by Becker-Ross and Florek. These spectrometers use a compact double monochromator with a prism pre-monochromator and an echelle grating monochromator for high resolution. A linear charge-coupled device (CCD) array with 200 pixels is used as the detector. The second monochromator does not have an exit slit; hence the spectral environment at both sides of the analytical line becomes visible at high resolution. As typically only 3–5 pixels are used to measure the atomic absorption, the other pixels are available for correction purposes. One of these corrections is that for lamp flicker noise, which is independent of wavelength, resulting in measurements with very low noise level; other corrections are those for background absorption, as will be discussed later. == Background absorption and background correction == The relatively small number of atomic absorption lines (compared to atomic emission lines) and their narrow width (a few pm) make spectral overlap rare; there are only few
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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examples known that an absorption line from one element will overlap with another. Molecular absorption, in contrast, is much broader, so that it is more likely that some molecular absorption band will overlap with an atomic line. This kind of absorption might be caused by un-dissociated molecules of concomitant elements of the sample or by flame gases. We have to distinguish between the spectra of di-atomic molecules, which exhibit a pronounced fine structure, and those of larger (usually tri-atomic) molecules that don't show such fine structure. Another source of background absorption, particularly in ET AAS, is scattering of the primary radiation at particles that are generated in the atomization stage, when the matrix could not be removed sufficiently in the pyrolysis stage. All these phenomena, molecular absorption and radiation scattering, can result in artificially high absorption and an improperly high (erroneous) calculation for the concentration or mass of the analyte in the sample. There are several techniques available to correct for background absorption, and they are significantly different for LS AAS and HR-CS AAS. === Background correction techniques in LS AAS === In LS AAS background absorption can only be corrected using instrumental techniques, and all of them are based on two sequential measurements: firstly, total absorption (atomic plus background), secondly, background absorption only. The difference of the two measurements gives the net atomic absorption. Because of this, and because of the use of additional devices in the spectrometer, the signal-to-noise ratio of background-corrected signals is always significantly inferior compared to uncorrected signals. It should also be pointed out that in LS AAS there is no way to correct for (the rare case of) a direct overlap of two atomic lines. In essence, there are three techniques used for background correction in LS AAS: ==== Deuterium background correction ==== This
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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|
is the oldest and still most commonly used technique, particularly for flame AAS. In this case, a separate source (a deuterium lamp) with broad emission is used to measure the background absorption over the entire width of the exit slit of the spectrometer. The use of a separate lamp makes this technique the least accurate one, as it cannot correct for any structured background. It also cannot be used at wavelengths above about 320 nm, as the emission intensity of the deuterium lamp becomes very weak. The use of deuterium HCL is preferable compared to an arc lamp due to the better fit of the image of the former lamp with that of the analyte HCL. ==== Smith-Hieftje background correction ==== This technique (named after their inventors) is based on the line-broadening and self-reversal of emission lines from HCL when high current is applied. Total absorption is measured with normal lamp current, i.e., with a narrow emission line, and background absorption after application of a high-current pulse with the profile of the self-reversed line, which has little emission at the original wavelength, but strong emission on both sides of the analytical line. The advantage of this technique is that only one radiation source is used; among the disadvantages are that the high-current pulses reduce lamp lifetime, and that the technique can only be used for relatively volatile elements, as only those exhibit sufficient self-reversal to avoid dramatic loss of sensitivity. Another problem is that background is not measured at the same wavelength as total absorption, making the technique unsuitable for correcting structured background. ==== Zeeman-effect background correction ==== An alternating magnetic field is applied at the atomizer (graphite furnace) to split the absorption line into three components, the π component, which remains at the same position as the original absorption
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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line, and two σ components, which are moved to higher and lower wavelengths, respectively. Total absorption is measured without magnetic field and background absorption with the magnetic field on. The π component has to be removed in this case, e.g. using a polarizer, and the σ components do not overlap with the emission profile of the lamp, so that only the background absorption is measured. The advantages of this technique are that total and background absorption are measured with the same emission profile of the same lamp, so that any kind of background, including background with fine structure can be corrected accurately, unless the molecule responsible for the background is also affected by the magnetic field and using a chopper as a polariser reduces the signal to noise ratio. While the disadvantages are the increased complexity of the spectrometer and power supply needed for running the powerful magnet needed to split the absorption line. === Background correction techniques in HR-CS AAS === In HR-CS AAS background correction is carried out mathematically in the software using information from detector pixels that are not used for measuring atomic absorption; hence, in contrast to LS AAS, no additional components are required for background correction. ==== Background correction using correction pixels ==== It has already been mentioned that in HR-CS AAS lamp flicker noise is eliminated using correction pixels. In fact, any increase or decrease in radiation intensity that is observed to the same extent at all pixels chosen for correction is eliminated by the correction algorithm. This obviously also includes a reduction of the measured intensity due to radiation scattering or molecular absorption, which is corrected in the same way. As measurement of total and background absorption, and correction for the latter, are strictly simultaneous (in contrast to LS AAS), even the fastest
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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|
changes of background absorption, as they may be observed in ET AAS, do not cause any problem. In addition, as the same algorithm is used for background correction and elimination of lamp noise, the background corrected signals show a much better signal-to-noise ratio compared to the uncorrected signals, which is also in contrast to LS AAS. ==== Background correction using a least-squares algorithm ==== The above technique can obviously not correct for a background with fine structure, as in this case the absorbance will be different at each of the correction pixels. In this case, HR-CS AAS is offering the possibility to measure correction spectra of the molecule(s) that is (are) responsible for the background and store them in the computer. These spectra are then multiplied with a factor to match the intensity of the sample spectrum and subtracted pixel by pixel and spectrum by spectrum from the sample spectrum using a least-squares algorithm. This might sound complex, but first of all the number of di-atomic molecules that can exist at the temperatures of the atomizers used in AAS is relatively small, and second, the correction is performed by the computer within a few seconds. The same algorithm can actually also be used to correct for direct line overlap of two atomic absorption lines, making HR-CS AAS the only AAS technique that can correct for this kind of spectral interference. == See also == Absorption spectroscopy Beer–Lambert law Inductively coupled plasma mass spectrometry Laser absorption spectrometry == References == == Further reading == B. Welz, M. Sperling (1999), Atomic Absorption Spectrometry, Wiley-VCH, Weinheim, Germany, ISBN 3-527-28571-7. A. Walsh (1955), The application of atomic absorption spectra to chemical analysis, Spectrochim. Acta 7: 108–117. J.A.C. Broekaert (1998), Analytical Atomic Spectrometry with Flames and Plasmas, 3rd Edition, Wiley-VCH, Weinheim, Germany. B.V. L'vov (1984),
|
{
"page_id": 2637,
"source": null,
"title": "Atomic absorption spectroscopy"
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Twenty-five years of furnace atomic absorption spectroscopy, Spectrochim. Acta Part B, 39: 149–157. B.V. L'vov (2005), Fifty years of atomic absorption spectrometry; J. Anal. Chem., 60: 382–392. H. Massmann (1968), Vergleich von Atomabsorption und Atomfluoreszenz in der Graphitküvette, Spectrochim. Acta Part B, 23: 215–226. W. Slavin, D.C. Manning, G.R. Carnrick (1981), The stabilized temperature platform furnace, At. Spectrosc. 2: 137–145. B. Welz, H. Becker-Ross, S. Florek, U. Heitmann (2005), High-resolution Continuum Source AAS, Wiley-VCH, Weinheim, Germany, ISBN 3-527-30736-2. H. Becker-Ross, S. Florek, U. Heitmann, R. Weisse (1996), Influence of the spectral bandwidth of the spectrometer on the sensitivity using continuum source AAS, Fresenius J. Anal. Chem. 355: 300–303. J.M. Harnly (1986), Multi element atomic absorption with a continuum source, Anal. Chem. 58: 933A-943A. Skoog, Douglas (2007). Principles of Instrumental Analysis (6th ed.). Canada: Thomson Brooks/Cole. ISBN 0-495-01201-7. == External links == Media related to Atomic absorption spectroscopy at Wikimedia Commons
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Speculative evolution is a subgenre of science fiction and an artistic movement focused on hypothetical scenarios in the evolution of life, and a significant form of fictional biology. It is also known as speculative biology and it is referred to as speculative zoology in regards to hypothetical animals. Works incorporating speculative evolution may have entirely conceptual species that evolve on a planet other than Earth, or they may be an alternate history focused on an alternate evolution of terrestrial life. Speculative evolution is often considered hard science fiction because of its strong connection to and basis in science, particularly biology. Speculative evolution is a long-standing trope within science fiction, often recognized as beginning as such with H. G. Wells's 1895 novel The Time Machine, which featured several imaginary future creatures. Although small-scale speculative faunas were a hallmark of science fiction throughout the 20th century, ideas were only rarely well-developed, with some exceptions such as Stanley Weinbaum's Planetary series, Edgar Rice Burroughs's Barsoom, a fictional rendition of Mars and its ecosystem published through novels from 1912 to 1941, and Gerolf Steiner's Rhinogradentia, a fictional order of mammals created in 1957. The modern speculative evolution movement is generally agreed to have begun with the publication of Dougal Dixon's 1981 book After Man, which explored a fully realized future Earth with a complete ecosystem of over a hundred hypothetical animals. The success of After Man spawned several "sequels" by Dixon, focusing on different alternate and future scenarios. Dixon's work, like most similar works that came after them, were created with real biological principles in mind and were aimed at exploring real life processes, such as evolution and climate change, through the use of fictional examples. Speculative evolution's possible use as an educational and scientific tool has been noted and discussed through the decades
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following the publication of After Man. Speculative evolution can be useful in exploring and showcasing patterns present in the present and in the past. By extrapolating past trends into the future, scientists can research and predict the most likely scenarios of how certain organisms and lineages could respond to ecological changes. In some cases, attributes and creatures first imagined within speculative evolution have since been discovered. A filter feeder anomalocarid was illustrated by artist John Meszaros in the 2013 book All Your Yesterdays by John Conway, C. M. Kosemen and Darren Naish. In the year following publication, a taxonomic study proved the existence of the filter feeding anomalocarid Tamisiocaris. == History == === Early works === Explorations of hypothetical worlds featuring future, alternate or alien lifeforms is a long-standing trope in science fiction. One of the earliest works usually recognized as representing one of speculative evolution is H. G. Wells's science fiction novel The Time Machine, published in 1895. The Time Machine, set over eight hundred thousand years in the future, features post-human descendants in the form of the beautiful but weak Eloi and the brutish Morlocks. Further into the future, the protagonist of the book finds large crab-monsters and huge butterflies. Science fiction authors who wrote after Wells often used fictional creatures in the same vein, but most such imaginary faunas were small and not very developed. Edgar Rice Burroughs, who wrote in the early 20th century, can like Wells be considered an early speculative evolution author. Although his fictional ecosystems were still relatively small in scope, they were the settings of many of his novels and as such quite well-developed. In particular, Burroughs's Barsoom, a fictional version of the planet Mars which appeared in ten novels published from 1912 to 1941, featured a Martian ecosystem with a variety
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of alien creatures and several distinct Martian cultures and ethnic groups. Stanley Weinbaum's Planetary series also includes significantly conceptualized and developed alien life. Frederik Pohl wrote that before Weinbaum, science fiction's aliens "might be catmen, lizard-men, antmen, plantmen or rockmen; but they were, always and incurably, men. Weinbaum changed that. ... it was the difference in orientation – in drives, goals and thought processes – that made the Weinbaum-type alien so fresh and rewarding in science fiction in the mid-thirties." In 1930, Olaf Stapledon published a "future history", Last and First Men: A Story of the Near and Far Future, describing the history of humanity from the present onwards, across two billion years and eighteen human species, of which Homo sapiens is the first. Besides conventional environment-driven evolution -during which offshoots of humanity experienced both elevated and the total loss of sentience - the book anticipates the science of genetic engineering, and is an early instance of the fictional group mind idea. Published in 1957, German zoologist Gerolf Steiner's book Bau und Leben der Rhinogradentia (translated into English as The Snouters: The Form and Life of the Rhinogrades) described the fictional evolution, biology and behavior of an imaginary order of mammals, the Rhinogradentia or "rhinogrades". The Rhinogrades are characterized by a nose-like feature called a "nasorium", the form and function of which vary significantly between species, akin to Darwin's finches and their beak specialization. This diverse group of fictional animals inhabits a series of islands in which they have gradually evolved, radiating into most ecological niches. Satirical papers have been published continuing Steiner's imagined world. Although the work does feature an entire speculative ecosystem, its impact is dwarfed by the later works due to its limited scope, only exploring the life of an island archipelago. In 1976, the Italian author
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and illustrator Leo Lionni published Parallel Botany, a "field guide to imaginary plants", presented with academic-style mentions of genuine people and places. Parallel Botany has been compared to the 1972 book Invisible Cities by Italo Calvino, in which Marco Polo in a dialogue with Kublai Khan describes 55 cities, which, like Lionni's "parallel" plants, are "only as real as the mind's ability to conceptualize them". === Movement === One of the significant "founding" works of speculative evolution is After Man by Dougal Dixon, published in 1981. To this day, After Man is recognized as the first truly large-scale speculative evolution project involving a whole world and a vast array of species. Furthering its significance is the fact that the book was made very accessible by being published by mainstream publishers and being fully illustrated with color images. As such, After Man is often seen as having firmly established the idea of creating entire speculative worlds. Through the decades following After Man's publication, Dixon remained one of the sole authors of speculative evolution, publishing two more books in the same vein as After Man; The New Dinosaurs in 1988 and Man After Man in 1990. Dixon cited The Time Machine as his primary inspiration, being unaware of Steiner's work, and devised After Man as a popular-level book on the processes of evolution that instead of using the past to tell the story projected the processes into the future. A central idea of After Man, besides a wave of extinction following humans, is convergent evolution as new species bear a close resemblance to their unrelated predecessors. When designing the various animals of the book, Dixon looked at the different types of biomes on the planet and what adaptations animals living there have, designing new animals descended from modern day ones with the
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same set of adaptations. The success of After Man inspired Dixon to continue writing books that explained factual scientific processes through fictional examples. The New Dinosaurs was in essence a book about zoogeography, something the general public would be unfamiliar with, using a world in which the non-avian dinosaurs had not gone extinct. Man After Man, explored climate change over the course of the next few million years by showcasing its effects through the eyes of future human descendants. Today, many artists and writers work on speculative evolution projects online, often in the same vein as Dixon's works. Speculative evolution continues to endure a somewhat mainstream presence through films and TV shows featuring hypothetical and imaginary creatures, such as The Future is Wild (2002), Primeval (2007–2011), Avatar (2009), Terra Nova (2011), and Alien Worlds (2020). The modern explosion of speculative evolution has been termed by British paleontologist Darren Naish as the "Speculative Zoology Movement". == As an educational and scientific tool == Although primarily characterized as entertainment, speculative evolution can be used as educational tool to explain and illustrate real natural processes through using fictional and imaginary examples. The worlds created are often built on ecological and biological principles inferred from the real evolutionary history of life on Earth and readers can learn from them as such. For example, all of Dixon's speculative works are aimed at exploring real processes, with After Man exploring evolution, The New Dinosaurs zoogeography and both Man After Man and Greenworld (2010) exploring climate change, offering an environmental message. In some cases, speculative evolution artists have successfully predicted the existence of organisms that were later discovered to resemble something real. Many of the animals featured in Dixon's After Man are still considered plausible ideas, with some of them (such as specialized rodents and semi-aquatic primates)
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being reinforced with recent biology studies. A creature dubbed "Ceticaris", conceived by artist John Meszaros as a filter-feeding anomalocarid, was published in the 2013 book All Your Yesterdays, and in 2014, the actual Cambrian anomalocarid Tamisiocaris was discovered to have been a filter-feeder. In honor of Meszaros's prediction, Tamisiocaris was included in a new clade named the Cetiocaridae. Dougal Dixon's The New Dinosaurs was heavily influenced by paleontological ideas developing during its time, such as the ongoing dinosaur renaissance, and as such many of the dinosaurs in the book are energetic and active creatures rather than sluggish and lumbering. Dixon extrapolated on the ideas of paleontologists such as Robert Bakker and Gregory S. Paul when creating his creatures and also used patterns seen in the actual evolutionary history of the dinosaurs and pushing them to an extreme. Perhaps because of this, many of the animals in the book are similar to actual Mesozoic animals that were later discovered. Many of the dinosaurs in it are feathered, something not widely accepted at the time of its publication but seen as likely today. Similarly, After Man in 1981 represents a sort of time capsule of geological thought before global warming was fully discerned, but Dixon also portrays a sixth mass extinction or Anthropocene before it was commonplace to do so. Speculative evolution can be useful in exploring and showcasing patterns present in the present and in the past, and there is a useful aspect to hypothesizing on the form of future and alien life. By extrapolating past trends into the future, scientists could research and predict the most likely scenarios of how certain organisms and lineages could respond to ecological changes. As such, speculative evolution facilitates authors and artists to develop realistic hypotheses of the future. In some scientific fields, speculation is
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essential in understanding what is being studied. Paleontologists apply their own understanding of natural processes and biology to understand the appearances and lifestyles of extinct organisms that are discovered, varying in how far their speculation goes. For instance, All Yesterdays and its sequel All Your Yesterdays (2017) explores highly speculative renditions of real (and in some cases hypothetical) prehistoric animals that do not explicitly contradict any of the recovered fossil material. The speculation undertaken for All Yesterdays and its sequel has been compared to that of Dixon's speculative evolution works, though its objective was to challenge modern conservative perceptions and ideas of how dinosaurs and other prehistoric creatures lived, rather than designing whole new ecosystems. The books have inspired a modern artistic movement of artists going beyond conventional paleoart tropes, expanding into increasingly speculative renditions of prehistoric life. Additionally, the evolutionary history of fictional organisms has been used as a tool in biology education. Caminalcules, named after Joseph H. Camin, are a group of animal-like lifeforms, consisting of 77 purported extant and fossil species that were invented as a tool for understanding phylogenetics. The classification of Caminalcules, as well as other fictional creatures such as dragons and aliens, have been used as analogies to teach concepts in evolution and systematics. Speculative evolution is sometimes presented in museum exhibitions. For instance, both After Man and The Future is Wild has been presented in exhibition form, educating museum visitors on the principles of biology and evolution through using their own fictional future creatures. == Subsets == === Extraterrestrial life === A popular subset of speculative evolution is the exploration of possible realistic extraterrestrial life and ecosystems. Speculative evolution writings focusing on extraterrestrial life, like the blog Furahan Biology, use realistic scientific principles to describe the biomechanics of hypothetical alien life. Although commonly
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identified with terms such as "astrobiology", "xenobiology" or "exobiology", these terms designate actual scientific fields largely unrelated to speculative evolution. Though 20th century work in exobiology sometimes formulated "audacious" ideas about extraterrestrial forms of life. Astrophysicists Carl Sagan and Edwin Salpeter speculated that a "hunters, floaters and sinkers" ecosystem could populate the atmospheres of gas giant planets like Jupiter, and scientifically described it in a 1976 paper. In extraterrestrial-focused speculative biology, lifeforms are often designed with the intention to populate planets wildly different from Earth, and in such cases concerns like chemistry, astronomy and the laws of physics become just as important to consider as the usual biological principles. Very exotic environments of physical extremes may be explored in such scenarios. For example, Robert Forward's 1980 Dragon's Egg develops a tale of life on a neutron star, and the resulting high-gravity, high-energy environment with an atmosphere of iron vapor and mountains 5-100 millimeters high. Once the star cools down and stable chemistry develops, life evolves extremely quickly, and Forward imagines a civilization of "cheela" that lives a million times faster than humans. In some cases, artists and writers exploring possible alien life conjure similar ideas independent of each other, often attributed to studying the same biological processes and ideas. Such occasions can be called "convergent speculation", similar to the scientific idea of convergent evolution. Perhaps the most famous speculative work on a hypothetical alien ecosystem is Wayne Barlowe's 1990 book Expedition, which explores the fictional exoplanet Darwin IV. Expedition was written as a report of a 24th-century expedition that had been led to the planet by a team composed of both humans and intelligent aliens and used paintings and descriptive texts to create and describe a fully realized extraterrestrial ecosystem. Barlowe later served as an executive producer of a TV
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adaptation of the book, Alien Planet (2005) where exploration of Darwin IV is instead carried out by robotic probes and the segments detailing the ecosystems of the planet are intercut with interviews with scientists, such as Michio Kaku, Jack Horner and James B. Garvin. Other examples of speculative evolution focused on extraterrestrial life include Dougal Dixon's 2010 book Greenworld, TV programmes such as 1997 the BBC2/Discovery Channel special Natural History of an Alien and the 2005 Channel 4/National Geographic programme Extraterrestrial as well as a variety of personal web-based artistic projects, such as C. M. Kosemen's "Snaiad" and Gert van Dijk's "Furaha", envisioning the biosphere of entire alien worlds. Through science fiction, the speculative biology of extraterrestrial organisms has a strong presence in popular culture. The eponymous monster of Alien (1979), particularly its life cycle from egg to parasitoid larva to 'Xenomorph', is thought to be based on the real habits of parasitoid wasps in biology. Further, H. R. Giger's design of the Alien incorporated the features of insects, echinoderms and fossil crinoids, while concept artist John Cobb suggested acid blood as a biological defense mechanism. James Cameron's 2009 film Avatar constructed a fictional biosphere full of original, speculative alien species; a team of experts ensured that the lifeforms were scientifically plausible. The creatures of the movie took inspiration from Earth species as diverse as pterosaurs, microraptors, great white sharks, and panthers, and combined their traits to create an alien world. Darren Naish praised the creature design of 2022's Avatar: The Way of Water as well, admitting suspension of disbelief on the humanoid Na'vi protagonists. He notes the other creatures, aliens and their anatomies and lifestyles are inspired by evolution and ecology to a significant degree, with probable inspirations such as mycorrhizal fungi, marine reptiles, and simian evolution. According to
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Naish, "the series will be a mainstay in discussions about creature design and speculative biology for some time yet." === Alternative evolution === Similar to alternate history, alternative evolution is the exploration of possible alternate scenarios that could have played out in the Earth's past to give rise to alternate lifeforms and ecosystems, popularly the survival of non-avian dinosaurs to the present day. As humanity is often not a part of the worlds envisioned through alternative evolution, it has sometimes been characterized as non-anthropocentric. Although dinosaurs surviving to the age of humans has been adapted as a plot point in numerous science fiction stories since at least 1912, beginning with Arthur Conan Doyle's The Lost World, the idea of exploring the fully fledged alternate ecosystems that would develop in such a scenario truly began with the publication of Dixon's The New Dinosaurs in 1988, in which dinosaurs were not some lone stragglers of known species that had survived more or less unchanged for the last 66 million years, but diverse animals that had continued to evolve beyond the Cretaceous. In the vein of Dixon's The New Dinosaurs imagination, a now largely defunct, but creatively significant collaborative online project the Speculative Dinosaur Project followed in the same zoological worldbuilding tradition. Since 1988, alternative evolution has sometimes been applied in popular culture. The creatures in the 2005 film King Kong were fictitious descendants of real animals, with Skull Island being inhabited by dinosaurs and other prehistoric fauna. Inspired by Dougal Dixon's works, the designers imagined what 65 million years or more of isolated evolution might have done to dinosaurs. Concept art for the film was published in the book The World of Kong: A Natural History of Skull Island (2005), which explored the world of the film from a biological perspective, envisioning
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Skull Island as a surviving fragment of ancient Gondwana. Prehistoric creatures on a declining, eroding island had evolved into "a menagerie of nightmares". A hypothetical natural history of dragons is a popular subject of speculative zoology, being explored in works such as Peter Dickinson's The Flight of Dragons (1979), the 2004 mockumentary The Last Dragon and the Dragonology series of books. === Future evolution === The evolution of organisms in the Earth's future is a popular subset of speculative evolution. A relatively common theme in future evolution is civilizational collapse and/or humans becoming extinct due to an anthropogenic extinction event caused by environmental degradation. After such a mass extinction event, the remaining fauna and flora evolve into a variety of new forms. Although the foundations of this subset were laid by Wells's The Time Machine already in 1895, it is generally agreed that it was definitively established by Dixon's After Man in 1981, which explored a fully realized future ecosystem set 50 million years from the present. Dixon's third work on speculative evolution, Man After Man (1990) is also an example of future evolution, this time exploring an imagined future evolutionary path of humanity. Peter Ward's Future Evolution (2001) makes a scientifically accurate approach to the prediction of patterns of evolution in the future. Ward compares his predictions with those of Dixon and Wells. He tries to understand the mechanism of mass extinctions and the principles of recovery of ecosystems. A key point is that "champion supertaxa" who diversify and speciate at a greater rate, will inherit the world after mass extinctions. Ward quotes the paleontologist Simon Conway Morris, who points out that the fantastical or even whimsical creatures devised by Dougal Dixon, echo nature's tendency to converge on the same body plans. While Ward calls Dixon's visions "semi-whimsical" and
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compares them to Wells' initial visions in The Time Machine, he nonetheless continues the use of analogous evolution, which is a larger trend in speculative zoology. Future evolution has also been explored on TV, with the mockumentary series The Future is Wild in 2002, for which Dixon was a consultant (and author of the companion book), and the series Primeval (2007–2011), a drama series in which imagined future animals occasionally appeared. Ideas of future evolution are also frequently explored in science fiction novels, such as in Kurt Vonnegut's 1985 science fiction novel Galápagos, which imagines the evolution of a small surviving group of humans into a sea lion-like species. Stephen Baxter's 2002 science fiction novel Evolution follows 565 million years of human evolution, from shrewlike mammals 65 million years in the past to the ultimate fate of humanity (and its descendants, both biological and non-biological) 500 million years in the future. C. M. Kosemen's 2008 All Tomorrows similarly explores the future evolution of humanity. Speculative biology and the future evolution of the human species are significant in bio art. === Seed worlds === Seed worlds, or seeded worlds, are another popular subset of the genre. It involves a terraformed planet or a habitable, yet uninhabited planet being "seeded" by already existing species of animals, plants and fungi, which will speciate in order to fill the different niches by adaptive radiation. The focus can be on one or multiple species, but usually more taxa are present on the project's planet, that won't be covered in as much detail. One of the most well-known works in this category is Serina: A Natural History of the World of Birds by Dylan Bajda, in which the focal species is the domestic canary, Serinus canaria domestica, who is the progenitor of all other bird species
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that come later. A minor species that later becomes more relevant is the guppy (Poecilia), whose descendants become terrestrial tripods and compete against the birds after a severe mass extinction which killed 99% of all species on the moon. Another relevant seed world, Batrachiterra, involves various species of frogs seeded by humans on the fictional planet Heqet, originally for the purpose of studying batrachotoxin. == See also == Astrobiology – the interdisciplinary study of the possibility of life elsewhere in the universe. Bestiary – popular in the Middle Ages, bestiaries combined descriptions of real animals with descriptions of fantastical ones, sometimes likened to speculative biology. Contingency (evolutionary biology) – the scientific study of evolutionary outcomes differing due to differences in history. Future history – imagined future historical events and predictions. Global catastrophic risk and Human extinction – often tends to precede works featuring hypothetical animals that could one day inhabit Earth in the distant future. Hypothetical types of biochemistry – hypothesized life based on molecules other than carbon. Paleoart – artwork reconstructing prehistoric animals, often seen as closely related to speculative biology given the inherent speculation required to reconstruct long-dead organisms. == References == == External links == Encyclopedia Galactica. A speculative evolution project by Finnish artist Ken Ferjik exploring the lifeforms of several fictional planets. Furaha: Natural History of the planet v Phoenicis IV. A speculative evolution project by Dutch artist Gert van Dijk exploring the fictional planet Furaha and its lifeforms. Life on Snaiad. A speculative evolution project by Turkish artist C. M. Kosemen exploring the fictional planet of Snaiad and its lifeforms. Serina: A Natural History of the World of Birds. A speculative evolution project envisioning an alien planet in which all animals have descended from mundane and commonly-kept species, in particular the Common Canary. All Your
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Yesterdays, the sequel to All Yesterdays and a free downloadable book featuring speculative renditions of extinct animals. The Neocene project. A collaborative speculative evolution project exploring Earth's life as imagined 25 million years in the future. Archived site of Project Nereus. A speculative evolution project by Evan Black exploring the fictional planet Nereus and its lifeforms. Archived site of The Speculative Dinosaur Project. A collaborative speculative evolution project exploring Earth as imagined if the K-T extinction event had not occurred. Also Russian translation of this project and saved English version are available. Sagan 4. A collaborative speculative evolution project founded in 2006, in which a community of volunteers have worked together to develop thousands of species which all originated from a single cell.
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Chargaff's rules (given by Erwin Chargaff) state that in the DNA of any species and any organism, the amount of guanine should be equal to the amount of cytosine and the amount of adenine should be equal to the amount of thymine. Further, a 1:1 stoichiometric ratio of purine and pyrimidine bases (i.e., A+G=T+C) should exist. This pattern is found in both strands of the DNA. They were discovered by Austrian-born chemist Erwin Chargaff in the late 1940s. == Definitions == === First parity rule === The first rule holds that a double-stranded DNA molecule, globally has percentage base pair equality: A% = T% and G% = C%. The rigorous validation of the rule constitutes the basis of Watson–Crick base pairs in the DNA double helix model. === Second parity rule === The second rule holds that both Α% ≈ Τ% and G% ≈ C% are valid for each of the two DNA strands. This describes only a global feature of the base composition in a single DNA strand. == Research == The second parity rule was discovered in 1968. It states that, in single-stranded DNA, the number of adenine units is approximately equal to that of thymine (%A ≈ %T), and the number of cytosine units is approximately equal to that of guanine (%C ≈ %G). In 2006, it was shown that this rule applies to four of the five types of double stranded genomes; specifically it applies to the eukaryotic chromosomes, the bacterial chromosomes, the double stranded DNA viral genomes, and the archaeal chromosomes. It does not apply to organellar genomes (mitochondria and plastids) smaller than ~20–30 kbp, nor does it apply to single stranded DNA (viral) genomes or any type of RNA genome. The basis for this rule is still under investigation, although genome size may play
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a role. The rule itself has consequences. In most bacterial genomes (which are generally 80–90% coding) genes are arranged in such a fashion that approximately 50% of the coding sequence lies on either strand. Wacław Szybalski, in the 1960s, showed that in bacteriophage coding sequences purines (A and G) exceed pyrimidines (C and T). This rule has since been confirmed in other organisms and should probably be now termed "Szybalski's rule". While Szybalski's rule generally holds, exceptions are known to exist. The biological basis for Szybalski's rule is not yet known. The combined effect of Chargaff's second rule and Szybalski's rule can be seen in bacterial genomes where the coding sequences are not equally distributed. The genetic code has 64 codons of which 3 function as termination codons: there are only 20 amino acids normally present in proteins. (There are two uncommon amino acids—selenocysteine and pyrrolysine—found in a limited number of proteins and encoded by the stop codons—TGA and TAG respectively.) The mismatch between the number of codons and amino acids allows several codons to code for a single amino acid—such codons normally differ only at the third codon base position. Multivariate statistical analysis of codon use within genomes with unequal quantities of coding sequences on the two strands has shown that codon use in the third position depends on the strand on which the gene is located. This seems likely to be the result of Szybalski's and Chargaff's rules. Because of the asymmetry in pyrimidine and purine use in coding sequences, the strand with the greater coding content will tend to have the greater number of purine bases (Szybalski's rule). Because the number of purine bases will, to a very good approximation, equal the number of their complementary pyrimidines within the same strand and, because the coding sequences occupy
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80–90% of the strand, there appears to be (1) a selective pressure on the third base to minimize the number of purine bases in the strand with the greater coding content; and (2) that this pressure is proportional to the mismatch in the length of the coding sequences between the two strands. The origin of the deviation from Chargaff's rule in the organelles has been suggested to be a consequence of the mechanism of replication. During replication the DNA strands separate. In single stranded DNA, cytosine spontaneously slowly deaminates to adenosine (a C to A transversion). The longer the strands are separated the greater the quantity of deamination. For reasons that are not yet clear the strands tend to exist longer in single form in mitochondria than in chromosomal DNA. This process tends to yield one strand that is enriched in guanine (G) and thymine (T) with its complement enriched in cytosine (C) and adenosine (A), and this process may have given rise to the deviations found in the mitochondria. Chargaff's second rule appears to be the consequence of a more complex parity rule: within a single strand of DNA any oligonucleotide (k-mer or n-gram; length ≤ 10) is present in equal numbers to its reverse complementary nucleotide. Because of the computational requirements this has not been verified in all genomes for all oligonucleotides. It has been verified for triplet oligonucleotides for a large data set. Albrecht-Buehler has suggested that this rule is the consequence of genomes evolving by a process of inversion and transposition. This process does not appear to have acted on the mitochondrial genomes. Chargaff's second parity rule appears to be extended from the nucleotide-level to populations of codon triplets, in the case of whole single-stranded Human genome DNA. A kind of "codon-level second Chargaff's parity rule"
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is proposed as follows: Examples — computing whole human genome using the first codons reading frame provides: 36530115 TTT and 36381293 AAA (ratio % = 1.00409). 2087242 TCG and 2085226 CGA (ratio % = 1.00096), etc... In 2020, it is suggested that the physical properties of the dsDNA (double stranded DNA) and the tendency to maximum entropy of all the physical systems are the cause of Chargaff's second parity rule. The symmetries and patterns present in the dsDNA sequences can emerge from the physical peculiarities of the dsDNA molecule and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. == Percentages of bases in DNA == The following table is a representative sample of Erwin Chargaff's 1952 data, listing the base composition of DNA from various organisms and support both of Chargaff's rules. An organism such as φX174 with significant variation from A/T and G/C equal to one, is indicative of single stranded DNA. == See also == Genetic codes == References == == Further reading == Szybalski W, Kubinski H, Sheldrick P (1966). "Pyrimidine clusters on the transcribing strands of DNA and their possible role in the initiation of RNA synthesis". Cold Spring Harbor Symposia on Quantitative Biology. 31: 123–127. doi:10.1101/SQB.1966.031.01.019. PMID 4966069. Lobry JR (1996). "Asymmetric substitution patterns in the two DNA strands of bacteria". Mol. Biol. Evol. 13 (5): 660–665. doi:10.1093/oxfordjournals.molbev.a025626. PMID 8676740. Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH (1999). "Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases". Nucleic Acids Res. 27 (7): 1642–1649. doi:10.1093/nar/27.7.1642. PMC 148367. PMID 10075995. McLean MJ, Wolfe KH, Devine KM (1998). "Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes". J Mol Evol. 47 (6): 691–696. Bibcode:1998JMolE..47..691M. CiteSeerX 10.1.1.28.9035. doi:10.1007/PL00006428. PMID 9847411. S2CID 12917481.
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}
|
McInerney JO (1998). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proc Natl Acad Sci USA. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. PMC 27958. PMID 9724767. == External links == CBS Genome Atlas Database Archived 2016-05-16 at the Portuguese Web Archive — contains hundreds of examples of base skews and had problems. The Z curve database of genomes — a 3-dimensional visualization and analysis tool of genomes.
|
{
"page_id": 526941,
"source": null,
"title": "Chargaff's rules"
}
|
A water bath is laboratory equipment made from a container filled with heated water. It is used to incubate samples in water at a constant temperature over a long period of time. Most water baths have a digital or an analogue interface to allow users to set a desired temperature, but some water baths have their temperature controlled by a current passing through a reader. Uses include warming of reagents, melting of substrates, determination of boiling point, or incubation of cell cultures. It is also used to enable certain chemical reactions to occur at high temperature. Water baths are preferred heat sources for heating flammable chemicals, as their lack of open flame prevents ignition. Different types of water baths are used depending on application. For all water baths, it can be used up to 99.9 °C. When the required temperature is above 100 °C, alternative methods such as oil bath, silicone oil bath or sand bath may be used. == Precautions == It is not recommended to use water bath with moisture sensitive or pyrophoric reactions. Do not heat a bath fluid above its flash point. Water level should be regularly monitored, and filled with distilled water only. This is required to prevent salts from depositing on the heater. Disinfectants can be added to prevent growth of organisms. If application involves liquids that give off fumes, it is recommended to operate water bath in fume hood or in a well ventilated area. The cover is closed to prevent evaporation and to help reaching high temperatures. == Types of water bath == === Circulating water baths === Circulating water baths (also called stirrers ) are ideal for applications when temperature uniformity and consistency are critical, such as enzymatic and serologic experiments. Water is thoroughly circulated throughout the bath resulting in a
|
{
"page_id": 26413670,
"source": null,
"title": "Laboratory water bath"
}
|
more uniform temperature. === Non-circulating water baths === This type of water bath relies primarily on convection instead of water being uniformly heated. Therefore, it is less accurate in terms of temperature control. In addition, there are add-ons that provide stirring to non-circulating water baths to create more uniform heat transfer. === Shaking water baths === This type of water bath has extra control for shaking, which moves liquids around. This shaking feature can be turned on or off. In microbiological practices, constant shaking allows liquid-grown cell cultures grown to constantly mix with the air. Some key benefits of shaking water bath are user-friendly operation via keypad, convenient bath drains, adjustable shaking frequencies, bright LED-display, optional lift-up bath cover, power switch integrated in keypad and warning and cut-off protection for low/high temperature. == Water bath technologies == The bath is a fundamental product in any laboratory. Over the years, water baths have evolved from basic analog tools to advanced digital machines capable of sophisticated and programmable controls, functions, and capabilities. Key features in water baths often include: Multi-language operation User-settable limit values "Eco modes" which save energy after set programs are completed User-settable alarms: audible, visible or both Displays of actual and/or set point temperatures Programmable pre-sets for frequently used temperatures Integrated timers Hinged gable covers Calibration off-set capabilities Stainless reservoirs Reservoir drains Primary and automatic safety thermostats Compatible with waterless alloy bath beads == Additional images == == See also == Thermal immersion circulator Heated bath Hot plate Sand bath Oil bath == References ==
|
{
"page_id": 26413670,
"source": null,
"title": "Laboratory water bath"
}
|
Crystallopathy is a harmful state or disease associated with the formation and aggregation of crystals in tissues or cavities, or in other words, a heterogeneous group of diseases caused by intrinsic or environmental microparticles or crystals, promoting tissue inflammation and scarring. == Composition == Crystallopathies can be associated with four main kinds of crystalline structures: liquid non-aggregating crystal solutions, amorphous nano-scale solid particles, crystalline micro-scale solid particles, and polycrystalline larger solid structures. They can be composed of various minerals, metabolites, proteins, and microparticles, including the following: == Location == In principle, crystal formation can happen anywhere in the body. Well-known places are excretory organs where concentrations get high easily, like in the biliary and urinary tracts, but crystalline structures are also formed in intracellular and extracellular spaces of tissues, like within the arterial wall in atherosclerosis. For example, mechanical obstruction by mineral stones causes nephrolithiasis, urolithiasis, cholecystolithiasis, choledocholithiasis, docholithiasis, and sialolithiasis, and acute inflammation caused by crystals in joints causes gout and pseudogout. Renal diseases are also common in crystallopathies, including: == Mechanisms == Local supersaturation is a common trigger of crystallization, and when the nucleus of the crystalline structure is formed, crystals can self-perpetuate and cause more crystallization and aggregation. Main mechanisms by which the formed crystals and aggregates cause pathological states and ultimately disease are acute necroinflammation, chronic tissue remodelling, and mechanical obstruction. Necroinflammation is an autoamplifying process where crystals are toxic to cells (cytotoxicity) and cause cell death (necrosis and regulated cell death) and a local and systemic inflammatory response. Cytotoxicity includes actin depolymerization, free radical and reactive oxygen species synthesis, and autophagy. Crystals can also directly activate inflammation via Mincle receptors, calcium and potassium signalling, calpains, cathepsin beta, proteases, and NLPR3 inflammasomes. Cells undergo cell death via three main mechanisms: necroptosis via RIPK1, FADD, RIPK3, and
|
{
"page_id": 63834727,
"source": null,
"title": "Crystallopathy"
}
|
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