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Search by property

A list of all pages that have property "Description" with value "-5B-5BFile:1PM-3B2D-3B3G-3B4U-3B5S-3B6Rot-2D.png-7C300px-5D-5D". Since there have been only a few results, also nearby values are displayed.

Showing below up to 125 results starting with #1.

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List of results

  • Pressure  + ('''Pressure''' is a fundamental quantity e'''Pressure''' is a fundamental quantity expressing energy per volume. The SI unit of pressure is generally pascal [Pa] = [J·m<sup>-3</sup>]. The term 'stress' (mechanical stress) is used as a synonym for pressure ([[Bureau International des Poids et Mesures 2019 The International System of Units (SI) |SI]]). Pressure is known in physics as mechanical pressure, which is force per area, ''p'' = ''F''·''A''<sup>-1</sup> [Pa] = [N·m<sup>-2</sup>]. In physical chemistry, gas pressure is defined as ''p'' = ''n''·''V''<sup>-1</sup>·''RT'', where the [[concentration]] is ''c'' = ''n''·''V''<sup>-1</sup> [mol·m<sup>-3</sup>], ''R'' is the [[gas constant]], and ''T'' is the absolute temperature, and ''RT'' is expressed in units of chemical force [J·mol<sup>-1</sup>]. van't Hoff's osmotic pressure assumes the same form applied to dissolved substances diffusing across a semipermeable membrane, but concentrations should be replaced by [[activity |activities]]. The activity of dissolved gases is expressed by the [[partial pressure]], where the [[solubility]] can be seen as an activity coefficient. Pressure appears explicitely or implicitely in all chapters of physics and physical chemistry. In contrast to the universal counterparts energy and force, however, the general connections between various isomorphic expressions of pressure remain poorly understood: Pressure is the concentration of the [[force]] at the point of [[action]]. More generally, pressure is the force times concentration at the interphase of interaction.]]. More generally, pressure is the force times concentration at the interphase of interaction.)
  • Temperature plot empty  + ('''Problem:''' Layout "01 Calibration Exp.'''Problem:''' Layout "01 Calibration Exp. Gr3-Temp" is selected, a third plot is displayed on the screen but it remains empty (no plot is shown). Newer versions of [[DatLab]] include pre-installed layouts which do not recognize some channel designations from older O2k series.hannel designations from older O2k series.)
  • Proficiency test  + ('''Proficiency testing''' PT is an evaluat'''Proficiency testing''' PT is an evaluation of participant performance against pre-established criteria by means of interlaboratory comparisons. Some PT providers in the medical area use the term “External Quality Assessment (EQA)” for their proficiency testing schemes, or for their broader programmes, or both. Internal PT strategies may be implemented into laboratory science as practical steps towards PT to achieve reproducibility.eps towards PT to achieve reproducibility.)
  • Proline dehydrogenase  + ('''Proline dehydrogenase''' (ProDH), L-pro'''Proline dehydrogenase''' (ProDH), L-proline:quinone oxidoreductase, is located on the inner side of the [[mtIM]], oxidizing [[proline]] to delta-1-pyrroline-5-carboxylate, with reduction of FAD to FADH<sub>2</sub> and direct entry into the [[Q-junction]], exerting an additive effect of convergent pathways. ProDH is widely distributed in a variety of organisms, is a source of ROS, and may play a role in carcinogenesis. source of ROS, and may play a role in carcinogenesis.)
  • Proton slip  + ('''Proton slip''' is a property of the pro'''Proton slip''' is a property of the proton pumps (Complexes CI, CIII, and CIV) when the [[proton]] slips back to the matrix side within the proton pumping process. Slip is different from the [[proton leak]], which depends on Δ''p'' and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the [[biochemical coupling efficiency]] of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by [[LEAK respiration]] or LEAK oxygen flux, ''L''. Compare: [[Proton leak]].[Proton leak]].)
  • PubMed  + ('''PubMed''' is a free search tool for articles in the life sciences field.)
  • Publication efficiency  + ('''Publication efficiency''' is the fracti'''Publication efficiency''' is the fraction ''F''<sub>r,a/p</sub> of reproducible publications ''N''<sub>r</sub> which are among the number ''N''<sub>a</sub> of publications that receive attention and meaningful interpretation, per total count ''N''<sub>p</sub> of all published communications. Publication efficiency ''F''<sub>r,a/p</sub> = ''F''<sub>r/p</sub>·''F''<sub>a/p</sub> is low due to (''1'') the reproducibility crisis expressed as low reproducibility efficiency ''F''<sub>r/p</sub> = ''N''<sub>r</sub>/''N''<sub>p</sub>, and (''2'') the inflation crisis expressed as low attention efficiency ''F''<sub>a/p</sub> = ''N''<sub>a</sub>/''N''<sub>p</sub>. Estimates of these partial efficiencies vary from field to field. With ''F''<sub>r/p</sub>=0.15 and ''F''<sub>a/p</sub>=0.05, the current publication efficiency is as low as 0.0075, or only 0.75 % of all presently published communictions are reproducible and receive attention and meaningful interpretation. Reduction of the number of irreproducible zero-value publications is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.ons is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.)
  • Pyruvate carboxylase  + ('''Pyruvate carboxylase''' synthesizes [[oxaloacetate]]'''Pyruvate carboxylase''' synthesizes [[oxaloacetate]] from [[pyruvate]] and CO<sub>2</sub> as an [[anaplerosis |anaplerotic reaction]] in the mitochondrial matrix of the liver and kidney of higher animals, representing an alternative to the [[malic enzyme]] pathway to oxaloacetate or the [[phosphoenolpyruvate carboxykinase]] reaction (compare glyoxylate cycle in plants and microorganisms). Carboxylation of pyruvate to oxaloacetate requires Mg-ATP. Acetyl CoA is a strong positive modulator. PC can form pyruvate from oxaloacetate to remove an excess of oxaloacetate which inhibits succinate dehydrogenase.f oxaloacetate which inhibits succinate dehydrogenase.)
  • Pyruvate dehydrogenase  + ('''Pyruvate dehydrogenase''' is the first '''Pyruvate dehydrogenase''' is the first component enzyme of the [[pyruvate dehydrogenase complex]], which catalyzes oxidative decarboxylation of [[pyruvate]] in the mt-matrix, and yields [[acetyl-CoA]]. PDH is known as the mitochondrial gatekeeper in the core energy pathway of electron flow into the tricarboxylic acid cycle.on flow into the tricarboxylic acid cycle.)
  • Q calibration - DatLab  + ('''Q calibration''')
  • Q-cycle  + ('''Q-cycle''' refers to the sequential oxi'''Q-cycle''' refers to the sequential oxidation and reduction of the electron carrier Coenzyme Q (CoQ or [[ubiquinone]]) in mitochondria or plastoquinones in the photosynthetic system. Originally, the concept of the Q-cycle was proposed by [[Mitchell P|Peter D Mitchell]]. Following several modifications, the Q-cycle is established, describing how [[CIII]] translocates hydrogen ions against the protonmotive force. The reduced CoQ ([[quinol |ubiquinol]] QH<sub>2</sub>) binds to the Q<sub>o</sub> site of CIII, while the oxidized CoQ ([[ubiquinone]] Q) to the Q<sub>i</sub> site of CIII. First, QH<sub>2</sub> reduces the iron-sulfur protein and feeds cytochrome ''c''<sub>1</sub> with one electron. The other electron is transferred to the ''b''<sub>L</sub> heme and reduces the ''b''<sub>H</sub> heme, which transfers the electron to ubiquinone at the Q<sub>i</sub>-site which is reduced to a [[semiquinone]]. A second QH<sub>2</sub> is required to fully reduce semiquinone to ubiquinol. At the end of the Q-cycle, four protons leave the mt-matrix and enter the intermembrane space, and the reduced cytochrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Q<sub>i</sub>-site can be reused by binding to the Q<sub>o</sub>-site of CIII.chrome ''c'' transfers electrons to CIV. The ubiquinol generated at the Q<sub>i</sub>-site can be reused by binding to the Q<sub>o</sub>-site of CIII.)
  • Quenching  + ('''Quenching''' is the name given to any p'''Quenching''' is the name given to any process that reduces [[fluorescence]] intensity. Molecular oxygen is a [[fluorescence]] and [[phosphorescence]] quencher for some substances – a phenomenon that has been made use of in constructing optical probes for measuring oxygen.cting optical probes for measuring oxygen.)
  • Quinol  + ('''Quinol''' is a class of ''reduced'' org'''Quinol''' is a class of ''reduced'' organic compounds derived from quinone (oxidized form) by two-electron and two-proton reduction. In the mitochondrial electron transfer system, ubiquinol or reduced [[coenzyme Q]] can be found, while in the photosynthetic systems plastoquinols (particularly PQ<sub>9</sub>) are common. These redox compounds exist in three different redox states: [[quinone]] (oxidized), quinol (reduced), and an intermediate [[semiquinone]].[[semiquinone]].)
  • Quinone  + ('''Quinone''' is a class of ''oxidized'' o'''Quinone''' is a class of ''oxidized'' organic compounds with a fully conjugated cyclic dione structure derived from aromatic compounds. [[Ubiquinone]] or coenzmye Q is the naturally occurring quinone in the mitochondrial [[ETS]], while in the photosynthetic system plastoquinones are common. The quinone is reduced either to an unstable semiquinone by one hydrogen atom or to a quinol by two electrons and two protons.a quinol by two electrons and two protons.)
  • Rapamycin  + ('''Rapamycin''' is an inhibitor of the mam'''Rapamycin''' is an inhibitor of the mammalian/mechanistic target of rapamycin, complex 1 (mTORC1). Rapamycin induces autophagy and dyscouples mitochondrial respiration. Rapamycin delays senescence in human cells, and extends lifespan in mice without detrimental effects on mitochondrial fitness in skeletal muscle. mitochondrial fitness in skeletal muscle.)
  • Reactive nitrogen species  + ('''Reactive nitrogen species''', RNS, are nitric oxide-derived oxidants. The main source of RNS is [[nitric oxide]] (NO•). NO• plays an important role in cell signaling and in oxidative-nitrosative stress.)
  • Reactive oxygen species  + ('''Reactive oxygen species''', ROS, are mo'''Reactive oxygen species''', ROS, are molecules derived from molecular [[oxygen]], including free oxygen radicals, which are more reactive than O<sub>2</sub>. Physiologically and pathologically important ROS include [[superoxide]], the [[hydroxyl radical]] and [[hydroxide ion]], [[hydrogen peroxide]] and other [[peroxides]]. These are important in cell signalling, oxidative defence mechanisms and [[oxidative stress]].[[oxidative stress]].)
  • Reference material  + ('''Reference material''' (RM) is material '''Reference material''' (RM) is material or substance one or more of whose property values are sufficiently homogeneous and well established to be used for the calibration of an apparatus, the assessment of a measurement procedure, or for assigning values to materials (adapted from VIM: 1993, 6.13). The adjective 'homogeneous' refers to the physical homogeneity between macroscopic parts of the material, not to any microheterogeneity between molecules of the analyte.'''Primary reference material''' is reference material having the highest metrological qualities and whose value is determined by means of a primary reference measurement procedure. The concept "primary calibrator" is subordinate to "calibrator" (see 3.7) and to "primary reference material". 3.7) and to "primary reference material".)
  • References in BEC https-format  + ('''References in BEC https-format''' show '''References in BEC https-format''' show (''1'') the list of authors, (''2'') the year of publication in parentheses, (''3'') the title of the publication, and (''4'') the https://doi.org/ link. Removing all the unnecessary detail of journal name and pages, the focus is on authors, year, and title of the reference, which is a concept in line with [[DORA]]. The https-link then does the full job. In exceptional cases when there is no such link, the following formats would apply: a https://pubmed.ncbi.nlm.nih.gov/ link, a link directly to an Open Access pdf, or the old conventional format for the reference. Scientific journals apply ''yesterday's concepts'' in the various formats of references with bewildering abbreviations of journals, volumes, issues, page numbers. We can do ''today's job'' much better using the BEC https-format: </br><small></br># Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. https://doi.org/10.1371/journal.pone.0228692</br># Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. https://doi.org/10.1161/CIRCRESAHA.114.303819. </br># Buranyi S (2017) Is the staggeringly profitable business of scientific publishing bad for science? https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science </br># Cardoso LHD, Doerrier C, Gnaiger E (2021) Magnesium Green for fluorometric measurement of ATP production does not interfere with mitochondrial respiration. https://doi.org/10.26124/bec:2021-0001 </br># Day S, Rennie S, Luo D, Tucker JD (2020) Open to the public: paywalls and the public rationale for open access medical research publishing. https://doi.org/10.1186/s40900-020-0182-y</br># Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. https://doi.org/10.1016/S0034-5687(01)00307-3 </br># ….</br></small></br>Compare with a conventional reference format in: Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005ic publication. https://doi.org/10.26124/bec:2021-0005)
  • Reliability  + ('''Reliability''' relates the magnitude of'''Reliability''' relates the magnitude of the measurement error in observed measurements (i.e., precision or intermediate precision) to the inherent variability in the ‘error-free’, ‘true’, or underlying level of the quantity between subjects. The value of the reliability takes a value between 0 and 1. When the variability value is zero, indicates that all the variability in the measurements is due to measurement error. And, on the contrary, when the value is 1 indicates that there is a zero error in the measurement error. It is also known as the intraclass correlation, as it equals the correlation between any two measurements made on the same subject.two measurements made on the same subject.)
  • Repetitions  + ('''Repetitions''' of an [[experiment]]'''Repetitions''' of an [[experiment]] or [[assay]] are designed to obtain statistical information on the methodological [[precision]] of the measurements. A number of repetitions, ''n'', of measurements are performed on the same sample, applying an identical experimental protocol to subsamples, without providing any information on variability between samples.nformation on variability between samples.)
  • Replica  + ('''Replica''' are designed in scientific [[study |studies]]'''Replica''' are designed in scientific [[study |studies]] to evaluate the effect of uncontrolled variability on a result obtained from an [[experiment]] on a single [[sample]], to describe the variability and distribution of experimental results, and to obtain statistical information such as the median or average for a defined [[sample size]]. It may be useful to make a terminological distinction between ''replica'' of experiments, ''N'', designed to obtain statistical information on the [[population]], and ''[[repetitions]]'' of [[experiment]]s or [[assay]]s, ''n'', designed to obtain statistical information on the methodological [[precision]] of the measurements. The terms [[study]], [[experiment]] and [[assay]] have to be defined carefully in this context.e to be defined carefully in this context.)
  • Research  + ('''Research''' is a term composed of '''se'''Research''' is a term composed of '''search''' and '''re'''. What does this tell us? The best comparison of the English with a German word is ''Untersuchung'', composed of ''suchung'' (search) and ''unter'' (below). The term ''search'' (suchen) is straightforward to understand and comparable in both languages. The prefix ''re'' and ''unter'' are more difficult to reconcile, yet in both languages these perfixes reveal complementary if not nearly identical messages. ''re'' means {''Quote''} back to the original place; again, anew, once more {''end of Quote''} [1], whereas ''unter'' means ''below'' or ''underneath''. Re-search, therefore, is not simply the search or investigation of some topic or problem, it means essentially doing the search again and again (re -> re-producibility) and penetrating ''below'' a simple search by reaching out for an underlying level of the search. The ''re'' in re-search and re-producibility has to be extended ultimately from a single re-search group to inter-laboratory re-investigation. This tells us, therefore, that while ''search'' is valuable, ''re-search'' provides the necessary validation. This re-evaluation of confirmative re-search should be re-cognized as the most important strategy to address the [[reproducibility crisis]].[[reproducibility crisis]].)
  • Resorufin  + ('''Resorufin''' is a fluorescence probe us'''Resorufin''' is a fluorescence probe used in various biological assays. Among others, it is the product obtained in the [[Horseradish_peroxidase| Horseradish peroxidase]]-catalyzed assay using [[Amplex_red| Amplex Red]] for the measurement of [[Hydrogen_peroxide| H<sub>2</sub>O<sub>2</sub>]] production.[[Hydrogen_peroxide| H<sub>2</sub>O<sub>2</sub>]] production.)
  • Respiratory complexes  + ('''Respiratory Complexes''' are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. [[Respiratory Complexes#Respiratory Complexes - more than five |» '''MiPNet article''']])
  • Respiratory state  + ('''Respiratory states''' of [[mitochondrial preparations]]'''Respiratory states''' of [[mitochondrial preparations]] and [[living cells]] are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the [[coupling-control state]] and the [[electron-transfer-pathway state]].[[electron-transfer-pathway state]].)
  • Respirometry  + ('''Respirometry''' is the quantitative mea'''Respirometry''' is the quantitative measurement of respiration. ''Respiration is therefore a combustion, a very slow one to be precise'' (Lavoisier and Laplace 1783). Thus the ''basic idea of using calorimetry to explore the ''sources'' and ''dynamics'' of heat changes were present in the origins of bioenergetics'' ([[Gnaiger_1983_J Exp Zool|Gnaiger 1983]]). Respirometry provides an ''indirect'' calorimetric approach to the measurement of metabolic heat changes, by measuring oxygen uptake (and carbon dioxide production and nitrogen excretion in the form of ammonia, urea, or uric acid) and converting the oxygen consumed into an [[enthalpy]] change, using the [[oxycaloric equivalent]]. Liebig (1842) showed that the substrate of oxidative respiration was protein, carbohydrates, and fat. ''The sum of these chemical changes of materials under the influence of living cells is known as [[metabolism]]'' (Lusk 1928). The amount (volume STP) of carbon dioxide expired to the amount (volume STP) of oxygen inspired simultaneously is the respiratory quotient, which is 1.0 for the combustion of carbohydrate, but less for lipid and protein. Voit (1901) summarized early respirometric studies carried out by the ''Munich school'' on patients and healthy controls, concluding that ''the metabolism in the body was not proportional to the combustibility of the substances outside the body, but that protein, which burns with difficulty outside, metabolizes with the greatest ease, then carbohydrates, while fats, which readily burns outside, is the most difficultly combustible in the organism.'' Extending these conclusions on the ''sources'' of metabolic heat changes, the corresponding ''dynamics'' or respiratory control was summarized (Lusk 1928): ''The absorption of oxygen does not cause metabolism, but rather the amount of the metabolism determines the amount of oxygen to be absorbed. .. metabolism regulates the respiration.''.. metabolism regulates the respiration.'')
  • Resting metabolic rate  + ('''Resting respiration''' or '''resting me'''Resting respiration''' or '''resting metabolic rate''' (RMR) is measured under standard conditions of an 8–12-h fast and a 12-h abstinence from exercise. In an exemplary study ([[Haugen 2003 Am J Clin Nutr]]), "subjects rested quietly in the supine position in an isolated room with the temperature controlled to 21–24° C. RMR was measured for 15–20 min. Criteria for a valid RMR was a minimum of 15 min of steady state, determined as a <10% fluctuation in oxygen consumption and <5% fluctuation in respiratory quotient". The main difference between RMR and BMR ([[basal metabolic rate]]) is the position of the subject during measurement. Resting metabolic rate is the largest component of the daily energy budget in most human societies and increases with physical training state ([[Speakman 2003 Proc Nutr Soc]]).man 2003 Proc Nutr Soc]]).)
  • Resveratrol  + ('''Resveratrol''' is a natural bioactive phenol prouced by several plants with antioxidant and anti-inflammatory effects. Dietary intake as nutraceutical is discussed for targeting mitochondria with a wide spectrum of action in degenerative diseases.)
  • Risk management  + ('''Risk management''' is the identification, assessment, and prioritization of risks.)
  • Rotenone  + ('''Rotenone''' is an inhibitor of [[Complex I]] (CI) and thus inhibits NADH oxidation. It inhibits the transfer of electrons from iron-sulfur clusters in CI to ubiquinone via binding to the ubiquinone binding site of CI. See also [[Succinate pathway]].)
  • Ruthenium red  + ('''Ruthenium red''' (synonym: ammoniated r'''Ruthenium red''' (synonym: ammoniated ruthenium oxychloride) inhibits the mitochondrial Ca<sup>2+</sup> uniporter. However, in addition it has been shown to interact with and inhibit a large number of other proteins, including ion channels particularly of the Transient Receptor Potential Vanilloid (TRPV) family [1], Ca<sup>2+</sup>-ATPases, and, importantly, the voltage-dependent anion channel (VDAC) [2]. and, importantly, the voltage-dependent anion channel (VDAC) [2].)
  • SF6847  + ('''SF6847''' (C<sub>18</sub>H&'''SF6847''' (C<sub>18</sub>H<sub>22</sub>N<sub>2O</sub>), also known as tyrphostin A9 or malonoben, is a protonophore and a very potent [[uncoupler]] of [[oxidative phosphorylation]], being used in the nM range. Like all uncouplers, SF6847 concentrations must be titrated carefully to evaluate the [[Uncoupler#Optimum_uncoupler_concentration|optimum concentration]] for maximum stimulation of mitochondrial respiration, particularly to avoid inhibition of respiration at higher concentrations.ion, particularly to avoid inhibition of respiration at higher concentrations.)
  • SGp-pathway control state  + ('''SGp''': [[Succinate]] & [[Glycerophosphate]]. '''MitoPathway control state:''' SGp; obtained with OctPGMSGp(Rot) '''SUIT protocol:''' [[SUIT-001]] and ((SUIT-002)
  • SUIT  + ('''SUIT''' is the abbreviation for '''S''''''SUIT''' is the abbreviation for '''S'''ubstrate-'''U'''ncoupler-'''I'''nhibitor '''T'''itration. SUIT protocols are used with mt-preparations to study respiratory control in a sequence of coupling and pathway control states induced by multiple titrations within a single experimental assay. These studies use biological samples economically to gain maximum information with a minimum amount of cells or tissue. with a minimum amount of cells or tissue.)
  • Safranin  + ('''Safranin''' is one of the most establis'''Safranin''' is one of the most established dyes for measuring [[mitochondrial membrane potential]] by [[fluorometry]]. It is an [[extrinsic fluorophores |extrinsic fluorophore]] with an excitation wavelength of 495 nm and emission wavelength of 587 nm. Safranin is a potent inhibitor of [[NADH electron transfer-pathway state |N-linked respiration]] and of the [[phosphorylation system]].</br></br>''Synonyms:'' Safranin O, Safranin Y, Safranin T, Gossypimine, Cotton Red, Basic Red2nin T, Gossypimine, Cotton Red, Basic Red2)
  • Salicylhydroxamic acid  + ('''Salicylhydroxamic acid''' (SHAM; synony'''Salicylhydroxamic acid''' (SHAM; synonym: 2-Hydroxybenzohydroxamic acid N,2-Dihydroxybenzamide) is an inhibitor of the [[alternative oxidase]] (AOX). When AOX is blocked by SHAM, electrons are forced through the CIII-cytochrome ''c'' oxidase pathway, allowing observation of the operation of the CIII-CIV pathway without AOX activity.the CIII-CIV pathway without AOX activity.)
  • Sample mass concentration  + ('''Sample mass [[concentration]]''' is ''C''<sub>''m''<sub>s</sub></sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·m<sup>-3</sup>].)
  • Sample size  + ('''Sample size''' is an ambiguous term. (1'''Sample size''' is an ambiguous term. (1) Size can be measured as an extensive quantity in terms of [[mass]] ''m''<sub>S</sub> [kg], [[volume]] ''V''<sub>S</sub> [m<sup>3</sup>], or [[energy]] ''E''<sub>S</sub> [J] of a pure [[sample]] S. If the sample consists of countable [[entity |entities]] ''X'', the [[count]] ''N''<sub>''X''</sub> [x] in sample S is an elementary quantity, in contrast to the extensive quantities used as indicators of sample size. (2) In statistics, however, the term 'sample size' does not refer to the individual sample, but indicates on the contrary the number of samples investigated or sampled from a study group. ''N'' is the number of [[sample]]s collected and assayed to obtain representative statistical information on the [[population]]. The population size defines the upper limit of the statistical sample size.[[population]]. The population size defines the upper limit of the statistical sample size.)
  • Saponin  + ('''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]]'''Saponin''' is a mild detergent that [[Permeabilization of plasma membrane|permeabilizes plasma membranes]] completely and selectively due to their high cholesterol content, whereas mt-membranes with lower cholesterol content are affected only at higher concentrations. Applied for [[Permeabilized tissue or cells|permeabilization of muscle fibres]].[[Permeabilized tissue or cells|permeabilization of muscle fibres]].)
  • Save and Disconnect  + ('''Save and Disconnect''': Stops data acquisition and disconnects from the O2k (only for DatLab 7))
  • Save as - DatLab  + ('''Save as''' a DatLab file. When disconnected from the O2k, save the file under a different file name, optionally in a different directory.)
  • Save - DatLab  + ('''Save''' a DatLab file. When disconnecte'''Save''' a DatLab file. When disconnected from the O2k, save any changes made under the identical file name overwriting the previous file. Such changes do not affect the raw data of the experiment, but relate to calibrations, experimental protocol, marks, events, and layout.</br></br>'''Temporary backup files''' are generated by DatLab in the current user's temp directory, indicated by adding tmp.$$$ to the file name. These files are retained only if the PC has failed during data analysis. During data acquisition, the data are written continuously onto the file, hence backup files are not necessary under these conditions. are not necessary under these conditions.)
  • Scaling factor  + ('''Scaling factor''' determines the multiplication factor that is applied to the time derivative of the signal.)
  • Scaling - DatLab  + ('''Scaling''' a graph in [[DatLab]]'''Scaling''' a graph in [[DatLab]] provides flexibility to vary the display of the plots and create Graph layouts. It allows viewing a data plot in differently scaled graphs, zooming the signal and time scales, and scrolling along the axes of the graph provide maximum information on the current experiment. This does not influence the format of stored data. Different ranges for the axes change the appearance of data dramatically. It is highly recommended to use reference layouts. </br></br>»''Compare:'' [[Select plots - DatLab]].[Select plots - DatLab]].)
  • Select O2k - DatLab  + ('''Select O2k - DatLab''')
  • Selectivity  + ('''Selectivity''' is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.)
  • Semiquinone  + ('''Semiquinone''' is an unstable free radical derived either from the removal of one hydrogen atom with its electron from [[quinol]] (reduced form), or by the addition of a single hydrogen atom to a [[quinone]] (oxidized form).)
  • Sensitivity  + ('''Sensitivity''' refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification.)
  • Serial port  + ('''Serial port''' describes the connection'''Serial port''' describes the connection between O2k and Computer. </br>With the [[USB-Cable 2.0\Type A-B]] connected, select '''Serial port''' in the [[Connection window]]. Depending on the [[O2k series]], it is possible to connect with a '''Serial port''' or [[USB port]].[[USB port]].)
  • Shredder-Accessory Box  + ('''Shredder-Accessory Box''': for storage and shipping of Shredder accessories.)
  • Sirtuins  + ('''Sirtuins''' are NAD<sup>+</sup'''Sirtuins''' are NAD<sup>+</sup>-dependent deacetylases which play a prominent role as metabolic regulators. Their dependence on intracellular levels of NAD<sup>+</sup> (NAD<sup>+</sup> activates sirtuin activity, whereas NADH inhibits it) makes them suitable as sensors that can detect cellular energy status.</br>[[Sirtuins#Sirtuin_family |» '''MiPNet article''']][[Sirtuins#Sirtuin_family |» '''MiPNet article''']])
  • Azide  + ('''Sodium azide''' is an inhibitor of [[Complex IV]]/cytochrome ''c'' oxidase (CIV, COX, CcO).)
  • Sodium fluoride  + ('''Sodium fluoride (NaF)''' is used in combination with [[beryllium sulfate]] to form beryllium trifluoride (BeF<sup>3−</sup>), to inhibit the [[ATP synthase]] if it is exposed by disruption of the mitochondrial membranes.)
  • Sodium orthovanadate  + ('''Sodium vanadate (Na<sub>3</sub>VO<sub>4</sub>)''' is used as an ATPase inhibitor.)
  • Solution protocols  + ('''Solution protocols''' contain media, substrates, uncouplers, inhibitors used in [[SUIT|SUIT protocols]], permeabilization agents, etc.)
  • Specific quantity  + ('''Specific quantities''' are obtained whe'''Specific quantities''' are obtained when the [[extensive quantity]] is divided by system size, in contrast to [[intensive quantity|intensive quantities]]. ''The adjective'' specific ''before the name of an extensive quantity is often used to mean divided by mass'' ([[Cohen 2008 IUPAC Green Book |Cohen et al 2008]]). A mass-specific quantity (''e.g.'', mass-specific flux is flow divided by mass of the system) is independent of the extent of non-interacting homogenous subsystems. If mass-specific oxygen flux is constant and independent of system size (expressed as mass), then there is no interaction between the subsystems. The well-established scaling law in respiratory physiology reveals a strong interaction of oxygen consumption and body mass by the fact that mass-specific basal metabolic rate (oxygen flux) does not increase proportionally and linearly with body mass. Maximum mass-specific oxygen flux, ''V''<sub>O2max</sub>, is less mass-dependent across a large range of body mass of different mammalian species (Weibel and Hoppeler 2005).ifferent mammalian species (Weibel and Hoppeler 2005).)
  • Spectrophotometry  + ('''Spectrophotometry''' is the use of a [[spectrophotometer]]'''Spectrophotometry''' is the use of a [[spectrophotometer]] to measure the transmittance, reflectance or remittance of a material as a function of wavelength. See [[transmission spectrophotometry]], [[reflectance spectrophotometry]] and [[remission spectrophotometry]].[[remission spectrophotometry]].)
  • Spectroscopy  + ('''Spectroscopy''' is a broader term than [[spectrophotometry]] in that it is concerned with the investigation and measurement of spectra produced when matter interacts with or emits any form electromagnetic radiation.)
  • Speed  + ('''Speed''', ''v'' [m·s<sup>-1</s'''Speed''', ''v'' [m·s<sup>-1</sup>], is the [[distance]], ''s'' [m], covered by a particle per unit time, irrespective of geometrical direction in space. Therefore, speed is not a [[vector]], in contrast to [[velocity]].</br> ''v'' = d''s''/d''t'' [m·s<sup>-1</sup>][velocity]]. ''v'' = d''s''/d''t'' [m·s<sup>-1</sup>])
  • Spermidine  + ('''Spermidine''' is a polycationic bioacti'''Spermidine''' is a polycationic bioactive polyamine mainly found in wheat germ, soybean and various vegetables, involved in the regulation of mitophagy, cell growth and cell death. Like other caloric restriction mimetics, spermidine is effective in cardioprotection, neuroprotection and anticancer immunosuppression by preserving mitochondrial function and control of autophagy.ondrial function and control of autophagy.)
  • Stability  + ('''Stability''' determines the accuracy of intensity and [[absorbance]] measurements as a function of time. Instability (see [[drift]] introduces systematic errors in the [[accuracy]] of [[fluorescence]] and [[absorbance]] measurements.)
  • Standard operating procedures  + ('''Standard operating procedures''' are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.)
  • State 1  + ('''State 1''' is the first respiratory sta'''State 1''' is the first respiratory state in an oxygraphic protocol described by [[Chance_1955_JBC-III|Chance and Williams (1955)]], when isolated mitochondria are added to mitochondrial respiration medium containing oxygen and inorganic phosphate, but no ADP and no reduced respiratory substrates. In State 1, [[LEAK respiration]] may be supported to some extent by undefined endogenous substrates, which are oxidized and slowly exhausted. After oxidation of endogenous substrates, only residual oxygen consumption remains ([[ROX]]).[[ROX]]).)
  • State 5  + ('''State 5''' is the [[respiratory state]]'''State 5''' is the [[respiratory state]] obtained in a protocol with isolated mitochondria after a sequence of [[State 1]] to [[State 4]], when the concentration of O<sub>2</sub> is depleted in the closed oxygraph chamber and zero oxygen (the anaerobic state) is reached ([[Chance 1955 JBC-III|Chance and Williams, 1955]]; Table I).</br></br>State 5 is defined in the original publication in two ways: ''State 5 may be obtained by antimycin A treatment or by anaerobiosis'' (Chance and Williams, 1955; page 414). [[Antimycin A]] treatment yields a State 5 equivalent to a state for measurement of [[residual oxygen consumption]], ROX (which may also be induced by [[rotenone]]+[[myxothiazol]]; [[Gnaiger 2009 Int J Biochem Cell Biol|Gnaiger 2009]]). Setting State 5 equivalent to ROX or anoxia (Chance and Williams 1955) can be rationalized only in the context of measurement of cytochrome redox states, whereas in the context of respiration State 5 is usually referred to as [[anoxic]].[[anoxic]].)
  • Stirrer power  + ('''Stirrer power''' is switched on and off during operation of the [[Oroboros O2k]] in [[DatLab]] by pressing [F11] (left chamber) and [F12] (right chamber), respectively. This is functional only with a stirrer bar added to each O2k chamber.)
  • Stopper-Shaft conical\white PVDF\central Port  + ('''Stopper-Shaft conical\white [[PVDF]]'''Stopper-Shaft conical\white [[PVDF]]\central Port''': PVDF shaft with one central capillary and conical base, receptacle on the top for collecting excess medium during closing the O2k-Chamber and during titration; component of [[Stopper\white PVDF\conical Shaft\central Port]].</br></br>'''Discontinued'''[[Stopper\white PVDF\conical Shaft\central Port]]. '''Discontinued''')
  • Stray light  + ('''Stray light''' is defined as the detect'''Stray light''' is defined as the detected light of any wavelength that lies outside the [[bandwidth]] of the selected wavelength. In the presence of '''stray light''' of intensity ''I''<sub>''s''</sub>, the equation for [[transmittance]] (''T'') becomes ''T'' = (''I'' + ''I''<sub>''s''</sub>)/(''I''<sub>''0''</sub> + ''I''<sub>''s''</sub>) where ''I''<sub>''0''</sub> is the incident light intensity and ''I'' is the transmitted light intensity. Clearly, the lower the value of ''I'', the more dominant becomes the '''stray light''' term and so can cause errors in the quantification of low [[fluorescence]] signals or at high levels of [[absorbance]].[[absorbance]].)
  • Strobilurin  + ('''Strobilurin''': {''Quote''} Strobilurin'''Strobilurin''': {''Quote''} Strobilurins are a group of chemical compounds used in agriculture as fungicides. They are part of the larger group of QoI inhibitors, which act to inhibit {''end of Quote'': [http://en.wikipedia.org/wiki/Strobilurin]} respiratory [[Complex III]].[[Complex III]].)
  • Submitochondrial particles  + ('''Submitochondrial particles''' (smtp) co'''Submitochondrial particles''' (smtp) consist of membrane fragments which retain most of the enzymatic machinery required in electron transfer and [[oxidative phosphorylation]]. Such membrane fragments are continuous closed vesicles formed by resealing of mt-membrane fragments after disruption of the mitochondrial structure. smtp are used to isolate the inner-[[membrane-bound ET pathway]] (mETS) from the upstream modules of the [[Electron transfer pathway]] (ETS) which are located in the mt-matrix and outer mt-membrane (transporters). smtp are obtained by treatment of mitochondria with membrane-dispersing agents such as digitonin at high concentration or by sonic irradiation.igh concentration or by sonic irradiation.)
  • Subsample  + ('''Subsamples''' can be obtained (1) from '''Subsamples''' can be obtained (1) from a homogenous [[sample]] (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of [[assay]] (e.g. for measurement of respiration and enzyme activities), and (ii) a number of [[repetitions]], ''n'', of the same assay on the same sample.n'', of the same assay on the same sample.)
  • Subscripts in physical chemistry  + ('''Subscripts in physical chemistry''' are'''Subscripts in physical chemistry''' are used to differentiate symbols of different quantities. While these subscripts need to be short to be readable, they have to be distinct and well defined. Several subscripts relate to fundamental terms and concepts, summarized in a list below. and concepts, summarized in a list below.)
  • Pathway control ratio  + ('''Substrate control ratios''' are [[flux control ratio]]'''Substrate control ratios''' are [[flux control ratio]]s ''FCR'', at a constant mitochondrial [[coupling-control state]]. Whereas there are only three well-defined coupling-control states of mitochondrial respiration, ''L'', ''P'', ''E'' ([[LEAK respiration]], [[OXPHOS]], [[Electron transfer pathway]]), numerous [[Electron-transfer-pathway state]]s are possible. </br></br>Careful selection of the reference state, ''J''<sub>ref</sub>, is required, for which some guidelines may be provided without the possibility to formulate general rules. ''FCR'' are best defined by taking ''J''<sub>ref</sub> as the maximum flux (e.g. [[NS |NS<sub>''E''</sub>]]), such that flux in various other respiratory states, ''J<sub>i</sub>'', is smaller or equal to ''J''<sub>ref</sub>. However, this is not generally possible with ''FCR''. For instance, the [[N/S pathway control ratio]] (at constant coupling-control state) may be larger or smaller than 1.0, depending on the mitochondrial source and various mitochondrial injuries. The [[S-pathway control state]] may be selected preferentially as ''J''<sub>ref</sub>, if mitochondria with variable [[N]]-linked injuries are studied. In contrast, the [[reference state]], ''Z'', is strictly defined for [[flux control efficiency]].[[flux control efficiency]].)
  • Succinate dehydrogenase  + ('''Succinate dehydrogenase''' is a [[TCA cycle]]'''Succinate dehydrogenase''' is a [[TCA cycle]] enzyme converting [[succinate]] to [[fumarate]] while reducing FAD to FADH<sub>2</sub>. SDH is the largest component of the mt-inner membrane [[Complex II]] (CII) and thus part of the TCA cycle and [[electron transfer pathway]].[[electron transfer pathway]].)
  • Succinyl-CoA ligase  + ('''Succinyl-CoA ligase''' (SUCLA or SUCLG)'''Succinyl-CoA ligase''' (SUCLA or SUCLG) is a TCA cycle enzyme converting succinyl-CoA + ADP or (GDP) + Pi to [[succinate]] + ATP (GTP). Two different isoforms exsist: SUCLA (EC: 6.2.1.5) is the ATP-forming isoenzyme, SUCLG (EC: 6.2.1.4) is the GTP-forming isoenzyme. Both reactions are reversible. This reaction is attributed to mitochondrial substrate-level phosphorylation, which is considered as an alternative way of ATP synthesis because it is partially independent from the respiratory chain and from the mitochondrial proton motive force.rom the mitochondrial proton motive force.)
  • Sulfide quinone reductase  + ('''Sulfide quinone reductase''' (SQR) is i'''Sulfide quinone reductase''' (SQR) is involved in electron transfer from sulfide which is used as a hydrogen donor by the mitochondrial respiratory system. SQR is associated with a [[dioxygenase]] and a [[sulfur transferase]] to release thiosulfate (H<sub>2</sub>S<sub>2</sub>O<sub>3</sub>).(H<sub>2</sub>S<sub>2</sub>O<sub>3</sub>).)
  • Sulfite oxidase  + ('''Sulfite oxidase''' (SO) is a dimeric en'''Sulfite oxidase''' (SO) is a dimeric enzyme, located in the intermembrane space of mitochondria, with each monomer containing a single Mo cofactor and cyt b5-type heme [1]. SO catalyzes the oxidation of sulfite to sulfate as the terminal step in the metabolism of sulfur amino acids and is vital for human health. Inherited mutations in SO result in severe neurological problems, stunted brain growth, and early death [2]. </br></br>Function: SO catalyzes the terminal reaction in the oxidative degradation of sulfur amino acids with the formation of a sulfate, electrons pass to cytochrom ''c'' and are further utilized in the respiratory system.</br></br>Sulfite + O<sub>2</sub> + H<sub>2</sub>O --> Sulfate + H<sub>2</sub>O<sub>2</sub> </br></br>Localization: The level of expression of SO differs in various tissues with main predominant localization in liver, kidney, skeletal muscle, heart, placenta, and brain in humans and liver, kidney, heart, brain, and lung in rats [3]. </br></br>Deficiency: SO is vital for metabolic pathways of sulfur amino acids (cysteine and methionine). Complete lack of this enzyme, typically caused by gene mutation, leads to lethal disease called sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.ed sulfite oxidase deficiency characterized by neurological abnormalities with brain atrophy.)
  • Synchronous time axes  + ('''Synchronous time axes''' sets, if ticked, the time axes of all graphs at an identical range and offset, which is particularly useful while panning.)
  • T-Shirt: Oroboros black/organic cotton  + ('''T-Shirt Oroboros black/organic cotton''': An Oroboros on the front.)
  • TIP2k and O2k-upgrade\B  + ('''TIP2k and O2k-Upgrade\B''': Titration-Injection microPump TIP2k, including the electronic upgrade of the O2k-main unit returned to workshop (Series B-D). '''Discontinued''')
  • TIP2k cooling box  + ('''TIP2k-Cooling Box''': Cooling box for TIP2k syringes. '''Discontinued''')
  • TIP2k-Needle Safety Support  + ('''TIP2k-Needle Safety Support''': for safe storage of TIP2k-needles when not required during the experiment. This item is a standard component of the [[TIP2k-Module]].)
  • TMRM  + ('''TMRM''' (tetramethylrhodamine methyl es'''TMRM''' (tetramethylrhodamine methyl ester) is an [[extrinsic fluorophores|extrinsic fluorophore]] used as a probe to determine changes in [[Mitochondrial_membrane_potential|mitochondrial membrane potential]]. TMRM is a lipophilic cation that is accumulated in the mitochondrial matrix in proportion to Δ''ψ''<sub>mt</sub>. Upon accumulation of the dye it exhibits a red shift in its absorption and fluorescence emission spectrum. The fluorescence intensity is quenched when the dye is accumulated in the mitochondrial matrix.en the dye is accumulated in the mitochondrial matrix.)
  • Tetrahydrofolate  + ('''Tetrahydrofolate''', THF, is the substrate in mitochondrial folate-mediated 1C metabolism, an [[NADH-linked pathway]] leading to the formation of formate which is exported to the cytosol.)
  • Tetraphenylphosphonium  + ('''Tetraphenylphosphonium''' (TPP<sup>+</sup>). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for [[Mitochondrial membrane potential | measuring the mitochondrial membrane potential]].)
  • Thenoyltrifluoroacetone  + ('''Thenoyltrifluoroacetone''' TTFA is a noncompetitive inhibitor of CII binding on the quinone-binding (SDHC/SDHD).)
  • Thioredoxin reductase  + ('''Thioredoxin reductase''' (TrxR) is a family of enzymes able to reduce thioredoxin in mammals.)
  • Time resolution  + ('''Time resolution''' in respirometric measurements is influenced by three parameters: the [[response time of the POS]], the data sampling interval and the number of points used for flux calculation.)
  • Traceability  + ('''Traceability''' is the property of the '''Traceability''' is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10].nties [SOURCE: VIM:1993, definition 6.10].)
  • Trueness of measurement  + ('''Trueness of measurement''' is the close'''Trueness of measurement''' is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the [[measurand]].[[measurand]].)
  • Trueness  + ('''Trueness''' is understood as the lack of [[bias]] and the instrument calibration procedures are the key factor on establishing and correcting it.)
  • USB-RS232 Serial Adapter  + ('''USB-RS232 Serial Adapter''', for connec'''USB-RS232 Serial Adapter''', for connecting the [[RS232-Cable]] attached to the [[O2k-Main Unit]] (Series A-D) to the USB port of the PC or laptop. This is not required for O2k-Series E, nor when using a PC or laptop with a serial RS232 port. '''Discontinued'''th a serial RS232 port. '''Discontinued''')
  • Uncertainty of measurement  + ('''Uncertainty of measurement''' is a para'''Uncertainty of measurement''' is a parameter, associated with the result of a [[measurement]], that characterizes the dispersion of the values that could reasonably be attributed to the [[measurand]]. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression.at are combined into one final expression.)
  • Uncoupling protein 1  + ('''Uncoupling protein 1''' (UCP1) is also '''Uncoupling protein 1''' (UCP1) is also called thermogenin and is predominantly found in brown adipose tissue (BAT). UCP1 belongs to the gene family of [[uncoupling proteins]]. It is vital for the maintenance of body temperature, especially for small mammals. As the essential component of non-shivering thermogenesis, it possesses the ability to build and open a pore in the inner mitochondrial membrane through which protons may flow along their electrochemical gradient, generated by respiration, bypassing the ATP-producing re-entry site at the F1F0-ATP synthase. Thereby the energy stored in the electrochemical gradient is dissipated as heat.rochemical gradient is dissipated as heat.)
  • Uncoupling protein 2  + ('''Uncoupling protein 2''' (UCP2) belongs to the gene family of [[uncoupling proteins]]. Whereas [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]], this may not be the case for UCP2.)
  • Uncoupling proteins  + ('''Uncoupling proteins''' (UCPs) are mitoc'''Uncoupling proteins''' (UCPs) are mitochondrial anion carrier proteins that can be found in the inner mitochondrial membranes of animals and plants. [[Uncoupling protein 1 |UCP1]] acts as an [[uncoupler]] by dissipating the electrochemical proton gradient ([[mitochondrial membrane potential]]), generated by the [[electron transfer pathway]] by pumping protons from the mitochondrial matrix to the mitochondrial intermembrane space. to the mitochondrial intermembrane space.)
  • Units in figures and tables  + ('''Units in figures and tables''' are spec'''Units in figures and tables''' are specified together with the numerical values. The ''value'' of a quantity ''Q'' is the product of a [[number]] ''N'' and a [[unit]] ''u''<sub>''Q''</sub>. Abstract units ''u''<sub>''Q''</sub> (such as dm<sup>3</sup>=L, kg, J) are linked to measured quantities (such as volume, mass, energy): </br> Eq.(1) ''Q''<sub>''u''</sub> = ''N''·''u''<sub>''Q''</sub></br></br>The multiplication in Eq.(1) can be handled like any mathematical equation and re-arranged to the form which indicates the meaning (left) of a number (right): </br> Eq.(2a) ''Q''<sub>''u''</sub>/''u''<sub>''Q''</sub> = ''N''</br> Eq.(2b) ''N''<sub>''X''</sub>/x = ''N''</br></br>When numbers are given on the axes of figures and in tables, the corresponding labels should be indicated according to Eq.(2), where Eq.(2a) applies to measured quantities, whereas Eq.(2b) relates to the countable quantity, i.e. [[count]] with unit [x]. For example, the axis label for volume-specific oxygen flux may be written as ''J''<sub>''V'',O<sub>2</sub></sub> / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''<sub>O<sub>2</sub></sub> / [amol/(s·x)].s ''J''<sub>''V'',O<sub>2</sub></sub> / [pmol/(s·mL)] and cell-count specific oxygen flow as ''I''<sub>O<sub>2</sub></sub> / [amol/(s·x)].)
  • Velocity  + ('''Velocity''', '''''v''''' [m·s<sup>'''Velocity''', '''''v''''' [m·s<sup>-1</sup>], is the [[speed]] in a defined spatial direction, and as such velocity is a [[vector]]. Velocity is the [[advancement]] in distance per unit time,</br> '''''v''''' ≡ d'''''z''''' ∙ d''t''<sup>-1</sup> [m·s<sup>-1</sup>] d'''''z''''' ∙ d''t''<sup>-1</sup> [m·s<sup>-1</sup>])
  • Viable cells  + ('''Viable cells''' vce are characterized by an intact plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>).)
  • Viton  + ('''Viton'''® is a fluoroelastomer with excellent resistance to aggressive fuels and chemicals. Viton is resistant against oxygen diffusion which makes it an ideal material for high-resolution respirometry (Viton O-rings).)
  • Volume  + ('''Volume''' ''V'' is a derived quantity b'''Volume''' ''V'' is a derived quantity based on the SI base quantity [[length]] [m] and is expressed in terms of [[SI base units]] in the derived unit cubic meter [m<sup>3</sup>]. The liter [L = dm<sup>3</sup>] is a conventional unit of volume for concentration and is used for most solution chemical kinetics. The volume ''V'' contained in a system (experimental chamber) is separated from the environment by the system boundaries; this is called the volume of the system, and described in practical language as big/small (derived from [[length]], [[height]]) or voluminous. Systems are defined at constant volume or constant [[pressure]]. For a pure sample S, the volume ''V''<sub>S</sub> of the pure sample equals the volume ''V'' of the system, ''V''<sub>S</sub> = ''V''. For [[sample]] s in a mixture, the ratio ''V''<sub>s</sub>·''V''<sup>-1</sup> is the nondimensional [[volume fraction]] ''Φ''<sub>s</sub> of sample s. Quantities divided by volume are [[concentration]]s of sample s in a mixture, such as [[count]] concentration ''C<sub>X</sub>'' = ''N<sub>X</sub>''·''V''<sup>-1</sup> [x·L<sup>-1</sup>], and amount of substance concentration ''C''<sub>B</sub> = ''n''<sub>B</sub>·''V''<sup>-1</sup> [mol·L<sup>-1</sup>]. Mass concentration is [[density]] ''ρ''<sub>s</sub> = ''m''<sub>s</sub>·''V''<sup>-1</sup> [kg·L<sup>-1</sup>]. In closed compressible systems (with a gas phase), the concentration of the gas increases, when pressure-volume [[work]] is performed on the system.is performed on the system.)
  • Wavelength averaging  + ('''Wavelength averaging''' is the averagin'''Wavelength averaging''' is the averaging of several adjacent data points across the recorded spectrum (spectral [[smoothing]]), to improve the [[signal-to-noise ratio]]. For example, if the instrument recorded 5 data points per nm, the average of the 5 points can be taken for each successive nm across the range of the spectrum to give a 5-point smoothing. This method clearly reduces the wavelength [[resolution]].[[resolution]].)
  • Work  + ('''Work''' [J] is a specific form of [[energy]]'''Work''' [J] is a specific form of [[energy]] in the First Law of thermodynamics, and a specific form of [[exergy]] in the Second Law of thermodynamics, performed by a closed or open system on its surroundings (the environment). This is the definition of ''external'' work, which is zero in [[isolated system]]s. The term exergy includes external and internal work. Mechanical work is force [N] times path length [m]. The internal-energy change of a closed system, d''U'', is due to external exchange (e) of work and heat, and external total work (et, including pressure-volume work) is the internal-energy change minus heat,</br> d<sub>et</sub>''W'' = d''U'' - d<sub>e</sub>''Q''b>et</sub>''W'' = d''U'' - d<sub>e</sub>''Q'')
  • Zero calibration  + ('''Zero calibration''' is, together with [[air calibration]]'''Zero calibration''' is, together with [[air calibration]], one of the two steps of the POS calibration. It is performed in the [[closed chamber]] after all the oxygen has been depleted by the addition of [[dithionite]] or by respiration of [[Isolated mitochondria |imt]] or [[Living cells |cells]]. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.ent experiments performed on the same day.)
  • DatLab 2  + ('''[[DatLab]] 2''' (DL2) is a MS-DOS programe. DL2 is still used for analysis of [[oxygen kinetics]], after exporting files recorded in recent DatLab versions. A user-friendly O2-kinetics module is in preparation (DL8).)
  • Substrates as electron donors  + ('''[[Substrate]]'''[[Substrate]]s as electron donors''' are reduced fuel compounds ''S''<sub>red</sub> that are oxidized to an oxidized product ''P''<sub>ox</sub> during H<sup>+</sup>-linked electron transfer, ''S''<sub>red</sub> → ''P''<sub>ox</sub> + 2{H<sup>+</sup> + e<sup>-</sup>}. Mitochondrial respiration depends on a continuous flow of electron-supplying substrates across the mitochondrial membranes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.anes into the matrix space. Many substrates are strong anions that cannot permeate lipid membranes and hence require carriers.)
  • Base quantities and count  + ('''[[Template:Base quantities and count]]''')
  • ArXiv preprint server  + ('''arXiv''' is a classic preprint server i'''arXiv''' is a classic preprint server initiated in 1991 by Paul Ginsparg. {''Quote''} arXiv.org is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by Cornell University with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators. {''end of Quote''}. arXiv rejects abstracts that are submitted without accompanying paper. are submitted without accompanying paper.)
  • BioRxiv preprint server for biology  + ('''bioRxiv''' (pronounced "bio-archive") i'''bioRxiv''' (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It was launched in 2013 by Cold Spring Harbor Laboratory Press in New York, and is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. bioRxiv is intended for rapid sharing of new research. Some review articles contain new data/analyses and may therefore be deemed appropriate. Reviews that solely summarize existing knowledge are not appropriate and neither are term papers, book excerpts, and undergraduate dissertations.excerpts, and undergraduate dissertations.)
  • PH calibration buffers  + ('''pH calibration buffers''' are prepared to obtain two or more defined pH values for calibration of pH electrodes and pH indicator dyes.)
  • PH combination electrode 150/6 mm  + ('''pH combination electrode''', 150 mm shaft, 6 mm diameter, incl. connection cable with BNC plug. '''Discontinued''' * Replaced by [[O2k-pH ISE-Module]].)
  • PH combination electrode 70/5 mm  + ('''pH-Combination Electrode\70/5 mm''', 70 mm shaft, 5 mm diameter, for 30251-24 stopper. ''' Discontinued ''' * Replaced by [[O2k-pH ISE-Module]].)
  • PX calibration - DatLab  + ('''pX calibration''')
  • Hydroxybutyrate  + ('''β-hydroxybutyrate''' or 3-hydroxybutyrate is a ketone body that can be used as a [[NADH electron transfer-pathway state|NADH-linked substrate]]. The β-hydroxybutyrate dehydrogenase produces acetoacetate while reducing NAD<sup>+</sup> to [[NADH]]. <br>)
  • Complex I-linked substrate state  + (''See'' '''[[N-pathway control state]]''' (previous: CI-linked) versus '''[[Complex I]]''')
  • CI control ratio  + (''See'' '''[[N/NS pathway control ratio]]''')
  • Complex I&II-linked substrate state  + (''See'' '''[[NS-pathway control state]]''' (previous: CI<small>&</small>II-linked))
  • Substrate control efficiency  + (''See'' '''[[Pathway control efficiency]]''')
  • Substrate control ratio  + (''See'' '''[[Pathway control ratio]]''')
  • Complex II-linked substrate state  + (''See'' '''[[S-pathway control state]] (previous: CII-linked))
  • CII control ratio  + (''See'' '''[[S/NS pathway control ratio]]''')
  • Group  + (''See'' '''[[population]]'''.)
  • Phosphate  + (''See:'' '''[[Inorganic phosphate]]''')
  • Autoxidation  + (''This definition is insufficient and need''This definition is insufficient and needs elaboration.''</br></br>Autoxidation is a slow process implying oxidation of carbohydrates through oxygen in open air, leading to a primary formation of peroxides and hydroperoxides. UV radiation can speed up this process.s. UV radiation can speed up this process.)
  • Cellular substrates  + ((1) Cellular substrates ''in vivo'', endogenous; '''Ce'''. (2) Cellular substrates ''in vivo'', with exogenous substrate supply from culture medium or serum; '''Cm'''. * ''This page needs an update.'')
 (-5B-5BFile:1PM-3B2D-3B3G-3B4U-3B5S-3B6Rot-2D.png-7C300px-5D-5D)
  • Natoms O  + (0.5 nmol O<sub>2</sub>; in bioenergetics a variety of expressions is used for units of amount of half a nmol molecular oxygen (natoms oxygen; natoms O; ng.atom O; nmol O), with the identical meaning: 0.5 nmol O<sub>2</sub>.)
  • BAM15  + (2-fluorophenyl){6-[(2-fluorophenyl)amino](2-fluorophenyl){6-[(2-fluorophenyl)amino](1,2,5-oxadiazolo[3,4-e]pyrazin-5-yl)}amine ('''BAM15''') is a protonophore or uncoupler of [[Oxidative phosphorylation|oxidative phosphorylation]] detected in a screen for uncoupling agents exerting less toxicity than commonly used uncouplers and first described by [[Kenwood 2013 Mol Metab|Kennwood et al. 2013]]. In their comparison of BAM15 with FCCP it was shown to increase oxygen flux to a similar extent as the classical uncoupler, to display a much broader range of concentrations inducing maximum respiration, to stimulate no formation of H<sub>2</sub>O<sub>2</sub>, to leave cellular membrane potential unaffected, and to ultimately exert less cytotoxicity.e potential unaffected, and to ultimately exert less cytotoxicity.)
  • 3-Mercaptopropionic acid  + (3-Mercaptopropionic acid (MPA) inhibits long chain [[acyl-CoA dehydrogenase]]s (ACADs).)
  • Mitochondrial states and rates - terminology beyond MitoEAGLE 2020  + (666 coauthors of the 'MitoEAGLE white paper' [1] collaborated to reach a consensus on terminology related to mitochondrial respiratory states and rates. This page is intended to prepare a questionnaire and follow-up publication.)
  • Mitochondria Interest Group  + (<br/> [[File:MIG.gif|128 px|left]]<br/> </br>[[File:MIG.gif|128 px|left]]</br>The '''Mitochondria Interest Group''' (MIG) is an Inter-Institute Interest Group at the National Institutes of Health (NIH), with members worldwide! MIG is concerned with all aspects of the mitochondrion and diseases in which the mitochondrion is involved. We hold monthly meetings, usually on the second Monday of the month (except when it is a Federal holiday or other special exceptions). </br></br>[email protected] is an Email list moderated by Ph.D. Steven Zullo as an interactive information platform, with free subscritpion to this mitochondrial network. List members are reminded of their responsibility to critically evaluate the content of the postings. The information, opinions, data, and statements contained herein are not necessarily those of the U. S. Government, the National Institutes of Health (NIH), or MIG and should not be interpreted, acted on or represented as such.be interpreted, acted on or represented as such.)
  • Custom label  + (A '''Custom label''' can be entered in this box to rename the axis label. Two lines are available for the axis name and unit.)
  • Digital Object Identifier  + (A '''Digital Object Identifier''', DOI, isA '''Digital Object Identifier''', DOI, is a persistent identifier used to uniquely identify online publications in order to ensure they remain traceable, searchable and citable over the long term. Compared to other types of persistent identifiers, the DOI system is widespread and well established in the life sciences arena, and it provides widely accepted visible proof that a publication is citable.sible proof that a publication is citable.)
  • Layout for DatLab graphs  + (A '''Layout''' in [[DatLab]]A '''Layout''' in [[DatLab]] selected in the Layout menu yields a standardized display of graphs and [[Plot - DatLab |plots]] displayed with specific [[Scaling - DatLab|scalings]]. The graph layout defines initial settings, which can be modified for plots [Ctrl+F6] and scaling [F6]. A modified layout can be saved as user layout without changing the standard layouts.out without changing the standard layouts.)
  • Lower O2 limit - DatLab  + (A '''Lower O2 limit [µM]''' can be definedA '''Lower O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration drops below this limit. It reminds the user that re-oxygenation of the O2k-chamber may be required. For the lower O<sub>2</sub> concentration limit, the [[critical oxygen pressure |critical oxygen concentration]] should be considered, which differs between isolated mitochondria, large cells, and permeabilized muscle fibers. A higher limit should be chosen when high oxygen flux is expected, e.g. prior to uncoupler titration. A lower limit is acceptable prior to inhibition of respiration causing low oxygen flux.ptable prior to inhibition of respiration causing low oxygen flux.)
  • National Standards Body  + (A '''National Standards Body''' is the national member of the [[International Organization for Standardization]] (ISO).)
  • Notified Body  + (A '''Notified Body''' is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.)
  • Quality audit  + (A '''Quality Audit''' is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.)
  • Stand alone application  + (A '''Stand alone application''' is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network.)
  • Upper O2 limit - DatLab  + (A '''Upper O2 limit [µM]''' can be defined for each O2k-chamber, to trigger an automatic warning when the experimental O<sub>2</sub> concentration rises beyond this limit.)
  • Web application  + (A '''Web application''' is a computer software where the [[user interface]] gets accessed by the user through a web browser.)
  • Canonical ensemble  + (A '''canonical ensemble''' is the group ofA '''canonical ensemble''' is the group of compartments enclosed in an isolated system '''H''', with a smaller compartment A<sub>1</sub> in thermal equilibrium with a larger compartment A<sub>2</sub> which is the heat reservoir at temperature ''T''. When A<sub>1</sub> is large in the canonical sense, if its state can be described in terms of macroscopic thermodynamic quantities of ''V'', ''T'', and ''p'' merging with the state described as a probability distribution.T'', and ''p'' merging with the state described as a probability distribution.)
  • Closed system  + (A '''closed system''' is a system with bouA '''closed system''' is a system with boundaries that allow external exchange of energy (heat and work), but do not allow exchange of matter. A limiting case is light and electrons which cross the system boundary when work is exchanged in the form of light or electric energy. If the surroundings are maintained at constant temperature, and heat exchange is rapid to prevent the generation of thermal gradients, then the closed system is isothermal. A frequently considered case are closed isothermal systems at constant pressure (and constant volume with aqueous solutions). Changes of closed systems can be partitioned according to internal and external sources. Closed systems may be homogenous (well mixed and isothermal), continuous with gradients, or [[Discontinuous system|discontinuous]] with compartments (heterogenous).[[Discontinuous system|discontinuous]] with compartments (heterogenous).)
  • Coenzyme  + (A '''coenzyme''' or cosubstrate is a [[cofactor]]A '''coenzyme''' or cosubstrate is a [[cofactor]] that is attached loosely and transiently to an enzyme, in contrast to a [[prosthetic group]] that is attached permanently and tightly. The coenzyme is required by the corresponding enzyme for its activity (IUPAC definition). A coenzyme is 'a low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons' (IUPAC definition).l groups or electrons' (IUPAC definition).)
  • Cofactor  + (A '''cofactor''' is 'an organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely ([[coenzyme]]) or tightly ([[prosthetic group]])' (IUPAC definition).)
  • Coupling-control protocol  + (A '''coupling-control protocol CCP''' induA '''coupling-control protocol CCP''' induces different [[coupling control state]]s at a constant [[electron-transfer-pathway state]]. [[Residual oxygen consumption]] (''Rox'') is finally evaluated for ''Rox'' correction of flux. The CCP may be extended, when further respiratory states (e.g. cell viability test; CIV assay) are added to the coupling control module consisting of three coupling control states. The term '''phosphorylation control protocol''', PCP, has been introduced synonymous for CCP.</br>» [[Coupling_control_protocol#From_PCP_to_CCP |'''MiPNet article''']][Coupling_control_protocol#From_PCP_to_CCP |'''MiPNet article''']])
  • Dataset  + (A '''dataset''' is a collection of data. In the context of databases a dataset represents the collection of entries in a database-table. In this table columns represent [[Attribute|attributes]] and rows display the according values of the entries.)
  • Decimal marker and spaces between groups of numerals  + (A '''decimal marker''' is used to separateA '''decimal marker''' is used to separate the integral part of numbers from the decimal part. The SI recommends: "the symbol for the decimal marker shall be either the point on the line or the comma on the line". In English language versions, the dot (point on the line) should be used uniquely as the decimal marker. To avoid ambiguities, BEC follows the SI recommendation that “Numbers may be divided in groups of three in order to facilitate reading; neither dots nor commas are ever inserted in the spaces between groups” (pages 183-184).he spaces between groups” (pages 183-184).)
  • Detector  + (A '''detector''' is a device that convertsA '''detector''' is a device that converts the light falling upon it into a current or voltage that is proportional to the light intensity. The most common devices in current use for [[fluorometry]] and [[spectrophotometry]] are [[photodiodes]] and [[photodiode arrays]].[[photodiode arrays]].)
  • Difference spectrum  + (A '''difference spectrum''' is an [[absorbance spectrum]]A '''difference spectrum''' is an [[absorbance spectrum]] obtained by subtracting that of one substance from that of another. For example, a '''difference spectrum''' may be plotted of the [[absorbance spectrum]] obtain ed from reduced [[cytochrome c]] and subtracting the [[absorbance spectrum]] from the same concentration of [[cytochrome c]] in its oxidised state. The [[difference spectrum]] may be used to quantify the amount to which the [[cytochrome c]] is reduced. This can be achieved with the aid of a [[reference spectrum]] (or spectra) and the [[least squares method]].[[least squares method]].)
  • Directive  + (A '''directive''' is a legal act of the European Union, which requires member states to achieve a particular result without dictating the means of achieving that result.)
  • Dispersion devices  + (A '''dispersion device''' diffracts light A '''dispersion device''' diffracts light at different angles according to its wavelength. Traditionally, prisms and [[diffraction gratings]] are used, the latter now being the most commonly used device in a [[spectrofluorometer]] or [[spectrophotometer]].[[spectrophotometer]].)
  • Fluorophore  + (A '''fluorophore''' is a fluorescent substA '''fluorophore''' is a fluorescent substance that may occur naturally ([[intrinsic fluorophores]]) or that may be added to a sample or preparation whereby the fluorescence intensity is proportional to the concentration of a specific species or parameter within the sample. These are [[extrinsic fluorophores]], also referred to as fluorescent markers., also referred to as fluorescent markers.)
  • Free radicals  + (A '''free radical''' is any atom or molecuA '''free radical''' is any atom or molecule that contains one or more unpaired electrons in an orbital. The degree of chemical reactivity depends on the localization of unpaired electrons. Free radicals are extremely reactive, and they can either donate or accept an electron from other molecules. Free radicals that include oxygen radicals and derivatives of oxygen are [[reactive oxygen species]] (ROS). Likewise, [[reactive nitrogen species]] (RNS) are nitric oxide-derived compounds. ROS/RNS include oxygen/nitrogen free radicals and non-radicals that are easily converted into radicals. Mitochondria are a main endogenous source of free radicals in cells and consequently are exposed to oxidative-nitrosative damage. Electron transfer in the electron transfer-pathway (ET-pathway) is not perfect, leading an electron leakage. This electron leakage permits the formation of ROS such as [[superoxide]] anion (O2•−), [[hydrogen peroxide]] (H<sub>2</sub>O<sub>2</sub>) and the hydroxyl radical (HO•)./sub>O<sub>2</sub>) and the hydroxyl radical (HO•).)
  • Harmonized standard  + (A '''harmonized standard''' is a European [[standard]] developed by a recognized European Standards Organisation: CEN, CENELEC, or ETSI.)
  • Healthy reference population  + (A '''healthy reference population''', HRP,A '''healthy reference population''', HRP, establishes the baseline for the relation between body mass and height in healthy people of zero underweight or overweight, providing a reference for evaluation of deviations towards underweight or overweight and obesity. The WHO Child Growth Standards (WHO-CGS) on height and body mass refer to healthy girls and boys from Brazil, Ghana, India, Norway, Oman and the USA. The Committee on Biological Handbooks compiled data on height and body mass of healthy males from infancy to old age (USA), published before emergence of the fast-food and soft-drink epidemic. Four allometric phases are distinguished with distinct allometric exponents. At heights above 1.26 m/x the allometric exponent is 2.9, equal in women and men, and significantly different from the exponent of 2.0 implicated in the body mass index, BMI [kg/m<sup>2</sup>].e body mass index, BMI [kg/m<sup>2</sup>].)
  • High signal at zero oxygen  + (A '''high signal at zero oxygen''' may be A '''high signal at zero oxygen''' may be observed during [[zero calibration]] (R0). First, check the quality of the [[dithionite]] solution. The following instructions show how to distinguish between a defective sensor head and an electrical leak current.ensor head and an electrical leak current.)
  • Light-emitting diode  + (A '''light-emitting diode''' (LED) is a liA '''light-emitting diode''' (LED) is a light source (semiconductor), used in many every-day applications and specifically in [[fluorometry]]. LEDs are available for specific spectral ranges across wavelengths in the [http://en.wikipedia.org/wiki/Light-emitting_diode#Colors_and_materials visible, ultraviolet, and infrared range].visible, ultraviolet, and infrared range].)
  • Measurement process  + (A '''measurement process''' or a '''measurement''' is a set of operations to determine the value of a [[quantity]].)
  • Measuring equipment  + (A '''measuring equipment''' is a measuring instrument, software, measurement standard, reference material or auxiliary apparatus, or a combination thereof, necessary to realize a measurement process.)
  • Medical device  + (A '''medical device''' is an instrument, aA '''medical device''' is an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article, including a component part, or accessory which is (1) intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or (2) intended to affect the structure or any function of the body of man or other animals, and which does not achieve any of its primary intended purposes through chemical action within or on the body of man or other animals and which is not dependent upon being metabolized for the achievement of any of its primary intended purposes.t of any of its primary intended purposes.)
  • Metabolic control variable  + (A '''metabolic control variable''' ''X'' cA '''metabolic control variable''' ''X'' causes the transition between a [[background state]] Y (background rate ''Y<sub>X</sub>'') and a [[reference state]] Z (reference rate ''Z<sub>X</sub>''). ''X'' may be a stimulator or activator of flux, inducing the step change from background to reference steady state (Y to Z). Alternatively, ''X'' may be an inhibitor of flux, absent in the reference state but present in the background state (step change from Z to Y).ate but present in the background state (step change from Z to Y).)
  • Model  + (A '''model''' regarding databases is the representation of a real world object in a computer understandable language. A '''model''' can be defined by the structure of its [[dataset]] and the relations to other '''models'''.)
  • Norm  + (A '''norm''' is a rule that is enforced by members of a community.)
  • Number  + (A '''number''' ''N'' (or ''n'') is a [[count]]A '''number''' ''N'' (or ''n'') is a [[count]] ''N''<sub>''X''</sub> [x] divided by the [[elementary entity]] ''U''<sub>''X''</sub> [x]. ''X'' must represent the same entity in both occurences. The elementary unit [x] cancels in the division by simplification, such that numbers (for example, numbers 8 or 24) are abstracted from the counted entity ''X''. The concept of number is tightly entangled with units, counts and entities.pt of number is tightly entangled with units, counts and entities.)
  • Numeral  + (A '''numeral''' is the symbol representingA '''numeral''' is the symbol representing a specific [[number]]. A numeral is the figure of a number, with different notation types used as a figure (VIII and 8 for Roman and Arabic numerals; 八 and 捌 for practical and financial Chinese). A numeral may consist of one or more characters or digits. 60 and 60.00 are different numerals consisting of two and four digits, respectively, which represent the same number sixty. Sixty is the name of the number 60, with the meaning 'number 60'. ''N'' is not a numeral but a symbol representing the entity 'number'. The equation ''N''=60 assignes the numerical value 60 to the entity 'number'. The numeral 60 is a symbol for a pure number that equals 6 times 10 (or 2 times 30; or 1 times 60).6 times 10 (or 2 times 30; or 1 times 60).)
  • Plot - DatLab  + (A '''plot''' in DatLab represents a specific [[O2k signals and output|channel]] in the graph. To change the [[Layout for DatLab graphs]] go to [Graph]/'''[[Select plots - DatLab |Select plots]]''' to open the '''Graph layout''' window.)
  • Polarization voltage  + (A '''polarization voltage''' of 600 mV to A '''polarization voltage''' of 600 mV to 800 mV is applied between anode and cathode of the [[polarographic oxygen sensor]], resulting in a current when oxygen is consumed. The current is converted by the electronics to a voltage (raw signal) which must not be confused with the polarization voltage.be confused with the polarization voltage.)
  • Population  + (A '''population''' (or '''group''') defines the [[sample type]] of an [[experiment]], before sample preparation. The population (or group) size represents the upper limit of the [[sample size]], ''N''.)
  • Preprint  + (A '''preprint''' is {''Quote''} a way in wA '''preprint''' is {''Quote''} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {''end of Quote''}. Preprints are disseminated without peer review, e.g. in the preprint server [[MitoFit Preprints]]. In contrast, the journal [[Bioenergetics Communications]] publishes peer-reviewed articles, which preferentially are communicated in advance in MitoFit Preprints.municated in advance in MitoFit Preprints.)
  • Product  + (A '''product''' in a chemical reaction has a positive [[stoichiometric number]] since it is produced, whereas a [[substrate]] has a negative stoichiometric number since it is consumed.)
  • Prosthetic group  + (A '''prosthetic group''' is a [[cofactor]]A '''prosthetic group''' is a [[cofactor]] that is attached permanently and tightly or even covalently to an enzyme and that is regenerated in each enzymatic turnover. Thus a prostethic group is distinguished from a [[coenzyme]] or cosubstrate that is attached loosely and transiently. Like a coenzyme, the prosthetic group is required by an enzyme for its activity. A prosthetic group is 'a tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity' (IUPAC definition).</br></br>FMN/FMNH<sub>2</sub> and FAD/FADH<sub>2</sub> are prosthetic groups of [[Complex I]] and [[Complex II]], respectively.[[Complex II]], respectively.)
  • Quantity  + (A '''quantity''' is the attribute of a pheA '''quantity''' is the attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively. A [[dimension |dimensional]] quantity is a number (variable, parameter, or constant) connected to its dimension, which is different from 1. {''Quote''} The value of a quantity is generally expressed as the product of a number and a unit. The unit is simply a particular example of the quantity concerned which is used as a reference, and the number is the ratio of the value of the quantity to the unit. {''end of Quote'': Bureau International des Poids et Mesures 2019 The International System of Units (SI), p. 127)}.ernational System of Units (SI), p. 127)}.)
  • Reference spectrum  + (A '''reference spectrum''' for a substance is an [[absorbance spectrum]] of the same substance at a known concentration and [[redox state]].)
  • Requirement  + (A '''requirement''' is a singular documented physical or functional need that a particular design, product or process must be able to perform.)
  • Sample  + (A '''sample''' is one or more parts taken A '''sample''' is one or more parts taken from an ensemble that is studied. A sample is either stored for later quantification or prepared and possibly separated into subsamples, which are enclosed in a system for qualitative or quantitative investigation. A pure sample S is a pure gas, pure liquid or pure solid of a defined elementary [[entity]]-type. A pure biological sample is a cell type, tissue, or organism without its solid, liquid or gaseous environment. Then the system used to investigate sample S contains only entities of entity-type S, and the [[volume]] ''V''<sub>S</sub> [L] and [[mass]] ''m''<sub>S</sub> [kg] of the pure (sub)sample S are identical to the volume ''V'' and mass ''m'' of the experimental [[system]]. A pure sample S may be mixed with other components to be investigated as a solution, mixture, or suspension, indicated by the symbol s in contrast to the pure sample S. A sample s is obtained in combination with other components, such that the [[volume]] ''V''<sub>s</sub> [L] and [[mass]] ''m''<sub>s</sub> [kg] of the sample s are larger than the volume ''V''<sub>S</sub> and mass ''m''<sub>S</sub> of the pure sample S. For example, the number of cells ''N''<sub>ce</sub> [Mx] can be counted in a sample s of a cell suspension, whereas the mass ''m''<sub>ce</sub> [mg] of cells requires a pure sample S of cells to be measured on a mass-balance. Clarity of statistical representation is improved, if the symbol ''N'' is used for the number of [[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats.[[primary sample]]s taken from a study group, and the symbol ''n'' is used for the number of subsamples studied as technical repeats.)
  • Scalar  + (A '''scalar''' is a pysicochemical quantitA '''scalar''' is a pysicochemical quantity that is fully described by its magnitude. A potential difference, differences of concentration or pressure are scalars, whereas a potential gradient is a [[vector]]. Similarly, the [[protonmotive force]] and metabolic oxygen [[flux]] are scalars, whereas the fundamental [[force]]s of physics and [[velocity]] are vectors.[[velocity]] are vectors.)
  • Solutions  + (A '''solution''' is {''Quote''}: A liquid A '''solution''' is {''Quote''}: A liquid or solid phase containing more than one substance, when for convenience one (or more) substance, which is called the solvent, is treated differently from the other substances, which are called solutes. When, as is often but not necessarily the case, the sum of the mole fractions of solutes is small compared with unity, the solution is called a dilute solution. A superscript attached to the ∞ symbol for a property of a solution denotes the property in the limit of infinite dilution {''end of Quote'': [http://goldbook.iupac.org/S05746.html IUPAC Gold Book]}.</br>[[Solutions#Stock-.2C_storage-_and_working-solutions:_How_do_they_differ.3F |» '''MiPNet article''']]Solutions#Stock-.2C_storage-_and_working-solutions:_How_do_they_differ.3F |» '''MiPNet article''']])
  • Spectrofluorometer  + (A '''spectrofluorometer''' makes use of a A '''spectrofluorometer''' makes use of a [[spectrometer]] to measure and analyse the fluorescent emission spectra from a [[fluorophore]]. It will typically differ from an [[absorbance]] [[spectrophotometer]] in that it will have a larger [[slit width]] (to increase [[sensitivity]]) and use a longer [[integration time]]. The configuration of the illuminating and receiving optics also differ from [[spectrophotometry]] in that the excitation source is directed perpendicularly to the position of the emission [[detector]] so that the intensity of the excitation signal reaching the [[detector]] is minimised.[[detector]] is minimised.)
  • Spectrophotometer  + (A '''spectrophotometer''' is an instrumentA '''spectrophotometer''' is an instrument that consists of an entrance slit, a dispersion device (see [[dispersion devices]] and a [[detector]] for the purpose of measuring the intensity of light emerging from a sample across a given wavelength range. A [[light source]] is also necessary in order for the instrument to function, and this may be located within the instrument or from an external source using [[lightguides]] or other [[optics]].[[optics]].)
  • Standard  + (A '''standard''' is an established [[norm]] or [[requirement]] in regard to a defined system. It can consist of a formal document that establishes uniform criteria, methods, processes and practices.See also [[Harmonized standard]].)
  • Stirrer test  + (A '''stirrer test''' is performed in the [[Oroboros O2k]]A '''stirrer test''' is performed in the [[Oroboros O2k]] for quick evaluation of the performance of the [[OroboPOS]] and for [[POS calibration - dynamic|dynamic calibration]]. Stirring is stopped in both chambers and restarted after a selected period. The default period is 30 s, for experiments at 37 °C. At lower experimental temperature, this period should be prolonged (60 s at 25 °C). In the [[O2k-Open Support#O2k_Quality_Control |SOP (O2k Quality Control)]] for the [[O2k-Open_Support#1._O2_sensor_test|O<sub>2</sub> sensor test]], the stirrer test is performed in the 'open' chamber in conjunction with [[Air calibration]]. In general, the stirrer test can be performed equally with an open or closed chamber. Upon automatic re-start of the stirrer (On), the increase of the oxygen signal should be rapid and monoexponential.the oxygen signal should be rapid and monoexponential.)
  • Three-electrode system  + (A '''three-electrode system''' is the setuA '''three-electrode system''' is the setup used in the [[Q-Sensor]], which is an integral part of the [[Q-Module]]. This system is used in voltammetry (including [[cyclic voltammetry]]) to study the current as a function of the applied potential using three different electrodes: 1) the working electrode 2) the reference electrode, and 3) the counter electrode. In the [[Q-Sensor]], the working or detecting electrode is a glassy carbon (GC) electrode that is set to a given potential and makes contact with the analyte. The potential of the working electrode is controlled by the constant potential of the a silver/silver chloride (Ag/AgCl) reference electrode, which does not pass any current. The applied potential on the surface of the GC should be sufficient to either oxidize reduced analyte (in this case [[Coenzyme Q]]) or to reduce oxidized analyte. Thus, the counter electrode is a platinum electrode (Pt) that passes a current to counter these redox events by completing the circuit that is rate-limited by electron transfer on the GC. To determine the reduced Q fraction the GC electrode is set at the oxidation peak potential, which can be determined with [[cyclic voltammetry]].[[cyclic voltammetry]].)
  • Tissue homogenate  + (A '''tissue homogenate''' (thom) is obtained through mechanical micro-disruption of fresh tissue and the cell membranes are mechanically permeabilized.)
  • User code - DatLab  + (A '''user''' code or name is entered upon starting [[DatLab]]. This window pops up automatically after opening DatLab. Usernames are connected with personal [[Layout for DatLab graphs |graph layouts]].)
  • Vector  + (A '''vector''' is a pysicochemical quantitA '''vector''' is a pysicochemical quantity with magnitude and spatial direction of a [[gradient]]. Symbols for vectors are written in bold face. For example, [[velocity]], '''''v''''', and the fundamental [[force]]s of physics, '''''F''''', are vectors. An infinitesimal area is a vector, d'''''A''''', perpendicular to the plane. d'''''A''''', perpendicular to the plane.)
  • Working measurement standard  + (A '''working measurement standard''' is a standard that is used routinely to calibrate or check material measures, measuring instruments or reference materials [SOURCE: VIM:1993, 6.7].)
  • In vitro diagnostic medical device  + (A [[medical device]]A [[medical device]] is an '''in vitro diagnostic medical device (IVD)''' if it is a reagent, calibrator, control material, kit, specimen receptacle, software, instrument, apparatus, equipment or system, whether used alone or in combination with other diagnostic goods for in vitro use.h other diagnostic goods for in vitro use.)
  • Steady state  + (A [[system]]A [[system]] is in a '''steady state''' if the state variables of a dynamic system do not change over time due to exchange processes with the environment, which compensate for internal dissipative transformations — such as chemical reactions or diffusion — and thus prevent any changes of the system and externalize dissipative changes to the environment. The dynamic nature of the steady state differentiates it from the thermodynamic equilibrium state. {''Quote''} Steady states can be obtained only in [[open system]]s, in which changes by internal transformations, ''e.g.'', O<sub>2</sub> consumption, are instantaneously compensated for by external fluxes across the system boundary, ''e.g.'', O<sub>2</sub> supply, thus preventing a change of O<sub>2</sub> concentration in the system (Gnaiger 1993). Mitochondrial [[respiratory states]] monitored in [[closed system]]s satisfy the criteria of pseudo-steady states for limited periods of time, when changes in the system ([[concentration]]s of O<sub>2</sub>, fuel substrates, ADP, P<sub>i</sub>, H<sup>+</sup>) do not exert significant effects on metabolic fluxes (respiration, phosphorylation). Such pseudo-steady states require respiratory media with sufficient buffering capacity and substrates maintained at kinetically-saturating concentrations, and thus depend on the kinetics of the processes under investigation. {''end of Quote'': [[BEC 2020.1]]}. Whereas fluxes may change at a steady state over time, concentrations are maintained constant. The 'respiratory steady state' (Chance and Williams 1955) is characterized by constant fluxes (O<sub>2</sub> flux, H<sub>2</sub>O<sub>2</sub> flux) and measured variables of state (cytochrome redox states, Q redox state, NADH redox state, mitochondrial membrane potential). [[High-resolution respirometry]] allows for the measurement of several parameters (''e.g.'' O<sub>2</sub> flux, H<sub>2</sub>O<sub>2</sub> flux, mitochondrial membrane potential) at pseudo-steady states, when changes of [[concentration]]s in the [[closed system]] do not exert any control on fluxes. Combination with the [[TIP2k-Module| Titration-Injection microPump (TIP2k)]] allows operation with programmable titration regimes at steady-state ADP concentration (Gnaiger 2001), oxygen concentration (oxystat mode; Gnaiger et al 2000, Harrison et al 2015) or steady-state pH (pH-stat more), yielding an expanded flexibility in experimental design by combining the technical advantages of closed and [[open system]]s approaches.en system]]s approaches.)
  • Uninterrupted power supply  + (A back-up power supply may be required to secure '''uninterrupted power supply'''.)
  • Graph control - DatLab  + (A combination of mouse and keyboard commands provides convenient control of graphs in DatLab 8.)
  • SUIT: Browse DL-Protocols and templates  + (A comprehensive library of SUIT protocols A comprehensive library of SUIT protocols including DatLab example traces, instructions, brief explanatory texts, links to relevant pages, representative diagrams and templates for data evaluation can be browsed from inside DatLab 7.4. Click on menu [Protocols]\SUIT: Browse DL-Protocols and templates to open a folder with all the [[MitoPedia: SUIT|SUIT protocols]] provided with the DatLab 7.4. [[Run DL-Protocol/Set O2 limit| DL-Protocols]] (DLP) for different [[MitoPedia: Sample preparations|sample preparations]] can be chosen to assess multiple sequences of respiratory [[Coupling control state|coupling control ]] and [[Electron-transfer-pathway state|ET-pathway ]] states. DL-Protocols posses unique D## codes and comprise a fixed sequence of events and marks which cannot be changed by the user. However, the users can edit titration volumes and concentrations in the Overview window of a DL-protocol, save the overview, and export the file as a [[Export DL-Protocol User (*.DLPU)|user-specific DL-Protocol]] [File / Export / A or B: Export DL-Protocol User (*.DLPU)]. In DatLab 7.4, fixed sequence of events and marks can be changed (Skip/Added) in a SUIT protocol by the user. Moreover, editions of text, instructions, concentrations and titration volumes of injections in a specific DL-Protocol can be edited and saved as [[Export DL-Protocol User (*.DLPU)|user-specific DL-Protocol]] [File]\Export\DL-Protocol User (*.DLPU). For more information, see: [[Enable DL-Protocol editing]].[[Enable DL-Protocol editing]].)
  • Inside the O2k  + (A glance '''inside the [[Oroboros O2k]]''')
  • TPP+ inhibitory effect  + (A major task in establishing a procedure fA major task in establishing a procedure for measurement of [[mitochondrial membrane potential]] using probe molecules is the evaluation of inhibitory concentrations of the probe molecule on the activity of respiration. The '''TPP<sup>+</sup> inhibitory effect''' (this also applies to TPMP<sup>+</sup> and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP<sup>+</sup>, and for restriction of experimental TPP<sup>+</sup> concentrations below the inhibitory range.ion of experimental TPP<sup>+</sup> concentrations below the inhibitory range.)
  • Experiment  + (A number of replica, ''N'', of '''experimeA number of replica, ''N'', of '''experiment'''s on one [[sample type]] is designed to obtain statistical information about the involved [[population]](s) and to test hypotheses about a population and about differences between populations, when experiments are carried out on different sample types. An experiment may involve various [[assay]]s, ''e.g.'', a respirometric assay and an assay for protein determination.ay and an assay for protein determination.)
  • Project  + (A scientific project is a collection of [[experiment| experiments]]A scientific project is a collection of [[experiment| experiments]] designed to proof or disproof a specific hypothesis. The [[experiment| experiments]] will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental [[assay| assays]] (''i.e.'', observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough [[replica| data collection]].[1] Popper K (2002) The logic of scientific discover. Routledge Classics. ISBN: 978-0-415-27843-0outledge Classics. ISBN: 978-0-415-27843-0)
  • User - DatLab  + (A user name is)
  • Light source  + (A variety of '''light sources''' are availA variety of '''light sources''' are available for [[fluorometry]] and [[spectrophotometry]]. These include deuterium, mercury and xenon arc lamps and quartz halogen bulbs dependent upon the wavelengths required. However, the advent of [[light emitting diode]]s has greatly increased the possibilities for the application of [[fluorometry]] and [[spectrophotometry]] to areas that were previously not practicable, and at a much reduced cost.t practicable, and at a much reduced cost.)
  • Elasticity  + (According to David Fell, "Elasticities areAccording to David Fell, "Elasticities are properties of individual enzymes and not the metabolic system. The elasticity of an enzyme to a metabolite is related to the slope of the curve of the enzyme's rate plotted against metabolite concentration, taken at the metabolite concentrations found in the pathway in the metabolic state of interest. It can be obtained directly as the slope of the logarithm of the rate plotted against the logarithm of the metabolic concentration. The elasticity will change at each point of the curve (s,v) and must be calculated for the specific concentration of the metabolite (s) that will give a specific rate (r) of the enzyme activity" (See Figure).</br></br></br>[[File:Elasticity_Measurement.jpg]][[File:Elasticity_Measurement.jpg]])
  • O2k control  + (After selection of an O2k setup in the '''O2k control''' [F7] window, followed by a left-click '''Send to O2k''', only the following control functions are routinely required during experimental operations.)
  • Amperometric,Amp  + (After selection of the Amperometric, Amp cAfter selection of the Amperometric, Amp channel in the '''[[O2k configuration]]''', an Amperometric, Amp tab will appear in the '''O2k control''' [F7] window. Set the desired light intensity (0-1600) in the field ´Fluo intensity´ and the desired amplification of the signal (1-1000) in the field ´Gain for Fluo sensor´in the Amperometric, Amp window followed by a left-click '''Send to O2k'''. Switching off the [[Illumination on/off|illumination]] before each fluorometric measurement is routinely required.ometric measurement is routinely required.)
  • Connection window  + (After starting [[DatLab]] either the '''Connection window''' opens automatically by default or open [[O2k control]] by pressing [F7] and select the communication port.)
  • Absorbance  + (Also known as attenuation or extinction, 'Also known as attenuation or extinction, '''absorbance''' (''A'') is a measure of the difference between the [[incident light]] intensity (''I''<sub>0</sub>) and the intensity of light emerging from a sample (''I''). It is defined as:</br></br>''A'' = log (''I''<sub>0</sub>/''I'') is defined as: ''A'' = log (''I''<sub>0</sub>/''I''))
  • Intrinsic fluorophores  + (An '''Intrinsic flourophore''' is a naturally occurring [[fluorophore]] of which [[NADH]], aromatic amino acids and flavins are examples.)
  • Absorption spectrum  + (An '''absorption spectrum''' is similar to an [[absorbance spectrum]] of a sample, but plotted as a function of [[absorption]] against wavelength.)
  • Entity  + (An '''entity''' of type ''X'' is somethingAn '''entity''' of type ''X'' is something that can measured as an [[extensive quantity]] or counted as an [[elementary entity]]. The term entity with symbol ''X'', therefore, has a general meaning, including but not limited to elementary entities ''U''<sub>''X''</sub>. The distinction can be emphasized by using the term entity-type ''X'', to avoid confusion of an entity ''X'' with the more restricted definition of elementary entity ''U''<sub>''X''</sub> as a ''single'' countable object or event.ub>''X''</sub> as a ''single'' countable object or event.)
  • Events - DatLab  + (An '''event''' in [[DatLab]]An '''event''' in [[DatLab]] is a defined point in time, labelled by a name (1 to 10 characters). An event applies to all plots of the selected O2k-Chamber. The event is shown by a vertical line in the graph and the label of the event is shown on the top (DatLab 6 and lower: on the bottom). The default name is the sequential number of the event. It is recommended to edit event labels with a minimum number of characters, and to explain the abbreviation in the 'Definition' box. The final concentration and titration volume can be entered into the corresponding boxes, if the event relates to the titration of a substance. A short comment can be entered to describe the event in detail. </br>'''Set events''' - Manual events are entered (real-time, connected to the O2k) by pressing [F4] at the time of the event (e.g. to indicate a manual titration into the chamber). An event belongs either to chamber A, chamber B, or both. Instrumental events are added automatically, e.g. when the stirrer (A or B) or illumination (both chambers) is switched on or off.</br>After setting a new event the Edit event window pops up. Pressing F4 defines the time point of the event. Full attention can then be paid to the experiment. Edit the event later, as it is possible to insert an event at any chosen moment of the plotted record of the experiment by placing the cursor anywhere in the graph at the selected time point by pressing Ctrl and clicking the left mouse button.</br>'''Edit event''' - Left click on the name of an existing event to open the Edit event window to edit or Delete event.</br>In events obtained from a selected [[DL-Protocols |protocol]], the entire sequence of consecutive events is defined with event names, definitions, concentrations and titration volumes.</br>'''Name''' - Enter an event name of 1 to 10 characters. Short names (e.g. O instead of Open) are recommended.</br>''' Comment''' - Further information can be entered into the text field.</br>Select O2k-chamber A, B or both. The Event will be shown on plots for both or one selected chamber.</br>»[[DL-Protocols#DL-Protocol_principles|Protocol events]][DL-Protocols#DL-Protocol_principles|Protocol events]])
  • Examination  + (An '''examination''' is a set of operations having the object of determining the value or characteristics of a property. In some disciplines (e.g. microbiology) an examination is the total activity of a number of tests, observations or measurements.)
  • Experimental code  + (An '''experimental code''' can be entered in the [[Sample - DatLab|Sample]] window, containing up to 10 digits.)
  • Interlaboratory comparison  + (An '''interlaboratory comparison''' is the organization, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions.)
  • Journal issue  + (An '''issue''' of a journal or periodical is a number, which typically indicates how many times a [[Journal volume |volume]] of the journal has been published in sequence.)
  • Open system  + (An '''open system''' is a system with bounAn '''open system''' is a system with boundaries that allow external exchange of energy and matter; the surroundings are merely considered as a source or sink for quantities transferred across the system boundaries ([[external flow]]s, ''I''<sub>ext</sub>).[[external flow]]s, ''I''<sub>ext</sub>).)
  • Outlier  + (An '''outlier''' is a member of a set of vAn '''outlier''' is a member of a set of values which is inconsistent with other members of that set. An outlier can arise by chance from the expected population, originate from a different population, or be the result of an incorrect recording or other blunder. Many schemes use the term outlier to designate a result that generates an action signal. This is not the intended use of the term. While outliers will usually generate action signals, it is possible to have action signals from results that are not outliers [SOURCE: ISO 5725‑1:1994, modified].liers [SOURCE: ISO 5725‑1:1994, modified].)
  • Outlier-skewness index  + (An '''outlier-skewness index''' ''OSI'' isAn '''outlier-skewness index''' ''OSI'' is defined for evaluation of the distribution of data sets with outliers including separate clusters or skewness in relation to a normal distribution with equivalence of the average and median. The ''OSI'' is derived from [http://www.statisticshowto.com/pearsons-coefficient-of-skewness/ Pearson’s coefficient of skewness] 2:</br></br>: Pearson 2 coefficient = 3 · (average-median)/SD</br></br>The outlier-skewness index ''OSI'' introduces the absolute value of the arithmetic mean, ''m'' = ABS(average + median)/2, for normalization:</br></br>: ''OSI'' = (average-median)/(''m'' + SD) </br></br>: ''OSI'' = (average-median)/[ABS(average+median)/2 + SD]</br></br>At the limit of a zero value of ''m'', the ''OSI'' equals the Pearson 2 coefficient (without the multiplication factor of 3). At high ''m'' with small standard deviation (SD), the ''OSI'' is effectively the difference between the average and the median normalized for ''m'', (average-median)/''m''.malized for ''m'', (average-median)/''m''.)
  • Uncoupler  + (An '''uncoupler''' is a protonophore ([[CCCP]]An '''uncoupler''' is a protonophore ([[CCCP]], [[FCCP]], [[DNP]], [[SF6847]]) which cycles across the inner mt-membrane with transport of protons and dissipation of the electrochemical proton gradient. Mild uncoupling may be induced at low uncoupler concentrations, the noncoupled state of [[ET capacity]] is obtained at optimum uncoupler concentration for maximum flux, whereas at higher concentrations an uncoupler-induced inhibition is observed. uncoupler-induced inhibition is observed.)
  • Endothermic  + (An [[energy]]An [[energy]] transformation is '''endothermic''' if the [[enthalpy]] change of a closed system is positive when the process takes place in the forward direction and heat is absorbed from the environment under isothermal conditions (∆<sub>e</sub>''Q'' > 0) without performance of work (∆<sub>e</sub>''W'' = 0). The same energy transformation is [[exothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]].ergonic]].)
  • Exothermic  + (An [[energy]]An [[energy]] transformation is '''exothermic''' if the [[enthalpy]] change of a closed system is negative when the process takes place in the forward direction and heat is lost to the environment under isothermal conditions (∆<sub>e</sub>''Q'' < 0) without performance of work (∆<sub>e</sub>''W'' = 0). The same energy transformation is [[endothermic]] if it proceeds in the backward direction. Exothermic and endothermic transformations can proceed spontaneously without coupling only, if they are [[exergonic]].ergonic]].)
  • Assay  + (An experimental '''assay''' is a method toAn experimental '''assay''' is a method to obtain a measurement with a defined instrument on a [[sample]] or [[subsample]]. Multiple assay types may be applied on the same sample or subsample, if the measurement does not destroy it. For instance, the wet weight of a permeabilized muscle fibre preparation can be determined based on a specific laboratory protocol (gravimetric assay), maintaining the functional integrity of the sample, which then can be used in a respirometric assay, followed by a spectrophotometric assay for measurement of protein content. The experimental design determines which types of assays have to be applied for a complete experiment. Destructive assays, such as determination of protein content or dry weight, can be applied on a sample only after performing a respirometric assay, or on a separate subsample. The experimental variability is typically dominated by the assay with the lowest [[resolution]] or signal to noise ratio. The signal to noise ratio may be increased by increasing the number, ''n'', of [[repetitions]] of measurements on subsamples. Evaluation of procedural variation ('experimental noise') due to instrumental resolution and handling requires subsampling from homogenous samples.uires subsampling from homogenous samples.)
  • Sample type  + (An experimental '''sample type''' is the object of an [[experiment]]. A sample type is defined by the specifications of the [[population]] and by a specific sample preparation (see [[MitoPedia: Sample preparations]]).)
  • Science - the concept  + (As per the 2017 UNESCO Recommendation on SAs per the 2017 UNESCO Recommendation on Science and Scientific Researchers, the term ‘science’ signifies the enterprise whereby humankind, acting individually or in small or large groups, makes an organized attempt, in cooperation and in competition, by means of the objective study of observed phenomena and its validation through sharing of findings and data and through peer review, to discover and master the chain of causalities, relations or interactions; brings together in a coordinated form subsystems of knowledge by means of systematic reflection and conceptualization; and thereby furnishes itself with the opportunity of using, to its own advantage, understanding of the processes and phenomena occurring in nature and society.phenomena occurring in nature and society.)
  • Conflict of interest  + (As stated on the [https://www.bioenergeticAs stated on the [https://www.bioenergetics-communications.org/index.php/bec/BECPolicies#Journal_policies_on_conflicts_of_interest_.2F_competing_interests Bioenergetics Communications' policy], a '''conflict of interest''' may be of non-financial or financial nature. Examples of conflicts of interest include (but are not limited to):</br>:::* Individuals receiving funding, salary or other forms of payment from an organization, or holding stocks or shares from a company, whose financial situation might be influenced by the publication of the findings;</br>:::* Individuals, their funding organization or employer holding (or applying for) related patents;</br>:::* Official affiliations and memberships with interest groups relating to the content of the publication;</br>:::* Political, religious, or ideological competing interests.</br>For authors, any conflict of interest is declared at the time of submission and included in the published manuscript. For editors and reviewers, conflicts should be taken into account before accepting an assignment.to account before accepting an assignment.)
  • STPD  + (At '''standard temperature and pressure drAt '''standard temperature and pressure dry''' (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, ''V''<sub>m</sub>, and ''V''<sub>m,O<sub>2</sub></sub> is 22.414 and 22.392 L∙mol<sup>-1</sup>, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (''V''<sub>O<sub>2</sub>max</sub> [mL O<sub>2</sub>·min<sup>-1</sup>]) to SI units [µmol O<sub>2</sub>·s<sup>-1</sup>]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), ''V''<sub>m,O<sub>2</sub></sub> is 24.038 L∙mol<sup>-1</sup>. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol<sup>-1</sup> and 22.689 L∙mol<sup>-1</sup> for O<sub>2</sub>.;/sup>. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol<sup>-1</sup> and 22.689 L∙mol<sup>-1</sup> for O<sub>2</sub>.)
  • Copyright  + (Authors retain the copyright for the conteAuthors retain the copyright for the contents of their manuscripts published in [[Bioenergetics Communications]]. {''Quote''} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain '''copyright''' and receive credit for their work, while allowing anyone to read and reuse their work. {''end of Quote''}d and reuse their work. {''end of Quote''})
  • Mitophagy  + (Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. » [[Mitophagy#Mitochondrial_mitophagy | '''MiPNet article''']])
  • Barth Syndome  + (Barth Syndome (BTHS) is an X-linked genetiBarth Syndome (BTHS) is an X-linked genetic condition that is caused by a mutation in the tafazzin gene (taz). This mutation causes cardiolipin abnormalities, cardiomyopathy, neutropenia, muscle weakness, growth delay, and exercise intolerance.</br></br>[https://www.barthsyndrome.org/about-barth-syndrome/overview-of-barth-syndrome Weblink]</br> Contributed by [[Sparagna GC]] 2016-04-24[[Sparagna GC]] 2016-04-24)
  • Biological contamination  + (Biological contamination may be caused by microbial growth in the O2k-Chamber or in the experimental medium.)
  • Bovine serum albumin  + (Bovine serum albumin is a membrane stabiliBovine serum albumin is a membrane stabilizer, oxygen radical scavenger, and binds Ca<sup>2+</sup> and free fatty acids, hence the rather expensive essentially free fatty acid free BSA is required in mitochondrial isolation and respiration media. Sigma A 6003 fraction V.lation and respiration media. Sigma A 6003 fraction V.)
  • Full screen  + (By clicking/enabling '''Full screen''' in By clicking/enabling '''Full screen''' in the Graph-menu in DatLab the currently selected graph is shown alone on the full screen (On) or together with the other defined graphs (Off). Full screen is particularly useful for a single channel overview and for Copy to clipboard [ALT+G B].rview and for Copy to clipboard [ALT+G B].)
  • Calcium retention capacity  + (Calcium retention capacity (CaRC) is a meaCalcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca<sup>2+</sup>), primarily in the form of calcium phosphates, in the mitochondrial matrix. By storing calcium in the form of osmotically inactive precipitates the mitochondria contribute to the buffering of cytosolic free Ca<sup>2+</sup> levels and thereby to the regulation of calcium-dependent cellular processes. Alterations of CaRC are important in stress phenomena associated with energy limitation and have been linked to neurodegenerative diseases [[Starkov 2010 FEBS J |(Starkov 2013 FEBS J).]]</br>Experimentally, CaRC has been indirectly assessed by determination of respiratory rates of isolated mitochondria which were exposed to continuously increasing doses of Ca<sup>2+</sup> by use of the [[TIP2k-Module| Titration-Injection microPump TIP2k]]. The upper limit of CaRC was observed as a sudden decrease of respiration presumed to reflect opening of the permeability transition pore [[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]][[Hansson_2010_J_Biol_Chem |(Hansson 2010 J Biol Chem).]])
  • POS calibration - dynamic  + (Calibration of the sensor response time. See also [[POS calibration - static]].)
  • Cataplerosis  + (Cataplerosis is the exit of TCA cycle intermediates from the mt-matrix space.)
  • Living cells  + (Cell viability in '''living cells''' shoulCell viability in '''living cells''' should be >95 % for various experimental investigations, including cell respirometry. Viable cells (vce) are characterized by an intact plasma membrane barrier function. The total cell count (''N''<sub>ce</sub>) is the sum of viable cells (''N''<sub>vce</sub>) and dead cells (''N''<sub>dce</sub>). In contrast, the plasma membrane can be permeabilized selectively by mild detergents ([[digitonin]]), to obtain the [[Mitochondrial preparations |mt-preparation]] of [[permeabilized cells]] used for [[cell ergometry]]. Living cells are frequently labelled as ''intact cells'' in the sense of the total cell count, but ''intact'' may suggest dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury.t dual meanings of ''viable'' or unaffected by a disease or mitochondrial injury.)
  • DatLab error messages  + (Common '''DatLab error messages''' and according actions and solutions are listed here.)
  • Citrate synthase  + (Condensation of [[oxaloacetate]]Condensation of [[oxaloacetate]] with acetyl-CoA yields citrate as an entry into the [[TCA cycle]]. CS is located in the mt-matrix. CS activity is frequently used as a functional marker of the amount of mitochondria (mitochondrial elementary marker, ''mtE'') for normalization of respiratory flux.'') for normalization of respiratory flux.)
  • O2k configuration  + (Configure or modify the settings for the OConfigure or modify the settings for the O2k sensors</br></br>In '''O2k configuration''', channels (amperometric and potentiometric) can be switched on/off by selecting the according tick box. The Power-O2k number (P1, P2, ..) and numbers for O2 sensors, Amp sensors, pX electrodes and pX reference electrodes are entered or edited here. With the [[O2k-FluoRespirometer]] (O2k-Series H and higher), the serial numbers of the [[Smart Fluo-Sensor|Smart Fluo-Sensors]] are shown automatically under [Amperometric, Amp]. The O2k configuration window pops up when DatLab starts and "Connect to O2k" is pressed for the first time. It is also accessible from the menu "Oroboros O2k" and from within the [[O2k control]] and [[Mark statistics - DatLab|Mark statistics]] windows.[[Mark statistics - DatLab|Mark statistics]] windows.)
  • Cross-linked respiratory states  + (Coordinated respiratory [[SUIT|SUIT protocols]]Coordinated respiratory [[SUIT|SUIT protocols]] are designed to include '''cross-linked respiratory states''', which are common to these protocols. Different SUIT protocols address a variety of respiratory control steps which cannot be accomodated in a single protocol. Cross-linked respiratory states are included in each individual coordinated protocol, such that these states can be considered as replicate measurements, which also allow for harmonization of data obtained with these different protocols.a obtained with these different protocols.)
  • Energy metabolism  + (Core '''energy metabolism''' is the integrCore '''energy metabolism''' is the integrated biochemical process supplying the cell with ATP, utilizing ATP for various forms of work including biogenesis, maintaining ion and redox balance, and in specific organisms or tissues dissipating heat for temperature regulation.ssipating heat for temperature regulation.)
  • Set Power O2k number - DatLab  + (Create an identifier for your Power O2k instrument. Since it is displayed in the status panel (bottom right) and in axis labels, it should be a short code, any combination of digits and letters is allowed.)
  • Keyboard shortcuts - DatLab  + (DatLab provides several keyboard shortcuts to allow for quick access to many functions and settings without using a mouse.)
  • DatLab-Upgrading to DatLab 6  + (DatLab-Upgrading to DatLab 6: including free follow-up updates for DatLab 6 for the next two years)
  • O2k channel labels  + (Default channel labels can now be changed,Default channel labels can now be changed, and new labels set by the user. E.g., rename the Amperometric channel, Amp, to 'H2O2' for H2O2 measurements by fluorometry; rename the potentiometric channel, pX, to TPP+ for mitochondrial membrane measurements with the O2k-pH ISE-Module.</br>For changing the label, go to menu [Oroboros O2k]\O2k channel labels and set the new channel label as desired. and set the new channel label as desired.)
  • Test  + (Descr)
  • Q-pools  + (Different '''Q-pools''' are more or less cDifferent '''Q-pools''' are more or less clearly distinguished in the cell, related to a variety of models describing degress of Q-pool behavior. (''1'') [[CoQ]]-pools are distinguished according to their compartmentation in the cell: mitochondrial CoQ (mtCoQ) and CoQ in other organelles versus plasma-membrane CoQ. (''2'') The total mitochondrial CoQ-pool mtCoQ is partitioned into an [[ETS]]-reactive Q-pool, Q<sub>ra</sub>, and an inactive mtCoQ-pool, Q<sub>ia</sub>. (''2a'') The Q<sub>ra</sub>-pool is fully reduced in the form of quinol QH<sub>2</sub> under anoxia, and fully oxidized in the form of quinone in aerobic [[mitochondrial preparations]] incubated without [[CHNO-fuel substrate]]s. Intermediate redox states of Q<sub>ra</sub> are sensitive to pathway control and coupling control of mitochondrial electron transfer and [[OXPHOS]]. (''2b'') The Q<sub>ia</sub>-pool remains partially reduced and oxidized independent of aerobic-anoxic transitions. The redox state of Q<sub>ia</sub> is insensitive to changes in mitochondrial respiratory states. (''3'') The Q<sub>ra</sub>-pool is partitioned into Q with Q-pool behavior according to the fluid-state model (synonymous: random-collision model) and Q tightly bound to supercomplexes according to the solid-state model. The two models describe the extremes in a continuum of homogenous or heterogenous Q-pool behavior. The CII-Q-CIII segment of the [[S-pathway]] is frequently considered to follow homogenous Q-pool behavior participating in the Q<sub>hom</sub>-pool, whereas the CI-Q-CIII segment of the [[N-pathway]] indicates [[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Q<sub>het</sub>-pool.[[supercomplex]] organization and metabolic channeling with different degrees of Q-pool heterogeneity contributing to the Q<sub>het</sub>-pool.)
  • Dilution effect  + (Dilution of the concentration of a compound or sample in the experimental chamber by a titration of another solution into the chamber.)
  • Biochemical threshold effect  + (Due to threshold effects, even a large defect diminishing the velocity of an individual enzyme results in only minor changes of pathway flux.)
  • Electron leak  + (Electrons that escape the [[electron transfer pathway]]Electrons that escape the [[electron transfer pathway]] without completing the reduction of oxygen to water at cytochrome ''c'' oxidase, causing the production of [[Reactive_oxygen_species |ROS]]. The rate of electron leak depends on the topology of the complex, the redox state of the moiety responsible of electron leakiness and usually on the protonmotive force ([[Protonmotive force|Δ''p'']]). In some cases, the [[Protonmotive force|Δ''p'']] dependance relies more on the ∆pH component than in the ∆''Ψ''.e on the ∆pH component than in the ∆''Ψ''.)
  • Proton leak  + (Flux of protons driven by the protonmotiveFlux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the [[ATP synthase]] and thus contributing to [[LEAK respiration]]. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive [[force]]. Compare: [[Proton slip]].[[Proton slip]].)
  • Shipping an O2k  + (For '''shipping an O2k or parts''', standaFor '''shipping an O2k or parts''', standard operating procedures have to be followed to avoid damage of the instrument and unexpected delays. The [[O2k-Main Unit]] must be shipped only in [[Packing\O2k-Box 1]], without [[O2k-chamber]]s and without [[OroboPOS]]. Two [[O2k-Chamber Holder]]s, two [[OroboPOS-Holder]]s and two [[OroboPOS-Connector]]s are attached to the O2k-Main Unit for transport.tached to the O2k-Main Unit for transport.)
  • DatLab-Analysis templates  + (Go in DatLab to [[Mark statistics - DatLab|Mark statistics]]Go in DatLab to [[Mark statistics - DatLab|Mark statistics]] (F2), select which type of marks you want to export ("All marks in plot" or "DL-Protocol marks", with 3 possibilities each), then click on [Copy to clipboard] to copy selected values and paste them to a '''DatLab-Analysis template''' for numerical and graphical data analysis.for numerical and graphical data analysis.)
  • Hydronium ion  + (H<sup>+</sup> forms the '''hydronium ion''' H<sub>3</sub>O<sup>+</sup>, which in turn is further solvated by water molecules in clusters such as H<sub>5</sub>O<sub>2</sub><sup>+</sup> and H<sub>9</sub>O<sub>4</sub><sup>+</sup>.)
  • Energy  + (Heat and work are forms of '''energy''' [1Heat and work are forms of '''energy''' [1 cal = 4.184 J]. Energy [J] is a fundamental term that is used in physics and physical chemistry with various meanings [1]. These meanings become explicit in the following equations relating to systems at constant [[volume]] (d''V'' = 0) or constant gas [[pressure]] (d''p'' = 0). Energy is exchanged between a system and the environment across the system boundaries in the form of [[heat]], d<sub>e</sub>''Q'', total or available [[work]], d<sub>et</sub>''W'' (or d<sub>et</sub>''W''), and [[matter]], d<sub>mat</sub>''U'' (or d<sub>mat</sub>''H'') [2], </br></br> d''U'' = (d<sub>e</sub>''Q'' + d<sub>et</sub>''W'') + d<sub>mat</sub>''U'' ; d''V'' = 0 [Eq. 1a]</br></br> d''H'' = (d<sub>e</sub>''Q'' + d<sub>e</sub>''W'') + d<sub>mat</sub>''H'' ; d''p'' = 0 [Eq. 1b]</br></br>Whereas d''U'' (or d''H'') describe the [[internal-energy]] change (or [[enthalpy]] change) of the ''system'', heat and work are ''external'' energy changes (subscript e; et: external total; e: external excluding pressure-volume work), and d<sub>mat</sub>''U'' (or d<sub>mat</sub>''H'') are the exchange of matter expressed in internal-energy (or enthaply) equivalents. In closed systems, d<sub>mat</sub>''U'' = 0 (d<sub>mat</sub>''H'' = 0). The energy balance equation [Eq. 1] is a form of the First Law of Thermodynamics, which is the law of conservation of internal-energy, stating that energy cannot be generated or destroyed: energy can only be transformed into different forms of work and heat, and transferred in the form of matter.</br></br>Notably, the term '''energy''' is general and vague, since energy may be associated with either the first or second law of thermodynamics. Work is a form of energy exchange [Eq. 1], but can be seen as [[exergy]] exchange in conjunction with d<sub>e</sub>''G'' = d<sub>e</sub>''W'' in a closed system [Eq. 3b].</br></br>An equally famous energy balance equation considers energy changes of the system only, in the most simple form for isothermal systems (d''T'' = 0):</br></br> d''U'' = d''A'' + ''T''∙d''S'' = d''U'' + d''B'' [Eq. 2a]</br></br> d''H'' = d''G'' + ''T''∙d''S'' = d''G'' + d''B'' [Eq. 2b]</br></br>The internal-energy change, d''U'' (enthalpy change, d''H'') is the sum of ''free'' energy change ([[Helmholtz energy]], d''A''; or Gibbs energy = [[exergy]] change, d''G'') and ''bound'' energy change ([[bound energy]], d''B'' = ''T''∙d''S''). The bound energy is that part of the energy change that is always bound to an exchange of heat.</br></br>A third energy balance equation accounts for changes of the system in terms of irreversible internal processes (i) occuring within the system boundaries, and reversible external processes (e) of transfer across the system boundaries (at constant gas pressure),</br></br> d''H'' = d<sub>i</sub>''H'' + d<sub>e</sub>''H'' [Eq. 3a]</br></br> d''G'' = d<sub>i</sub>''G'' + d<sub>e</sub>''G'' [Eq. 3b]</br></br>The energy conservation law of thermodynamics (first law) can be formulated as d<sub>i</sub>''H'' = 0 (at constant gas pressure), whereas the generally negative sign of the [[dissipated energy]], d<sub>i</sub>''G'' ≡ d<sub>i</sub>''D'' ≤ 0, is a formulation of the second law of thermodynamics. Insertion into Eq. 3 yields,</br></br> d''H'' = d<sub>e</sub>''H'' [Eq. 4a]</br></br> d''G'' = d<sub>i</sub>''D'' + d<sub>e</sub>''W'' + d<sub>mat</sub>''G'' [Eq. 4b]</br></br>When talking about energy transformations, the term energy is used in a general sense without specification of these various forms of energy. the second law of thermodynamics. Insertion into Eq. 3 yields, d''H'' = d<sub>e</sub>''H'' [Eq. 4a] d''G'' = d<sub>i</sub>''D'' + d<sub>e</sub>''W'' + d<sub>mat</sub>''G'' [Eq. 4b] When talking about energy transformations, the term energy is used in a general sense without specification of these various forms of energy.)