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List of results

• Vector  + (A '''vector''' is a pysicochemical quantit … A '''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.'', O₂ consumption, are instantaneously compensated for by external fluxes across the system boundary, ''e.g.'', O₂ supply, thus preventing a change of O₂ 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 O₂, fuel substrates, ADP, P_i, H⁺) 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 (O₂ flux, H₂O₂ 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.'' O₂ flux, H₂O₂ 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 f … A 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⁺ inhibitory effect''' (this also applies to TPMP⁺ and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP⁺, and for restriction of experimental TPP⁺ concentrations below the inhibitory range.ion of experimental TPP⁺ concentrations below the inhibitory range.)
• Experiment  + (A number of replica, ''N'', of '''experime … A 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.)
• User - DatLab  + (A user name is)
• Light source  + (A variety of '''light sources''' are avail … A 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 are … According 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 - DatLab 7  + (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 c … After 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''₀) and the intensity of light emerging from a sample (''I''). It is defined as:</br></br>''A'' = log (''I''₀/''I'') is defined as: ''A'' = log (''I''₀/''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 something … An '''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''_''X''. 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''_''X'' 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 boun … An '''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''_ext).[[external flow]]s, ''I''_ext).)
• Outlier  + (An '''outlier''' is a member of a set of v … An '''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'' is … An '''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 (∆_e''Q'' > 0) without performance of work (∆_e''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 (∆_e''Q'' < 0) without performance of work (∆_e''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 to … An 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 S … As 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.bioenergetic … As 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 dr … At '''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''_m, and ''V''_m,O₂ is 22.414 and 22.392 L∙mol^-1, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (''V''_O₂max [mL O₂·min^-1]) to SI units [µmol O₂·s^-1]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), ''V''_m,O₂ is 24.038 L∙mol^-1. 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^-1 and 22.689 L∙mol^-1 for O₂.;/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^-1 and 22.689 L∙mol^-1 for O₂.)
• Copyright  + (Authors retain the copyright for the conte … Authors 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 geneti … Barth 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 stabili … Bovine serum albumin is a membrane stabilizer, oxygen radical scavenger, and binds Ca²⁺ 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 mea … Calcium retention capacity (CaRC) is a measure of the capability of mitochondria to retain calcium (Ca²⁺), 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 Ca²⁺ 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 Ca²⁺ 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''' shoul … Cell 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''_ce) is the sum of viable cells (''N''_vce) and dead cells (''N''_dce). 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.)
• Exit - DatLab 7  + (Close DatLab files and '''quit''' the program.)
• Close and delete file - DatLab  + (Close and delete a file.)
• 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.)