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At least 91 records · Page 5

On the uncertainty in single molecule fluorescent lifetime and energy emission measurements

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least square methods agree and are optimal when the number of detected photons is large however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67% of those can be noise and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous poisson processes, we derive the exact joint arrival time probably density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. the ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background nose and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Brown, Emery N.↗

On the Uncertainty in Single Molecule Fluorescent Lifetime and Energy Emission Measurements

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least squares methods agree and are optimal when the number of detected photons is large, however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67 percent of those can be noise, and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous Poisson processes, we derive the exact joint arrival time probability density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. The ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background noise and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Brown, Emery N.↗

Determination of cytoplasmic calcium concentration in Dryopteris spores: a developmentally non-disruptive technique for loading of the calcium indicator fura-2

Germination of Dryopteris spores is mediated by the physiologically active, far-red-absorbing form of phytochrome, Pfr, and external Ca2+ is necessary for the transduction of the light signal. Because knowledge about the cytoplasmic calcium ion concentration, [Ca2+]i, is of great importance for understanding the role of calcium during signal transduction, this value was measured using fura-2 in fern spores undergoing the normal developmental progression into germination. Fura-2 was loaded into the spores by electroporation, which does not disrupt the normal process of germination. The intensity of the fluorescence emission of the loaded fura-2 was analysed by a microspectrophotometric assay of single spores, and successful loading could be obtained by the application of ten electrical pulses (field strength 7.5 kV cm-1, half-life (time constant) 230 microseconds). Fura-2 was alternately excited by light of wavelengths 355 and 385 nm through an inverted fluorescence microscope, and the emitted fura-2 fluorescence was collected by a silicon-intensified video camera. The cytoplasmic calcium ion concentration was calculated from the ratio of the camera output obtained for both wavelengths and displayed by a pseudo-color technique. Spores responded to changes of the extracellular Ca2+ concentration, and this observation is considered as evidence that fura-2 is loaded into the cytoplasm. The substitution of a low external [Ca2+] (1 mM ethyleneglycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA)) by 1 mM CaCl2 caused a fast increase of [Ca2+]i from approx. 50 nM to above 500 nM. In contrast, the subsequent substitution of CaCl2 by EGTA decreased [Ca2+]i again below 100 nM within 0.5 h. Furthermore, the application of ionomycin could initiate a change in [Ca2+]i according to the Ca2+ gradient established between the extracellular medium and cytoplasm. In spores sown on a Ca(2+) -free medium, [Ca2+]i, analysed in a buffer containing EGTA, was found to be around 50 nM during the first days of cultivation, independent of the irradiation protocol. However, if spores were grown in darkness on a Ca(2+) -containing medium and analysed in EGTA, [Ca2+]i was significantly higher (> or = 500 nM). In red-light-irradiated spores, [Ca2+]i was found to decrease with increasing time after irradiation, and was determined to be less than 100 nM when analysis was done 44 h after germination was initiated by the light treatment.

NASA Discipline Plant Biology↗

Spectrophotometry near the atmospheric cutoff of the strongest Bowen resonance fluorescence lines of O III in two planetary nebulae

Spectrophotometric results are presented for the stronger, well-resolved Bowen O III resonance fluorescence emission lines in the planetary nebulae 7027 and NGC 7662 down to and including the intrinsically strong line at 3133 A. These data are combined with results from the IUE atlas of spectra and similar results for the longer wavelength lines by Likkel and Aller (1986) to give the first full coverage of the Bowen lines. Good agreement is found with fluorescence theory for the primary cascade lines, except for the Likkel and Aller results. The efficiency of conversion of the exciting He II Ly-alpha into O III lines is determined, and values comparable to other planetary nebulae are found.

O'Dell, C. R.↗

Time-Resolved Ultraviolet Spectroscopy of The M-Dwarf GJ 876 Exoplanetary System

Extrasolar planets orbiting M-stars may represent our best chance to discover habitable worlds in the coming decade. The ultraviolet spectrum incident upon both Earth-like and Jovian planets is critically important for proper modeling of their atmospheric heating and chemistry. In order to provide more realistic inputs for atmospheric models of planets orbiting low-mass stars, we present new near- and far-ultraviolet (NUV and FUV) spectroscopy of the M-dwarf exoplanet host GJ 876 (M4V). Using the COS and STIS spectrographs on board the Hubble Space Telescope, we have measured the 1150-3140 A spectrum of GJ 876. We have reconstructed the stellar H1 Ly alpha emission line profile, and find that the integrated Ly alpha flux is roughly equal to the rest of the integrated flux (1150-1210 A + 1220-3140 A) in the entire ultraviolet bandpass (F(Ly alpha)/F(FUV+NUV) equals approximately 0.7). This ratio is approximately 2500x greater than the solar value. We describe the ultraviolet line spectrum and report surprisingly strong fluorescent emission from hot H2 (T(H2) greater than 2000 K). We show the light curve of a chromospheric + transition region flare observed in several far-UV emission lines, with flare/quiescent flux ratios greater than or equal to 10. The strong FUV radiation field of an M-star (and specifically Ly alpha) is important for determining the abundance of O2--and the formation of biomarkers-in the lower atmospheres of Earth-like planets in the habitable zones of low-mass stars.

France, Kevin↗

Hydrogen Molecules in SN 1987A

The observations of CO and SiO in the infrared spectrum of SN 1987A clearly indicate that molecules can form in the debris of a supernova explosion. Since H2 is not easily observable we compute its abundance theoretically. For conditions typical of the inner (v less than 2500 km/s) envelope of SN 1987A, the fraction of H that is in molecular form rises to approx. 1% by t approx. 800 days. For t less than 500 days the formation is dominated by the gas-phase reactions H + H(+) yields H2(+) + hv; H2(+) + H yields H2 + H(+). Thereafter, the formation is dominated by the reactions H + e yields H(-) + hv; H(-) + H yields H2 + e. At early times the H(-) may absorb approx. 10%-30% of visible photons, contributing to the apparent paucity of H alpha emission. For t greater than 1000 days the abundance of H2 'freezes out' due to the slowing of all reactions. The opacity of the supernova envelope in the range 912 less than lambda less than or approx. equal to 1400 A (the upper limit depending on temperature) is dominated by resonance scattering in the Lyman and Werner bands of H2. The resulting fluorescence emission bands of H2 in the range 1150 less than lambda less than 1650 A may be observable in the UV spectra of supernovae at late times.

Culhane, Michael↗

Time-Resolved Ultraviolet Spectroscopy of the M-Dwarf GJ 876 Exoplanetary System

Extrasolar planets orbiting M-stars may represent our best chance to discover habitable worlds in the coming decade. The ultraviolet spectrum incident upon both Earth-like and Jovian planets is critically important for proper modeling of their atmospheric heating and chemistry. In order to provide more realistic inputs for atmospheric models of planets orbiting low-mass stars, we present new near- and far-ultraviolet (NUV and FUV) spectroscopy of the M-dwarf exoplanet host GJ 876 (U4V). Using the COS and STIS spectrographs aboard the Hubble Space Telescope, we have measured the 1150 - 3140 Ang. spectrum of GJ 876. We have reconstructed the stellar H I Ly-alpha emission line profile, and find that the integrated Ly-apha flux is roughly equal to the rest of the integrated flux (1150 - 1210 Ang + 1220 - 3140 Ang) in the entire ultraviolet bandpass (F(Ly-alpha)/F(FUV+NUV) approximately equals 0.7). This ratio is approximately 2500 x greater than the solar value. We describe the ultraviolet line spectrum and report surprisingly strong fluorescent emission from hot H2 (T(H2) > 2000 K). We show the light-curve of a chromospheric + transition region flare observed in several far-UV emission lines, with flare/ quiescent flux ratios :2: 10. The strong FUV radiation field of an M-star (and specifically Ly-alpha) is important for determining the abundance of O2 - and the formation of biomarkers - in the lower atmospheres of Earth-like planets in the habitable zones of low-mass stars.

France, Kevin↗

Observations of emission lines in M supergiants

Copernicus observations of Mg 2 h and k emission lines from M giants and supergiants are described. Supergiants with extensive circumstellar gas shells show an asymmetric k line. The asymmetry is ascribed to superimposed lines of Fe 1 and Mn 1. The Mg 2 line width fit the Wilson-Bappu relation derived from observations of G and K Stars. Results of correlated ground-based observations include (1) the discovery of K 1 fluorescent emission from the Betelgeuse shell; (2) extimates of the mass-loss rates; and (3) the proposal that silicate dust grains must account for the major fraction of the Si atoms in the Betelgeuse shell.

Lambert, D. L.↗

New Methods for Retrieval of Chlorophyll Red Fluorescence from Hyperspectral Satellite Instruments: Simulations and Application to GOME-2 and SCIAMACHY

Global satellite measurements of solar-induced fluorescence (SIF) from chlorophyll over land and ocean have proven useful for a number of different applications related to physiology, phenology, and productivity of plants and phytoplankton. Terrestrial chlorophyll fluorescence is emitted throughout the red and far-red spectrum, producing two broad peaks near 683 and 736nm. From ocean surfaces, phytoplankton fluorescence emissions are entirely from the red region (683nm peak). Studies using satellite-derived SIF over land have focused almost exclusively on measurements in the far red (wavelengths greater than 712nm), since those are the most easily obtained with existing instrumentation. Here, we examine new ways to use existing hyperspectral satellite data sets to retrieve red SIF (wavelengths less than 712nm) over both land and ocean. Red SIF is thought to provide complementary information to that from the far red for terrestrial vegetation. The satellite instruments that we use were designed to make atmospheric trace-gas measurements and are therefore not optimal for observing SIF; they have coarse spatial resolution and only moderate spectral resolution (0.5nm). Nevertheless, these instruments, the Global Ozone Monitoring Instrument 2 (GOME-2) and the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY), offer a unique opportunity to compare red and far-red terrestrial SIF at regional spatial scales. Terrestrial SIF has been estimated with ground-, aircraft-, or satellite-based instruments by measuring the filling-in of atmospheric andor solar absorption spectral features by SIF. Our approach makes use of the oxygen (O2) gamma band that is not affected by SIF. The SIF-free O2 gamma band helps to estimate absorption within the spectrally variable O2 B band, which is filled in by red SIF. SIF also fills in the spectrally stable solar Fraunhofer lines (SFLs) at wavelengths both inside and just outside the O2 B band, which further helps to estimate red SIF emission. Our approach is then an extension of previous approaches applied to satellite data that utilized only the filling-in of SFLs by red SIF. We conducted retrievals of red SIF using an extensive database of simulated radiances covering a wide range of conditions. Our new algorithm produces good agreement between the simulated truth and retrievals and shows the potential of the O2 bands for noise reduction in red SIF retrievals as compared with approaches that rely solely on SFL filling. Biases seen with existing satellite data, most likely due to instrumental artifacts that vary in time, space, and with instrument, must be addressed in order to obtain reasonable results. Our 8-year record of red SIF observations over land with the GOME-2 allows for the first time reliable global mapping of monthly anomalies. These anomalies are shown to have similar spatiotemporal structure as those in the far red, particularly for drought-prone regions. There is a somewhat larger percentage response in the red as compared with the far red for these areas that are drought sensitive. We also demonstrate that good-quality ocean fluorescence line height retrievals can be achieved with GOME-2, SCIAMACHY, and similar instruments by utilizing the full complement of radiance measurements that span the red SIF emission feature.

spatiotemporal structure↗

Scattering of Solar X-Rays by Jupiter and Saturn

Soft X-ray emission has been observed from the disk of both Jupiter and Saturn as well as from the auroral regions of these planets. The low-latitude disk emission as observed by ROSAT, the Chandra X-Ray Observatory, and XMM-Newton appears to be uniformly distributed across the disk and to be correlated with solar activity. These characteristics suggest that the source of the disk x-rays are: (1) elastic scattering of solar X-rays by atmospheric neutrals (2) absorption of solar X-rays in the carbon K-shell followed by fluorescent emission. The carbon atoms are found in methane molecules located below the homopause. In this paper we present the results of calculations of the scattering albedo and of the emitted x-ray intensity for a range of atmospheric abundances and for a number of solar irradiance spectra. The model calculations are compared with recent x-ray observations of Jupiter and Saturn.

Cravens, T. E.↗

Native Fluorescence Detection Methods and Detectors for Naphthalene and/or Other Volatile Organic Compound Vapors

Naphthalene, benzene, toluene, xylene, and other volatile organic compounds have been identified as serious health hazards. This is especially true for personnel working with JP8 jet fuel and other fuels containing naphthalene as well as other hazardous volatile organic compounds (VOCs). Embodiments of the invention are directed to methods and apparatus for near-real-time in-situ detection and accumulated dose measurement of exposure to naphthalene vapor and other hazardous gaseous VOCs. The methods and apparatus employ excitation of fluorophors native or endogenous to compounds of interest using light sources emitting in the ultraviolet below 300 nm and measurement of native fluorescence emissions in distinct wavebands above the excitation wavelength. The apparatus of some embodiments are cell-phone-sized sensor/dosimeter "badges" to be worn by personnel potentially exposed to naphthalene or other hazardous VOCs. The badge sensor of some embodiments provides both real time detection and data logging of exposure to naphthalene or other VOCs of interest from which both instantaneous and accumulated dose can be determined. The badges employ a new native fluorescence based detection method to identify and differentiate VOCs. The particular focus of some embodiments are the detection and identification of naphthalene while other embodiments are directed to detection and identification of other VOCs like aromatic hydrocarbons such as benzene, toluene, and xylene.

Hug, William F.↗

Connections Between Jet Formation and Multiwavelength Spectral Evolution in Black Hole Transients

Multiwavelength observations are the key to understand conditions of jet formation in Galactic black hole transient (GBHT) systems. By studying radio and optical-infrared evolution of such systems during outburst decays, the compact jet formation can be traced. Comparing this with X-ray spectral and timing evolution we can obtain physical and geometrical conditions for jet formation, and study the contribution of jets to X-ray emission. In this work, first X-ray evolution - jet relation for XTE J1752-223 will be discussed. This source had very good coverage in X-rays, optical, infrared and radio. A long exposure with INTEGRAL also allowed us to study gamma-ray behavior after the jet turns on. We will also show results from the analysis of data from GX 339-4 in the hard state with SUZAKU at low flux levels. The fits to iron line fluorescence emission show that the inner disk radius increases by a factor of greater than 27 with respect to radii in bright states. This result, along with other disk radius measurements in the hard state will be discussed within the context of conditions for launching and sustaining jets.

Kakemci, Emrah↗

Altered excitation energy transfer between phycobilisome and photosystems in the absence of ApcG, a small linker peptide, in Synechocystis sp. PCC 6803, a cyanobacterium

Phycobilisome (PBS) is a large pigment-protein complex in cyanobacteria and red algae responsible for capturing sunlight and transferring its energy to photosystems (PS). Spectroscopic and structural properties of various PBSs have been widely studied, however, the nature of so-called complex-complex interactions between PBS and PSs remains much less explored. In this work, we have investigated the function of a newly identified PBS linker protein, ApcG, some domain of which, together with a loop region (PB-loop in ApcE), is possibly located near the PBS-PS interface. Using Synechocystis sp. PCC 6803, we generated an ApcG deletion mutant and probed its deletion effect on the energetic coupling between PBS and photosystems. Steady-state and time-resolved spectroscopic characterization of the purified ΔApcG-PBS demonstrated that ApcG removal weakly affects the photophysical properties of PBS that the spectroscopic properties of terminal energy emitters are comparable to those of PBS from wild-type. However, analysis of fluorescence decay imaging datasets reveals that ApcG deletion induces disruptions within the allophycocyanin (APC) core, resulting in the emergence (splitting) of two spectrally diverse subgroups with some short-lived APC. Profound spectroscopic changes of the whole ΔApcG mutant cell, however, emerge during state transition, a dynamic process of light scheme adaptation. The mutant cells in State I show a substantial increase in PBS-related fluorescence. On the other hand, global analysis of time-resolved fluorescence demonstrates that in general ApcG deletion does not alter or inhibit state transitions if it is interpreted only in terms of the changes of the PSII and PSI fluorescence emission intensity. Furthermore, the results revealed yet–to–be discovered mechanism of ApcG-docking induced excitation energy transfer regulation within PBS or to Photosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Discovery of iron line emission in the Hercules X-1 low-state spectrum with HEAO 1

Results are reported for HEAO 1 observations of Her X-1 which confirm the existence of the iron line-emission feature discovered with OSO 8 in the high-state spectrum and also reveal an iron emission feature in the low-state spectrum. The iron line-emission feature in the low-state spectrum was detected at a significance level greater than 5 sigmas and is characterized by a line energy of 6.4 keV, an equivalent width larger than that of the high-state line, a binary phase dependence of the line intensity, and a line width that is intrinsically narrow in contrast to the broad high-state line. The observed line energy and narrow line width are shown to be consistent with an interpretation in terms of fluorescence emission due to X-ray heating. It is suggested that HZ Her contributes no more than about 10% of the predicted line flux, that this emission is reflected from a highly ionized plasma, and that a hot coronal gas is an important source of the low-state X-rays.

Pravdo, S. H.↗

Calibration of the SHERLOC Deep Ultraviolet Fluorescence–Raman Spectrometer on the Perseverance Rover

We describe the wavelength calibration of the spectrometer for the scanning of habitable environments with Raman and luminescence for organics and chemicals (SHERLOC) instrument onboard NASA’s Perseverance Rover. SHERLOC utilizes deep ultraviolet Raman and fluorescence (DUV R/F) spectroscopy to enable analysis of samples from the Martian surface. SHERLOC employs a 248.6 nm deep ultraviolet laser to generate Raman-scattered photons and native fluorescence emission photons from near-surface material to detect and classify chemical and mineralogical compositions. The collected photons are focused on a charge-coupled device and the data are returned to Earth for analysis. The compact DUV R/F spectrometer has a spectral range from 249.9 nm to 353.6 nm (200 cm1 to 12, 000 cm1) (with a spectral resolution of 0.296 nm (40 cm1)). The compact spectrometer uses a custom design to project a high-resolution Raman spectrum and a low-resolution fluorescence spectrum on a single charge-coupled device. The natural spectral separation enabled by deep ultraviolet excitation enables wavelength separation of the Raman/fluorescence spectra. The SHERLOC spectrometer was designed to optimize the resolution of the Raman spectral region and the wavelength range of the fluorescence region. The resulting illumination on the charge-coupled device is curved, requiring a segmented, nonlinear wavelength calibration in order to understand the mineralogy and chemistry of Martian materials.

Kyle Uckert↗

Evolution of Iron K Alpha Line Emission in the Black Hole Candidate GX 339-4

GX 339-4 was regularly monitored with the Rossi X-Ray Timing Explorer during a period (in 1999) when its X-ray flux decreased significantly (from 4.26 x 10(exp -10) to 7.6 x 10(exp -12) ergs in the 3-20 keV band), as the source settled into the 'off state.' Our spectral analysis revealed the presence of a prominent iron K alpha line in the observed spectrum of the source for all observations. The line shows an interesting evolution: it is centered at approx. 6.4 keV when the measured flux is above 5 x 10(exp -1) ergs per sq cm/s but is shifted to approx. 6.7 keV at lower fluxes. The equivalent width of the line appears to increase significantly toward lower fluxes, although it is likely to be sensitive to calibration uncertainties. While the fluorescent emission of neutral or mildly ionized iron atoms in the accretion disk can perhaps account for the 6.4 keV line, as is often invoked for black hole candidates, it seems difficult to understand the 6.7 keV line with this mechanism because the disk should be less ionized at lower fluxes (unless its density changes drastically). On the other hand, the 6.7 keV line might be due to a recombination cascade of hydrogen- or helium-like iron ions in an optically thin, highly ionized plasma. We discuss the results in the context of proposed accretion models.

Feng, Y. X.↗

Molecular Hydrogen Fluorescence in IC 63

This grant has supported the acquisition, reduction and analysis of data targeting the structure and excitation of molecular hydrogen in the reflection nebula IC 63 and in particular the fluorescent emission seen in the UV. In addition to manpower for analyzing the FUSE data, the grant supported the (attempted) acquisition of supporting ground-based data. We proposed for and received observing time for two sets of ground based, data; narrow band imaging ([S II], [O III) at KPNO (July 2002; Observer: Burgh) and imaging spectro-photometry of several of the near-infrared rotation-vibration lines of H2 at the IRTF (October 2003; Observer: Andersson). Unfortunately, both of these runs were failures, primarily because of bad weather, and did not result in any useful data. We combined the FUSE observations with rocket borne observations of the star responsible for exciting the H2 fluorescence in IC 63: gamma Cas, and with archival HUT observations of IC 63, covering the long-wavelength part of the molecular hydrogen fluorescence.

Andersson, B-G↗

New Evidence for Efficient Collisionless Heating of Electrons at the Reverse Shock of a Young Supernova Remnant

Although collisionless shocks are ubiquitous in astrophysics, certain key aspects of them are not well understood. In particular, the process known as collisionless electron heating, whereby electrons are rapidly energized at the shock front, is one of the main open issues in shock physics. Here, we present the first clear evidence for efficient collisionless electron heating at the reverse shock of Tycho's supernova remnant (SNR), revealed by Fe K diagnostics using high-quality X-ray data obtained by the Suzaku satellite. We detect K beta (3p yields 1s) fluorescence emission from low-ionization Fe ejecta excited by energetic thermal electrons at the reverse shock front, which peaks at a smaller radius than Fe K alpha (2p yields 1s) emission dominated by a relatively highly ionized component. Comparisons with our hydrodynamical simulations imply instantaneous electron heating to a temperature 1000 times higher than expected from Coulomb collisions alone. The unique environment of the reverse shock, which is propagating with a high Mach number into rarefied ejecta with a low magnetic field strength, puts strong constraints on the physical mechanism responsible for this heating and favors a cross-shock potential created by charge deflection at the shock front. Our sensitive observation also reveals that the reverse shock radius of this SNR is about 10% smaller than the previous measurement using the Fe K alpha morphology from the Chandra observations. Since strong Fe K beta fluorescence is expected only from low-ionization plasma where Fe ions still have many 3p electrons, this feature is key to diagnosing the plasma state and distribution of the immediate postshock ejecta in a young SNR.

Fe K diagnostics↗