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- ItemDenoising for Improved Parametric MRI of the Kidney: Protocol for Nonlocal Means Filtering(Totowa, NJ : Humana Press, 2021) Starke, Ludger; Tabelow, Karsten; Niendorf, Thoralf; Pohlmann, Andreas; Pohlmann, Andreas; Niendorf, ThoralfIn order to tackle the challenges caused by the variability in estimated MRI parameters (e.g., T2* and T2) due to low SNR a number of strategies can be followed. One approach is postprocessing of the acquired data with a filter. The basic idea is that MR images possess a local spatial structure that is characterized by equal, or at least similar, noise-free signal values in vicinities of a location. Then, local averaging of the signal reduces the noise component of the signal. In contrast, nonlocal means filtering defines the weights for averaging not only within the local vicinity, bur it compares the image intensities between all voxels to define “nonlocal” weights. Furthermore, it generally compares not only single-voxel intensities but small spatial patches of the data to better account for extended similar patterns. Here we describe how to use an open source NLM filter tool to denoise 2D MR image series of the kidney used for parametric mapping of the relaxation times T2* and T2. This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.
- ItemNanoscale Spatiotemporal Diffusion Modes Measured by Simultaneous Confocal and Stimulated Emission Depletion Nanoscopy Imaging(Washington, DC : ACS Publ., 2018-6-12) Schneider, Falk; Waithe, Dominic; Galiani, Silvia; Bernardino de la Serna, Jorge; Sezgin, Erdinc; Eggeling, ChristianThe diffusion dynamics in the cellular plasma membrane provide crucial insights into molecular interactions, organization, and bioactivity. Beam-scanning fluorescence correlation spectroscopy combined with super-resolution stimulated emission depletion nanoscopy (scanning STED–FCS) measures such dynamics with high spatial and temporal resolution. It reveals nanoscale diffusion characteristics by measuring the molecular diffusion in conventional confocal mode and super-resolved STED mode sequentially for each pixel along the scanned line. However, to directly link the spatial and the temporal information, a method that simultaneously measures the diffusion in confocal and STED modes is needed. Here, to overcome this problem, we establish an advanced STED–FCS measurement method, line interleaved excitation scanning STED–FCS (LIESS–FCS), that discloses the molecular diffusion modes at different spatial positions with a single measurement. It relies on fast beam-scanning along a line with alternating laser illumination that yields, for each pixel, the apparent diffusion coefficients for two different observation spot sizes (conventional confocal and super-resolved STED). We demonstrate the potential of the LIESS–FCS approach with simulations and experiments on lipid diffusion in model and live cell plasma membranes. We also apply LIESS–FCS to investigate the spatiotemporal organization of glycosylphosphatidylinositol-anchored proteins in the plasma membrane of live cells, which, interestingly, show multiple diffusion modes at different spatial positions.
- ItemDiffusion and interface effects during preparation of all-solid microstructured fibers(Basel : MDPI AG, 2014) Kobelke, J.; Bierlich, J.; Wondraczek, K.; Aichele, C.; Pan, Z.; Unger, S.; Schuster, K.; Bartelt, H.All-solid microstructured optical fibers (MOF) allow the realization of very flexible optical waveguide designs. They are prepared by stacking of doped silica rods or canes in complex arrangements. Typical dopants in silica matrices are germanium and phosphorus to increase the refractive index (RI), or boron and fluorine to decrease the RI. However, the direct interface contact of stacking elements often causes interrelated chemical reactions or evaporation during thermal processing. The obtained fiber structures after the final drawing step thus tend to deviate from the targeted structure risking degrading their favored optical functionality. Dopant profiles and design parameters(e.g., the RI homogeneity of the cladding) are controlled by the combination of diffusion and equilibrium conditions of evaporation reactions. We show simulation results of diffusion and thermal dissociation in germanium and fluorine doped silica rod arrangements according to the monitored geometrical disturbances in stretched canes or drawn fibers. The paper indicates geometrical limits of dopant structures in sub-μm-level depending on the dopant concentration and the thermal conditions during the drawing process. The presented results thus enable an optimized planning of the preform parameters avoiding unwanted alterations in dopant concentration profiles or in design parameters encountered during the drawing process.
- ItemSpin pumping at interfaces with ferro- and paramagnetic Fe60Al40films acting as spin source and spin sink(Melville, NY : American Inst. of Physics, 2022) Strusch, T.; Lenz, K.; Meckenstock, R.; Bali, R.; Ehrler, J.; Lindner, J.; Fassbender, J.; Farle, M.; Potzger, K.; Semisalova, A.We present a study of spin pumping efficiency and determine the spin mixing conductance and spin diffusion length in thin bilayer films based on 3d transition metal alloy Fe60Al40. Due to its magnetostructural phase transition, Fe60Al40 can be utilized as a ferromagnetic (FM) or paramagnetic (PM) material at the same temperature depending on its structural order; thus a thin Fe60Al40 film can act as a spin source or a spin sink when interfaced with a paramagnet or a ferromagnet, respectively. Ferromagnetic resonance measurements were performed in a frequency range of 5-35 GHz on bilayer films composed of FM-Fe60Al40/Pd and PM-Fe60Al40/Ni80Fe20 (permalloy). The increase in damping with the thickness of the paramagnetic layer was interpreted as a result of spin pumping into the paramagnet. We determine the spin mixing conductance g P d ↑↓ = (3.8 ± 0.5) × 10 18 m - 2 at the FM-Fe60Al40/Pd interface and the spin diffusion length λ P d = 9.1 ± 2.0 nm in Pd. For the PM-Fe60Al40/permalloy interface, we find a spin mixing conductance g F e A l ↑↓ = (2.1 ± 0.2) × 10 18 m - 2 and a spin diffusion length λ F e A l = 11.9 ± 0.2 nm for PM-Fe60Al40. The demonstrated bi-functionality of the Fe60Al40 alloy in spin pumping structures may be promising for spintronic applications.
- ItemError estimates for nonlinear reaction-diffusion systems involving different diffusion length scales(Bristol : IOP Publ., 2016) Reichelt, SinaWe derive quantitative error estimates for coupled reaction-diffusion systems, whose coefficient functions are quasi-periodically oscillating modeling the microstructure of the underlying macroscopic domain. The coupling arises via nonlinear reaction terms and we allow for different diffusion length scales, i.e. whereas some species have characteristic diffusion length of order 1 other species may diffuse with the order of the characteristic microstructure-length scale. We consider an effective system, which is rigorously obtained via two-scale convergence, and we derive quantitative error estimates.
- ItemHigh photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy(Bristol : IOP Publ., 2020) Schneider, Falk; Hernandez-Varas, Pablo; Lagerholm, B. Christoffer; Shrestha, Dilip; Sezgin, Erdinc; Roberti, M. Julia; Ossato, Giulia; Hecht, Frank; Eggeling, Christian; Urbančič, IztokProbing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells. © The Author(s). Published by IOP Publishing Ltd.
- ItemCarbon and Neon Ion Bombardment Induced Smoothing and Surface Relaxation of Titania Nanotubes(Basel : MDPI, 2021) Kupferer, Astrid; Mensing, Michael; Lehnert, Jan; Mändl, Stephan; Mayr, Stefan G.Titania nanotube arrays with their enormous surface area are the subject of much attention in diverse fields of research. In the present work, we show that not only 60 keV and 150 keV ion bombardment of amorphous titania nanotube arrays yields defect creation within the tube walls, but it also changes the surface morphology: the surface relaxes and smoothens in accordance with a curvature-driven surface material’s transport mechanism, which is mediated by radiation-induced viscous flow or radiation-enhanced surface diffusion, while the nanotubes act as additional sinks for the particle surface currents. These effects occur independently of the ion species: both carbon and neon ion bombardments result in comparable surface relaxation responses initiated by an ion energy of 60 keV at a fluence of 1 × 1016 ions/cm2. Using atomic force microscopy and contact angle measurements, we thoroughly study the relaxation effects on the surface topography and surface free energy, respectively. Moreover, surface relaxation is accompanied by further amorphization in surface-near regions and a reduction in the mass density, as demonstrated by Raman spectroscopy and X-ray reflectivity. Since ion bombardment can be performed on global and local scales, it constitutes a versatile tool to achieve well-defined and tunable topographies and distinct surface characteristics. Hence, different types of nanotube arrays can be modified for various applications.
- ItemTRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data(London : F1000 Research Ltd, 2021) Reina, Francesco; Wigg, John M.A.; Dmitrieva, Mariia; Lefebvre, Joël; Rittscher, Jens; Eggeling, ChristianSingle particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox – 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
- ItemNitric oxide density distributions in the effluent of an RF argon APPJ: Effect of gas flow rate and substrate(Bristol : IOP, 2014) Iseni, S.; Zhang, S.; Van Gessel, A.F.H.; Hofmann, S.; Van Ham, B.T.J.; Reuter, S.; Weltmann, K.-D.; Bruggeman, P.J.The effluent of an RF argon atmospheric pressure plasma jet, the so-called kinpen, is investigated with focus on the nitric-oxide (NO) distribution for laminar and turbulent flow regimes. An additional dry air gas curtain is applied around the plasma effluent to prevent interaction with the ambient humid air. By means of laser-induced fluorescence (LIF) the absolute spatially resolved NO density is measured as well as the rotational temperature and the air concentration. While in the laminar case, the transport of NO is attributed to thermal diffusion; in the turbulent case, turbulent mixing is responsible for air diffusion. Additionally, measurements with a molecular beam mass-spectrometer (MBMS) absolutely calibrated for NO are performed and compared with the LIF measurements. Discrepancies are explained by the contribution of the NO2 and N2O to the MBMS NO signal. Finally, the effect of a conductive substrate in front of the plasma jet on the spatial distribution of NO and air diffusion is also investigated.
- ItemStructure and stability of the magnetic solar tachocline(College Park, MD : Institute of Physics Publishing, 2007) Rüdiger, G.; Kitchatinov, L.L.Rather weak fossil magnetic fields in the radiative core can produce the solar tachocline if the field is almost horizontal in the tachocline region, i.e. if the field is confined within the core. This particular field geometry is shown to result from a shallow (≲1 Mm) penetration of the meridional flow existing in the convection zone into the radiative core. Two conditions are thus crucial for a magnetic tachocline theory: (i) the presence of meridional flow of a few metres per second at the base of the convection zone, and (ii) a magnetic diffusivity inside the tachocline smaller than 108 cm 2 s-1. Numerical solutions for the confined poloidal fields and the resulting tachocline structures are presented. We find that the tachocline thickness runs as Bp-1/2 with the poloidal field amplitude falling below 5% of the solar radius for Bp > 5 mG. The resulting toroidal field amplitude inside the tachocline of about 100 G does not depend on the Bp. The hydromagnetic stability of the tachocline is only briefly discussed. For the hydrodynamic stability of latitudinal differential rotation we found that the critical 29% of the 2D theory of Watson (1981 Geophys. Astrophys. Fluid Dyn. 16 285) are reduced to only 21% in 3D for marginal modes of about 6 Mm radial scale. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.