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- ItemUnveiling vertebrate development dynamics in frog Xenopus laevis using micro-CT imaging(Oxford University Press, 2024-07-17) Lázňovský, Jakub; Kavková, Michaela; Reis, Alice Helena; Robovská-Havelková, Pavla; Maia, Lorena Agostini; Křivánek, Jan; Zikmund, Tomáš; Kaiser, Jozef; Buchtová, Marcela; Harnoš, JakubBackground Xenopus laevis, the African clawed frog, is a versatile vertebrate model organism in various biological disciplines, prominently in developmental biology to study body plan reorganization during metamorphosis. However, a notable gap exists in the availability of comprehensive datasets encompassing Xenopus' late developmental stages.Findings This study utilized micro-computed tomography (micro-CT), a noninvasive 3-dimensional (3D) imaging technique with micrometer-scale resolution, to explore the developmental dynamics and morphological changes in Xenopus laevis. Our approach involved generating high-resolution images and computed 3D models of developing Xenopus specimens, spanning from premetamorphosis tadpoles to fully mature adults. This dataset enhances our understanding of vertebrate development and supports various analyses. We conducted a careful examination, analyzing body size, shape, and morphological features, focusing on skeletogenesis, teeth, and organs like the brain and gut at different stages. Our analysis yielded valuable insights into 3D morphological changes during Xenopus' development, documenting details previously unrecorded. These datasets hold the solid potential for further morphological and morphometric analyses, including segmentation of hard and soft tissues.Conclusions Our repository of micro-CT scans represents a significant resource that can enhance our understanding of Xenopus' development and the associated morphological changes in the future. The widespread utility of this amphibian species, coupled with the exceptional quality of our scans, which encompass a comprehensive series of developmental stages, opens up extensive opportunities for their broader research application. Moreover, these scans can be used in virtual reality, 3D printing, and educational contexts, further expanding their value and impact. Graphical Abstract Summary: X-ray tomography was used to examine the African clawed frog (Xenopus laevis). This extensive dataset of specimens from tadpoles to adult frogs opens avenues to novel insights into the changes and developmental dynamics of selected structures, leading eventually to an improved understanding of this crucial animal model.
- ItemImaging the elemental distribution within human malignant melanomas using Laser-Induced Breakdown Spectroscopy(Elsevier, 2024-06-29) Kopřivová, Hana; Kiss, Kateřina; Krbal, Lukáš; Stejskal, Václav; Buday, Jakub; Pořízka, Pavel; Kaška, Milan; Ryška, Aleš; Kaiser, JozefThe diagnosis of malignant melanoma, often an inconspicuous but highly aggressive tumor, is most commonly done by histological examination, while additional diagnostic methods on the level of elements and molecules are constantly being developed. Several studies confirmed differences in the chemical composition of healthy and tumor tissue. Our study presents the potential of the LIBS (Laser -Induced -Breakdown Spectroscopy) technique as a diagnostic tool in malignant melanoma (MM) based on the quantitative changes in elemental composition in cancerous tissue. Our patient group included 17 samples of various types of malignant melanoma and one sample of healthy skin tissue as a control. To achieve a clear perception of results, we have selected two biogenic elements (calcium and magnesium), which showed a dissimilar distribution in cancerous tissue from its healthy surroundings. Moreover, we observed indications of different concentrations of these elements in different subtypes of malignant melanoma, a hypothesis that requires confirmation in a more extensive sample set. The information provided by the LIBS Imaging method could potentially be helpful not only in the diagnostics of tumor tissue but also be beneficial in broadening the knowledge about the tumor itself.
- ItemProLEED Studio: software for modeling low-energy electron diffraction patterns(INT UNION CRYSTALLOGRAPHY, 2024-02-01) Procházka, Pavel; Čechal, JanLow-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.
- ItemShifty invisibility cloaks(Optica Publishing Group, 2024-01-01) Courtial, Johannes; Bělín, Jakub; Soboňa, Matúš; Locher, Maik; Tyc, TomášWe recently presented what we believe are new cloaking strategies [Belin et al., Opt. Express 27, 37327 (2019)], abstracted from the properties of an ideal-lens cloak that exists in theory only. Key to the cloaking strategies is that objects on the cloak's inside are imaged to its outside. In the simplest case, interior objects appear simply shifted, forming a "shifty cloak". Here we connect our work to several previous investigations of shifty cloaks and other shifty devices, designed using standard transformation optics, thereby bringing our cloaking strategies closer to experimental realization. We investigate to the best of our knowledge novel combinations of shifty cloaks, specifically Janus devices and optical wormholes. Finally, we demonstrate an experimental realization of a paraxial shifty cloak.
- ItemAnalytical electron microscopy analysis of insulating and metallic phases in nanostructured vanadium dioxide(Royal Society of Chemistry, 2024-05-03) Krpenský, Jan; Horák, Michal; Kabát, Jiří; Planer, Jakub; Kepič, Peter; Křápek, Vlastimil; Konečná, AndreaVanadium dioxide (VO2) is a strongly correlated material that exhibits the insulator-to-metal transition (IMT) near room temperature, which makes it a promising candidate for applications in nanophotonics or optoelectronics. However, creating VO2 nanostructures with the desired functionality can be challenging due to microscopic inhomogeneities that can significantly impact the local optical and electronic properties. Thin lamellas, produced by focused ion beam milling from a homogeneous layer, provide a useful prototype for studying VO2 at the truly microscopic level using a scanning transmission electron microscope (STEM). High-resolution imaging is used to identify structural inhomogeneities while electron energy-loss spectroscopy (EELS) supported by statistical analysis helps to detect VxOy stoichiometries with a reduced oxidation number of vanadium at the areas of thickness below 70 nm. On the other hand, the thicker areas are dominated by vanadium dioxide, where the signatures of the IMT are detected in both core-loss and low-loss EELS experiments with in situ heating. The experimental results are interpreted with ab initio and semi-classical calculations. This work shows that structural inhomogeneities such as pores and cracks present no harm to the desired optical properties of VO2 samples. We utilize analytical electron microscopy with in situ heating to observe the insulator-metal transition in vanadium dioxide and to identify additional vanadium oxides across the sample exhibiting nanoscopic pores and cracks.