Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly,diffractGUIdetermines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly,ringGUIidentifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. BothdiffractGUIandringGUIemploy methods of computer vision for a fast, robust and accurate analysis. Thirdly,cellVieweris an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes.diffractGUIandcellViewercan be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly fromDigitalMicrograph(Gatan Inc.).

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Extracellular matrix (ECM) hydrogels prepared by tissue decellularization have been reported as natural injectable materials suitable for neural tissue repair. In this study, we prepared ECM hydrogel derived from human umbilical cord (UC) and evaluated its composition and mechanical and biological properties in comparison with the previously described ECM hydrogels derived from porcine urinary bladder (UB), brain, and spinal cord. The ECM hydrogels did not differ from each other in the concentration of collagen, while the highest content of glycosaminoglycans as well as the shortest gelation time was found for UC-ECM. The elastic modulus was then found to be the highest for UB-ECM. In spite of a different origin, topography, and composition, all ECM hydrogels similarly promoted the migration of human mesenchymal stem cells (MSCs) and differentiation of neural stem cells, as well as axonal outgrowth in vitro. However, only UC-ECM significantly improved proliferation of tissue-specific UC-derived MSCs when compared with the other ECMs. Injection of UC-ECM hydrogels into a photothrombotic cortical ischemic lesion in rats proved its in vivo gelation and infiltration with host macrophages. In summary, this study proposes UC-ECM hydrogel as an easily accessible biomaterial of human origin, which has the potential for neural as well as other soft tissue reconstruction.

Non-thermal plasmas hold great promise for a variety of biomedical applications. To ensure safe clinical application of plasma, a rigorous analysis of plasma-induced effects on cell functions is required. Yet mechanisms of bacteria deactivation by non-thermal plasma remain largely unknown. We therefore analyzed the influence of low-temperature atmospheric plasma on Gram-positive and Gram-negative bacteria. Using scanning electron microscopy, we demonstrate that both Grampositive and Gram-negative bacteria strains in a minute were completely destroyed by helium plasma. In contrast, mesenchymal stem cells (MSCs) were not affected by the same treatment. Furthermore, histopathological analysis of hematoxylin and eosin-stained rat skin sections from plasma-treated animals did not reveal any abnormalities in comparison to control ones. We discuss possible physical mechanisms leading to the shred of bacteria under non-thermal plasma irradiation. Our findings disclose how helium plasma destroys bacteria and demonstrates the safe use of plasma treatment for MSCs and skin cells, highlighting the favorability of plasma applications for chronic wound therapy. V C 2015 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4907624]Deactivation of bacteria and control of cellular nanomechanics can be done by different physical factors, including: mechanical forces, 1 laser irradiation, 2 high-gradient magnetic field, 3-5 pulses of electric field, 6 ultrasound, 7 and atmospheric non-thermal plasma. 8,9 However, the mechanisms of these effects and factors related to regulation of bacteria proliferation and death have been poorly investigated and not fully understood. Interactions between bacteria (cells) and plasmas can be carried out by means of any of plasma's agents: neutral gas, charged particles, excited atoms/molecules, reactive species (such as NO, O 3 , OH, and O 2 À ), UV light, electrical field, and ion bombarding. Thus, various constituents of plasma can affect biological, physical, and chemical processes in mammalian cell cultures, tissue, and microorganisms.In the last several decades, the problem of antibiotic resistance emerged as a rapidly growing public health issue. 10 Therefore, there is an indispensable need for the design and development of novel alternatives to antibiotics. In this regard, non-thermal plasma represents an important and effective alternative approach in overcoming resistant microorganisms. 11,12 The use of non-thermal atmospheric pressure plasma devices in clinical practice requires operating regimes that can be easily controlled and adjusted during treatments. Moreover, some side effects of the developed plasma devices, in particular, on the respiratory organs or the overheating of healthy tissues, can be expected. These unfavorable effects can be reduced by tuning of the physical properties of plasma generators. A burst of studies indicate a great potential of low temperature plasmas use in a wide variety of biological and medical applications, 12 specifically in wound healing. 9,13 Concomitantl...

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