Tomas Zikmund

Central European Institute of Technology-Czech Republic | CEITEC · Brno University of Technology

The development of craniofacial skeletal structures is fascinatingly complex and elucidation of the underlying mechanisms will not only provide novel scientific insights, but also help develop more effective clinical approaches to the treatment and/or prevention of the numerous congenital craniofacial malformations. To this end, we performed CAGE-s...

Computational modeling plays an important role in assessment of biomaterial structures, living tissue and their mechanical properties. Microstructure investigation of bone tissue needs high-level computational models based on μ-CT images. A crucial factor when creating a computational model is image processing using tissue segmentation. The most co...

Metallic porous structures (scaffolds) produced by additive manufacturing represent an important class of personalised implants used in load-bearing orthopaedic applications. As such, their fatigue performance must be excellent to prevent the need for revision surgery. This paper provides insight into the high-cycle fatigue behaviour of novel titan...

Misalignment of the rotation axis causes severe artifacts in X-ray computed tomography. Calibration of this parameter is often insufficient for sub-micron resolution measurements and needs to be corrected during the post-processing. This correction can be accelerated by various automatic methods. These vary in mechanisms and performance, making the...

Cross-section preparation of painting micro-samples is part of their routine analysis. This type of preparation can be used for several analytical techniques, such as scanning electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, and optical microscopy. These techniques offer high-resolution imaging and/or elemental info...

Scanning electron microscopy (SEM) is a common method for the analysis of painting micro-samples. The high resolution of this technique offers precise surface analysis and can be coupled with an energy-dispersive spectrometer for the acquisition of the elemental composition. For light microscopy and SEM analysis, the painting micro-samples are comm...

Spontaneous bleeds are a leading cause of death in the pediatric JAG1-related liver disease Alagille syndrome (ALGS). We asked whether there are sex differences in bleeding events in patients, whether Jag1Ndr/Ndr mice display bleeds or vascular defects, and whether discovered vascular pathology can be confirmed in patients non-invasively. We perfor...

Characterization of brain infarct lesions in rodent models of stroke is crucial to assess stroke pathophysiology and therapy outcome. Until recently, the analysis of brain lesions was performed using two techniques: (1) histological methods, such as TTC (Triphenyltetrazolium chloride), a time-consuming and inaccurate process; or (2) MRI imaging, a...

Aging of lithium-ion batteries is especially important for applications such as battery electric vehicles, where they constitute a major part of the total cost and practically determine product lifetime. One of the main problems during cycle aging is the swelling of the electrode stack, as this results in increased mechanical stresses inside batter...

Archeological ceramic is full of information from the socio-economic relations within a society to the food storage practices. Various admixtures are added to enhance specific properties of the ceramic. Hay is an under evaluated admixture and when fired, the organic part partially or fully “disappears”, thus making it harder to identify. The organi...

Archeological ceramic is full of information from the socio-economic relations within a society to the food storage practices. Various admixtures are added to enhance specific properties of the ceramic. Hay is an under evaluated admixture and when fired, the organic part partially or fully “disappears”, thus making it harder to identify. The organi...

Adrenal glands are the major organs releasing catecholamines and regulating our stress response. The mechanisms balancing generation of adrenergic chromaffin cells and protecting against neuroblastoma tumors are still enigmatic. Here we revealed that serotonin (5HT) controls the numbers of chromaffin cells by acting upon their immediate progenitor...

Reef-building corals are endangered animals with a complex colonial organization. Physiological mechanisms connecting multiple polyps and integrating them into a coral colony are still enigmatic. Using live imaging, particle tracking, and mathematical modeling, we reveal how corals connect individual polyps and form integrated polyp groups via spec...

Selective laser melting (SLM) is an additive manufacturing technology suitable for producing cellular lattice structures using fine metal powder and a laser beam. However, the shape and dimensional deviations occur on the thin struts during manufacturing, influencing the mechanical properties of the structure. There are attempts in the literature t...

Background:Lightless caves can harbour a wide range of living organisms. Cave animals have evolved a set of morphological, physiological, and behavioural adaptations known as troglomorphisms, enabling their survival in the perpetual darkness, narrow temperature and humidity ranges, and nutrient scarcity of the subterranean environment. In this stud...

Characterization of brain infarct lesion in rodent models of stroke is crucial to assess the outcome of stroke therapies and to study the disease pathophysiology. However, so far it has been mostly performed by: 1) histological methods, a time-consuming process that lead to significant flaws; or 2) via MRI imaging, which is faster, yielding 3D info...

Background Reptiles exhibit a large heterogeneity in teeth morphology. The main variability comprises the different tooth shape, the type of tooth attachment to the underlying bone, or the ability to replace the teeth. Findings Here, we provide full datasets of microtomography scans and 3D models of reptilian dentitions and skulls. We selected rep...

Spinal fusion is a surgical procedure used to join two or more vertebrae to prevent movement between them. This surgical procedure is considered in patients suffering from a wide range of degenerative spinal diseases or vertebral fractures. The success rate of spinal fusion is frequently evaluated subjectively using X-ray computed tomography. The p...

One of the critical factors that may significantly contribute to X-ray computed tomography measurement uncertainty is the misalignment of CT system components from ideal geometry assumed by tomographic reconstruction. It is proven to cause image artifacts, inhomogeneous magnification, thus leading to dimensional measurement errors. There is a lack...

In computed tomography, artifacts caused by metal objects pose a major challenge, as they severely degrade the final image. Reduction of these artifacts is a topic of ongoing research, and many possible approaches have been developed so far. Among these, projection completion methods are effective and reasonably simple to implement compared to othe...

The spatial resolution is still one of the essential parameters quantified in X-ray micro Computed Tomography for industrial applications. There is a number of approaches, how can be the spatial resolution determined. Our paper presents two of them: evaluation of the ruby sphere according to the ASTM E1695–95 guideline and bar pattern recognition i...

Characterization of brain infarct lesion in rodent models of stroke is crucial to assess the outcome of stroke therapies and to study the disease pathophysiology. However, so far it has been mostly performed by: 1) histological methods, a time-consuming process that lead to significant flaws and tissue distortion; or 2) via MRI imaging, which is fa...

This paper deals with the research of the Selective Laser Melting (SLM) scanning strategy to produce lattice structures from AlSi10Mg powder material. Nowadays, most of the SLM end-users use the laser strategy and parameters recommended by powder or machine suppliers to produce different components. However, this setup can cause material and shape...

Hollow SDD particles raise challenges with respect toappropriate and meaningful particle characterization. Whilstmeasurements of particle size and bulk density provide someinformation, the results can be confounded due to incorrectassumptions. Correspondingly, any correlation to powder/formulation properties may be erroneous or misleading.Quantitat...

X-ray computed tomography is a common tool for non-destructive testing and analysis. One major application of this imaging technique is 3D porosity identification and quantification, which involves image segmentation of the analysed dataset. This segmentation step, which is most commonly performed using a global thresholding algorithm, has a major...

X-ray computed tomography is a 3D imaging technique that is able to provide information about both inner and outer parts of battery cells without their destruction. We will present this technique allowing us access to the batteries data in the whole range of scales – from the analysis of entire cells down to microstructure of electrodes. We will fo...

Adverse effects of high dietary phosphorus on bone health have been observed in both animal and human studies. The aim of the investigation was to examine chronic effect of high phosphorus diet on the apical mandibular cortical thickness and volume in a hystricomorph rodent (Octodon degus) using micro-computed tomography. Male degus were randomly d...

The pro-survival MCL1 protein is overexpressed in many cancers, including B-cell non-Hodgkin lymphomas (B-NHL). S63845 is a highly specific inhibitor of MCL1. We analyzed mechanisms of sensitivity/resistance to S63845 in preclinical models of diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). Annexin V-based cytotoxic assays, western...

X-ray computed-tomography is an established inspection technique for cultural heritage objects, but it is rarely used for painted micro-samples. These small, delicate, and complex parts of historical objects offer important and unique insights to conservators and restorers, but there is no standard method for preparing them nondestructively and wit...

Multi-level visualization of U-Zr mineralization in sandstones is discussed, aiming at the identification of mineral phases, imaging of their distribution using 2D and 3D projections, and quantification of the presence of U-rich domains. For this purpose, uranium-bearing sediments with anomalous concentrations of Zr, Nb ± Fe, Sr were studied (Břevn...

Many growth factors have been studied as additives accelerating lumbar fusion rates in different animal models. However, their low hydrolytic and thermal stability both in vitro and in vivo limits their workability and use. In the proposed work, a stabilized vasculogenic and prohealing fibroblast growth factor-2 (FGF2-STAB®) exhibiting a functional...

Achondroplasia is the most prevalent genetic form of dwarfism in humans and is caused by activating mutations in FGFR3 tyrosine kinase. The clinical need for a safe and effective inhibitor of FGFR3 is unmet, leaving achondroplasia currently incurable. Here, we evaluated RBM-007, an RNA aptamer previously developed to neutralize the FGFR3 ligand FGF...

Alagille syndrome (ALGS) is generally thought of as a pediatric cholestatic liver disease, but spontaneous bleeds are a major cause of death. Here, we investigated bleeding in patients and a mouse model for ALGS (Jag1Ndr/Ndr mice) and asked whether phenotypes identified in mice could be detected in patients non-invasively. Jag1Ndr/Ndr mice spontane...

Amyloid plaques are small (~ 50 μm), highly-dense aggregates of amyloid beta (Aβ) protein in brain tissue, supposed to play a key role in pathogenesis of Alzheimer’s disease (AD). Plaques´ in vivo detection, spatial distribution and quantitative characterization could be an essential marker in diagnostics and evaluation of AD progress. However, cur...

Background X-ray microtomography (μCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological informatio...

Aims The aim of this study was to answer the question whether our newly developed injectable biodegradable “self-setting” polymer-composite as a bone adhesive is a good “bone-glue” candidate to efficiently fix comminuted fractures of pig femoral bones used as an ex-vivo experimental model. Methods Mechanical properties of adhesive prepared from α-...

Purpose This paper aims to focus on the evaluation of a polymer concrete as a three-dimensional (3D) printing material. An associated company has developed plastic concrete made from reused unrecyclable plastic waste. Its intended use is as a construction material. Design/methodology/approach The concrete mix, called PolyBet, composed of polypropy...

Patient-specific approach is gaining a wide popularity in computational simulations of biomechanical systems. Simulations (most often based on the finite element method) are to date routinely created using data from imaging devices such as computed tomography which seemingly very complex and sophisticated. However, using a computed tomography in fi...

Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed...

In this article, we introduce a new ring artifacts reduction procedure that combines several ideas from existing methods into one complex and robust approach with a goal to overcome their individual weaknesses and limitations. The procedure differentiates two types of ring artifacts according to their cause and character in computed tomography (CT)...

Amyloid plaques are small (~50 μm), highly-dense aggregates of amyloid beta (Aβ) protein in brain tissue, supposed to play a key role in pathogenesis of Alzheimer’s disease (AD). Plaques´ in vivo detection, spatial distribution and quantitative characterization could be an essential marker in diagnostics and evaluation of AD progress. However, curr...

Coordinated development of muscles, tendons, and their attachment sites ensures emergence of functional musculoskeletal units that are adapted to diverse anatomical demands among different species. How these different tissues are patterned and functionally assembled during embryogenesis is poorly understood. Here, we investigated the morphogenesis...

3D concrete printing technology (3DCP) is a relatively new technology that was first established in the 1990s. The main weakness of the technology is the interface strength between the extruded layers, which are deposited at different time intervals. Consequently, the interface strength is assumed to vary in relation to the time of concrete casting...

The author would like to correct the co-author’s name from “Josef Kaiser” to “Jozef Kaiser” and the last author name “Tomas Zikmund” is repeated twice in the online published article. The correct authors list is mentioned below.

In the manufacture of wires designed for the welding of low-alloy fine-grain steels, multiple internal discontinuities appear during some periods that are the cause of major failures (cracking) of the wires. To establish the causes of this phenomenon, a complex analysis was performed making use of light and electron microscopy, metallography, micro...

Bone presents different systemic functionalities as calcium phosphate reservoir, organ protection, among others. For that reason, the bone health conditions are essential to keep in equilibrium the metabolism of several body systems. Different technologies exist to diagnose bone conditions with invasive methods based on ionizing radiation. Therefor...

This work provides the benchmarking of two additive manufacturing (AM) technologies suitable for the fabrication of commercially pure titanium scaffolds for bone tissue engineering, i.e., selective laser melting (SLM) and robocasting. SLM is a powder bed fusion technique that is industrially used for the AM of titanium parts, while robocasting is a...

The investigation of archaeological samples, such as ancient ceramics, provides more details about the past. In this work, we suggest a new approach for the calibration of a depth profiling of ceramic fragments with glazed layers. X-ray Micro Computed Tomography (μCT) serves as a calibration method for a depth-profile analysis using Laser-Induced B...

The inhalation route has a substantial influence on the fate of inhaled particles. An outbreak of infectious diseases such as COVID-19, influenza or tuberculosis depends on the site of deposition of the inhaled pathogens. But the knowledge of respiratory deposition is important also for occupational safety or targeted delivery of inhaled pharmaceut...

An innovative approach to a non-destructive lock mechanism examination by means of X-ray computed tomography (CT) was involved in a careful opening of a locked 19th century chest missing the key, as an interdisciplinary cooperation with the restorers. In regard of the exploration and conservation of such locked objects, their opening is important t...

Secondary palate development is characterized by the formation of two palatal shelves on the maxillary prominences, which fuse in the midline in mammalian embryos. However, in reptilian species, such as turtles, crocodilians, and lizards, the palatal shelves of the secondary palate develop to a variable extent and morphology. While in most Squamate...

X-ray phase contrast imaging (PCI) is sensitive to phase shift of X-rays induced by sample. This is advantageous for low X-ray absorption samples such as polymers, biomaterials, tissues, scaffolds etc. We show propagation-based phase-contrast X-ray computed tomography imaging (PBI) in a specific configuration with the wide-cone angle (>50∘), polych...

A very bright and long bolide was observed over the eastern part of the Czech Republic during late local evening on December 9, 2014. This bolide was recorded by professional instruments in the Czech part of the European Fireball Network. Three meteorites weighing in total 87 g were found in the predicted area and were named Žďár nad Sázavou. The c...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Coordinated development of muscles, tendons, and their attachment sites ensures emergence of functional musculoskeletal units that are adapted to diverse anatomical demands among different species. How these different tissues are patterned and functionally assembled during embryogenesis is poorly understood. Here, we investigated the morphogenesis...

Background: In mammals, odontogenesis is regulated by transient signaling centers known as enamel knots (EKs), which drive the dental epithelium shaping. However, the developmental mechanisms contributing to formation of complex tooth shape in reptiles are not fully understood. Here, we aim to elucidate whether signaling organizers similar to EKs...

BACKGROUND AND AIMS: Alagille syndrome, like several other liver diseases, is characterized by malformation of lumenized structures, such as the circulatory or biliary systems. Liver architecture has typically been studied through 2D sections and, more recently, using thick tissue sections combined with immunofluorescence. We aimed to develop a rob...

Corticothalamic axons express Contactin-2 (CNTN2/TAG-1), a neuronal recognition molecule of the immunoglobulin superfamily involved in neurogenesis, neurite outgrowth, and fasciculation. TAG-1, which is expressed transiently by cortical pyramidal neurons during embryonic development, has been shown to be fundamental for axonal recognition, cellular...

3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usual...