Trees are natural objects, where deviations through the branches amplify geometric data for 3D representation and bring challenges to various applications dealing with 3D models, such as compression, visualization, symmetry detection, and radiative transfer simulation. This data article describes dataset of approximately symmetric 3D tree models with manually identified predominant symmetry plane in each tree model. Parameters for procedural tree synthesis were manually adjusted to produce approximately bilaterally symmetric trees which are grouped into species with distinct features. In the last step, each tree was manually annotated with approximate symmetry plane. This dataset contains geometric data of branches, manually defined parameters for tree synthesis method, point clouds, and a division plane with a score of bilateral symmetry strength. The generated trees can be used as benchmark data for verification of approximate reflectional symmetry detection methods. Additionally, generated 3D tree models can be used for other applications requiring pregenerated trees, such as compression of tree models, instancing, decimation methods, and radiative transfer simulation and modeling.

• Klíčová slova
• 3D tree modeling, Approximate symmetry, Symmetry detection, Tree synthesis,
• Publikační typ
• časopisecké články MeSH

Three-dimensional (3D) printing has showed great potential for the construction of electrochemical sensor devices. However, reported 3D-printed biosensors are usually constructed by physical adsorption and needed immobilizing reagents on the surface of functional materials. To construct the 3D-printed biosensors, the simple modification of the 3D-printed device by non-expert is mandatory to take advantage of the remote, distributed 3D printing manufacturing. Here, a 3D-printed electrode was prepared by fused deposition modeling (FDM) 3D printing technique and activated by chemical and electrochemical methods. A glucose oxidase-based 3D-printed nanocarbon electrode was prepared by covalent linkage method to an enzyme on the surface of the 3D-printed electrode to enable biosensing. X-ray photoelectron spectroscopy and scanning electron microscopy were used to characterize the glucose oxidase-based biosensor. Direct electrochemistry glucose oxidase-based biosensor with higher stability was then chosen to detect the two biomarkers, hydrogen peroxide and glucose by chronoamperometry. The prepared glucose oxidase-based biosensor was further used for the detection of glucose in samples of apple cider. The covalently linked glucose oxidase 3D-printed nanocarbon electrode as a biosensor showed excellent stability. This work can open new doors for the covalent modification of 3D-printed electrodes in other electrochemistry fields such as biosensors, energy, and biocatalysis.

• Klíčová slova
• 3D-printed electrode, Covalent modification, Electrochemical detection, Glucose, Hydrogen peroxide,
• MeSH
• 3D tisk * MeSH
• Aspergillus niger enzymologie   MeSH
• biosenzitivní techniky * metody   MeSH
• elektrochemické techniky * metody   přístrojové vybavení   MeSH
• elektrody * MeSH
• enzymy imobilizované * chemie   metabolismus   MeSH
• glukosa * analýza   chemie   MeSH
• glukosaoxidasa * chemie   metabolismus   MeSH
• limita detekce MeSH
• Malus chemie   MeSH
• peroxid vodíku * chemie   analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• enzymy imobilizované * MeSH
• glukosa * MeSH
• glukosaoxidasa * MeSH
• peroxid vodíku * MeSH

In the context of climate change conditions, addressing the shifting composition of forest stands and changes in traditional forest management practices are necessary. For this purpose, understanding the biomass allocation directly influenced by crown architecture is crucial. In this paper, we want to demonstrate the possibility of 3D mensuration of canopy architecture with the digitizer sensor Fastrak Polhemus and demonstrate its capability for assessing important structural information for forest purposes. Scots pine trees were chosen for this purpose, as it is the most widespread tree species in Europe, which, paradoxically, is very negatively affected by climate change. In our study, we examined young trees since the architecture of young trees influences their growth potential. In order to get the most accurate measurement of tree architecture, we evaluated the use of the Fastrak Polhemus magnetic digitizer to create a 3D model of individual trees and perform a subsequent statistical analysis of the data obtained. It was found that the stand density affects the number of branches in different orders and the heights of the trees in the process of natural regeneration. Regarding the branches, in our case, the highest number of branch orders was found in the clear-cut areas (density = 0.0), whereas the lowest branching was on-site with mature stands (density = 0.8). The results showed that the intensity of branching (assessed as the number of third-order branches) depends on the total number of branches of the tree of different branch orders but also on stand density where the tree is growing. An important finding in this study was the negative correlation between the tree branching and the tree height. The growth in height is lower when the branching expansion is higher. Similar data could be obtained with Lidar sensors. However, the occlusion due to the complexity of the tree crown would impede the information from being complete when using the magnetic digitizer. These results provide vital information for the creation of structural-functional models, which can be used to predict and estimate future tree growth and carbon fixation.

• Klíčová slova
• 3D model, Fastrak Polhemus, Pinus sylvestris, shading, tree architecture,
• MeSH
• biomasa MeSH
• klimatické změny MeSH
• lesy * MeSH
• stromy * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH

The paper deals with modeling the liver perfusion intended to improve quantitative analysis of the tissue scans provided by the contrast-enhanced computed tomography (CT). For this purpose, we developed a model of dynamic transport of the contrast fluid through the hierarchies of the perfusion trees. Conceptually, computed time-space distributions of the so-called tissue density can be compared with the measured data obtained from CT; such a modeling feedback can be used for model parameter identification. The blood flow is characterized at several scales for which different models are used. Flows in upper hierarchies represented by larger branching vessels are described using simple 1D models based on the Bernoulli equation extended by correction terms to respect the local pressure losses. To describe flows in smaller vessels and in the tissue parenchyma, we propose a 3D continuum model of porous medium defined in terms of hierarchically matched compartments characterized by hydraulic permeabilities. The 1D models corresponding to the portal and hepatic veins are coupled with the 3D model through point sources, or sinks. The contrast fluid saturation is governed by transport equations adapted for the 1D and 3D flow models. The complex perfusion model has been implemented using the finite element and finite volume methods. We report numerical examples computed for anatomically relevant geometries of the liver organ and of the principal vascular trees. The simulated tissue density corresponding to the CT examination output reflects a pathology modeled as a localized permeability deficiency.

• Klíčová slova
• Bernoulli equation, Darcy flow, Dynamic contrast-enhanced computed tomography, Liver perfusion, Porous media, Transport equation,
• MeSH
• analýza metodou konečných prvků MeSH
• biologické modely MeSH
• jaterní oběh * fyziologie   MeSH
• játra krevní zásobení   diagnostické zobrazování   MeSH
• kontrastní látky farmakokinetika   MeSH
• lidé MeSH
• matematické pojmy MeSH
• počítačová rentgenová tomografie statistika a číselné údaje   MeSH
• počítačová simulace MeSH
• poréznost MeSH
• vylepšení rentgenového snímku metody   MeSH
• zobrazování trojrozměrné statistika a číselné údaje   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kontrastní látky MeSH

During pregnancy, oxygen diffuses from maternal to fetal blood through villous trees in the placenta. In this paper, we simulate blood flow and oxygen transfer in feto-placental capillaries by converting three-dimensional representations of villous and capillary surfaces, reconstructed from confocal laser scanning microscopy, to finite-element meshes, and calculating values of vascular flow resistance and total oxygen transfer. The relationship between the total oxygen transfer rate and the pressure drop through the capillary is shown to be captured across a wide range of pressure drops by physical scaling laws and an upper bound on the oxygen transfer rate. A regression equation is introduced that can be used to estimate the oxygen transfer in a capillary using the vascular resistance. Two techniques for quantifying the effects of statistical variability, experimental uncertainty and pathological placental structure on the calculated properties are then introduced. First, scaling arguments are used to quantify the sensitivity of the model to uncertainties in the geometry and the parameters. Second, the effects of localized dilations in fetal capillaries are investigated using an idealized axisymmetric model, to quantify the possible effect of pathological placental structure on oxygen transfer. The model predicts how, for a fixed pressure drop through a capillary, oxygen transfer is maximized by an optimal width of the dilation. The results could explain the prevalence of fetal hypoxia in cases of delayed villous maturation, a pathology characterized by a lack of the vasculo-syncytial membranes often seen in conjunction with localized capillary dilations.

• MeSH
• biologické modely * MeSH
• choriové klky embryologie   MeSH
• difuze MeSH
• kapiláry metabolismus   fyziologie   MeSH
• krevní oběh * MeSH
• kyslík metabolismus   MeSH
• lidé MeSH
• placenta krevní zásobení   MeSH
• plod krevní zásobení   MeSH
• těhotenství MeSH
• zobrazování trojrozměrné * MeSH
• Check Tag
• lidé MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kyslík MeSH

The complex architecture of the liver biliary network represents a structural prerequisite for the formation and secretion of bile as well as excretion of toxic substances through bile ducts. Disorders of the biliary tract affect a significant portion of the worldwide population, often leading to cholestatic liver diseases. Cholestatic liver disease is a condition that results from an impairment of bile formation or bile flow to the gallbladder and duodenum. Cholestasis leads to dramatic changes in biliary tree architecture, worsening liver disease and systemic illness. Recent studies show that the prevalence of cholestatic liver diseases is increasing. The availability of well characterized animal models, as well as development of visualization approaches constitutes a critical asset to develop novel pathogenetic concepts and new treatment strategies.

• MeSH
• cholestáza diagnostické zobrazování   patofyziologie   MeSH
• lidé MeSH
• mikroskopie elektronová rastrovací metody   MeSH
• modely nemocí na zvířatech * MeSH
• teoretické modely MeSH
• žlučové cesty diagnostické zobrazování   fyziologie   patofyziologie   MeSH
• žlučové ústrojí diagnostické zobrazování   fyziologie   patofyziologie   MeSH
• zobrazování trojrozměrné metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Chloroplast number per cell is a frequently examined quantitative anatomical parameter, often estimated by counting chloroplast profiles in two-dimensional (2D) sections of mesophyll cells. However, a mesophyll cell is a three-dimensional (3D) structure and this has to be taken into account when quantifying its internal structure. We compared 2D and 3D approaches to chloroplast counting from different points of view: (i) in practical measurements of mesophyll cells of Norway spruce needles, (ii) in a 3D model of a mesophyll cell with chloroplasts, and (iii) using a theoretical analysis. We applied, for the first time, the stereological method of an optical disector based on counting chloroplasts in stacks of spruce needle optical cross-sections acquired by confocal laser-scanning microscopy. This estimate was compared with counting chloroplast profiles in 2D sections from the same stacks of sections. Comparing practical measurements of mesophyll cells, calculations performed in a 3D model of a cell with chloroplasts as well as a theoretical analysis showed that the 2D approach yielded biased results, while the underestimation could be up to 10-fold. We proved that the frequently used method for counting chloroplasts in a mesophyll cell by counting their profiles in 2D sections did not give correct results. We concluded that the present disector method can be efficiently used for unbiased estimation of chloroplast number per mesophyll cell. This should be the method of choice, especially in coniferous needles and leaves with mesophyll cells with lignified cell walls where maceration methods are difficult or impossible to use.

• Klíčová slova
• Chloroplast counting, Norway spruce (Picea abies L. Karst.), confocal microscopy, coniferous needle structure, disector method, mesophyll, profile counting, stereology.,
• MeSH
• biologické modely MeSH
• chloroplasty metabolismus   MeSH
• mezofylové buňky cytologie   metabolismus   MeSH
• smrk MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Purpose: To investigate the effect of patient specific vessel cooling on head and neck hyperthermia treatment planning (HTP). Methods and materials: Twelve patients undergoing radiotherapy were scanned using computed tomography (CT), magnetic resonance imaging (MRI) and contrast enhanced MR angiography (CEMRA). 3D patient models were constructed using the CT and MRI data. The arterial vessel tree was constructed from the MRA images using the 'graph-cut' method, combining information from Frangi vesselness filtering and region growing, and the results were validated against manually placed markers in/outside the vessels. Patient specific HTP was performed and the change in thermal distribution prediction caused by arterial cooling was evaluated by adding discrete vasculature (DIVA) modeling to the Pennes bioheat equation (PBHE). Results: Inclusion of arterial cooling showed a relevant impact, i.e., DIVA modeling predicts a decreased treatment quality by on average 0.19 °C (T90), 0.32 °C (T50) and 0.35 °C (T20) that is robust against variations in the inflow blood rate (|ΔT| < 0.01 °C). In three cases, where the major vessels transverse target volume, notable drops (|ΔT| > 0.5 °C) were observed. Conclusion: Addition of patient-specific DIVA into the thermal modeling can significantly change predicted treatment quality. In cases where clinically detectable vessels pass the heated region, we advise to perform DIVA modeling.

• Klíčová slova
• Hyperthermia, discrete vasculature, head and neck, hyperthermia treatment planning, thermal modelling,
• MeSH
• cévy anatomie a histologie   diagnostické zobrazování   MeSH
• indukovaná hypertermie * MeSH
• lidé MeSH
• magnetická rezonanční tomografie MeSH
• nádory hlavy a krku krevní zásobení   diagnostické zobrazování   terapie   MeSH
• počítačem asistovaná terapie MeSH
• počítačová rentgenová tomografie MeSH
• počítačové modelování podle konkrétního pacienta * MeSH
• studie proveditelnosti MeSH
• teplota MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Timber volume is an important asset, not only as an ecological component, but also as a key source of present and future revenues, which requires precise estimates. We used the Trimble TX8 survey-grade terrestrial laser scanner (TLS) to create a detailed 3D point cloud for extracting total tree height and diameter at breast height (1.3 m; DBH). We compared two different methods to accurately estimate total tree heights: the first method was based on a modified version of the local maxima algorithm for treetop detection, "HTTD", and for the second method we used the centers of stem cross-sections at stump height (30 cm), "HTSP". DBH was estimated by a computationally robust algebraic circle-fitting algorithm through hierarchical cluster analysis (HCA). This study aimed to assess the accuracy of these descriptors for evaluating total stem volume by comparing the results with the reference tree measurements. The difference between the estimated total stem volume from HTTD and measured stems was 2.732 m3 for European oak and 2.971 m3 for Norway spruce; differences between the estimated volume from HTSP and measured stems was 1.228 m3 and 2.006 m3 for European oak and Norway spruce, respectively. The coefficient of determination indicated a strong relationship between the measured and estimated total stem volumes from both height estimation methods with an R2 = 0.89 for HTTD and R2 = 0.87 for HTSP for European oak, and R2 = 0.98 for both HTTD and HTSP for Norway spruce. Our study has demonstrated the feasibility of finer-resolution remote sensing data for semi-automatic stem volumetric modeling of small-scale studies with high accuracy as a potential advancement in precision forestry.

• Klíčová slova
• 3D point cloud, circle fitting, forest biometrics, hierarchical cluster analysis, managed forest, modeling stem volume, stem-level assessment,
• Publikační typ
• časopisecké články MeSH

Climate, topography and the 3D structure of forests are major drivers affecting local species communities. However, little is known about how the specific functional traits of saproxylic (wood-living) beetles, involved in the recycling of wood, might be affected by those environmental characteristics.Here, we combine ecological and morphological traits available for saproxylic beetles and airborne laser scanning (ALS) data in Bayesian trait-based joint species distribution models to study how traits drive the distributions of more than 230 species in temperate forests of Europe.We found that elevation (as a proxy for temperature and precipitation) and the proportion of conifers played important roles in species occurrences while variables related to habitat heterogeneity and forest complexity were less relevant. Furthermore, we showed that local communities were shaped by environmental variation primarily through their ecological traits whereas morphological traits were involved only marginally. As predicted, ecological traits influenced species' responses to forest structure, and to other environmental variation, with canopy niche, wood decay niche and host preference as the most important ecological traits. Conversely, no links between morphological traits and environmental characteristics were observed. Both models, however, revealed strong phylogenetic signal in species' response to environmental characteristics.These findings imply that alterations of climate and tree species composition have the potential to alter saproxylic beetle communities in temperate forests. Additionally, ecological traits help explain species' responses to environmental characteristics and thus should prove useful in predicting their responses to future change. It remains challenging, however, to link simple morphological traits to species' complex ecological niches. Read the free Plain Language Summary for this article on the Journal blog.

• Klíčová slova
• Bayesian modelling, Coleoptera, HMSC, LiDAR, airborne laser scanning, environmental gradient, functional traits, phylogeny,
• Publikační typ
• časopisecké články MeSH