In the Czech part of the Upper Silesian Coal Basin (Moravian-Silesian region, Czech Republic), there are many deposits of endogenous combustion (e.g., localized burning soil bodies, landfills containing industrial waste, or slag rocks caused by mining processes). The Hedwig mining dump represents such an example of these sites where, besides the temperature and the concentrations of toxic gases, electric and non-electric quantities are also monitored within the frame of experimentally proposed and patented technology for heat collection (the so-called "Pershing" system). Based on these quantities, this paper deals with the determination and evaluation of negative heat sources and the optimization of the positive heat source dependent on measured temperatures within evaluation points or on a thermal profile. The optimization problem is defined based on a balance of the heat sources in the steady state while searching for a local minimum of the objective function for the heat source. From an implementation point of view, it is the interconnection of the numerical model of the heat collector in COMSOL with a user optimization algorithm in MATLAB using the LiveLink for MATLAB. The results are elaborated in five case studies based on the susceptibility testing of the numerical model by input data from the evaluation points. The tests were focused on the model behavior in terms of preprocessing for measurement data from each chamber of the heat collector and for the estimated value of temperature differences at 90% and 110% of the nominal value. It turned out that the numerical model is more sensitive to the estimates in comparison with the measured data of the chambers, and this finding does not depend on the type optimization algorithm. The validation of the model by the use of the mean-square error led to the finding of optimal value, also valid with respect to the other evaluation.

• Klíčová slova
• COMSOL multiphysics, MATLAB, borehole heat exchanger (BHE), liveLink for MATLAB, optimization, partial differential equation,
• Publikační typ
• časopisecké články MeSH

Textile yarns are the fundamental building blocks in the fabric industry. The measurement of the diameter of the yarn textile and fibers is crucial in textile engineering as the diameter size and distribution can affect the yarn's properties, and image processing can provide automatic techniques for faster and more accurate determination of the diameters. In this paper, facile and new methods to measure the yarn's diameter and its individual fibers diameter based on image processing algorithms that can be applied to microscopic digital images. Image preprocessing such as binarization and morphological operations on the yarn image were used to measure the diameter automatically and accurately compared to the manual measuring using ImageJ software. In addition to the image preprocessing, the circular Hough transform was used to measure the diameter of the individual fibers in a yarn's cross-section and count the number of fibers. The algorithms were built and deployed in a MATLAB (R2020b, The MathWorks, Inc., Natick, Massachusetts, United States) environment. The proposed methods showed a reliable, fast, and accurate measurement compared to other different image measuring softwares, such as ImageJ.

• Klíčová slova
• Hough transform, MATLAB, diameter, fiber, hairiness, image processing, yarn, yarn’s helix model,
• Publikační typ
• časopisecké články MeSH

The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation. Under the assumption of negligible water exchange between compartments, the time-dependent apparent diffusion coefficient can be directly computed from the solution of a diffusion equation subject to a time-dependent Neumann boundary condition. This paper describes a publicly available MATLAB toolbox called SpinDoctor that can be used 1) to solve the Bloch-Torrey partial differential equation in order to simulate the diffusion magnetic resonance imaging signal; 2) to solve a diffusion partial differential equation to obtain directly the apparent diffusion coefficient; 3) to compare the simulated apparent diffusion coefficient with a short-time approximation formula. The partial differential equations are solved by P1 finite elements combined with built-in MATLAB routines for solving ordinary differential equations. The finite element mesh generation is performed using an external package called Tetgen. SpinDoctor provides built-in options of including 1) spherical cells with a nucleus; 2) cylindrical cells with a myelin layer; 3) an extra-cellular space enclosed either a) in a box or b) in a tight wrapping around the cells; 4) deformation of canonical cells by bending and twisting; 5) permeable membranes; Built-in diffusion-encoding pulse sequences include the Pulsed Gradient Spin Echo and the Oscillating Gradient Spin Echo. We describe in detail how to use the SpinDoctor toolbox. We validate SpinDoctor simulations using reference signals computed by the Matrix Formalism method. We compare the accuracy and computational time of SpinDoctor simulations with Monte-Carlo simulations and show significant speed-up of SpinDoctor over Monte-Carlo simulations in complex geometries. We also illustrate several extensions of SpinDoctor functionalities, including the incorporation of T2 relaxation, the simulation of non-standard diffusion-encoding sequences, as well as the use of externally generated geometrical meshes.

• Klíčová slova
• Apparent diffusion coefficient, Bloch-torrey equation, Diffusion magnetic resonance imaging, Finite elements, Simulation,
• MeSH
• difuzní magnetická rezonance metody   MeSH
• lidé MeSH
• mozek * MeSH
• neurozobrazování metody   MeSH
• počítačová simulace MeSH
• software * MeSH
• teoretické modely * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

UNLABELLED: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination. AVAILABILITY AND IMPLEMENTATION: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox. CONTACT: ghagen@uccs.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• buňky Hep G2 MeSH
• fluorescence * MeSH
• fluorescenční mikroskopie metody   MeSH
• lidé MeSH
• mikrofilamenta ultrastruktura   MeSH
• osvětlení metody   MeSH
• počítačové zpracování obrazu MeSH
• software * MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Knowledge of soft tissue fiber structure is necessary for accurate characterization and modeling of their mechanical response. Fiber configuration and structure informs both our understanding of healthy tissue physiology and of pathological processes resulting from diseased states. This study develops an automatic algorithm to simultaneously estimate fiber global orientation, abundance, and waviness in an investigated image. To our best knowledge, this is the first validated algorithm which can reliably separate fiber waviness from its global orientation for considerably wavy fibers. This is much needed feature for biological tissue characterization. The algorithm is based on incremental movement of local regions of interest (ROI) and analyzes two-dimensional images. Pixels belonging to the fiber are identified in the ROI, and ROI movement is determined according to local orientation of fiber within the ROI. The algorithm is validated with artificial images and ten images of porcine trachea containing wavy fibers. In each image, 80-120 fibers were tracked manually to serve as verification. The coefficient of determination R2 between curve lengths and histograms documenting the fiber waviness and global orientation were used as metrics for analysis. Verification-confirmed results were independent of image rotation and degree of fiber waviness, with curve length accuracy demonstrated to be below 1% of fiber curved length. Validation-confirmed median and interquartile range of R2, respectively, were 0.90 and 0.05 for curved length, 0.92 and 0.07 for waviness, and 0.96 and 0.04 for global orientation histograms. Software constructed from the proposed algorithm was able to track one fiber in about 1.1 s using a typical office computer. The proposed algorithm can reliably and accurately estimate fiber waviness, curve length, and global orientation simultaneously, moving beyond the limitations of prior methods.

• Klíčová slova
• automated algorithm, collagen structure, fiber orientation, fiber waviness, image analysis, soft tissue analysis,
• MeSH
• algoritmy * MeSH
• kolagen MeSH
• prasata MeSH
• software * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kolagen MeSH

The COVID-19 outbreak led to the discovery of SARS-CoV-2 in sewage; thus, wastewater treatment plants (WWTPs) could have the virus in their effluent. However, whether SARS-CoV-2 is eradicated by sewage treatment is virtually unknown. Specifically, the objectives of this study include (i) determining whether a mixed matrixed membrane (MMM) is able to remove SARS-CoV-2 (polycarbonate (PC)-hydrous manganese oxide (HMO) and PC-silver nanoparticles (Ag-NP)), (ii) comparing filtration performance among different secondary treatment processes, and (iii) evaluating whether artificial neural networks (ANNs) can be employed as performance indicators to reduce SARS-CoV-2 in the treatment of sewage. At Shariati Hospital in Mashhad, Iran, secondary treatment effluent during the outbreak of COVID-19 was collected from a WWTP. There were two PC-Ag-NP and PC-HMO processes at the WWTP targeted. RT-qPCR was employed to detect the presence of SARS-CoV-2 in sewage fractions. For the purposes of determining SARS-CoV-2 prevalence rates in the treated effluent, 10 L of effluent specimens were collected in middle-risk and low-risk treatment MMMs. For PC-HMO, the log reduction value (LRV) for SARS-CoV-2 was 1.3-1 log10 for moderate risk and 0.96-1 log10 for low risk, whereas for PC-Ag-NP, the LRV was 0.99-1.3 log10 for moderate risk and 0.94-0.98 log10 for low risk. MMMs demonstrated the most robust absorption performance during the sampling period, with the least significant LRV recorded in PC-Ag-NP and PC-HMO at 0.94 log10 and 0.96 log10, respectively.

• Klíčová slova
• Artificial neural network, Mix matrix membrane, SARS-CoV-2, Wastewater treatment,
• MeSH
• COVID-19 * epidemiologie   MeSH
• kovové nanočástice * MeSH
• lidé MeSH
• neuronové sítě MeSH
• odpadní voda MeSH
• odpadní vody MeSH
• SARS-CoV-2 MeSH
• stříbro MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• odpadní voda MeSH
• odpadní vody MeSH
• stříbro MeSH

The microgrid (MG) faces significant security issues due to the two-way power and information flow. Integrating an Energy Management System (EMS) to balance energy supply and demand in Malaysian microgrids, this study designs a Fuzzy Logic Controller (FLC) that considers intermittent renewable sources and fluctuating demand patterns. FLC offers a flexible solution to energy scheduling effectively assessed by MATLAB/Simulink simulations. The microgrid consists of PV, battery, grid, and load. A Maximum Power Point Tracking (MPPT) controller helps to extract the maximum PV output and manages the power storage by providing or absorbing excess power. System analysis is performed by observing the State of Charge (SoC)of the battery and output power for each source. The grid supplies additional power if the battery and PV fail to meet the load demand. Total Harmonic Distortion (THD) analysis compares the performance of the Proportional-Integral Controller (PIC) and FLC. The results show that the PI controller design reduces the THD in the current signal, while FLC does not reduce the THD of the grid current when used in the EMS. However, FLC offers better control over the battery's SOC, effectively preventing overcharging and over-discharging. While PI reduces THD, FLC provides superior SOC control in a system comprising PV, battery, grid, and load. The findings demonstrate that the output current is zero when the SOC is higher than 80% or lower than 20%, signifying that no charging or discharging takes place to avoid overcharging and over-discharging. The third goal was accomplished by comparing and confirming that the grid current's THD for the EMS designed with both the PI Controller and the FLC is maintained below 5%, following the IEEE 519 harmonic standard, using the THD block in MATLAB Simulink. This analysis highlights FLC's potential to address demand-supply mismatches and renewable energy variability, which is crucial for optimizing microgrid performance.

• Klíčová slova
• Energy management system, Fuzzy logic controller, MATLAB simulink, Microgrid,
• Publikační typ
• časopisecké články MeSH

The potential nondestructive diagnostics of solid objects is discussed in this article. The whole process is accomplished by consecutive steps involving software analysis of the vibration power spectrum (eventually acoustic emissions) created during the normal operation of the diagnosed device or under unexpected situations. Another option is to create an artificial pulse, which can help us to determine the actual state of the diagnosed device. The main idea of this method is based on the analysis of the current power spectrum density of the received signal and its postprocessing in the Matlab environment with a following sample comparison in the Statistica software environment. The last step, which is comparison of samples, is the most important, because it is possible to determine the status of the examined object at a given time. Nowadays samples are compared only visually, but this method can't produce good results. Further the presented filter can choose relevant data from a huge group of data, which originate from applying FFT (Fast Fourier Transform). On the other hand, using this approach they can be subjected to analysis with the assistance of a neural network. If correct and high-quality starting data are provided to the initial network, we are able to analyze other samples and state in which condition a certain object is. The success rate of this approximation, based on our testing of the solution, is now 85.7%. With further improvement of the filter, it could be even greater. Finally it is possible to detect defective conditions or upcoming limiting states of examined objects/materials by using only one device which contains HW and SW parts. This kind of detection can provide significant financial savings in certain cases (such as continuous casting of iron where it could save hundreds of thousands of USD).

• Klíčová slova
• FFT, MatLab, Statistica, defect, power spectrum,
• MeSH
• akustika MeSH
• on-line systémy MeSH
• počítačové zpracování signálu MeSH
• software MeSH
• spektrální analýza metody   MeSH
• vibrace * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Artificial neural network based modeling is a generic approach to understand and correlate different complex parameters of biological systems for improving the desired output. In addition, some new inferences can also be predicted in a shorter time with less cost and labor. As terpenoid indole alkaloid pathway in Vinca minor is very less investigated or elucidated, a strategy of elicitation with hydroxylase and acetyltransferase along with incorporation of various precursors from primary shikimate and secoiridoid pools via simultaneous employment of cyclooxygenase inhibitor was performed in the hairy roots of V. minor. This led to the increment in biomass accumulation, total alkaloid concentration, and vincamine production in selected treatments. The resultant experimental values were correlated with algorithm approaches of artificial neural network that assisted in finding the yield of vincamine, alkaloids, and growth kinetics using number of elicits. The inputs were the hydroxylase/acetyltransferase elicitors and cyclooxygenase inhibitor along with various precursors from shikimate and secoiridoid pools and the outputs were growth index (GI), alkaloids, and vincamine. The approach incorporates two MATLAB codes; GRNN and FFBPNN. Growth kinetic studies revealed that shikimate and tryptophan supplementation triggers biomass accumulation (GI = 440.2 to 540.5); while maximum alkaloid (3.7 % dry wt.) and vincamine production (0.017 ± 0.001 % dry wt.) was obtained on supplementation of secologanin along with tryptophan, naproxen, hydrogen peroxide, and acetic anhydride. The study shows that experimental and predicted values strongly correlate each other. The correlation coefficient for growth index (GI), alkaloids, and vincamine was found to be 0.9997, 0.9980, 0.9511 in GRNN and 0.9725, 0.9444, 0.9422 in FFBPNN, respectively. GRNN provided greater similarity between the target and predicted dataset in comparison to FFBPNN. The findings can provide future insights to calculate growth index, alkaloids, and vincamine in combination to different elicits.

• Klíčová slova
• Artificial neural network, Generalized regression neural network, MATLAB, Vinca minor,
• MeSH
• alkaloidy biosyntéza   MeSH
• kořeny rostlin metabolismus   MeSH
• neuronové sítě * MeSH
• Vinca metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• alkaloidy MeSH

Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model's behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields.

• Klíčová slova
• MATLAB, SBML, model code, pharmacokinetics, reproducibility, systems biology,
• MeSH
• biologické modely * MeSH
• farmakokinetika * MeSH
• lidé MeSH
• počítačová simulace MeSH
• reprodukovatelnost výsledků MeSH
• software * MeSH
• systémová biologie * metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH