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- ItemMInfer: Bridging MetaboAnalyst and Jacobian analysis for metabolomic networks(Elsevier, 2025-02-13) Schwarzerová, Jana; Mate, Erdő Gabor; Idkowiak, Jakub; Olešová, Dominika; Kvasnička, Aleš; Dobesova, Dana; Friedecký, David; Provazník, Valentýna; Skarda, Jozef; Weckwerth, Wolfram; Nägele, ThomasMetabolomic interaction networks provide critical insights into the dynamic relationships between metabolites and their regulatory mechanisms. This study introduces MInfer, a novel computational framework that integrates outputs from MetaboAnalyst, a widely used metabolomic analysis tool, with Jacobian analysis to enhance the derivation and interpretation of these networks.
- ItemMethod Comparison for Bone Density in Multiple Myeloma Patients(Czech Society for Biomedical Engineering and Medical Informatics, 2024-09-30) Nohel, Michal; Mézl, Martin; Válek, Vlastimil; Dostál, Marek; Chmelík, JiříBone mineral density (BMD) is an important indicator of bone health, particularly in patients with conditions such as multiple myeloma. This study aims to compare three methodologies for quantifying BMD in vertebral regions affected by lytic lesions: two using data from conventional CT with different corrections for tissue composition, and one using data acquired on a dual-energy CT system. Method 1 is based on conventional CT with corrections using reference values for muscle and fat, Method 2 uses conventional CT with corrections based on the measured CT values of paraspinal muscle, and Method 3 is based on dual-energy CT. The Wilcoxon signed-rank test was used for statistical comparison, as the dataset did not follow a normal distribution. The results indicated significant differences between Methods 1 and 2 for BMD in regions of interest (ROIs) within lytic lesions, while no significant differences were found for other comparisons in this group. For vertebrae affected by multiple myeloma, significant differences were found between Methods 1 and 2, and Methods 2 and 3, but not between Methods 1 and 3. In healthy vertebrae, a significant difference was found only between Methods 2 and 3. When all ROIs were combined, significant differences were found between Methods 1 and 2, and Methods 2 and 3, with no difference between Methods 1 and 3. Future research will focus on objectively assessing the accuracy of these methods by comparing their results with a calibration phantom.
- ItemThe histone chaperones ASF1 and HIRA are required for telomere length and 45S rDNA copy number homeostasis(Wiley, 2024-10-14) Machelová, Adéla; Dadejová, Martina; Franek, Michal; Mougeot, Guillaume; Simon, Lauriane; Le Goff, Samuel; Duc, Celine; Bassler, Jasmin; Demko, Martin; Schwarzerová, Jana; Desset, Sophia; Probst, Aline; Dvořáčková, MartinaGenome stability is significantly influenced by the precise coordination of chromatin complexes that facilitate the loading and eviction of histones from chromatin during replication, transcription, and DNA repair processes. In this study, we investigate the role of the Arabidopsis H3 histone chaperones ANTI-SILENCING FUNCTION 1 (ASF1) and HISTONE REGULATOR A (HIRA) in the maintenance of telomeres and 45S rDNA loci, genomic sites that are particularly susceptible to changes in the chromatin structure. We find that both ASF1 and HIRA are essential for telomere length regulation, as telomeres are significantly shorter in asf1a1b and hira mutants. However, these shorter telomeres remain localized around the nucleolus and exhibit a comparable relative H3 occupancy to the wild type. In addition to regulating telomere length, ASF1 and HIRA contribute to silencing 45S rRNA genes and affect their copy number. Besides, ASF1 supports global heterochromatin maintenance. Our findings also indicate that ASF1 transiently binds to the TELOMERE REPEAT BINDING 1 protein and the N terminus of telomerase in vivo, suggesting a physical link between the ASF1 histone chaperone and the telomere maintenance machinery.
- ItemGenetic and phenotypic diversity of Flavobacterium psychrophilum isolates from Czech salmonid fish farms(BioMed Central, 2024-09-18) Vaibarova, Vera; Králová, Stanislava; Palíková, Miroslava; Schwarzerová, Jana; Nejezchlebová, Julie; Čejková, Darina; Čížek, AloisThe salmonid pathogen Flavobacterium psychrophilum poses a significant economic threat to global aquaculture, yet our understanding of its genetic and phenotypic diversity remains incomplete across much of its geographic range. In this study, we characterise the genetic and phenotypic diversity of 70 isolates collected from rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta m. fario) from fish farms in the Czech Republic between 2012 and 2019 to compare their genomic content with all draft or complete genomes present in the NCBI database (n=187).
- ItemEvaluation of the Spatial Structure of Windbreaks from Digital Photography(Polish Society of Ecological Engineering, 2024-09-01) Kučera, Josef; Fukalová, Petra; Středová, Hana; Blecha, Martin; Jakubíček, Roman; Chmelík, Jiří; Podhrázská, Jana; Středa, TomášThe loss of fertile soil due to wind erosion has major impacts on the landscape and the environment. Its intensity and extent depend on many factors, where vegetation cover, soil moisture and wind intensity play key roles. Climatic conditions are constantly developing towards a higher extremity. Episodes of drought associated with a higher risk of wind erosion are longer and more frequent. For farmers, this results in higher demands for management in order to increase resistance against the negative effects of wind erosion. Windbreaks effectively protect the soil by reducing wind speed. This paper describes the automation of the current procedure for the evaluation of the spatial structure of windbreaks by means of advanced image signal analysis (2D) and the subsequent use of machine learning for further classification of spatial structure parameters (optical porosity). Software called Windbreak which enables the evaluation of optical porosity, including the assessment of canopy height, has been developed. The program allows working with digital photographs at the original resolution. The output from the Windbreak software can be also used as input values for determining the effectiveness of windbreaks.