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- ItemCpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome(Elsevier, 2025-05-21) Bartas, Martin; Petrovič, Michal; Brázda, Václav; Trenz, Oldřich; Ďurčanský, Aleš; Šťastný, JiříWith continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation, with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use, scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of the obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/ #/analyse/cpg.
- ItemTowards efficient waste management: identification of waste flow chains in micro-regional detail through monitored data(Springer, 2024-06-18) Němcová, Lucie; Pluskal, Jaroslav; Šomplák, Radovan; Kůdela, JakubCountries around the world are gradually implementing the transition to a circular economy in waste management. This effort should be initiated already at the waste producers. It is necessary to plan and monitor waste management in as much detail as possible, i.e. at the level of micro-regions. At present, only indicators at the national level are analysed, as more detailed data at the micro-regional level are often not available or are burdened with significant errors and inconsistencies. The calculation of waste management indicators for micro-regions will allow to identify the potential for increasing material or energy recovery and to plan the necessary infrastructure directly to these locations instead of blanket and often ineffective legislative actions. This paper presents an approach for determining the producer-treatment linkage, i.e., provides information about each produced waste, where it was treated, and in what way. Such information is often not available based on historical waste management data as there are repeated waste transfers and often aggregated within a micro-region. The network flow approach is based on an iterative procedure combining a simulation with multi-criteria optimization. The chosen criteria replicate expert estimates in investigated issue such as minimum flow splitting, and minimum transfer micro-regions. A data reconciliation is performed where the deviation from all simulations is minimized, given that the capacity constraints of nodes and arcs resulting from the database must be satisfied. The approach is tested on a generated sample task to evaluate the precision and time complexity of the developed tool. Finally, the presented approach is applied to address a case study in the Czech Republic, within which it is possible to identify treatment location and methods for waste from individual regions.
- ItemMaterials That Do Not Form Any Defects After WEDM(MDPI, 2024-12-06) Mouralová, Kateřina; Fries, Jiří; Beneš, Libor; Houška, PavelWire Electric Discharge Machining (WEDM) is an unconventional machining technology that uses electrical impulses to generate very high temperatures to cut material. The WEDM process hence causes some unfortunate defects, such as cracks and burnt cavities, which can impact the correct functionality of the machined pieces and shorten their service life. This study was carried out to understand which materials remain defect-free after WEDM. The examined materials were the Ampcoloy 35 copper alloy, the high-entropy steels FeCoCrMnNi and FeCoCrMnNiC0.2, and the B1914 and Nimonic 263 nickel alloys. The influence of the machining parameters, namely the pulse off time, gap voltage, discharge current, pulse on time, and wire feed, on the cutting speed and the surface topography of the machined piece was investigated. The surface morphology, the state of the subsurface layer in a cross-section, and the number of diffused elements from the wire electrode were analysed. All the analysed materials were found completely suitable for WEDM machining as they do not form any surface or subsurface defects.
- ItemThe Machinability of Different Albromet W130 Plates Thicknesses by WEDM to the Required Surface Roughness Value(MDPI, 2024-12-06) Mouralová, Kateřina; Beneš, Libor; Zahradníček, Radim; Fries, Jiří; Manová, AndreaWire Electrical Discharge Machining (WEDM) technology represents an unconventional but vital manufacturing technology in many different industrial branches. The automotive industry and its many significant requirements bring the need to manufacture inserts and mould segments for plastic injections from Albromet W130 material, with a required roughness, Ra, from 4.5 to 5 mu m so that subsequent profile etching can be eliminated. A planned experiment of 60 rounds was carried out to discover the optimal machining parameters, namely, the pulse-off time, gap voltage, discharge current, pulse-on time, and wire speed in order for the thickness of 10 to 100 mm (after 10 mm) to demonstrate the required roughness. The goal was to evaluate the surface roughness, maximise the cutting speed, and manufacture it without surface or subsurface defects. The evaluation of the planned experiment led to the establishment of optimised WEDM machining parameters with which thicknesses of 10-100 mm will always be produced with the required roughness, Ra, from 4.5 to 5 mu m and with the highest possible cutting speed. It was also proven that the machining does not lead to surface or subsurface defects, and thus, the service life of the manufactured parts will not be affected.
- ItemAnalysis of the time slot length impact of selected data link layer protocols on energy resource consumption in wireless sensor networks(Lublin University of Technology, 2025-01-01) Dymora, Paweł; Mazurek, Mirosław; Łyczko, Kamil; Hadaš, ZdeněkThe paper analyzes the effect of time slots on the correctness of packet delivery for selected media access conmedium access protocol), and X-MAC protocol (enhanced MAC protocol compared to B-MAC). In the study, reliability, and power consumption were used as indicators of the quality of the protocol variant. The length of the time slot was shown to affect the consumption of energy resources of the nodes. For all network sizes considered, it was shown that the best results were achieved by the L-MAC protocol, which also proved to be the most energyefficient with a low ratio of energy resource consumption. The X-MAC protocol has significant advantages and can be easily implemented on nodes running packet-switched wireless transceivers.