1. Tailoring the crystalline and amorphous phase ratios of TiO2 through the use of organic additives during hydrothermal synthesisNejc Rozman, Andrijana Sever Škapin, David Maria Tobaldi, Goran Dražić, Peter Nadrah, 2024, izvirni znanstveni članek Povzetek: The photocatalytic properties of TiO2 are primarily determined by its crystallinity and crystalline phase ratios. To improve the photocatalytic properties of TiO2, greater control over the formation of crystalline and amorphous phases during synthesis is therefore required. In this study, we demonstrate how the addition of minute amounts of three organic compounds (isopropanol, acetone and acetic acid) during hydrothermal treatment affects the amorphous and crystalline phase ratios: the addition of isopropanol or acetone accelerates the phase transition from anatase and brookite to rutile, whereas the addition of acetic acid inhibits the transformation of anatase to rutile, increasing the content of amorphous phase compared to samples where no organic compound was added. We show that the combination of the organic compound added, along with the duration of the hydrothermal treatment, can be used to tailor the phase composition of TiO2, so as to obtain either: i) TiO2 with a high content of both rutile and amorphous phase, ii) TiO2 with a high rutile content and iii) TiO2 with different ratios of all four phases, when the duration of synthesis is short (2–4 h). The materials synthesized exhibited high photocatalytic activity (in most cases higher than P25), which is attributed to the beneficial phase composition and high specific surface area.
Ključne besede: sol-gel processes, X-ray methods, chemical properties, TiO2, photocatalysis
Objavljeno v DiRROS: 14.08.2024; Ogledov: 43; Prenosov: 87
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2. In-depth comparison of adeno-associated virus containing fractions after CsCl ultracentrifugation gradient separationMojca Janc, Kaja Zevnik, Ana Dolinar, Tjaša Jakomin, Maja Štalekar, Katarina Bačnik, Denis Kutnjak, Magda Tušek-Žnidarič, Lorena Zentilin, Dmitri G. Fedorov, David Dobnik, 2024, izvirni znanstveni članek Povzetek: Recombinant adeno-associated viruses (rAAVs) play a pivotal role in the treatment of genetic diseases. However, current production and purification processes yield AAV-based preparations that often contain unwanted empty, partially filled or damaged viral particles and impurities, including residual host cell DNA and proteins, plasmid DNA, and viral aggregates. To precisely understand the composition of AAV preparations, we systematically compared four different single-stranded AAV (ssAAV) and self-complementary (scAAV) fractions extracted from the CsCl ultracentrifugation gradient using established methods (transduction efficiency, analytical ultracentrifugation (AUC), quantitative and digital droplet PCR (qPCR and ddPCR), transmission electron microscopy (TEM) and enzyme-linked immunosorbent assay (ELISA)) alongside newer techniques (multiplex ddPCR, multi-angle light-scattering coupled to size-exclusion chromatography (SEC-MALS), multi-angle dynamic light scattering (MADLS), and high-throughput sequencing (HTS)). Suboptimal particle separation within the fractions resulted in unexpectedly similar infectivity levels. No single technique could simultaneously provide comprehensive insights in the presence of both bioactive particles and contaminants. Notably, multiplex ddPCR revealed distinct vector genome fragmentation patterns, differing between ssAAV and scAAV. This highlights the urgent need for innovative analytical and production approaches to optimize AAV vector production and enhance therapeutic outcomes.
Ključne besede: recombinant adeno-associated viruses (rAAVs), CsCl ultracentrifugation gradient, analytical methods, digital droplet PCR (ddPCR), transmission electron microscopy (TEM), analytical ultracentrifugation (AUC), size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS), Illumina sequencing, virology
Objavljeno v DiRROS: 07.08.2024; Ogledov: 92; Prenosov: 73
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3. Extraction of DNA from different sample types - a practical approach for GMO testingJana Žel, Tina Demšar, Dejan Štebih, Mojca Milavec, Kristina Gruden, 2015, izvirni znanstveni članek Povzetek: Current methods based on DNA targets for the detection, identification and quantification of genetically modified organisms (GMOs) involve extraction of the DNA. Different extraction procedures have been developed for the great variety
of samples from food, feed, seeds and particular plant parts. This makes the operation of routine analytical laboratories complex and workloads heavy. Here we present a decision-making system, developed over many years of GMO testing on different samples, that result in the application of only a few extraction methods for the majority of samples. Developed decision-making system enables quicker and more cost effective testing of GMOs. In addition, the performance of DNA extraction resulting from the use of the selected extraction methods is presented for use in subsequent testing of GMOs by real time PCR methods. This approach can be used as a model for similar systems based on nucleic acid analysis in food, feed, seeds and plants.
Ključne besede: extraction methods, genetically modified organisms, GMO, decision- making system (biology), GMO testing, cetyltrimethylammonium bromide, CTAB
Objavljeno v DiRROS: 29.07.2024; Ogledov: 99; Prenosov: 86
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4. PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databasesTianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa, 2022, izvirni znanstveni članek Povzetek: PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology.
Ključne besede: PaintOmics 4, web tools, datasets, analysis methods, molecular biology
Objavljeno v DiRROS: 17.07.2024; Ogledov: 124; Prenosov: 126
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5. Evaluation of DNA extraction methods for reliable quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosaAlexandra Bogožalec Košir, Dane Lužnik, Viktorija Tomič, Mojca Milavec, 2023, izvirni znanstveni članek Povzetek: Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
Ključne besede: nucleic acid, dPCR, DNA extraction methods, Gram-negative bacteria
Objavljeno v DiRROS: 12.07.2024; Ogledov: 138; Prenosov: 148
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6. Singular $p$-biharmonic problem with the Hardy potentialAmor Drissi, Abdeljabbar Ghanmi, Dušan Repovš, 2024, izvirni znanstveni članek Povzetek: The aim of this paper is to study existence results for a singular problem involving the $p$-biharmonic operator and the Hardy potential. More precisely, by combining monotonicity arguments with the variational method, the existence of solutions is established. By using the Nehari manifold method, the multiplicity of solutions is proved. An example is also given to illustrate the importance of these results.
Ključne besede: p-biharmonic equation, variational methods, existence of solutions, Hardy potential, Nehari manifold, fibering map
Objavljeno v DiRROS: 08.07.2024; Ogledov: 175; Prenosov: 73
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7. Experimental investigation of the shear force capacity of prismatic cross laminated timber beamsHenrik Danielsson, Tomaž Pazlar, Erik Serrano, Boris Azinović, 2024, izvirni znanstveni članek Povzetek: Experimental tests of Cross Laminated Timber (CLT) under in-plane beam loading conditions are presented. The influence of the element layup, the individual lamination width, and the beam overhang at the supports on the shear force capacity was investigated. All the CLT beams had the same gross cross section, and a 4-point-bending test setup was used. The experimentally determined load-bearing capacities are compared with the load-bearing capacities resulting from analytical methods proposed for structural design, focusing on shear failure in the crossing areas of flatwise bonded laminations (shear failure mode III). The test results indicate no or very small influence of the element layup and the lamination width on the shear force capacity. These results partly contradict the predictions of the proposed design methods. Of the three studied beam geometry parameters, the beam overhang at the support had the greatest influence on the load-bearing capacity.
Ključne besede: cross laminated timber, CLT, beam, shear testing, shear capacity, design methods
Objavljeno v DiRROS: 15.04.2024; Ogledov: 366; Prenosov: 180
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8. Influence of test methodology on the characterization of the parallel-to-grain timber embedment strength and foundation modulus of dowelsCaroline D. Aquino, Rodrigues Leonardo G., Michael Schweigler, Meta Kržan, Zheng Li, Jorge M. Branco, 2024, izvirni znanstveni članek Povzetek: A reliable determination of the embedment strength and foundation modulus of timber elements is critical for the design and safety assessment of joints in timber structures. However, the existence of various test configurations for characterising the embedding properties of large diameter steel fasteners in timber elements poses challenges in directly comparing and utilising available test data. This paper aims to provide an insight into the influence of embedment property test methods, comparing experimental results from different test setups within the guidelines of the EN 383 and ASTM D 5764-97a standards for European softwood species, Scots pine wood (Pinus sylvestris) and Norway spruce (Picea abies). In addition to the test guidelines, the thickness of the specimen and the application of the load was evaluated within the protocols. A comprehensive statistical analysis was performed to identify statistically significant differences between the groups evaluated. The results of the analysis revealed disagreement between the standards in the evaluation of the strength of the embedding, highlighting the potential bias inserted by the experimental setup and protocol. Furthermore, it was proven that the thickness of the specimens influences both the embedding strength and the foundation modulus of the wood species tested. Finally, no distinctions were observed between tensile and compressive loading within the guidelines of the EN 383 standard.
Ključne besede: embedment strength, foundation modulus, dowel-type connections, test methods
Objavljeno v DiRROS: 15.04.2024; Ogledov: 289; Prenosov: 146
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9. Researching the change in the weight of split oak firewood due to different drying methodsAmina Gačo, 2021, objavljeni znanstveni prispevek na konferenci Povzetek: In this paper, the influences of stacking methods and drying places of split oak firewood in winter conditions (Quercus cerris) have been experimentally and theoretically investigated, due to the great importance of use in heating with such wood. The research was conducted on a sample of 48 pieces of logs with bark made of freshly cut oak. The logs were obtained by mechanized technology with the help of grafting by a hydraulic splitter and a chainsaw. Each log was measured for a research length of 0.30 m, marked with numbers 1-24. On each log, the weight was measured on a scale of 5 kg with an accuracy of 0.5 grams. Drying of logs was performed in two places. The first drying place was in outdoor conditions, sheltered from the snow and ventilated. The second place was indoors, at approximately constant room temperature. The logs were stacked in a crossed way for better air circulation. They were dried between 15/12/2020 and 15/02/2021, a total of 62 days. The average initial weight of logs dried in the facility was 1130.3 g, in the dried state the average weight was 952.87 g, which represented 84.3% of the original weight. The average initial weight of logs dried in outdoor conditions was 1192.125 g, in the dried state 1076.37 g, which represented 90.29% of the original weight. The average initial water content in the logs dried in the facility was 37.9%, in the dried state it was 27.5%. For logs dried in outdoor conditions, the average initial amount of water was 36.6%, in the dried state the average amount of water was 31.2%.
Ključne besede: weight, drying methods, splitting firewood, oak, stacking methods
Objavljeno v DiRROS: 09.04.2024; Ogledov: 645; Prenosov: 461
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10. Additive manufacturing multi-material components of SAF 2507 duplex steel and 15-5 PH martensitic stainless steelMartina Koukolíková, Pavel Podaný, Sylwia Rzepa, Michal Brázda, Aleksandra Kocijan, 2023, izvirni znanstveni članek Povzetek: The study reports the successful deposition of 15–5 precipitation-hardened (PH) martensitic steel on SAF 2507 duplex stainless steel (and vice versa) to form functionally graded materials (FGMs) using powder-based, directed-energy-deposition (DED) technology. The evolution of the microstructure and the mechanical properties of the 15–5 PH/SAF 2507 functionally graded material in the as-built state were investigated systematically. The results proved that the microstructural transition zone (MTZ) is formed above the fusion line due to the dilution effect of both steels. The phase composition of the MTZ consists of ferrite and, in comparison to the base materials, an increased amount of austenite. The interface has the lowest hardness owing to the formation of a significant proportion of the austenitic phase. However, the tensile mechanical properties were not affected by the interface as failure occurred in both SAF 2507 and at the interface regions. The research presents a promising application of FGMs in a horizontal configuration to form a high - quality, metallurgical joint between heterogeneous materials. This study introduces a novel approach by additive manufacturing (AM) of heterogeneous multi-materials, merging the favorable properties of duplex SAF 2507 and martensitic 15-5 PH stainless steels through superior metallurgical bonding. The combination of SAF 2507 and 15-5 PH in a functionally graded material has not been previously explored, as the existing studies deal with the duplex stainless steels SAF 2507 and either martensitic stainless-steel 15-5 PH deposited separately by laser powder-bed-fusion (L-PBF) or DED methods. This research pioneers the investigation of these materials in tandem, paving the way for the development of novel FGMs with optimized properties for specific applications. The resulting FGM exhibits exceptional corrosion resistance and high strength, making it highly versatile for applications in diverse industries such as offshore oil and gas production, aerospace, aviation, and chemical processing equipment.
Ključne besede: directed energy deposition, functionally graded materials, miniaturized specimen testing methods, SAF 2507, 15-5 PH
Objavljeno v DiRROS: 04.04.2024; Ogledov: 282; Prenosov: 113
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