1. The influence of storage conditions and DNA extraction protocol on the results of molecular analysis of the European spruce bark beetle (Ips typographus L.)Zina Devetak, Andreja Kavčič, Maarten De Groot, Barbara Piškur, 2023, original scientific article Abstract: One of the key steps of the molecular identification of bark beetles is obtaining a sufficient quantity of high-quality DNA extract. In this study, we investigated the influence of different storage procedures for Ips typographus (L.) specimens and various DNA extraction protocols on the quantity and quality of DNA intended for use in molecular diagnostics. Adult beetles were frozen at -20 °C, either dry or in ethanol. We tested four different protocols for DNA extraction. We compared the quantity of extracted DNA and assessed its quality with PCR and Sanger sequencing. Different storage protocols had no significant effect on the quantity of DNA extracted. However, freezing specimens in ethanol provided higher-quality DNA for molecular applications. Only two of the extraction protocols produced sequenceable amplicons, and the difference in the amount of extracted DNA between them was not significant. We propose the optimal combination of storing specimens in ethanol at -20°C and using the Nucleospin Insect DNA extraction kit from Macherey Nagel, enabling a timeefficient identification process.
Keywords: early detection, specimen storage, total DNA extraction, PCR, polymerase chain reaction, Sanger sequencing, molecular diagnostics
Published in DiRROS: 02.02.2024; Views: 442; Downloads: 135
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2. Electrochemical corrosion tests on steel in alkali-activated materialsNina Gartner, Miha Hren, Tadeja Kosec, Andraž Legat, 2021, published scientific conference contribution Abstract: One of the potential alternatives to Ordinary Portland Cement (OPC) are Alkali-Activated Materials (AAMs). The service life of reinforced concrete structures greatly depends on the corrosion resistance of embedded steel reinforcement. Due to the wide range of AAMs and their diverse properties, corrosion processes of steel in these materials are relatively unknown. Corrosion monitoring methods or their interpretations in certain cases cannot be directly transferred from the ones for OPC materials. The chemical compositions of pore solution in different AAMs influence the results of electrochemical measurements and their interpretations. Within this research, three different alkali-activated mortar mixes were prepared, based on fly ash, slag or metakaolin. Pore solutions were extracted from each mortar andchemical analysis was acquired. Different electrochemical corrosion measurements were performed on steel submerged to synthetic pore solutions. In parallel, ordinary carbon steel reinforcing bar was installed in the same types of alkali-activated mortar mixes. Specimens were exposed to wet/dry cycles with saline solution and periodic measurements of electrochemical impedance spectroscopy (EIS) were performed. Measured parameters in both systems were analysedand compared. It was concluded that electrochemical measurements in pore solutions can provide basic overview on corrosion behaviour in different AAMs environments. Periodic EIS measurements enabled monitoring of corrosion initiation and propagation on steel reinforcement in AAMs, although the information on the corrosion type is missing. Interpretation of results depends on visual analysis of corrosion damages after the end of exposure, providing information on corrosion type and intensity. The continuation of research on corrosion monitoring techniques will be performed by using Electrical Resistance (ER) sensors and Coupled Multi-Electrode Array (CMEA) sensors.
Keywords: corrosion, alkali-activated mortars, pore solution extraction, electrochemical corrosion techniques, visual analysis
Published in DiRROS: 22.01.2024; Views: 208; Downloads: 114
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3. Recovery of phosphorus and metals from the ash of sewage sludge, municipal solid waste, or wood biomass : a review and proposals for further useSara Tominc, Vilma Ducman, Wolfgang Wisniewski, Terttu Luukkonen, Kirkelund Gunvor M., Ottosen Lisbeth M., 2023, original scientific article Abstract: This review provides an overview of methods to extract valuable resources from the ash fractions of sewage sludge, municipal solid waste, and wood biomass combustion. The resources addressed here include critical raw materials, such as phosphorus, base and precious metals, and rare earth elements for which it is increasingly important to tap into secondary sources in addition to the mining of primary raw materials. The extraction technologies prioritized in this review are based on recycled acids or excess renewable energy to achieve an optimum environmental profile for the extracted resources and provide benefits in the form of local industrial symbioses. The extraction methods cover all scarce and valuable chemical elements contained in the ashes above certain concentration limits. Another important part of this review is defining potential applications for the mineral residues remaining after extraction. Therefore, the aim of this review is to combine the knowledge of resource extraction technology from ashes with possible applications of mineral residues in construction and related sectors to fully close material cycle loops.
Keywords: critical raw materials, extraction, sewage sludge ash, municipal solid waste incineration ash, wood biomass ash
Published in DiRROS: 03.11.2023; Views: 360; Downloads: 133
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4. FooDis : a food-disease relation mining pipelineGjorgjina Cenikj, Tome Eftimov, Barbara Koroušić-Seljak, 2023, original scientific article Abstract: Nowadays, it is really important and crucial to follow the new biomedical knowledge that is presented in scientific literature. To this end, Information Extraction pipelines can help to automatically extract meaningful relations from textual data that further require additional checks by domain experts. In the last two decades, a lot of work has been performed for extracting relations between phenotype and health concepts, however, the relations with food entities which are one of the most important environmental concepts have never been explored. In this study, we propose FooDis, a novel Information Extraction pipeline that employs state-of-the-art approaches in Natural Language Processing to mine abstracts of biomedical scientific papers and automatically suggests potential cause or treat relations between food and disease entities in different existing semantic resources. A comparison with already known relations indicates that the relations predicted by our pipeline match for 90% of the food-disease pairs that are common in our results and the NutriChem database, and 93% of the common pairs in the DietRx platform. The comparison also shows that the FooDis pipeline can suggest relations with high precision. The FooDis pipeline can be further used to dynamically discover new relations between food and diseases that should be checked by domain experts and further used to populate some of the existing resources used by NutriChem and DietRx.
Keywords: text mining, relation extraction, named entity recognition, named entity linking, food-disease relations
Published in DiRROS: 25.05.2023; Views: 363; Downloads: 170
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5. From language models to large-scale food and biomedical knowledge graphsGjorgjina Cenikj, Lidija Strojnik, Risto Angelski, Nives Ogrinc, Barbara Koroušić-Seljak, Tome Eftimov, 2023, original scientific article Abstract: Knowledge about the interactions between dietary and biomedical factors is scattered throughout uncountable research articles in an unstructured form (e.g., text, images, etc.) and requires automatic structuring so that it can be provided to medical professionals in a suitable format. Various biomedical knowledge graphs exist, however, they require further extension with relations between food and biomedical entities. In this study, we evaluate the performance of three state-of-the-art relation-mining pipelines (FooDis, FoodChem and ChemDis) which extract relations between food, chemical and disease entities from textual data. We perform two case studies, where relations were automatically extracted by the pipelines and validated by domain experts. The results show that the pipelines can extract relations with an average precision around 70%, making new discoveries available to domain experts with reduced human effort, since the domain experts should only evaluate the results, instead of finding, and reading all new scientific papers.
Keywords: biomedical knowledge graphs, relation-mining pipelines, relation extraction, validation
Published in DiRROS: 17.05.2023; Views: 388; Downloads: 157
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