1. Decision support for the comparative evaluation and selection of analytical methods : detection of genetically modified organisms as an exampleDavid Dobnik, Kristina Gruden, Jana Žel, Yves Bertheau, Arne Holst-Jensen, Marko Bohanec, 2018, izvirni znanstveni članek Povzetek: The selection of the best-fit-for-purpose analytical method to be implemented in the laboratory is difficult due to availability of multiple methods, targets, aims of detection, and different kinds and sources of more or less reliable information. Several factors, such as method performance, practicability, cost of setup, and running costs need to be considered together with personnel training when selecting the most appropriate method. The aim of our work was to prepare a flexible multicriteria decision analysis model suitable for evaluation and comparison of analytical methods used for the purpose of detecting and/or quantifying genetically modified organisms, and to use this model to evaluate a variety of changing analytical methods. Our study included selection of PCR-, isothermal-, protein-, microarray-, and next-generation sequencing-based methods in simplex and/or multiplex formats. We show that the overall result of their fitness for purpose is relatively similar; however, individual criteria or a group of related criteria exposed more substantial differences between the methods. The proposed model of this decision support system enables easy modifications and is thus suitable for any other application of complex analytical methods.
Ključne besede: multicriteria decision analysis, genetically modified organisms, method evaluation, DEXi, decision support system, DSS
Objavljeno v DiRROS: 24.07.2024; Ogledov: 127; Prenosov: 151
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2. An insight into the feeding ecology of Serranus Scriba, a Shallow water mesopredator in the Northern Adriatic Sea, with a non-destructive methodAna Lokovšek, Martina Orlando-Bonaca, Domen Trkov, Lovrenc Lipej, 2022, izvirni znanstveni članek Povzetek: Serranus scriba is a common member of the coastal fish community in the Adriatic Sea, but knowledge about its feeding ecology is scarce. The aim of this paper is to present new evidence about its food preferences and feeding habits. An innovative non-destructive method of fecal pellet analysis was used for this study. This method does not require sacrificing specimens and the fish can be released back into the sea alive after the laboratory work. The results demonstrated that S. scriba mainly preys on decapods, followed by polychaetes, isopods, fish, mollusks and swarming shrimps. The calculated index of trophic diversity (ITD) value of 0.89 indicates that it is an opportunistic feeder that feeds on a wide range of different prey. According to the calculated trophic level of 3.43, which is higher than that of other members of the community, S. scriba is also an important piscivorous predator. With age, S. scriba undergoes an ontogenetic shift. The proportion of crustaceans, gastropods and polychaetes decreases with age and body size, while the proportion of fish increases.
Ključne besede: coastal fishes, diet, non-destructive method, non-lethal method, painted comber, northern Adriatic
Objavljeno v DiRROS: 17.07.2024; Ogledov: 119; Prenosov: 109
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3. Evaluation of methods and processes for robust monitoring of SARS-CoV-2 in wastewaterOlivera Maksimović, Živa Lengar, Zala Kogej Zwitter, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2022, izvirni znanstveni članek Povzetek: The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
Ključne besede: waste water, method evolution, virus detection, SARS-CoV-2
Objavljeno v DiRROS: 17.07.2024; Ogledov: 116; Prenosov: 101
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4. Treatment patterns and real-world evidence for stage III non-small cell lung cancer in Central and Eastern EuropeMilada Zemanova, Marko Jakopović, Karmen Stanič, Małgorzata Łazar-Poniatowska, Martina Vrankar, Petronela Rusu, Tudor Ciuleanu, Davorin Radosavljevic, Krisztina Bogos, Sergiusz Nawrocki, 2020, izvirni znanstveni članek Povzetek: The aim of this project was to collect real-world evidence and describe treatment patterns for stage III non-small cell lung cancer in Central and Eastern Europe. Based on real-world evidence, an expert opinion was developed, and the unmet needs and quality indicators were identified. Patients and methods. A systematic literature search and a multidisciplinary expert panel of 10 physicians from 7 countries used a modified Delphi process to identify quality indicators and unmet needs in patients with stage III non-small cell lung cancer. The profound questionnaire was used to characterize treatment patterns used for stage III non-small cell lung cancer, and a systematic review identified patterns in Central and Eastern Europe. The first questionnaire was completed by a group of medical oncologists, radiation oncologists and pneumologists. The panel of experts attended an in-person meeting to review the results of the questionnaire and to process a second round Delphi. An additional survey was then compiled and completed by the panel. Results. A complete consensus was reached by the panel of experts on a set of evidence-based clinical recommendations. The experience-based questionnaire generated a highly variable map of treatment patterns within the region. A list of unmet needs and barriers to quality care were developed with near-unanimous consent of the panel of experts. Conclusions. The current landscape of diagnostic and therapeutic approaches in Central and Eastern European countries is highly variable. We identified several significant barriers, mainly related to the availability of diagnostic and imaging methods and low rates of chemoradiotherapy with curative intention as initial treatment for unresectable stage III NSCLC.
Ključne besede: non-small cell lung cance, stage III, treatment patterns, Delphi method
Objavljeno v DiRROS: 16.07.2024; Ogledov: 121; Prenosov: 78
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5. Evaluation of two-dimensional dose distributions for pre-treatment patient-specific IMRT dosimetryĐeni Smilović Radojčić, David Rajlić, Božidar Casar, Manda Švabić Kolacio, Nevena Obajdin, Dario Faj, Slaven Jurković, 2018, izvirni znanstveni članek Povzetek: The accuracy of dose calculation is crucial for success of the radiotherapy treatment. One of the methods that represent the current standard for patient-specific dosimetry is the evaluation of dose distributions measured with an ionization chamber array inside a homogeneous phantom using gamma method. Nevertheless, this method does not replicate the realistic conditions present when a patient is undergoing therapy. Therefore, to more accurately evaluate the treatment planning system (TPS) capabilities, gamma passing rates were examined for beams of different complexity passing through inhomogeneous phantoms. Materials and methods The research was performed using Siemens Oncor Expression linear accelerator, Siemens Somatom Open CT simulator and Elekta Monaco TPS. A 2D detector array was used to evaluate dose distribution accuracy in homogeneous, semi-anthropomorphic and anthropomorphic phantoms. Validation was based on gamma analysis with 3%/3mm and 2%/2mm criteria, respectively. Results Passing rates of the complex dose distributions degrade depending on the thickness of non-water equivalent material. They also depend on dose reporting mode used. It is observed that the passing rate decreases with plan complexity. Comparison of the data for all set-ups of semi-anthropomorphic and anthropomorphic phantoms shows that passing rates are higher in the anthropomorphic phantom. Conclusions Presented results raise a question of possible limits of dose distribution verification in assessment of plan delivery quality. Consequently, good results obtained using standard patient specific dosimetry methodology do not guarantee the accuracy of delivered dose distribution in real clinical cases
Ključne besede: IMRT, 2D dose verification, gamma method, antropomorphic phantom
Objavljeno v DiRROS: 10.06.2024; Ogledov: 205; Prenosov: 102
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7. Assessment of local radial basis function collocation method for diffusion problems structured with multiquadrics and polyharmonic splinesIzaz Ali, Umut Hanoglu, Robert Vertnik, Božidar Šarler, 2024, izvirni znanstveni članek Povzetek: This paper aims to systematically assess the local radial basis function collocation method, structured with multiquadrics (MQs) and polyharmonic splines (PHSs), for solving steady and transient diffusion problems. The boundary value test involves a rectangle with Dirichlet, Neuman, and Robin boundary conditions, and the initial value test is associated with the Dirichlet jump problem on a square. The spectra of the free parameters of the method, i.e., node density, timestep, shape parameter, etc., are analyzed in terms of the average error. It is found that the use of MQs is less stable compared to PHSs for irregular node arrangements. For MQs, the most suitable shape parameter is determined for multiple cases. The relationship of the shape parameter with the total number of nodes, average error, node scattering factor, and the number of nodes in the local subdomain is also provided. For regular node arrangements, MQs produce slightly more accurate results, while for irregular node arrangements, PHSs provide higher accuracy than MQs. PHSs are recommended for use in diffusion problems that require irregular node spacing.
Ključne besede: meshless method, polyharmonic splines, multiquadrics, augmentation, heat diffusion equation
Objavljeno v DiRROS: 04.04.2024; Ogledov: 355; Prenosov: 141
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8. Keep it simple : improving the ex situ culture of Cystoseira s.l. to restore macroalgal forestsAna Lokovšek, Valentina Pitacco, Domen Trkov, Leon Lojze Zamuda, Annalisa Falace, Martina Orlando-Bonaca, 2023, izvirni znanstveni članek Povzetek: Brown algae from genus Cystoseira s.l. form dense underwater forests that represent the most productive areas in the Mediterranean Sea. Due to the combined effects of global and local stressors such as climate change, urbanization, and herbivore outbreaks, there has been a severe decline in brown algal forests in the Mediterranean Sea. Natural recovery of depleted sites is unlikely due to the low dispersal capacity of these species, and efficient techniques to restore such habitats are needed. In this context, the aims of our study were (1) to improve and simplify the current ex situ laboratory protocol for the cultivation of Gongolaria barbata by testing the feasibility of some cost-effective and time-efficient techniques on two donor sites of G. barbata and (2) to evaluate the survival and growth of young thalli during the laboratory phase and during the most critical five months after out-planting. Specifically, the following ex situ cultivation methods were tested: (A) cultivation on clay tiles in mesocosms with culture water prepared by three different procedures (a) filtered seawater with a 0.22 μm filter membrane, (b) filtered seawater with a 0.7 μm filter membrane (GF), and (c) UV-sterilized water, and (B) cultivation on clay tiles in open laboratory systems. After two weeks, all thalli were fixed to plastic lantern net baskets suspended at a depth of 2 m in the coastal sea (hybrid method), and the algal success was monitored in relation to the different donor sites and cultivation protocol. The satisfactory results of this study indicate that UV-sterilized water is suitable for the cultivation of G. barbata in mesocosm, which significantly reduces the cost of the laboratory phase. This opens the possibility of numerous and frequent algal cultures during the reproductive period of the species. Additionally, if the young thalli remain in the lantern net baskets for an extended period of several months, they can grow significantly in the marine environment without being exposed to pressure from herbivorous fish.
Ključne besede: gojenje ex situ, obnova habitata, izboljšanje metodologije, gozdički rjavih alg, ex situ cultivation, mesocosm, open system, method improvement, brown algal forests restoration
Objavljeno v DiRROS: 29.03.2024; Ogledov: 366; Prenosov: 249
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9. Lessons learned from the monitoring of retaining structures, built in demanding geotechnical conditions in SloveniaPavel Žvanut, Janko Logar, 2019, objavljeni znanstveni prispevek na konferenci Povzetek: A typical retaining structure built with large-diameter bored piles in soft clastic rock, and sup-ported by pre-stressed permanent ground anchors, is discussed. Step-by-step back analyses were performed. A simplified geological structure was first used in the analyses, together with a simple Mohr-Coulomb model. The results were compared with more complex analyses using a Hardening Soil model and a more detailed geological structure. Much better results were obtained with the use of the HS model, which is more suitable for the modelling of rock of such a type, but even with the use of the MC model the final results were quite good, making the use of the observational method attractive for engineers.
Ključne besede: geotechnics, gretaining structures, bored piles, numerical modelling, finite element method, observational method
Objavljeno v DiRROS: 27.03.2024; Ogledov: 312; Prenosov: 156
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10. Application of a meshless space-time adaptive approach to phase-field modelling of polycrystalline solidificationTadej Dobravec, Boštjan Mavrič, Božidar Šarler, 2023, objavljeni znanstveni prispevek na konferenci Povzetek: We have developed a 2-D numerical meshless adaptive approach for phase-field modelling of dendritic solidification. The quadtree-based approach decomposes the computational domain into quadtree sub-domains of different sizes. The algorithm generates uniformly-distributed computational nodes in each quadtree sub-domain. We apply the meshless radial basis function generated finite difference method and the forward Euler scheme to discretise governing equations in each computational node. The fixed ratio between the characteristic size and the node spacing of a quadtree sub-domain ensures space adaptivity. The adaptive time-stepping accelerates the calculations further. In the framework of previous research studies, we used the approach to solve quantitative phase-field models for single dendrite growth in pure melts and dilute binary alloys. In the present study, we upgrade the solution procedure for the modelling growth of multiple differently oriented dendrites. Along with the space-time adaptive approach, we apply non-linear preconditioning of the phase-field equation to increase computational efficiency. We investigate a novel numerical approach's accuracy and computational efficiency by simulating the equiaxed dendrite growth from a dilute binary alloy.
Ključne besede: dendritic growth, phase-field method, meshless methods, polycrystalline solidification
Objavljeno v DiRROS: 21.03.2024; Ogledov: 364; Prenosov: 142
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