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1.
Building and applying quantitative adverse outcome pathway models for chemical hazard and risk assessment
Edward J. Perkins, Roman Ashauer, Lyle Burgoon, Rory Conolly, Brigitte Landesmann, Cameron Mackay, Cheryl A. Murphy, Nathan Pollesch, James R. Wheeler, Anže Županič, Stefan Scholz, 2019, pregledni znanstveni članek

Povzetek: An important goal in toxicology is the development of new ways to increase the speed, accuracy, and applicability of chemical hazard and risk assessment approaches. A promising route is the integration of in vitro assays with biological pathway information. We examined how the adverse outcome pathway (AOP) framework can be used to develop pathway-based quantitative models useful for regulatory chemical safety assessment. By using AOPs as initial conceptual models and the AOP knowledge base as a source of data on key event relationships, different methods can be applied to develop computational quantitative AOP models (qAOPs) relevant for decision making. A qAOP model may not necessarily have the same structure as the AOP it is based on. Useful AOP modeling methods range from statistical, Bayesian networks, regression, and ordinary differential equations to individual-based models and should be chosen according to the questions being asked and the data available. We discuss the need for toxicokinetic models to provide linkages between exposure and qAOPs, to extrapolate from in vitro to in vivo, and to extrapolate across species. Finally, we identify best practices for modeling and model building and the necessity for transparent and comprehensive documentation to gain confidence in the use of qAOP models and ultimately their use in regulatory applications. Environ Toxicol Chem 2019;38:1850–1865. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Ključne besede: Quantitative Adverse Outcome pathways, TKTD modelling, alternatives to animal testing, predictive toxicology, species extrapolation, prioritization of chemicals
Objavljeno v DiRROS: 06.08.2024; Ogledov: 16; Prenosov: 13
.pdf Celotno besedilo (1,11 MB)
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2.
DELWAVE 1.0 : deep learning surrogate model of surface wave climate in the Adriatic Basin
Peter Mlakar, Antonio Ricchi, Sandro Carniel, Davide Bonaldo, Matjaž Ličer, 2024, izvirni znanstveni članek

Povzetek: We propose a new point-prediction model, the DEep Learning WAVe Emulating model (DELWAVE), which successfully emulates the behaviour of a numerical surface ocean wave model (Simulating WAves Nearshore, SWAN) at a sparse set of locations, thus enabling numerically cheap large-ensemble prediction over synoptic to climate timescales. DELWAVE was trained on COSMO-CLM (Climate Limited-area Model) and SWAN input data during the period of 1971–1998, tested during 1998–2000, and cross-evaluated over the far-future climate time window of 2071–2100. It is constructed from a convolutional atmospheric encoder block, followed by a temporal collapse block and, finally, a regression block. DELWAVE reproduces SWAN model significant wave heights with a mean absolute error (MAE) of between 5 and 10 cm, mean wave directions with a MAE of 10–25°, and a mean wave period with a MAE of 0.2 s. DELWAVE is able to accurately emulate multi-modal mean wave direction distributions related to dominant wind regimes in the basin. We use wave power analysis from linearised wave theory to explain prediction errors in the long-period limit during southeasterly conditions. We present a storm analysis of DELWAVE, employing threshold-based metrics of precision and recall to show that DELWAVE reaches a very high score (both metrics over 95 %) of storm detection. SWAN and DELWAVE time series are compared to each other in the end-of-century scenario (2071–2100) and compared to the control conditions in the 1971–2000 period. Good agreement between DELWAVE and SWAN is found when considering climatological statistics, with a small (≤ 5 %), though systematic, underestimate of 99th-percentile values. Compared to control climatology over all wind directions, the mismatch between DELWAVE and SWAN is generally small compared to the difference between scenario and control conditions, suggesting that the noise introduced by surrogate modelling is substantially weaker than the climate change signal.
Ključne besede: surrogate modelling, deep learning, DEep Learning WAVe Emulating model, DELWAVE, Simulating WAves Nearshore, SWAN
Objavljeno v DiRROS: 05.08.2024; Ogledov: 48; Prenosov: 39
.pdf Celotno besedilo (9,04 MB)
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3.
Turbulence observations in the Gulf of Trieste under moderate wind forcing and different water column stratification
Francesco Marcello Falcieri, Lakshmi Kantha, Alvise Benetazzo, Andrea Bergamasco, Davide Bonaldo, Francesco Barbariol, Vlado Malačič, Mauro Sclavo, Sandro Carniel, 2016, izvirni znanstveni članek

Povzetek: The oceanographic campaign CARPET2014 (Characterizing Adriatic Region Preconditionig EvenTs), (30 January–4 February 2014) collected the very first turbulence data in the Gulf of Trieste (northern Adriatic Sea) under moderate wind (average wind speed 10 m s−1) and heat flux (net negative heat flux ranging from 150 to 400 W m−2). Observations consisted of 38 CTD (Conductivity, Temperature, Depth) casts and 478 microstructure profiles (grouped into 145 ensembles) with three sets of yoyo casts, each lasting for about 12 consecutive hours. Averaging closely repeated casts, such as the ensembles, can lead to a smearing effect when in the presence of a vertical density structure with strong interfaces that can move up or down between subsequent casts under the influence of tides and internal waves. In order to minimize the smearing effect of such displacements on mean quantities, we developed an algorithm to realign successive microstructure profiles to produce sharper and more meaningful mean profiles of measured turbulence parameters. During the campaign, the water column in the gulf evolved from well-mixed to stratified conditions due to Adriatic waters intruding at the bottom along the gulf's south-eastern coast. We show that during the warm and relatively dry winter, the water column in the Gulf of Trieste, even under moderate wind forcing, was not completely mixed due to the influence of bottom waters intruding from the open sea. Inside the gulf, two types of water intrusions were found during yoyo casts: one coming from the northern coast of the Adriatic Sea (i.e. cooler, fresher and more turbid) and one coming from the open sea in front of the Po Delta (i.e. warmer, saltier and less turbid). The two intrusions had different impacts on turbulence kinetic energy dissipation rate profiles. The former, with high turbidity, acted as a barrier to wind-driven turbulence, while the latter, with low sediment concentrations and a smaller vertical density gradient, was not able to suppress downward penetration of turbulence from the surface.
Ključne besede: hydrology, oceanographic data, numerical modelling, wind forcing, turbulence
Objavljeno v DiRROS: 01.08.2024; Ogledov: 95; Prenosov: 115
.pdf Celotno besedilo (2,99 MB)
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4.
Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato
Živa Ramšak, Anna Coll Rius, Tjaša Stare, Oren Tzfadia, Špela Baebler, Yves Van de Peer, Kristina Gruden, 2018, izvirni znanstveni članek

Povzetek: To develop novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modeling represents a powerful tool that can unravel properties of complex biological systems. In this study, we aimed to use network modeling to better understand immune signaling in potato (Solanum tuberosum). For this, we first built on a reliable Arabidopsis (Arabidopsis thaliana) immune signaling model, extending it with the information from diverse publicly available resources. Next, we translated the resulting prior knowledge network (20,012 nodes and 70,091 connections) to potato and superimposed it with an ensemble network inferred from time-resolved transcriptomics data for potato. We used different network modeling approaches to generate specific hypotheses of potato immune signaling mechanisms. An interesting finding was the identification of a string of molecular events illuminating the ethylene pathway modulation of the salicylic acid pathway through Nonexpressor of PR Genes1 gene expression. Functional validations confirmed this modulation, thus supporting the potential of our integrative network modeling approach for unraveling molecular mechanisms in complex systems. In addition, this approach can ultimately result in improved breeding strategies for potato and other sensitive crops.
Ključne besede: network modelling, potato, molecular biology
Objavljeno v DiRROS: 01.08.2024; Ogledov: 92; Prenosov: 122
.pdf Celotno besedilo (1,77 MB)
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Scaphoideus titanus forecasting and management : quo vadis?
Elena Gonella, Giovanni Benelli, Nathalie Arricau-Bouvery, Domenico Bosco, Meta Virant-Doberlet, 2024, pregledni znanstveni članek

Povzetek: Scaphoideus titanus Ball (Hemiptera: Cicadellidae) is a major pest for European viticulture due to its high efficiency in the transmission of one of the most destructive pathogens for grapevine, namely flavescence dorée phytoplasmas. Although it plays a major role in spreading this disease, S. titanus is part of a complex epidemiological cycle involving several alternative vectors with variable relevance for phytoplasma spread. Here we provide an updated review on S. titanus monitoring and modelling, as well as the available tools for management of this pest and for limiting phytoplasma transmission and, thus, also spread. Insecticide-based control is examined; additional emphasis is placed on innovative and low-impact control approaches, such as vibrational mating disruption, biocontrol, and methods to reduce vector competence. We also discuss the main emerging challenges to the implementation of effective and sustainable control programs against S. titanus.
Ključne besede: epidemiology, pest monitoring, modelling, Integrated Pest Management, vibrational mating disruption, biological control, plant resistance elicitors, RNA-interference, symbiotic control, entomology, insects, plant protection
Objavljeno v DiRROS: 23.07.2024; Ogledov: 96; Prenosov: 72
.pdf Celotno besedilo (814,31 KB)
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7.
Experimental evidence of long-term oceanic circulation reversals without wind influence in the North Ionian Sea
Angelo Rubino, Miroslav Gačić, Manuel Bensi, Vedrana Kovacevic, Vlado Malačič, Milena Menna, Maria Eletta Negretti, Joel Sommeria, Davide Zanchettin, Ricardo V. Barreto, Laura Ursella, Vanessa Cardin, Giuseppe Civitarese, Mirko Orlić, Boris Petelin, Giuseppe Siena, 2020, izvirni znanstveni članek

Povzetek: Under the emerging features of interannual-to-decadal ocean variability, the periodical reversals of the North Ionian Gyre (NIG), driven mostly by the mechanism named Adriatic-Ionian Bimodal Oscillating System (BiOS), are known as impacting on marine physics and biogeochemistry and potentially influencing short-term regional climate predictability in the Eastern Mediterranean. Whilst it has been suggested that local wind forcing cannot explain such variability, aspects of the alternative hypothesis indicating that NIG reversals mainly arises from an internal ocean feedback mechanism alone remain largely debated. Here we demonstrate, using the results of physical experiments, performed in the world’s largest rotating tank and numerical simulations, that the main observed feature of BiOS, i.e., the switch of polarity of the near-surface circulation in the NIG, can be induced by a mere injection of dense water on a sloping bottom. Hence, BiOS is a truly oceanic mode of variability and abrupt polarity changes in circulation can arise solely from extreme dense water formation events.
Ključne besede: physical oceanography, climate and Earth system modelling
Objavljeno v DiRROS: 19.07.2024; Ogledov: 110; Prenosov: 94
.pdf Celotno besedilo (1,81 MB)
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8.
Virtual modelling of novel applicator prototypes for cervical cancer brachytherapy
Primož Petrič, Robert Hudej, Noora Al-Hammadi, Barbara Šegedin, 2016, izvirni znanstveni članek

Povzetek: Standard applicators for cervical cancer Brachytherapy (BT) do not always achieve acceptable balance between target volume and normal tissue irradiation. We aimed to develop an innovative method of Targetvolume Density Mapping (TDM) for modelling of novel applicator prototypes with optimal coverage characteristics. Patients and methods. Development of Contour-Analysis Tool 2 (CAT-2) software for TDM generation was the core priority of our task group. Main requests regarding software functionalities were formulated and guided the coding process. Software validation and accuracy check was performed using phantom objects. Concepts and terms for standardized workflow of TDM post-processing and applicator development were introduced. Results. CAT-2 enables applicator-based co-registration of Digital Imaging and Communications in Medicine (DICOM) structures from a sample of cases, generating a TDM with pooled contours in applicator-eye-view. Each TDM voxel is assigned a value, corresponding to the number of target contours encompassing that voxel. Values are converted to grey levels and transformed to DICOM image, which is transported to the treatment planning system. Iso-density contours (IDC) are generated as lines, connecting voxels with same grey levels. Residual Volume at Risk (RVR) is created for each IDC as potential volume that could contain organs at risk. Finally, standard and prototype applicators are applied on the TDM and virtual dose planning is performed. Dose volume histogram (DVH) parameters are recorded for individual IDC and RVR delineations and characteristic curves generated. Optimal applicator configuration is determined in an iterative manner based on comparison of characteristic curves, virtual implant complexities and isodose distributions. Conclusions. Using the TDM approach, virtual applicator prototypes capable of conformal coverage of any target volume, can be modelled. Further systematic assessment, including studies on clinical feasibility, safety and effectiveness are needed before routine use of novel prototypes can be considered.
Ključne besede: cervical cancer, brachytherapy, applicators, virtual modelling
Objavljeno v DiRROS: 09.05.2024; Ogledov: 216; Prenosov: 113
.pdf Celotno besedilo (671,88 KB)

9.
Modelling intumescent coatings for the fire protection of structural systems : a review
Andrea Lucherini, Donatella de Silva, 2024, pregledni znanstveni članek

Povzetek: Purpose Intumescent coatings are nowadays a dominant passive system used to protect structural materials in case of fire. Due to their reactive swelling behaviour, intumescent coatings are particularly complex materials to be modelled and predicted, which can be extremely useful especially for performance-based fire safety designs. In addition, many parameters influence their performance, and this challenges the definition and quantification of their material properties. Several approaches and models of various complexities are proposed in the literature, and they are reviewed and analysed in a critical literature review. Design/methodology/approach Analytical, finite-difference and finite-element methods for modelling intumescent coatings are compared, followed by the definition and quantification of the main physical, thermal, and optical properties of intumescent coatings: swelled thickness, thermal conductivity and resistance, density, specific heat capacity, and emissivity/absorptivity. Findings The study highlights the scarce consideration of key influencing factors on the material properties, and the tendency to simplify the problem into effective thermo-physical properties, such as effective thermal conductivity. As a conclusion, the literature review underlines the lack of homogenisation of modelling approaches and material properties, as well as the need for a universal modelling method that can generally simulate the performance of intumescent coatings, combine the large amount of published experimental data, and reliably produce fire-safe performance-based designs. Research limitations/implications Due to their limited applicability, high complexity and little comparability, the presented literature review does not focus on analysing and comparing different multi-component models, constituted of many model-specific input parameters. On the contrary, the presented literature review compares various approaches, models and thermo-physical properties which primarily focusses on solving the heat transfer problem through swelling intumescent systems. Originality/value The presented literature review analyses and discusses the various modelling approaches to describe and predict the behaviour of swelling intumescent coatings as fire protection for structural materials. Due to the vast variety of available commercial products and potential testing conditions, these data are rarely compared and combined to achieve an overall understanding on the response of intumescent coatings as fire protection measure. The study highlights the lack of information and homogenisation of various modelling approaches, and it underlines the research needs about several aspects related to the intumescent coating behaviour modelling, also providing some useful suggestions for future studies.
Ključne besede: intumescent coatings, fire protection, modelling, structural fire engineering, fire safety, performance-based design
Objavljeno v DiRROS: 17.04.2024; Ogledov: 258; Prenosov: 119
.pdf Celotno besedilo (790,21 KB)
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10.
Lessons learned from the monitoring of retaining structures, built in demanding geotechnical conditions in Slovenia
Pavel 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: 292; Prenosov: 139
.pdf Celotno besedilo (1,67 MB)
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