1. Making PBPK models more reproducible in practiceElena Domínguez-Romero, Stanislav Mazurenko, Martin Scheringer, Vitor A. P. Martins dos Santos, Chris T Evelo, Mihail Anton, John M. Hancock, Anže Županič, Maria Suarez-Diez, 2024, izvirni znanstveni članek Povzetek: Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model’s behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields.
Ključne besede: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Objavljeno v DiRROS: 07.11.2024; Ogledov: 138; Prenosov: 62
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2. Crack size in coating and moisture problems comparing thermally modified and native spruce window frame profiles using hygrothermal simulationGregor Vidmar, Rožle Repič, Boštjan Lesar, Miha Humar, 2024, izvirni znanstveni članek Povzetek: Fungal growth and degradation of wood may be caused by damage in the surface coating. The larger the cracks, the greater in principle the possibility of moisture-induced problems. Measuring basic unknown material parameters and employing hygrothermal simulations, the suitability and the maximum acceptable vertical crack size in the surface coating for a given bottom window profile made of thermally modified (TM) spruce(wood) with that made of native spruce were compared for location Ljubljana. Validation with the field test data was the second objective of the respective research. The average calculated maximum moisture content in TM spruce is about 4% (kg/kg) lower than that of native spruce. The 3 mm wide crack in the surface coating of a window frame made of native spruce is of the highest concern, whereas a 9 mm wide crack in the coating of a TM spruce profile is still acceptable. As far as moisture content is concerned in our study the TM spruce window frames were proved to be significantly more suitable for installation than the corresponding frames made of native Norway spruce. It was shown that isopleth, VTT and biohygrothermal models for mould growth do not properly capture the comparison between both materials, mainly because they classify both in the same material class/substrate category and they do not consider the material moisture content.
Ključne besede: hygrothermal simulations, mould growth modelling, cracks in surface coating, thermally modified wood, wooden window frame
Objavljeno v DiRROS: 16.10.2024; Ogledov: 201; Prenosov: 372
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3. Modelling of deformable polymer to be used for joints between infill masonry walls and R. C. framesMatija Gams, Arkadiusz Kwiecień, Jože Korelc, Theodoros Rousakis, Alberto Viskovic, 2017, objavljeni znanstveni prispevek na konferenci Povzetek: In the paper an idea to use a deformable polymer material for the joint between R.C. frames and masonry infills is presented. As an early step of testing the idea, experimental tests of the polymer in monotonic uniaxial tension at different load rates are performed and analyzed. The load rates range from very fast (8.3 mm/s) to very slow (0.00083 mm/s). The material exhibits a very strong strain rate effect and viscous behavior. In the second part of the paper a numerical model is developed and implemented into a finite element to simulate the results of the tests. The model is based on a new family of strain measures, called the Darjani-Naghdabadi strain measures and a classical viscosity formulation. Almost perfect model predictions up to collapse at 50-150% elongation are obtained by using calibration based on minimization of error.
Ključne besede: masonry infills, deformable polymer joint, viscosity, modelling
Objavljeno v DiRROS: 19.08.2024; Ogledov: 363; Prenosov: 158
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4. Building and applying quantitative adverse outcome pathway models for chemical hazard and risk assessmentEdward 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: 251; Prenosov: 179
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5. DELWAVE 1.0 : deep learning surrogate model of surface wave climate in the Adriatic BasinPeter 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: 272; Prenosov: 194
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6. Turbulence observations in the Gulf of Trieste under moderate wind forcing and different water column stratificationFrancesco 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: 364; Prenosov: 319
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7. Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potatoŽiva 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: 324; Prenosov: 254
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8. Estimating exposure to extremely low frequency magnetic fields near high-voltage power lines and assessment of possible increased cancer risk among Slovenian children and adolescentsTina Žagar, Blaž Valič, Tadej Kotnik, Sara Korat, Sonja Tomšič, Vesna Zadnik, Peter Gajšek, 2023, izvirni znanstveni članek Ključne besede: exposure assessment, childhood cancer, extremely low frequency magnetic fields, modelling, high voltage power lines
Objavljeno v DiRROS: 25.07.2024; Ogledov: 305; Prenosov: 655
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9. 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: 318; Prenosov: 214
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10. Experimental evidence of long-term oceanic circulation reversals without wind influence in the North Ionian SeaAngelo 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: 333; Prenosov: 229
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