1. PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice" : Version v2Elena 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, zaključena znanstvena zbirka raziskovalnih podatkov Povzetek: Physiologically-based pharmacokinetic (PBPK) model code associated to the journal article by: E. Domínguez-Romero, S. Mazurenko, M. Scheringer, V. A. P. Martins dos Santos, C. T. Evelo, M. Anton, J. M. Hancock, A. Županič, M. Suarez-Diez, entitled: Making PBPK models more reproducible in practice (Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae569, https://doi.org/10.1093/bib/bbae569).
The code is provided in MATLAB and SBML formats. The following files can be found here:
"PBPK_code_EDR_et_al_vs4.m": model code in MATLAB format. This is the 4th version of the code. The mathematical model is described by Domínguez-Romero et al., and more succinctly explained within the code (annotations). When this code is run in MATLAB, we obtain the next file:
"Model_variables_numeric_results.xls": numeric results obtained by model simulation in MATLAB.
"SM2_PBPK_code_EDR_et_al_final4_test_trigger.xml": model code in SBML format, obtained by conversion of the MATLAB code, by using "Model ODE Converter for Creating Automated SBML Interoperability (MOCCASIN)” (Gómez et al., 2016) and COPASI tools (Tiwari et al., 2021). More details about the conversion can be found in Domínguez-Romero et al. (2024).
Ključne besede: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Objavljeno v DiRROS: 08.05.2026; Ogledov: 109; Prenosov: 82
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3. In situ evaluation of an active-passive sampling (APS) technique for monitoring psychoactive compounds in effluent wastewaterAllen Jun Anies, Maria Laimou-Geraniou, Maarten Quireyns, Taja Verovšek, David John Heath, Ester Heath, Raewyn M. Town, 2026, izvirni znanstveni članek Povzetek: Monitoring of psychoactive drugs and their metabolites in wastewater is critical to understanding their environmental fate and potential impacts. Passive sampling offers a complementary approach to conventional composite sampling, providing time-integrated monitoring, while offering insights into bioavailable fractions of compounds. This study evaluates the applicability of an active-passive sampling (APS) approach for monitoring eight psychoactive compounds in effluent wastewater, integrating field deployments with predictive modelling of sorbent-to-water partition coefficients (K[sw]). APS and diffusive gradients in thin films (DGT) samplers, equipped with hydrophilic-lipophilic balanced (HLB) and mixed-mode cation exchange (MCX) sorbents were deployed alongside daily composite sampling during 2023-2024 monitoring campaigns in Belgium and Slovenia. APS exhibited non-linear uptake kinetics indicative of non-ideal sink behaviour and additional mass-transfer limitations, including interfacial effects, while DGT uptake remained predominantly diffusion-controlled over the deployment periods. K[SW] values were predicted using tree-based machine-learning models (Random Forest and XGBoost), enabling robust interpretation of APS data under near-equilibrium conditions. APS and DGT measurements generally showed good agreement, though APS concentrations were systematically higher for most compounds, with differences influenced by sorbent type and environmental factors. The controlled laminar flow of APS enhanced sorption consistency under variable wastewater conditions. Comparisons with composite sampling highlighted the complementary nature of these approaches, with APS providing additional insights on bioavailable and particle-bound fractions. Overall, APS presents a robust and versatile tool for monitoring psychoactive compounds, supporting quantitative assessment of contaminant dynamics, bioavailability, and fate in aquatic systems.
Ključne besede: wastewater monitoring, diffusive gradients in thin films, psychoactive compounds, uptake kinetics, predictice modelling
Objavljeno v DiRROS: 16.03.2026; Ogledov: 246; Prenosov: 171
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4. Integrating computational fluid dynamics into organ-on-chip systems: a glioblastoma-centred design and validation frameworkHooman Taleban, Xinzhong Li, Zulfiqur Ali, Karunakaran Kalesh, Jai Prakash, Tugba Bagci-Onder, Barbara Breznik, 2026, pregledni znanstveni članek Povzetek: Glioblastoma GBM: Glioblastoma multiforme (GBM) remains one of the most lethal and treatment-resistant brain cancers, driven in part by the complexity of its tumour microenvironment (TME). While organ-on-chip (OoC) platforms offer more physiologically relevant models than traditional 2D or static 3D systems, their design remains largely empirical, lacking predictive control over flow conditions, biochemical gradients, and mechanical cues. Computational Fluid Dynamics (CFD) has emerged as a powerful tool to enhance the design, precision, and biological fidelity of OoC platforms. This comprehensive review highlights current limitations in replicating GBM’s biological complexity and technical constraints in device fabrication and maintenance, mapping them to specific CFD strategies. It synthesises current strategies into a structured workflow for integrating CFD into the design, optimisation, and validation of microfluidic tumour models—bridging engineering precision with biological complexity. In addition, validation frameworks reported in the literature are highlighted and mapped onto GBM-on-chip applications have been recommended, drawing on widely recognised international standards for engineering validation and regulatory modelling practices. Finally, this review positions CFD as a core component of GBM-on-chip development and explores how its integration with AI-based optimisation can advance the creation of more predictive, scalable, and biologically relevant in vitro tumour models.
Ključne besede: AI, computational fluid dynamics, glioblastoma, In silicosimulation, in vitro modelling, microfluidic perfusion, organ-on-chip, tumour microenvironment
Objavljeno v DiRROS: 13.02.2026; Ogledov: 426; Prenosov: 209
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5. Life cycle environmental and cost modelling to support the development of national renovation roadmapsBen Jacobs, Els Van de moortel, Damien Trigaux, Gašper Stegnar, Ana Marija Spindler, Marjana Lutman, Meta Kržan, Karen Allacker, 2025, objavljeni znanstveni prispevek na konferenci Povzetek: In the context of the European Green Deal, achieving a climate-neutral building stock by 2050 has become a key objective. The 2024-revision of the Energy Performance of Buildings Directive (EPBD) highlights this goal by requiring EU Member States to transform their long-term renovation strategies into practical National Renovation Plans. The LIFE project GreenRenoV8 supports the practical implementation of the EPBD by developing a scalable, cost-effective methodology for deep, sustainable building renovation. By combining the environmental performance with the economic implications (both investment and life cycle cost), the project aims to identify the most cost-effective renovation strategies. GreenRenoV8 focuses on five EU Member States: Austria, Belgium (Flanders region), Greece, Italy and Slovenia. A stock modelling approach is used, starting with the identification of representative building archetypes per country. For each archetype, specific renovation strategies are developed and their life cycle environmental impact, investment cost and life cycle cost are assessed. The results are extrapolated to the national level to determine the most cost-effective measures and to prioritize these. The modelling moreover incorporates seismic resilience where required. This paper describes the approach taken within the GreenRenoV8 project to support evidence-based renovation planning that maximizes environmental impact reduction and cost-effectiveness across the EU.
Ključne besede: energy efficiency, life-cycle costing, life-cycle assessment, building stock modelling, sustainable renovation, carbon-neutral buildings
Objavljeno v DiRROS: 27.01.2026; Ogledov: 362; Prenosov: 230
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6. Climate-driven habitat shifts in brown algal forests: insights from the Adriatic SeaDaša Donša, Danijel Ivajnšič, Lovrenc Lipej, Domen Trkov, Borut Mavrič, Valentina Pitacco, Ana Fortič, Ana Lokovšek, Milijan Šiško, Martina Orlando-Bonaca, 2026, izvirni znanstveni članek Povzetek: Brown algal forests (Cystoseira sensu lato) are key habitat-forming components of temperate rocky coasts but have experienced widespread decline across the Mediterranean Sea. This study investigates the current distribution and potential future shifts in brown algal forests across the Adriatic Sea under ongoing climate change. We combined non-destructive field-based mapping along the Slovenian coastline with remote-sensing products and spatial environmental predictors to model basin-wide habitat suitability. A multiscale geographically weighted regression (MGWR) framework was applied to account for spatial non-stationarity and to explicitly capture the fact that environmental drivers of habitat suitability operate at different spatial scales—an assumption that global models such as GAM or standard GWR cannot adequately address. Habitat suitability maps were generated for present-day conditions and projected under mid- and late-century climate scenarios. The results reveal pronounced latitudinal gradients, identify areas of ongoing canopy decline in the northern Adriatic, and highlight parts of the southern Adriatic as potential climate refugia. Overall, the study demonstrates a likely north–south contraction of suitable habitat for brown algal forests and underscores the value of multiscale spatial modelling for informing marine spatial planning, conservation prioritization, and climate- adaptive restoration under European policy frameworks.
Ključne besede: brown algal forests, Cystoseira s.l., habitat suitability, spatial modelling, Adriatic Sea, climate change, shifts
Objavljeno v DiRROS: 21.01.2026; Ogledov: 356; Prenosov: 288
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7. Life cycle environmental and cost modelling to support the development of national renovation roadmapsBen Jacobs, Els Van de moortel, Damien Trigaux, Gašper Stegnar, Ana Marija Spindler, Marjana Lutman, Meta Kržan, Karen Allacker, 2025, objavljeni znanstveni prispevek na konferenci Ključne besede: energy efficiency, life-cycle costing, life-cycle assessment, building stock modelling, sustainable renovation, carbon-neutral buildings
Objavljeno v DiRROS: 12.01.2026; Ogledov: 318; Prenosov: 201
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8. Modelling flow and transport to assess the influence of subsurface geometry on Alpine karst aquifer vulnerabilityBarbara Fleck, Lukas Plan, Bernhard Grasemann, Cyril Mayaud, 2025, izvirni znanstveni članek Povzetek: Karst areas are highly susceptible to contamination due to rapid recharge and throughflow caused by their heterogeneous structure with unknown networks of conduits embedded in a matrix of low conductivity. Vulnerability methods have been used to ensure adequate protection of drinking water resources. However, most of the studies assessing the vulnerability of karst aquifers consider it as a constant value in time and, therefore, under special hydrological conditions in space, which is an oversimplification of reality. In this work, the behaviour of an Alpine karst system characterised by rapid flow and transfer through vertical shafts has been studied by discrete numerical modelling using MODFLOW 6. Six numerical models have been designed with the aim of representing simple common geometrical configurations found in Alpine karst systems. These models simulate how the flow and transport response at the system outlet is influenced by the aquifer geometry and recharge conditions. The results confirm that the arrival of the tracer at the spring strongly depends on the conduit geometry and the recharge conditions. This demonstrates that karst aquifer vulnerability cannot be defined as a constant value but should be specifically assessed depending on the spatio-temporal conditions.
Ključne besede: Alpine karst system, numerical flow and transport modelling, vulnerability, overflow, MODFLOW 6
Objavljeno v DiRROS: 10.01.2026; Ogledov: 487; Prenosov: 248
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9. Identification of a PCE contamination source in an intergranular aquifer using a simulation–optimisation framework: a case study of Ljubljana polje, SloveniaMitja Janža, 2025, izvirni znanstveni članek Povzetek: Identification of contamination sources is critical for effective remediation planning in contaminated aquifers. This study presents a simulation–optimisation framework that was developed to reconstruct the release history and identify the potential source location after tetrachloroethene (PCE) concentrations that exceeded regulatory limits were detected in production and monitoring wells at the Hrastje well field. The approach integrates a physically based groundwater flow and solute transport model with an evolutionary algorithm to estimate unknown source parameters. The method was tested under realistic field conditions, accounting for the complexity and uncertainty of the subsurface environment. In the optimisation procedure, parameter values converged towards optimal estimates, and the simulated PCE concentrations in monitored wells showed good agreement with the observed values. The delineated source location and the reconstructed temporal and spatial dynamics of PCE contamination in the aquifer provide essential guidance for decision makers in designing and prioritising remediation strategies. By narrowing the potential source area, more targeted and cost-effective field investigations can be planned. The developed model offers a practical tool for evaluating alternative remediation scenarios, supporting adaptive water resource management and safeguarding the drinking water supply.
Ključne besede: groundwater contamination, remediation planning, drinking water protection, well field management, modelling
Objavljeno v DiRROS: 09.01.2026; Ogledov: 635; Prenosov: 348
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10. Measuring biological age : insights from omics studiesEva Kočar, Robert Šket, Ana Halužan Vasle, Gorazd Avguštin, Evgen Benedik, Barbara Koroušić-Seljak, Pavle Simić, Antonio Martinko, Shawnda A. Morrison, Maroje Sorić, Mihaela Skrt, Tomaž Polak, Tine Tesovnik, Barbara Jenko Bizjan, Jernej Kovač, Tadej Battelino, Damjana Rozman, Nataša Poklar Ulrih, Bojana Bogovič Matijašić, Gregor Jurak, Miha Moškon, Tadeja Režen, 2026, pregledni znanstveni članek Povzetek: Biological ageing is a systemic, multifactorial process driven by progressive molecular and cellular alterations whose complexity necessitates systems-level approaches. Advances in high-throughput omics technologies now allow simultaneous quantification of millions of biomolecules from a single specimen, enabling longitudinal, integrative profiling across multiple molecular layers. This review synthesizes recent progress in applying genomics, epigenomics, metabolomics and microbiomics to ageing research, highlighting their contributions to biomarker discovery, mechanistic insight, and translational opportunities. Genomic studies reveal genetic variants that promote extreme longevity, while epigenetic clocks provide robust predictors of biological age. The blood proteome can be used to calculate proteome-based scores and evaluate temporal changes in ageing trajectories in an organ- and sex-specific manner. Metabolomic signatures identify key metabolites reflecting ageing trajectories, and microbiome research demonstrates that gut microbial composition mirrors and modulates biological ageing, with microbiome clocks emerging. The omics approaches have further elucidated the impact of exercise and diet providing evidence that interventions can reduce biological age. The integration of multi-omics with clinical and lifestyle data, powered by machine learning and artificial intelligence, is paving the way for a holistic definition of biological age and the development of personalized healthy ageing strategies. This review highlights how the omics technologies and computational modelling are transforming ageing biology into strategies for personalized healthy ageing.
Ključne besede: ageing, biological ageing, omics, physical fitness, nutrition, computational modelling
Objavljeno v DiRROS: 08.01.2026; Ogledov: 630; Prenosov: 229
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