51. 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, original scientific article Abstract: 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.
Keywords: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Published in DiRROS: 07.11.2024; Views: 63; Downloads: 29
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56. Vrednotenje pritiskov in vplivov na morski ekosistem Krajinskega parka Debeli rtič, s poudarkom na območju podvodnega grebena : zaključno poročiloAna Fortič, Borut Mavrič, Martina Orlando-Bonaca, Lovrenc Lipej, 2024, final research report Keywords: morska biologija, vplivi, Krajinski park Debeli rtič, morski ekosistemi, morska biodiverziteta, morska biološka raznovrstnost, poročila
Published in DiRROS: 06.11.2024; Views: 75; Downloads: 29
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57. On the presence of the less known arminid nudibranch Dermatobranchus rubidus (Gould, 1852) in the Adriatic SeaTea Knapič, Rino Stanić, Borut Mavrič, Lovrenc Lipej, 2024, original scientific article Abstract: Two cases of the occurrence of the alien heterobranch species, Dermatobranchus rubidus (Gould, 1852) are reported for the Adriatic Sea. The first record originates from June 2019 from the island of Brač (Croatia, Middle Adriatic Sea), when a specimen was found during the collection of clams, while the second specimen was sighted at Fiesa (Gulf of Trieste, Northern Adriatic Sea) in October 2023, photographed on coarse sand bottom. These are the first records for the Adriatic Sea and indications of the possible establishment of this species in the Mediterranean Sea. Due to its cryptic behaviour and perhaps nocturnal habits, it is difficult to assess whether the species has been overlooked so far or whether it is extending its distribution in the Mediterranean.
Keywords: first Adriatic record, occurrence
Published in DiRROS: 06.11.2024; Views: 67; Downloads: 37
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58. Impact of indoor air pollution on DNA damage and chromosome stability : a systematic reviewLuka Kazensky, Katarina Matković, Marko Gerić, Bojana Žegura, Gordana Pehnec, Goran Gajski, 2024, review article Abstract: Indoor air pollution is becoming a rising public health problem and is largely resulting from the burning of solid fuels and heating in households. Burning these fuels produces harmful compounds, such as particulate matter regarded as a major health risk, particularly affecting the onset and exacerbation of respiratory diseases. As exposure to polluted indoor air can cause DNA damage including DNA sd breaks as well as chromosomal damage, in this paper, we aim to provide an overview of the impact of indoor air pollution on DNA damage and genome stability by reviewing the scientific papers that have used the comet, micronucleus, and γ-H2AX assays. These methods are valuable tools in human biomonitoring and for studying the mechanisms of action of various pollutants, and are readily used for the assessment of primary DNA damage and genome instability induced by air pollutants by measuring different aspects of DNA and chromosomal damage. Based on our search, in selected studies (in vitro, animal models, and human biomonitoring), we found generally higher levels of DNA strand breaks and chromosomal damage due to indoor air pollutants compared to matched control or unexposed groups. In summary, our systematic review reveals the importance of the comet, micronucleus, and γ-H2AX assays as sensitive tools for the evaluation of DNA and genome damaging potential of different indoor air pollutants. Additionally, research in this particular direction is warranted since little is still known about the level of indoor air pollution in households or public buildings and its impact on genetic material. Future studies should focus on research investigating the possible impact of indoor air pollutants in complex mixtures on the genome and relate pollutants to possible health outcomes.
Keywords: indoor air quality, genome damage, comet assay, micronucleus assay, γ-H2AX assay, health risk
Published in DiRROS: 06.11.2024; Views: 70; Downloads: 35
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59. Winners or losers? Two academic years in experiences of COVID-19 pandemicIvana Milovanović, Radenko Matić, Brigita Banjac, Saša Pišot, 2024, original scientific article Abstract: Background. The COVID-19 pandemic declared on March 11th, 2020, has had a substantial impact on the lives of all over the world. The student population, being one of the most vulnerable and substile ones, was forced to face specific unexpected circumstances for the first time in their lives. Objective. In this paper, the authors explored the reflections of the COVID-19 experience and basic segments of everyday life of university students after the first academic year under pandemic measures and a follow-up year with their subjective perception of to what extent their lives have changed and how they were able to adapt to COVID-19 emergency measures. Design. The field research was conducted among students in two European countries: Slovenia and Serbia. The qualitative semi-structured interviews with students (N=20, 50% male) were executed in June-July 2020 and June-July 2021. Results. The basic segments of students' daily lives underwent significant changes, yet they successfully coped and adapted to the COVID-19 emergency measures. Notably, improvements were observed in study strategies, reducing fear and loneliness. Above all, the primary longing was for social contact and gathering with friends. In their private lives, they were more concerned about opportunities but on the other hand, they gained more free time for various non-academic activities. Finally, sports science students have proven better-coping mechanisms with extraordinary circumstances. Conclusion. This study contributes to a deeper understanding of the changes in the daily lives of students during the first and second waves of the COVID-19 pandemic.
Keywords: students, everyday practice, e-learning, perspective of the future, fear, loneliness, COVID-19 pandemic measures, public health
Published in DiRROS: 06.11.2024; Views: 90; Downloads: 63
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60. Evidence driven indoor air quality improvement : an innovative and interdisciplinary approach to improving indoor air qualityMario Lovrić, Goran Gajski, Jessica Fernández-Agüera, Mira Pöhlker, Bojana Žegura, Matjaž Novak, Alja Štern, Katja Kološa, Martina Štampar, 2024, review article Abstract: Indoor air pollution is a recognized emerging threat, claiming millions of lives annually. People are constantly exposed to ambient and indoor air pollution. The latest research shows that people in developed countries spend up to 90% of their time indoors and almost 70% at home. Although impaired IAQ represents a significant health risk, it affects people differently, and specific populations are more vulnerable: children, the elderly, and people with respiratory illnesses are more sensitive to these environmental risks. Despite rather extensive research on IAQ, most of the current understanding about the subject, which includes pollution sources, indoor–outdoor relationships, and ventilation/filtration, is still quite limited, mainly because air quality monitoring in the EU is primarily focused on ambient air quality and regulatory requirements are lacking for indoor environments. Therefore, the EDIAQI project aims to improve guidelines and awareness for advancing the IAQ in Europe and beyond by allowing user-friendly access to information about indoor air pollution exposures, sources, and related risk factors. The solution proposed with EDIAQI consists of conducting a characterization of sources and routes of exposure and dispersion of chemical, biological, and emerging indoor air pollution in multiple cities in the EU. The project will deploy cost-effective/user-friendly monitoring solutions to create new knowledge on sources, exposure routes, and indoor multipollutant body burdens. The EDIAQI project brings together 18 organizations from 11 different European countries that provide interdisciplinary skills and expertise in various fields, including environmental science and technology, medicine, and toxicology, as well as policy design and public engagement.
Keywords: indoor air pollution, health risk, vulnerable populations, IAQ (Indoor Air Quality), EDIAQI project, monitoring solutions, exposure routes
Published in DiRROS: 06.11.2024; Views: 89; Downloads: 52
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