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42. Variety of general position problems in graphsJing Tian, Sandi Klavžar, 2025, original scientific article Abstract: Let $X$ be a vertex subset of a graph $G$. Then $u, v\in V(G)$ are $X$-positionable if $V(P)\cap X \subseteq \{u,v\}$ holds for any shortest $u,v$-path $P$. If each two vertices from $X$ are $X$-positionable, then $X$ is a general position set. The general position number of $G$ is the cardinality of a largest general position set of $G$ and has been already well investigated. In this paper a variety of general position problems is introduced based on which natural pairs of vertices are required to be $X$-positionable. This yields the total (resp. dual, outer) general position number. It is proved that the total general position sets coincide with sets of simplicial vertices, and that the outer general position sets coincide with sets of mutually maximally distant vertices. It is shown that a general position set is a dual general position set if and only if its complement is convex. Several sufficient conditions are presented that guarantee that a given graph has no dual general position set. The total general position number, the outer general position number, and the dual general position number of arbitrary Cartesian products are determined.
Keywords: general position, total general position, outer general position, dual general position, Cartesian product of graphs, strong resolving graph, convex subgraph
Published in DiRROS: 07.11.2024; Views: 47; Downloads: 19
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43. 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: 35; Downloads: 17
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48. 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: 45; Downloads: 17
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49. 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: 53; Downloads: 26
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50. 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: 59; Downloads: 25
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