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1.
Addressing the sense of school belonging among all students? : a systematic literature review
Urška Štremfel, Klaudija Šterman Ivančič, Igor Peras, 2024, review article

Abstract: The sense of school belonging plays an important role in students’ academic, behavioural, and psychological outcomes. Based on a systematic review, following the PRISMA 2020 guidelines and examining 86 studies conducted between 1990 and February 2023, the article addresses two research questions: (a) what are the predictors of the sense of school belonging at the individual, micro, meso, exo, macro, and chrono levels of the bioecological model of human development; (b) do these predictors differ based on students’ individual characteristics, and if so, how. The findings reveal individual factors as important predictors of school belonging and indicate the lack of studies that take into consideration the interplay of different (micro, meso, exo, macro, chrono) levels in addressing the sense of school belonging. Considering the complexity and multi-factorial nature of the sense of school belonging, it calls upon further research, which would support the development of evidence-based interventions for fostering school belonging among different groups of students, particularly those who are at risk of feeling alienated from school, and thus promote equity in education.
Keywords: education, sense of school belonging, predictors, bioecological model of human development, equity, systematic review
Published in DiRROS: 27.01.2025; Views: 78; Downloads: 38
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2.
Evaluating alternative transformation pathways of wood-based bioeconomy : application of an input–output model
Domen Arnič, Efstratios Loizou, Špela Ščap, Peter Prislan, Luka Juvančič, 2024, original scientific article

Abstract: The wood-based bioeconomy is one of the main pillars of sustainable transformation and decarbonisation of the economy, as it promotes the use of renewable resources, reduces reliance on fossil fuels, and supports the development of eco-friendly industries. The paper provides quantitative insight into the potential impacts of transformation of the wood-based bioeconomy in Slovenia, a small, export-oriented economy with ample, but sub-optimally used, forest resources. The analysis uses an input–output (I-O) model to estimate I-O multipliers of sectors representing the wood-based bioeconomy and to capture their direct and indirect impacts on the Slovenian economy. The baseline performance of the wood bioeconomy sectors and their potential to induce economic activity (Scenario A) are estimated with an adjusted I-O model (based on the national I-O table for 2015), in which hybrid sectors are divided into conventional and bio-based segments. Alternative transformation pathways are translated into four additional scenarios. While Scenario B foresees progress in efficiency and integration within the existing structure of transactions, Scenario C (increased energy use of wood biomass) and Scenarios D/D+ (technology- and capital-intensive restructuring) represent two extreme restructuring pathways of the sector. The results of scenario analysis with the I-O model show that the changes in the input requirement structure of the Slovenian wood-based bioeconomy could result in up to a 17% increase in total output, up to a 20% increase in the number of employees, and up to a 16% increase in incomes, all of them attributed to the most optimistic scenario (D+). The results of the study provide quantified assessments underpinning strategic planning for the wood-based bioeconomy, both in the industry and public policy spheres.
Keywords: wood-based bioeconomy, input–output model, transformation pathways, impact analysis, strategic planning
Published in DiRROS: 09.01.2025; Views: 114; Downloads: 65
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3.
Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost
Filip Buric, Sandra Viknander, Xiaozhi Fu, Oliver Lemke, Oriol Gracia Carmona, Jan Zrimec, Lukasz Szyrwiel, Michael Mülleder, Markus Ralser, Aleksej Zelezniak, 2025, original scientific article

Abstract: Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, an amino acid sequence is tailored to meet the required abundance of a proteome, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here we show that the amino acid sequence alone encodes over half of protein abundance variation across all domains of life, ranging from bacteria to mouse and human. With an attempt to go beyond predictions, we trained a manageable-size Transformer model to interpret latent factors predictive of protein abundances. Intuitively, the model's attention focused on the protein's structural features linked to stability and metabolic costs related to protein synthesis. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations which increase predicted abundance have significantly altered protein polarity and hydrophobicity, underscoring a connection between protein structural features and abundance. Through molecular dynamics simulations we revealed that abundance-enhancing mutations possibly contribute to protein thermostability by increasing rigidity, which occurs at a lower synthesis cost.
Keywords: molecular biology, biotechnology, bioinformatics, deep learning, gene expression, synthetic biology, protein abundance, amino acid sequence, evolutionary selection, transformer model, MGEM (Mutation guided by an embedded manifold)
Published in DiRROS: 17.12.2024; Views: 147; Downloads: 63
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4.
Mitochondria can substitute for parvalbumin to lowercytosolic calcium levels in the murine fast skeletal muscle
Lorenzo Marcucci, Leonardo Nogara, Marta Canato, Elena Germinario, Anna Raffaello, Michela Carraro, Paolo Bernardi, Laura Pietrangelo, Simona Boncompagni, Feliciano Protasi, Nazareno Paolocci, Carlo Reggiani, 2024, original scientific article

Abstract: Aim: Parvalbumin (PV) is a primary calcium buffer in mouse fast skeletal musclefibers. Previous work showed that PV ablation has a limited impact on cytosolicCa2+ ([Ca2+]cyto) transients and contractile response, while it enhances mitochon-drial density and mitochondrial matrix-free calcium concentration ([Ca2+]mito).Here, we aimed to quantitatively test the hypothesis that mitochondria act tocompensate for PV deficiency.Methods: We determined the free Ca 2+ redistribution during a 2 s 60 Hz tetanicstimulation in the sarcoplasmic reticulum, cytosol, and mitochondria. Via a re-action–diffusion Ca 2+ model, we quantitatively evaluated mitochondrial uptakeand storage capacity requirements to compensate for PV lack and analyzed pos-sible extracellular export.Results: [Ca 2+]mito during tetanic stimulation is greater in knock-out (KO)(1362 ± 392 nM) than in wild-type (WT) (855 ± 392 nM), p < 0.05. Under the as-sumption of a non-linear intramitochondrial buffering, the model predicts an ac-cumulation of 725 μmoles/Lfiber (buffering ratio 1:11 000) in KO, much higherthan in WT (137 μmoles/Lfiber, ratio 1:4500). The required transport rate via mi-tochondrial calcium uniporter (MCU) reaches 3 mM/s, compatible with availableliterature. TEM images of calcium entry units and Mn2+ quenching showed a greater capacity of store- operated calcium entry in KO compared to WT. However,levels of [Ca 2+]cyto during tetanic stimulation were not modulated to variations ofextracellular calcium.Conclusions: The model-based analysis of experimentally determined calciumdistribution during tetanic stimulation showed that mitochondria can act as abuffer to compensate for the lack of PV. This result contributes to a better under-standing of mitochondria's role in modulating [Ca2+]cyto in skeletal muscle fibers.
Keywords: calcium, mitochondria, mouse skeletal muscle fibers, parvalbumin, reaction-diffusion model
Published in DiRROS: 13.11.2024; Views: 199; Downloads: 2932
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Making PBPK models more reproducible in practice
Elena 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: 284; Downloads: 96
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10.
Uporabnost nacionalnih podatkov laserskega skeniranja in cikličnega aerofotografiranja pri zaznavanju gozdnih vrzeli
Anže Martin Pintar, Mitja Skudnik, 2024, original scientific article

Abstract: Gozdna tla zastirajo drevesne krošnje in gozdna vrzel je vsaka večja ali manjša površina tal, ki je ne prekrivajo krošnje zgornjega sloja dreves. Velikost vrzeli vpliva na to, katera drevesna vrsta se bo pomladila, pa tudi na vertikalno in horizontalno strukturo gozda. Na Pohorju (Pahernikova gozdna posest, za katero so značilni gozdovi, v katerih se na majhnih površinah pojavljajo drevesa različnih premerov in starosti) smo analizirali možnosti samodejnega zaznavanja vrzeli na podlagi podatkov laserskega skeniranja Slovenije (LSS) in cikličnega aerofotografiranja Slovenije (CAS). Uporabili smo digitalna modela krošenj (DMK), pridobljena iz obeh virov podatkov. Skupna natančnost zaznavanja tudi najmanjših vrzeli (manjših od 50 m2) na podlagi podatkov LSS je znašala 94,4 %, na podlagi podatkov CAS pa 83,1 %. Na podlagi podatkov LSS je mogoče zaznati večje število in površino vrzeli, prav tako so vrzeli, pridobljene na podlagi podatkov LSS, bolj razčlenjene in podolgovate. Zaznavanje vrzeli s podatki CAS in LSS je medsebojno bolj primerljivo pri najmanjših površinah vrzeli 100 m2, natančnost zaznave takšnih vrzeli je 85,4 oziroma 94,4 %. Rezultati kažejo, da je ob odsotnosti podatkov LSS uporaba podatkov CAS za določanje vrzeli smiselna na velikopovršinski ravni in pri zaznavanju vrzeli, večjih od 100 m2.
Keywords: raznomerni in raznodobni gozdovi, digitalni model krošenj, gozdna vrzel, zaznavanje, lasersko skeniranje Slovenije, ciklično aerofotografiranje Slovenije
Published in DiRROS: 29.10.2024; Views: 181; Downloads: 122
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