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1.
From permits to samples : addressing key challenges for high-quality reference genome generation in Europe
Katja Reichel, Jaakko Pohjoismäki, Jonas J. Astrin, Astrid Böhne, Chiara Bortoluzzi, Elena Bužan, Javier del Campo, Claudio Ciofi, Camilla B. Di-Nizo, Pradeep K. Divakar, 2026, pregledni znanstveni članek

Opis: High-quality reference genome assemblies have become essential for deepening our understanding of biodiversity, yet obtaining them for many species remains surprisingly challenging. Drawing on experiences from the European Reference Genome Atlas (ERGA) community, we focus on permit and sample-handling procedures leading up to nucleic acid sequencing, covering tasks such as ensuring ethical and legal compliance, verifying accurate species identification, maintaining sample integrity during transport, and isolating high-quality DNA or nuclei. While many of the challenges and solutions we discuss are broadly relevant, our regulatory and logistical examples are primarily from Europe. By synthesising practical guidance, we highlight the crucial importance of taxonomic expertise, proper vouchering and biobanking, rigorous cold-chain management or alternative preservation methods, and emphasise adherence to packaging and shipping requirements for biological materials. We showcase examples spanning diverse regions, taxa and source materials, which underscore the importance of context-specific strategies and internationally harmonised protocols, particularly for metadata reporting. Our recommendations aim to support both small-scale projects and large initiatives, directing collective efforts to facilitate efficient sampling, vouchering and sample processing for future genomic studies.
Ključne besede: permits, samples, genomics
Objavljeno v RUP: 21.01.2026; Ogledov: 90; Prenosov: 3
.pdf Celotno besedilo (1,22 MB)
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2.
Razlika med zgodnjo in pozno obravnavo otrok z motnjo avtističnega spektra : sistematični pregled literature
Petra Zakrajšek, Vesna Posavčević, 2025, pregledni znanstveni članek

Opis: Sistematični pregled literature preučuje učinke zgodnje in pozne obravnave otrok z motnjo avtističnega spektra na njihov razvoj. Namen pregleda je bil sintetizirati in opisati razvojne izide, povezane z zgodnjo diagnozo in intervencijo, ter izide, povezane s pozno diagnozo in intervencijo pri otrocih z motnjo avtističnega spektra. V pregled je bilo vključenih 11 raziskav v angleškem jeziku, ki so primerjale učinek zgodnje in pozne diagnoze ter preučevale učinkovitost različnih intervencij motnje avtističnega spektra. V pregledu so bile uporabljene tri baze podatkov (PubMed, ScienceDirect in Web of Science), pri čemer so bile vključene raziskave, objavljene med letoma 2020 in 2024. Kakovost izbranih raziskav je bila ocenjena s standardiziranima kontrolnima seznamoma casp (Critical Appraisal Skills Programme) in jbi (Joanna Briggs Institute). Rezultati kažejo, da zgodnja diagnoza in intervencija pomembno izboljšata izide na področju socialnega, kognitivnega, gibalnega, čustvenega razvoja in razvoja vedenjskih značilnosti otrok z motnjo avtističnega spektra. Otroci, ki so bili deležni zgodnje obravnave, so dosegli boljše rezultate na področjih socialne komunikacije, prilagoditvenega vedenja, kognitivnih sposobnosti, finih motoričnih veščin in jezikovnih spretnosti. Nasprotno je pozna diagnoza pogosto povezana z resnejšimi simptomi in večjimi razvojnimi zaostanki. Ključna ugotovitev je, da je zgodnja intervencija ključna za zmanjšanje simptomov motnje avtističnega spektra in izboljšanje kakovosti življenja otrok, medtem ko lahko pozna diagnoza vodi do dolgotrajnih negativnih posledic. Pregled poudarja pomen pravočasne obravnave za optimalen razvoj otroka z motnjo avtističnega spektra in predlaga smernice za nadaljnje raziskovanje, ki temeljijo na preučevanju dolgoročnih učinkov različnih intervencij.
Ključne besede: motnja avtističnega spektra, zgodnja intervencija, pozna intervencija, zgodnja diagnoza, pozna diagnoza, razvoj otroka
Objavljeno v RUP: 21.01.2026; Ogledov: 86; Prenosov: 0
.pdf Celotno besedilo (265,01 KB)

3.
Dataset of sentiment tagged language resources for Macedonian language
Sofija Kochovska, Jernej Vičič, Branko Kavšek, 2026, izvirni znanstveni članek

Opis: Macedonian is a South Slavic language spoken by about 2 million people, primarily in North Macedonia and among diaspora communities worldwide. It’s known for a few distinctive features. Most notably, it uses definite articles attached to the end of nouns, for example, kniga (a book) becomes knigata (the book). Furthermore, it doesn’t use grammatical cases, which makes its grammar relatively straightforward compared to other Slavic languages. The dataset comprises two lists of sentiment annotated words that present the core of the Macedonian sentiment-annotated lexicon, a list of the stopwords, and a list of Affirmative and non-Affirmative words (AnAwords) composed mostly of intensifiers and diminishers, and a list of polarity shifters. The main usage of the presented materials is in rule-based sentiment analysis, but the usage of some of the lists can be much broader.
Ključne besede: Macedonian language, sentiment analysis, sentiment lexicon, sentiment analys, rule-based methods, natural language processing, low-resource languages, AnA words, stopwords, intensifiers, diminishers, polarity shifters
Objavljeno v RUP: 20.01.2026; Ogledov: 78; Prenosov: 2
.pdf Celotno besedilo (251,79 KB)
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4.
Psychotherapists’ mindful awareness and self-regulation in the prevention of empathic distress
Eva Benda, Maša Žvelc, 2025, izvirni znanstveni članek

Opis: Objectives The aims of our research were to explore how psychotherapists recognize and experience empathic distress (ED), investigate their self-regulation strategies used within and outside psychotherapy sessions, and explore the role of mindful awareness during sessions in relation to self-regulation and ED. Methods We employed a qualitative, grounded theory methodology. We conducted interviews with eight Slovenian female integrative psychotherapists. Results Therapists reported experiencing intense emotions and physical reactions during empathic distress (ED), including anxiety, irritability, apathy, self-critique, resistance to work, fatigue, and physical pain. Many described prolonged periods of unrecognized ED. We found that mindful body awareness, a decentered perspective, and co-regulating with the client within therapy sessions were significant self-regulation strategies for therapists. Therapists also emphasized the importance of self-regulation before and after sessions and the value of supervision. Mindfulness, other meditation practices, and social- izing were highlighted as significant out-of-session regulation strategies for the prevention of ED. Conclusions This study highlights the critical need for psychotherapists to have tools for the early recognition of empathic distress. It introduces the Empathic Distress Prevention Model for Psychotherapists, emphasizing the role of mindful body awareness and other self-regulation strategies during therapy sessions, along with self-care outside of therapy. By addressing in-session self-regulation, rarely explored in psychotherapy literature, this study contributes novel insights with applications for therapists’ well-being, practice, education, and supervision.
Ključne besede: self regulation, mindfulness, empathic distress, well-being, decentered perspective, psychotherapy
Objavljeno v RUP: 20.01.2026; Ogledov: 67; Prenosov: 3
.pdf Celotno besedilo (817,02 KB)
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5.
On the Q‐polynomial property of bipartite graphs admitting a uniform structure
Blas Fernández, Roghayeh Maleki, Štefko Miklavič, Giusy Monzillo, 2026, izvirni znanstveni članek

Ključne besede: subconstituent algebra, uniform posets, Q-polynomial structures
Objavljeno v RUP: 16.01.2026; Ogledov: 128; Prenosov: 2
.pdf Celotno besedilo (410,55 KB)
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6.
Biodiversity genomics research practices require harmonising to meet stakeholder needs in conservation
Elena Bužan, Christian de Guttry, Chiara Bortoluzzi, Nathaniel R. Street, Kay Lucek, Anna Rosling, Lino Ometto, Alice Mouton, Luísa S. Marins, María José Ruiz-López, José Melo-Ferreira, Elisabet Ottosson, Camila J. Mazzoni, Robert M. Waterhouse, 2025, izvirni znanstveni članek

Opis: Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.
Ključne besede: best practices, biodiversity genomics, genome-wide genetic diversity, stakeholder engagement, standardisation, whole genome resequencing data
Objavljeno v RUP: 16.01.2026; Ogledov: 131; Prenosov: 2
.pdf Celotno besedilo (808,17 KB)
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7.
Type-based computation of knowledge graph statistics
Iztok Savnik, Kiyoshi Nitta, Riste Škrekovski, Nikolaus Augsten, 2025, izvirni znanstveni članek

Opis: We propose a formal model of a knowledge graph (abbr. KG) that classifies the ground triples into sets that correspond to the triple types. The triple types are partially ordered by the sub-type relation. Consequently, the sets of ground triples that are the interpretations of triple types are partially ordered by the subsumption relation. The types of triple patterns restrict the sets of ground triples, which need to be addressed in the evaluation of triple patterns, to the interpretation of the types of triple patterns. Therefore, a schema graph of a KG should include all triple types that are likely to be determined as the types of triple patterns. The stored schema graph consists of the selected triple types that are stored in a KG and the complete schema graph includes all valid triple types of KG. We propose choosing the schema graph, which consists of the triple types from a strip around the stored schema graph, i.e., the triple types from the stored schema graph and some adjacent levels of triple types with respect to the sub-type relation. Given a selected schema graph, the statistics are updated for each ground triple t from a KG. First, we determine the set of triple types stt from the schema graph that are affected by adding a triple t to an RDF store. Finally, the statistics of triple types from the set stt are updated.
Ključne besede: knowledge graphs, RDF stores, graph database systems
Objavljeno v RUP: 16.01.2026; Ogledov: 145; Prenosov: 2
.pdf Celotno besedilo (677,80 KB)
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8.
A pan-European citizen science study shows population size, climate and land use are related to biased morph ratios in the heterostylous plant Primula veris
Tsipe Aavik, Triin Reitalu, Marianne Kivastik, Iris Reinula, Sabrina Träger, Evelyn Uuemaa, Marta Barberis, Arjen Biere, Sílvia Castro, Sara A. O. Cousins, Živa Fišer, 2026, izvirni znanstveni članek

Opis: The distylous plant Primula veris has long served as a model species for studying heterostyly, that is the occurrence of multiple floral morphs within a population to ensure outcrossing. Habitat loss, reduced plant population sizes, and climate change have raised concerns about the impact of these factors on morph ratios and the related consequences on fitness of heterostylous species. We studied the deviation of floral morphs of P. veris from isoplethy (i.e. equal frequency) in response to plant population size, landscape context and climatic factors, based on a pan-European citizen science campaign involving observations from 28 countries. In addition, we examined the relative frequency of morphs to determine whether landscape and climatic factors disrupt morph frequencies or whether a specific morph has an advantage over the other. Theory predicts equal frequencies of short-styled S-morphs and long-styled L-morphs in populations at equilibrium. However, data from >3000 populations showed a substantial morph deviation from isoplethy and a significant excess of S-morphs (9% higher compared to L-morphs). Deviation of morph frequency from equilibrium was substantially stronger in smaller populations and was not affected by morph identity. Higher summer precipitation and land use intensity were associated with an increased prevalence of S-morphs. Five populations containing individuals exhibiting short homostyle phenotypes (with the style and anthers in low positions) were found. Genotyping of the individuals at CYP734A50 gene of the S locus, which determines the length of the style and the position of anthers of P. veris, revealed no mutations in this region. Our results based on an unprecedented geographic sampling suggest that changes in land use and climate may be responsible for non-equilibrium morph frequencies. This large-scale citizen science initiative sets foundations for future studies to clarify whether the unexpected excess of S-morphs is due to partial intra-morph compatibility, disruption of heterostyly or survival advantage of S-morphs. Synthesis. Human-induced environmental change may affect biodiversity indirectly through altering reproductive traits, which can also lead to reduced fitness and genetic diversity. Further research should consider the possible role of pollinators in mediating the ecological and evolutionary consequences of recent landscape and climatic shifts on plant reproductive traits.
Ključne besede: citizen science, flower, heterostily
Objavljeno v RUP: 16.01.2026; Ogledov: 116; Prenosov: 2
.pdf Celotno besedilo (2,66 MB)
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9.
Enhanced precision in axle configuration inference for bridge weigh-in-motion systems using computer vision and deep learning
Domen Šoberl, Jan Kalin, Andrej Anžlin, Maja Kreslin, Klen Čopič Pucihar, Matjaž Kljun, Doron Hekič, Aleš Žnidarič, 2025, izvirni znanstveni članek

Opis: Heavy goods vehicles (HGVs) have a significant impact on road and bridge infrastructure, with overloaded vehicles accelerating structural deterioration and increasing safety risks. Bridge weigh-in-motion (B-WIM) systems estimate gross vehicle weight (GVW) using strain measurements, but inaccuracies in axle configuration recognition can reduce reliability. This study presents a low-cost computer vision (CV) extension for existing B-WIM installations that verifies strain-inferred axle configurations using traffic camera images and flags GVW estimates as reliable or unreliable. Experiments on a data set of over 30,000 HGV records show that by combining convolutional neural networks with strain-based heuristics, GVW reliability can improve from 96.7% to 99.89%, effectively excluding nearly all erroneous measurements. The approach operates without interrupting ongoing B-WIM operations and can be applied retrospectively to historical data. Limitations include the inability to detect raised axles (RAs), which the method excludes as unreliable. This method provides a practical, high-precision enhancement for structural health monitoring of bridges.
Ključne besede: B-WIM, computer vision, deep learning
Objavljeno v RUP: 16.01.2026; Ogledov: 107; Prenosov: 3
.pdf Celotno besedilo (2,01 MB)
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10.
Occupancy of artificial shelters by European tree frog (Hyla arborea) in Škocjanski zatok Nature Reserve : a non-invasive sampling method in ecologically sensitive habitats
Martin Senič, Matic Jančič, Jure Jugovic, Kevin Rečnik, Sara Zupan, Martina Lužnik, 2025, izvirni znanstveni članek

Opis: Monitoring amphibians in non-breeding habitats is constrained by low detectability and potential disturbance to sensitive ecosystems. We tested the effectiveness of artificial shelters - PVC pipes - as a non-invasive method for monitoring the European tree frog (Hyla arborea) outside the breeding season in Škocjanski zatok Nature Reserve (Koper, Slovenia). Over three years (2022–2024), we installed 40- and 50-mm diameter shelter pipes at 24 sites and conducted regular inspections. A total of 338 encounters of the focal species were recorded, with frogs of all sizes using the shelters. Overall shelter occupancy declined across years, possibly reflecting a combination of factors including reduced recruitment, vegetation changes, demographic fluctuations, and weather conditions. A statistically significant trend was observed, with narrower (40-mm) shelter pipes having 1.6 to 1.7 times more captures than wider (50-mm) ones, despite no significant difference in the body size of frogs occupying each type. By using PVC artificial shelters, we greatly enhanced the detectability of H. arborea in the Škocjanski zatok Nature Reserve compared to classical monitoring methods such as acoustic surveys or dip-netting. Importantly, a non-invasive approach using artificial shelters minimized the risk of disturbance to breeding and migratory birds, which is essential in areas with high avifaunal conservation value. Our results support the broader use of artificial shelters for monitoring arboreal amphibians in ecologically sensitive areas and suggest future research should explore finer-scale shelter design to improve detection and ecological interpretation across life stages.
Ključne besede: Hyla arborea, artificial shelters, PVC pipes, amphibian monitoring, protected areas
Objavljeno v RUP: 14.01.2026; Ogledov: 119; Prenosov: 2
.pdf Celotno besedilo (928,26 KB)
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