1. Evidence-based unification of potato gene models with the UniTato collaborative genome browserMaja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Francesca Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek, 2024, original scientific article Abstract: Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant re-analysis, and leads to missing or wrongly annotated genes. Here, we unify the recent potato double monoploid v4 and v6 gene models by developing an automated merging protocol, resulting in a Unified poTato genome model (UniTato). We subsequently established an Apollo genome browser (unitato.nib.si) that enables public access to UniTato and further community-based curation. We demonstrate how the UniTato resource can help resolve problems with missing or misplaced genes and can be used to update or consolidate a wider set of gene models or genome information. The automated protocol, genome annotation files, and a comprehensive translation table are provided at github.com/NIB-SI/unitato. Keywords: bioinformatics analysis, plant genome annotation, gene model annotations, Phureja group, GFF files, poTato genome model, UniTato Published in DiRROS: 11.06.2024; Views: 49; Downloads: 60
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2. Stress knowledge map : a knowledge graph resource for systems biology analysis of plant stress responsesCarissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Anže Županič, Kristina Gruden, 2024, original scientific article Abstract: Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology. Keywords: Stress knowledge map, knowledge graph, knowledge network, entry point, plant digital twin, plant stress responses, plant signaling, systems biology Published in DiRROS: 11.06.2024; Views: 58; Downloads: 39
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3. Computed tomographic perfusion imaging for the prediction of response and survival to transarterial chemoembolization of hepatocellular carcinomaPeter Popović, Ana Leban, Klara Kregar, Manca Garbajs, Rok Dežman, Matjaž Bunc, 2018, original scientific article Keywords: hepatocellular carcinoma, computed tomography perfusion imaging, drug-eluting beads transarterial chemoembolization, response to treatment, survival Published in DiRROS: 11.06.2024; Views: 54; Downloads: 26
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4. Site-specific dataset of mining and metallurgical residues for resource managementCarlo Cormio, Marta Fernández-Alonso, Peter Cleall, Soraya Heuss-Aßbichler, Daniela Guglietta, Danielle Sinnett, Katalin Szabó, Gorazd Žibret, Maria Teresa Carvalho, Ulrich Kral, Tim T. Werner, Bruno Lemiere, 2024, other scientific articles Abstract: This geospatial dataset provides a compilation of findings from an evidence-based review of site-specific resource assessments of mining and metallurgical residues. Information pertaining to location, target material, geological knowledge, extractability, resource classification and stakeholder perspectives was collected from publicly available reports, articles, academic theses, and databases. The dataset includes 44 relevant data attributes from 64 mining and metallurgical sites in 27 countries. Resource classification is available for 38 sites. The dataset can be used by evaluators of recovery projects, authorities that provide permits, as well as by decision makers in support of developing regulatory policies. The dataset facilitates future addition of sites by the research community and can be further used as a starting point to bridge the estimates on recoverable quantities to the United Nations Framework Classification (UNFC). The UNFC is a universally applicable scheme for the sustainable management of all energy, primary and secondary mineral resources. Its use is stimulated by the European Commission and is intended to be adopted by geological surveys to harmonize the data on the availability of primary and secondary raw materials in Europe in future. Keywords: resources, reserves, mining waste, secondary raw materials, tailings, geodatabase, circular economy, resource assessment Published in DiRROS: 10.06.2024; Views: 33; Downloads: 6
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5. Guanidine modification improves functions of natural RNA-targeting alkaloidsTamaki Endoh, Sagar Satpathi, Yutong Chen, Saki Matsumoto, Tatsuya Ohyama, Peter Podbevšek, Janez Plavec, Kazumitsu Onizuka, Fumi Nagatsugi, Naoki Sugimoto, 2024, original scientific article Published in DiRROS: 10.06.2024; Views: 37; Downloads: 14
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6. pISA-tree : a data management framework for life science research projects using a standardised directory treeMarko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll Rius, Špela Baebler, Kristina Gruden, 2022, original scientific article Keywords: pISA-tree, ISA model, data management, research data, metadata Published in DiRROS: 05.06.2024; Views: 105; Downloads: 70
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7. Digital PCR for the characterization of reference materialsMegan H. Cleveland, Hua-Jun He, Mojca Milavec, Young-Kyung Bae, Peter M. Vallone, Jim F. Huggett, 2024, review article Abstract: Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials. Keywords: digital PCR, dPCR, reference materials, UV-spectroscopy Published in DiRROS: 03.06.2024; Views: 111; Downloads: 48
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8. Implant-prosthetic rehabilitation after radiation treatment in head and neck cancer patients : a case-series report of outcomeJasna Cotič, Jure Jamšek, Milan Kuhar, Nataša Ihan Hren, Andrej Kansky, Mutlu Özcan, Peter Jevnikar, 2017, original scientific article Abstract: Background. Slovenia has a high burden of head and neck cancer. Patients are mostly treated with surgery followed by radiation therapy. Advanced surgical and prosthodontic techniques have expanded the rehabilitation options. The aim of the study was to review the outcome of implant-prosthetic treatment after radiation therapy. Patients and methods. Twenty irradiated head and neck cancer patients who received a removable implantsupported denture at the University Medical Centre Ljubljana were included in the study. Kaplan-Meier survival analysis, Cox proportional hazard models and logistic regression were used to assess the implant survival and success rate. Results. Twenty patients had 100 implants inserted. The estimated implant survival rate was 96% after 1 year and 87% after 5 years. Failures were mostly observed before loading (91.2%). Implants inserted in the transplanted bone were significantly more likely to fail. Out of 89 implants supporting the dentures, 79 implants (88.7%) were successful, meaning that they were functionally loaded and exhibited no pain, radiolucency or progressive bone loss. Prosthetic treatment was significantly less successful in older patients. The attachment system and the number of implants did not have a statistically significant influence on the success rate. Conclusions. Implant-supported dentures have been shown to be a reliable treatment modality after head and neck cancer surgery and radiation therapy. Possible early failures should be communicated with the patients. Keywords: head and neck cancer, radiation therapy, dental implants Published in DiRROS: 03.06.2024; Views: 72; Downloads: 32
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9. A novel mutation in the FOXC2 gene : a heterozygous insertion of adenosine (c.867insA) in a family with lymphoedema of lower limbs without distichiasisTanja Planinšek Ručigaj, Matija Rijavec, Jovan Miljković, Julij Šelb, Peter Korošec, 2017, original scientific article Keywords: primary lymphedema, FOXC2 mutation, distichiasis, lower limbs lymphedema Published in DiRROS: 31.05.2024; Views: 83; Downloads: 56
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10. Poročilo o izvedbi naloge javnega naročila: »Monitoring ogljika v gozdnih tleh, mokriščih in urbanih tleh« - MEJNIK 4 : končno poročiloAleksander Marinšek, Daniel Žlindra, Mitja Ferlan, Erika Kozamernik, Boštjan Mali, Peter Horvat, Eva Zagorac, Nastja Mesarec, Janez Bergant, Borut Vrščaj, Primož Simončič, 2023, final research report Keywords: monitoring, ogljik, gozdna tla, mokrišča, urbana tla Published in DiRROS: 24.05.2024; Views: 138; Downloads: 141
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