21. Verzioniranje in uporaba Git, GitHub/GitLabKatja Meden, 2024, druge monografije in druga zaključena dela Ključne besede: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, raziskovalni podatki, nadzor različic, spletna orodja, infrastruktura, odprti podatki, Git, odprtokodni programi
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22. Autoimmune mast cell activation test as a diagnostic tool in chronic spontaneous urticariaAna Koren, Luka Dejanović, Matija Rijavec, Peter Kopač, Mojca Bizjak, Mihaela Zidarn, Mitja Košnik, Peter Korošec, 2024, izvirni znanstveni članek Povzetek: first_pagesettingsOrder Article Reprints
Open AccessArticle
Autoimmune Mast Cell Activation Test as a Diagnostic Tool in Chronic Spontaneous Urticaria
by Ana Koren 1,*ORCID,Luka Dejanović 1ORCID,Matija Rijavec 1,2ORCID,Peter Kopač 1,3ORCID,Mojca Bizjak 1ORCID,Mihaela Zidarn 1,3,Mitja Košnik 1,3ORCID andPeter Korošec 1,4
1
University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
2
Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
3
Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
4
Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(17), 9281; https://doi.org/10.3390/ijms25179281
Submission received: 25 July 2024 / Revised: 23 August 2024 / Accepted: 25 August 2024 / Published: 27 August 2024
(This article belongs to the Special Issue Progression of Allergy and Immune Response)
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Abstract
Chronic spontaneous urticaria (CSU) is associated with skin mast cell activation, and its triggering mechanisms are not completely elucidated. Evidence suggests an autoimmune component of CSU. Our aim was to assess the usefulness of an autoimmune mast cell activation test (aiMAT) for diagnosing and differentiating CSU into different subtypes. We enrolled 43 patients with active, uncontrolled CSU before starting treatment with omalizumab and 15 controls. Patients were evaluated based on omalizumab response. aiMATs were performed using non-IgE-sensitized (NS) or myeloma IgE-sensitized (S) LAD2 cells, which were then stimulated with CSU/control sera (25 µL and 10 µL). The expression of CD63 was assessed with flow cytometry. CD63 response on NS-LAD2 was significantly increased in CSU patients compared to controls after the stimulation with 25 µL CSU/control sera (p = 0.0007) and with 10 µL CSU/control sera (p = 0.0001). The ROC curve analysis demonstrated an area under the curve (AUC) of 0.82. The cutoff for autoimmune-non-IgE-sensitized-MAT was 40.3% CD63+ LAD2, which resulted in 73.3% sensitivity and 81.4% specificity. CD63 response on S-LAD2 was significantly increased in CSU patients compared to controls after the stimulation with 25 µL CSU/control sera (p = 0.03). The ROC curve analysis demonstrated an AUC of 0.66. The cutoff for the autoimmune-myeloma IgE-sensitized-MAT was 58.4% CD63+ cells, which resulted in 62.8% sensitivity and 66.7% specificity. Overall, 36 out of 43 (84%) patients responded to omalizumab, and 7 (16%) were nonresponders. We found no differences between LAD2 CD63 response and response to omalizumab. In conclusion, aiMAT could represent a new diagnostic tool in CSU. Additional studies are needed to evaluate the potential benefits during omalizumab therapy.
Ključne besede: mast cell activation test, LAD2, chronic spontaneous urticaria, omalizumab, CD63 expression
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27. Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophagesNejc Stopnišek, Stina Hedžet, Tomaž Accetto, Maja Rupnik, 2025, izvirni znanstveni članek Povzetek: Background Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.
Ključne besede: prophage detection, Bacteroides, Phocaeicola, gut microbiome, prophage diversity, Caudoviricetes, antibiotic resistance, phage-bacteria interactions, temporal stability
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28. Addressing the paradox of rest with innovative technologiesRado Pišot, Uroš Marušič, Luka Šlosar, 2025, drugi znanstveni članki Povzetek: The paradox of rest lies in its dual nature: essential for recovery yet potentially harmful when prolonged. Prolonged physical inactivity (PI) significantly contributes to non-communicable diseases (NCDs). Studies show nearly a third of adults worldwide were insufficiently active in 2022, with the economic costs of PI projected to reach INT$520 billion by 2030. Bedrest models have illuminated the rapid onset of insulin resistance, general functional decline and muscle atrophy associated with PI, particularly in hospitalised older adults. Innovative technologies, such as extended reality (XR), offer promising solutions for mitigating the effects of PI and can enhance non-physical rehabilitation techniques such as motor imagery and action observation. These technologies provide immersive, personalised therapeutic experiences that engage multiple senses, transforming passive recovery into an active process and addressing both the physical and cognitive consequences of inactivity. Results of bedrest study showed significant preservation of muscle mass, improved strength and enhanced insulin sensitivity in the intervention group compared to controls. These findings highlight the potential of XRbased strategies in addressing structural and functional declines during inactivity. As part of the Interreg VI-A Italia-Slovenija project X-BRAIN.net, advanced XR-equipped active rooms were developed to aid post-stroke rehabilitation in acute care settings. XR technologies, particularly VR, have shown promise in providing dynamic and adaptable therapeutic environments that facilitate early and targeted interventions. Future advancements focus on integrating XR with brain-computer interfaces (BCIs) and synchronised visual-haptic neurofeedback, enhancing sensorimotor cortical activation and improving rehabilitation outcomes. Comprehensive multimodal approaches, including nutritional, physical and non-physical interventions, are emerging as effective strategies to personalise and optimise patient recovery.
Ključne besede: physical inactivity, functional and cognitive decline, rehabilitation, extended reality, multimodal interventions
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29. Raziskovalna infrastruktura za jezikovne vire in tehnologije CLARIN.SITomaž Erjavec, 2024, druge monografije in druga zaključena dela Ključne besede: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, raziskovalni podatki, uprabljanje podatkov, spletna orodja, infrastruktura, odprti podatki, CLARIN, raziskovalni podatki, jezikovni viri
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30. GIS orodja : praktična predstavitev uporabe orodij za delo s prostorskimi podatkiSimon Koblar, 2024, druge monografije in druga zaključena dela Ključne besede: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, raziskovalni podatki, uprabljanje podatkov, spletna orodja, infrastruktura, odprti podatki
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