1. Significance of nuclear factor - kappa beta activation on prostate needle biopsy samples in the evaluation of Gleason score 6 prostatic carcinoma indolenceMarko Zupančič, Boris Pospihalj, Snežana Cerović, Barbara Gazić, Primož Drev, Marko Hočevar, Andraž Perhavec, 2020, original scientific article Abstract: The goal of our study was to find out whether the immunohistochemical expression of nuclear factor-kappa beta (NF-%B) p65 in biopsy samples with Gleason score 3 + 3 = 6 (GS 6) can be a negative predictive factor for Prostate cancer (PCa) indolence. Patients and methods Study was conducted on a retrospective cohort of 123 PCa patients with initial total PSA % 10 ng/ml, number of needle biopsy specimens % 8, GS 6 on biopsy and T1/T2 estimated clinical stage who underwent laparoscopic radical prostatectomy and whose archived formalin-fixed and paraffin-embedded (FFPE) prostate needle biopsy specimens were used for additional immunohistochemistry staining for detection of NF-%B p65. Both cytoplasmic and nuclear NF-%B p65 expression in biopsy cores with PCa were correlated with postoperative pathological stage, positive surgical margins, GS and biochemical progression of disease. Results After follow-up of 66 months, biochemical progression (PSA % 0.2 ng/ml) occurred in 6 (5.1%) patients, 3 (50%) with GS 6 and 3 (50%) with GS 7 after radical prostatectomy. Both cytoplasmic and nuclear NF-%B p65 expressions were not significantly associated with pathological stage, positive surgical margin and postoperative GS. Patients with positive cytoplasmic NF-kB reaction had significantly more frequent biochemical progression than those with negative cytoplasmic NF-kB reaction with PSA 0.2 ng/ml as cutoff point (p = 0.015) and a trend towards more biochemical progression with PSA % 0.05 ng/ml as cutoff point (p = 0.068). Conclusions Cytoplasmic expression of NF-%B is associated with more biochemical progression and might be an independent prognostic factor for recurrence-free survival (RFS), but further studies including larger patient cohorts are needed to confirm these initial results.
Keywords: prostate cancer, needle biopsy, nuclear factor-kappa beta, Gleason
Published in DiRROS: 12.07.2024; Views: 21; Downloads: 13
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2. Highly specific qPCR and amplicon sequencing method for detection of quarantine citrus pathogen Phyllosticta citricarpaapplicable for air samplesJanja Zajc, Zala Kogej Zwitter, Sara Fišer, Cene Gostinčar, Antonio Vicent, Anaïs Galvañ Domenech, Luca Riccioni, Neil Boonham, Maja Ravnikar, Polona Kogovšek, 2023, original scientific article Abstract: The fungus Phyllosticta citricarpa is a quarantine pathogen in the EU and is of high economic importance in many parts of the world where favourable climate conditions drive the development of citrus black spot (CBS) disease. Disease symptoms include necrotic lesions on leaves and fruits. Low disease pressure can reduce crop market-ability, while higher disease pressure can cause premature fruit drop, significantly increasing crop losses. The wind-dispersed spores of P. citricarpa are especially prob-lematic for rapid pathogen dispersal, but also provide an opportunity for early detec-tion of the disease spreading into a new area. In this study we have developed and validated a quantitative PCR (qPCR) assay based on the TEF1-α sequence. Specificity testing demonstrated that it is currently the only qPCR assay that does not cross- react with closely related Phyllosticta species. The assay is sensitive and can detect a single copy of the TEF1 gene in a reaction, it is highly repeatable and reproducible and can be used for testing of the sticky tapes from spore traps as well as citrus fruit sam-ples. High-throughput sequencing (HTS) of the DNA barcodes ITS1 and TEF1 was also explored for the detection and discrimination of P. citricarpa. The limit of detection of the HTS was 1000 spores on a daily spore trap tape. This study makes an important improvement to the diagnostics of the CBS and the methods developed can also be applied to improve the surveillance and early detection of the pathogen when linked to spore samplers in the field.
Keywords: detection, fungal spore sampling, internal transcribed region (ITS), translation elongation factor 1-α (TEF1)
Published in DiRROS: 12.07.2024; Views: 21; Downloads: 19
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3. Insulin-like growth factor 1 receptor expression in advanced non-small-cell lung cancer and its impact on overall survivalMojca Humar, Izidor Kern, Gregor Vlačić, Vedran Hadžić, Tanja Čufer, 2017, original scientific article Keywords: insulin-like growth factor 1 receptor, type 2 diabetes mellitus, advanced non-small-cell lung cancer, overall survival
Published in DiRROS: 03.06.2024; Views: 135; Downloads: 80
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4. Long-term survival in glioblastoma : methyl guanine methyl transferase (MGMT) promoter methylation as independent favourable prognostic factorUroš Smrdel, Mara Popović, Matjaž Zwitter, Emanuela Boštjančič, Andrej Zupan, Viljem Kovač, Damjan Glavač, Drago Bokal, Janja Jerebic, 2016, original scientific article Abstract: In spite of significant improvement after multi-modality treatment, prognosis of most patients with glioblastoma remains poor. Standard clinical prognostic factors (age, gender, extent of surgery and performance status) do not clearly predict long-term survival. The aim of this case-control study was to evaluate immuno-histochemical and genetic characteristics of the tumour as additional prognostic factors in glioblastoma. Long-term survivor group were 40 patients with glioblastoma with survival longer than 30 months. Control group were 40 patients with shorter survival and matched to the long-term survivor group according to the clinical prognostic factors. All patients underwent multimodality treatment with surgery, postoperative conformal radiotherapy and temozolomide during and after radiotherapy. Biopsy samples were tested for the methylation of MGMT promoter (with methylation specific polymerase chain reaction), IDH1 (with immunohistochemistry), IDH2, CDKN2A and CDKN2B (with multiplex ligation-dependent probe amplification), and 1p and 19q mutations (with fluorescent in situ hybridization). Methylation of MGMT promoter was found in 95% and in 36% in the long-term survivor and control groups, respectively (p < 0.001). IDH1 R132H mutated patients had a non-significant lower risk of dying from glioblastoma (p= 0.437), in comparison to patients without this mutation. Other mutations were rare, with no significant difference between the two groups. Molecular and genetic testing offers additional prognostic and predictive information for patients with glioblastoma. The most important finding of our analysis is that in the absence of MGMT promoter methylation, longterm survival is very rare. For patients without this mutation, alternative treatments should be explored.
Keywords: glioblastoma, long-term survival, methyl guanine methyl transferase, MGMT, prognostic factor
Published in DiRROS: 30.04.2024; Views: 198; Downloads: 187
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5. Application of multivariate statistical methods for determining geochemical trends of elements on the territory of SloveniaRobert Šajn, Mateja Gosar, Jasminka Alijagić, Tamara Teršič, 2024, original scientific article Abstract: The main objective of this study is to map multi-element geochemical anomalies in soil on a regional scale. We aimed to determine and evaluate the baseline geochemical values and main geochemical trends in soil that may serve as reference values against any future changes. A total of 817 topsoil samples (0–10 cm) were collected in a 5 × 5 km grid and analyzed for 35 elements using ICP-ES after multi-acid digestions (HClO4/HNO3/HCl/HF) and 53 elements using ICP-MS after modified aqua regia digestion (HCl/HNO3/H2O). The analytical results for the two different digestion methods (multi-acid digestion vs. aqua regia) were also compared for each chemical element. Multivariate statistical methods were applied to identify the geochemical trends and main sources of trace elements over the territory of Slovenia. Based on these results, seven natural and one mixed natural/anthropogenic geochemical association were established. The contents and trends of the determined factors are presented according to 8 natural units, 4 drainage areas, and geological units characteristic of Slovenia. The identified anthropogenic geochemical association combines toxic elements (Ag, Bi, Cd, Hg, P, Pb, S, Sn, and Zn). Increased values of these elements can be found in mining areas and metallurgic centers, in Quaternary sediments of the Sava River, and Adriatic Basin as the consequence of past mining activities and in the Julian Alps, where their origin could be connected to the atmospheric deposition.
Keywords: soil, geochemical mapping, distribution of geochemical elements, factor analysis, cluster analysis
Published in DiRROS: 04.01.2024; Views: 371; Downloads: 88
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6. Candidate pathogenicity factor/effector proteins of ‘Candidatus Phytoplasma solani’ modulate plant carbohydrate metabolism, accelerate the ascorbate–glutathione cycle, and induce autophagosomesMarina Dermastia, Špela Tomaž, Rebeka Strah, Tjaša Lukan, Anna Coll Rius, Barbara Dušak, Timotej Čepin, Aleš Kladnik, Maja Zagorščak, Kristina Gruden, Maruša Pompe Novak, 2023, original scientific article Abstract: The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including ‘Candidiatus Phytoplasma solani’ are unknown. Six putative pathogenicity factors/effectors from six different strains of ‘Ca. P. solani’ were selected by bioinformatic analysis. The way in which they manipulate the host cellular machinery was elucidated by analyzing Nicotiana benthamiana leaves after Agrobacterium-mediated transient transformation with the pathogenicity factor/effector constructs using confocal microscopy, pull-down, and co-immunoprecipitation, and enzyme assays. Candidate pathogenicity factors/effectors were shown to modulate plant carbohydrate metabolism and the ascorbate–glutathione cycle and to induce autophagosomes. PoStoSP06, PoStoSP13, and PoStoSP28 were localized in the nucleus and cytosol. The most active effector in the processes studied was PoStoSP06. PoStoSP18 was associated with an increase in phosphoglucomutase activity, whereas PoStoSP28, previously annotated as an antigenic membrane protein StAMP, specifically interacted with phosphoglucomutase. PoStoSP04 induced only the ascorbate–glutathione cycle along with other pathogenicity factors/effectors. Candidate pathogenicity factors/effectors were involved in reprogramming host carbohydrate metabolism in favor of phytoplasma own growth and infection. They were specifically associated with three distinct metabolic pathways leading to fructose-6-phosphate as an input substrate for glycolysis. The possible significance of autophagosome induction by PoStoSP28 is discussed.
Keywords: autophagosome, effector, glycolysis, pathogenicity factor, StAMP
Published in DiRROS: 24.08.2023; Views: 637; Downloads: 283
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7. Measurements of bridge dynamic amplification factor using bridge weigh-in-motion dataJan Kalin, Aleš Žnidarič, Andrej Anžlin, Maja Kreslin, 2022, original scientific article Abstract: The dynamic component of bridge traffic loading is commonly taken into account with a Dynamic Amplification Factor (DAF)—the ratio between the dynamic and static load effects on a bridge. In the design codes, this factor is generally more conservative than in reality. Recently a new method of cal- culation of this factor had been developed. Data from 15 different bridges have been analysed since then and this paper presents the results of the analyses. The background for Bridge Weigh-in-Motion is given, and the most recent method for DAF calculation is described. The sites from which the data originated are presented, and the selection of data discussed. The results of the analyses are presented and discussed and some examples of DAF calculations are shown. Data from the considered sites have invariably demonstrated a DAF decrease with increasing axle load. This is a significant result, especially for assessment of existing structures, since it is beneficial to use measured structural param- eters to optimise structural analysis.
Keywords: bridge loads, bridge weigh-in-motion, dynamic amplication factor, dynamic analysis, measurement, traffic loading
Published in DiRROS: 14.07.2023; Views: 421; Downloads: 235
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8. Private forest owner willingness to mobilise wood from dense, small-diameter tree standsMatevž Triplat, Satu Helenius, Ruben Laina, Nike Krajnc, Thomas Kronholm, Zdenka Ženko, Teppo Hujala, 2023, original scientific article Abstract: Forests are a source of renewable biomass, and their utilisation will play a vital role in the transition towards a climate-neutral economy. Small-diameter tree management could contribute to this transition via providing renewable biomass for sustainable uses and fostering tree growth towards long-lifecycle bioproducts. The utilisation of small-diameter trees in the EU is still low since new technologies and work models are required to make the operations economically profitable, environmentally sound, and socially attractive. The supply of biomass from small-diameter tree stands is dependent on forest owners with diverse perceptions on their forests and diverse ownership objectives. However, there is scarce research on forest owner perceptions on small-diameter tree management, which encompasses home consumption, self-active work, and commercial forestry services. A survey in four EU countries was designed to identify the main factors affecting the motivation of forest owners to mobilise biomass from small-diameter stands. Factor and clustering analyses were used to identify four forest owner segments: weakly-engaged traders, well-being seekers, self-active profit-seekers, and well-informed service users. The willingness to utilise biomass from small-diameter tree stands and participate in the market was shaped by forest owner knowledge of forestry, economic and socio-cultural motivations, and sensitivity to service offerings. Forest owner preferences for market participation are heterogenous, and thus different policy implementation approaches are needed and proposed.
Keywords: customer profiles, factor analysis, forestry services, management objectives, biomass, communication strategies
Published in DiRROS: 05.01.2023; Views: 824; Downloads: 344
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9. Mutational burden, MHC-I expression and immune infiltration as limiting factors for in situ vaccination by TNF[alfa] and IL-12 gene electrotransferUrška Kamenšek, Katja Uršič Valentinuzzi, Boštjan Markelc, Maja Čemažar, Vita Šetrajčič Dragoš, Gregor Serša, 2021, original scientific article Abstract: In situ vaccination is a promising immunotherapeutic approach, where various local ablative therapies are used to induce an immune response against tumor antigens that are released from the therapy-killed tumor cells. We recently proposed using intratumoral gene electrotransfer for concomitant transfection of a cytotoxic cytokine tumor necrosis factor-% (TNF%) to induce in situ vaccination, and an immunostimulatory cytokine interleukin 12 (IL-12) to boost the primed immune response. Here, our aim was to test the local and systemic effectiveness of the approach in tree syngeneic mouse tumor models and associate it with tumor immune profiles, characterized by tumor mutational burden, immune infiltration and expression of PD-L1 and MHC-I on tumor cells. While none of the tested characteristic proved predictive for local effectiveness, high tumor mutational burden, immune infiltration and MHC-I expression were associated with higher abscopal effectiveness. Hence, we have confirmed that both the abundance and presentation of tumor antigens as well as the absence of immunosuppressive mechanisms are important for effective in situ vaccination. These findings provide important indications for future development of in situ vaccination based treatments, and for the selection of tumor types that will most likely benefit from it.
Keywords: in situ vaccination, gene electrotransfer, interleukin 12, tumor necrosis factor [alfa]
Published in DiRROS: 19.09.2022; Views: 646; Downloads: 224
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10. Real-world testing practices, treatment patterns and clinical outcomes in patients from Central Eastern Europe with EGFR-mutated advanced non-small cell lung cancer : a retrospective chart review study (REFLECT)Urška Janžič, Nina Turnšek, Mircea Dediu, Ivan Shterev Donev, Roxana Lupu, Gabriela Teodorescu, Tudor Ciuleanu, Adam Płużański, 2022, original scientific article Abstract: The targeted therapy with tyrosine kinase inhibitors (TKIs) against the epidermal growth factor receptor mutation (EGFRm) in advanced non-small cell lung cancer (NSCLC) changed the treatment paradigm. REFLECT study (NCT04031898) explored EGFR/T790M testing and treatment patterns in EGFRm NSCLC patients receiving first- or second-generation (1G/2G) EGFR TKIs as front-line (1L) in eight countries. Pooled data from Central Eastern Europe (CEE) countries from this study (Bulgaria, Poland, Romania, Slovenia) are presented here. This physician-led chart review study was conducted in patients with confirmed-EGFRm NSCLC initiating 1L 1G/2G EGFR TKIs between 2015–2018. The CEE cohort included 389 patients receiving 1L erlotinib (37%), afatinib (34%), and gefitinib (29%). Overall, 320 (82%) patients discontinued 1L, and 298 (77%) progression events were registered. Median progression free survival on 1L TKIs was 14.0 (95% CI: 12.6–15.6) months. Median overall survival from 1L start was 26.6 (95% CI: 24.1–29.0) months. Attrition rate between 1L and next line was 30%. Among patients with 1L progression, 200 (67%) were tested for T790M and 58% were positive. This first CEE analysis of treatments and outcomes in EGFRm NSCLC patients highlights the importance of using the most efficacious therapies currently available in 1L to reduce attrition and improve patient outcomes.
Keywords: lung neoplasms, non-small cell lung carcinoma, Eastern Europe, real-world study, REFLECT study, epidermal growth factor receptor, lung cancer
Published in DiRROS: 09.09.2022; Views: 645; Downloads: 269
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