31. Managing the deluge of newly discovered plant viruses and viroids : an optimized scientific and regulatory framework for their characterization and risk analysisNuria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi, Mark Paul Selda Rivarez, Johan Rollin, Ferran Salavert Pamblanco, Coline Temple, Miguel A. Aranda, Denis Kutnjak, Maja Ravnikar, 2023, izvirni znanstveni članek Povzetek: The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
Ključne besede: plant viruses and viroids, high throughput sequencing (HTS), biological characterization, plant health, regulatory agencies, Pest Risk Analysis (PRA), virus disease
Objavljeno v DiRROS: 12.07.2024; Ogledov: 22; Prenosov: 9
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32. Consensus molecular subtypes (CMS) in metastatic colorectal cancer : personalized medicine decisionMartina Reberšek, 2020, pregledni znanstveni članek Povzetek: Colorectal cancer (CRC) is one of the most common types of cancer in the world. Metastatic disease is still incurable in most of these patients, but the survival rate has improved by treatment with novel systemic chemotherapy and targeted therapy in combination with surgery. New knowledge of its complex heterogeneity in terms of genetics, epigenetics, transcriptomics and microenvironment, including prognostic and clinical characteristics, led to its classification into various molecular subtypes of metastatic CRC, called consensus molecular subtypes (CMS). The CMS classification thus enables the medical oncologists to adjust the treatment from case to case. They can determine which type of systemic chemotherapy or targeted therapy is best suited to a specific patient, what dosages are needed and in what order. Conclusions. CMS in metastatic CRC are the new tool to include the knowledge of molecular factors, tumour stroma and signalling pathways for personalized, patient-orientated systemic treatment in precision medicine.
Ključne besede: metastatic colorectal cancer, heterogeneity, biomarkers, consensus molecular subtype
Objavljeno v DiRROS: 12.07.2024; Ogledov: 17; Prenosov: 6
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33. Does regular quality control improve the quality of surgery in Slovenian breast cancer screening program?Andraž Perhavec, Sara Milićević, Barbara Perić, Janez Žgajnar, 2020, izvirni znanstveni članek Povzetek: The aim of our study was to evaluate the quality of surgery of Slovenian breast cancer screening program (DORA) using the requested EU standards. Furthermore, we investigated whether regular quality control over the 3-year period improved the quality of surgical management. Patients and methods. Patients who required surgical management within DORA between January 1st, 2016 and December 31st, 2018 were included in the retrospective study. Quality indicators (QIs) were adjusted mainly according to European Society of Breast Cancer Specialists (EUSOMA) and European Breast Cancer Network (EBCN) recommendations. Five QIs for therapeutic and two for diagnostic surgeries were selected. Additionally, variability in achieving the requested QIs among surgeons was analysed. Results. Between 2016 and 2018, 14 surgeons performed 1421 breast procedures in 1398 women. There were 1197 therapeutical (for proven breast cancer) and 224 diagnostic surgical interventions respectively. Overall, the minimal standard was met in two QIs for therapeutic and none for diagnostic procedures. A statistically significant improvement in three QIs for therapeutic and in one QI for diagnostic procedures was observed however, indicating that regular quality control improves the quality of surgery. A high variability in achieving the requested QIs was observed among surgeons, which remained high throughout the study period. Conclusions. Adherence to all selected surgical QIs in patients from screening program is difficult to achieve, especially to those specifically defined for screen-detected lesions. Regular quality control may improve results over time. Reducing the number of surgeons dedicated to breast pathology may reduce variability of management inside the institution.
Ključne besede: breast surgery, mammography, screening program, quality control
Objavljeno v DiRROS: 12.07.2024; Ogledov: 25; Prenosov: 8
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34. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: prostate cancer, needle biopsy, nuclear factor-kappa beta, Gleason
Objavljeno v DiRROS: 12.07.2024; Ogledov: 21; Prenosov: 13
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35. Worldwide tests of generic attractants, a promising tool for early detection of non-native cerambycid speciesAlain Roques, Lili Ren, Davide Rassati, Juan Shi, Evgueni Akulov, Alenka Žunič Kosi, 2023, izvirni znanstveni članek Povzetek: A large proportion of the insects which have invaded new regions and countries are emerging species, being found for the first time outside their native range. Being able to detect such species upon arrival at ports of entry before they establish in non-native countries is an urgent challenge. The deployment of traps baited with broad-spectrum semiochemical lures at ports-of-entry and other high-risk sites could be one such early detection tool. Rapid progress in the identification of semiochemicals for cerambycid beetles during the last 15 years has revealed that aggregation-sex pheromones and sex pheromones are often conserved at global levels for genera, tribes or subfamilies of the Cerambycidae. This possibly allows the development of generic attractants which attract multiple species simultaneously, especially when such pheromones are combined into blends. Here, we present the results of a worldwide field trial programme conducted during 2018–2021, using traps baited with a standardised 8-pheromone blend, usually complemented with plant volatiles. A total of 1308 traps were deployed at 302 sites covering simultaneously or sequentially 13 European countries, 10 Chinese provinces and some regions of the USA, Canada, Australia, Russia (Siberia) and the Caribbean (Martinique). We intended to test the following hypotheses: 1) if a species is regularly trapped in significant numbers by the blend on a continent, it increases the probability that it can be detected when it arrives in other countries/continents and 2) if the blend exerts an effective, generic attraction to multiple species, it is likely that previously unknown and unexpected species can be captured due to the high degree of conservation of pheromone structures within related taxa. A total of 78,321 longhorned beetles were trapped, representing 376 species from eight subfamilies, with 84 species captured in numbers greater than 50 individuals. Captures comprised 60 tribes, with 10 tribes including more than nine species trapped on different continents. Some invasive species were captured in both the native and invaded continents. This demonstrates the potential of multipheromone lures as effective tools for the detection of ‘unexpected’ cerambycid invaders, accidentally translocated outside their native ranges. Adding new pheromones with analogous well-conserved motifs is discussed, as well as the limitations of using such blends, especially for some cerambycid taxa which may be more attracted by the trap colour or other characteristics rather than to the chemical blend.
Ključne besede: pheromone trapping, invasion, early detection, Holarctic, multi-pheromone blend
Objavljeno v DiRROS: 12.07.2024; Ogledov: 21; Prenosov: 11
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36. Sarcopenia and myosteatosis at presentation adversely affect survival after esophagectomy for esophageal cancerMatevž Srpčič, Taja Jordan, Karteek Popuri, Mihael Sok, 2020, izvirni znanstveni članek Ključne besede: esophageal cancer, esophagectomy, muscle depletion, myosteatosis, sarcopenia, survival
Objavljeno v DiRROS: 12.07.2024; Ogledov: 25; Prenosov: 7
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37. Long term response of electrochemotherapy with reduced dose of bleomycin in elderly patients with head and neck non-melanoma skin cancerČrt Jamšek, Gregor Serša, Maša Omerzel, Aleš Grošelj, 2020, izvirni znanstveni članek Povzetek: . Electrochemotherapy (ECT) is a local cancer treatment based on electroporation where the electric field is used to enhance cell membrane permeability and thereby facilitating the transition of chemotherapeutic agents into the cell. For the treatment of non-melanoma skin cancer, a standard dosage of 15,000 IU/m2 bleomycin (BLM) is used. The aim of the present study was to evaluate the long-term ECT response in the group of elderly patients with non-melanoma skin cancer treated with a reduced dose of BLM in comparison to the outcome in the patients treated with the standard dose of BLM. Patients and methods. Twenty-eight patients older than 65 years, with a total of 52 non-melanoma skin lesions were included in the study. Twelve patients (24 lesions) in the experimental group received a reduced dose of BLM (10,000 IU/m2), 16 patients (28 lesions) were treated with a standard dose of BLM (15,000 IU/m2). Results. No statistically significant difference in tumor control was observed between both groups. In the experimental group, tumors recurred in 39.0% of treated lesions in a median follow-up time of 28 months. In the control group, the recurrence rate of treated lesions was 15.4% in a median follow-up time of 40 months. Conclusions. ECT with a reduced dose of BLM is a feasible treatment option for elderly patients with equal efficacy to standard dose treatment and should be considered as a treatment modality in advanced aged patients with comorbidities, where overall life expectancy is poor
Ključne besede: electrochemotherapy, bleomycin, non-melanoma skin cancer
Objavljeno v DiRROS: 12.07.2024; Ogledov: 17; Prenosov: 5
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38. Tomato brown rugose fruit virus in aqueous environments : survival and significance of water-mediated transmissionNataša Mehle, Katarina Bačnik, Irena Bajde, Jakob Brodarič, Adrian Fox, Ion Gutiérrez-Aguirre, Miha Kitek, Denis Kutnjak, Yue Lin Loh, Olivera Maksimović, Maja Ravnikar, Elise Vogel, Christine Vos, Ana Vučurović, 2023, izvirni znanstveni članek Povzetek: Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control.
Ključne besede: tomato brown rugose fruit virus, tomato, hydroponics, water-linked epidemiology, survival
Objavljeno v DiRROS: 12.07.2024; Ogledov: 18; Prenosov: 10
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39. Three-dimensional MRI evaluation of the effect of bladder volume on prostate translocation and distortionŽiga Snoj, Andrew B. Gill, Leonardo Rundo, Nikola Sushentsev, Tristan Barrett, 2020, izvirni znanstveni članek Ključne besede: prostate translocation, prostate distortion, gland deformation, bladder volume, magnetic resonance imaging, radiation therapy planning
Objavljeno v DiRROS: 12.07.2024; Ogledov: 13; Prenosov: 10
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40. Pulsed low dose-rate irradiation response in isogenic HNSCC cell lines with different radiosensitivityVesna Todorović, Ajda Prevc, Martina Nikšić Žakelj, Monika Savarin, Simon Buček, Blaž Grošelj, Primož Strojan, Maja Čemažar, Gregor Serša, 2020, izvirni znanstveni članek Povzetek: . Management of locoregionally recurrent head and neck squamous cell carcinomas (HNSCC) is challenging due to potential radioresistance. Pulsed low-dose rate (PLDR) irradiation exploits phenomena of increased radiosensitivity, low-dose hyperradiosensitivity (LDHRS), and inverse dose-rate effect. The purpose of this study was to evaluate LDHRS and the effect of PLDR irradiation in isogenic HNSCC cells with different radiosensitivity. Materials and methods. Cell survival after different irradiation regimens in isogenic parental FaDu and radioresistant FaDu-RR cells was determined by clonogenic assay; post irradiation cell cycle distribution was studied by flow cytometry; the expression of DNA damage signalling genes was assesed by reverse transcription-quantitative PCR. Results. Radioresistant Fadu-RR cells displayed LDHRS and were more sensitive to PLDR irradiation than parental FaDu cells. In both cell lines, cell cycle was arrested in G2/M phase 5 hours after irradiation. It was restored 24 hours after irradiation in parental, but not in the radioresistant cells, which were arrested in G1-phase. DNA damage signalling genes were under-expressed in radioresistant compared to parental cells. Irradiation increased DNA damage signalling gene expression in radioresistant cells, while in parental cells only few genes were under-expressed. Conclusions. We demonstrated LDHRS in isogenic radioresistant cells, but not in the parental cells. Survival of LDHRSpositive radioresistant cells after PLDR was significantly reduced. This reduction in cell survival is associated with variations in DNA damage signalling gene expression observed in response to PLDR most likely through different regulation of cell cycle checkpoints.
Ključne besede: DNA damage, isogenic cell lines, low dose irradiation, pulsed low dose-rate irradiation, radiosensitivity
Objavljeno v DiRROS: 12.07.2024; Ogledov: 15; Prenosov: 7
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