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1.
Breast cancer risk prediction using Tyrer-Cuzick algorithm with an 18-SNPs polygenic risk score in a European population with below-average breast cancer incidence
Tjaša Oblak, Petra Škerl, Benjamin J. Narang, Rok Blagus, Mateja Krajc, Srdjan Novaković, Janez Žgajnar, 2023, izvirni znanstveni članek

Povzetek: Goals: To determine whether an 18 single nucleotide polymorphisms (SNPs) polygenic risk score (PRS18) improves breast cancer (BC) risk prediction for women at above-average risk of BC, aged 40-49, in a Central European population with BC incidence below EU average. Methods: 502 women aged 40-49 years at the time of BC diagnosis completed a questionnaire on BC risk factors (as per Tyrer-Cuzick algorithm) with data known at age 40 and before BC diagnosis. Blood samples were collected for DNA isolation. 250 DNA samples from healthy women aged 50 served as a control cohort. 18 BC-associated SNPs were genotyped in both groups and PRS18 was calculated. The predictive power of PRS18 to detect BC was evaluated using a ROC curve. 10-year BC risk was calculated using the Tyrer-Cuzick algorithm adapted to the Slovenian incidence rate (S-IBIS): first based on questionnaire-based risk factors and, second, including PRS18. Results: The AUC for PRS18 was 0.613 (95 % CI 0.570-0.657). 83.3 % of women were classified at above-average risk for BC with S-IBIS without PRS18 and 80.7 % when PRS18 was included. Conclusion: BC risk prediction models and SNPs panels should not be automatically used in clinical practice in different populations without prior population-based validation. In our population the addition of an 18SNPs PRS to questionnaire-based risk factors in the Tyrer-Cuzick algorithm in general did not improve BC risk stratification, however, some improvements were observed at higher BC risk scores and could be valuable in distinguishing women at intermediate and high risk of BC.
Ključne besede: early breast cancer, polygenic risk score, risk prediction
Objavljeno v DiRROS: 21.03.2024; Ogledov: 57; Prenosov: 21
.pdf Celotno besedilo (1,54 MB)

2.
The influence of storage conditions and DNA extraction protocol on the results of molecular analysis of the European spruce bark beetle (Ips typographus L.)
Zina Devetak, Andreja Kavčič, Maarten De Groot, Barbara Piškur, 2023, izvirni znanstveni članek

Povzetek: One of the key steps of the molecular identification of bark beetles is obtaining a sufficient quantity of high-quality DNA extract. In this study, we investigated the influence of different storage procedures for Ips typographus (L.) specimens and various DNA extraction protocols on the quantity and quality of DNA intended for use in molecular diagnostics. Adult beetles were frozen at -20 °C, either dry or in ethanol. We tested four different protocols for DNA extraction. We compared the quantity of extracted DNA and assessed its quality with PCR and Sanger sequencing. Different storage protocols had no significant effect on the quantity of DNA extracted. However, freezing specimens in ethanol provided higher-quality DNA for molecular applications. Only two of the extraction protocols produced sequenceable amplicons, and the difference in the amount of extracted DNA between them was not significant. We propose the optimal combination of storing specimens in ethanol at -20°C and using the Nucleospin Insect DNA extraction kit from Macherey Nagel, enabling a timeefficient identification process.
Ključne besede: early detection, specimen storage, total DNA extraction, PCR, polymerase chain reaction, Sanger sequencing, molecular diagnostics
Objavljeno v DiRROS: 02.02.2024; Ogledov: 331; Prenosov: 101
.pdf Celotno besedilo (1,17 MB)
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3.
Temporal and spatial variability of phloem structure in Picea abies and Fagus sylvatica and its link to climate
Jožica Gričar, Jernej Jevšenak, Kyriaki Giagli, Klemen Eler, Dimitrios Tsalagkas, Vladimir Gryc, Hanuš Vavrčík, Katarina Čufar, Peter Prislan, 2024, izvirni znanstveni članek

Povzetek: Using a unique 8-year data set (2010–2017) of phloem data, we studied the effect of temperature and precipitation on the phloem anatomy (conduit area, widths of ring, early and late phloem) and xylem-ring width in two coexisting temperate tree species, Picea abies and Fagus sylvatica, from three contrasting European temperate forest sites. Histometric analyses were performed on microcores taken from tree stems in autumn. We found high interannual variability and sensitivity of phloem anatomy and xylem-ring widths to precipitation and temperature; however, the responses were species- and site-specific. The contrasting response of xylem and phloem-ring widths of the same tree species to weather conditions was found at the two Slovenian sites generally well supplied with precipitation, while at the driest Czech site, the influence of weather factors on xylem and phloem ring widths was synchronised. Since widths of mean annual xylem and phloem increments were narrowest at the Czech site, this site is suggested to be most restrictive for the radial growth of both species. By influencing the seasonal patterns of xylem and phloem development, water availability appears to be the most important determinant of tissue- and species-specific responses to local weather conditions.
Ključne besede: wood anatomy, early phloem, European beech, late phloem, Norway spruce, sieve element area, xylem-ring width
Objavljeno v DiRROS: 19.01.2024; Ogledov: 185; Prenosov: 84
.pdf Celotno besedilo (5,31 MB)
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4.
Efficacy of trapping protocols for Agrilus jewel beetles : a multi-country assessment
Giacomo Santoiemma, David Williams, Everett G. Booth, Giacomo Cavaletto, James Connell, Gianfranco Curletti, Maarten De Groot, Sarah M. Devine, Abigail Enston, Joseph A. Francese, Eva Groznik, Tine Hauptman, 2024, izvirni znanstveni članek

Povzetek: The genus Agrilus is one of the most diverse insect genera worldwide. The larval feeding activity causes extensive damage in both forests and orchards. In addition, more than 30 species have been introduced outside their native range so far, including the emerald ash borer Agrilus planipennis Fairmaire. Thus, the availability of efficient trapping protocols for early detection of Agrilus species at entry points is of utmost importance. In this study we tested whether trapping protocols developed for surveillance of A. planipennis in North America were also effective for other Agrilus species. In particular, through a multi-country assessment we compared the efficacy of detecting Agrilus species on: (i) green glue-coated prism traps vs. green Fluon-coated multi-funnel traps when baited with the green leaf volatile (Z)-3-hexenol or left unbaited; and (ii) green multi-panel traps vs. green multi-panel traps baited with dead adult Agrilus beetles (decoys). A total of 23,481 individuals from 45 Agrilus species were caught. Trap design significantly affected both species richness and abundance of Agrilus species in several of the countries where the trapping experiments were carried out, and green prism traps outperformed green multi-funnel traps in most cases. On the contrary, the addition of a (Z)-3-hexenol lure or dead adult beetle decoys on to traps did not improve trap catches. Our study highlights that reliable trap models to survey Agrilus species are already available, but also that there is the clear need to further investigate chemical ecology of Agrilus species to develop semiochemical lures that can improve detection efficacy.
Ključne besede: biosecurity, early detection, forest pests, lures, traps, visual stimuli, Agrilus, beetles
Objavljeno v DiRROS: 19.01.2024; Ogledov: 153; Prenosov: 105
.pdf Celotno besedilo (3,11 MB)
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5.
Trends in specialized palliative care referrals at an oncology center from 2007 to 2019
Lučka Boltežar, Barbara Jezeršek Novaković, Maja Ebert Moltara, 2021, izvirni znanstveni članek

Ključne besede: palliative care, primary site of cancer, early referral
Objavljeno v DiRROS: 21.09.2022; Ogledov: 386; Prenosov: 224
.pdf Celotno besedilo (1,80 MB)
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6.
Where to search: the use of opportunistic data for the detection of an invasive forest pest
Maarten De Groot, Nikica Ogris, Mark van der Meij, Michael J.O. Pocock, 2022, izvirni znanstveni članek

Povzetek: Early detection is important for the management of invasive alien species. In the last decade citizen science has become an important source of such data. Here, we used opportunistic records from the “LIFE ARTEMIS” citizen science project, in which people submitted records from places where they observed tree pests, to understand the distribution of a rapidly-spreading forest pest: the oak lace bug (Corythucha arcuata) in Slovenia. These citizen science records were not distributed randomly. We constructed a species distribution model for C. arcuata that accounted for the biased distribution of citizen science by using the records of other tree pests and diseases from the same project as pseudo-absences (so-called constrained pseudo-absences), and compared this to a model with pseudo-absences selected randomly from across Slovenia. We found that the constrained pseudo-absence model showed that C. arcuata was more likely to be found in east, in places with more oak trees and at lower elevations, and also closer to highways and railways, indicating introduction and dispersal by accidental human transport. The outputs from the model with random pseudo-absences were broadly similar, although estimates from this model tended to be higher and less precise, and some factors that were significant (proximity to minor roads and human settlements) were artefacts of recorder bias, showing the importance of taking the distribution of recording into account wherever possible. The finding that C. arcuata is more likely to be found near highways allows us to design advice for where future citizen science should be directed for efficient early detection.
Ključne besede: Oak lace bug, ecological modelling, citizen science, invasive alien species, early detection, Corythucha arcuata
Objavljeno v DiRROS: 08.09.2022; Ogledov: 469; Prenosov: 234
.pdf Celotno besedilo (2,79 MB)
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7.
Vismodegib in locally advanced basal cell carcinoma in Slovenia
Tanja Mesti, Maša Sever, Janja Ocvirk, 2022, izvirni znanstveni članek

Povzetek: Background: Vismodegib is a first-in-class inhibitor of the hedgehog pathway for treatment of locally advanced basal cell carcinoma (laBCC) and metastatic BCC. Objectives: The purpose of this study is to report outcomes of patients with laBCC, with basal cell carcinoma nevus syndrome (Gorlin Goltz syndrome [G-G Syn]) treated with vismodegib in routine clinical practice in Slovenia in 8.3-year period. Methods: In this retrospective cohort study, we analyzed baseline characteristics, outcomes, and treatment-related adverse events from locally advanced BCC. The patients were divided into two cohorts: 39 laBCC or multiple BCC patients and 7 patients with G-G Syn who were treated with vismodegib from November 2012 till January 2021. Results: During 100-month period, 46 patients were diagnosed with laBCC (26), multiple BCC (13), and G-G Syn (7), all inappropriate for surgery or radiotherapy. Baseline characteristics: median age was 72.8 years in laBCC + multiple BCC cohort and 47.4 years in G-G Syn cohort. The objective response rate was 80% in laBCC + multiple BCC and 86% in G-G Syn cohort. Disease control rate (DCR) was 95% in laBCC + multiple BCC and 100% in G-G Syn cohort. Median duration of treatment was 9.9 months (range: 1.5-43.1) in laBCC and multiple BCC cohort and 19.5 months (range: 3.6-94.1) in G-G Syn cohort. Majority of treatment-emergent adverse events (TEAEs) in laBCC or multiple BCC cohort were grade 1 or 2 (96%), only 4% of AEs were grade 3. Majority of TEAEs in G-G Syn cohort were also grade 1 or 2 (87%), 13% of AEs were grade 3. No grade 4 or 5 vismodegib-related AEs were reported. Conclusion: Vismodegib has shown meaningful efficacy with DCR from 95% to 100% in patients with laBCC, multiple BCC, and G-G Syn in Slovenia. TEAEs were successfully alleviated with multidisciplinary approach and early supportive care.
Ključne besede: basal cell carcinoma, early supportive care, Gorlin Goltz syndrome, multidisciplinary approach
Objavljeno v DiRROS: 07.09.2022; Ogledov: 430; Prenosov: 203
.pdf Celotno besedilo (448,27 KB)
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8.
Combined effects of early season leaf removal and climatic conditions on aroma precursors in Sauvignon blanc grapes
Paolo Sivilotti, Branka Škvarč, Lorena Butinar, Melita Sternad Lemut, Klemen Lisjak, Andreja Vanzo, 2017, izvirni znanstveni članek

Povzetek: Early leaf removal around the cluster zone is a common technique applied in cool climate viticulture, to regulate yield components and improve fruit quality. Despite the increasing amount of information on early leaf removal and its impact on total soluble solids, anthocyanins and polyphenols, less is known regarding aroma compounds. In order to verify the hypothesis that defoliation, applied before or after flowering, could impact the biosynthesis of thiol precursors, we performed a two year (2013 and 2014) experiment on Sauvignon blanc. We provided evidence that differential accumulation of thiols precursors in berries is affected by the timing of defoliation and this impact was related to modifications in biosynthetic pathway. Furthermore, the possible interaction between leaf removal treatment and seasonal weather conditions, and its effect on the biosynthesis of volatile precursors are discussed. Our results suggested that in Sauvignon blanc the relative proportion of 4-S-glutathionyl-4-methylpentan-2-one (G-4MSP) and 3-S-glutathionylhexan-1-ol (G-3SH) precursors can be affected by defoliation, and this could be related to the induction of two specific genes encoding glutathione-S-transferases (VvGST3 and VvGST5), while no significant effects on basic fruit chemical parameters, polyphenols and methoxypyrazines were ascertained under our experimental conditions.
Ključne besede: early leaf removal, cluster exposure, thiol precursors, methoxypyrazines, Vitis vinifera
Objavljeno v DiRROS: 06.09.2022; Ogledov: 422; Prenosov: 186
URL Povezava na celotno besedilo

9.
COVID-19 pandemic impact on cytopathology practice in the post-lockdown period : an international, multicenter study
Elena Vigliar, Pasquale Pisapia, Filippo Dello Iacovo, Izidor Kern, William C. Faquin, Martha Bishop Pitman, 2022, izvirni znanstveni članek

Povzetek: Background. In a previous worldwide survey, the authors showed a drastic reduction in the number of cytological specimens processed during the coronavirus disease 2019 “lockdown” period along with an increase in malignancy rates. To assess the continued impact of the pandemic on cytological practices around the world, they undertook a second follow-up worldwide survey collecting data from the post-lockdown period (2020). Methods. Participants were asked to provide data regarding their cytopathology activity during the first 12 weeks of their respective national post-lockdown period (2020), which ranged from April 4 to October 31. Differences between the post-lockdown period and the corresponding 2019 period were evaluated, and the authors specifically focused on rates of malignant diagnoses. Results. A total of 29 respondents from 17 countries worldwide joined the survey. Overall, a lower number of cytological specimens (n = 236,352) were processed in comparison with the same period in 2019 (n = 321,466) for a relative reduction of 26.5%. The overall malignancy rate showed a statistically significant increase (12,442 [5.26%] vs 12,882 [4.01%]; P < .001) during the same time period. Similar results were obtained if both malignancy and suspicious for malignancy rates were considered together (15,759 [6.58%] vs 16,011 [4.98%]; P < .001). Conclusions. The data showed a persistent reduction in the cytological specimen volume during the post-lockdown period (2020). However, the relative increase in the cytological workload in the late part of the post-lockdown is a promising finding of a slow return to normality.
Ključne besede: covid-19, neoplasms, early detection of cancer, lung -- pathology -- cytology, diagnostic screening programs, fine-needle biopsy, cytopathology, fine-needle aspiration, malignancy rate
Objavljeno v DiRROS: 07.02.2022; Ogledov: 761; Prenosov: 240
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10.
Zgodnje odkrivanje raka dojk
T... Kumar, 1994, objavljeni znanstveni prispevek na konferenci

Ključne besede: Diagnosis early
Objavljeno v DiRROS: 14.05.2021; Ogledov: 876; Prenosov: 241
.pdf Celotno besedilo (424,33 KB)

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