421. Detection and localization of hyperfunctioning parathyroid glands on [18F]fluorocholine PET/CT using deep learning – model performance and comparison to human expertsLeon Jarabek, Jan Jamšek, Anka Cuderman, Sebastijan Rep, Marko Hočevar, Tomaž Kocjan, Mojca Jensterle Sever, Žiga Špiclin, Žiga Maček Ležaić, Filip Cvetko, Luka Ležaič, 2022, original scientific article Abstract: In the setting of primary hyperparathyroidism (PHPT), [18F]fluorocholine PET/CT (FCH-PET) has excellent diagnostic performance, with experienced practitioners achieving 97.7% accuracy in localising hyperfunctioning parathyroid tissue (HPTT). Due to the relative triviality of the task for human readers, we explored the performance of deep learning (DL) methods for HPTT detection and localisation on FCH-PET images in the setting of PHPT. Patients and methods. We used a dataset of 93 subjects with PHPT imaged using FCH-PET, of which 74 subjects had visible HPTT while 19 controls had no visible HPTT on FCH-PET. A conventional Resnet10 as well as a novel mPETResnet10 DL model were trained and tested to detect (present, not present) and localise (upper left, lower left, upper right or lower right) HPTT. Our mPETResnet10 architecture also contained a region-of-interest masking algorithm that we evaluated qualitatively in order to try to explain the model’s decision process. Results. The models detected the presence of HPTT with an accuracy of 83% and determined the quadrant of HPTT with an accuracy of 74%. The DL methods performed statistically worse (p < 0.001) in both tasks compared to human readers, who localise HPTT with the accuracy of 97.7%. The produced region-of-interest mask, while not showing a consistent added value in the qualitative evaluation of model’s decision process, had correctly identified the foreground PET signal. Conclusions. Our experiment is the first reported use of DL analysis of FCH-PET in PHPT. We have shown that it is possible to utilize DL methods with FCH-PET to detect and localize HPTT. Given our small dataset of 93 subjects, results are nevertheless promising for further research Keywords: primary hyperparathyroidism, deep learning, nuclear medicine Published in DiRROS: 25.07.2024; Views: 258; Downloads: 89
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423. Real-world outcomes, treatment patterns and T790M testing rates in non-small cell lung cancer patients treated with first-line first- or second-generation epidermal growth factor receptor tyrosine kinase inhibitors from the Slovenian cohort of the REFLECT studyNina Turnšek, Rok Devjak, Natalija Edelbaher, Ilonka Osrajnik, Mojca Unk, Dušanka Vidovič, Tina Jerič, Urška Janžič, 2022, original scientific article Abstract: Background. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective treatments for EGFR mutation-positive (EGFRm) non-small cell lung cancer (NSCLC). However, routine clinical practice is different between countries/institutions. Patients and methods. The REFLECT study (NCT04031898) is a retrospective medical chart review that explored real-life treatment and outcomes of EGFRm NSCLC patients receiving first-line (1L) first-/second-generation (1G/2G) EGFR TKIs in 8 countries. This study included adult patients with documented advanced/metastatic EGFRm NSCLC with 1L 1G/2G EGFR TKIs initiated between Jan 2015 – Jun 2018. We reviewed data on clinical characteristics, treatments, EGFR/T790M testing patterns, and survival outcomes. Here, we report data from 120 medical charts in 3 study sites from Slovenia. Results. The Slovenian cohort (median age 70 years, 74% females) received 37% erlotinib, 32% afatinib, 31% gefitinib. At the time of data collection, 94 (78%) discontinuations of 1L TKI, and 89 (74%) progression events on 1L treatment were reported. Among patients progressing on 1L, 73 (82%) were tested for T790M mutation yielding 50 (68%) positive results, and 62 (85%) received 2L treatment. 82% of patients received osimertinib. Attrition rate between 1L and 2L was 10%. The median (95% CI) real-world progression free survival on 1L EGFR TKIs was 15.6 (12.6, 19.2) months; median overall survival (95% CI) was 28.9 (25.0, 34.3) months. Conclusions. This real-world study provides valuable information about 1G/2G EGFR TKIs treatment outcomes and attrition rates in Slovenian EGFRm NSCLC patients. The reduced attrition rate and improved survival outcomes empha-size the importance of 1L treatment decision. Keywords: real-world study, non-small cell lung cancer, epidermal growth factor receptor, lung cancer Published in DiRROS: 25.07.2024; Views: 122; Downloads: 59
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425. Early isolated subarachnoid hemorrhage versus hemorrhagic infarction in cerebral venous thrombosisJan Kobal, Ksenija Cankar, Kristijan Ivanušič, Borna Vudrag, Katarina Šurlan Popović, 2022, original scientific article Abstract: Background: Cerebral venous thrombosis (CVT) is a rare cerebral vascular disease, the presentation of which is highly variable clinically and radiologically. A recent study demonstrated that isolated subarachnoid hemorrhage (iSAH) in CVT is not as rare as thought previously and may have a good prognostic significance. Hemorrhagic venous infarction, however, is an indicator of an unfavorable outcome. We therefore hypothesized that patients who initially suffered iSAH would have a better clinical outcome than those who suffered hemorrhagic cerebral infarction. Patients and methods: We selected patients hospitalized due to CVT, who presented either with isolated SAH or cerebral hemorrhagic infarction at admission or during the following 24 hours: 23 (10 men) aged 22-73 years. The data were extracted from hospital admission records, our computer data system, and the hospital radiological database. Results: The iSAH group consisted of 8 (6 men) aged 49.3 ± 16.2 and the hemorrhagic infarction group included 15 (4 men) aged 47.9 ± 16.8. Despite having a significantly greater number of thrombosed venous sinuses/deep veins (Mann-Whitney Rank Sum Test, p = 0.002), the isolated SAH group had a significantly better outcome on its modified Rankin Score (mRs) than the hemorrhagic infarction group (Mann-Whitney Rank Sum Test, p = 0.026). Additional variables of significant impact were edema formation (p = 0.004) and sulcal obliteration (p = 0.014). Conclusions: The patients who suffer iSAH initially had a significantly better outcome prognosis than the hemorrhagic infarction patients, despite the greater number of thrombosed sinuses/veins in the iSAH group. A possible explanation might include patent superficial cerebral communicating veins. Keywords: cerebral venous thrombosis, hemorrhagic brain infarction, subarachnoid hemorrhage Published in DiRROS: 25.07.2024; Views: 150; Downloads: 91
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426. Novel ▫$TiO_2$▫-supported gold nanoflowers for efficient photocatalytic ▫$NO_x$▫ abatementŠpela Slapničar, Gregor Žerjav, Janez Zavašnik, Matevž Roškarič, Matjaž Finšgar, Albin Pintar, 2024, original scientific article Abstract: t: In this study, we pioneered the synthesis of nanoflower-shaped TiO2 -supported Au photocatalysts and investigated their properties. Au nanoflowers (Au NFs) were prepared by a Na-citrate and hydroquinone-based preparation method, followed by wet impregnation of the derived Au NFs on the surface of TiO2 nanorods (TNR). A uniform and homogeneous distribution of Au NFs was observed in the TNR + NF(0.7) sample (lower Na-citrate concentration), while their distribution was heterogeneous in the TNR + NF(1.4) sample (higher Na-citrate concentration). The UV-Vis DR spectra revealed the size- and shape-dependent optical properties of the Au NFs, with the LSPR effect observed in the visible region. The solid-state EPR spectra showed the presence of Ti3+, oxygen vacancies and electron interactions with organic compounds on the catalyst surface. In the case of the TNR + NF(0.7) sample, high photocatalytic activity was observed in the H2 -assisted reduction of NO2 to N2 at room temperature under visible-light illumination. In contrast, the TNR + NF(1.4) catalyst as well as the heat-treated samples showed no ability to reduce NO2 under visible light, indicating the presence of deformed Au NFs limiting the LSPR effect. These results emphasized the importance of the choice of synthesis method, as this could strongly influence the photocatalytic activity of the Au NFs Published in DiRROS: 25.07.2024; Views: 174; Downloads: 131
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427. The truncated moment problem on curves $y = q(x)$ and $yx^\ell = 1$Aljaž Zalar, 2024, original scientific article Abstract: In this paper, we study the bivariate truncated moment problem (TMP) on curves of the form $y = q(x), q(x) \in \mathbb{R} [x], \deg q ≥ 3$ and $yx^\ell = 1, \ell \in \mathbb{N}$ \ $\{1\}$. For even degree sequences, the solution based on the size of moment matrix extensions was first given by Fialkow [Fialkow L. Solution of the truncated moment problem with variety $y = x^3$. Trans Amer Math Soc. 2011;363:3133–3165.] using the truncated Riesz–Haviland theorem [Curto R, Fialkow L. An analogue of the Riesz–Haviland theorem for the truncated moment problem. J Funct Anal. 2008;255:2709–2731.] and a sum-of-squares representations for polynomials, strictly positive on such curves [Fialkow L. Solution of the truncated moment problem with variety $y = x^3$. Trans Amer Math Soc. 2011;363:3133–3165.; Stochel J. Solving the truncated moment problem solves the moment problem. Glasgow J Math. 2001;43:335–341.]. Namely, the upper bound on this size is quadratic in the degrees of the sequence and the polynomial determining a curve. We use a reduction to the univariate setting technique, introduced in [Zalar A. The truncated Hamburger moment problem with gaps in the index set. Integral Equ Oper Theory. 2021;93:36.doi: 10.1007/s00020-021-02628-6.; Zalar A. The truncated moment problem on the union of parallel lines. Linear Algebra Appl. 2022;649:186–239. doi.org/10.1016/j.laa.2022.05.008.; Zalar A. The strong truncated Hamburger moment problem with and without gaps. J Math Anal Appl. 2022;516:126563. doi: 10.1016/j.jmaa.2022. 126563.], and improve Fialkow’s bound to $\deg q − 1$ (resp. $\ell + 1$) for curves $y = q(x)$ (resp. $yx^\ell = 1$). This in turn gives analogous improvements of the degrees in the sum-of-squares representations referred to above. Moreover, we get the upper bounds on the number of atoms in the minimal representing measure, which are $k \deg q$ (resp. $k(\ell+ 1)$) for curves $y = q(x)$ (resp. $yx^\ell = 1$) for even degree sequences, while for odd ones they are $k \deg q − \bigl \lceil \frac{\deg q}{2} \bigr \rceil$ (resp. $k(\ell + 1) − \bigl \lfloor \frac{\ell}{2} \bigr \rfloor + 1$) for curves $y = q(x)$ (resp. $yx^\ell = 1$). In the even case, these are counterparts to the result by Riener and Schweighofer [Riener C, Schweighofer M. Optimization approaches to quadrature:a new characterization of Gaussian quadrature on the line and quadrature with few nodes on plane algebraic curves, on the plane and in higher dimensions. J Complex. 2018;45:22–54., Corollary 7.8], which gives the same bound for odd degree sequences on all plane curves. In the odd case, their bound is slightly improved on the curves we study. Further on, we give another solution to the TMP on the curves studied based on the feasibility of a linear matrix inequality, corresponding to the univariate sequence obtained, and finally we solve concretely odd degree cases to the TMP on curves $y = x^\ell, \ell = 2, 3,$ and add a new solvability condition to the even degree case on the curve $y = x^2$. Keywords: truncated moment problems, K-moment problems, K-representing measure, minimal measure, moment matrix extensions, positivstellensatz, linear matrix inequality Published in DiRROS: 25.07.2024; Views: 149; Downloads: 130
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428. Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus YDenis Kutnjak, Santiago F. Elena, Maja Ravnikar, 2017, original scientific article Abstract: RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).
IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes. Keywords: Potato virus Y, experimental evolution, genetic drift, natural selection, sRNA deep sequencing Published in DiRROS: 24.07.2024; Views: 171; Downloads: 75
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429. Cucujus cinnaberinus (Scopoli, 1763) at its terra typica in Slovenia : historical overview, distribution patterns and habitat selectionAl Vrezec, Špela Ambrožič Ergaver, Andrej Kobler, Andrej Kapla, Maarten De Groot, 2017, original scientific article Abstract: The saproxylic beetle, Cucujus cinnaberinus, has received increasing research attention in Europe since the adoption of the Habitats Directive and establishment of the Natura 2000 network. The history of the species has been investigated as well as the influence of abiotic and biotic variables on the distribution of C. cinnaberinus in Slovenia which is at the limit of its range and also terra typica for the species. The species was first described in 1763 by Joannes A. Scopoli in Carniola, a duchy of the Habsburg Monarchy. Today, most of the territory of Carniola is situated within Slovenia. C. cinnaberinus is particularly common in the eastern part of the country, but very scarce in the mountainous western part. According to historical and recent distribution patterns of C. cinnaberinus in the former Carniolan territory, the region of Ribnica-Kočevje in southern Slovenia is proposed as the most probable type locality of the species. Although the bulk of the C. cinnaberinus population in Slovenia is confined to the lowlands, the species has been found up to 1095 m a.s.l., albeit at a much lower abundance due to the influence of climate and forest structure. Although C. cinnaberinus is a quite an opportunistic species regarding host tree selection, it has been shown to exhibit a preference for Tilia, Populus and Robinia. It is suspected that the high abundance of C. cinnaberinus in lowland floodplain forests is due to the recent human-induced increase in preferred fast-growing and short-lived host trees, i.e. the planting of poplar trees and spread of invasive Black Locust (Robinia pseudoacacia) after the 1960s. In contrast, in montane forests, preferred host trees (e.g. Tilia) represent < 1 % of all growing stock. Although montane C. cinnaberinus populations are rare, they could still be important for the conservation of the species, since montane habitats cover the largest area within the species’ distribution range. Keywords: saproxylic beetle, Natura 2000, type locality, Carniola, altitudinal distribution, host tree selection, macrohabitat, large-scale survey Published in DiRROS: 24.07.2024; Views: 589; Downloads: 138
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430. Comparison between proteome and transcriptome response in potato (Solanum tuberosum L.) leaves following potato virus Y (PVY) infectionTjaša Stare, Katja Stare, Wolfram Weckwerth, Stefanie Wienkoop, Kristina Gruden, 2017, original scientific article Abstract: Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it. Keywords: proteomics, transcriptomics, potato, potato virus Y Published in DiRROS: 24.07.2024; Views: 183; Downloads: 182
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