1. DINCAE 1.0 : a convolutional neural network with error estimates to reconstruct sea surface temperature satellite observationsAlexander Barth, Aida Alvera-Azcárate, Matjaž Ličer, Jean-Marie Beckers, 2020, izvirni znanstveni članek Povzetek: A method to reconstruct missing data in sea surface temperature data using a neural network is presented. Satellite observations working in the optical and infrared bands are affected by clouds, which obscure part of the ocean underneath. In this paper, a neural network with the structure of a convolutional auto-encoder is developed to reconstruct the missing data based on the available cloud-free pixels in satellite images. Contrary to standard image reconstruction with neural networks, this application requires a method to handle missing data (or data with variable accuracy) in the training phase. The present work shows a consistent approach which uses the satellite data and its expected error variance as input and provides the reconstructed field along with its expected error variance as output. The neural network is trained by maximizing the likelihood of the observed value. The approach, called DINCAE (Data INterpolating Convolutional Auto-Encoder), is applied to a 25-year time series of Advanced Very High Resolution Radiometer (AVHRR) sea surface temperature data and compared to DINEOF (Data INterpolating Empirical Orthogonal Functions), a commonly used method to reconstruct missing data based on an EOF (empirical orthogonal function) decomposition. The reconstruction error of both approaches is computed using cross-validation and in situ observations from the World Ocean Database. DINCAE results have lower error while showing higher variability than the DINEOF reconstruction.
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2. One-step reverse-transcription digital PCR for reliable quantification of different pepino mosaic virus genotypesNataša Mehle, Larisa Gregur, Alexandra Bogožalec Košir, David Dobnik, 2020, izvirni znanstveni članek Povzetek: In recent years, pepino mosaic virus (PepMV) has rapidly evolved from an emerging virus to an endemic pathogen, as it causes significant loses to tomato crops worldwide. At present, the main control strategy for prevention of PepMV disease in tomato production remains based on strict hygiene measures. To prevent damage caused by PepMV, cross-protection is used in some countries. Reliable characterisation, detection and quantification of the pathogen are vital for disease control. At present, reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) is generally used for this purpose. However, quantitative use of RT-qPCR is linked to standardised reference materials, which are not available for PepMV. In addition, many factors can influence RT-qPCR efficiencies and lead to lower accuracy of the quantification. In this study, well-characterised PepMV-genotype-specific RT-qPCR assays were transferred to two digital PCR (dPCR) platforms. dPCR-based assays allow absolute quantification without the need for standard curves, and due to the binary nature of the reaction, dPCR also overcomes many of the other drawbacks of RT-qPCR. We have shown that these newly developed and validated PepMV-genotype-specific dPCR assays are suitable candidates for higher-order methods for quantification of PepMV RNA, as they show lower measurement variability, with sensitivity and specificity comparable to RT-qPCR.
Ključne besede: digital PCR, pepino mosaic virus, quantification, genotype specific
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3. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environmentKatarina Bačnik, Denis Kutnjak, Anja Pecman, Nataša Mehle, Magda Tušek-Žnidarič, Ion Gutiérrez-Aguirre, Maja Ravnikar, 2020, izvirni znanstveni članek Povzetek: Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation.
Ključne besede: wastewater, virome, high-throughput sequencing, plant viruses, tobamoviruses, infectivity
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4. Cancer-related fatigue : causes and current treatment optionsMelissa S. Y. Thong, Cornelis J. F. van Noorden, Karen Steindorf, Volker Arndt, 2020, izvirni znanstveni članek Povzetek: Fatigue is a symptom commonly experienced by survivors of cancer through all stages of the disease trajectory. Survivors identify fatigue as a significant problem which is not adequately addressed by healthcare providers [1•]. Being fatigued has a greater negative impact on functioning and health-related quality of life (HRQoL) than other symptoms such as pain or depression [2, 3]. Fatigued survivors are more likely to have reduced employment participation [4, 5], greater financial stress [6], and higher healthcare utilization [6, 7]. Moreover, fatigue may reduce survival; feeling fatigued at diagnosis [6, 8] and during survivorship [9] is associated with higher mortality.
This review aims to provide a summary on the current state of research on cancer-related fatigue (CRF) of survivors with local disease treated with curative intent. We briefly summarize the prevalence, definition, evaluation, and etiology of CRF. Due to the volume of research on CRF treatments, we provide a non-exhaustive overview of treatments for CRF published within the last 5 years (guidelines, meta-analyses, reviews, randomized trials).
Ključne besede: cancer-related fatigue, cytokines, physical activity, pharmacologic, complementary and alternative medicine
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5. Physical activity and cancer risk. Actual knowledge and possible biological mechanismsMihaela Jurdana, 2021, pregledni znanstveni članek Povzetek: Scientific evidence has shown that an increase in regular physical activity is associated with a decrease in the development of many types of cancer. Potential mechanisms that link physical activity to reduced cancer risk include a decrease in systemic inflammation, hyperinsulinemia, insulin-like growth factor (IGF-I), sex hormones, pro-inflammatory leptin and other obesity-related cytokines, and a significant increase in anti-inflammatory adiponectin levels. In addition, physical activity improves immune function and the composition and diversity of the gastrointestinal microbiota. Moderate physical activity is important for cancer protection, but the most significant changes in the inflammatory profile are conferred by physical activity performed at higher intensities. Thus, there is a need for further investigation into the type, intensity, and duration of physical activity for the prevention of some types of cancer and the development of effective recommendations.
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6. PLANiTS : a curated sequence reference dataset for plant ITS DNA metabarcodingElisa Banchi, Claudio Gennaro Ametrano, Samuele Greco, David Stanković, Lucia Muggia, Alberto Pallavicini, 2020, izvirni znanstveni članek Povzetek: DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering.
Ključne besede: DNA metabarcoding, reference datasets
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8. Experimental evidence of long-term oceanic circulation reversals without wind influence in the North Ionian SeaAngelo Rubino, Miroslav Gačić, Manuel Bensi, Vedrana Kovacevic, Vlado Malačič, Milena Menna, Maria Eletta Negretti, Joel Sommeria, Davide Zanchettin, Ricardo V. Barreto, Laura Ursella, Vanessa Cardin, Giuseppe Civitarese, Mirko Orlić, Boris Petelin, Giuseppe Siena, 2020, izvirni znanstveni članek Povzetek: Under the emerging features of interannual-to-decadal ocean variability, the periodical reversals of the North Ionian Gyre (NIG), driven mostly by the mechanism named Adriatic-Ionian Bimodal Oscillating System (BiOS), are known as impacting on marine physics and biogeochemistry and potentially influencing short-term regional climate predictability in the Eastern Mediterranean. Whilst it has been suggested that local wind forcing cannot explain such variability, aspects of the alternative hypothesis indicating that NIG reversals mainly arises from an internal ocean feedback mechanism alone remain largely debated. Here we demonstrate, using the results of physical experiments, performed in the world’s largest rotating tank and numerical simulations, that the main observed feature of BiOS, i.e., the switch of polarity of the near-surface circulation in the NIG, can be induced by a mere injection of dense water on a sloping bottom. Hence, BiOS is a truly oceanic mode of variability and abrupt polarity changes in circulation can arise solely from extreme dense water formation events.
Ključne besede: physical oceanography, climate and Earth system modelling
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9. The performance of the Xpert Bladder Cancer Monitor Test and voided urinary cytology in the follow-up of urinary bladder tumorsTomaž Smrkolj, Urška Čegovnik Primožič, Teja Fabjan, Saša Šterpin, Joško Osredkar, 2021, izvirni znanstveni članek Povzetek: Background: Cystoscopy in complement with urinary cytology represents the gold standard for the follow-up of patients with urinary bladder tumours. Xpert Bladder Cancer Monitor Test (XBC) is a novel mRNA-based urine test for bladder cancer surveillance. The aim of the study was to evaluate the performance of the XBC and voided urinary cytology (VUC) in the follow-up of bladder tumours. Patients and methods. The XBC was performed on stabilized voided urine and VUC was performed on urine samples. The results were compared to cystoscopic findings and histopathological results after transurethral resection of the bladder lesion. Results. For the prediction of malignant histopathological result sensitivity, the specificity and negative predictive value were 76.9%, 97.5% and 93.0% for the XBC and 38.4%, 97.5% and 83.3%, respectively for VUC. For the prediction of suspicious or positive cystoscopic finding sensitivity, the specificity and negative predictive value were 75.0%, 95.2%, and 93.0% respectively for the XBC and 41.7%, 97.6%, and 85.4% for VUC. The sensitivities for papilary urothelial neoplasms of low malignant potential (PUNLMP), low- and high-grade tumours were 0.0%, 66.7% and 100.0% for the XBC and 0.0%, 66.7% and 42.9%, respectively for VUC. Conclusions: The XBC showed significantly higher overall sensitivity and negative predictive value than VUC and could be used to increase the recommended follow-up cystoscopy time intervals. Complementing the XBC and voided urinary cytology does not improve performance in comparison to the XBC alone.
Ključne besede: cystoscopy, Xpert BC monitor test, urinary bladder neoplasm, voided urinary cytology
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10. Long term results of follow-up after HPV self-sampling with devices Qvintip and HerSwab in women non-attending cervical screening programmeTeodora Bokan, Urška Ivanuš, Tine Jerman, Iztok Takač, Darja Arko, 2021, izvirni znanstveni članek Povzetek: We are presenting the results of the Slovenian human papillomaviruses (HPV) self-sampling pilot study in colposcopy population of National Cervical Cancer Screening Programme ZORA for the first time. One-year and four-year follow-up results are presented for two different self-sampling devices. Participants and methods. A total of 209 women were enrolled in the study at colposcopy clinic. Prior to the gynaecological examination, all women performed self-collected vaginal swab at the clinic; 111 using Qvintip and 98 using HerSwab self-sampling device. After self-sampling, two cervical smears were taken by a clinician; first for conventional cytology and second for HPV test. After that, all women underwent colposcopy and a cervical biopsy if needed. We compared sensitivity, specificity, and predictive values of cytology (at the cut-off atypical squamous cells of undetermined significance or more [ASC-US+]) and HPV test (on self- and clinician-taken samples) for the detection of cervical intraepithelial neoplasia grade 2 or more (CIN2+) after one and four years of follow-up. Hybrid Capture 2 (HC2) assay was used for all HPV testing. Results. The mean age of 209 women was 37.6 years and HPV positivity rate 67.0% (140/209), 36.9 years and 70.3% (78/111) in the Qvintip group and 38.4 years and 63.3% (62/98) in the HerSwab group, respectively. Overall, percent agreement between self and clinician-taken samples was 81.8% (kappa 0.534) in the Qvintip and 77.1% (kappa 0.456) in the HerSwab group. In the Qvintip group, the longitudinal sensitivity, specificity, positive and negative predictive values were 71.8%, 75.0%, 83.6%, 60.0% for cytology; 83.1%, 51.3%, 75.6% and 62.5% for HPV test of self-taken samples and 94.4%, 57.5%, 79.8% and 85.2% for HPV test on clinician-taken samples. In the HerSwab group, the corresponding results were 71.7%, 46.7%, 61.3%, 58.3% for cytology; 75.0%, 47.7%, 62.9% and 61.8% for HPV test on self-taken samples and 94.3%, 44.4%, 66.7% and 87.0% for clinician-taken samples, respectively. Conclusions. The results confirm that HPV self-sampling is not as accurate as clinician sampling when HC2 is used. All HPV tests showed a higher sensitivity in detecting CIN2+ compared to cytology. Due to non-inferior longitudinal sensitivity of HPV self-sampling compared to cytology, HPV self-sampling might be an option for non-attenders to the National Cancer Screening Programme.
Ključne besede: HPV self-sampling, cytology, high-grade intraepithelial lesion, screening programmes
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