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Povzetek: Personalized medicine is promising a revolution for medicine and human biology in the 21st century. The scientific foundation for this revolution is accomplished by analyzing biological high-throughput data sets from genomics, transcriptomics, proteomics, and metabolomics. Currently, access to these data has been limited to either rather simple Web-based tools, which do not grant much insight or analysis by trained specialists, without firsthand involvement of the physician. Here, we present the novel Web-based tool “BioMiner,” which was developed within the scope of an international and interdisciplinary project (SYSTHER†) and gives access to a variety of high-throughput data sets. It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities. BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer. A public instance of BioMiner along with the database is available at http://systherDB.microdiscovery.de/, login and password: “systher”; a tutorial detailing the usage of BioMiner can be found in the Supplementary File.
Ključne besede: data mining, multiomics data integration, biomarker detection, pathway visualization, personalized medicine, cancer
Objavljeno v DiRROS: 26.07.2024; Ogledov: 32; Prenosov: 30
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Povzetek: In this article, we investigate the potential for detection and characterization of sinkholes under dense forest cover by using airborne laser scanning data. Laser pulse returns from the ground provide important data for the estimation of digital elevation model (DEM), which can be used for further processing. The main objectives of this study were to map and determine the geomorphometric characteristics of a large number of sinkholes and to investigate the correlations between geomorphology and vegetation in areas with such characteristics. The selected study area has very low anthropogenic influences and is particularly suitable for studying undisturbed karst sinkholes. The information extracted from this study regarding the shapes and depths of sinkholes show significant directionality for both orientation of sinkholes and their distribution over the area. Furthermore, significant differences in vegetation diversity and composition occur inside and outside the sinkholes, which indicates their presence has important ecological impacts.
Ključne besede: sinkholes, geomorphology, vegetation
Objavljeno v DiRROS: 26.07.2024; Ogledov: 47; Prenosov: 26
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Povzetek: Enteric viruses are commonly present in environmental waters and represent the major cause of waterborne infections and outbreaks. Since traditional wastewater treatments fail to remove enteric viruses in the water purification process, they are released daily into environmental waters. Monolithic supports have enabled chromatography to enter the field of virology. They have been successfully used in virus purification and concentration. In this work quaternary amine (QA) methacrylate monoliths were exploited to remove enteric viruses from wastewater treatment plant effluent. Expectedly, chromatographic processing of such a complex medium was troublesome, even for monoliths, characterized by extremely large pore dimensions. This problem was solved by introducing a pre-step chromatography using hydroxyl (OH) methacrylate monoliths. This way, molecules, that would hinder virus binding to the anion-exchanger monolith, were removed. As a result, the OH pre-column reduced backpressure increase on the subsequent anion-exchanger column, and increased both QA column binding capacity and life time. Wastewater effluent samples were successfully purified from five waterborne enteric viruses (rotavirus, norovirus genogroup I and II, astrovirus, sapovirus), below the detection limit of RT-qPCR. The breakthrough of the rotavirus binding capacity was not reached for concentrations that significantly exceeded those expected in effluent waters. The obtained results confirm that methacrylate monoliths can be a valuable tool for simultaneous removal of different waterborne viruses from contaminated water sources.
Ključne besede: monolith chromatography, waterborne, virus, removal, wastewater, qPCR
Objavljeno v DiRROS: 26.07.2024; Ogledov: 29; Prenosov: 12
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Povzetek: In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
Ključne besede: flavescence dorée, homogenization, loop-mediated isothermal amplification, on-site application, validation
Objavljeno v DiRROS: 26.07.2024; Ogledov: 38; Prenosov: 34
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Povzetek: Zaradi možnih negativnih zdravstvenih posledic presejalnih programov in velikih sredstev, vloženih vanje, je pomembno spremljati njihovo učinkovitost. Umrljivost v ciljni populaciji je eden od kazalnikov, ki služi za prikaz dolgoročne učinkovitosti organiziranih populacijskih presejalnih programov – po 10 do 20 letih se pričakuje padec umrljivosti v ciljni populaciji za 20 % do 30 %. Ena od glavnih omejitev kazalnika umrljivosti je, predvsem pri rakih z dobrim preživetjem, da pokaže učinkovitost presejanja šele v daljšem časovnem obdobju. Mnogokrat se zato za oceno učinkovitosti populacijskih presejalnih programov za raka uporablja analiza preživetja, pri kateri so rezultati dostopni prej. Tudi analiza preživetja ima svoje omejitve, saj se lahko v rezultate prikradejo številne pristranosti (npr. pristranost časa trajanja, prednosti in prediagnosticiranja). Nedavno smo slovenski raziskovalci predlagali nov analitični pristop, ki omogoča primerjavo preživetja pri rakih, ki so oz. niso odkriti v presejalnem programu, z upoštevanjem vseh pomembnih pristranosti. Izračunana preživetja so osnova za izračun pridobljenih let življenja, to je mere, ki izraža dodatno število let življenja, ki bi jih osebe preživele zaradi vključitve v presejalni program.V testnem primeru smo ocenili učinke uvedbe Državnega prese-jalnega program za raka dojk DOR A, ki smo ga prvim prebival-kam ponudili leta 2008, na celotno populacijo pa je bil razširjen leta 2018. Ženske, ki so bile povabljene v program DOR A v obdobju 2008–2018, so do leta 2022 pridobile skupaj 90,6 leta življenja, če bi bile v program DOR A že od leta 2008 vključene vse ženske, pa bi pridobile 552,7 leta življenja. Z vsakim dodatnim letom opazovanja, ko posamezne ženske od vključitve v program DOR A preživijo, se seštevek pridobljenih let življenja poveča.Nova metoda bo v pomoč pri upravljanju obstoječih presejalnih programov za raka, njihovi promociji in vrednotenju učinkov pri spremembah presejalnih politik.
Ključne besede: presejalni programi, kakovost, register raka
Objavljeno v DiRROS: 26.07.2024; Ogledov: 28; Prenosov: 7
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