41. Host range and symptomatology of Pepino mosaic virus strains occurring in EuropeDag-Ragnar Blystad, René van der Vlugt, Ana Alfaro-Fernández, María del Carmen Córdoba, Gábor Bese, Dimitrinka Hristova, Henryk Pospieszny, Nataša Mehle, Maja Ravnikar, Laura Tomassoli, Christina Varveri, Steen Lykke Nielsen, 2015, original scientific article Abstract: Pepino mosaic virus (PepMV) has caused great concern in the greenhouse tomato industry after it was found causing a new disease in tomato in 1999. The objective of this paper is to investigate alternative hosts and compare important biological characteristics of the three PepMV strains occurring in Europe when tested under different environmental conditions. To this end we compared the infectivity and symptom development of three, well characterized isolates belonging to three different PepMV strains, EU-tom, Ch2 and US1, by inoculating them on tomato, possible alternative host plants in the family Solanaceae and selected test plants. The inoculation experiments were done in 10 countries from south to north in Europe. The importance of alternative hosts among the solanaceous crops and the usefulness of test plants in the biological characterization of PepMV isolates are discussed. Our data for the three strains tested at 10 different European locations with both international and local cultivars showed that eggplant is an alternative host of PepMV. Sweet pepper is not an important host of PepMV, but potato can be infected when the right isolate is matched with a specific cultivar. Nicotiana occidentalis 37B is a useful indicator plant for PepMV studies, since it reacts with a different symptomatology to each one of the PepMV strains.
Keywords: Pepino mosaic virus, potexvirus, strains, host plants, test plants
Published in DiRROS: 26.07.2024; Views: 50; Downloads: 33
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42. BioMinerJoachim Selbig, Kristina Gruden, Michal Or-Guil, Christian Schichor, Chris Bauer, Karol Stec, Alexander Glintschert, Johannes Schuchhardt, 2015, original scientific article Abstract: 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.
Keywords: data mining, multiomics data integration, biomarker detection, pathway visualization, personalized medicine, cancer
Published in DiRROS: 26.07.2024; Views: 55; Downloads: 39
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43. Survey results on nucleic acid tests of infectious diseases : present status and need for rapid and near-patient diagnosticsJörg Neukammer, Martin Hussels, Andreas Kummrow, Alison S. Devonshire, Carole A. Foy, Jim F. Huggett, Helen C. Parkes, Jana Žel, Mojca Milavec, Heinz Schimmel, Wolfgang Unger, Müslüm Akgöz, Timothy D. McHugh, Viktorija Tomič, Hans-Peter Grunert, Heinz Zeichhardt, 2015, original scientific article Abstract: This survey discusses current and emerging isothermal and rapid polymerase chain reaction (PCR) based nucleic acid amplification methods for near-patient diagnostics.
To assess the clinical need of rapid diagnostics for infectious diseases based on nucleic acid tests (NATs) we performed and analysed a questionnaire among laboratories participating in corresponding INSTAND ring trials for external quality assurance. The questions concerning new amplification technologies like isothermal nucleic acid amplification, potentially suited to significantly decrease turnaround times, were complemented by questions to evaluate the present status of NATs. Besides end-users, companies were also addressed by sending out a manufacturer specific questionnaire.
Analysis of the answers from 48 laboratories in 14 European countries revealed that a much shorter turnaround time is requested for selected pathogens compared to about 2 h or longer when applying temperature cycling amplification, i.e. PCR. In this context, most frequently mentioned were methicillin-resistant Staphylococcus aureus (MRSA), norovirus, influenza A and B viruses, cytomegalovirus (CMV) as well as hepatitis B virus (HBV) and hepatitis C virus (HCV). At present, 8% of the laboratories having participated in this survey apply isothermal amplification of nucleic acids to identify infectious pathogens.
Keywords: nucleic acid tests, infectious diseases, virus detection, bacteria detection, isothermal nucleic acid amplification, status report, questionnaire, NAT, PCR
Published in DiRROS: 26.07.2024; Views: 56; Downloads: 31
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44. Using lidar data to analyse sinkhole characteristics relevant for understory vegetation under forest cover-case study of a high karst area in the Dinaric mountainsMilan Kobal, Irena Bertoncelj, Francesco Pirotti, Igor Dakskobler, Lado Kutnar, 2015, original scientific article Abstract: 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.
Keywords: sinkholes, geomorphology, vegetation
Published in DiRROS: 26.07.2024; Views: 60; Downloads: 32
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45. Rak neznanega izvora : nas izvor bolezni še zanimaErika Matos, Snežana Pavlović Djokić, Srdjan Novaković, Marina Čakš, Rok Devjak, Nežka Hribernik, Kaja Cankar, 2024, professional article Abstract: Rak neznanega izvora (RNI) je opredeljen kot karcinom ali nediferencirana neoplazma, pri kateri z naborom standardnih diagnostičnih postopkov ni mogoče odkriti izvornega mesta bolezni. Tradicionalno RNI delimo v dve podskupini, pri čemer le približno 15 % primerov predstavlja prognostično ugodno skupino. Velika večina bolnikov spada v prognostično neugodno skupino in ima ob prvi prezentaciji obsežno breme bolezni. Možnosti zdravljenja so omejene, izidi bolnikov, zdravljenih z empirično kemoterapijo (KT) s platino ali taksani, pa so še vedno slabi, srednje celokupno preživetje je manj kot 10 mesecev. Za mnoge bolnike ostaja optimalna izbira najboljše možno podporno zdravljenje. Novi pristopi k obravnavi teh bolnikov se zdijo obetavni in so temeljit premik v paradigmi zdravljenja RNI; od zdravljenja, specifičnega za organ/tkivo, k zdravljenju, usmerjenemu na posameznega bolnika, ki temelji na genomskih spremembah njegovega tumorja. Prispevek povzema trenutne dokaze o uporabi vsakega od teh pristopov. Predstavljeno je tudi zdravljenje treh bolnikov z neugodnim RNI.
Keywords: rak neznanega izvora, molekularne značilnosti, biološki označevalci
Published in DiRROS: 26.07.2024; Views: 63; Downloads: 16
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46. Methacrylate monolith chromatography as a tool for waterborne virus removalNejc Rački, Petra Kramberger, Andrej Steyer, Jernej Gašperšič, Aleš Štrancar, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2015, original scientific article Abstract: 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.
Keywords: monolith chromatography, waterborne, virus, removal, wastewater, qPCR
Published in DiRROS: 26.07.2024; Views: 47; Downloads: 20
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47. Onkološko zdravstveno svetovanje na daljavoAleksandra Grbič, Dajana Glavan, Sara Brodarič, Irena Oblak, 2024, review article Abstract: Izhodišče: V začetku leta 2023 smo v okviru klicnega centra vzpostavili zdravstveno svetovanje z namenom opolnomočenja in podpore bolnikov ter njihovih bližnjih. V raziskavi smo analizirali pogostost in stopnjo pojavljanja simptomov, povezanih z boleznijo in zdravljenjem, z uporabo ocenjevalnega protokola in nadaljnjih napotitev glede na izraženost težav.
Metode: Izvedena je bila retrospektivna analiza telefonskih klicev na linijo zdravstvenega svetovanja v klicnem centru od 1. 10. 2023 do 31. 1. 2024. Za zbiranje podatkov o klicateljih je bilo potrjeno in uporabljeno ocenjevalno orodje v podatkovni bazi Redcap. Za izračun odstotnih deležev smo uporabili program Microsoft® Excel® for Office 365 in opisno statistiko.
Rezultati: Vzorec je vključeval 144 telefonskih klicev, kar je predstavljalo 60 % telefonskih klicev bolnikov in 39 % klicev bol-nikovih bližnjih. Vzrok telefonskih klicev je bil v 60,4 % posledica neželenih učinkov sistemskega zdravljenja, ki so bili najpogostejši do tedna dni od prejetja zadnjega zdravljenja. V analizi telefon-skih klicev so bili najpogosteje izraženi simptomi bolečina (10 %), slabost (10 %), izguba apetita (7 %), driska (7 %). Na podlagi tega je bilo izvedenih 144 zdravstvenih svetovanj, 87 napotitev na osebnega zdravnika ali lečečega onkologa in 14 napotitev na nujno medicinsko pomoč.
Zaključek: Zdravstveno svetovanje na daljavo je treba uporabiti kot priložnost za zagotavljanje dostopnosti do informacij in pravo-časne zdravstvene oskrbe prek informacijskih in telekomunikacij-skih sistemov, saj vpliva na spodbujanje samooskrbe, zmanjšanje števila hospitalizacij, znižanje stroškov zdravstvene oskrbe in nenazadnje na kakovost življenja onkoloških bolnikov.
Keywords: zdravstveno svetovanje, oddaljen dostop, ocenjevalni triažni protokol
Published in DiRROS: 26.07.2024; Views: 42; Downloads: 13
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48. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevinePolona Kogovšek, Jennifer Hodgetts, J. Hall, Nina Prezelj, Petra Nikolić, Nataša Mehle, Rok Lenarčič, Ana Rotter, M. Dickinson, Neil Boonham, Marina Dermastia, Maja Ravnikar, 2015, original scientific article Abstract: 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.
Keywords: flavescence dorée, homogenization, loop-mediated isothermal amplification, on-site application, validation
Published in DiRROS: 26.07.2024; Views: 54; Downloads: 48
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49. Načrt središča za Jugovzhodno EvropoYannis Fallas, Nikolaos Ntavos, Panagiotis Karagiannis, Dimitris Tsimplinas, Georgios Ntalos, Polona Hafner, Andreja Vedenik, Jožica Gričar, Iva Božić, Danijela Šarić Bartolović, Ivan Ambroš, 2024, treatise, preliminary study, study Keywords: transport lesa, dobre prakse, inovacije, trajnost
Published in DiRROS: 26.07.2024; Views: 62; Downloads: 2 |
50. Ocena pridobljenih let življenja v populacijskih presejalnih programih za rakaVesna Zadnik, Maja Pohar Perme, Tina Žagar, Bor Vratanar, Katja Jarm, Katarina Lokar, Maja Jurtela, Sonja Tomšič, 2024, professional article Abstract: 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.
Keywords: presejalni programi, kakovost, register raka
Published in DiRROS: 26.07.2024; Views: 47; Downloads: 12
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