1. 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: 109; Downloads: 92
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2. Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCRPolona Kogovšek, Nataša Mehle, Anja Pugelj, Tjaša Jakomin, Hans-Josef Schroers, Maja Ravnikar, Marina Dermastia, 2017, original scientific article Abstract: A fluorescence-based real-time loop-mediated isothermal amplification (LAMP) assay for ‘Candidatus Phytoplasama solani’ (Bois noir phytoplasma; BNp) detection was developed and optimised for rapid laboratory and on-site BNp detection. This assay is highly specific, rapid and as sensitive as qPCR. It was validated according to European and Mediterranean Plant Protection Organisation recommendations. In addition, 286 grapevine leaf samples from the 2015 growing season were tested with this new real-time LAMP assay and an assay previously developed for detection of Flavescence dorée phytoplasma (FDp). These LAMP assays for detection of both BNp and FDp used without any DNA extraction step, which is a required step for qPCR analysis, were comparably effective to qPCR, and positive results were obtained in less than 35 min.
Keywords: real-time LAMP, grapevine yellows phytoplasma, validation
Published in DiRROS: 24.07.2024; Views: 122; Downloads: 90
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3. Status and trends in the rate of introduction of marine non-indigenous species in European seasArgyro Zenetos, Konstantinos Tsiamis, Marika Galanidi, Natacha Carvalho, Cátia Bartilotti, Borut Mavrič, Martina Orlando-Bonaca, 2022, original scientific article Abstract: nvasive alien species are a major worldwide driver of biodiversity change. The current study lists verified records of non-indigenous species (NIS) in European marine waters until 2020, with the purpose of establishing a baseline, assessing trends, and discussing appropriate threshold values for good environmental status (GES) according to the relevant European legislation. All NIS records were verified by national experts and trends are presented in six-year assessment periods from 1970 to 2020 according to the European Union Marine Strategy Framework Directive. Altogether, 874 NIS have been introduced to European marine waters until 2020 with the Mediterranean Sea and North-East Atlantic Ocean hosting most of the introductions. Overall, the number of new introductions has steadily increased since 2000. The annual rate of new introductions reached 21 new NIS in European seas within the last six-year assessment period (2012–2017). This increase is likely due to increased human activities and research efforts that have intensified during the early 21st century within European Seas. As Europe seas are not environmentally, nor geographically homogenous, the setting of threshold values for assessing GES requires regional expertise. Further, once management measures are operational, pathway-specific threshold values would enable assessing the effectiveness of such measures.
Keywords: non-indigenous species, European seas, regional seas, MSFD, good environmental status, validation, uncertainties
Published in DiRROS: 18.07.2024; Views: 119; Downloads: 159
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4. What did we achieve with VALITEST an EU project on validation in plant pest diagnostics?Charlotte Trontin, Barbara Agstner, Denise Altenbach, Géraldine Anthoine, Hanna Baginska, Ian Brittain, A Chabirand, Anne-Marie Chappé, P. Dahlin, Tanja Dreo, C. Freye-Minks, Camilo Gianinazzi, Catherine Harrison, Glyn Jones, Marco Stefan Kaiser, Marta Luigi, Sébastien Massart, Nataša Mehle, Monica Mezzalama, Hanna Mouaziz, Maja Ravnikar, Tom Raaymakers, Jean-Philippe Renvoise, Mathieu Rolland, Marta Santos, Sam Seddas, René van der Vlugt, Ana Vučurović, Françoise Petter, 2022, original scientific article Keywords: plant pest diagnostics, validation, test performance study, high-throughput, sequencing, reference material, training
Published in DiRROS: 17.07.2024; Views: 111; Downloads: 54
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5. Validated inventories of non-indigenous species (NIS) for the Mediterranean Sea as tools for regional policy and patterns of NIS spreadMarika Galanidi, Mehdi Aissi, Malek Ali, Ali Bakalem, Michel Bariche, Angela G. Bartolo, Borut Mavrič, Martina Orlando-Bonaca, 2023, original scientific article Abstract: This work presents refined, updated subregional and regional non-indigenous species (NIS) inventories for the Mediterranean Sea, validated by national and taxonomic experts, with species records observed until December 2020. These datasets will be used as the baselines for the implementation of the Integrated Monitoring and Assessment Programme for the Mediterranean (IMAP) and the Mediterranean Quality Status Report 2023. In total, 1006 non-indigenous species have been found in Mediterranean marine and brackish waters. The highest numbers of NIS were observed in Israel, Türkiye, Lebanon and Italy. Approximately 45 species were categorized as data deficient, either due to lack of consensus on their alien status or the validity of their identification. Polychaeta, Foraminifera and macroalgae were the groups with the highest numbers of controversial species. There was a general increase in the yearly rate of new NIS introductions after the late 1990s, which appears to be slowing down in the last decade, but this may be confounded by reporting lags and differential research efforts. Between 1970 and 2020 there has been a steep increase in the proportion of shared species present throughout all four Mediterranean subregions, which are predominantly transported via shipping and recreational boating. While Lessepsian species are gradually spreading westwards and northwards, there is still a considerable invasion debt accumulating in the eastern and central Mediterranean.
Keywords: non-indigenous species, Mediterranean Sea, validation, non-indigenous species inventories, NIS, Integrated Monitoring and Assessment Programme for the Mediterranean, IMAP
Published in DiRROS: 12.07.2024; Views: 134; Downloads: 122
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6. Effects of specific parameters on simulations of energy use and air temperatures in offices equipped with radiant heating/cooling panelsSabina Jordan, Jože Hafner, Martina Zbašnik-Senegačnik, Andraž Legat, 2019, original scientific article Abstract: When creating a simulation model to assess the performance of buildings, there is usually a lack of feedback information. Only in the case of measurements of a real building is a direct comparison of the measured values and simulated results possible. Parameter data related to users’ behavior or other events can also be obtained. Their evaluated frequency, magnitude and duration, along with boundary conditions, are crucial for the results. It is clear that none of them can be predicted very accurately. Most of them, however, are needed for computer modeling. In this paper we analyzed the well-defined TRNSYS simulation model of offices equipped with radiant ceiling panels for heating and cooling. The model was based on real case offices and was validated based on measurements for 1 year. The analysis included simulations in order to define what effect the parameters related mainly to users have on the energy use and the indoor air temperatures. The study confirmed that specific human activities influence the annual energy use to a relatively small degree and that their effects often counteract. It also confirmed the even more important fact that although small, these activities can influence the thermal comfort of users. It is believed that despite the fact that this research was based on an analysis of offices equipped with radiant ceiling panels, most of the results could be applied generally.
Keywords: measurements, modeling, simulation, validation, analysis, energy use, temperature
Published in DiRROS: 15.09.2023; Views: 494; Downloads: 238
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7. Validation of combinatorial evaluation of strain-gauge amplifier linearityMiha Hiti, 2020, original scientific article Abstract: This paper describes a validation of a combinatorial calibration technique based calibration procedure for strain-gauge amplifier calibration. The deviation between two strain-gauge amplifiers at calibration using the combinatorial technique is compared to the deviation between the same two amplifiers at calibration on a force calibration machine as a transducer-amplifier chain under unchanged conditions, serving as an amplifier linearity comparator. This enables the validation to be confirmed with a suitable expanded measurement uncertainty of 3 nV/V.
Keywords: strain-gauge amplifier, calibration, combinatorial technique, validation
Published in DiRROS: 21.08.2023; Views: 448; Downloads: 171
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8. From language models to large-scale food and biomedical knowledge graphsGjorgjina Cenikj, Lidija Strojnik, Risto Angelski, Nives Ogrinc, Barbara Koroušić-Seljak, Tome Eftimov, 2023, original scientific article Abstract: Knowledge about the interactions between dietary and biomedical factors is scattered throughout uncountable research articles in an unstructured form (e.g., text, images, etc.) and requires automatic structuring so that it can be provided to medical professionals in a suitable format. Various biomedical knowledge graphs exist, however, they require further extension with relations between food and biomedical entities. In this study, we evaluate the performance of three state-of-the-art relation-mining pipelines (FooDis, FoodChem and ChemDis) which extract relations between food, chemical and disease entities from textual data. We perform two case studies, where relations were automatically extracted by the pipelines and validated by domain experts. The results show that the pipelines can extract relations with an average precision around 70%, making new discoveries available to domain experts with reduced human effort, since the domain experts should only evaluate the results, instead of finding, and reading all new scientific papers.
Keywords: biomedical knowledge graphs, relation-mining pipelines, relation extraction, validation
Published in DiRROS: 17.05.2023; Views: 574; Downloads: 228
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9. Reliability and validity of 30-15 intermittent fitness test for cardiorespiratory fitness assessment among infantry members of Slovenian armed forces : ǂa ǂstudy protocolArmin Paravlić, Boštjan Šimunič, Rado Pišot, Samo Rauter, Janez Vodičar, 2022, original scientific article Abstract: Introduction: Cardiorespiratory fitness (CRF) testing is routinely performed by most armed and tactical forces around the world as part of their recruitment process for new members or simply as an annual examination of their personnel. A 2-mile run (2MR) test is among the most commonly used. However, as it is performed outdoors, weather, climate, and terrain can influence the results and often limit the maximum performance. Also, this test has been shown to be difficult for individuals because the pacing strategy is self-paced. As such, it does not reflect the real situation on the battlefield, where most activities are externally driven by the environment and the enemy. Therefore, we believe that the 30-15 Intermittent Fitness Test (30-15IFT) may be a suitable tool for measuring CRF and battle readiness of military personnel. Moreover, given the importance of visual attention to military personnel we aim to investigate the differences in visual attention between better and less physically prepared infantry members and its corresponding response to maximal endurance running test. Methods and analysis: This randomized cross-over study using a within-subjects test-retest design will enroll 32 infantry members of the Slovenian Armed Forces. To investigate the reliability and validity of the 30-15IFT test, an incremental treadmill test (TR), a 2MR test, and two identical 30-15IFT will be performed in randomized order. Additionally, participants will be subsequently divided into two groups based on their score on the Army Physical Fitness Test (APFT), whereas differences in visual attention will be assessed by using the d2 test. The primary analysis will assess differences in key physiological outcomes between the different CRF tests (TR vs. 2MR vs. 30-15IFT). In addition, the relative reliability of all dependent variables between two 30-15IFT trials will be estimated by interclass correlation coefficient (ICC), while relationship between maximal oxygen uptake, heart rate and maximal running speed of 30-15IFT, TR and 2MR will be assessed using Pearson’s correlation.
Keywords: Slovenian armed forces, running endurance, visual attention, cardiorespiratory fitness assessment, intermittent fitness tests, reliability, validation
Published in DiRROS: 27.07.2022; Views: 784; Downloads: 440
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10. Passive shoulder exoskeletons : more effective in the lab than in the field?Sander De Bock, Jo Ghillebert, Renée Govaerts, Shirley A. Elprama, Uroš Marušič, Ben Serrien, An Jacobs, Joost Geeroms, Romain Meeusen, Kevin De Pauw, 2021, original scientific article Abstract: Shoulder exoskeletons potentially reduce overuse injuries in industrial settings including overhead work or lifting tasks. Previous studies evaluated these devices primarily in laboratory setting, but evidence of their effectiveness outside the lab is lacking. The present study aimed to evaluate the effectiveness of two passive shoulder exoskeletons and explore the transfer of laboratory-based results to the field. Four industrial workers performed controlled and in-field evaluations without and with two exoskeletons, ShoulderX and Skelex in a randomized order. The exoskeletons decreased upper trapezius activity (up to 46%) and heart rate in isolated tasks. In the field, the effects of both exoskeletons were less prominent (up to 26% upper trapezius activity reduction) while lifting windscreens weighing 13.1 and 17.0 kg. ShoulderX received high discomfort scores in the shoulder region and usability of both exoskeletons was moderate. Overall, both exoskeletons positively affected the isolated tasks, but in the field the support of both exoskeletons was limited. Skelex, which performed worse in the isolated tasks compared to ShoulderX, seemed to provide the most support during the in-field situations. Exoskeleton interface improvements are required to improve comfort and usability. Laboratory-based evaluations of exoskeletons should be interpreted with caution, since the effect of an exoskeleton is task specific and not all infield situations with high-level lifting will equally benefit from the use of an exoskeleton. Before considering passive exoskeleton implementation, we recommend analyzing joint angles in the field, because the support is inherently dependent on these angles, and to perform in-field pilot tests. This paper is the first thorough evaluation of two shoulder exoskeletons in a controlled and infield situation.
Keywords: assistive devices, exoskeletons, ergonomics, industrial plants, system validation
Published in DiRROS: 28.02.2022; Views: 832; Downloads: 607
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