101. ELIXIR and toxicology : a community in development [version 2; peer review: 2 approved]Marvin Martens, Rob Stierum, EL Schymanski, Chris T Evelo, Anže Županič, 2023, pregledni znanstveni članek Povzetek: Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology, and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
Ključne besede: toxicology, ELIXIR, interoperability, FAIR
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102. New approach methodologies to facilitate and improve the hazard assessment of non-genotoxic carcinogens : a PARC projectMarc Audebert, Ann-Sophie Assmann, Amaya Azqueta, Pavel Babica, Emilio Benfenati, Martina Štampar, Bojana Žegura, 2023, pregledni znanstveni članek Povzetek: Carcinogenic chemicals, or their metabolites, can be classified as genotoxic or non-genotoxic carcinogens (NGTxCs). Genotoxic compounds induce DNA damage, which can be detected by an established in vitro and in vivo battery of genotoxicity assays. For NGTxCs, DNA is not the primary target, and the possible modes of action (MoA) of NGTxCs are much more diverse than those of genotoxic compounds, and there is no specific in vitro assay for detecting NGTxCs. Therefore, the evaluation of the carcinogenic potential is still dependent on long-term studies in rodents. This 2-year bioassay, mainly applied for testing agrochemicals and pharmaceuticals, is time-consuming, costly and requires very high numbers of animals. More importantly, its relevance for human risk assessment is questionable due to the limited predictivity for human cancer risk, especially with regard to NGTxCs. Thus, there is an urgent need for a transition to new approach methodologies (NAMs), integrating human-relevant in vitro assays and in silico tools that better exploit the current knowledge of the multiple processes involved in carcinogenesis into a modern safety assessment toolbox. Here, we describe an integrative project that aims to use a variety of novel approaches to detect the carcinogenic potential of NGTxCs based on different mechanisms and pathways involved in carcinogenesis. The aim of this project is to contribute suitable assays for the safety assessment toolbox for an efficient and improved, internationally recognized hazard assessment of NGTxCs, and ultimately to contribute to reliable mechanism-based next-generation risk assessment for chemical carcinogens.
Ključne besede: non-genotoxic carcinogens, NGTxC, new approach methodologies, NAM, PARC
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103. CRISPR/Cas-mediated plant genome editing : outstanding challenges a decade after implementationTeodoro Cardi, Jana Murovec, Allah Bakhsh, Vladislava Galović, Tjaša Lukan, Kubilay Yıldırım, Milica Zlatković, Katrijn Van Laere, 2023, pregledni znanstveni članek Povzetek: The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
Ključne besede: CRISPR applications, CRISPR platforms, gene regulations, mutant detection, plant regeneration
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104. The importance of population contextual data for large-scale biomonitoring using an apex predator : the Tawny Owl (Strix aluco)Urška Ratajc, Rui Lourenço, Silvia Espín, Pablo Sánchez Virosta, Simon Birrer, Dani Studler, Chris Wernham, Al Vrezec, 2023, pregledni znanstveni članek Povzetek: Top predators are often used as sentinel species in contaminant monitoring due to their exposure and vulnerability to persistent, bioaccumulative and, in some cases, biomagnificable contaminants. Some of their ecological traits can vary in space and time, and are known to influence the contamination levels and therefore information on ecological traits should be used as contextual data for correct interpretation of large-scale contaminant spatial patterns. These traits can explain spatiotemporal variation in contaminant exposure (traits such as diet and dispersal distances) or contaminant impacts (traits such as population trend and clutch size). The aim of our research was to review the spatial variation in selected contextual parameters in the Tawny Owl (Strix aluco), a species identified by the COST Action European Raptor Biomonitoring Facility as one of the most suitable candidates for pan-European biomonitoring. A considerable variation in availability of published and unpublished contextual data across Europe was found, with diet being the most extensively studied trait. We demonstrate that the Tawny Owl is a suitable biomonitor at local scale but also that taking spatial variation of other contextual data (e.g. diet) into account is necessary. We found spatial gaps in knowledge about the species ecology and biology in Southern Europe, along with gaps in certain population parameters (e.g. population trends) in several countries. Based on our findings, we proposed a minimal recommended scheme for monitoring of population contextual data as one of the first steps towards a pan-European monitoring scheme using the Tawny Owl.
Ključne besede: raptors, sentinel species, contamination exposure, contamination impact, diet, minimal recommended monitoring scheme
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105. DELWAVE 1.0 : deep learning surrogate model of surface wave climate in the Adriatic BasinPeter Mlakar, Antonio Ricchi, Sandro Carniel, Davide Bonaldo, Matjaž Ličer, 2024, izvirni znanstveni članek Povzetek: We propose a new point-prediction model, the DEep Learning WAVe Emulating model (DELWAVE), which successfully emulates the behaviour of a numerical surface ocean wave model (Simulating WAves Nearshore, SWAN) at a sparse set of locations, thus enabling numerically cheap large-ensemble prediction over synoptic to climate timescales. DELWAVE was trained on COSMO-CLM (Climate Limited-area Model) and SWAN input data during the period of 1971–1998, tested during 1998–2000, and cross-evaluated over the far-future climate time window of 2071–2100. It is constructed from a convolutional atmospheric encoder block, followed by a temporal collapse block and, finally, a regression block. DELWAVE reproduces SWAN model significant wave heights with a mean absolute error (MAE) of between 5 and 10 cm, mean wave directions with a MAE of 10–25°, and a mean wave period with a MAE of 0.2 s. DELWAVE is able to accurately emulate multi-modal mean wave direction distributions related to dominant wind regimes in the basin. We use wave power analysis from linearised wave theory to explain prediction errors in the long-period limit during southeasterly conditions. We present a storm analysis of DELWAVE, employing threshold-based metrics of precision and recall to show that DELWAVE reaches a very high score (both metrics over 95 %) of storm detection. SWAN and DELWAVE time series are compared to each other in the end-of-century scenario (2071–2100) and compared to the control conditions in the 1971–2000 period. Good agreement between DELWAVE and SWAN is found when considering climatological statistics, with a small (≤ 5 %), though systematic, underestimate of 99th-percentile values. Compared to control climatology over all wind directions, the mismatch between DELWAVE and SWAN is generally small compared to the difference between scenario and control conditions, suggesting that the noise introduced by surrogate modelling is substantially weaker than the climate change signal.
Ključne besede: surrogate modelling, deep learning, DEep Learning WAVe Emulating model, DELWAVE, Simulating WAves Nearshore, SWAN
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106. From the sea to aquafeed : a perspective overviewOrhan Tufan Eroldogan, Brett Glencross, Lucie Novoveská, Susana P. Gaudêncio, Buki Rinkevich, Giovanna Cristina Varese, Maria F. Carvalho, Deniz Tasdemir, Ivo Safarik, Soren Laurentius Nielsen, Céline Rebours, Lada Lukić-Bilela, Johan Robbens, Evita Strode, Berat Z. Haznedaroglu, Marlen I. Vasquez, Ivana Čabarkapa, Slađana Rakita, Katja Klun, Ana Rotter, 2023, pregledni znanstveni članek Povzetek: Aquaculture has been one of the fastest-growing food production systems sectors for over three decades. With its growth, the demand for alternative, cheaper and high-quality feed ingredients is also increasing. Innovation investments on providing new functional feed alternatives have yielded several viable alternative raw materials. Considering all the current feed ingredients, their circular adaption in the aquafeed manufacturing industry is clearly of the utmost importance to achieve sustainable aquaculture in the near future. The use of terrestrial plant materials and animal by-products predominantly used in aquafeed ingredients puts a heavily reliance on terrestrial agroecosystems, which also has its own sustainability concerns. Therefore, the aquafeed industry needs to progress with functional and sustainable alternative raw materials for feed that must be more resilient and consistent, considering a circular perspective. In this review, we assess the current trends in using various marine organisms, ranging from microorganisms (including fungi, thraustochytrids, microalgae and bacteria) to macroalgae and macroinvertebrates as viable biological feed resources. This review focuses on the trend of circular use of resources and the development of new value chains. In this, we present a perspective of promoting novel circular economy value chains that promote the re-use of biological resources as valuable feed ingredients. Thus, we highlight some potentially important marine-derived resources that deserve further investigations for improving or addressing circular aquaculture.
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107. Computerized cognitive training in the older workforce : effects on cognition, life satisfaction, and productivityZdenka Milič Žepič, Voyko Kavcic, Bruno Giordani, Uroš Marušič, 2024, izvirni znanstveni članek Povzetek: Background: The accelerated aging of the world’s population will lead to an increase in the number of older people in the workforce. Computerized Cognitive Training (CCT) is effective in improving cognitive outcomes, but its benefits for older workers remain controversial. We investigate the real-world efficacy of CCT in the workplace, focusing on employees aged 50+ years from a public sector agency. Methods: Case managers (n = 82) were randomized to either an intervention group (24 40 min CCT sessions two times per week) or a waiting list passive control group. Cognitive ability, well-being, job satisfaction, and productivity outcome measures were collected and assessed before and after CCT or the comparable control wait time. Results: Participants undergoing CCT improved on a task of executive functioning (p = 0.04). There was a trend toward a change in work productivity after CCT (p = 0.09), with the control group showing a significant decrease (p = 0.02), while the intervention group remained stable. Conclusions: CCT during office hours has a positive effect on cognition and well-being without affecting productivity among white-collar office workers. CCT could be considered as an intervention to support the older workforce in managing the cognitive and behavioral challenges of changing workplace demands.
Ključne besede: older employees, 50+, computerized cognitive training (CCT), productivity, well-being
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108. Adjusting the operational potential window as a tool for prolonging the durability of carbon-supported Pt-alloy nanoparticles as oxygen reduction reaction electrocatalystsTina Đukić, Leonard Moriau, Iva Klofutar, Martin Šala, Luka Pavko, Francisco Javier Gonzalez Lopez, Francisco Ruiz-Zepeda, Andraž Pavlišič, Miha Hotko, Matija Gatalo, Nejc Hodnik, 2024, izvirni znanstveni članek Objavljeno v DiRROS: 05.08.2024; Ogledov: 57; Prenosov: 24
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109. Sequestration of membrane cholesterol by cholesterol-binding proteins inhibits SARS-CoV-2 entry into Vero E6 cellsMagdalena Kulma, Aleksandra Šakanović, Apolonija Bedina Zavec, Simon Caserman, Neža Omersa, Gašper Šolinc, Sara Orehek, Iva Hafner Bratkovič, Urška Kuhar, Brigita Slavec, Uroš Krapež, Matjaž Ocepek, Toshihide Kobayashi, Katarzyna Kwiatkowska, Roman Jerala, Marjetka Podobnik, Gregor Anderluh, 2024, izvirni znanstveni članek Objavljeno v DiRROS: 05.08.2024; Ogledov: 55; Prenosov: 28
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110. First contribution to the knowledge of coralline algae distribution in the Slovenian circalittoral zone (northern Adriatic)Annalisa Falace, Sara Kaleb, Martina Orlando-Bonaca, Borut Mavrič, Lovrenc Lipej, 2011, izvirni znanstveni članek Povzetek: Authors present new data on the coralline algal flora from Slovenia. They come from recent inspection of the Slovenian part of the Gulf of Trieste where peculiar communities, such as the biocoenosis of the coastal detritic bottom, the agglomeration of bioconcretions known in the area under the name of "trezze" or "tengue", and the bank of Mediterranean stony coral Cladocora caespitosa, occur. In such communities 11 coralligenous red algae were found. Five of them, Hydrolithon boreale, Lithothamnion minervae, L. philippii, L. sonderi and Neogoniolithon brassica-florida are newly recorded for Slovenia.
Ključne besede: coralline algae, Cladocora caespitosa, circalittoral, northern Adriatic, Slovenia
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