Forward-directed genetic screens are extremely powerful in identifying novel genes involved in a specific biological process, including various chromatin regulatory pathways. However, the traditional ways of genetic mapping are time- and cost-demanding. Recently, the whole process was revolutionized by the development of mapping-by-sequencing (MBS) protocols. In MBS, the causal mutations and their positions within genes are identified directly by whole-genome sequencing and bioinformatics analysis of the bulk of mutant plants selected based on the mutant phenotype from a segregating population. MBS increases precision and economizes the mapping. Here, we describe a general protocol and provide practical tips on how to proceed with the mapping-by-sequencing on the example of Arabidopsis forward-directed genetic screen designed to identify mutants sensitive to a specific type of DNA damage. The described protocol is generally applicable to a wide range of genetic screens in various inbreeding species with a reference genome sequence.

• Klíčová slova
• DNA damage repair, DNA-protein crosslinks, Forward genetics, Genetic mapping, High-throughput sequencing, Mapping-by-sequencing, SNP calling, Zebularine,
• MeSH
• Arabidopsis * genetika   MeSH
• fenotyp MeSH
• genom rostlinný MeSH
• mapování chromozomů * metody   MeSH
• mutace MeSH
• sekvenování celého genomu metody   MeSH
• výpočetní biologie metody   MeSH
• vysoce účinné nukleotidové sekvenování * metody   MeSH
• Publikační typ
• časopisecké články MeSH

OBJECTIVES: Pharmacovigilance efforts for COVID-19 vaccines have largely focused on severe adverse events (AEs), while nonserious, yet distressing, AEs, such as oral AEs, remain underexamined. This study aimed to analyse oral AE reporting patterns in the German national pharmacovigilance database. METHODS: A retrospective analysis of individual case safety reports (ICSRs) from the Paul-Ehrlich-Institut (PEI) database was conducted for December 2020 to December 2023. The absolute reporting ratio was calculated as cases per 1000 ICSRs for each oral AE. Secondary analyses included: (1) cross-database comparisons with the U.S. Vaccine Adverse Event Reporting System (VAERS); (2) disproportionality analysis using a hybrid approach combining frequentist and Bayesian conditions to establish signals of disproportionate reporting (SDRs); (3) subgroup analyses based on demographic and vaccine-related factors; and (4) multivariable regression to adjust for potential confounders. RESULTS: Gustatory AEs, such as ageusia and dysgeusia; other oral sensory AEs, including oral paraesthesia and oral hypoaesthesia; and specific mucosal AEs, such as oral herpes and aphthous stomatitis, were the most frequently reported oral AEs in the PEI dataset. Cross-database analysis not only confirmed the prominence of gustatory and other sensory AEs but also highlighted differences, with VAERS reporting higher rates of swollen tongue and lip swelling. Disproportionality analysis identified 21 oral AEs as true SDRs. Female susceptibility was evident in several oral AEs, and age-stratified analysis revealed higher reporting among minors and seniors compared to middle-aged adults. Differences in oral AE reporting between mRNA and viral vector vaccines lacked a consistent pattern, and booster doses were associated with increased reporting of select oral AEs. CONCLUSIONS: Within the limitations of passive surveillance data, this study highlights the need for further research on oral AEs using self-controlled case-series designs for clinically significant events. Integrating oral AEs into vaccine safety monitoring could improve postmarketing surveillance, while validated AEs may warrant inclusion in product information for transparency.

• Klíčová slova
• Adverse Drug Reaction Reporting Systems, COVID-19 vaccines, Germany, Oral manifestations, Pharmacovigilance,
• MeSH
• COVID-19 * prevence a kontrola   MeSH
• databáze faktografické MeSH
• dítě MeSH
• dospělí MeSH
• farmakovigilance * MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• nemoci úst * epidemiologie   chemicky indukované   etiologie   MeSH
• předškolní dítě MeSH
• retrospektivní studie MeSH
• senioři MeSH
• systémy pro sběr zpráv o nežádoucích účincích léků MeSH
• vakcinace * škodlivé účinky   MeSH
• vakcíny proti COVID-19 * škodlivé účinky   MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Německo epidemiologie   MeSH
• Názvy látek
• vakcíny proti COVID-19 * MeSH

Forest management is inherently complex, requiring a multi-dimensional approach to set management goals that balance the competing demands of ecosystem services, public expectations, and scientific-political considerations. This study addresses the necessity for recognising, prioritizing, and spatially stratifying ecosystem services (ES) based on technical suitability, stakeholder involvement, and the categories of sustainability within Turkey's forest ecosystem management framework in Yalnızçam case study area. By leveraging Multi-Criteria Decision Analysis (MCDA) methods, particularly the Delphi technique with Analytical Hierarchy Process (AHP), this research captures both scientific ground and perspectives of various sectors with a stratification model to determine ES provisions. The iterative framework includes ES identification and prioritization steps, culminating in their spatial stratification of forest stands with geographic information system. The results indicate that ES stratification highlighted the primary focus on biodiversity conservation (78.5%) and water protection (13.3%), with minimal provision for timber production (7.9%) and soil protection (0.04%), and none for climate regulation, eco-tourism, and non-wood forest products. This approach enables a more efficient spatial zoning strategy, balancing technical and socio-cultural factors, and streamlining decision-making processes crucial for sustainable forest management paradigm.

• Klíčová slova
• AHP, Forest management planning, ecosystem services, forest stratification,
• MeSH
• biodiverzita MeSH
• delfská metoda MeSH
• ekosystém * MeSH
• geografické informační systémy MeSH
• lesnictví * metody   MeSH
• lesy MeSH
• metody pro podporu rozhodování MeSH
• socioekonomické faktory MeSH
• zachování přírodních zdrojů * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Turecko MeSH

Materials informatics (MI) has gained attention as a data-driven approach to accelerating material optimization in several fields. By leveraging computational methods, recent advancements in artificial intelligence, and large datasets, MI is poised to significantly accelerate the development of various materials. This approach drives innovative solutions, offers new insights into composition-property relationships, and potentially redefines the standards for material testing and selection. Consequently, MI has become a powerful alternative to traditional experimentation, offering more systematic and efficient pathways for materials innovation. Despite its success in other domains, only a handful of studies have used MI in dental materials research, which has long relied on iterative, labor-intensive empirical testing to make incremental improvements. This narrative review summarizes the fundamental principles of MI while showcasing its emerging role in dental materials research. We also discuss advantages of MI compared with traditional pipelines; current limitations, such as data scarcity and the challenges of translating in vitro findings to clinical outcomes; and future perspectives.

• Klíčová slova
• Bayesian optimization, CAD-CAM, artificial intelligence, deep learning/machine learning, materials science(s), restorative materials,
• MeSH
• informatika v zubním lékařství * metody   MeSH
• lidé MeSH
• testování materiálů MeSH
• umělá inteligence MeSH
• zubní materiály * chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• zubní materiály * MeSH

Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

• MeSH
• databáze faktografické * MeSH
• ekosystém MeSH
• enzymy * MeSH
• fosfolipidy * MeSH
• mastné kyseliny * MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• Publikační typ
• časopisecké články MeSH
• dataset MeSH
• Názvy látek
• enzymy * MeSH
• fosfolipidy * MeSH
• mastné kyseliny * MeSH
• půda MeSH

Trait-based ecology relies on high-quality, well-documented data to explore how plant traits relate to environmental conditions, community assembly, and ecosystem functioning. However, the reuse and synthesis of trait data across studies remain limited by several constraints: a lack of detailed metadata, heterogeneous protocols, absence of individual-level measurements, and underrepresentation of certain trait types-particularly below-ground traits. Many existing datasets also lack the environmental details necessary to investigate trait-environment relationships at local scales. Here, we present FAIRTraits, a comprehensive dataset that addresses these limitations by compiling 189,452 records of quantitative trait measurements collected between 1997 and 2023 from 1955 populations of 240 vascular plant species in the Northern Mediterranean Basin, a region known both for its exceptional biodiversity and as a climate change hotspot. All data were collected by a single research group using consistent and well-documented field and laboratory protocols, ensuring internal consistency across traits, species, sites, and years. FAIRTraits includes 180 traits measured at the individual or replicate level, with no aggregation. It features an unprecedented diversity of traits spanning all major plant organs-leaves, stems, roots, and reproductive parts. These include widely used traits such as specific leaf area and plant height, but also traits that are rarely reported, especially below-ground traits related to root morphology, as well as mechanical properties, phenology, and microbial associations. In addition to raw measurements, species are annotated with categorical descriptors (e.g., life form, photosynthetic pathway, and successional status), and species-level values taken from a Mediterranean flora, for key traits such as reproductive phenology and maximum height. To support analyses that account for environmental variability, each observation is linked to detailed descriptors of the plot where the individual was sampled, including climate data, soil physicochemical properties, and disturbance regime. Full metadata on sampling protocols and measurement methods are provided for every trait and environmental variable. FAIRTraits was built in compliance with the FAIR principles of data management (Findable, Accessible, Interoperable, and Reusable). Metadata are described using the Ecological Metadata Language (EML); trait definitions are standardized using community-endorsed semantic resources. The data are archived across two interoperable repositories: GBIF (via Darwin Core and trait-specific extensions) for taxon-trait associations and InDoRES for environmental and contextual data. These efforts ensure long-term preservation, data traceability, and seamless integration with plant trait databases such as BROT or TRY, and cross-organism initiatives such as the Open Traits Network or the Encyclopedia of Life. FAIRTraits offers a robust, richly documented, and reusable resource for investigating plant functional strategies, trait-environment relationships, and scaling from individuals to communities and ecosystems. It also provides a concrete example of how trait datasets can meet the highest standards of data quality and interoperability-serving as a model for future community-led initiatives in functional ecology. The FAIRTraits database is released under the CC-BY Attribution 4.0 International license.

• Klíčová slova
• FAIR principles, Mediterranean Biogeographic Region, biodiversity standards, ecosystem properties, environmental conditions, gas exchange, leaf, stem, root and reproductive traits, litter mass loss, phenology, plant functional traits, terminological resources, trait‐based ecology,
• MeSH
• databáze faktografické * MeSH
• fyziologie rostlin * MeSH
• rostliny * klasifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• dataset MeSH
• Geografické názvy
• Středomoří MeSH

SUMMARY: MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualization and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels. AVAILABILITY AND IMPLEMENTATION: The MOLEonline application is freely available at https://moleonline.cz with no login requirement, its source code is stored at GitHub under the MIT licence at https://github.com/sb-ncbr/moleonline-web, and archived at Figshare at https://doi.org/10.6084/m9.figshare.29816174.

• MeSH
• databáze proteinů MeSH
• internet MeSH
• konformace proteinů MeSH
• proteiny * chemie   MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• výpočetní biologie * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny * MeSH

Stereotactic arrhythmia radioablation (STAR) for ventricular tachycardia (VT) is a non-invasive treatment modality to reduce the VT burden by delivering a single high radiation dose to the arrhythmogenic substrate. Identification and delineation of the arrhythmogenic substrate, definition of the radiation target, and transfer of this target across different imaging modalities from the invasive electroanatomic map (EAM) to the planning computed tomography (CT) scan are key to the success of therapeutic radiation. The VT substrate is identified using EAM data and co-localized with radiological correlates of the ventricular scar. Precise transfer to the non-ECG-gated treatment planning CT is essential for safe and effective STAR delivery. Current challenges include translating the endocardial or epicardial EAM surface target into a 3D cardiac target volume (CTV), reconciling different acquisition methods (e.g., (exhale-gated) EAM, contrast-enhanced ECG-gated CT angiography, and non-gated non-contrast planning CT), and achieving accurate CTV transfer using multi-modal image integration. Early approaches relied on manual delineation using side-by-side EAM and CT rendering, leading to poor reproducibility and potential treatment failure. Emerging (semi)auto-segmentation software based on the American Heart Association (AHA) 17-segment left ventricular model offers promise but lacks standardized weighing of identified segments and methods for handling partially involved segments. More recently, 2D-to-3D and 3D-to-3D target transfer methods, including commercial and in-house computer-aided tools, have been developed to address these difficulties. Currently, a standardized workflow has not been established. This review addresses the need to standardize CTV definitions and transfer workflows, assessing available tools and proposing quality assurance measures based on recommendations of the STOPSTORM.eu consortium.

• Klíčová slova
• Catheter ablation, Stereotactic arrhythmia radioablation, Target volume transfer, Ventricular tachycardia,
• MeSH
• komorová tachykardie * diagnostické zobrazování   radioterapie   chirurgie   MeSH
• lidé MeSH
• plánování radioterapie pomocí počítače * metody   MeSH
• počítačová rentgenová tomografie * metody   MeSH
• radiochirurgie * metody   MeSH
• software * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Understanding T-cell receptor (TCR) specificity is not only essential for fundamental research, but could open up novel avenues for diagnostics, cancer immunotherapy, and the targeted treatment of autoimmune diseases. The immune system responds to challenges through groups of T-cells with similar TCR sequences. In recent years, searching for TCRs with an enrichment of similar sequences - neighbors - in a TCR repertoire has become a standard procedure for antigen-specific TCR identification. This study provides a systematic comparison of computational algorithms-ALICE, TCRNET, GLIPH2, and tcrdist3-that leverage neighborhood enrichment for antigen-specific TCR identification. Using published murine datasets from Lymphocytic choriomeningitis virus (LCMV) infection and novel datasets from Sputnik V vaccination and Mycobacterium tuberculosis (Mtb) infection, we evaluated the performance of these algorithms. To facilitate reproducible analysis, we developed TCRgrapher, an R library that integrates these pipelines into a user-friendly framework. TCRgrapher enables efficient identification of antigen-specific TCRs from single repertoire snapshots and supports flexible parameter customization. Our comparative analysis revealed that ALICE and TCRNET consistently outperformed GLIPH2 and tcrdist3 across most datasets, achieving higher area under precision-recall curve. While murine datasets provide valuable insights into algorithm performance, caution is advised when extrapolating these results to other species or different experimental conditions. TCRgrapher is freely available on GitHub (https://github.com/KseniaMIPT/tcrgrapher), offering researchers a robust tool for investigating TCR specificity and advancing immunological studies.

• Klíčová slova
• TCR repertoire, TCR specificity, immunoinformatics, software,
• MeSH
• algoritmy * MeSH
• antigeny * imunologie   MeSH
• lidé MeSH
• Mycobacterium tuberculosis imunologie   MeSH
• myši MeSH
• receptory antigenů T-buněk * imunologie   genetika   MeSH
• virus lymfocytární choriomeningitidy imunologie   MeSH
• výpočetní biologie * metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antigeny * MeSH
• receptory antigenů T-buněk * MeSH

BACKGROUND: Recent studies have demonstrated that prolonged sperm storage adversely affects offspring through epigenetics, yet its broader effects on other molecular levels such as transcription and proteomics in progeny have been rarely explored. RESULTS: We employed comprehensive multi-omics approaches to uncover storage-induced epigenetic changes in sperm and their effects on embryonic development and offspring health. Sperm from common carp (Cyprinus carpio) was stored in vitro in artificial seminal plasma for 14 days, and the impacts of storage on functional properties of sperm and progeny development were investigated. We combined DNA methylome, transcriptomic and proteomic data to elucidate the potential mechanisms by which sperm storage influences progeny development. Prolonged in vitro storage significantly reduced sperm motility and fertilising ability which coincided with changes in the DNA methylation pattern. Integrated analyses of the offspring DNA methylome, comparative transcriptomics and cardiac performance measurements revealed storage-induced alterations of genes associated with nervous system development, myocardial morphogenesis and cellular responses to stimuli. Proteomic analyses showed that in addition to visual perception and nervous system function, pathways of the immunity system were also enriched. Results provide strong evidence of the epigenetic inheritance of the offspring's performances when short-term stored sperm was used for fertilisation. CONCLUSIONS: Short-term sperm storage induces heritable molecular and phenotypic changes in offspring, raising concerns over the potential intergenerational consequences of assisted reproductive practices in aquaculture and possibly other vertebrates.

• Klíčová slova
• Epigenetic inheritance, Epigenetics, Fish sperm, Offspring development, Sperm ageing,
• MeSH
• embryonální vývoj * MeSH
• epigeneze genetická MeSH
• kapři * genetika   fyziologie   embryologie   MeSH
• metylace DNA MeSH
• multiomika MeSH
• proteomika MeSH
• spermie * fyziologie   metabolismus   MeSH
• transkriptom MeSH
• uchování spermatu * škodlivé účinky   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH