BACKGROUND: Digitising and aggregating local floristic data is a critical step in the study of biodiversity. The integrative web-based platform Pladias, designed to cover a wide range of data on vascular plants, was recently developed in the Czech Republic. The combination of occurrence data with species characteristics opens many opportunities for data analysis and synthesis. NEW INFORMATION: This article describes the relational structure of the Pladias database service (PladiasDB) and the context of the platform architecture. The structure is relatively complex, as our goal was to cover: (i) species occurrence records, including their management, validation and export of revised species distribution maps, (ii) data on species characteristics with quality control tools using defined data types and (iii) separate user interfaces (UI) for professionals and the general public. We discuss the approaches chosen to model individual elements in PladiasDB and summarise the experience gained during the first five years of operation of the Pladias platform.

• Klíčová slova
• Czech Republic, botany, database, flora, occurrence, plant, relational database model, species, trait, tree hierarchy, vegetation,
• Publikační typ
• časopisecké články MeSH

The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures using R packages provided by inspected platforms. If neither of these was available, we used the public interface of individual databases. For almost half (12) of the databases analyzed, we did not find any formalized taxa hierarchy data structure, providing only biological information about taxon membership in higher ranks, which is not fully formalizable and thus not generally usable. The least effective Adjacency List model (storing parentId of a taxon) dominates among the remaining providers. This study demonstrates the lack of attention paid by current biodiversity databases to modeling taxon hierarchy, particularly to making it available to researchers in the form of a hierarchical data structure within the data provided. For biodiversity relational databases, the Closure Table type is the most suitable of the known data models, which also corresponds to the ontology concept. However, its use is rather sporadic within the biodiversity databases ecosystem.

• MeSH
• biodiverzita * MeSH
• databáze faktografické * MeSH
• Publikační typ
• časopisecké články MeSH
• technické zprávy MeSH

Two values of thermal requirements, the lower developmental threshold (LDT), that is, the temperature at which development ceases, and the sum of effective temperatures, that is, day degrees above the LDT control the development of ectotherms and are used in phenology models to predict time at which the development of individual stages of a species will be completed. To assist in the rapid development of phenology models, we merged a previously published database of thermal requirements for insects, gathered by online search in CAB Abstracts, with independently collected data for insects and mites from original studies. The merged database comprises developmental times at various constant temperatures on 1,054 insect and mite species, many of them in several populations, mostly pests and their natural enemies, from all over the world. We show that closely related species share similar thermal requirements and therefore, for a species with unknown thermal requirements, the value of LDT and sum of effective temperatures of its most related species from the database can be used.

• MeSH
• biologické modely MeSH
• druhová specificita MeSH
• hmyz růst a vývoj   MeSH
• roztoči růst a vývoj   MeSH
• teplota MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Studies on climate change impacts are essential for identifying vulnerabilities and developing adaptation options. However, such studies depend crucially on the availability of reliable climate data. In this study, we introduce the climatological database called FORESEE (Open Database for Climate Change Related Impact Studies in Central Europe), which was developed to support the research of and adaptation to climate change in Central and Eastern Europe: the region where knowledge of possible climate change effects is inadequate. A questionnaire-based survey was used to specify database structure and content. FORESEE contains the seamless combination of gridded daily observation-based data (1951-2013) built on the E-OBS and CRU TS datasets, and a collection of climate projections (2014-2100). The future climate is represented by bias-corrected meteorological data from 10 regional climate models (RCMs), driven by the A1B emission scenario. These latter data were developed within the frame of the ENSEMBLES FP6 project. Although FORESEE only covers a limited area of Central and Eastern Europe, the methodology of database development, the applied bias correction techniques, and the data dissemination method, can serve as a blueprint for similar initiatives.

• Klíčová slova
• Central and Eastern Europe, bias correction, climatological database,
• Publikační typ
• časopisecké články MeSH

Advancements in deep learning speech representations have facilitated the effective use of extensive unlabeled speech datasets for Parkinson's disease (PD) modeling with minimal annotated data. This study employs the non-fine-tuned wav2vec 1.0 architecture to develop machine learning models for PD speech diagnosis tasks, such as cross-database classification and regression to predict demographic and articulation characteristics. The primary aim is to analyze overlapping components within the embeddings on both classification and regression tasks, investigating whether latent speech representations in PD are shared across models, particularly for related tasks. Firstly, evaluation using three multi-language PD datasets showed that wav2vec accurately detected PD based on speech, outperforming feature extraction using mel-frequency cepstral coefficients in the proposed cross-database classification scenarios. In cross-database scenarios using Italian and English-read texts, wav2vec demonstrated performance comparable to intra-dataset evaluations. We also compared our cross-database findings against those of other related studies. Secondly, wav2vec proved effective in regression, modeling various quantitative speech characteristics related to articulation and aging. Ultimately, subsequent analysis of important features examined the presence of significant overlaps between classification and regression models. The feature importance experiments discovered shared features across trained models, with increased sharing for related tasks, further suggesting that wav2vec contributes to improved generalizability. The study proposes wav2vec embeddings as a next promising step toward a speech-based universal model to assist in the evaluation of PD.

• Klíčová slova
• Parkinson’s disease, classification, cross-database, feature importance, regression, wav2vec,
• MeSH
• databáze faktografické * MeSH
• deep learning MeSH
• lidé středního věku MeSH
• lidé MeSH
• Parkinsonova nemoc * patofyziologie   MeSH
• řeč * fyziologie   MeSH
• senioři MeSH
• strojové učení MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND AND OBJECTIVE: Obstructive sleep apnoea (OSA) and hyperlipidaemia are independent risk factors for cardiovascular disease. This study investigates the association between OSA and prevalence of hyperlipidaemia in patients of the European Sleep Apnea Database (ESADA) cohort. METHODS: The cross-sectional analysis included 11 892 patients (age 51.9 ± 12.5 years, 70% male, body mass index (BMI) 31.3 ± 6.6 kg/m2 , mean oxygen desaturation index (ODI) 23.7 ± 25.5 events/h) investigated for OSA. The independent odds ratio (OR) for hyperlipidaemia in relation to measures of OSA (ODI, apnoea-hypopnoea index, mean and lowest oxygen saturation) was determined by means of general linear model analysis with adjustment for important confounders such as age, BMI, comorbidities and study site. RESULTS: Hyperlipidaemia prevalence increased from 15.1% in subjects without OSA to 26.1% in those with severe OSA, P < 0.001. Corresponding numbers in patients with diabetes were 8.5% and 41.5%, P < 0.001. Compared with ODI quartile I, patients in ODI quartiles II-IV had an adjusted OR (95% CI) of 1.33 (1.15-1.55), 1.37 (1.17-1.61) and 1.33 (1.12-1.58) (P < 0.001), respectively, for hyperlipidaemia. Obesity was defined as a significant risk factor for hyperlipidaemia. Subgroups of OSA patients with cardio-metabolic comorbidities demonstrated higher prevalence of HL. In addition, differences in hyperlipidaemia prevalence were reported in European geographical regions with the highest prevalence in Central Europe. CONCLUSION: Obstructive sleep apnoea, in particular intermittent hypoxia, was independently associated with the prevalence of hyperlipidaemia diagnosis.

• Klíčová slova
• cholesterol, hyperlipidaemia, hypoxia, obesity, sleep apnoea,
• MeSH
• hyperlipidemie epidemiologie   MeSH
• kardiovaskulární nemoci epidemiologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• obezita epidemiologie   MeSH
• obstrukční spánková apnoe epidemiologie   MeSH
• polysomnografie MeSH
• prevalence MeSH
• průřezové studie MeSH
• rizikové faktory MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa epidemiologie   MeSH

Small fish species, such as zebrafish and medaka, are increasingly gaining popularity in basic research and disease modeling as a useful alternative to rodent model organisms. However, the tracking options for fish within a facility are rather limited. In this study, we present an aquatic species tracking database, Zebrabase, developed in our zebrafish research and breeding facility that represents a practical and scalable solution and an intuitive platform for scientists, fish managers, and caretakers, in both small and large facilities. Zebrabase is a scalable, cross-platform fish tracking database developed especially for fish research facilities. Nevertheless, this platform can be easily adapted for a wide variety of aquatic model organisms housed in tanks. It provides sophisticated tracking, reporting, and management functions that help keep animal-related records well organized, including a QR code functionality for tank labeling. The implementation of various user roles ensures a functional hierarchy and customized access to specific functions and data. In addition, Zebrabase makes it easy to personalize rooms and racks, and its advanced statistics and reporting options make it an excellent tool for creating periodic reports of animal usage and productivity. Communication between the facility and the researchers can be streamlined by the database functions. Finally, Zebrabase also features an interactive breeding history and a smart interface with advanced visualizations and intuitive color coding that accelerate the processes.

• Klíčová slova
• Django, Python, facility database, husbandry, tracking, zebrafish,
• MeSH
• automatizované zpracování dat MeSH
• chov zvířat metody   organizace a řízení   MeSH
• dánio pruhované * MeSH
• databáze faktografické MeSH
• laboratorní zvířata * MeSH
• monitorování životního prostředí MeSH
• software * MeSH
• vodní hospodářství metody   organizace a řízení   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country, locality, responsible author, sampling dates, sampling method, and life habits of both canopy and recruit species are provided. This database will allow researchers to test ecological, biogeographical, and evolutionary hypotheses related to plant recruitment interactions. There are no copyright restrictions on the data set; please cite this data paper when using these data in publications.

• Klíčová slova
• ecological networks, facilitation, plant-plant interactions, recruitment, replacement,
• MeSH
• biologická evoluce MeSH
• cévnaté rostliny * MeSH
• ekosystém * MeSH
• lidé MeSH
• rostliny MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Sequences of immunoglobulin (Ig) domains of adhesive molecule GSAMS from the living fossil sponge Geodia cydonium were compared with the important motif of peptide protein kinase substrates and inhibitors (PKSI), detail PKSI sequences, and a common template sequence, derived from structures determined previously. We found the site-restricted sequence similarities to these peptide sequences predominantly in the GSAM Ig1 domain of GSAMS in the domain region related to corresponding Ig similarities detected earlier. Additional sequence block-related analysis revealed the presence of CDR1-like segments within PKSI-related regions and resulted in the detection of increased numbers of hypermutation motifs just in the CDR1-like segment of GSAM Ig1 (GSAM(cdrl.1)). In the following database searches with PKSI-related regions and GSAM(cdr1.1) we looked for: (i) peptide similarities present in the context of Ig domains or related structures in a large range of species from Archaea to Vertebrata, and (ii) some special nucleotide similarities.

• MeSH
• aminokyselinové motivy MeSH
• aminokyseliny analýza   MeSH
• biologická evoluce MeSH
• databáze faktografické MeSH
• imunoglobuliny genetika   metabolismus   MeSH
• inhibitory proteinkinas * MeSH
• molekuly buněčné adheze chemie   genetika   MeSH
• Porifera genetika   MeSH
• proteinkinasy metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin * MeSH
• sekvenční seřazení MeSH
• somatická hypermutace imunoglobulinových genů MeSH
• zkameněliny MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• imunoglobuliny MeSH
• inhibitory proteinkinas * MeSH
• molekuly buněčné adheze MeSH
• proteinkinasy MeSH

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

• Klíčová slova
• data sharing, global biodiversity modeling, global change, habitat destruction, land use,
• Publikační typ
• časopisecké články MeSH