• MeSH
• klinické laboratorní techniky MeSH
• nemocniční informační systémy MeSH
• Publikační typ
• kongresy MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie
• lékařská informatika

Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.

• MeSH
• databáze genetické MeSH
• databáze nukleových kyselin MeSH
• Eukaryota * genetika   MeSH
• fylogeneze MeSH
• geny rRNA genetika   MeSH
• RNA ribozomální 18S genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

This paper describes an evaluation framework that allows a standardized and quantitative comparison of IVUS lumen and media segmentation algorithms. This framework has been introduced at the MICCAI 2011 Computing and Visualization for (Intra)Vascular Imaging (CVII) workshop, comparing the results of eight teams that participated. We describe the available data-base comprising of multi-center, multi-vendor and multi-frequency IVUS datasets, their acquisition, the creation of the reference standard and the evaluation measures. The approaches address segmentation of the lumen, the media, or both borders; semi- or fully-automatic operation; and 2-D vs. 3-D methodology. Three performance measures for quantitative analysis have been proposed. The results of the evaluation indicate that segmentation of the vessel lumen and media is possible with an accuracy that is comparable to manual annotation when semi-automatic methods are used, as well as encouraging results can be obtained also in case of fully-automatic segmentation. The analysis performed in this paper also highlights the challenges in IVUS segmentation that remains to be solved.

• MeSH
• databáze faktografické normy   MeSH
• internacionalita MeSH
• interpretace obrazu počítačem metody   normy   MeSH
• intervenční ultrasonografie metody   normy   MeSH
• lidé MeSH
• nemoci koronárních tepen ultrasonografie   MeSH
• referenční hodnoty MeSH
• reprodukovatelnost výsledků MeSH
• senzitivita a specificita MeSH
• směrnice pro lékařskou praxi jako téma * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

UNLABELLED: Nowadays the most used pipeline for protein identification consists in the comparison of the MS/MS spectra to reference databases. Search algorithms compare obtained spectra to an in silico digestion of a sequence database to find exact matches. In this context, the database has a paramount importance and will determine in a great deal the number of identifications and its quality, being this especially relevant for non-model plant species. Using a single Viridiplantae database (NCBI, UniProt) and TAIR is not the best choice for non-model species since they are underrepresented in databases resulting in poor identification rates. We demonstrate how it is possible to improve the rate and quality of identifications in two orphan species, Quercus ilex and Pinus radiata, by using SEQUEST and a combination of public (Viridiplantae NCBI, UniProt) and a custom-built specific database which contained 593,294 and 455,096 peptide sequences (Quercus and Pinus, respectively). These databases were built after gathering and processing (trimming, contiging, 6-frame translation) publicly available RNA sequences, mostly ESTs and NGS reads. A total of 149 and 1533 proteins were identified from Quercus seeds and Pinus needles, representing a 3.1- or 1.5-fold increase in the number of protein identifications and scores compared to the use of a single database. Since this approach greatly improves the identification rate, and is not significantly more complicated or time consuming than other approaches, we recommend its routine use when working with non-model species. BIOLOGICAL SIGNIFICANCE: In this work we demonstrate how the construction of a custom database (DB) gathering all available RNA sequences and its use in combination with Viridiplantae public DBs (NCBI, UniProt) significantly improve protein identification when working with non-model species. Protein identification rate and quality is higher to those obtained in routine procedures based on using only one database (commonly Viridiplantae from NCBI), as we demonstrated analyzing Quercus seeds and Pine needles. The proposed approach based on the building of a custom database is not difficult or time consuming, so we recommend its routine use when working with non-model species. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

• MeSH
• borovice genetika   metabolismus   MeSH
• databáze proteinů * MeSH
• dub (rod) genetika   metabolismus   MeSH
• proteom genetika   metabolismus   MeSH
• proteomika metody   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza proteinů metody   MeSH
• sekvenční analýza RNA metody   MeSH
• semena rostlinná genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• dataset MeSH
• práce podpořená grantem MeSH

Tento prehľadový článok zdôrazňuje kľúčovú úlohu hmotnosti a rozmerov orgánov ako základných ukazovateľov pri diagnostike v súdnom lekárstve a pato- lógii. Zmeny hmotnosti orgánov slúžia ako základné markery patologických stavov a pomáhajú súdnym lekárom a patológom pri interpretácii nálezov z pitvy. Prehľad zdôrazňuje dôležitosť presnosti pri stanovovaní referenčných hodnôt orgánov, berúc do úvahy faktory, ako sú špecifické referenčné hodnoty pre po- puláciu a rovnako tak korelácie s telesnými parametrami. Okrem toho skúma vplyv obezity na hmotnosti orgánov, pričom zdôrazňuje potrebu aktualizovania databáz, ktoré presne odrážajú rôzne populácie. Článok podčiarkuje nedostatočnosť spoliehania sa na zastarané zdroje a obhajuje vytvorenie komplexnej a aktualizovanej databázy hmotností a rozmerov orgánov pre lokálnu populáciu, ktorá je nevyhnutná pre presnú forenznú interpretáciu výsledkov pitvy.

This review article highlights the crucial role of organ weights and dimensions as key indicators in forensic diagnosis. Organ weight changes serve as valuable markers for pathological conditions, aiding forensic doctors in interpreting autopsy findings. The review emphasizes the importance of precision in establish- ing organ reference values, considering factors like population-specific norms and correlations with body parameters. Furthermore, it explores the impact of obesity on organ weights, emphasizing the need for updated databases that accurately reflect diverse populations. The article underscores the inadequacy of relying on outdated sources and advocates for creating a comprehensive and updated database of organ weights and dimensions for the local population, essential for accurate forensic interpretations.

• MeSH
• obezita patologie   MeSH
• pitva * metody   MeSH
• referenční hodnoty MeSH
• tělesné váhy a míry klasifikace   MeSH
• velikost orgánu * MeSH
• Publikační typ
• přehledy MeSH

The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists-a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.

• MeSH
• Archaea * MeSH
• Bacteria genetika   MeSH
• Eukaryota * genetika   MeSH
• fylogeneze MeSH
• geny rRNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• enzymy MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie

Radon risk mapping at building sites in the Czech Republic indicate an advisable level of protection of buildings against the penetration of radon from the geological basement. Various techniques and instruments are used for the measurement of radon in soil gas. A national radon chamber and three radon reference sites in Central Bohemia enable radon data standardisation. Tests of field radon measurements and the reported radon activity concentration in soil gas at the reference sites are based on comparisons with other organisations and with a database of reference site measurements. The radon reference sites have been used for various investigations of radon in soil gas during the period 2000-07.

• MeSH
• dávka záření MeSH
• financování organizované MeSH
• monitorování radiace normy   přístrojové vybavení   MeSH
• plyny analýza   MeSH
• radiační ochrana normy   přístrojové vybavení   MeSH
• radioaktivní látky znečišťující půdu analýza   MeSH
• radioaktivní látky znečišťující vzduch analýza   MeSH
• radon analýza   MeSH
• referenční hodnoty MeSH
• reprodukovatelnost výsledků MeSH
• senzitivita a specificita MeSH
• znečištění vzduchu ve vnitřním prostředí analýza   prevence a kontrola   MeSH
• Geografické názvy
• Česká republika MeSH

Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High-quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1-5P' DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high-quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.

• MeSH
• členovci genetika   MeSH
• databáze nukleových kyselin * MeSH
• entomologie MeSH
• polymerázová řetězová reakce MeSH
• respirační komplex IV genetika   MeSH
• sekvenční analýza DNA MeSH
• soudní vědy * MeSH
• taxonomické DNA čárové kódování * MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Světová databázová centra se svými databázemi jsou často pro běžného uživatele hůře dostupná ne z důvodu jejich komerčního charakteru, ale že o nich uživatel nemá povědomí. Přehled databázových center, která mají ve své nabídce lékařské nebo farmaceutické databáze, často unikátní a specializované. Role lékařské knihovny ve zprostředkování přístupu k těmto databázím.

The world database vendors with their databases are not known usually for typical users of scientific information, because the centers are based on fee, and also there are other organisational barriers. The brief overview of database vendors, which offers medical or pharmaceutical databases, often unique and specialized. The role of medical libraries in the brokerage of access. Search and reference services.

• MeSH
• databáze jako téma MeSH
• farmaceutické databáze MeSH
• informační služby MeSH
• lékařství MeSH