• Publikační typ
• abstrakt z konference MeSH

SUMMARY: ShinySOM offers a user-friendly interface for reproducible, high-throughput analysis of high-dimensional flow and mass cytometry data guided by self-organizing maps. The software implements a FlowSOM-style workflow, with improvements in performance, visualizations and data dissection possibilities. The outputs of the analysis include precise statistical information about the dissected samples, and R-compatible metadata useful for the batch processing of large sample volumes. AVAILABILITY AND IMPLEMENTATION: ShinySOM is free and open-source, available online at gitlab.com/exaexa/ShinySOM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• algoritmy * MeSH
• metadata MeSH
• průběh práce MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• antropologie metody   MeSH
• databáze nukleových kyselin MeSH
• genom lidský genetika   MeSH
• lidé MeSH
• metadata MeSH
• mitochondriální DNA analýza   genetika   MeSH
• starobylá DNA * analýza   izolace a purifikace   MeSH
• vývoj člověka MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• přehledy MeSH

BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.

• MeSH
• alely * MeSH
• Arabidopsis * genetika   MeSH
• data mining * metody   MeSH
• datové soubory jako téma * MeSH
• frekvence genu MeSH
• genotyp MeSH
• Glycine max * genetika   MeSH
• internet * MeSH
• kukuřice setá * genetika   MeSH
• metadata MeSH
• mutace MeSH
• pigmentace genetika   MeSH
• rostlinné geny genetika   MeSH
• software * MeSH
• substituce aminokyselin MeSH
• vegetační klid genetika   MeSH
• vizualizace dat MeSH
• Publikační typ
• časopisecké články MeSH

Background: Our previous study analyzed the age trajectory of mortality (ATM) in 14 European countries, while this study aimed at investigating ATM in other continents and in countries with a higher level of mortality. Data from 11 Non-European countries were used. Methods: The number of deaths was extracted from the WHO mortality database. The Halley method was used to calculate the mortality rates in all possible calendar years and all countries combined. This method enables us to combine more countries and more calendar years in one hypothetical population. Results: The age trajectory of total mortality (ATTM) and also ATM due to specific groups of diseases were very similar in the 11 non-European countries and in the 14 European countries. The level of mortality did not affect the main results found in European countries. The inverse proportion was valid for ATTM in non-European countries with two exceptions. Slower or no mortality decrease with age was detected in the first year of life, while the inverse proportion model was valid for the age range (1, 10) years in most of the main chapters of ICD10. Conclusions: The decrease in child mortality with age may be explained as the result of the depletion of individuals with congenital impairment. The majority of deaths up to the age of 10 years were related to congenital impairments, and the decrease in child mortality rate with age was a demonstration of population heterogeneity. The congenital impairments were latent and may cause death even if no congenital impairment was detected.

• Publikační typ
• časopisecké články MeSH

Background: In humans, the mortality rate dramatically decreases with age after birth, and the causes of death change significantly during childhood. In the present study, we attempted to explain age-associated decreases in mortality for congenital anomalies of the central nervous system (CACNS), as well as decreases in total mortality with age. We further investigated the age trajectory of mortality in the biologically related category "diseases of the nervous system" (DNS). Methods: The numbers of deaths were extracted from the mortality database of the World Health Organization (WHO) for the following nine countries: Denmark, Finland, Norway, Sweden, Austria, the Czech Republic, Hungary, Poland, and Slovakia. Because zero cases could be ascertained over the age of 30 years in a specific age category, the Halley method was used to calculate the mortality rates in all possible calendar years and in all countries combined. Results: Total mortality from the first day of life up to the age of 10 years and mortality due to CACNS within the age interval of [0, 90) years can be represented by an inverse proportion with a single parameter. High coefficients of determination were observed for both total mortality (R2 = 0.996) and CACNS mortality (R2 = 0.990). Our findings indicated that mortality rates for DNS slowly decrease with age during the first 2 years of life, following which they decrease in accordance with an inverse proportion up to the age of 10 years. The theory of congenital individual risk (TCIR) may explain these observations based on the extinction of individuals with more severe impairments, as well as the bent curve of DNS, which exhibited an adjusted coefficient of determination of R¯2 = 0.966. Conclusion: The coincidence between the age trajectories of all-cause and CACNS-related mortality may indicate that the overall decrease in mortality after birth is due to the extinction of individuals with more severe impairments. More deaths unrelated to congenital anomalies may be caused by the manifestation of latent congenital impairments during childhood.

• Publikační typ
• časopisecké články MeSH

Background: Mortality rate rapidly decreases with age after birth, and, simultaneously, the spectrum of death causes show remarkable changes with age. This study analyzed age-associated decreases in mortality rate from diseases of all main chapters of the 10th revision of the International Classification of Diseases. Methods: The number of deaths was extracted from the mortality database of the World Health Organization. As zero cases could be ascertained for a specific age category, the Halley method was used to calculate the mortality rates in all possible calendar years and in all countries combined. Results: All causes mortality from the 1st day of life to the age of 10 years can be represented by an inverse proportion model with a single parameter. High coefficients of determination were observed for total mortality in all populations (arithmetic mean = 0.9942 and standard deviation = 0.0039). Slower or no mortality decrease with age was detected in the 1st year of life, while the inverse proportion method was valid for the age range [1, 10) years in most of all main chapters with three exceptions. The decrease was faster for the chapter "Certain conditions originating in the perinatal period" (XVI).The inverse proportion was valid already from the 1st day for the chapter "Congenital malformations, deformations and chromosomal abnormalities" (XVII).The shape of the mortality decrease was very different for the chapter "Neoplasms" (II) and the rates of mortality from neoplasms were age-independent in the age range [1, 10) years in all populations. Conclusion: The theory of congenital individual risks of death is presented and can explain the results. If it is valid, latent congenital impairments may be present among all cases of death that are not related to congenital impairments. All results are based on published data, and the data are presented as a supplement.

• Publikační typ
• časopisecké články MeSH

Bibliometrické údaje jsou základem nejen pro měření vědeckého výstupu, ale i pro softwarové nástroje, které pomáhají vědcům orientovat se ve stále rychleji rostoucí záplavě článků. Tyto nástroje pracují různými způsoby s metadaty bibliografických záznamů v databázích odborných publikací. Příspěvek představuje dva z těcchto nástrojů – VOSviewer a Connected Papers.

Bibliometric data are the basis not only for measuring scientific output, but also for software tools that help scientists navigate the ever-increasing flood of articles. These tools work in different ways with the metadata of bibliographic records in databases of scientific publications. This paper introduces two of these tools, VOSviewer and Connected Papers.

• MeSH
• formuláře a záznamy - kontrola a vedení MeSH
• mezinárodní spolupráce MeSH
• on-line systémy MeSH
• referenční standardy MeSH
• řízení kvality MeSH
• ukládání a vyhledávání informací MeSH
• Publikační typ
• příručky MeSH

• Konspekt
• Kancelář
• NLK Obory
• knihovnictví, informační věda a muzeologie

Srozumitelná publikace nabízí ucelený přehled o současných možnostech efektivního využití informačních a komunikačních technologií (ICT) ve firmách a jiných organizacích. Manažeři, podnikatelé, studenti VŠ a další uživatelé informačních systémů (IS) se seznámí s možnými přístupy k aktualizaci IS a ICT, s klíčovými aplikacemi, s informačními systémy pro řízení podniků, aplikacemi pro ukládání a analýzu dat, se zajišťováním datové kvality a významu metadat. Autorka se věnuje i problematice CRM a CPM systémů. Kniha dále informuje o možnostech rozvoje podnikání s ICT, o e-businessu, o základní klasifikaci a očekávaných trendech, a také o bezpečnosti IS, o aktuálních hrozbách a o přípravě bezpečnostní politiky firmy. Velkou předností knihy je srozumitelná, ucelená a přitom stručná deskripce dané problematiky tak, aby byla pochopitelná studentům a uživatelům bez hlubších znalostí informatiky, kteří mají zájem o zvýšení kvality podnikatelských a obchodních procesů využitím ICT.