This work presents an automated data-mining model for age-at-death estimation based on 3D scans of the auricular surface of the pelvic bone. The study is based on a multi-population sample of 688 individuals (males and females) originating from one Asian and five European identified osteological collections. Our method requires no expert knowledge and achieves similar accuracy compared to traditional subjective methods. Apart from data acquisition, the whole procedure of pre-processing, feature extraction and age estimation is fully automated and implemented as a computer program. This program is a part of a freely available web-based software tool called CoxAGE3D. This software tool is available at https://coxage3d.fit.cvut.cz/ Our age-at-death estimation method is suitable for use on individuals with known/unknown population affinity and provides moderate correlation between the estimated age and actual age (Pearson's correlation coefficient is 0.56), and a mean absolute error of 12.4 years.

• MeSH
• data mining MeSH
• faciální stigmatizace MeSH
• lidé MeSH
• obličej MeSH
• pánevní kosti * diagnostické zobrazování   MeSH
• software MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články 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

Age-at-death estimation of adult skeletal remains is a key part of biological profile estimation, yet it remains problematic for several reasons. One of them may be the subjective nature of the evaluation of age-related changes, or the fact that the human eye is unable to detect all the relevant surface changes. We have several aims: (1) to validate already existing computer models for age estimation; (2) to propose our own expert system based on computational approaches to eliminate the factor of subjectivity and to use the full potential of surface changes on an articulation area; and (3) to determine what age range the pubic symphysis is useful for age estimation. A sample of 483 3D representations of the pubic symphyseal surfaces from the ossa coxae of adult individuals coming from four European (two from Portugal, one from Switzerland and Greece) and one Asian (Thailand) identified skeletal collections was used. A validation of published algorithms showed very high error in our dataset-the Mean Absolute Error (MAE) ranged from 16.2 and 25.1 years. Two completely new approaches were proposed in this paper: SASS (Simple Automated Symphyseal Surface-based) and AANNESS (Advanced Automated Neural Network-grounded Extended Symphyseal Surface-based), whose MAE values are 11.7 and 10.6 years, respectively. Lastly, it was demonstrated that our models could estimate the age-at-death using the pubic symphysis over the entire adult age range. The proposed models offer objective age estimates with low estimation error (compared to traditional visual methods) and are able to estimate age using the pubic symphysis across the entire adult age range.

• MeSH
• data mining MeSH
• dospělí MeSH
• lidé MeSH
• soudní antropologie metody   MeSH
• symphysis pubica * MeSH
• určení kostního věku metody   MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

• MeSH
• big data MeSH
• data mining metody   MeSH
• expertní systémy MeSH
• lékařská informatika metody   trendy   MeSH
• správnost dat MeSH
• strojové učení MeSH
• umělá inteligence * MeSH

Human-nature relationships are an important aspect of leisure research. Previous studies also reported that nature-related activities have a health benefit. In this study, we surveyed US-American birdwatchers at two time points during the COVID pandemic (independent samples). During the beginning of the COVID pandemic in spring 2020, we analyzed their comments with an AI sentiment analysis. Approximately one year later (winter 2020/21), during the second wave, the study was repeated, and a second data set was analyzed. Here we show that during the ongoing pandemic, the sentiments became more negative. This is an important result because it shows that despite the positive impact of nature on mental health, the sentiments become more negative in the enduring pandemic.

• MeSH
• COVID-19 * MeSH
• lidé MeSH
• pandemie MeSH
• postoj MeSH
• postojová analýza MeSH
• SARS-CoV-2 MeSH
• sociální média * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Spojené státy americké MeSH

Developments in information technology have impacted on all areas of modern life and in particular facilitated the growth of globalisation in commerce and communication. Within the drugs area this means that both drugs discourse and drug markets have become increasingly digitally enabled. In response to this, new methods are being developed that attempt to research and monitor the digital environment. In this commentary we present three case studies of innovative approaches and related challenges to software-automated data mining of the digital environment: (i) an e-shop finder to detect e-shops offering new psychoactive substances, (ii) scraping of forum data from online discussion boards, (iii) automated sentiment analysis of discussions in online discussion boards. We conclude that the work presented brings opportunities in terms of leveraging data for developing a more timely and granular understanding of the various aspects of drug-use phenomena in the digital environment. In particular, combining the number of e-shops, discussion posts, and sentiments regarding particular substances could be used for ad hoc risk assessments as well as longitudinal drug monitoring and indicate "online popularity". The main challenges of digital data mining involve data representativity and ethical considerations.

• MeSH
• data mining MeSH
• léčivé přípravky * MeSH
• lidé MeSH
• monitorování léčiv MeSH
• obchod MeSH
• poruchy spojené s užíváním psychoaktivních látek * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Intensive care unit (ICU) is a very special unit of a hospital, where healthcare professionals provide treatment and, later, close follow-up to the patients. It is crucial to estimate mortality in ICU patients from many viewpoints. The purpose of this study is to classify the status of patients with acute kidney injury (AKI) in ICU as early mortality, late mortality, and survival by the application of Classification and Regression Trees (CART) algorithm to the patients' attributes such as blood urea nitrogen, creatinine, serum and urine neutrophil gelatinase-associated lipocalin (NGAL), alkaline phosphatase, lactate dehydrogenase (LDH), gamma-glutamyl transferase, laboratory electrolytes, blood gas, mean arterial pressure, central venous pressure and demographic details of patients. This study was conducted 50 patients with AKI who were followed up in the ICU. The study also aims to determine the significance of relationship between the attributes used in the prediction of mortality in CART and patients' status by employing the Kruskal-Wallis H test. The classification accuracy, sensitivity, and specificity of CART for the tested attributes for the prediction of early mortality, late mortality, and survival of patients were 90.00%, 83.33%, and 91.67%, respectively. The values of both urine NGAL and LDH on day 7 showed a considerable difference according to the patients' status after being examined by the Kruskal-Wallis H test.

• MeSH
• akutní poškození ledvin * mortalita   MeSH
• algoritmy MeSH
• biologické markery analýza   MeSH
• data mining metody   MeSH
• dospělí MeSH
• klasifikace MeSH
• laktátdehydrogenasy analýza   MeSH
• lidé MeSH
• lipokalin-2 analýza   MeSH
• metody pro podporu rozhodování MeSH
• mortalita v nemocnicích * MeSH
• prognóza MeSH
• rozhodovací podpůrné systémy pro řízení MeSH
• rozhodovací stromy MeSH
• statistika jako téma MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH

Background: The beginning of the coronavirus disease (COVID-19) epidemic dates back to December 31, 2019, when the first cases were reported in the People's Republic of China. In the Czech Republic, the first three cases of infection with the novel coronavirus were confirmed on March 1, 2020. The joint effort of state authorities and researchers gave rise to a unique team, which combines methodical knowledge of real-world processes with the know-how needed for effective processing, analysis, and online visualization of data. Objective: Due to an urgent need for a tool that presents important reports based on valid data sources, a team of government experts and researchers focused on the design and development of a web app intended to provide a regularly updated overview of COVID-19 epidemiology in the Czech Republic to the general population. Methods: The cross-industry standard process for data mining model was chosen for the complex solution of analytical processing and visualization of data that provides validated information on the COVID-19 epidemic across the Czech Republic. Great emphasis was put on the understanding and a correct implementation of all six steps (business understanding, data understanding, data preparation, modelling, evaluation, and deployment) needed in the process, including the infrastructure of a nationwide information system; the methodological setting of communication channels between all involved stakeholders; and data collection, processing, analysis, validation, and visualization. Results: The web-based overview of the current spread of COVID-19 in the Czech Republic has been developed as an online platform providing a set of outputs in the form of tables, graphs, and maps intended for the general public. On March 12, 2020, the first version of the web portal, containing fourteen overviews divided into five topical sections, was released. The web portal's primary objective is to publish a well-arranged visualization and clear explanation of basic information consisting of the overall numbers of performed tests, confirmed cases of COVID-19, COVID-19-related deaths, the daily and cumulative overviews of people with a positive COVID-19 case, performed tests, location and country of infection of people with a positive COVID-19 case, hospitalizations of patients with COVID-19, and distribution of personal protective equipment. Conclusions: The online interactive overview of the current spread of COVID-19 in the Czech Republic was launched on March 11, 2020, and has immediately become the primary communication channel employed by the health care sector to present the current situation regarding the COVID-19 epidemic. This complex reporting of the COVID-19 epidemic in the Czech Republic also shows an effective way to interconnect knowledge held by various specialists, such as regional and national methodology experts (who report positive cases of the disease on a daily basis), with knowledge held by developers of central registries, analysts, developers of web apps, and leaders in the health care sector.

• Klíčová slova
• webová aplikace,
• MeSH
• analýza dat MeSH
• Betacoronavirus MeSH
• COVID-19 * MeSH
• data mining * MeSH
• epidemie statistika a číselné údaje   MeSH
• hlášení nemocí MeSH
• informační systémy * MeSH
• koronavirové infekce * MeSH
• lidé MeSH
• Check Tag
• lidé MeSH
• Geografické názvy
• Česká republika MeSH

Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database. In total, 760 487 protein domains from 42 371 protein models were mapped to hg19 coordinates and made publicly available for search or download (www.prot2hg.com). In addition, this annotation was implemented into the genomics research platform GENESIS in order to query nearly 8000 exomes and genomes of families with rare Mendelian disorders (tgp-foundation.org). When applied to patient genetic data, we found that rare (<1%) variants in the Genome Aggregation Database were significantly more annotated onto a protein domain in comparison to common (>1%) variants. Similarly, variants described as pathogenic or likely pathogenic in ClinVar were more likely to be annotated onto a domain. In addition, we tested a dataset consisting of 60 causal variants in a cohort of patients with epileptic encephalopathy and found that 71% of them (43 variants) were propagated onto protein domains. In summary, we developed a resource that annotates variants in the coding part of the genome onto conserved protein domains in order to increase variant prioritization efficiency.Database URL: www.prot2hg.com.

• MeSH
• anotace sekvence metody   MeSH
• data mining metody   MeSH
• databáze genetické * MeSH
• datové kurátorství metody   MeSH
• genetická variace * MeSH
• genom lidský genetika   MeSH
• genomika metody   MeSH
• internet MeSH
• lidé MeSH
• proteinové domény genetika   MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Siderophores represent important microbial virulence factors and infection biomarkers. Their monitoring in fermentation broths, bodily fluids, and tissues should be reproducible. Similar isolation, characterization, and quantitation studies can often have conflicting results, and without proper documentation of sample collection, data processing, and analysis methods, it is difficult to reexamine the data and reconcile these differences. In this Springer Nature Protocol, we present the procedure optimized for ferricrocin/triacetylfusarinine C extraction from biological material as well as for tissue fixation and cryosectioning for optical microscopy and for both elemental and molecular mass spectrometry imaging. Special attention is paid to siderophore data mining from conventional and product ion mass spectra, liquid chromatography, and mass spectrometry imaging datasets, performed here by our free software called CycloBranch.

• MeSH
• Aspergillus fumigatus metabolismus   MeSH
• biologické markery analýza   MeSH
• chromatografie kapalinová metody   MeSH
• data mining metody   MeSH
• datové soubory jako téma MeSH
• ferrichrom analogy a deriváty   izolace a purifikace   metabolismus   MeSH
• fixace tkání metody   MeSH
• hmotnostní spektrometrie metody   MeSH
• invazivní plicní aspergilóza diagnóza   mikrobiologie   MeSH
• kryoultramikrotomie metody   MeSH
• krysa rodu rattus MeSH
• kyseliny hydroxamové izolace a purifikace   metabolismus   MeSH
• lidé MeSH
• modely nemocí na zvířatech MeSH
• siderofory izolace a purifikace   metabolismus   MeSH
• software MeSH
• železité sloučeniny izolace a purifikace   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH