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
New strains of non-vannellid flattened amoebae isolated from fish, an invertebrate and the marine environment were studied together with Flabellula citata Schaeffer, 1926 selected by morphology as a reference strain. The study revealed a paucity of features distinguishing individual strains at the generic level, but clearly evidenced mutual phylogenetic relationships within the assemblage of strains as well as their affiliation to the Leptomyxida. In this study, the SSU rDNA dataset of leptomyxids was expanded and a new branching pattern was presented within this lineage of Amoebozoa. Sequences of three newly introduced strains clustered in close relationship with the type strain of F. citata, the type species of the genus. Three strains, including one resembling Flamella sp., were positioned within a sister-group containing Paraflabellula spp. Results of phylogenetic analysis confirmed doubts of previous authors regarding generic assignment of several Rhizanmoeba and Ripidomnyxa strains.
- MeSH
- amébiáza genetika parazitologie veterinární MeSH
- Amoeba izolace a purifikace klasifikace ultrastruktura MeSH
- fylogeneze MeSH
- malé podjednotky ribozomu genetika MeSH
- molekulární sekvence - údaje MeSH
- nemoci ryb genetika parazitologie MeSH
- polymerázová řetězová reakce MeSH
- protozoální DNA genetika klasifikace MeSH
- ribozomální DNA genetika klasifikace MeSH
- ryby genetika parazitologie MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční seřazení MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
Small subunit rRNA sequences were obtained from 38 representatives mainly of the nematode orders Spirurida (Camallanidae, Cystidicolidae, Daniconematidae, Philometridae, Physalopteridae, Rhabdochonidae, Skrjabillanidae) and, in part, Ascaridida (Anisakidae, Cucullanidae, Quimperiidae). The examined nematodes are predominantly parasites of fishes. Their analyses provided well-supported trees allowing the study of phylogenetic relationships among some spirurine nematodes. The present results support the placement of Cucullanidae at the base of the suborder Spirurina and, based on the position of the genus Philonema (subfamily Philoneminae) forming a sister group to Skrjabillanidae (thus Philoneminae should be elevated to Philonemidae), the paraphyly of the Philometridae. Comparison of a large number of sequences of representatives of the latter family supports the paraphyly of the genera Philometra, Philometroides and Dentiphilometra. The validity of the newly included genera Afrophilometra and Caranginema is not supported. These results indicate geographical isolation has not been the cause of speciation in this parasite group and no coevolution with fish hosts is apparent. On the contrary, the group of South-American species of Alinema, Nilonema and Rumai is placed in an independent branch, thus markedly separated from other family members. Molecular data indicate that the skrjabillanid subfamily Esocineminae (represented by Esocinema bohemicum) should be either elevated to the rank of an independent family or Daniconematidae (Mexiconema africanum) should be decreased to Daniconematinae and transferred to the family Skrjabillanidae. Camallanid genera Camallanus and Procamallanus, as well as the subgenera Procamallanus and Spirocamallanus are confirmed to be paraphyletic. Paraphyly has also been found within Filarioidea, Habronematoidea and Thelazioidea and in Cystidicolidae, Physalopteridae and Thelaziidae. The results of the analyses also show that Neoascarophis, Spinitectus and Rhabdochona are monophyletic, in contrast to the paraphyletic genus Ascarophis. They further confirm the independence of two subgenera, Rhabdochona and Globochona, in the genus Rhabdochona. The necessity of further studies of fish-parasitizing representatives of additional nematode families not yet studied by molecular methods, such as Guyanemidae, Lucionematidae or Tetanonematidae, is underscored.
- MeSH
- DNA helmintů genetika chemie MeSH
- financování organizované MeSH
- fylogeneze MeSH
- hlístice genetika klasifikace patogenita MeSH
- molekulární sekvence - údaje MeSH
- nematodózy parazitologie veterinární MeSH
- nemoci ryb parazitologie MeSH
- ribozomální DNA genetika chemie MeSH
- ryby MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA veterinární MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
Background: Classifying diseases into ICD codes has mainly relied on human reading a large amount of written materials, such as discharge diagnoses, chief complaints, medical history, and operation records as the basis for classification. Coding is both laborious and time consuming because a disease coder with professional abilities takes about 20 minutes per case in average. Therefore, an automatic code classification system can significantly reduce the human effort. Objectives: This paper aims at constructing a machine learning model for ICD-10 coding, where the model is to automatically determine the corresponding diagnosis codes solely based on free-text medical notes. Methods: In this paper, we apply Natural Language Processing (NLP) and Recurrent Neural Network (RNN) architecture to classify ICD-10 codes from natural language texts with supervised learning. Results: In the experiments on large hospital data, our predicting result can reach F1-score of 0.62 on ICD-10-CM code. Conclusion: The developed model can significantly reduce manpower in coding time compared with a professional coder.
- MeSH
- automatizované zpracování dat metody MeSH
- deep learning * MeSH
- elektronické zdravotní záznamy MeSH
- mezinárodní klasifikace nemocí * MeSH
- neuronové sítě (počítačové) MeSH
- strojové učení MeSH
- ukládání a vyhledávání informací metody statistika a číselné údaje MeSH
- vizualizace dat MeSH
- zpracování přirozeného jazyka MeSH
- Publikační typ
- práce podpořená grantem MeSH
- MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- Myxozoa anatomie a histologie klasifikace genetika fyziologie MeSH
- nemoci ryb epidemiologie MeSH
- parazitární nemoci u zvířat epidemiologie parazitologie MeSH
- ribozomální DNA genetika MeSH
- ryby parazitologie MeSH
- žlučník parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Indický oceán epidemiologie MeSH
- Saudská Arábie MeSH
Ferroptosis is a recently described programmed cell death mechanism that is characterized by the buildup of iron (Fe)-dependent lipid peroxides in cells and is morphologically, biochemically, and genetically distinct from other forms of cell death, having emerged to play an important role in cancer biology. Ferroptosis has significant importance during cancer treatment because of the combination of factors, including suppression of the glutathione peroxidase 4 (Gpx4), cysteine deficiency, and arachidonoyl (AA) peroxidation, which cause cells to undergo ferroptosis. However, the physiological significance of ferroptosis throughout development is still not fully understood. This current review is focused on the factors and molecular mechanisms with the diagrammatic illustrations of ferroptosis that have a role in the initiation and sensitivity of ferroptosis in various malignancies. This knowledge will open a new road for research in oncology and cancer management.
- MeSH
- ferroptóza * MeSH
- fosfolipidová hydroperoxidglutathionperoxidasa MeSH
- lidé MeSH
- lipidové peroxidy MeSH
- nádory * farmakoterapie metabolismus MeSH
- peroxidace lipidů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
