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Systematic and Applied Microbiology May 2024Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise...
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov.
Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 and Flavobacterium bizetiae, 99.0 % for strain F-65 and Flavobacterium branchiarum, 98.7 % for strain F-126 and Flavobacterium tructae, 98.2 % for strain F-323 and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 shared 100 % identical 16S rRNA genes, while strains F-323 and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 , F-65 , F-70 , F126 and F-323 represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 (=JCM 34194 = KCTC 82254 ), Flavobacterium pisciphilum sp. nov. F-65 (=JCM 34197 = KCTC 82257 ), Flavobacterium flavipigmentatum sp. nov. F-70 (Fl-33 = Fl-77 = JCM 34198 = KCTC 82258 ), Flavobacterium lipolyticum sp. nov. F-126 (JCM 34199 = KCTC 82259 ) and Flavobacterium cupriresistens sp. nov. F-323 (Fl-318 = JCM 34200 = KCTC 82260 ), are proposed.
PubMed: 38761464
DOI: 10.1016/j.syapm.2024.126518 -
The Science of the Total Environment Jul 2024Although seaweeds rank among the most productive vegetated habitats globally, their inclusion within Blue Carbon frameworks is at its onset, partially because they...
Although seaweeds rank among the most productive vegetated habitats globally, their inclusion within Blue Carbon frameworks is at its onset, partially because they usually grow in rocky substrates and their organic carbon (C) is mostly exported and stored beyond their habitat and thus, demonstrating its long-term storage is challenging. Here, we studied the sedimentary C storage in macroalgal forests dominated by Gongolaria barbata and in adjacent seagrass Cymodocea nodosa mixed with Caulerpa prolifera algae meadows, and bare sand habitats in Mediterranean shallow coastal embayments. We characterized the biogeochemistry of top 30 cm sedimentary deposits, including sediment grain-size, organic matter and C contents, C burial rates and the provenance of sedimentary C throughout stable carbon isotopes (δC) and pyrolysis analyses. Sediment C stocks and burial rates (since 1950) in G. barbata forests (mean ± SE, 3.5 ± 0.2 kg C m accumulated at 15.5 ± 1.6 g C m y) fall within the range of those reported for traditional Blue Carbon Ecosystems. Although the main species contributing to sedimentary C stocks in all vegetated habitats examined was C. nodosa (36 ± 2 %), macroalgae contributed 49 % (19 ± 2 % by G. barbata and 30 ± 3 % by C. prolifera) based on isotope mixing model results. Analytical pyrolysis confirmed the presence of macroalgae-derived compounds in the sediments, including N-compounds and α-tocopherol linked to G. barbata and C. prolifera, respectively. The sedimentary C burial rate linked to macroalgae within the macroalgal forests examined ranged from 5.4 to 9.5 g C m y (7.4 ± 2 g C m y). This study provides empirical evidence for the long-term (∼70 years) sequestration of macroalgae-derived C within and beyond seaweed forests in Mediterranean shallow coastal embayments and thereby, supports the inclusion of macroalgae in Blue Carbon frameworks.
Topics: Seaweed; Forests; Carbon Sequestration; Carbon; Mediterranean Sea; Environmental Monitoring; Ecosystem; Geologic Sediments
PubMed: 38750738
DOI: 10.1016/j.scitotenv.2024.173219 -
Brain and Behavior May 2024
Topics: Humans; Attention Deficit Disorder with Hyperactivity; Sensation
PubMed: 38747736
DOI: 10.1002/brb3.3501 -
RoFo : Fortschritte Auf Dem Gebiete Der... May 2024Worldwide, the study and examination of human remains and the circumstances of their acquisition for anatomical collection have received great interest. As part of...
Worldwide, the study and examination of human remains and the circumstances of their acquisition for anatomical collection have received great interest. As part of provenance research projects, a large number of collections are being investigated to determine whether the human remains have been acquired in a correct or unlawful way because the people could have been killed in order to be used as "anthropological objects" for research purposes and to become so-called "specimens". These topics have also been addressed by the Institute of Anatomy at the University Medical Center Rostock. The role of radiology in this interdisciplinary project will be presented using selected examples.The anatomical collection at the University of Rostock includes 40 human skulls, 14 plaster casts, 6 Egyptian mummy heads, and 1 full-body mummy. In addition to the examination by a historian, an anthropologist, and forensic pathologists, additional computed tomography was carried out on nine skulls and the full-body mummy. Micro-computed tomography was also carried out on seven skulls in order to enable a look behind the mummification material and tissue remains.(Micro-)computed tomography was able to close diagnostic gaps and the results presented some rather unexpected findings.Due to interdisciplinary collaboration, individual fates could be determined, which provided information about the individual's life and death circumstances. None of the examined individuals showed evidence of colonial-era injustice or the use of violence that would have led to their inclusion in the collection. (Micro-)computed tomography was a valuable addition to this provenance research project. · Computed tomography enhances interdisciplinary provenance research projects.. · Computed tomography enables a non-destructive examination of human remains.. · The future of research and presentation of human remains will increasingly be virtual.. · Steinhagen I, Brinker U, Kolbe V et al. The role of radiology in provenance research - experiences from the collaboration between radiology and anatomy at the University of Rostock and future perspectives. Fortschr Röntgenstr 2024; DOI 10.1055/a-2303-0312.
PubMed: 38744319
DOI: 10.1055/a-2303-0312 -
Journal of the American Medical... Jun 2024Error analysis plays a crucial role in clinical concept extraction, a fundamental subtask within clinical natural language processing (NLP). The process typically...
BACKGROUND
Error analysis plays a crucial role in clinical concept extraction, a fundamental subtask within clinical natural language processing (NLP). The process typically involves a manual review of error types, such as contextual and linguistic factors contributing to their occurrence, and the identification of underlying causes to refine the NLP model and improve its performance. Conducting error analysis can be complex, requiring a combination of NLP expertise and domain-specific knowledge. Due to the high heterogeneity of electronic health record (EHR) settings across different institutions, challenges may arise when attempting to standardize and reproduce the error analysis process.
OBJECTIVES
This study aims to facilitate a collaborative effort to establish common definitions and taxonomies for capturing diverse error types, fostering community consensus on error analysis for clinical concept extraction tasks.
MATERIALS AND METHODS
We iteratively developed and evaluated an error taxonomy based on existing literature, standards, real-world data, multisite case evaluations, and community feedback. The finalized taxonomy was released in both .dtd and .owl formats at the Open Health Natural Language Processing Consortium. The taxonomy is compatible with several different open-source annotation tools, including MAE, Brat, and MedTator.
RESULTS
The resulting error taxonomy comprises 43 distinct error classes, organized into 6 error dimensions and 4 properties, including model type (symbolic and statistical machine learning), evaluation subject (model and human), evaluation level (patient, document, sentence, and concept), and annotation examples. Internal and external evaluations revealed strong variations in error types across methodological approaches, tasks, and EHR settings. Key points emerged from community feedback, including the need to enhancing clarity, generalizability, and usability of the taxonomy, along with dissemination strategies.
CONCLUSION
The proposed taxonomy can facilitate the acceleration and standardization of the error analysis process in multi-site settings, thus improving the provenance, interpretability, and portability of NLP models. Future researchers could explore the potential direction of developing automated or semi-automated methods to assist in the classification and standardization of error analysis.
Topics: Electronic Health Records; Natural Language Processing; Humans; Classification; Medical Errors
PubMed: 38742455
DOI: 10.1093/jamia/ocae101 -
Comprehensive Reviews in Food Science... May 2024Food authentication and contamination are significant concerns, especially for consumers with unique nutritional, cultural, lifestyle, and religious needs. Food...
Food authentication and contamination are significant concerns, especially for consumers with unique nutritional, cultural, lifestyle, and religious needs. Food authenticity involves identifying food contamination for many purposes, such as adherence to religious beliefs, safeguarding health, and consuming sanitary and organic food products. This review article examines the issues related to food authentication and food fraud in recent periods. Furthermore, the development and innovations in analytical techniques employed to authenticate various food products are comprehensively focused. Food products derived from animals are susceptible to deceptive practices, which can undermine customer confidence and pose potential health hazards due to the transmission of diseases from animals to humans. Therefore, it is necessary to employ suitable and robust analytical techniques for complex and high-risk animal-derived goods, in which molecular biomarker-based (genomics, proteomics, and metabolomics) techniques are covered. Various analytical methods have been employed to ascertain the geographical provenance of food items that exhibit rapid response times, low cost, nondestructiveness, and condensability.
Topics: Animals; Humans; Food Analysis; Food Contamination; Metabolomics; Proteomics
PubMed: 38741454
DOI: 10.1111/1541-4337.13360 -
BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Neoplasms; England; Community Pharmacy Services; Early Detection of Cancer; Pharmacies
PubMed: 38740425
DOI: 10.1136/bmj-2023-077087 -
Journal of AOAC International May 2024The identification of the geographical origin of Polygonatum cyrtonema Hua is of particular importance because the quality and market value of Polygonatum cyrtonema Hua...
BACKGROUND
The identification of the geographical origin of Polygonatum cyrtonema Hua is of particular importance because the quality and market value of Polygonatum cyrtonema Hua from different production areas are highly variable due to differences in the growing environment and climatic conditions.
OBJECTIVE
This study utilized near-infrared spectra (NIR) of Polygonatum cyrtonema Hua (n = 400) to develop qualitative models for effective differentiation of Polygonatum cyrtonema Hua from various regions.
METHODS
The models were produced under different conditions to distinguish the origins distinctly. Ten pre-processing methods have been used to pre-process the original spectra (OS) and to select the most optimal spectral pre-processing method. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA) were employed to determine appropriate models. For simplicity, the pretreated full spectrum was calculated by different wavelength selection methods, and the four most significant variables were selected as discriminant indicator variables.
RESULTS
The results show that Polygonatum cyrtonema Hua from different regions can be effectively distinguished using spectra from a series of samples analyzed by OPLS-DA. The accuracy of the OPLS-DA model is also satisfactory, with a good differentiation rate.
CONCLUSION
The study findings indicate the feasibility of using spectroscopy in combination with multivariate analysis to identify the geographical origins of Polygonatum cyrtonema Hua.
HIGHLIGHTS
The utilization of near-infrared spectroscopy combined with chemometrics exhibits high efficacy in discerning the provenance of herbal medicines and foods, thereby facilitating quality assurance measures.
PubMed: 38733574
DOI: 10.1093/jaoacint/qsae036 -
Journal of Materials Chemistry. A May 2024Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by full control of the data gathering process. In...
Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by full control of the data gathering process. In this work, we demonstrate tooling which bridges these two aspects, and illustrate its use in a case study of automated battery cycling. We successfully interface off-the-shelf battery cycling hardware with the computational workflow management software AiiDA, allowing us to control experiments, while ensuring trust in the data by tracking its provenance. We design user interfaces compatible with this tooling, which span the inventory, experiment design, and result analysis stages. Other features, including monitoring of workflows and import of externally generated and legacy data are also implemented. Finally, the full software stack required for this work is made available in a set of open-source packages.
PubMed: 38725523
DOI: 10.1039/d3ta06889g -
International Journal of Systematic and... May 2024Two yellow-coloured strains, F-29 and F-340, were isolated from fish farms in Antalya and Mugla in 2015 and 2017 during surveillance studies. The 16S rRNA gene sequence...
Two yellow-coloured strains, F-29 and F-340, were isolated from fish farms in Antalya and Mugla in 2015 and 2017 during surveillance studies. The 16S rRNA gene sequence analysis showed that both strains belong to the genus . A polyphasic approach involving a comprehensive genome analysis was employed to ascertain the taxonomic provenance of the strains. The overall genome-relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus were found to be well below the established thresholds of 70 and 95 %, respectively. The whole-genome-based phylogenetic analysis revealed that strain F-29 is closely related to (dDDH 39.3 % and ANI 89.4 %), while strain F-340 has a close relationship with the type strain of (dDDH 25.6 % and ANI 81.5 %). Both strains were psychrotolerant with an optimum growth temperature of 25 °C. The chemotaxonomic characteristics of the strains were typical of the genus . Both strains had phosphatidylethanolamine, aminolipids and unidentified lipids in their polar lipid profile and MK-6 as the isoprenoid quinone. The major fatty acids were iso-C and anteiso-C. The genome size of the strains was 3.5 Mb, while G+C contents were 35.3 mol% for strain F-29 and 33.4 mol% for strain F-340. Overall, the characterizations confirmed that both strains are representatives of two novel species within the genus , for which the names sp. nov. and sp. nov. are proposed, with F-29 (JCM 34193=KCTC 82253) and F-340 (JCM 34203=KCTC 82263) as the type strains, respectively.
Topics: Flavobacterium; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Bacterial Typing Techniques; DNA, Bacterial; Animals; Nucleic Acid Hybridization; Sequence Analysis, DNA; Vitamin K 2; Fishes; Genome, Bacterial; Aquaculture; Phosphatidylethanolamines
PubMed: 38717929
DOI: 10.1099/ijsem.0.006369