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720 results for “Identification data”
Figure 17 from: Tibpromma S, Hyde K, Bhat J, Mortimer P, Xu J, Promputtha I, Doilom M, Yang J, Tang A, Karunarathna S (2018) Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 33: 25-67. https://doi.org/10.3897/mycokeys.33.23670
Figure 17 - Mycoleptodiscus endophyticus (MFLU 18-0001, holotype). a Colony on MEA media b, c Mycelia masses d–f Vegetative hyphae in culture. Scale bars: 10 μm (b–d), 5 μm (e, f).
Figure 4 from: Tibpromma S, Hyde K, Bhat J, Mortimer P, Xu J, Promputtha I, Doilom M, Yang J, Tang A, Karunarathna S (2018) Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 33: 25-67. https://doi.org/10.3897/mycokeys.33.23670
Figure 4 - Endopandanicola thailandica (MFLU 18-0021, holotype). a Mycelia masses b, c Clamp connections. Scale bars: 10 μm (a), 5 μm (b, c).
Data From "Radar-Based Deep Learning for Debris Flow Identification amid the Environmental Disturbances"
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Data from: Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification. 2) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring. 3) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R2 were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as expensive as morphology-based identification. 4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.
Data from: Identification of resistance to bacterial leaf blight in the U.S. Department of Agriculture Collard Collection
Bacterial leaf blight incited by Pseudomonas cannabina pv. alisalensis (Pca) is a devastating disease with incidence reports worldwide and a wide host range capable of infecting all commercially valuable Brassica crops. With no chemical control options available, the most effective form of disease control is host plant resistance, but thus far resistant germplasm has only been identified in Brassica juncea L. (mustard greens). We report the first screening of Brassica oleracea L. var. viridis germplasm, including leafy green collard and collard-like accessions, for resistance to bacterial leaf blight by artificial inoculation of Pca in greenhouse trials. All commercial cultivars tested displayed an intermediate disease response resulting in leaf lesion development that renders the product unmarketable. Two sources of significant resistance were identified in the U.S. Department of Agriculture (USDA) viridis collection, which provides a valuable source of resistance alleles for collard cultivar development and introgression into other B. oleracea crops.
Data from: Portable bacteria-capturing chip for direct surface-enhanced Raman scattering identification of urinary tract infection pathogens
Acute urinary tract infections (UTIs) are one of the most common nosocomial bacterial infections, which affect almost 50% of the population at least once in their lifetime. UTIs may lead to lethal consequences if they are left undiagnosed and untreated properly. Early, rapid and accurate uropathogens detection methods play a pivotal role in clinical process. In this work, a portable bacteria-grasping surface-enhanced Raman scattering (SERS) chip for identification of three species of uropathogens (E. coli CFT 073, P. aeruginosa PAO1, and P. mirabilis PRM1) directly from culture matrix was reported. The chip was firstly modified with a positively-charged NH3+ group, which enable itself grasp the negatively-charged bacterial cells through the electrostatic adsorption principle. After the bacterial cells were captured by the chip, concentrated Ag nanoparticles (NPs) were used to obtain their Raman fingerprint spectra with recognizable characteristic peaks and good reproducibility. With the help of chemometric method such as discriminant analysis (DA), the SERS based chip allows a rapid, successful identification of three species of UTI bacteria with a minimal bacterial concentration (105 cells/mL) required for clinical diagnostics. In addition, this chip could spot the bacterial SERS fingerprints information directly from LB culture medium and artificial urine without sample pre-treatment. The portable bacteria-grasping SERS based chip provides a possibility for fast and easy detection of uropathogens, and viability of future development in healthcare applications.
Data from: Identification of habitat-specific biomes of aquatic fungal communities using a comprehensive nearly full-length 18S rRNA dataset enriched with contextual data
Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
Data from: Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
<p><b>Background:</b> Although the effects of macrophages and CD8 T cell infiltration on clinical outcomes have been widely reported, the association between immunity-associated gene with them for hepatocellular carcinoma (HCC) remains unclear.</p> <p><b>Materials and methods: </b>The ssGSEA served for quantifying the macrophages as well as CD8 T cell infiltration in the HCC samples obtained from TCGA database. Kaplan-Meier(KM) survival assay was used to determine the associations between macrophages and CD8 T cell infiltration with OS. LASSO Cox regressive method assisted in developing an immune gene signature as well as building a risk score. The performance was evaluated by the time-dependent ROC together with the KM survival analysis. The ICGC database were adopted for external verification. CIBERSORT was applied to the correlation analysis on the immune-related signature and the immunocyte infiltration. GSEA were employed exploring the underlying molecular mechanisms.</p> <p><b>Results:</b> Increased CD8+ T cell infiltration was associated with longer OS, whereas a greater infiltration of macrophages was related to shorter OS. There were 398 differential expression genes (DEGs) between the high- and low infiltration groups with the "edgeR" package. A prognostic signature consisted of 10 immune genes was built in TCGA and examined in ICGC. The uniform cutoff (0.927) was adopted for separating sufferers into the high-risk(HR) and low-risk(LR) groups. The ROC curves revealed that the AUC data for this signature predicting 1,2,3,4 and 5 year were all above 0.7 in both TCGA and ICGC cohort and patients in the HR<sub> </sub>group exhibited evidently weaker prognostic results compared with the LR group. The HR<sub> </sub>group presented evidently greater Tregs and Macrophage M0 relative to the LR group, whereas the LR group saw the enrichment of CD8 T cells.</p> <p><b>Conclusion:</b> The immune signature associated with macrophages as well as CD8 T cell infiltration has reliable prognostic and predictive value for HCC patients.</p>
Raw data- IDENTIFICATION PERFORMANCE DURING QUARANTINE BY COVID 19 PANDEMIC: INFLUENCE OF EMOTIONAL VARIABLES AND SLEEP QUALITY
<p>The raw data supporting the conclusions of this article</p>
Data of "Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning"
<p>This is the data and assosiated in-house code for the paper:</p> <p>Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning</p> <p>Sander Roet, Christopher D. Daub, and Enrico Riccardi</p> <p>Journal of Chemical Theory and Computation <strong>2021</strong> <em>17</em> (10), 6193-6202</p> <p>DOI: 10.1021/acs.jctc.1c00458</p>
Figure 1 from: Sonet G, Jordaens K, Braet Y, Bourguignon L, Dupont E, Backeljau T, de Meyer M, Desmyter S (2013) Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France. ZooKeys 365: 307-328. https://doi.org/10.3897/zookeys.365.6027
Figure 1 - Best matches obtained for each species using five different search procedures:Barcode fragment (642–658 bp) submitted to GenBank (1) and the public records of BOLD (2); barcode fragment submitted to the species level records of BOLD, including early-released sequences (3); barcode fragment and keyword "barcode" submitted to GenBank (4) and longer COI fragment (1412–1534 bp) submitted to GenBank (5). Numbers of haplotypes used as queries are between parentheses. Longer COI fragments were obtained for all species except for Protophormia terraenovae.
Final Taxonomy for personality identification using SNS data
<p>blinded_for_Review</p>
Data for article entitled 'Anti-hiatus tendencies in Spanish: Rate of occurrence and phonetic identification'', published in Linguistics
<p>see the article</p>
iGEM Leiden 2023 - MALDI-TOF data for PHA identification
<p>Raw data of MALDI-TOF experiment aimed at identifying PHA in <em>Methylobacterium extorquens</em> AM1.</p>
Data Collection for Stress Identification
ClinicalTrials.gov study NCT02574871. IPD Sharing: Not stated. Countries: 0. Publications: 5.
Data from: Two-step pyrolysis-gas chromatography method with mass spectrometric detection for identification of tattoo ink ingredients and counterfeit products
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Data from: Identification of genetic defects in 33 probands with Stargardt disease by WES-based bioinformatics gene panel analysis
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Data from: Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
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Data from: Genome-wide identification of microsatellites and transposable elements in the dromedary camel genome using whole genome sequencing data
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.