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720 results for “Identification data”
Data for "Identification of Karst Spring Hydrographs Using Laboratory and Numerical Simulations Considering Combined Discrete-Continuum Approaches"
<p>This is the dataset for "Identification of Karst Spring Hydrographs Using Laboratory and Numerical Simulations Considering Combined Discrete-Continuum Approaches”.</p>
FIGURE 1 in On identification errors in Scytalopus speluncae (Ménétriés) and S. pachecoi Maurício from southern Brazil with new data on distribution and biogeography of these taxa (Aves: Rhinocryptidae)
FIGURE 1. Specimens of tapaculos from southern Brazil with disputed identification. Above, adult male of Scytalopus pachecoi (MHNCI 5491) previously wrongly identified as S. speluncae. Below, immature male of S. speluncae (MHNCI 3452) erroneously identified as S. pachecoi by other authors. The white arrow points to the upper primary coverts and alula, which are light brown/buff with a wide blackish stripe along the feather shaft, a condition characteristic of young S. speluncae and never present in S. pachecoi.
FIGURE 2 in On identification errors in Scytalopus speluncae (Ménétriés) and S. pachecoi Maurício from southern Brazil with new data on distribution and biogeography of these taxa (Aves: Rhinocryptidae)
FIGURE 2. Global distributions of S. speluncae (dark gray) and S. pachecoi (light gray) based on published records, mainly from Maurício et al. (2010, 2014). Dotted ellipse-like line encircles a small area where the two species are sympatric. Scytalopus speluncae: 1 = R. L. Taborda; 2 = Limoeiro. Scytalopus pachecoi: 3 = Fazenda Tunas; 4 = Fazenda Mangueira de Pedra (see text for details). Abbreviations for Brazilian states: RS, Rio Grande do Sul; SC, Santa Catarina; PR, Paraná; SP, São Paulo; RJ, Rio de Janeiro; ES, Espírito Santo; MG, Minas Gerais; MS, Mato Grosso do Sul; for other countries (in bold font): URU, Uruguay; ARG, Argentina; PAR, Paraguay.
Raw data of "Identification of two unannotated miRNAs in classic Hodgkin lymphoma cell lines" article.
<p>This is the dataset with used raw data regarding preparation of the manuscript entitled "Identification of two unannotated miRNAs in classic Hodgkin lymphoma cell lines" (10.1371/journal.pone.0283186).</p>
Test data for the shared task Ideology and Power Identification in Parliamentary Debates 2024
<p>This dataset contains a selection of speeches from <a href="https://www.clarin.eu/parlamint">ParlaMint</a> corpora (version 4.0) as the test set for the shared task on "<a href="https://touche.webis.de/clef24/touche24-web/ideology-and-power-identification-in-parliamentary-debates.html">Ideology and Power Identification in Parliamentary Debates</a>" in <a href="https://clef2024.imag.fr/">CLEF 2024</a>. The format of the files are similar to the <a title="training set" href="10450640">training set</a>, with the exception that the labels are not provided in this data set.</p>
Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies"
<p>Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies." The datasets contain nanopore and Sanger sequencing data (including the electropherograms) as well as EPI2ME and NGSpeciesID analysis.</p>
States of genome assembly supporting data for complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.
<p>Assemblies for each isolate and assembly stage is in .gfa and .fasta format.</p> <p>the best SPAdes assembly is also included in the .zip files.</p> <p>1) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong.<br> 2) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong and error corrected with Canu<br> 3) Unicycler with illumina data and Nanopore data from the first and second sequencing run, filtered with FiltLong.<br> 4) manual finshing of assembly 3. <br> Methods are described in the paper and at the github repository (https://github.com/thsyd/bfassembly)</p> <p> </p>
Computational Data for Identification of an allosteric binding site on the Glycine Transporter, GlyT2
<p>Input structures and gromacs trajectories for Identification of an allosteric binding site on the Glycine Transporter, GlyT2, for bioactive lipid analgensics</p>
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7). in An integrative taxonomic revision of the genus Triphosa Stephens, 1829 (Geometridae: Larentiinae) in the Middle East and Central Asia, with description of two new species
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7).
Image data used for publication "Species-level image classification with convolutional neural network enable insect identification from habitus images "
<p>Image-crops of specimens from insect drawers</p> <p>In 2017 we scanned 208 insect drawers containing the collection of british carabids from the Natural History Museum London and extracted crops from the scanned images. This database contain 63.364 specimens that we used to train, validate and test a convolutional neural network.</p> <p>Each folder is named as the gbif id number. E.g. Carabus problematicus is 4470555: https://www.gbif.org/species/4470555</p>
Data Sets for: Trace elements in aerosol from Northwest Pacific marginal sea, Indian Ocean and South Pacific to Antarctica: Spatial variability and source identification
<p>This dataset includes the concentrations of trace elements in aerosols, along with location and time information, collected during a cruise from November 2021 to April 2022. The cruise covered the Pacific, the Indian Ocean, the Southern Ocean.</p>
Datos de identificación y aspectos metodológicos de los estudios seleccionados/ Identification data and methodological aspects of the selected studies
<p>Datos de identificación y aspectos metodológicos de los estudios seleccionados/ Identification data and methodological aspects of the selected studies</p> <p><span>Una década de investigación sobre la eficacia de las prácticas de educación inclusiva y el DUA en la universidad. </span><span>Revisión sistemática de la literatura.</span></p> <p><em><span>A decade of research on the effectiveness of inclusive education practices and UDL in universities. Systematic literature review.</span></em></p> <p><span><span>María Pineda-Martínez</span></span></p>
Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms
<p>Metadata files for our final analysis as part of the "<span><span>Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms" study.</span></span></p>
Data from: "Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015
Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus tephrosceles), which is a highly threatened monkey due to habitat loss. We analyzed blood samples from 24 individuals from Kibale National Park (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of which 58,814,906 passed the filtering steps. Using the program STACKS v. 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had a mean observed heterozygosity of 0.25. These data will be used to study the effects of habitat fragmentation on genomic diversity, dispersal, and disease transmission in this species. Our approach provides a good example of the potential of RAD sequencing in studies of wild primate populations.
Data from: Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional-level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus that obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of airborne dispersed fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost-efficient way to include fungi as a part of large-scale biodiversity assessments and monitoring programs.
Data from: Strain identification and quorum sensing inhibition characterization of marine-derived Rhizobium sp. NAO1
A novel strategy for combating pathogens is through the ongoing development and use of anti-quorum sensing (QS) treatments such as therapeutic bacteria or their anti-QS substances. Relatively little is known about the bacteria that inhabit the open ocean and of their potential anti-pathogenic attributes; thus, in an initiative to identify these types of therapeutic bacteria, planktonic microbes from the North Atlantic Ocean were collected, isolated, cultured and screened for anti-QS activity. Screening analysis identified one such strain, Rhizobium sp. NAO1. Extracts of Rhizobium sp. NAO1 were identified via ultra-performance liquid chromatography (UPLC) analysis. They were shown to contain N-acyl homoserine lactone (AHL)-based QS analogues (in particular, the N-butyryl homoserine lactone (C4-AHL) analogue) and could disrupt biofilm formation by Pseudomonas aeruginosa PAO1. QS inhibition was confirmed using confocal scanning laser microscopy and growth curves, and it was shown to occur in a dose-dependent manner without affecting bacterial growth. Secondary metabolites of Rhizobium sp. NAO1 inhibited PAO1 pathogenicity by downregulating AHL-mediated virulence factors such as elastase activity and siderophore production. Furthermore, as a result of biofilm structure damage, the secondary metabolite products of Rhizobium sp. NAO1 significantly increased the sensitivity of PAO1 to aminoglycoside antibiotics. Our results demonstrated that Rhizobium sp. strain NAO1 has the ability to disrupt P. aeruginosa PAO1 biofilm architecture, in addition to attenuating P. aeruginosa PAO1 virulence factor production and pathogenicity. Therefore, the newly identified ocean-derived Rhizobium sp. NAO1 has the potential to serve as a QS inhibitor and may be a new microbial resource for drug development.
Data from: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape
The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain, and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful DNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season, and distance from forest) varied between the three responses. Nuclear microsatellite amplification of DNA from jaguar faeces had lower success rates (15–44%) compared with those of the mtDNA marker. Our results show that DNA identification of carnivore species from faecal samples works efficiently in the Amazon forest and can provide data on species occurrence as well as a valuable tool for genetic, ecological and conservation studies.
Data from: A framework for the identification of long-term social avoidance in longitudinal datasets
Animal sociality is of significant interest to evolutionary and behavioural ecologists, with efforts focused on the patterns, causes and fitness outcomes of social preference. However, individual social patterns are the consequence of both attraction to (preference for) and avoidance of conspecifics. Despite this, social avoidance has received far less attention than social preference. Here, we detail the necessary steps to generate a spatially explicit, iterative null model which can be used to identify non-random social avoidance in longitudinal studies of social animals. We specifically identify and detail parameters which will influence the validity of the model. To test the usability of this model, we applied it to two longitudinal studies of social animals (Eastern water dragons (Intellegama leseurii) and bottlenose dolphins (Tursiops aduncus) to identify the presence of social avoidances. Using this model allowed us to identify the presence of social avoidances in both species. We hope that the framework presented here inspires interest in addressing this critical gap in our understanding of animal sociality, in turn allowing for a more holistic understanding of social interactions, relationships and structure.
Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
Background: Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results: Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
Data from: Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs
<p>The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis (LoD), which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record, our results suggest patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.