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1,007 results for “single use”
Data from: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA
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Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads
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Data from: Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet
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Data from: Identifying litchi (Litchi chinensis Sonn.) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers
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Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
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Data from: Ecological forensics: using single point stable isotope values to infer seasonal schedules of animals after two diet switches
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Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
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Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
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High throughput measurement of single HeLa cell volume growth and cell cycle progression using FXm
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A dataset of long-term consistency values of resting-state fMRI connectivity maps in a single individual derived at multiple sites and vendors using the Canadian Dementia Imaging Protocol
<p>This dataset contains preprocessed resting state fMRI data (.nii.gz) with accompanying confound files (.tsv) from the Single Individual volunteer for Multiple Observations across Networks (SIMON; http://fcon_1000.projects.nitrc.org/indi/retro/SIMON.html) dataset that has been minimally preprocessed using the NeuroImaging Analysis Kit (NIAK; http://niak.simexp-lab.org/build/html/PREPROCESSING.html). Preprocessing steps included: (1) Slice timing correction; (2) Estimation of rigid-body motion in fMRI runs, both within- and between sessions; (3) Linear or non-linear coregistration of the structural scan in stereotaxic space; (4) Individual coregistration between structural and functional scans; (5) Resampling of functional scans in stereotaxic space. Confound files (.tsv) have been included for purposes of scrubbing and regression of confounds using NIAK or other analysis software, allowing for further processing without conflicts.</p>
Model and observational dataset used in Tsiringakis, A. , Holtslag, A.A.M., Grimmond, S. and Steeneveld, G.J. Surface and atmospheric driven variability of the single-layer urban canopy model under clear sky conditions over London, Journal of Geophysical Research: Atmospheres
<p>This dataset contains:</p> <p>- Model output from the single-column version of the Weather Research and Forecasting model v3.8.1.</p> <p>- Observations from the KSSW tower (King's College London, United Kingdom) used for model evaluation.</p> <p>- The Single-column Urban Boundary Layer Inter-comparison Model Experiment (SUBLIME) case study description and external forcing file for the single-column version of Weather Research and Forecasting model.</p> <p>This dataset is used in :</p> <p>~Tsiringakis, A., Holtslag, A.A.M., Grimmond, S. and Steeneveld, G.J. Surface and atmospheric driven variability of the single-layer urban canopy model under clear sky conditions over London. Journal of Geophysical Research: Atmospheres</p>
The molecular diversity of phagotrophic Euglenids examined using single-cell methods
<p>Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, andphagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose.We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from <em>Urceolus, Jenningsia, Chasmostoma</em>, and <em>Sphenomonas</em>, and expanded coverage for <em>Dinema</em> and <em>Heteronema</em> sensu lato, amongst others. <em>Urceolus</em> monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. <em>Heteronema vittatum</em> and similar cells branch separately from <em>Heteronema</em> (c.f.) <em>globuliferum</em> and <em>Teloprocta/Heteronema scaphurum</em>, while <em>Dinema</em> appears as 2–3 clades. <em>Sphenomonas</em> is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.</p>
Raw data associated with the article: "Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets.", NAR, Puchtler et.al.
<p>All data taken in the production of the corresponding paper: "Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets."</p> <p>The associated manuscript describes a method for DNA sequencing which involves the sequential release of nucleotides from a single, immobilised strand of DNA via pyrophosphorolysis (PPL). Released nucleotides, in the form of dNTPs, are captured in microdroplets which are manipulated using an optical-EWOD platform. A detection chemistry within each droplet releases a specific dye depending on which dNTPs are present, allowing the optical read-out of bases within each droplet. Hence, by capturing bases sequentially within droplets as they are cleaved from the strand of DNA, the sequence can be optically identified.</p>
Data Repository: Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes
<p>Data repository for the scMappR manuscript:</p> <p>Abstract from biorXiv (https://www.biorxiv.org/content/10.1101/2020.08.24.265298v1.full).</p> <p>RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN.</p>
Data from: Reliability of single-use PEEP-valves attached to self-inflating bags during manual ventilation of neonates – an in vitro study
Introduction International resuscitation guidelines suggest to use positive end-expiratory pressure (PEEP) during manual ventilation of neonates. Aim of our study was to test the reliability of self-inflating bags (SIB) with single-use PEEP valves regarding PEEP delivery and the effect of different peak inflation pressures (PIP) and ventilation rates (VR) on the delivered PEEP. Methods Ten new single-use PEEP valves from 5 manufacturers were tested by ventilating an intubated 1kg neonatal manikin containing a lung model with a SIB that was actuated by an electromechanical plunger device. Standard settings: PIP 20cmH2O, VR 60/min, flow 8L/min. PEEP settings of 5 and 10cmH2O were studied. A second test was conducted with settings of PIP 40cmH2O and VR 40/min. The delivered PEEP was measured by a respiratory function monitor (CO2SMO+). Results Valves from one manufacturer delivered no relevant PEEP and were excluded. The remaining valves showed a continuous decay of the delivered pressure during expiration. The median (25th and 75th percentile) delivered PEEP with standard settings was 3.4(2.7–3.8)cmH2O when set to 5cmH2O and 6.1(4.9–7.1)cmH2O when set to 10cmH2O. Increasing the PIP from 20 to 40 cmH2O led to a median (25th and 75th percentile) decrease in PEEP to 2.3(1.8–2.7)cmH2O and 4.3(3.2–4.8)cmH2O; changing VR from 60 to 40/min led to a PEEP decrease to 2.8(2.1–3.3)cmH2O and 5.0(3.5–6.2)cmH2O for both PEEP settings. Conclusion Single-use PEEP valves do not reliably deliver the set PEEP. PIP and VR have an effect on the delivered PEEP. Operators should be aware of these limitations when manually ventilating neonates.
Data from: Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets
DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
Data from: High-performance single-walled carbon nanotube transparent conducting film fabricated by using low feeding rate of ethanol solution
We report floating catalyst chemical vapor deposition synthesis of single-walled carbon nanotubes (SWCNTs) for high performance transparent conducting films (TCFs) using low feeding rate of precursor solution. Herein, ethanol acts as carbon source, ferrocene and thiophene as catalyst precursor and growth promoter, respectively. By adopting a low feeding rate of 4 μl/min, the fabricated TCFs present one of the lowest sheet resistances of ca. 78 ohm/sq. at 90% transmittance. Optical characterizations demonstrate that the mean diameter of high quality SWCNTs is up to 2 nm. Additionally, electron microcopy observations provide the evidences that the mean length of SWCNT bundles is as long as 28.4 μm while the mean bundle diameter is only 5.3 nm. Moreover, very few CNT loops can be found in the film. Remarkably, the fraction of individual SWCNTs climbs up to 24.6%. All those morphology data account for the superior optoelectronic performance of our SWCNT TCFs.
Data from: QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers
Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long-distance migrants typically have longer wings than short-distance migrants and sedentary species, and long-winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large-scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within-population variation of relative wing length (h2 = 0.74 ± 0.05) is associated with standing genetic variation in at least six genomic regions (one genome-wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co-locate with Wnt growth factors and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and RhoV). Our findings therefore suggest that standing genetic variation in the Wnt genes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.
Data from: Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule–coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.
Data from: Single mechanosensory neurons encode lateral displacements using precise spike timing and thresholds
During locomotion, animals rely on multiple sensory modalities to maintain stability. External cues may guide behavior, but they must be interpreted in the context of the animal's own body movements. Mechanosensory cues that can resolve dynamic internal and environmental conditions, like those from vertebrate vestibular systems or other proprioceptors, are essential for guided movement. How do afferent proprioceptor neurons transform movement into a neural code? In flies, modified hindwings known as halteres detect forces produced by body rotations, and are essential for flight. The mechanisms by which haltere neurons transform forces resulting from three-dimensional body rotations into patterns of neural spikes are unknown, however. We use intracellular electrodes to record from haltere primary afferent neurons during a range of haltere motions. We find that spike timing activity of individual neurons changes with displacement, and propose a mechanism by which single neurons can encode three-dimensional haltere movements during flight.
ScienceDex guides
Understand access before you commit
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.