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1,007 results for “single use”
Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.
Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
Supplementary information to "ScRNA-IMM: Single-cell RNA-Seq Imputation method using Mean/Median Imputation"
Open the record for dataset details and reuse information.
Healthy woodchuck genome with viral sequences appended used for single-cell RNA-seq analysis
Open the record for dataset details and reuse information.
Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing
<p>Source data for our circSC manuscript.</p>
Label-Free Differentiation of Living versus Dead Single Yeast Cells using Broadband Electrical Impedance Spectroscopy
<p>Data to support manuscript.</p>
Data from: Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data
1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (PURC: "Pipeline for Untangling Reticulate Complexes") that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multilabeled species tree for a subset of our accessions. We amplified four ~1kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. PURC infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly-polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads PURC was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
Single-electron spin resonance in a nanoelectronic device using a global field
<p><span class="pre-line-wrapping ng-binding">Spin-based silicon quantum electronic circuits offer a scalable platform for quantum computation, combining the manufacturability of semiconductor devices with the long coherence times afforded by spins in silicon. Advancing from current few-qubit devices to silicon quantum processors with upwards of a million qubits, as required for fault-tolerant operation, presents several unique challenges, one of the most demanding being the ability to deliver microwave signals for large-scale qubit control. Here we demonstrate a potential solution to this problem by using a three-dimensional dielectric resonator to broadcast a global microwave signal across a quantum nanoelectronic circuit. Critically, this technique utilizes only a single microwave source and is capable of delivering control signals to millions of qubits simultaneously. We show that the global field can be used to perform spin resonance of single electrons confined in a silicon double quantum dot device, establishing the feasibility of this approach for scalable spin qubit control.</span></p>
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
<p>This dataset contains gene expression values, i. e. transcript counts, of 278 intestinal epithelial cells.</p>
Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon
<p>Processed data use in the the Mellon manuscript</p> <p>The following scanpy anndata objects are also available</p> <ol> <li>preprocessed_t-cell-depleted-bm-rna.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data, cell-state densities, B-cell primed and lineage accessibility scores.</li> <li>preprocessed_t-cell-depleted-bm-atac.h5ad: Anndata object for the RNA modality of the T-cell depleted bone marrow multiome dataset with normalized data, cell type annotations, clusters, cell-state densities, B-cell primed and lineage peaks.</li> <li>preprocessed_t-cell-depleted-bm-rna-metacells.h5ad: Anndata object with metacells for the RNA modality of the T-cell depleted bone marrow multiome dataset .</li> <li>preprocessed_mouse-gastrulation-atlas.h5ad: Anndata object of the preprocessed mouse gastrulation data with normalized data, cell type annotations, clusters, pseudo time, fate propensities, MAGIC imputed expression data,</li> </ol>
Red blood cell trapping using single-beam acoustic tweezers in the Rayleigh regime
<p>Here are the datasets and original code used for the title 'Red blood cell trapping using single-beam acoustic tweezers in the Rayleigh regime.'</p>
Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"
<p>Data and scripts accompanying the paper <em>Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp</em>.</p> <ul> <li>d.zip contains raw MS data from samples run on timsTOF SCP.</li> <li>raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240).</li> <li>mzML.zip contains raw MS data in mzML format from all samples.</li> <li>sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data.</li> <li>sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData.</li> <li>example_subset.zip contains csv files for short example datasets displayed in the paper.</li> <li>scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs.</li> <li>build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation.</li> </ul> <p>These file descriptions are also available in the README.txt file.</p>
Clinical Study of a Single-Use, Point-of-Care Molecular Diagnostic Device for the Detection of Neisseria Gonorrhoeae (NG), Trichomonas Vaginalis (TV), and Chlamydia Trachomatis (CT) Utilizing Vaginal
ClinicalTrials.gov study NCT03596151. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Single-Armed Use of ViviGen Cellular Bone Matrix in Patients Undergoing Posterolateral Lumbar Surgery
ClinicalTrials.gov study NCT04007094. IPD Sharing: NO. Countries: 1. Publications: 0.
Combined Use of Apatinib Mesylate and Vinorelbine Versus Single Use of Vinorelbine in Triple-negative Breast Cancer
ClinicalTrials.gov study NCT03932526. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Consumer Perception of an Experimental Mouthwash After a Single Use in Dry Mouth Subjects
ClinicalTrials.gov study NCT03005041. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Single-Use Negative Pressure Wound Therapy System vs. Traditional Negative Pressure Wound Therapy System (tNPWT)
ClinicalTrials.gov study NCT02470806. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Volume Versus Concentration: Clinical Effectiveness of Single Shot Quadrates Lumborum Block Using Either a High Volume/Low Concentration or Low Volume/High Concentration Injectate for Total Hip Arthro
ClinicalTrials.gov study NCT04259645. IPD Sharing: NO. Countries: 1. Publications: 0.
An Open Single-centre Investigation Evaluating Efficacy in Second Degree Partial Thickness Burns Using a Silicone Contact Layer Containing Silver.
ClinicalTrials.gov study NCT01734317. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.