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3,696 results for “reference”
The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.
<p><em>The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.</em></p>
Selected references for analyzing the urban metabolism term and the urban metabolism concept
<p>This file contains textual data and metadata collected within the framework of a research project on the concept of urban metabolism headed by Professor Daniela Perrotti and supported by the Belgian Fund for Scientific Reseach F.R.S-FNRS under Grant n° MIS-F.4536.22. </p> <p> </p>
LDIC 2024 - List of References
<p>List of references used for the conference paper "A Bibliometric Analysis of Literature on Emission inventories in Seaports: A Study of related Literature".</p>
Dataset for "Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"
<p><strong>存放"Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"文章中的相关数据。</strong></p> <p>包括blastn出来的原始output文件;mtDNA-like short segments fastq文件;ATAC-seq的fastq文件;</p> <p>以及文章中提及的supplementary 表格和bed文件</p>
Ultrasonic Pulse Transmission Tests: Datasets - Test Series 3, Reference Tests on Air
<p>The test series was created to receive information about the impact of the behaviour of two different piezoelectric shear wave sensors on the measurement results of ultrasonic pulse transmission tests. The approach for the test series was to vary the parameters pulse-width and the shear-wave-sensor-type. This results in a two-dimensional test parameter grid (pulse-width versus shear-wave-sensor-type). Tests were performed for each grid point in order to receive information needed to optimize the pulse width, but also a possible dependency between material and sensor behaviour. The material tested was the air of the laboratory environment. The test method used was the ultrasonic pulse transmission method with combined compression- and shear wave measurements. All test data and metadata are summarized into datasets using GNU Octave's open binary file format.</p>
Ultrasonic Pulse Transmission Tests: Datasets - Test Series 7, Reference Tests on Aluminium Cylinder
<p>The test series was created in order to validate the stability and functionality of the test device and to create a data reference for metals (aluminium cylinder). The approach for the test series was to vary the parameters number-of-samples-recorded and pulse-voltage. This results in a two-dimensional test parameter grid. Tests were performed several times for each grid point (number-of-samples-recorded versus pulse-voltage) in order to receive statistical information about the stability of the test results. The material tested was an aluminium cylinder with a diameter of 50 millimetres and a height of 50 millimetres. The test method used was the ultrasonic pulse transmission method with combined compression- and shear wave measurements. All test data and metadata are summarized into datasets using GNU Octave's open binary file format.</p>
Ultrasonic Pulse Transmission Tests: Datasets - Test Series 6, Reference Tests on Water
<p>The test series was created in order to validate the stability and functionality of the test device and to create a data reference for liquid materials (water). The approach for the test series was to vary the parameters number-of-samples-recorded, pulse-voltage and distance-between-actuator-and-sensor. This results in a three-dimensional test parameter grid. Tests were performed several times for each grid point (number-of-samples-recorded versus pulse-voltage versus distance-between-actuator-and-sensor) in order to receive statistical information about the stability of the test results. The material tested was water from the tap of the laboratory water supply system. The test method used was the ultrasonic pulse transmission method with combined compression- and shear wave measurements. All test data and metadata are summarized into datasets using GNU Octave's open binary file format.</p>
Ultrasonic Pulse Transmission Tests: Datasets - Test Series 5, Reference Tests on Air
<p>The test series was created in order to validate the stability and functionality of the test device and to create a data reference for aeriform materials (air). The approach for the test series was to vary the parameters number-of-samples-recorded, pulse-voltage and distance-between-actuator-and-sensor. This results in a three-dimensional test parameter grid. Tests were performed several times for each grid point (number-of-samples-recorded versus pulse-voltage versus distance-between-actuator-and-sensor) in order to receive statistical information about the stability of the test results. The material tested was the air in the laboratory room. The test method used was the ultrasonic pulse transmission method with combined compression- and shear wave measurements. All test data and metadata are summarized into datasets using GNU Octave's open binary file format.</p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
Gene prediction for: A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides
<div> <div> <div> <div>Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star,<em> Pycnopodia helianthoides</em>, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus <em>Pisaster</em>. These novel genomic resources for <em>Pycnopodia helianthoides</em> will underwrite population genomic, comparative genomic, and phylogenomic analyses — as well as their integration across scales — of SSW and environmental stressors. This data resource contains the files associated with gene prediction.</div> </div> </div> </div>
Fig. 44. Character 64. Uncal lateral lobes, states 0 and 1 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 44. Character 64. Uncal lateral lobes, states 0 and 1: (0) absent; (1) present.
Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella)
<p>Reference transcriptome sequences (superTranscripts) of a marine teleost fish <em>Parapercis pulchella</em>.</p> <p>This dataset is a part of our work, "Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (<em>Parapercis</em> pulchella)" published in <em>Marine Genomics</em>.</p> <p>https://doi.org/10.1016/j.margen.2024.101086</p> <p> If you use this dataset, plese cite the above paper.</p> <p>Raw RNA-seq data and <em>de novo </em>assembled sequences generated by Trinity have been deposited in NCBI/DDBJ/EMBL under accession PRJDB16534.</p> <p>This dataset is generated from Trinity raw-assembled sequences using superTranscripts method (Corset, Lace). </p> <p>Functional annotations were conducted using eggNog-mapper, KEEG Automatic Annotation Server (KAAS), and reciprocal BLAST best-hit analysis against medaka's protein sequences.</p> <p> </p> <p>The codes for generating these data are deposited in GitHub (<a href="https://github.com/yaoakifumi/Ppul-reference-transcriptome">https://github.com/yaoakifumi/Ppul-reference-transcriptome</a>).</p> <p> </p>
A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants
<p>Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.</p>
Stratification reference points for Luhansk region tree cover change (1996,2000,2013,2020)
<p><strong>Occupation of Environment: Long-Term Consequences of war in Ukraine on conservation of forested areas of Emerald Network in the Luhansk region - </strong>Generated sample points that reflect stratification type and landcover change for Luhansk region for tree cover change area estimation. The division into territories controlled by Ukraine and Russia made based on the demarcation line with consideration of the buffer zone, where Ukrainian institutions were disconnected due to the active warfare in purpose of separation of zones with interruption of Ukrainian environmental policies.</p>
Effect of egocentric and allocentric reference frames on spatial numerical associations
<p>From an embodied view of cognition, sensorimotor mechanisms are strongly involved in abstract processing, such as Arabic number meanings. For example, spatial cognition can influence number processing. These spatial-numerical associations (SNAs) have been deeply explored since the seminal spatial-numerical associations of response code (SNARC) effect (i.e., faster left/right sided responses to small/large magnitude numbers, respectively). While these SNAs along the transverse plane (left-to-right axis) have been extensively studied in cognitive sciences, no systematic assessment of other planes of the tridimensional space has been afforded. Moreover, there is no evidence of how SNAs organize themselves throughout the changes in spatial body-reference frames (egocentric and allocentric). Hence, this study aimed to explore how SNAs organize themselves along the transverse and sagittal planes when egocentric and allocentric changes are processed during body displacements in the environment. In the first experiment, the results revealed that when the participants used an egocentric reference, SNAs were observed only along the sagittal plane. In a second experiment that used an allocentric reference, the reversed pattern of results was observed: SNAs were present only along the transverse plane of the body. Overall, these findings suggest that depending on the spatial reference frames of the body, SNAs are strongly flexible.</p>
Genome and Transcriptome references based on hg19 from UCSC, 2015
<p>rsem.transcripts.nant2015.fa.gz - bgzipped FASTA reference of transcriptomes</p><p>genome.nant2015.fa.gz - bgzipped FASTA human genome reference, with several viral sequences added.</p><p>refseq.txt.gz - Exact sequence accessions and mapping coordinates for a RefSeq transcriptome based off the UCSC genome browser for hg19.</p><p>Coordinates are BED-style, with one row per transcript, and 1+ transcript per gene.</p><p>Column annotation</p><p>1. RefSeq Accession</p><p>2. Chromosome</p><p>3. Strand</p><p>4. thinStart (gene boundary, including UTR)</p><p>5. thinEnd (gene boundary, including UTR)</p><p>6. thickStart (CDS boundary)</p><p>7. thinStart (CDS boundary)</p><p>8. number of exons</p><p>9. comma separated exon starts</p><p>10. comma separate exon ends</p><p>11. common gene name</p><p>12. refseq gene id</p><p>13. 0 if non-primary transcript, 1 if primary transcript</p>
Physiological Reference Values of Total Arterial Impedance Derived From PRAM Monitoring
ClinicalTrials.gov study NCT07340333. IPD Sharing: NO. Countries: 1. Publications: 7.
A Study Evaluating the Safety and Efficacy of LentiGlobin BB305 Drug Product in β-Thalassemia Major (Also Referred to as Transfusion-dependent β-Thalassemia [TDT]) and Sickle Cell Disease
ClinicalTrials.gov study NCT02151526. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Comparison of Technegas and Xenon-133 Planar Lung Imaging in Subjects Referred for Ventilation Scintigraphy
ClinicalTrials.gov study NCT03054870. IPD Sharing: NO. Countries: 1. Publications: 0.
Comparing Smoking Cessation Interventions Among Underserved Patients Referred for Lung Cancer Screening
ClinicalTrials.gov study NCT04798664. IPD Sharing: YES. Countries: 1. Publications: 1.
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.