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3,696 results for “reference”
Supervised jet clustering reference data
<p>A set of MC simulated events for training/testing machine learning architectures for the task of supervised jet clustering.<br> In total 100,000 W' events and 100,000 q* events<br> Description:<br> * 13 TeV collision data simulated with pythia 8.183.<br> * wboson.txt contains events generated from a W' boson with a mass of 600 GeV, which decays 100% of the time to a W boson and a Z boson. The W boson is forced to decay haronically and the Z boson decays into neutrinos.<br> * qstar.txt contains events generated from a excited quark q* with a mass of 600 GeV, which decays 100% of the time to a quark and a Z boson. The Z boson is forced to decay into neutrinos.<br> * events in the text format<br> * each line in the text represent one event, which contains variable number of detector-stable particles.<br> * each particle contains 7 features in order: [px, py, pz, E, pdgID, is-from-W, is-in-leading-jet]. The first four features are the four momentum of the particle, and pdgID is the pag number of the particle. is-from-W is 1 if the particle coming from W boson and 0 otherwise. is-in-leading-jet is 1 if the particle is inside the leading jet reconstructed from the anti-kT jet algorithm (R=1.0).</p> <p> </p>
Dataset for A Modified Approach for Process-Integrated Reference Point Determination
<p>The Global Geodetic Observing System (GGOS) calls for continues and automated determination of the geometric reference points of space-geodetic techniques such as DORIS, GNSS, SLR and VLBI. Whereas the reference points of DORIS beacons and GNSS antennas can simply be measured by observing well-defined reference markers, the determination of SLR and VLBI reference points are a metrological challenge, because these reference points are inaccessible and non-materialized. Indirect methods are needed to estimate the reference points in a rigorous way, which fulfil the requirements on an automated and continues reference point determination of the Global Geodetic Observing System. In this investigation, a modified approach for reference point determination of SLR and VLBI telescopes is presented. The results of the new approach are compared to proven reference point models. The numerical deviations of the estimated reference point coordinates and the axis-offset are <<50 μm and demonstrate the equivalence of the new approach.</p>
Construction of a chromosome-scale long-read reference genome assembly for potato
<p><span><strong>Background:</strong> Worldwide, the cultivated potato, <i>Solanum tuberosum </i>L<i>.</i>, is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. <i>tuberosum </i>Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. </span></p> <p><span><strong>Findings: </strong>Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared to the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the numbersof contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. </span></p> <p><span><strong>Conclusions: </strong>Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.</span></p>
RVDB-prot, a reference viral protein database and its HMM profiles
<p>We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.</p>
External References of English Wikipedia (ref-wiki-en)
<p><strong>External References of English Wikipedia </strong>(<strong>ref-wiki-en</strong>) is a corpus of the plain-text content of 2,475,461 external webpages linked from the reference section of articles in English Wikipedia. Specifically:</p> <ul> <li>32,329,989 external reference URLs were extracted from a <a href="https://zenodo.org/record/3483254">2018 HTML dump of English Wikipedia</a>. Removing repeated and ill-formed URLs yielded 23,036,318 unique URLs.</li> <li>These URLs were filtered to remove file extensions for unsupported formats (videos, audio, etc.), yielding 17,781,974 downloadable URLs. The URLs were loaded into <a href="http://nutch.apache.org/">Apache Nutch</a> and continuously downloaded from August 2019 to December 2019, resulting in 2,475,461 successfully downloaded URLs. Not all URLs could be accessed. The order in which URLs were accessed was determined by Nutch, which partitions URLs by <a href="https://docs.oracle.com/javase/7/docs/api/java/net/URL.html#getHost()">host</a> and then randomly chooses amongst the URLs for each host.</li> <li>The content of these webpages were indexed in <a href="https://lucene.apache.org/solr/">Apache Solr</a> by Nutch. From Solr we extracted a JSON dump of the content.</li> <li>Many URLs offer a redirect; unfortunately Nutch does not index redirect information. This means that connecting the Wikipedia article (with the pre-direct link) to the downloaded webpage (at the post-redirect link) was complicated. However, by inspecting the order of download in the Nutch log files, we managed to recover links for 2,058,896 documents (83%) from their original Wikipedia article(s).</li> <li>We further managed to associate 3,899,953 unique Wikidata items with at least one external reference webpage in the corpus.</li> </ul> <p>The ref-en-wiki corpus is incomplete, i.e., we did not attempt to download all reference URLs for English Wikipedia. We thus also collect a smaller complete corpus for the external references of 5,000 Wikipedia articles (<strong>ref-wiki-en-5k</strong>). We sampled from 5 ranges of Wikidata items: Q1-10000, Q10001-100000, Q100001-1000000, Q1000001-10000000, and Q10000001-100000000. From each range we sampled 1000 items. We then scraped the external reference URLs for the Wikipedia article corresponding to these items and downloaded them. The resulting corpus contains 37,983 webpages.</p> <p>Each line of the corpus (ref-wiki-en, ref-wiki-en-5k) encodes the webpage of an external reference in JSON format. Specifically, we provide:</p> <ul> <li><em>tstamp</em>: When the webpage was accessed</li> <li><em>host</em>: The domain (FQDN post-redirect) from which the webpage was retrieved.</li> <li><em>title</em>: The title (meta) of the document</li> <li><em>url</em>: The URL (post-redirect) of the webpage</li> <li><em>Q</em>: The Q-code identifiers of the Wikidata items whose corresponding Wikipedia article is confirmed to link to this webpage.</li> <li><em>content</em>: A plain-text encoding of the content of the webpage.</li> </ul> <p>Below we provide an abbreviated example of a line from the corpus:</p> <pre><code>{"tstamp":"2019-09-26T01:22:43.621Z","host":"geology.isu.edu","title":"Digital Geology of Idaho - Basin And Range","url":"http://geology.isu.edu/Digital_Geology_Idaho/Module9/mod9.htm","Q":[810178],"content":"Digital Geology of Idaho - Basin And Range\n1 - Idaho Basement Rock\n2 - Belt Supergroup\n3 - Rifting & Passive Margin\n4 - Accreted Terranes\n5 - Thrust Belt\n6 - Idaho Batholith\n7 - North Idaho & Mining\n8 - Challis Volcanics\n9 - Basin and Range\n10 - Columbia River Basalts\n11 - SRP & Yellowstone\n12 - Pleistocene Glaciation\n13 - Palouse & Lake Missoula\n14 - Lake Bonneville Flood\n15 - Snake River Plain Aquifer\nBasin and Range Province - Teritiary Extension\nGeneral geology of the Basin and Range Province\nMechanisms of Basin and Range faulting\nIdaho Basin and Range south of the Snake River Plain\nIdaho Basin and Range north of the Snake River Plain\nLocal areas of active and recent Basin & Range faulting: Borah Peak\nPDF Slideshows: North of SRP , South of SRP , Borah Earthquake\nFlythroughs: Teton Valley , Henry's Fork , Big Lost River , Blackfoot , Portneuf , Raft River Valley , Bear River , Salmon Falls Creek , Snake River , Big Wood River\nVocabulary Words\nthrust fault\nBasin and Range\nSnake River Plain\nhalf-graben\ntransfer zone\n \n \n \n \nFly-throughs\nGeneral geology of the Basin and Range Province\nThe Basin and Range Province generally includes most of eastern California, eastern Oregon, eastern Washington, Nevada, western Utah, southern and western Arizona, and southeastern Idaho. ..."},</code></pre> <p>A summary of the files we make available:</p> <ul> <li><strong>ref-wiki-en.json.gz</strong>: 2,475,461 external reference webpages (JSON format)</li> <li><strong>ref-wiki-en_urls.txt.gz</strong>: 23,036,318 unique raw links to external references (plain-text format)</li> <li><strong>ref-wiki-en-5k.json.gz</strong>: 37,983 external reference webpages (JSON format)</li> <li><strong>ref-wiki-en-5k_urls.json.gz</strong>: 70,375 unique raw links to external references (plain-text format)</li> <li><strong>ref-wiki-en-5k_Q.txt.gz</strong>: 5,000 Wikidata Q identifiers forming the 5k dataset (plain-text format)</li> </ul> <p>Further details can be found in the publication:</p> <ul> <li><em>Suggesting References for Wikidata Claims based on Wikipedia's External References</em>. Paolo Curotto, Aidan Hogan. Wikidata Workshop @ISWC 2020.</li> </ul> <p>Further material relating to this publication (including code for a proof-of-concept interface) is <a href="http://aidanhogan.com/wikiref/">also available</a>.</p>
Raw data for reference flow experiments
<p>Raw results data for the reference flow study. Reference flow used public sequence data, where is specified in the manuscript, to generate the results. The figures shown in the manuscript were plotted using the provided processed data.</p> <p> </p> <p>Reference flow manuscript: https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4</p> <p>Reference flow software: https://github.com/langmead-lab/reference_flow</p> <p>Software for reference flow experiments: https://github.com/langmead-lab/reference_flow-experiments</p> <p>An archived version of the software for experiments: https://doi.org/10.5281/zenodo.4287729</p>
Reference flow VCF for pre-built genomes
<p>Pre-built genomes (in VCF format) for the RandFlow-LD and RandFlow-LD-26 methods in reference flow. The references can be built using the reference flow software (https://github.com/langmead-lab/reference_flow). An archival version of the software is available at http://doi.org/10.5281/zenodo.4287778</p> <p> </p> <p>The reference flow method is described at https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4</p>
V9_DeepSea (Deep Sea Reference Database)
<p>Deep Sea reference database for benthic protist communities: For the taxonomic assignment of our deep-sea sediment sample sequences, we used a reference database called V9_DeepSea. Besides V9 sequences from the Protist Ribosomal Reference database PR2 v4.11.1, we included 102 in-house Sanger-sequenced strains of which the majority was isolated from deep-sea (57 strains) and marine surface waters (32 strains).</p>
FIGURE 4 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 4. Ventral view of Bathyraja sexoculata sp. nov., ZMMU-P 24098, holotype, 346 mm TL, immature male, preserved. (A) head, (B) pelvic region, (C) tail
FIGURE 13 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 13. Plots of principal component (PC) scores for Bathyraja sexoculata sp. nov. and B. smirnovi, based on 12 measurements. (A) PCs 1 and 2, (B) PCs 3 and 4. Red stars, B. sexoculata; black dots, B. smirnovi from southern Sea of Japan; gray dots, B. smirnovi from northern Sea of Japan; white dots, B. smirnovi from Sea of Okhotsk
FIGURE 12 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 12. Plots of selected morphometric characters in Bathyraja sexoculata sp. nov. and B. smirnovi. (A) disc width, (B) disc length, (C) head length, (D) preoral length, (E) prenarial length, (F) internarial distance, (G) eye diameter, (H) tail length. Red stars, B. sexoculata; black dots, B. smirnovi from southern Sea of Japan; gray dots, B. smirnovi from northern Sea of Japan; white dots, B. smirnovi from Sea of Okhotsk
FIGURE 1 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 1. Collection sites of Bathyraja sexoculata sp. nov. (star) and B. smirnovi (circles) examined in this study. Black, gray, and white circles indicate specimens of B. smirnovi collected from southern Sea of Japan, northern Sea of Japan, and Sea of Okhotsk, respectively
FIGURE 15 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 15. Haplotype network for five Arctoraja species based on 557 bp of mitochondrial COI gene. Each circle represents a single haplotype; circle size represents number of individuals. Letters with numerals indicate haplotype codes
FIGURE 14 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 14. Neighbor-joining (NJ) tree for 21 Bathyraja species (including five species of the subgenus Arctoraja) and two Rhinoraja species, based on 557 bp of mitochondrial COI gene. Support values (≥50% bootstrap probability) indicated along branches. Asterisks (*) refer to sequences obtained from INSDC. Each node labeled with a catalogue number or an accession number (*) deposited in INSDC. Black arrow and dotted square indicate Bathyraja sexoculata and subgenus Arctoraja, respectively. Notoraja tobitukai included as outgroup
FIGURE 6 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 6. Uncatalogued fresh specimens (not kept after collection) of Bathyraja sexoculata sp. nov. collected from Simushir Island, Russia. Identification based on the photos. (A, B) adult male, (C, D) immature male
FIGURE 5 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 5. Paratypes of Bathyraja sexoculata sp. nov. (A, B) ZMMU-P 24096, paratype, 326 mm TL, immature male, preserved, (C, D) ZMMU-P 24097, paratype, 352 mm TL, immature male, fresh condition
FIGURE 3 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 3. Dorsal view of Bathyraja sexoculata sp. nov., ZMMU-P 24098, holotype, 346 mm TL, immature male, preserved. (A) head, (B) pelvic region, (C) tail end
FIGURE 7 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 7. Radiographs of Bathyraja sexoculata sp. nov., ZMMU-P 24098, holotype, 346 mm TL, immature male. (A) head, (B) pelvic region. ip = iliac processes, of = obturator foramen, pp = prepelvic process, pr = propterygium, rs = rostral shaft (rostral cartilage)
FIGURE 10 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 10. Bathyraja smirnovi. (A, B) ZIN 19051, paratype, 524 mm TL, immature female, off Magadan, Russia, northern Sea of Okhotsk, preserved, (C, D) FAKU 137702, 1094 mm TL, adult male, off Hokkaido, Japan, Sea of Okhotsk, fresh condition
FIGURE 9. Bathyraja smirnovi, BSKU 110851, 296 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 9. Bathyraja smirnovi, BSKU 110851, 296 mm TL, immature male, off Ishikawa Prefecture, Japan, southern Sea of Japan, fresh condition. (A) dorsal view, (B) ventral view
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.