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12,662 results for “linking”
10XG CRAM files for "Characterization of large-scale structural variants using Linked-Reads" (Part 1 of 2)
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
Illumina CRAM files for "Characterization of large-scale structural variants using Linked-Reads" (Part 2 of 2)
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
Illumina CRAM files for "Characterization of large-scale structural variants using Linked-Reads" (Part 1 of 2)
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
FIGURE 7 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 7. Records of Qorimayus alticola (blue dots) in Sierra de Famatina, La Rioja Province, western Argentina, together with known localities of the Chilean genera Nanophareus (red dots) and Metabalta (yellow dots). Regional divisions in Chile: Coquimbo (COQ); Valparaíso (VAL); Región Metropolitana de Santiago (MET); Libertador General Bernardo O'Higgins (OHI); Maule (MAU); Ñuble (ÑUB); Bío-Bío (BIO). Inset: position of the represented area in South America; La Rioja Province indicated in gray.
FIGURE 6 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 6. Distal end of penis, lateral views. A: Metabalta efformata Roewer, 1929, syntype ♂ (SMF), B–C: Detail of stylus and ventral process of stylus (VPS); C is slightly rotated dorsolaterally to see the subapical spines on the VPS shaft. D: Nanophareus bosqenublado Hara et al., 2012 (AMNH), E: Detail of stylus and VPS, F: Nanophareus palpalis Roewer, 1929, ♂ lectotype (SMF 986/1). Scales: 0.1 mm.
FIGURE 4 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 4. Right pedipalps, lateral view; all drawings at the same scale. A: Qorimayus alticola (Ringuelet, 1962) comb. nov., holotype ♂ (MACN). B: Metabalta efformata Roewer, 1929, syntype ♂ (SMF). C: Metabalta geniculata Roewer, 1929, syntype ♂ (SMF) D: Nanophareus bosqenublado Hara et al., 2012 (AMNH). Scale bars: 1 mm.
FIGURE 1 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 1. Cladistic relationships of Qorimayus gen. nov.: single most parsimonious tree obtained with implied weights (IW), k=6 (Ci: 0.37, Ri: 0.60, tree length: 376 steps). Character optimization: solid circles depict non-homoplasious states, open circles are homoplasious states. Small numbers on a circle indicate the character number (above the circle) and its state (below); larger numbers under relevant branches display values of bootstrap, jackknife and symmetric resample (B-J-SR), high support values in bold. Abbreviations for major clades (underlined): G: Gonyleptidae; PsG: Pachyloides-group; PG: Pachylus-group; PG+Eu: Pachylus-group plus Eusarcus spp.; MG: Metabalta-group; M+Na(+): Metabalta+Na(+); M: genus Metabalta; Na(+): Nanophareus, plus N+T; Na: genus Nanophareus; e-s: "eyes-separate" clade.
FIGURE 2 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 2. Qorimayus alticola (Ringuelet, 1962) comb. nov., holotype ♂ (MACN). A: Dorsal view (scutum, free tergites, che- licerae, base of right pedipalp and legs I–III, and right leg IV, from coxa to tibia). B: Ventral view (coxae IV, stigmatic segment, free sternites, right trochanter, femur and patella I). C–D: Ocular mound, C: right lateral view with front hump, D: posterior view. Scale bars: 1 mm.
FIGURE 5 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 5. Qorimayus alticola (Ringuelet, 1962) comb. nov., holotype ♂, distal end of penis. A: Dorsal view. B: Lateral view. C: Detail of stylus and ventral process of stylus (VPS). Macrosetae series are labelled as MS A, MS B, MS C, MS D and MS E, following the nomenclature of Kury & Villarreal (2015). Scales: 0.1 mm.
FIGURE 8 in Qorimayus, a new genus of relictual, high-altitude harvestmen from western Argentina (Arachnida, Opiliones, Gonyleptidae) reveals trans-Andean phylogenetic links
FIGURE 8. Habitat of Qorimayus alticola in the Río Oro canyon (La Rioja Province, Argentina). A: General view of the valley at ca. 2400 m a.s.l. B: Scrubland bordering the track to Mina El Oro, at one collecting site (2450 m a.s.l.).
The dataset of interatomic distances between the atoms, not linked with a covalent bond
<p><strong>non-bonded_b3lyp.txt non-bonded_B97-3c.txt non-bonded_PBEh-3c.txt </strong>- the datasets of the atomic pairs, not linked with a covalent bond. Each line in each file has the following format:</p> <p><em>Element Element </em>0<em> MoleculeId AtomId1 AtomId2</em></p> <p>Here <em>MoleculeId </em>is the same as identifiers used in the dataset of covalent bond lengths resulting from the first-principle calculations, available at <a href="https://doi.org/10.5281/zenodo.2631844">https://doi.org/10.5281/zenodo.2631844</a> (the underlying optimized molecular geometries are available via this link as well).</p>
Linking individual physiological indicators to the productivity of fish populations: A case study of Atlantic herring
<p>Raw data for i) heart rate measurements of Atlantic herring larvae reared at three different temperatures (7, 11 and 15°C); ii) compilation of Baltic herring larval growth rates measured in the field and in the laboratory; and iii) time series of thermal estimates (derived from satellite sea surface temperatures) in Greifswald Bay (Baltic Sea) between 1992 and 2017, as well as three herring productivity proxies in the area: weekly larval abundance in Greifswald Bay (one of the major spawning grounds), 1 yr-old juvenile abundance in the western Baltic basin, and the recruitment estimate from the International Council for the Exploration of the Sea (ICES) Herring Assessment Working Group for the Area South of 62°N.</p>
Figure 8 in A new species of Ahaetulla Link, 1807 (Serpentes: Colubridae: Ahaetullinae) from India
Figure 8. Habitat of Ahaetulla laudankia sp. nov. (a) Type locality Bangriposi, Mayurbhanj; and (b) Madhapur both in Odisha state, India.
Figure 5 in A new species of Ahaetulla Link, 1807 (Serpentes: Colubridae: Ahaetullinae) from India
Figure 5. Dorsal and lateral head profile of different species/populations of Ahaetulla with dermal appendages. (a) A. nasuta from low land Sri Lanka; (b) A. nasuta from highland southern Province Sri Lanka; (c) A. nasuta cf. isabellina from low land southern Tamil Nadu; (d) A. laudankia sp. nov.; (e) A. pulverulenta from Sri Lanka; and (f) A. anomala from Odisha, India. Image not to scale.
Figure 7 in A new species of Ahaetulla Link, 1807 (Serpentes: Colubridae: Ahaetullinae) from India
Figure 7. Hemipenis of Ahaetulla laudankia sp. nov. (ZSI-CZRC-6404); (a) asulcal view; (b) sulcal view; and (c) lateral view. Scale bar 10 mm.
Characterization of large-scale structural variants using Linked-Reads
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
News article mentions of 4chan from three weeks in 2017 and posts with links to these articles on 4chan/pol/
<p>This upload includes two dataset. The first comprises articles that mentioning "4chan" in its post body as retreived by Nexis Uni. We identified the three weeks in which the highest spikes in terms of the amount of articles occured in 2017 (see the image mentions_nexis_uni_2017_weeks.png ) and extracted the articles that were published within these. The dataset includes the article source, the article title, and the sentences where they mention 4chan to analyse the framing. We deleted the article bodies for copyright reasons. Two columns indicate the URL to the article if it appeared online. Additionally, we added a column with URLs to archive.is links of the same articles, in case they were archived.</p> <p>The second dataset consists of posts on the imageboard 4chan/pol/ that refer to one of the aforementioned URLs.</p>
Link to dataset related to article "Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells"
<p>Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of <em>cis</em>-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated <em>cis</em>-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.</p>
Learn2Link: Linking the Social and Academic Profiles of Researchers
<p>Data and code to reproduce work in Learn2Link: Linking the Social and Academic Profiles of Researchers.</p>
Linked COVID-19 Data: Geometries
<p>Linked COVID-19 <strong>Geometries</strong></p> <p>maintained at</p> <p><a href="https://github.com/Research-Squirrel-Engineers/COVID-19">https://github.com/Research-Squirrel-Engineers/COVID-19</a></p> <p>data origin by</p> <p>countries:</p> <p>data by <a href="https://github.com/AshKyd/geojson-regions">https://github.com/AshKyd/geojson-regions</a> extracted by <a href="https://geojson-maps.ash.ms/">https://geojson-maps.ash.ms/</a></p> <p>federal states:</p> <p><a href="https://gdz.bkg.bund.de/index.php/default/open-data/verwaltungsgebiete-1-2-500-000-stand-01-01-vg2500.html">https://gdz.bkg.bund.de/index.php/default/open-data/verwaltungsgebiete-1-2-500-000-stand-01-01-vg2500.html</a></p> <p>Verwaltungsgebiete 1:2 500 000, Stand 01.01. (VG2500)</p>
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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.