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1,514 results for “Widespread”
Fig. 1 in Do Antarctic populations represent local or widespread phylogenetic and ecological lineages? Complicated fate of bipolar moss concepts with Drepanocladus longifolius as a case study
Fig. 1 Geographical distribution of the studied accessions and detected genetic lineages corresponding to Drepanocladus longifolius (blue dots) and D. capillifolius (green triangles) according to present circumscription.
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
<p>This dataset contains supplemental tables and tracks for the study entitled: "Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation".</p> <ul> <li>Files <ul> <li>PMDs_CGIs.zip <ul> <li>The included files contain</li> <li>Genome positions of detected PMDs with their mean methylation (weighted mean, see Methods)</li> <li>Genome positions of CpG islands with their mean methylation (weighted mean)</li> <li>The "Brinkman" directory contains files from breast cancer data produced in this study</li> <li>The "normals" directory contains files from normal tissues (external data) analyzed in this study</li> <li>The "tumors" directory contains files from tumors (external data) analyzed in this study</li> <li>All genome positions are based on GRCh37/hg19 </li> <li>All files are TAB-delimited text files (.tsv)</li> </ul> </li> <li>DNAme_bigwigs.zip <ul> <li>The included files are BIGWIG files (http://genome.ucsc.edu/goldenPath/help/bigWig.html) for viewing the DNA methylation profiles in a genome browser such as UCSC (http://genome.ucsc.edu). Each file represents a whole-Genome Bisulfite Sequencing (WGBS) DNA methylation profile from one tumor used in this study. The used genome build was GRCh37/hg19. For every CpG with a coverage of at least 4 reads, the DNA methylation value (range: 0-1) is included.</li> </ul> </li> </ul> </li> <li>Methods <ul> <li>Detection of partially methylated domains (PMDs) in all whole-genome bisulfite sequencing (WGBS) methylation profiles throughout this study was done using the MethylSeekR package for R (1). Before PMD calling, CpGs overlapping common SNPs (dbSNP build 137) were removed. The alpha distribution (1) was used to determine whether PMDs were present at all, along with visual inspection of WGBS profiles. After PMD calling, the resulting PMDs were further filtered by removing regions overlapping with centromers (undetermined sequence content).</li> <li>Mean methylation values from WGBS inside CGIs were calculated using the ‘weighted methylation level’ (2).</li> <li>Mean methylation values from WGBS inside PMDs were calculated using the ‘weighted methylation level’ (2). Calculation of mean methylation within PMDs involved removing all CpGs overlapping with CpG island(-shores) and promoters, as the high CpG densities within these elements yield unbalanced mean methylation values, not representative of PMD methylation. </li> </ul> </li> <li>References <ul> <li>(1) Burger, L., Gaidatzis, D., Schübeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Research 41, (2013).</li> <li>(2) Schultz, M. D., Schmitz, R. J. & Ecker, J. R. ’Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends in Genetics 28, 583–585 (2012).</li> </ul> </li> </ul>
Fig. 2 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 2. Typical Haemoproteus plataleae stages from three infected white ibis (Eudocimus alba) from South Florida. All ibis were genetically confirmed to be infected with the EUDRUB01 lineage. A-E, an ibis from Juno Beach urban park; F, an ibis from Indian Creek urban park; and G-L, an ibis from the Solid Waste site. The latter bird had rare round forms (K-L), which were absent from other H. plataleae-infected ibis. Younger stages (C, H, I) had a an evident 'cleft' between the gametocyote and erythrocyte nucleus.
Fig. 3 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 3. Phylogenetic relationship of Haemoproteus plataleae from white ibis (Eudocimus albus) with other Haemoproteus spp.
Fig. 1 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 1. Box plots of parasitemia values of Haemoproteus plataleae in white ibis (Eudocimus albus) sampled from South Florida from 2010 to 2022 by year (A.), season (B.), and age (C. and D.). C. shows all ibis with general adult vs. juvenile age class designations and D. shows data for the subset of ibis that were aged to specific year for juveniles (1, 2, or 3 yrs old). Years 2015 and 2017 were significantly different from each other, but both were similar to other years. For remaining figures, factors that are differently colored are significantly different from each other. Note that the x-axis maximum varies between plots.
FIGURE 1 in Testing spatial and environmental factors to explain body shape variation in the widespread Central American Blackbelt cichlid Vieja maculicauda (Teleostei: Cichlidae)
FIGURE 1 | Points representing geographic location for the lots of Vieja maculicauda used in the current study. Straight black lines represent the approximate location of geological block divisions. Purple shading represents a modified version of IUCN redlist data for the distribution of this species (Lyons, 2019).
FIGURE 4 in Testing spatial and environmental factors to explain body shape variation in the widespread Central American Blackbelt cichlid Vieja maculicauda (Teleostei: Cichlidae)
FIGURE 4 | Canonical variate analysis and shape changes along both axes. Shape change has been magnified by two for increased visualization.
FIGURE 3 in Testing spatial and environmental factors to explain body shape variation in the widespread Central American Blackbelt cichlid Vieja maculicauda (Teleostei: Cichlidae)
FIGURE 3 | Principal component analysis of size-corrected shape and deformation grids along each axis.
FIGURE 2 in Testing spatial and environmental factors to explain body shape variation in the widespread Central American Blackbelt cichlid Vieja maculicauda (Teleostei: Cichlidae)
FIGURE 2 | Landmarks (in blue) and semilandmarks (in red) as placed on each specimen. Landmark positions are described on Tab. S1.
Supplemental data for "Widespread and rapid dynamics of subglacial water in the Canadian Arctic"
<h2>What's inside</h2> <p>This data set contains:</p> <ol> <li><strong>Inventory:</strong> The inventory of the active subglacial water bodies in the Canadian Arctic.</li> <li><strong>Workflows:</strong> Data analysis code that produces the study results. </li> <li><strong>Results:</strong> The derived ArcticDEM strip data and visualizations generated by this study.</li> </ol> <p>See "README.md" for more information.</p>
Fig. 2 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species
Fig. 2 Chronograms, resulting from BI analysis of the four selected Hypsugo marker sequences ND1 (a), CytB (b), COI (c), and 16 S RNA (d). Only lineage A and B were detected in all four marker datasets. The dots denote nodes with posterior probability value equal or above 0.95. Other nodes were below the value we designated as reliable to successfully infer phylogenetic relations between detected lineages (0.95). The scale bar indicates approximate age in millions of years
Fig. 3 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species
Fig. 3 Median-joining haplotype networks for the four marker sequences ND1 (a), CytB (b), COI (c), and 16 S RNA (d). Smaller coloured circles represent a single sequence, while the larger represent two or three. Hala refers to H. alaschanicus and Hstu to H. stubbei
Fig. 1 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species
Fig. 1 (a) Geographic origin of assigned Hyspugo savii sequences. For some sequences, only vague localities were available, and the placement therefore might be unprecise (see Online Resource 1). + marks the type locality of H. savii (Pisa, Italy). Projected lineage occurrence areas (coloured polygons) were created using buffer zones of approximately 200 km around each data point following anecdotal citations of migration distance (Juste and Paunović 2016; Dietz and Kiefer 2016) in QGIS v. 3.4.14. Question marks denote areas, where lineage distribution is at present unknown. (b) A H. savii individual photographed near Dragonja River, SW Slovenia, in 2018 by Jan Gojznikar. (c) MCC tree obtained by using the concatenated dataset. Posterior probabilities are shown next to their respective nodes. Value of the scale bar refers to million years before present. Squared tips indicate a concatenated sequence of a single individual, whilst triangles denote multiple concatenated sequences
Data for: Widespread forest-savanna coexistence but limited bistability at a landscape scale in Central Africa
<p>This directory contains the data used in the article **Zwaan et al. (2024) Widespread forest-savanna coexistence but limited bistability at a landscape scale in Central Africa** (DOI: <span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1088%2F1748-9326%2Fad8cef&data=05%7C02%7Ca.zwaan%40uu.nl%7C66d868876ad44e69715608dcf9c1c197%7Cd72758a0a4464e0fa0aa4bf95a4a10e7%7C0%7C0%7C638659857776731023%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=3Bk8nBksr5ZBWJF4nfBvx3yp1tbyZiy%2FLlnfwDCZwfE%3D&reserved=0">https://doi.org/10.1088/1748-9326/ad8cef</a></span>).</p> <p>This repository provides the datasets used for the figures and statistics in our research article. We hope that this data can be useful for other researchers. Feel free to explore and analyze the data as needed. If you use this data in your own research, please cite our article.</p> <p><br>**Contact**: For any questions or further information, please contact:<br>* Aart Zwaan<br>* Email: a.zwaan@uu.nl</p>
Linked collectors and determiners for: Taxonomy of widespread Neotropical species of Podisus Herrich-Schäffer (Hemiptera: Pentatomidae: Asopinae): redescription of P. distinctus (Stål, 1860) and revalidation of P. fuscescens (Dallas, 1851).
Natural history specimen data linked to collectors and determiners held within, "Taxonomy of widespread Neotropical species of Podisus Herrich-Schäffer (Hemiptera: Pentatomidae: Asopinae): redescription of P. distinctus (Stål, 1860) and revalidation of P. fuscescens (Dallas, 1851)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/85506694-60e1-40dc-88df-229cd4c9421d">https://bionomia.net/dataset/85506694-60e1-40dc-88df-229cd4c9421d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/85506694-60e1-40dc-88df-229cd4c9421d">https://gbif.org/dataset/85506694-60e1-40dc-88df-229cd4c9421d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Japeaeiella dollŋpartoniana, a New Widespread Lichen in the Appalachian Mountains of Eastern North America.
Natural history specimen data linked to collectors and determiners held within, "Japeaeiella dollŋpartoniana, a New Widespread Lichen in the Appalachian Mountains of Eastern North America". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/feb4164b-2c9c-4da6-acb3-326e2a5a34f2">https://bionomia.net/dataset/feb4164b-2c9c-4da6-acb3-326e2a5a34f2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/feb4164b-2c9c-4da6-acb3-326e2a5a34f2">https://gbif.org/dataset/feb4164b-2c9c-4da6-acb3-326e2a5a34f2</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Patterns of widespread decline in North American bumble bees.
Natural history specimen data linked to collectors and determiners held within, "Patterns of widespread decline in North American bumble bees". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8c04889e-a0ad-4f39-8623-06aa9cf0131d">https://bionomia.net/dataset/8c04889e-a0ad-4f39-8623-06aa9cf0131d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8c04889e-a0ad-4f39-8623-06aa9cf0131d">https://gbif.org/dataset/8c04889e-a0ad-4f39-8623-06aa9cf0131d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A taxonomic revision of Neodietrichia (Araneae: Linyphiidae), a rarely encountered but widespread spider taxon.
Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of Neodietrichia (Araneae: Linyphiidae), a rarely encountered but widespread spider taxon". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ffeccc89-779c-46c9-a4f7-842299585660">https://bionomia.net/dataset/ffeccc89-779c-46c9-a4f7-842299585660</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ffeccc89-779c-46c9-a4f7-842299585660">https://gbif.org/dataset/ffeccc89-779c-46c9-a4f7-842299585660</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A fresh start in ambersnail (Gastropoda: Succineidae) taxonomy: finding a foothold using a widespread species of Oxyloma.
Natural history specimen data linked to collectors and determiners held within, "A fresh start in ambersnail (Gastropoda: Succineidae) taxonomy: finding a foothold using a widespread species of Oxyloma". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/34e2ec3d-4fec-4e92-8363-f55c0df0aee0">https://bionomia.net/dataset/34e2ec3d-4fec-4e92-8363-f55c0df0aee0</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/34e2ec3d-4fec-4e92-8363-f55c0df0aee0">https://gbif.org/dataset/34e2ec3d-4fec-4e92-8363-f55c0df0aee0</a>. Formatted as a Frictionless Data package.
Fig. 8 in A fresh start in ambersnail (Gastropoda: Succineidae) taxonomy: finding a foothold using a widespread species of Oxyloma
Fig. 8. Oxyloma salleanum (L. Pfeiffer, 1850). Spring Garden Lake, Volusia County, Florida [O. effusum (L. Pfeiffer, 1853) topotypes]. A–B. Reproductive organs of specimen 2737 (NMV F 304258, shell height 11.0 mm) in ventral view, and male genitalia. C –D. Reproductive organs of specimen 2745 (NMV F 304259, 11.7 mm) in ventral view, and male genitalia. Details of the male genitalia of specimens 2737 and 2745 (B, D), with penial sheath opened to expose the epiphallus and penis with proximal appendix. Penis opened to show the spatial relationships of appendix and epiphallus openings to proximal penis, and the longitudinal folds bearing calcite rosettes embedded in the epithelium. Abbreviations: see Material and methods.
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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.