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Figure 3 in De novo mutations in the genome organizer CTCF cause intellectual disability
Figure 3. - Principal component analysis (PCA) of morphometric data. The ellipse highlights the group formed by the albino and normally pigmented specimens of the same size class. The albino is represented by the white square. Squares (N3 = 20-30 cm size-class); inverse triangles (N4 = 30-40 cm), circles (N5 = 40-50 cm), lozenges (N6 = 50-60 cm), and triangles (N7 = 60-70 cm).
Figure 2 in De novo mutations in the genome organizer CTCF cause intellectual disability
Figure 2. - Regressions of log of disc width vs. log of weight (A) and log of total length vs. log of weight (B) using the albino specimen and data from 28 female individuals of G. micrura. The albino specimen is represented by the white dot.
Loss of multi-level 3D genome organization during breast cancer progression - Processed LAD files
<p>This entry contains the processed LAD files produced as part of the following study:<br><strong>Loss of multi-level 3D genome organization during breast cancer progression</strong></p>
Loss of multi-level 3D genome organization during breast cancer progression - Third-party datasets
<p>This entry contains the following datasets:</p> <p>Datasets used by <a href="https://github.com/dixonlab/hic_breakfinder" target="_blank" rel="noopener">hic_breakfinder</a>:</p> <ul> <li>inter_expect_1Mb.hg38.txt</li> <li>intra_expect_100kb.hg38.txt</li> </ul> <p>FIles were originally downloaded from <a href="https://salkinstitute.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx" target="_blank" rel="noopener">this</a> URL.</p> <p>Datasets used by <a href="https://github.com/parklab/HiNT" target="_blank" rel="noopener">HiNT</a>:</p> <ul> <li>backgroundMatrices_hg38.zip</li> <li>refData_hg38.zip</li> </ul> <p>Files were originally downloaded from the following URLs: <a href="http://compbio.med.harvard.edu/hint/refData/" target="_blank" rel="noopener">link1</a>, <a href="http://compbio.med.harvard.edu/hint/backgroundMatrices/" target="_blank" rel="noopener">link2</a>.</p> <p>The above datasets are used by the data analysis workflows hosted at <a href="https://github.com/paulsengroup/2022-mcf10a-cancer-progression" target="_blank" rel="noopener">paulsengroup/2022-mcf10a-cancer-progression.</a><br>The results produced by running the workflows from the above repository were used as part of the following study:<br><strong>Loss of multi-level 3D genome organization during breast cancer progression</strong></p>
Fig. 5. Organic tentaculite remains. A, E in Organic remains of tentaculitids: New evidence from Upper Devonian of Poland
Fig. 5. Organic tentaculite remains. A, E?, F–H?, L?, M. Nowakiida. B, D, I–K. Styliolinida. C. Problematic. A, D–G, J, M, depth 4208 m, GIUS 4−3510 Do4208; B, C, H, I, K, L, depth 4264 m, GIUS 4−3511 Do4264.
Fig. 4 in Organic remains of tentaculitids: New evidence from Upper Devonian of Poland
Fig. 4. The different shape, size and microstructure of the early ontogenetic parts of mineral tentaculitids and the taxonomic consequence (from Farsan 2005, modified).
Fig. 3 in Organic remains of tentaculitids: New evidence from Upper Devonian of Poland
Fig. 3. Inner and outer structure of mineral tentaculite shell (from Larsson 1979 and Wood et al. 2004, modified).
Fig. 1 in Organic remains of tentaculitids: New evidence from Upper Devonian of Poland
Fig. 1. Localization of the investigated Dobrzyca 2 borehole; schematic geological Upper Devonian background after Turnau and Racki (1999).
Рис. 87–96. КопуΛятивные органы виΑов роΑа Zelotes. 87–88, 90–91, 93–94 – Z. gallicus; 89, 92, 95–96 – Z. pseudogallicus. 87–92 – паΛьпа самца вентраΛьно; 93–96 – эпигина: 93, 95 – вентраΛьно, 94, 96 – ΑорсаΛьно. ЭкземпΛяры: 87, 90 – из Αагонаки, АΑыгея; 88, 91, 93–94 – из Верхнего Зарамага, Северная Осетия; 89, 92, 95–96 – из Ростовской обΛасти. Масштабные Λинейки 0.25 мм. Figs 87–96. Copulatory organs of Zelotes spp. 87–88, 90–91, 93–94 – Z. gallicus; 89, 92, 95–96 – Z. pseudogallicus; 87–92 – male palp, ventral view; 93–96 – epigyne: 93, 95 – ventral view, 94, 96 – dorsal view. Specimens: 87, 90 – from Lagonaki, Adygea; 88, 91, 93–94 – from Verkhniy Zaramag, North Ossetia; 89, 92, 95–96 – from Rostov Region. Scale bars 0.25 mm. in A review of spiders of the genus Zelotes Gistel, 1848 of the subterraneus-group (Aranei: Gnaphosidae) from the Caucasus and Ciscaucasia
Рис. 87–96. КопуΛятивные органы виΑов роΑа Zelotes. 87–88, 90–91, 93–94 – Z. gallicus; 89, 92, 95–96 – Z. pseudogallicus. 87–92 – паΛьпа самца вентраΛьно; 93–96 – эпигина: 93, 95 – вентраΛьно, 94, 96 – ΑорсаΛьно. ЭкземпΛяры: 87, 90 – из Αагонаки, АΑыгея; 88, 91, 93–94 – из Верхнего Зарамага, Северная Осетия; 89, 92, 95–96 – из Ростовской обΛасти. Масштабные Λинейки 0.25 мм. Figs 87–96. Copulatory organs of Zelotes spp. 87–88, 90–91, 93–94 – Z. gallicus; 89, 92, 95–96 – Z. pseudogallicus; 87–92 – male palp, ventral view; 93–96 – epigyne: 93, 95 – ventral view, 94, 96 – dorsal view. Specimens: 87, 90 – from Lagonaki, Adygea; 88, 91, 93–94 – from Verkhniy Zaramag, North Ossetia; 89, 92, 95–96 – from Rostov Region. Scale bars 0.25 mm.
Рис. 80–86. КопуΛятивные органы Zelotes dagestanus Ponomarev, sp. n. 80–83 – паΛьпа самца: 80–82 – вентраΛьно, 83 – ΛатераΛьно; 84 – буΛьбус ΛатераΛьно; 85–86 – эпигина: 85 – вентраΛьно, 86 – ΑорсаΛьно. 80, 82–86 – экземпΛяры с бархана Сарыкум, Δагестан; 81 – экземпΛяр из окрестностей с. Гаша, Δагестан. Масштабная Λинейка 0.25 мм. Figs 80–86. Copulatory organs of Zelotes dagestanus Ponomarev, sp. n. 80–83 – male palp: 80–82 – ventral view, 83 – lateral view; 84 – bulbus, lateral view; 85–86 – epigyne: 85 – ventral view, 86 – dorsal view. 80, 82–86 – specimens from barkhan Sarykum, Dagestan; 81 – specimen from Gasha village environs, Dagestan. Scale bar 0.25 mm. in A review of spiders of the genus Zelotes Gistel, 1848 of the subterraneus-group (Aranei: Gnaphosidae) from the Caucasus and Ciscaucasia
Рис. 80–86. КопуΛятивные органы Zelotes dagestanus Ponomarev, sp. n. 80–83 – паΛьпа самца: 80–82 – вентраΛьно, 83 – ΛатераΛьно; 84 – буΛьбус ΛатераΛьно; 85–86 – эпигина: 85 – вентраΛьно, 86 – ΑорсаΛьно. 80, 82–86 – экземпΛяры с бархана Сарыкум, Δагестан; 81 – экземпΛяр из окрестностей с. Гаша, Δагестан. Масштабная Λинейка 0.25 мм. Figs 80–86. Copulatory organs of Zelotes dagestanus Ponomarev, sp. n. 80–83 – male palp: 80–82 – ventral view, 83 – lateral view; 84 – bulbus, lateral view; 85–86 – epigyne: 85 – ventral view, 86 – dorsal view. 80, 82–86 – specimens from barkhan Sarykum, Dagestan; 81 – specimen from Gasha village environs, Dagestan. Scale bar 0.25 mm.
Рис. 47–56. КопуΛятивные органы самцов. 47–48 – Zelotes fuscus; 49–56 – Z. subterraneus. 47, 49, 51–52, 54 – паΛьпы вентраΛьно; 48, 50, 53, 55–56 – буΛьбусы ΛатераΛьно. ЭкземпΛяры: 47–50 – из Северной Осетии: 47–48 – Тамиск, окрестности АΛагира, 49 – БаΑ, 50 – Бурон; 51 – из Хосты, КрасноΑарский край; 52–53 – из Южной Осетии; 54–56 – из КаΛужской обΛасти. Масштабная Λинейка 0.25 мм. Figs 47–56. Male copulatory organs. 47–48 – Zelotes fuscus; 49–56 – Z. subterraneus. 47, 49, 51–52, 54 – palps, ventral view; 48, 50, 53, 55–56 – bulbus, lateral view. Specimens: 47–50 – from North Ossetia: 47–48 – Tamisk, 49 – Bad, 50 – Buron; 51 – from Khosta, Krasnodar Region; 52–53 – from South Ossetia; 54–56 – Kaluga Region. Scale bar 0.25 mm. in A review of spiders of the genus Zelotes Gistel, 1848 of the subterraneus-group (Aranei: Gnaphosidae) from the Caucasus and Ciscaucasia
Рис. 47–56. КопуΛятивные органы самцов. 47–48 – Zelotes fuscus; 49–56 – Z. subterraneus. 47, 49, 51–52, 54 – паΛьпы вентраΛьно; 48, 50, 53, 55–56 – буΛьбусы ΛатераΛьно. ЭкземпΛяры: 47–50 – из Северной Осетии: 47–48 – Тамиск, окрестности АΛагира, 49 – БаΑ, 50 – Бурон; 51 – из Хосты, КрасноΑарский край; 52–53 – из Южной Осетии; 54–56 – из КаΛужской обΛасти. Масштабная Λинейка 0.25 мм. Figs 47–56. Male copulatory organs. 47–48 – Zelotes fuscus; 49–56 – Z. subterraneus. 47, 49, 51–52, 54 – palps, ventral view; 48, 50, 53, 55–56 – bulbus, lateral view. Specimens: 47–50 – from North Ossetia: 47–48 – Tamisk, 49 – Bad, 50 – Buron; 51 – from Khosta, Krasnodar Region; 52–53 – from South Ossetia; 54–56 – Kaluga Region. Scale bar 0.25 mm.
OMAP-21: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MICS on MACSima 1.5
<p>OMAP-21 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human tonsil samples. Tissue fixation and antigen retrieval is described in (<a href="https://www.biorxiv.org/content/biorxiv/early/2023/11/07/2023.10.27.564191.full.pdf">Spatial protein and RNA analysis on the same tissue section using MICS technology</a>). The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 47 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the human palatine tonsil. OMAP-21 follows closely OMAP-1 described for human lymph nodes (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-1-human-lymph-node-ibex.html">omap-1-human-lymph-node-ibex</a>) and OMAP-10 (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-10-palatine-tonsil-macsima.html">omap-10-palatine-tonsil-macsima</a>).</p> <p>All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The result of the analysis is included in the uploaded dataset. In brief, the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, this is the second OMAP for the MACSima system. A representative dataset created using OMAP-21 can be found here:<a href="https://doi.org/10.5281/zenodo.7875937"> </a><strong> 10.5281/zenodo.11281609 .</strong></p>
FIGURE 4 in Organization of the cephalic lateral-line canals in Electrophorus varii de Santana, Wosiacki, Crampton, Sabaj, Dillman, Mendes-Júnior & Castro e Castro, 2019 (Gymnotiformes: Gymnotidae)
FIGURE 4 | Images of CT scan of the head of Electrophorus varii. A. dorsal and B. left lateral views of the cranium show the ossification of the lateral-line canals. The ossified segments of canals are marked by colors. Yellow: infraorbital canal; navy blue: mandibular canal; green: otic canal; purple: pre-opercular canal; pink: supraorbital canal; light blue: supratemporal canal; red: otic pit ossicles. ANG-AR: Angulo-articular; CLT: cleithrum; DT: dentary; ENT: entopterygoid; FR: frontal bone; HYO: Hyomandibular; IOP: interopercle; MET: mesethmoid; MTP: metapterygoid; OP: opercle; PAR: parietal; PMX: premaxila; POP: preopercle; PTO: pterotic; QU: quadrate; SP: sphenotic; SYM: sympletic. Specimen size = 82 cm TL.
FIGURE 1 in Organization of the cephalic lateral-line canals in Electrophorus varii de Santana, Wosiacki, Crampton, Sabaj, Dillman, Mendes-Júnior & Castro e Castro, 2019 (Gymnotiformes: Gymnotidae)
FIGURE 1 | Sampling areas (Adolpho Ducke Reserve and Purupuru Lake, Amazonas, Brazil) where individuals of Electrophorus varii were captured. The white stars represent the exact sampling spots.
FIGURE 3 in Organization of the cephalic lateral-line canals in Electrophorus varii de Santana, Wosiacki, Crampton, Sabaj, Dillman, Mendes-Júnior & Castro e Castro, 2019 (Gymnotiformes: Gymnotidae)
FIGURE 3 | Organization of the cephalic lateral-line canals in adult Electrophorus varii. Arrangement of all canals in A. dorsal, B. lateral and C. ventral views. Yellow: infraorbital canal; navy blue: mandibular canal; green: otic canal; purple: pre-opercular canal; pink: supraorbital canal; light blue: supratemporal canal; grey: posterior lateral-line canal of the trunk; red: otic pit (OP) between cephalic and trunk canals. The photographs are from a juvenile that completed the development and is morphologically similar to an adult. The drawings are from an individual of 148 cm TL.
FIGURE 2 in Organization of the cephalic lateral-line canals in Electrophorus varii de Santana, Wosiacki, Crampton, Sabaj, Dillman, Mendes-Júnior & Castro e Castro, 2019 (Gymnotiformes: Gymnotidae)
FIGURE 2 | Ontogenetic development of the lateral-line canals in larvae and juveniles of Electrophorus varii, in lateral and dorsal views. A. 1.9 cm TL; B. 2.5 cm TL; C. 3.0 cm TL; D. 5.0 cm TL; E. 9.0 cm TL; F. 38 cm TL. Types of dashes indicate the (1) shallow and short grooves on the skin; (2) deep grooves; (3) segments of grooves start enclosure; (4) pores of canals on the skin. Yellow: infraorbital canal; navy blue: mandibular canal; green: otic canal; purple: pre-opercular canal; pink: supraorbital canal; light blue: supratemporal canal; grey: posterior lateral-line canal of the trunk and; red: otic pit between cephalic and trunk canals. Arrows indicate short grooves of the presumptive infraorbital and mandibular canals.
FIGURE 3 in Should the terms 'basal taxon' and 'transitional taxon' be extinguished from cladistic studies with extinct organisms?
FIGURE 3. Hypothetical data matrix and the most parsimonious tree obtained when it is analysed using parsimony.
FIGURE 2 in Should the terms 'basal taxon' and 'transitional taxon' be extinguished from cladistic studies with extinct organisms?
FIGURE 2. Simplified version of the cladogram of Figure 1 showing the relationships of the three main lineages of dinosaurs with focus on Sauropodomorpha. 'Sauropodomorpha A' and 'Sauropodomorpha B' represent two hypothetical taxa that are more closely related to Saturnalia than to Sauropoda. Ornithischia is represented by a single terminal taxon and Theropoda is represented by the living bird Gallus gallus.
FIGURE 1 in Should the terms 'basal taxon' and 'transitional taxon' be extinguished from cladistic studies with extinct organisms?
FIGURE 1. Simplified cladogram showing the relationships of the three main lineages of dinosaurs with focus on Sauropodomorpha. Letters A - F are related to clades treated in the main text. The assumed ages for the taxa of the tree are represented by rectangles thicker than other branches. Cladogenetic events (dichotomies) are not calibrated against geological time. Ornithischia is represented by the following taxa: Pisanosaurus, Heterodontosauridae, Eocursor, Thyreophora, Neornithischia. Theropoda is represented by the following taxa: Tawa, coelophysoids, Ceratosauria, Tetanurae. All other taxa represent Sauropodomorpha (here following the definition of Galton and Upchurch, 2004). Sauropoda (here following the definition of Salgado et al., 1997) is represented by Vulcanodon, Tazoudasaurus, Spinophorosaurus, Neosauropoda.
Estimated reflectance hyperspectral libraries for Vigo sediment sample, seafloor sand samples and marine organism
<h2>Abstract</h2> <p>Estimated reflectance hyperspectral libraries created for sand samples from seafloor at Vigo sea zone 1, 2 and 3, sediment samples from Vigo fieldwork Sept. 2023 and some Vigo marine organisms such as sea cucumber, sea pens, sea stars, coral, seaweed.</p> <p>This depository contains data generated within the European S34 project.</p> <h2>Metadata Information</h2> <table> <tbody> <tr> <td> <p><strong>Identification</strong></p> </td> </tr> <tr> <td> <p>Full Title</p> </td> <td> <p>Estimated reflectance hyperspectral libraries for Vigo sediment sample, seafloor sand samples and marine organism</p> </td> </tr> <tr> <td> <p>Abstract</p> </td> <td> <p>Estimated reflectance hyperspectral libraries created for sand samples from seafloor at Vigo sea zone 1, 2 and 3, sediment samples from Vigo fieldwork Sept. 2023 and some Vigo marine organisms such as sea cucumber, sea pens, sea stars, coral, seaweed.</p> </td> </tr> <tr> <td> <p>Keywords</p> </td> <td> <p>Reflectance hyperspectral signature, library, sediment, sand, sea cucumber, sea star, coral, seaweed</p> </td> </tr> <tr> <td> <p>Pilot area</p> </td> <td> <p>Ria de Vigo</p> </td> </tr> <tr> <td> <p>Associated resources</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Language</p> </td> <td> <p>English</p> </td> </tr> <tr> <td> <p>URL</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Categories</p> </td> <td> <p>Other</p> </td> </tr> <tr> <td> <p><strong>Temporal reference</strong></p> </td> </tr> <tr> <td> <p>Creation date (dd.mm.yyyy)</p> </td> <td> <p>25.05.2024</p> </td> </tr> <tr> <td> <p>Revision date (dd.mm.yyyy)</p> </td> <td> <p>25.05.2024</p> </td> </tr> <tr> <td> <p><strong>Quality and validity</strong></p> </td> </tr> <tr> <td> <p>Representation type</p> </td> <td> <p>Other</p> </td> </tr> <tr> <td> <p>Format</p> </td> <td> <p>CSV</p> </td> </tr> <tr> <td> <p>Lineage</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Spatial resolution</p> </td> <td> <p>0.25m</p> </td> </tr> <tr> <td> <p>Positional accuracy</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Maintenance information</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Coordinate system</p> </td> <td> <p>EPSG 3035</p> </td> </tr> <tr> <td> <p><strong>Constranits related to access and use</strong></p> </td> </tr> <tr> <td> <p>Use limitation</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Access constraint</p> </td> <td> <p>/</p> </td> </tr> <tr> <td> <p>Public/Private</p> </td> <td> <p>Public</p> </td> </tr> <tr> <td> <p><strong>Responsible organisation</strong></p> </td> </tr> <tr> <td> <p>Responsible Contact</p> </td> <td> <p>Ecotone AS, info@ecotone.com</p> </td> </tr> <tr> <td> <p>Responsible Party</p> </td> <td> <p>Ecotone AS</p> </td> </tr> <tr> <td> <p><strong>Metadata on metadata</strong></p> </td> </tr> <tr> <td> <p>Contact</p> </td> <td> <p>Ecotone AS, info@ecotone.com</p> </td> </tr> <tr> <td> <p>Metadata language</p> </td> <td> <p>English</p> </td> </tr> </tbody> </table>
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.