Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
66
datasets available to search
ShareScore release 0.9.0
Dataset results
66 results for “Proboscidean”
Proboscidean Palaeoproteomic Reference Dataset
<p>This entry contains the 'Proboscidean Palaeoproteomic Reference Dataset'.</p> <p>We used PaleoProPhyler ( https://github.com/johnpatramanis/Proteomic_Pipeline ) to generate a palaeoproteomic reference dataset of protein sequences from ancient and present-day Proboscidae. Using the first two modules of PaleoProPhyler, we translated more than 35 publicly available whole genomes from extant and extinct species. Details on the processing of the sequences can be found below.</p> <p> </p> <p>Which individuals / species are included?</p> <p>The full list of individuals, the original fastq repository location and the species included in the dataset are contained within the tab seperated file 'METATADATA.txt', that also contains headers. Most individuals of the dataset belong to one of these 3 species: <em>Loxodonta africana</em>,<em> Elephas maximus</em>, <em>Mammuthus primigenius. </em></p> <p> </p> <p>Which Proteins are included?</p> <p>We compiled a small initial list of 262 proteins that had been indentified in either teeth, bone or items made out of ivory. For each protein, both the canonical and all alternative protein coding isoforms (based on the Loxodonta africana reference proteome of Ensembl) were translated, leading to more than 350 unique protein sequences for each individual in the dataset. The protein list is available in the file 'proteins.txt'</p> <p> </p> <p>How were the proteins translated/generated?</p> <p>All genetic data were downloaded from ENA (https://www.ebi.ac.uk/ena/browser/home) as fastq files and mapped onto LoxAfr3, which is the latest annotated African elephant genome in Ensembl. The scripts used for the mapping are available here: https://github.com/johnpatramanis/Mapping_Scripts . We used the resulting bam files as input for PaleoProPhyler's module 1 & 2 , using LoxAfr3 as the reference proteome.</p> <p>Other files included in the zip folder:</p> <p>- ALL_PROT_REFERENCE.fa contains all of the sequences generated as part of the Proboscidean Palaeoproteomic Reference Dataset described above</p> <p>- PER_PROTEIN is a folder containing one fasta file for each protein within the Proboscidean Palaeoproteomic Reference Dataset, each protein fasta file has the sequences of all individuals for that particular protein</p> <p>- PER_SAMPLE is a folder containing one fasta file for each sample/individual within the Proboscidean Palaeoproteomic Reference Dataset, each sample fasta file has the sequences of all proteins for that particular sample.</p>
Fig. 11 in Shoulder height, body mass, and shape of proboscideans
Fig. 11. Left humerus of giant Mosbach mammoth (MNHM PW1947/23) from Middle Pleistocene, Mosbach, Germany; in lateral view.
Fig. 10 in Shoulder height, body mass, and shape of proboscideans
Fig. 10. Different growth curves for Loxodonta africana from average-sized to world record specimens based on isometric growth (red), Laws' (1975) equations for wild population in good conditions up to average size (brown), Homo sapiens (in optimal conditions) allometric growth (grey), and the proposed allometric growth curve for proboscideans in this study (black).
Fig. 6 in Shoulder height, body mass, and shape of proboscideans
Fig. 6. Femur length vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data).
Fig. 3 in Shoulder height, body mass, and shape of proboscideans
Fig. 3. Humerus lengths vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data). The ratios shaded in grey correspond to the maximal length of the humerus and the white ones to the articular length of the humerus.
Fig. 9 in Shoulder height, body mass, and shape of proboscideans
Fig. 9. Plot of height vs. weight for 561 male Homo sapiens in optimal conditions from 170 cm (low average) to 225 cm tall. Average growth curve (red line).
Fig. 2 in Shoulder height, body mass, and shape of proboscideans
Fig. 2. Scapula lengths vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data). The ratios shaded in grey correspond to the maximal length of the scapula and the white ones to the articular length of the scapula.
Fig. 5 in Shoulder height, body mass, and shape of proboscideans
Fig. 5. Radius length vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data).
Fig. 1 in Shoulder height, body mass, and shape of proboscideans
Fig. 1. Reconstruction of the forelimb of the Zhalainuoer III mammoth in anatomical position. The actual shoulder height (black): total height in anatomical position 3690 mm. The height obtained by adding the articular (green): manus (500 mm) + ulna (960 mm) + humerus (1233 mm) + scapula (1075 mm) = 3768 mm. Maximal lengths of different bone elements (red): manus (500 mm) + radius (985 mm) + humerus (1274 mm) + scapula (1115 mm) = 3874 mm. The actual shoulder height can be calculated by multiplying the result by 0.98 in the case of the sum of articular lengths and by 0.95 in the case of maximal lengths.
Fig. 4 in Shoulder height, body mass, and shape of proboscideans
Fig. 4. Ulna lengths vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data). The ratios shaded in grey correspond to the maximal length of the humerus, and the white ones to the articular length of the humerus.
Fig. 8 in Shoulder height, body mass, and shape of proboscideans
Fig. 8. Fibula length vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data).
Fig. 7 in Shoulder height, body mass, and shape of proboscideans
Fig. 7. Tibia length vs. skeletal shoulder height ratio of selected proboscideans based on the data collected in this study (Appendix 1, SOM: table 2; AL unpublished data).
Fig. 7 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 7. Dental elements of the proboscidean Chilgatherium harrisi Sanders, Kappelman, and Rasmussen, 2004, from the Upper Guang and Gahar Valley sections (late Oligocene), Chilga region, Ethiopia. A. Right P3 (CH9–22) reversed for consistency. B. Left P4 (CH9–7). C. Protoloph of left?M2 (CH12–4). D. Right M3 (CH35–1) reversed for consistency. E. Tritolophid of right m1 (CH35–3d) reversed for consistency. F. Left m2 (CH35–3a). G. Right m3 (CH35–3c) reversed for consistency. All in occlusal views. Dental elements of the proboscidean Arcanotherium savagei (Court, 1995), from the Evaporite Unit (early Oligocene) of Dor El Talha, Libya. H. Right p2, p3, m1, m3 and left p4, m2 (BMNH M. 82165) in occlusal view (p4 and m2 reversed for consistency).
Fig. 5 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 5. Ulnae of the proboscidean Arcanotherium savagei (Court, 1995), from the Idam Unit (early Oligocene) of Dor El Talha, Libya. A. Left ulna (BMNH M. 82176) in anterior (A1), lateral (A2), and proximal (A3) views. B. Left ulna (BMNH M. 82175), repaired since its first publication (Court 1995) in anterior (B1), lateral (B2), and proximal (B3) views.
Fig. 4 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 4. Atlas (BMNH M. 82173) of the proboscidean Arcanotherium savagei (Court, 1995) from the Idam Unit (early Oligocene) of Dor El Talha, Libya in anterior (A), posterior (B) dorsal (C), and lateral (D) views.
Fig. 1 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 1. Holotype mandible (BMNH M. 82163a, b, c) of the proboscidean Arcanotherium savagei (Court, 1995), from the Idam Unit (early Oligocene) of Dor El Talha, Libya in occlusal (A), lateral (B), reconstructed occlusal (C) views.
Fig. 2 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 2. Mandibular elements of the proboscidean Arcanotherium savagei (Court, 1995), from the Evaporite Unit (late Eocene) of Dor El Talha, Libya. A. Symphysis (BMNH M. 82164) in occlusal (A1), lateral (A2), and anterior (A3) views; uncrushed incisor loci are outlined in white on A3. B. Part of right mandibular ramus (BMNH M. 82166) with erupting m2 and p4 in occlusal (B1) and lateral (B2) views.
Fig. 6 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 6. Phylogenetic relationships among early tethytheres. Most parsimonious tree (L = 381; CI = 0.64; RI = 0.70) obtained from 207 morphological characters. Nodes are identified by letters (A to L). Bremer support is indicated in black under each node.
Fig. 3 in Reassessment of the generic attribution of Numidotherium savagei and the homologies of lower incisors in proboscideans
Fig. 3. Dental elements of the proboscidean Arcanotherium savagei (Court, 1995), from the Evaporite (A and C, late Eocene) and Idam (B, early Oligocene) units of Dor El Talha, Libya. A. Erupting left i1 (BMNH M. 82183) in occlusal (A1), lateral (A2), and anterior (A3) views. B. Right M1 (BMNH M. 82172) in buccal (B1), occlusal (B2), and lingual (B3) views. C. Right M2 (BMNH M. 82398) in buccal (C1), occlusal (C2), and lingual (C3) views. D. Left M3 (MNHN LBE 20) in buccal (D1), occlusal (D2), and lingual (D3) views.
Fig. 12 in A new large mammal from the Ypresian of Morocco: Evidence of surprising diversity of early proboscideans
Fig. 12. Character matrix of Daouitherium and other primitive lophodont proboscideans (see text: features 1–19) and most parsimonious cladogram resulting from parsimony analysis with Hennig86 program, with distribution of the derived features. Length = 56; CI = 85; RI = 82. This cladogram is unrooted. The significance of Daouitherium for the ancestral morphotype of proboscideans and the basal relationships of lophodont proboscidean taxa with respect to other proboscideans (e.g., Moeritherium, deinotheres) and tethytherians will be investigated separately with the study of the new material of Phosphatherium (work in preparation). Analysed features are additive and are weighted according to their relative importance (see matrix);howeverananalysisofthismatrixwithoutweightingthefeaturesdoes not change the resulting topology. Several reversions that are possible according to the algorithm have been discounted as being anatomically unlikely (features 1, 3, 4). Asterisk indicates convergent feature.
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.