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Fig. 5 in The complete mitogenome of Argas vulgaris (Filippova, 1961) and its phylogenetic status in subgenus Argas (Acari: Argasidae)
Fig. 5. Key morphological characters of female Ar. vulgaris. (a) Dorsal view of female Ar. vulgaris. (b) Ventral view of female Ar. vulgaris. (c) Posthypostomal seta, ventral view. (d) Details structure of the marginal cells between the dorsal and ventral surfaces. (e) Genital aperture of female Ar. vulgaris. (f) Ventral view of anus location. (g) Ventral view of capitulum. (h) Ventral view of hypostome of the dentition formula.
Fig. 4 in The complete mitogenome of Argas vulgaris (Filippova, 1961) and its phylogenetic status in subgenus Argas (Acari: Argasidae)
Fig. 4. Phylogenetic tree of Argas species based on the COI gene contained in the mitochondrial genome. Numbers at the nodes are bootstrap values of the ML analysis. The GenBank accession numbers are listed after the species names.
Fig. 3 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 3. Maximum likelihood tree (log likelihood = -2410.0522) of Corydoras samples with at least 90% similarity to the mitochondrial cytochrome oxidase I sequences of C. nattereri from the rio Suruí. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Bootstrap robustness is indicated next to selected branches. Samples of C. nattereri have the locality name appended to the sample ID (those for which mitogenomes were produced are from de rio "Surui"), outgroups have the genus name and other samples of Corydoras have the species epithet name appended to the ID code (Table 1).
Fig. 2 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 2. Sequencing depth over the complete mitogenomes of the three individuals of Corydoras nattereri: KT239008 (A), KT239009 (B), and KT239010 (C). Read counts (y-axis) are shown in logarithmic scale and sharp decreases correspond to the punctuation model of mitochondrial transcription (positions correspond to those shown in Fig. 1 and Table 3). Black vertical bars indicate position of gaps that were filled with Sanger sequencing (Table 2). Reads were mapped to the mitogenomes using Bowtie and visualized at the Integrative Genome Viewer (IGV, Bernt et al., 2013; Thorvaldsdóttir et al., 2013).
Fig. 1 in The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)
Fig. 1. Circular representation of the mitochondrial genome of Corydoras nattereri. Genes encoded in the heavy strand are shown in the outer circle and genes encoded in the light strand are offset inwards. The inner circle represents the CG-content. Figure was generated by the online server MitoFish, http://mitofish.aori.u-tokyo.ac.jp (Iwasaki et al., 2012).
Complete figure set for 'Radio Morphology of Gamma-ray Sources: Double-Lobed Radio Sources'
<p>This file is the online supplementary material for the data that will be published in the manuscript title "Radio Morphology of Gamma-ray Sources: Double-Lobed Radio Sources" by the Astrophysical Journal.</p>
Linked collectors and determiners for: Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013.
Natural history specimen data linked to collectors and determiners held within, "Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e">https://bionomia.net/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e">https://gbif.org/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar.
Natural history specimen data linked to collectors and determiners held within, "Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/799d241f-7891-4146-a38c-7809efa13368">https://bionomia.net/dataset/799d241f-7891-4146-a38c-7809efa13368</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/799d241f-7891-4146-a38c-7809efa13368">https://gbif.org/dataset/799d241f-7891-4146-a38c-7809efa13368</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: The millipede family Conotylidae in northwestern North America, with a complete bibliography of the family (Diplopoda, Chordeumatida, Heterochordeumatidea, Conotyloidea).
Natural history specimen data linked to collectors and determiners held within, "The millipede family Conotylidae in northwestern North America, with a complete bibliography of the family (Diplopoda, Chordeumatida, Heterochordeumatidea, Conotyloidea)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f7974bcf-11e7-4d1b-b09d-530dc2dbd54f">https://bionomia.net/dataset/f7974bcf-11e7-4d1b-b09d-530dc2dbd54f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f7974bcf-11e7-4d1b-b09d-530dc2dbd54f">https://gbif.org/dataset/f7974bcf-11e7-4d1b-b09d-530dc2dbd54f</a>. Formatted as a Frictionless Data package.
Complete Medline abstracts corpus between 2015-2019 annotated Whatizit text annotation tool
<p><strong>Background: </strong></p> <p>Whatizit is a text processing system that allows you to do text-mining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Identified terms are wrapped with XML tags that carry additional information, such as the primary keys to the databases where all the relevant information is kept. The wrapping XML is translated into HTML hypertext links. This service is highly appreciated by people who are reading literature and need to quickly find more information about a particular term, e.g. its Gene Ontology term.</p> <p>Whatizit is used in identifying formalized language patterns, specialized, syntactically formalized, technical notation. The annotation speed of a given pipeline is almost independent of the size of the vocabulary behind it and is currently based on pattern matching. In addition, several vocabularies can be integrated in a single pipeline.</p> <p><strong>Methodology:</strong></p> <p>The pipeline used is comprised of 175k Gene Ontology terms (preferred labels + synonyms).<br> The annotation on Medline 2015-2019 corpus is done with <em>Gene Ontology (GO)</em> integrated dictionary.</p> <p>The .zip file contains 10 XML files - each file is for half an year of MEDLINE annotated abstracts.<br> In addition to the abstract, the title is also annotated for further information enrichment.</p> <p>Respective DOIs, PMIDs are also included in the XML, when applicable.</p> <p><strong>Further development:</strong></p> <p>The XML files can be converted into JSON, JSON-LD format.</p> <p> </p> <p> </p>
Regression models generated by APRANK (computational prioritization of antigenic proteins and peptides from complete pathogen proteomes)
<p>Availability of highly parallelized immunoassays has renewed interest in the discovery of serology-based biomarkers for infectious diseases. Protein and peptide microarrays now provide a high-throughput platform for immunological screening of potential antigens and B-cell epitopes. However, there is still a need to prioritize relevant probes when designing these arrays. In this work we describe a computational method called APRANK (Antigenic Protein and Peptide Ranker) which integrates multiple molecular features to prioritize antigenic targets starting from a given pathogen proteome. These features include subcellular localization, presence of repetitive motifs, natively disordered regions, secondary structure, transmembrane spans and predicted interaction with the immune system. We applied this method to the prioritization of potential diagnostic antigens and peptides in a number of pathogen proteomes and human diseases: Borrelia burgdorferi (Lyme disease), Brucella melitensis (Brucellosis), Coxiella burnetii (Q fever), Escherichia coli (Gastroenteritis), Francisella tularensis (Tularemia), Leishmania braziliensis (Leishmaniasis), Leptospira interrogans (Leptospirosis), Mycobacterium leprae (Leprae), Mycobacterium tuberculosis (Tuberculosis), Plasmodium falciparum (Malaria), Porphyromonas gingivalis (Periodontal disease), Staphylococcus aureus (Bacteremia), Streptococcus pyogenes (Group A Streptococcal infections), Toxoplasma gondii (Toxoplasmosis) and Trypanosoma cruzi (Chagas Disease). After training a linear regression model the method achieves good to excellent performance on most species, measured by the enrichment of validated antigens at the top of the ranking. An unbiased validation using independent data sets shows APRANK is successful in predicting antigenicity for all pathogen species tested. We make APRANK available to facilitate the identification of novel diagnostic antigens in infectious diseases.</p>
FIG. 24 in Redescription of a Nearly Complete Skull of Plateosaurus (Dinosauria: Sauropodomorpha) from the Late Triassic of Trossingen (Germany)
FIG. 24. Vomers (with anterior ends of palatine and pterygoid) of Plateosaurus erlenbergiensis (AMNH FARB 6810). Abbreviations in appendix 2. A, left vomer in lateral view. B, left and right vomer in dorsal view. C, right vomer in lateral view. Abbreviations in appendix 2
FIG. 13 in Redescription of a Nearly Complete Skull of Plateosaurus (Dinosauria: Sauropodomorpha) from the Late Triassic of Trossingen (Germany)
FIG. 13. Left postorbital of Plateosaurus erlenbergiensis (AMNH FARB 6810). A, lateral; B, posterior; C, medial; D, anterior. Abbreviations in appendix 2.
FIG. 11 in Redescription of a Nearly Complete Skull of Plateosaurus (Dinosauria: Sauropodomorpha) from the Late Triassic of Trossingen (Germany)
FIG. 11. Left lacrimal of Plateosaurus erlenbergiensis (AMNH FARB 6810). A, dorsal; B, lateral; C, medial; D, ventral. Abbreviations in appendix 2.
FIG. 6 in Redescription of a Nearly Complete Skull of Plateosaurus (Dinosauria: Sauropodomorpha) from the Late Triassic of Trossingen (Germany)
FIG. 6. Right nasal of Plateosaurus erlenbergiensis (AMNH FARB 6810). A, lateral; B, dorsal; C, medial; D, ventral. Abbreviations in appendix 2.
Complete results of Procedure section in manuscript "PathML: A unified framework for whole-slide image analysis with deep learning"
<p>The results from a complete run of the Procedure section of the paper "PathML: A unified framework for whole-slide image analysis with deep learning".</p>
Confocal micrographs and complete dataset of neuromuscular junction morphology of pelvic limb muscles of the pig (Sus scrofa)
<p>This dataset entails the complete NMJ dataset for three pigs and the three muscles analysed for the publication "Comparative anatomy of the mammalian neuromuscular junction" (https://doi.org/10.1111/joa.13260). This includes spreadsheets (.csv) containing morphometric variables of neuromuscular junction morphology generated using NMJ-morph or aNMJ-morph, as well as muscle fibre diameter (MFD) data for completeness. The three muscles analysed are: extensor digitorum longus (EDL), peroneus longus (PL) and soleus (S). Data contains raw microscope images (.nd2), thresholded and cleaned images of pre- and post-synapse (.tif) and the thresholded and cleaned images of the intermediate muscle endplate (.tif) for the muscle soleus since the "aNMJ-morph" macro saves this intermediate image for measurement of endplate variables.</p> <p>The full data set description is in the readme_file.txt.</p>
STK Probability Matrix for the complete STK PamChip
<p>This dataset has a completed calculated posterior probabilities for each Kinase that could phosphorylate each peptide on the PamGene STK PamChip version 87102</p>
Figure 5. Novorostrum decorocrus Osawa, 1998 in Complete larval development of the rare porcellanid crab, Novorostrum decorocrus Osawa, 1998 (Crustacea: Decapoda: Anomura: Porcellanidae), reared under laboratory conditions
Figure 5. Novorostrum decorocrus Osawa, 1998, megalop. (A) Entire animal, dorsal; (B) rostrum, dorsal; (C) pterygostomian flap, left side, lateral; (D) thoracic sternites, ventral; (E) first pereiopod, dorsal; (F) third pereiopod, lateral; (G) chela of fifth pereiopod, dorsal; (H–K) pleopods on second to fifth abdominal somite, ventral; (L) telson and uropod, dorsal. Scale bars: 0.5 mm (A); 0.1 mm (B–J).
Figure 4. Novorostrum decorocrus Osawa, 1998 in Complete larval development of the rare porcellanid crab, Novorostrum decorocrus Osawa, 1998 (Crustacea: Decapoda: Anomura: Porcellanidae), reared under laboratory conditions
Figure 4. Novorostrum decorocrus Osawa, 1998, second zoea. (A) Antennule, ventral; (B) antenna, ventral; (C) mandibles (r, right; l, left), internal; (D) maxillule, ventral; (E, F) same, endopod, ventral; (G) maxilla, ventral; (H) first maxilliped, mesial; (I) second maxilliped, mesial; (J) third maxilliped, mesial; (K) pereiopods, mesial; (L) pleopod on second abdominal somite, ventral. Scale bars: 0.1 mm.
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.