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Plate 4 in Taxonomic Revision and Classification of Extant Holococcolithophores Previously Placed in the Genus Anthosphaera Kamptner emend. Kleijne 1991
Plate 4. Syracosphaera periperforata (Kleijne) Archontikis, Young, Cros comb. nov. HOL Scale bars = 1μm 1–2. Syracosphaera periperforata var. periperforata (Kleijne) Archontikis, Young, Cros HOL. 1. Coccosphere with highly arched CFCs (arrow a) and dome-shaped BCs that show an apical boss on top of their central distal cover (arrow b). 2. Detailed view showing the delicate structure of the CFCs' distal process. 3–4. Syracosphaera periperforata var. cylindrata Archontikis, Young, Cros var. nov. HOL. 3. Holotype; Complete coccosphere with high-arched CFCs (arrow a) and BCs of cylindrical shape that show no apical boss on top of their central structure; antapical coccoliths (arrow b) always bear an apical boss. 4. Paratype; detailed view showing the proximal (organic) base-plate and the rim of CFCs (arrow). 5–6. Syracosphaera periperforata var. tridentata Archontikis, Young, Cros var. nov. HOL. 5. Holotype; flattened coccosphere with CFCs that bear a low process with a three pointed upper/distal margin structure (arrow a), and a proximal rim with one to two rings of microcrystallites (arrow b); BCs present an apical boss on top of their distal cover. 6. Paratype.
Plate 1 in Taxonomic Revision and Classification of Extant Holococcolithophores Previously Placed in the Genus Anthosphaera Kamptner emend. Kleijne 1991
Plate 1. Syracosphaera molischii Schiller HOL Scale bars = 1μm 1–3. Syracosphaera molischii Schiller var. molischii HOL 1. Complete coccosphere. 2. Detailed view showing the ultrastructure (arrow) of CFCs. 3. Detailed view of BCs showing the angular microcrystallites of the central structure and the tiny perforations at the perforate cycle (arrow). 4–6. Syracosphaera molischii var. pertusa Archontikis, Young, Cros var. nov. HOL 4. Holotype; flattened coccosphere. 5. Paratype; coccosphere with BCs that bear larger (to that of S. molischii var. molischii HOL) perforations on their perforate cycle (arrow). 6. Detailed view of BCs with longitudinally arranged crystals at the central structure.
Plate 3 in Taxonomic Revision and Classification of Extant Holococcolithophores Previously Placed in the Genus Anthosphaera Kamptner emend. Kleijne 1991
Plate 3. Scale bars = 1μm 1–2. Syracosphaera lafourcadii (Lecal) Archontikis, Young, Cros comb. nov. HOL Complete coccospheres composed of CFCs that bear low distal processes (see arrows) and BCs with distal covers made of irregularly arranged crystallites. 3–4. Syracosphaera origami (Cros and McGrane) Archontikis, Young, Cros comb. nov. HOL Coccospheres with highly ornamented CFCs showing triangle-shaped distal processes (fig. 3, arrow) and BCs with an organic base-plate in proximal view (fig. 4, arrow a) and a rim that supports delicate struts of crystallites holding the origami-like paper boat distal covers (fig. 4, arrow b) in distal view.
Fig. 90-91 in Classification, Natural History, and Evolution of the Subfamily Peloniinae O (Coleoptera: Cleroidea: Cleridae). Part IX. Taxonomic revision of the New World genus Muisca S
Fig. 90-91: Metatarsus. (90) M. octonotata, ungues. (91) M. octonotata, 4th tarsomere.
Fig. 96 in Classification, Natural History, and Evolution of the Subfamily Peloniinae O (Coleoptera: Cleroidea: Cleridae). Part IX. Taxonomic revision of the New World genus Muisca S
Fig. 96: Geographic distribution of Muisca species as listed.
Uniprot datasets for training taxonomic classification
<p>The data is based on the UniProt-Swiss-Prot release 2020-04 dataset and contains data derived from amino acid sequences of human, bacterial and viral origin. From each original sequence we created multiple patches of length 100 using a sliding window. The data is stored in the FASTA format according to<br> <br> >{ID}_{patch index}|{class marker}<br> sequence<br> <br> with<br> <br> ID - denotes the ID of the original sequence in the UniProt-Swiss-Prot dataset<br> sequence - patch of length 100 of an amino acid sequence<br> patch_index - denotes the starting index of the given patch within the original sequence<br> class marker - indicates the taxonomic class<br> 0 - virus<br> 1 - bacteria<br> 2 - human / mammal<br> <br> The data is split into test, training and validation set which contain the following number of patches per class:<br> <br> <br> - train: 4.891.278<br> - test: 611.602<br> - val: 611.602</p>
Taxonomic classification based on k-mers
<p>DNA sequencing provides the possibility to obtain complete genomic DNA from environmental samples without the need for laboratory microbiological cultures. To this end, metagenomics, the direct DNA sequencing from microbial communities, has changed radically the field of microbiology, by unearthing a broad space of the planet’s microbial diversity, much of which remains unknown. Metagenomic approaches have become standard methods for identifying the biodiversity and the gene or metabolomic functionalities of bacterial and archaeal communities, with many applications not only in microbial ecology but also in public health as in clinical diagnostics and detection of pathogens. Yet, the decrease in the cost of high throughput sequencing and the great amount of microbial data produced every day, highlight one of the main biological questions: the taxonomic classification of metagenomic short reads. Which organisms are contained in a sample? Are there any features that can be used to identify them?</p> <p>To this end, many algorithms have been developed that achieve high speed, by counting k-mers, short sequence substrings of fixed-length k. In this way for the provided input sequences, a list of features can be computed that describes each one of them. Subsequently, the question now reforms to how can the produced k-mers be used for the taxonomic classification of the input sequences.</p> <p>Sample processing, sequencing, and core amplicon data analysis were performed by the Earth Microbiome Project (www.earthmicrobiome.org), and all amplicon sequence data and metadata have been made public through the EMP data portal (qiita.microbio.me/emp):</p> <ul> <li>Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., …, Jansson, J. K., Gilbert, J. A., Knight, R., & The Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551:457-463. doi:10.1038/nature24621.</li> </ul>
Taxonomic classification of seabird long bones using 3D shape: A method with wider potential in zooarchaeology
<p>Dataset of manually-placed landmark (.pts) files. </p> <p>Fixed landmarks and semilandmarks were placed on 3D digitised (.ply) models and exported in .pts file format from Landmark Editor 3.0 (Institute of Data Analysis and Visualization IDAV, University California Davis, USA) (Wiley et al., 2005). The .pts files can be read into R (R Core Team., 2021) using the Morpho::read.pts function (Schlager, 2017). </p> <p> </p> <p>R Core Team. (2021). R: A language and environment for statistical computing. (Version 4.0.2). R Foundation for Statistical Computing, Vienna, Austria. <a href="https://www.r-project.org/">https://www.r-project.org/.</a></p> <p>Schlager, S. (2017). Morpho and Rvcg–Shape Analysis in R: R-Packages for geometric morphometrics, shape analysis and surface manipulations. In <em>Statistical shape and deformation analysis</em> (pp. 217-256). Elsevier.</p> <p>Wiley, D. F., Amenta, N., Alcantara, D. A., Ghosh, D., Kil, Y. J., Delson, E., Harcourt-Smith, W., Rohlf, F. J., St. John, K., & Hamann, B. (2005). Evolutionary morphing. <em>IEEE Visualization 2005 - (VIS'05)</em>, pp.55.</p>
Data files and taxonomic classifiers for Pseudomonas syringae classification and virulence factor prediction
<p>PSSC.tree : core-genome tree of 2,161 high quality <em>Pseudomonas syringae</em> genomes</p> <p>metadata.csv: A CSV file containing taxonomic data, type strain designations, phylogroups as assigned in this study, LIN clusters assigned for classification purposes, presence/absence of key virulence factors, and metadata found in each genome’s Biosample record for all genomes found in PSSC.tree</p> <p>CLASSIFIER_xxx: QIIME 2 classifier artifacts trained on amplicons generated from primer sets indicated in file name</p> <p>xxx_VFOC.JSON: HMMER results for T3SS and effectors and WHOP genes, structured with both genome and gene product accession numbers as primary key, depending on file</p> <p> </p> <p> </p>
Fig. 1 in Taxonomic Revision and Classification of Extant Holococcolithophores Previously Placed in the Genus Anthosphaera Kamptner emend. Kleijne 1991
Fig. 1. Map of the sampling locations, where Anthosphaera was observed.
PyTorch model for taxonomic classification
<p>This is a trained PyTorch model for classifying an amino acid sequence's (preferably of length 100) taxonomic domain as viral (class 0), bacterial (class 1) or mammalian (class 2).</p> <p> </p>
Beating Naive Bayes at Taxonomic Classification
<p><a href="https://qiime2.org/">QIIME 2</a> Artifacts containing microbiome samples, organised by EMPO 3 classification.</p> <p>Downloaded from <a href="https://qiita.ucsd.edu/">Qiita</a>.</p>
FIGURE 17 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 17. Line drawings of spermatheca, spermathecal duct, and spermathecal gland of Zeanillus species. A—Z. carltoni (NZ, Otago, Mount Watkin); B—Z. lescheni (NZ, Otago, Waikaia Forest); C—Z. nanus (NZ, Otago, Balclutha), the structure is the same as in Fig. 16H and is repeated for purposes of comparison among species. Legend: sd—spermathecal duct. Scale bar = 0.1mm.
FIGURE 14 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 14. Line drawings of ring sclerite of Zeanillus species, male genitalia, dorsal aspect. A—Z. phyllobius (NZ, Canterbury, Ahuriri Scenic Reserve); B—Z. punctigerus (NZ, Canterbury, Orari Gorge); C—Z. nunni (NZ, Otago, Highway 87 at Rocklands Rd); D—Z. pallidus (NZ, Southland, Thomsons Bush); E—Z. pellucidus (NZ, Otago, Oamaru, Glen Warren Reserve); F—Z. nanus (NZ, Otago, Pisa Range); G—Z. montivagus (NZ, Otago, North Rough Ridge); H—Z. brouni (NZ, Otago, Oamaru, Glen Warren Reserve); I—Z. lescheni (NZ, Otago, Waikaia Forest); J—Z. carltoni (NZ, Otago, Mount Watkin). Legend: hd—handle of ring sclerite. Scale bar = 0.1mm.
FIGURE 16 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 16. Line drawings of spermatheca, spermathecal duct, and spermathecal gland of Zeanillus species. A—Z. phyllobius (NZ, Canterbury, Ahuriri Scenic Reserve); B—Z. punctigerus (NZ, Canterbury, Sharplin Falls); C—Z. nunni (NZ, Otago, Woodside Glen); D—Z. pellucidus (NZ, Otago, Oamaru, Glen Warren Reserve); E—Z. pallidus (NZ, Otago, Taieri Mouth); F—Z. brouni (NZ, Otago, Oamaru, Glen Warren Reserve); G—Z. montivagus (NZ, Otago, North Rough Ridge); H—Z. nanus (NZ, Otago, Balclutha). Legend: sd—spermathecal duct; sg—spermathecal gland; sp—spermatheca. Scale bar = 0.05mm.
FIGURE 15 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 15. Line drawings of right ovipositor sclerite, lateral aspect, of Zeanillus species. A—Z. phyllobius (NZ, Canterbury, Ahuriri Scenic Reserve); B—Z. punctigerus (NZ, Canterbury, Sharplin Falls); C—Z. nunni (NZ, Otago, Woodside Glen); D— Z. pallidus (NZ, Otago, Taieri Mouth); E—Z. pellucidus (NZ, Otago, Oamaru, Glen Warren Reserve); F—Z. brouni (NZ, Otago, Oamaru, Glen Warren Reserve); G—Z. carltoni (NZ, Otago, Mount Watkin); H—Z. lescheni (NZ, Otago, Waikaia Forest); I—Z. montivagus (NZ, Otago, North Rough Ridge); J—Z. nanus (NZ, Otago, Balclutha). Legend: es—ensiform seta; gc1—gonocoxite 1; gc2—gonocoxite 2; lt—laterotergite; ns—nematiform seta. Scale bar = 0.05mm.
FIGURE 13 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 13. Line drawings of aedeagus of Zeanillus species. Z. carltoni (NZ, Otago, Mount Watkin): A—median lobe, right lateral aspect, B—apical part of median lobe, dorsal aspect, C—left paramere, left lateral aspect, D—right paramere, right lateral aspect; Z. lescheni (NZ, Otago, Waikaia Forest): E—median lobe, right lateral aspect, F—apical part of median lobe, dorsal aspect, G—left paramere, left lateral aspect, H—right paramere, right lateral aspect; Z. nanus (NZ, Otago, Balclutha): I—median lobe, right lateral aspect, J—apical part of median lobe, dorsal aspect, K—left paramere, left lateral aspect, L—right paramere, right lateral aspect; Z. montivagus (NZ, Otago, North Rough Ridge): M—median lobe, right lateral aspect, Napical part of median lobe, dorsal aspect, O—left paramere, left lateral aspect, P—right paramere, right lateral aspect; Z. brouni (NZ, Otago, Oamaru, Glen Warren Reserve): Q—median lobe, right lateral aspect, R—apical part of median lobe, dorsal aspect, S—left paramere, left lateral aspect, T—right paramere, right lateral aspect. Legend: ds—dorsal sclerites; of—ostial field. Scale bar = 0.1mm.
FIGURE 12 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 12. Line drawings of aedeagus of Zeanillus species. Z. punctigerus (NZ, Canterbury, Sharplin Falls): A—median lobe, right lateral aspect, B—apical part of median lobe, dorsal aspect, C—left paramere, left lateral aspect, D—right paramere, right lateral aspect; Z. nunni (NZ, Otago, Evansdale): E—median lobe, right lateral aspect, F—apical part of median lobe, dorsal aspect, G—left paramere, left lateral aspect, H—right paramere, right lateral aspect; Z. phyllobius (NZ, Canterbury, Ahuriri Scenic Reserve): I—median lobe, right lateral aspect, J—apical part of median lobe, dorsal aspect, K—left paramere, left lateral aspect, L—right paramere, right lateral aspect; Z. pallidus (NZ, Otago, Taieri Mouth): M—median lobe, right lateral aspect, N—apical part of median lobe, dorsal aspect, O—left paramere, left lateral aspect, P—right paramere, right lateral aspect; Z. pellucidus (NZ, Otago, Oamaru, Glen Warren Reserve): Q—median lobe, right lateral aspect, R—apical part of median lobe, dorsal aspect, S—left paramere, left lateral aspect, T—right paramere, right lateral aspect. Legend: ao—apical orifice; bo—basal orifice; ds—dorsal sclerites, of—ostial field. Scale bar = 0.1mm.
FIGURE 7 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 7. Digital images of pterothorax and first abdominal ventrites, ventral aspect, of Zeanillus species. A—Z. phyllobius; B—Z. punctigerus; C—Z. nunni; D—Z. pallidus; E—Z. pellucidus; F—Z. brouni; G—Z. lescheni; H—Z. montivagus; I—Z. nanus. Legend: ipa—intercoxal process of abdominal ventrite 2; mes—metendosternite; mte—metanepisternum; mtvmetaventrite; v1–v2—abdominal ventrites 1–2. Scale bars = 0.2mm.
FIGURE 11 in A taxonomic review of the anilline genus Zeanillus Jeannel (Coleoptera: Carabidae: Bembidiini) of New Zealand, with descriptions of seven new species, re-classification of the species, and notes on their biogeography and evolution
FIGURE 11. Digital images of habitus of Zeanillus species, dorsal aspect. A—Z. phyllobius (NZ, Canterbury, Coopers Knob); B—Z. punctigerus (NZ, Canterbury, Sharplin Falls); C—Z. nunni (NZ, Otago, Highway 87 at Rocklands Road); D—Z. pallidus (NZ, Otago, Taieri Mouth); E—Z. pellucidus (NZ, Otago, Oamaru, Glen Warren Reserve); F—Z. brouni (NZ, Otago, Oamaru, Glen Warren Reserve); G—Z. carltoni (NZ, Otago, Mount Watkin); H—Z. lescheni (NZ, Otago, Waikaia Forest); I— Z. montivagus (NZ, Otago, North Rough Ridge): J—Z. nanus (NZ, Otago, Pisa Range). Scale bar = 1.0mm.
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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.