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scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution - Supplementary data and code
<p>Data and code to reproduce the analyses from the study: "scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution". </p>
Supplementary Materials for: Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China
<p>Supplementary Materials for</p><p><strong>Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China</strong></p><p>Adrian Jones, Daoyu Zhang, Steven E. Massey, Yuri Deigin, Louis R. Nemzer, Steven C. Quay</p>
FIGURES 23–31. Stenelmis puberula larva, 23 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences
FIGURES 23–31. Stenelmis puberula larva, 23) protergum, lateral depression with rimmed setiferous pits; 24) protergum, posterior angle; 25) long tergal seta; 26) meso- and metasternum, ventral view; 27) right fore-leg, ventral view; 28) left fore-leg, dorsal view; 29) fore-leg, detail of femur; 30) fore-leg, detail of tibia; 31) fore-leg, detail of tarsungulus.
FIGURES 12–22. Stenelmis puberula larva, 12 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences
FIGURES 12–22. Stenelmis puberula larva, 12) left mandible, ventral view; 13) right mandible, ventral view; 14) left maxilla, ventral view; 15) same, detail of prebasal tufted scales; 16) left maxilla, detail of lateral seta; 17) right maxilla – galea, lacinia, palpus, ventral view; 18) mouth parts, ventral view; 19) labium, ventral view; 20) labial palpus, ventral view; 21) same, detail of apical sensory field; 22) labium, dorsal view.
FIGURES 32–42. Stenelmis puberula larva, 32 in Stenelmis puberula Reitter (Coleoptera: Elmidae)-description of larva and its association with adults, using DNA sequences
FIGURES 32–42. Stenelmis puberula larva, 32) right mid-leg, dorsal view; 33) left hind-leg, dorsal view; 34) mid-leg, detail of tibia; 35) hind-leg, detail of femur-tibia articulation; 36) detail of abdominal forked scales; 37) detail of abdominal tergum, lateral view; 38) venter of abdominal segments; 39) abdominal tergites, dorsal view; 40) abdominal segment 9, dorsal view; 41) abdominal segment 9, lateral view; 42) abdominal operculum, hooks and anal gills.
FIGURE 17 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 17. Black adult male Bungarus candidus (UK B15) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Like the type specimen of Bungarus javanicus, it has a yellow ventral colouration and yellow spots on the vertebrals. Note unpigmented internasals and 5th and 6th supralabials of the right head side. Photo by Ulrich Kuch.
FIGURE 16 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 16. Close-up of a black adult male Bungarus candidus (UK BP4) from the area of Purwokerto, Central Java, Indonesia. Photo by Ulrich Kuch.
FIGURE 15 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 15. The most frequently encountered colour morph of "black" Bungarus candidus on Java represented by an adult male (UK BX3) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Photo by Ulrich Kuch.
FIGURE 13 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 13. Adult female Bungarus candidus (UK B34) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the anterior body and mosaic-like dark stippling on the posterior body and tail. Photo by Ulrich Kuch.
FIGURE 11 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 11. Adult male Bungarus candidus (UK B38) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the posterior half of the body. Photo by Ulrich Kuch.
FIGURE 14 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 14. Adult male Bungarus candidus (UK B35) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced bands on the posterior body and heavy pigmentation of all light interspaces and ventrolateral areas (opaque colouration is due to imminent shedding). Photo by Ulrich Kuch.
FIGURE 10 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 10. Regularly black-and-white banded juvenile Bungarus candidus from Desa Songgon, about 20 km SW of Banyuwangi, East Java, Indonesia. Note the characteristic light head pattern of juvenile specimens. Photo by Andrea Glässer-Trobisch and Dietmar Trobisch.
FIGURE 9 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 9. Black juvenile Bungarus candidus (ZMB 57702) from Banjar Berawa, Desa Canggu, Denpasar, Bali, Indonesia. Photo by Frank Tillack.
FIGURE 8 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 8. Ventral view of the partially leucistic juvenile Bungarus candidus (UK 96-1) from Linggarjati. Photo by Ulrich Kuch.
FIGURE 7 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 7. Juvenile Bungarus candidus (UK 96-1) from Linggarjati (Kabupaten Cirebon, West Java, Indonesia; 400– 500 m above sea level) with white snout, reduced black bands on anterior body, and white dorsals with dark tips on the rest of the body. Photo by Ulrich Kuch.
FIGURE 6 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 6. Contour map of Java and Madura (Bali, adjacent to the east, not shown). Capital letters indicate collecting areas: A, Losarang (near Indramayu); B, area of the type locality of Bungarus javanicus (near Mt. Ciremai, e.g., Linggarjati); C, Purwokerto basin; D, coastal plain near Cilacap. Dots and circles, respectively, mark collecting localities of additional examined specimens and literature records of black-and-white banded Bungarus candidus.
FIGURE 5 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 5. Black adult female Bungarus candidus (SMF 76271) from Linggarjati (Kabupaten Cirebon, West Java, Indonesia; 400–500 m above sea level). The colour pattern of this snake closely resembles that of the type specimen of Bungarus javanicus. Photo by Ulrich Kuch.
FIGURE 4 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 4. Kopstein's (1936) third specimen of Bungarus javanicus, the 'intermediary' snake from Linggarjati (ZRC 2.4379). Photo by Ulrich Kuch.
FIGURE 1 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 1. Line drawing of the type specimen of Bungarus javanicus. From the original description (Kopstein 1932).
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Zhejiang Province, eastern China
FIGURE 6. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.