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Figure 3 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 3. The gene order of mitochondrial coding sequences shared among all analysed millipede species in this study, which include all known species of Tropostreptus (T. droides, T. hamatus, T. kipunji, T. microcephalus, T. severus and T. sigmatospinus), in addition to Archispirostreptus gigas, Chaleponcus netus, Macrolenostreptus orestes, Prionopetalum kraepelini and Pseudotibiozus cerasopus. Colour key: red, ribosomal RNA (rRNA); pink, transfer RNA (tRNA); yellow, protein-coding sequences (CDS). Arrows indicate gene transcription orientation.
dudesdb_201709 - Fungi and Virus - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database for the set of Fungal and Viral complete genomes from NCBI RefSeq, dating from 2017-09. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
dudesdb_201709 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2017-09. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
dudesdb_201503 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database (.ddb for version 0.06 and .npz for version 0.07) for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2015-03. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
FIGURE 2 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations
FIGURE 2 | Phylogenetic analysis of 13 Corydoradinae and Hoplosternum littorale (Callichthyinae member) species as the outgroup based on the nucleotide sequences of 13 PCGs from the mitochondrial genome. Bootstrap values are shown next to nodes and the scale bar shows 0.03 changes. Population codes in Tab. 1.
FIGURE 1 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations
FIGURE 1 | A. Geographic location of the Scleromystax barbatus populations in coastal Atlantic Rainforest rivers. B. Male of S. barbatus. Photo by Caio Feltrin. C. Complete mitochondrial genome of S. barbatus from the AR population. Population codes in Tab. 1.
Cloud_ICA: A deterministic cloud-overlap algorithm for generating a complete set of independent column atmospheres
<p>In calculating solar radiation, climate models make many simplifications, in part to reduce computational cost and enable climate modeling, and in part from lack of understanding of critical atmospheric information. Whether known errors or unknown errors, the community's concern is how these could impact the modeled climate. The simplifications are well known and most have published studies evaluating them, but with individual studies it is difficult to compare. Here, we collect a wide range of such simplifications in either radiative transfer modeling or atmospheric conditions and assess potential errors within a consistent framework on climate‐relevant scales. We build benchmarking capability around a solar heating code (Solar‐J) that doubles as a photolysis code for chemistry and can be readily adapted to consider other errors and uncertainties. The broad classes here include: use of broad wavelength bands to integrate over spectral features; scattering approximations that alter phase function and optical depths for clouds and gases; uncertainty in ice‐cloud optics; treatment of fractional cloud cover including overlap; and variability of ocean surface albedo. We geographically map the errors in W m−2 using a full climate re‐creation for January 2015 from a weather forecasting model. For many approximations assessed here, mean errors are ∼2 W m−2 with greater latitudinal biases and are likely to affect a model's ability to match the current climate state. Combining this work with previous studies, we make priority recommendations for fixing these simplifications based on both the magnitude of error and the ease or computational cost of the fix.</p>
Figure 5 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 5. Comparison of the nucleotide sequences of the two putative control regions in the mitogenome of P. eriobotryae. The structural elements were recognized: repeat unit, TATA motif, TA(A)n motif, stem and loop, Poly T-stretch sequence, A + T-rich sequence and G(A)nT motif.
Figure 6 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 6. Gene rearrangement, transposition, inversion and inverse transposition. A. Comparison with the ancestor gene sequence of arthropods, Drosophila yakuba and P. eriobotryae gene sequence. B. Comparison with P. eriobotryae and other five known mitogenomes of Phlaeothripidae species. Yellow blocks show PCGs, blue ones show tRNA, red ones show rRNA and Colourless ones show CRs. Red dashes boxes represent conserve gene blocks. Red dotted ovals represent that the reverse transposition happened in the gene blocks. '+' indicates H-strand, and '-' indicates L-strand. Black arrows indicate the direction of gene translation.
Figure 1 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 1. The circular representation of the complete mitogenome of P. eriobotryae. The direction of gene transcription is indicated by the arrows. PCGs are showed as blue purple arrows, rRNA genes as green arrows, tRNA genes as pink purple arrow and CRs as orange arrows. The inner black circles show GC content and GC-skew plotted as the deviation from the average value of the entire sequence. The image was taken from slide-mounted specimen with an Olympus BX53 and edited manually in Adobe Photoshop 2022 v23.0.2.101.
Figure 4 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 4. Putative cloverleaf secondary structures of the 22 tRNAs of P. eriobotryae. The dot "." indicated mismatched base pairs.
Figure 3 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 3. The ratios of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks), and the ratio of Ka/Ks for each PCGs in the mitogenome of P. eriobotryae.
Figure 7 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 7. Phylogenetic tree of thrips obtained from Maximum-likelihood and MrBayes based on 13 PCGs dataset. The numbers on branches are superimposed with bootstrap support values (BP) and the Bayesian posterior probability (PP).
Figure 2 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae
Figure 2. Codons distribution and usage in the mitogenome of P. eriobotryae. A. Amino acid composition: codon families are provided on the x-axis; numbers of codons of each amino acid are provided on the y-axis. B. The relative synonymous codon usage (RSCU).
Fig. 7 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 7. Cladogram from the maximum likelihood rapid bootstrap analysis with bootstrap support values for each node.
Fig. 5 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 5. Amiid fish Amia sp., USNM 618000, from the Spring Site, Montana, USA; the Kishenehn Formation's Coal Creek Member, 43.5 Ma (Eocene). Dentary in left anterolateral view; three-dimensional model (A1), illustration with elements labeled, coronoid teeth outlined and indicated by arrows (A2). The letter following the anatomical abbreviation denotes the left (-l) element. Abbreviations: d, dentary; dsp, dermosphenotic; fr, frontal; l, lacrimal; n, nasal; po1, postinfraorbital.
Fig. 4 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 4. Amiid fish Amia sp., USNM 618000, from the Spring Site, Montana, USA; the Kishenehn Formation's Coal Creek Member, 43.5 Ma (Eocene). Skull in right ventrolateral view; three-dimensional model (A1), illustration with labeled elements (A2). The letter following the anatomical abbreviation denotes the left (-l) or right (-r) element. Abbreviations: ang, angular; ar, posterior articular element; bb, basibranchial; bop, branchiopercle; br, branchiostegal rays; cb, ceratobranchials; cl, cleithrum; d, dentary; dpt, dermopterotic; g, gular; hb, hypobranchials; l, lacrimal; m, mentomeckelian; mx, maxilla; n, nasal; op, opercle; pa, parietals; pmx, premaxilla; po1, po2, postinfraorbitals 1, 2; pop, preopercle; rar, retroarticular; ro, rostral; smx, supramaxilla; so, subinfraorbitals; sop, subopercle.
Fig. 2 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 2. Amiid fish Amia sp., USNM 618000, from the Spring Site, Montana, USA; the Kishenehn Formation's Coal Creek Member, 43.5 Ma (Eocene). A. Shale-imbedded skull in right ventrolateral view. B. Post-crania with the anterior end on the left. C. Three-dimensional model of the entire skeleton from left dorsolateral view. Abbreviations: cop, coprolite; mtg, metapterygium; pb, pelvic bone; pcfr, pectoral fin rays; pfr, principal fin rays; pp, parapophyses; ps, first pelvic fin ray; pvfr-l, left pelvic fin rays; rfr, rudimentary fin rays.
Fig. 6 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 6. Amiid fish Amia sp., USNM 618000, from the Spring Site, Montana, USA; the Kishenehn Formation's Coal Creek Member, 43.5 Ma (Eocene). Tail in left-lateral view; three-dimensional threshold model (A1), explanatory drawing with labeled elements (A2). Vertebral centra 61–68 are represented as impressions in the shale (see SOM: fig. S3). Abbreviations: ep, epurals; epx, epaxial; ha, haemal arch; hpx, hypaxial; hs, haemal spines; hyp1, hyp2, hypurals 1, 2; ihm, infrahaemal; na, neural arches; nsap, anterior process of neural spine; u1, u8, ural centra 1, 8.
Fig. 1 in The most complete amiid fish from the Coal Creek Member of the Eocene Kishenehn Formation in northwestern Montana
Fig. 1. Google Earth images showing the location of the USNM 618000 discovery site ("Spring Site") within Montana (A) and among other shale-bearing middle sequence localities (B). The Spring Site is located on the south bend of the river. Picture of the upper Spring Site showing where USNM 618000 was discovered (C).
ScienceDex guides
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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.