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Supplementary material 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Inferred secondary structure of 22 tRNA genes in the mitochondrial DNA of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata). :
FIGURE 4 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 4. Comparison diagram of mitochondrial gene arrangement patterns of nine millipede species. One-letter codes corresponding to the amino acids of the tRNAs are used. Diagram is adapted and modified from Brewer et al. (2013).
FIGURE 2 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 2. Potential stem and loop structures of the junctional sequences of (A) COI-COII, (B) ATP8-ATP6, (C) ND6- Cytb, (D) ND4L-ND4, and (E) ATP6-COIII, and (F) a non-coding region in the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937). The anticodon sequences are boxed, and termination codons or incomplete termination codons are drawn with an underline or side-line. The number of nucleotide sequences in each loop is shown.
FIGURE 1 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 1. The mitochondrial genome structures of Anaulaciulus koreanus (Verhoeff, 1937). The direction of transcription for each gene is shown by an arrow. The hatch-marked area is a large non-coding region.
FIGURE 3 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 3. Putative secondary structures of the 22 tRNAs observed from the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937)
Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.
Gene annotation of complete genome sequence of Achromobacter sp. strain E1
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DeepSEA complete datasets and code
<p><strong>Surveying antimicrobial resistance (AMR) is essential to track the evolution and spread of resistant genes/proteins since AMR is a major cause of death, being responsible for more deaths than HIV and malaria combined. Alignment-based annotation tools use strict similarity (>70%) cutoffs to distinguish between potential and AMR real sequences and only annotate proteins similar to those in their databases. DeepARG and AMRFinderPlus use artificial neural networks (ANN) and Hidden Markov Models (HMM) to annotate AMR proteins with remote homology. However, DeepARG needs a pre-processing step that aligns the query data and selects the most probable proteins, although the filtering uses looser cutoffs. HMMs also depend on multi-sequence alignment (MSA) and are focused on a single AMR class. Here we present DeepSEA, an alignment-free tool fitted on antimicrobial resistant proteins (APR) and non-resistant proteins (NRP) aligned and unaligned to ARP. Our results show that DeepSEA outperforms the current multi-class AMR classifiers. Furthermore, DeepSEA’s model can cluster AMR by resistant mechanisms, showing that the model's latent variables successfully captured distinguishing features of antibiotic resistance. Our tool annotated functionally validated tetracycline destructases (TDases) and confirmed the identification of a novel TDase found by HMM. </strong></p>
Complete dataset used in the study "A statistical approach to coronavirus classification based on nucleotide distributions"
<p>This is a complete dataset of parameters used in coronavirus classification based on distributions of nucleotide sequences as described in the study "A statistical approach to coronavirus classification based on nucleotide distributions"</p>
Supplementary File 4; Complete list of all wild herbivores, wild carnivores, wild primates and prosimians and wild rodents sampled in this study:
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Complete dataset for the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication"
<p>This dataset enlists all individual datapoints shown in the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication" (https://doi.org/10.1038/s41467-023-44157-3). For detailed information regarding the individual contributions please check the "Author information" section in the publication. </p>
Phylogenetic structure of moth communities (Geometridae, Lepidoptera) along a complete rainforest elevational gradient in Papua New Guinea"
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The VISTA Variables in the Vía Láctea eXtended (VVVX) ESO public survey: Completion of the observations and legacy - Appendix A
<p><strong>Table A.1. </strong>List the VVV+VVVX tiles and observed number of epochs. We present the tile names and centre coordinates in Equatorial and Galactic systems (see Fig. A.1 at the end for the spatial distribution). Columns 6 to 8 present the number of epochs observed in J, H and Ks during the VVV and VVVX campaigns. The first number is the total of epochs, and in parentheses the number of epochs observed in VVV and VVVX, respectively.</p>
Sequenced Raw Data: Untreated PTB (UTB) Cases, Completed ATT Treatment PTB (CTB) Cases, and Healthy Controls (HC)
<p>The FastQ datasets were generated using the Illumina MiSeq sequencing platform, specifically targeting the v3-v4 hypervariable region of the 16S rRNA gene, to facilitate high-resolution profiling of microbial communities.</p>
Automated Assessment of Mobile Programming Courses: Leveraging GitHub Classroom and Flutter for Enhanced Student Outcomes - Survey complete results
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JBCS - The complete list of categories and technologies
<p>JBCS - The complete list of categories and technologies</p>
The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae)
<p>ABSTRACT: Known colloquially as ‘Old Man’s Beard’, <em>Usnea</em> is a genus of lichenized Ascomycete fungi characterized by having a fruticose growth form and cartilaginous central axis. The complete mitochondrial genomes of <em>Usnea halei</em>, <em>U. mutabilis</em>, <em>U. subfusca</em>, <em>U. subgracilis</em>, and <em>U. subscabrosa</em> were sequenced using Illumina data and then assembled <em>de novo</em>. These mitogenomes ranged in size from 52,486 bp (<em>U. subfusca</em>) to 94,464 bp (<em>U. subgracilis</em>). All were characterized by having high levels of intronic and intergenic variation, such as ORFs that encode proteins with homology to two homing endonuclease types, LAGLIDADG and GIY-YIG. Genes annotated within these mitogenomes include 14 protein-coding genes, the large and small ribosomal subunits (LSU and SSU), and 23–26 tRNAs. Notably, the <em>atp9</em> gene was absent from each genome. Genomic synteny was highly conserved across the five species. Five conserved mitochondrial genes (<em>nad2</em>, <em>nad4</em>, <em>cox1</em>, <em>cox2</em>, and <em>cox3</em>) were used to infer a best estimate maximum likelihood phylogeny among these five <em>Usnea</em> and other relatives, which yielded relationships consistent with prior published phylogenies.</p>
Supplementary material 1 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Phylogenetic analysis : Explanation note: ML tree constructed based on the cox1 barcodes of genus Theretra using B. mori as outgroups. The asterisk represents the species researched presently.
Supplementary material 6 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S3. Amino acid alignment for sites under positive selection for cytb : Explanation note: The positions of each site are denoted on the top. An asterisk * denotes sites with posterior probability value ≥ 0.95 in Bayes Empirical Bayes (BEB) analysis.
Supplementary material 3 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S3. Nucleotide composition and skewness of different elements of the studied mitochondrial genome :
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.