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FIGURE 2 in Molecular Phylogenetic Analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin Sequences
FIGURE 2. Bayesian phylogenetic tree resulting from analysis of thirty-four the hexamerins sequences in insects. Next to nodes are bootstrap values. The outgroup species of proteins as follows: AmeHex70c: Apis mellifera, XM-392869; CfeHex2: Camponotus festinatus, AJ251271; BheHex: Bracon hebetor, I25974; AmeHex70b: Apis mellifera, AY601637; CfrHx1: Campodea fragilis, JX867269; CfrHx2: Campodea fragilis, JX867270; CspHex1: Campodea sp., CAX63173.
FIGURE 1 in Molecular Phylogenetic Analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin Sequences
FIGURE 1. Multiple alignment of Orthoptera hexamerin sequences. Putative hexamerins from L. migratoria (LmiHx2), R. microptera (RmiHx2), A. cinerea (AciHx2), C. italicus (CitHx2), M. wardi (MwaHx2), O. tibetanus (OtiHx2), C. versicolor (CveHx2), A. sinensis (AsiHx2), C. brunneus (CbrHx2), H. brunneriana (HbrHx1 and HbrHx2), X. japonicus (XjaHx1,2,4,5), P. soochowensis (PsoHx2), P. teretrirsostris (PteHx2), T. subulata (TsuHx1,2,5), Gryllotalpa sp. (GspHx1 and GspHx2), T. commodus (TcoHx1 and TcoHx2) and Ceuthophilus sp. (CespHx2 and CespHx3) were compared. The copper-binding histidines are shaded in gray; other strictly conserved residues are shaded in blue, Putative signal peptides are underlined.
FIGURE 3 in Molecular Phylogenetic Analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin Sequences
FIGURE 3. Neighbor-joining phylogenetic tree resulting from analysis of thirty-four the hexamerins sequences in insects. Next to nodes are bootstrap values.
Characterisation of core histone sequences and nuclear mobility using a reproducible research approach
<p>Dataset required to build the PhD thesis. Includes the public sequences that would otherwise be downloaded anew.</p>
variational-depth-from-focus: devCam sequences
<p>The 3 self-generated focal stack images datasets made using devCam.</p>
FIGURE 1 in A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences
FIGURE 1. Principal component analyses of male body measurements of Phyllomedusa camba (black) and P. chaparroi sp. nov. (grey). (A) Representation of the first two components of the raw measurements, and (B) of the residuals of a correlation with SVL.
FIGURE 6 in A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences
FIGURE 6. Adult of Phyllomedusa coelestis in life illustrating main differences (iris color, prominence of parotoid glands, dorsal skin texture, and color of lateral and hidden surfaces of limbs) to species of the P. tarsius group sensu this work. Photo by Santiago R. Ron, FaunaWebEcuador, under license CC (BY-NC 3.0).
FIGURE 5 in A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences
FIGURE 5. Close-up photos of heads of living individuals of (A) Phyllomedusa boliviana, San Sebastián, Santa Cruz, Bolivia (unvouchered); (B, C) P. camba, CM 157323; (D) P. chaparroi sp. nov., MUBI 13986; (E) P. coelestis, QCAZ 37884; (F) P. tarsius MHNLS 20216; (G) P. trinitatis; (H) P. venusta. Photographs are not to scale and are used to illustrate iris coloration only. Photo (A) by Arne Schulze, (E) by Santiago R. Ron, FaunaWebEcuador, under license CC (BY-NC 3.0), and (G) and (H) by F.J.M. Rojas-Runjaic.
FIGURE 4 in A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences
FIGURE 4. Dorsal (A) and ventral (B) views of preserved male holotype of Phyllomedusa chaparroi sp. nov. (MUBI 13986).
FIGURE 3 in A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences
FIGURE 3. Male holotype of Phyllomedusa chaparroi sp. nov. (MUBI 13986) in life: (A) dorsolateral view; (B) lateral view (note yellow markings on flank); (C) ventral view; (D) close-up photography of skin on mid-dorsum (note coarsely shagreen skin texture).
Data for: Sequence and structural diversity of mouse Y chromosomes
<p>SNV and small indel variant calls in VCF format; sample manifest as Excel spreadsheet.</p>
Sarcoidosis Microbiome Post-Processed Sequence Data
<p>16S, ITS, virome and shotgun sequencing data after demultiplexing, quality control, OTU formation (if relevant) and taxonomic assignment for the sarcoidosis microbiome project.</p> <p>This is intended to be used in conjunction with the code at https://github.com/eclarke/sarcoid-microbiome-paper to reproduce the analysis performed for the associated paper (citation pending acceptance/publication).</p> <p> </p> <p> </p>
FIGURE 4. Bayesian tree inferred using sequences D2–D3 in Morphological and molecular characterisation of Discotylenchus lorestanensis sp. n. (Nematoda: Tylenchidae) from Iran
FIGURE 4. Bayesian tree inferred using sequences D2–D3 region of the LSU rDNA gene. Posterior probabilities (pp) exceeding 0.5 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank accession numbers are listed for each taxon. Newly generated D2–D3 LSU rDNA sequences are in bold.
FIGURE 3 in Larvae of Ancyronyx Erichson, 1847 (Insecta: Coleoptera: Elmidae) from Sulawesi, using DNA sequences for the assignment of the larval stages
FIGURE 3. Ancyronyx schoedli, larva, dorsal (SEM photographs), A: head and pronotum; B: detail of pronotum with asperities and tubercles; C abdominal segments I–IV; D detail of abdominal segment III with lateral abdominal projections and setae; E: abdominal segment IX; F detail of abdominal apex.
FIGURE 4 in Larvae of Ancyronyx Erichson, 1847 (Insecta: Coleoptera: Elmidae) from Sulawesi, using DNA sequences for the assignment of the larval stages
FIGURE 4. Ancyronyx larvae, dorsal (SEM photographs), A: head and pronotum of A. tobada; B: head and pronotum of A. longiparamerus; C: details of abdominal segments I–III of A. tobada with tubercles, lateral abdominal projections, and setae; D: same aspect of A. longiparamerus; E: abdominal segments IX of A. tobada; F: abdominal segments IX of A. longiparamerus.
FIGURE 5 in Larvae of Ancyronyx Erichson, 1847 (Insecta: Coleoptera: Elmidae) from Sulawesi, using DNA sequences for the assignment of the larval stages
FIGURE 5. Ancyronyx toraja larva, dorsal (SEM photographs), A: head and pronotum; B: details of abdominal segments I–IV with tubercles, lateral abdominal projections, and setae; C: abdominal segment IX; D: detail of abdominal segment IX with 3 pairs of erected setae.
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 in A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 of Anthothela-like specimens. Bayesian posterior probabilities shown above branch, ML bootstrap values below branch; HKY+G (Bayesian results split freq = 0.0019, 10000000 gen, burnin=25000). (* indicates nodes present only in Bayesian analysis).
Integration of protein and coding sequences enables mutual augmentation of the language model
<p><strong>The file structure is as follows:</strong></p> <p>Project Root<br>├── TE_MRL<br>│ ├── MRL_dataset.zip<br>│ └── TE_dataset.zip<br>│<br>├── finetuned_model<br>│ ├── FoldP<br>│ ├── LocP<br>│ ├── SSP<br>│ └── SolP<br>│<br>├── tax_tsne<br>│ └── emb_3models.zip<br>│<br>└── training_data<br> ├── FoldP.csv<br> ├── LocP.csv<br> ├── SolP.csv<br> ├── SSP.pkl<br> └── pretrain_source_GCF.txt</p>
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>
Bruker rawdata acquired with the sequence a_MP2RAGE_CS_360
<div> <p>Raw datasets acquired on a mouse with brain metastasis which can be used to validate the reconstruction pipeline available here : <a href="https://github.com/CRMSB/SEQ_BRUKER_A_MP2RAGE_CS_360">https://github.com/aTrotier/PAPER_subspace_MESE</a></p> <p>The sequence used is a homemade 3D MP2RAGE + CS with a variable density poisson distribution along the ky-kz direction .</p> <p>This sequence and the corresponding reconstruction pipeline were developped at the CRMSB, UMR 5536, CNRS/University of Bordeaux</p> <p> </p> </div>
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.