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FIGURE 1 in Taxonomic study of Myrtaceae in forest fragments in Amazonian Maranhão, Brazil
FIGURE 1. Limits of Amazonian Maranhão and collection areas.
Healthy and cancer individuals from Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer
<p>Oxford Nanopore sequencing data from 61 samples described in manuscript "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer"<br><br></p> <p>All data are aligned to UCSC analysisSet hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/), and use 0-based coordinates.</p> <p><strong>Level 2:</strong> In order to provide combined fragmentation and methylation information, Biscuit was used to create “epiBED” files (see Methods). epiBED files contain each read on a separate line, with each DNA methylation call on the read. epiBED files can be used for combined methylation/fragmentomic analysis, and are compatible with the CelFiE-ISH software that was used for cell of origin deconvolution.</p> <p>Creation of Biscuit EpiBED files:<br>Biscuit (https://huishenlab.github.io/biscuit/) v. 1.4.1-dev was used with the command “biscuit epiread -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 1000000 hg38.analysisSet.fa”, where the reference is the same UCSC reference genome used for alignment. Files are available in the Zenodo repository listed in Data Availability.</p> <p><strong>Level 3</strong>: DNA methylation BED files. BED files created by modkit (see Methods) provide one line for each CpG covered, and can be used for basic DNA methylation analysis.<br><br>Creation of modkit BED files:<br>BED files were created using modkit (https://github.com/nanoporetech/modkit) v. 0.1.5 with the command “modkit pileup --cpg --combine-strands --ignore h --filter-threshold 0.9 --bedgraph". </p> <p> </p>
r.avaflow package for fragmentation
<p>Simulation package for fragmenting rock avalanches, including the relevant r.avaflow code and a start script.</p>
Investigating species composition in the Early Aurignacian of Le Piage (France) through collagen fingerprinting (ZooMS) of screen-recovered small bone fragments
<p>This link supplements the paper "Investigating species composition in the Early Aurignacian of Le Piage (France) through collagen fingerprinting (ZooMS) of screen-recovered small bone fragments" published in Paleoanthropology (https://paleoanthropology.org/ojs/index.php/paleo)</p> <p>We analysed with ZooMS (Zooarchaeology by mass Spectrometry) 1,050 bone fragments recovered through water sieving from an Early Aurignacian layer (37–34 ka cal. BP) in the site of Le Piage (Lot, France) to compare the taxonomic identifications of bone remains using traditional morphological attributes with remains identified using ZooMS, and discuss the implications of the taxonomic patterns that we uncovered. </p> <p>This page contains mzXml files of the spectra obtained and analysed within the scope of the published paper. The files are classified by runs, and the excel sheet entitled "Sample location (spectrum n°) in MS analyses" stipulates which mzXML files correspond to which specimen. This page also contains the simplified database reporting the identifications obtained through peptide mass fingerprinting (PMF) and a breakdown of deamidation values calculated with the Betacalc 3 published in Wilson et al. (2012).</p> <p><span><span>For any questions please contact Pauline Raymond (pauline.raymond@college-de-france.fr).</span><br><span>Please use the DOI when citing this dataset. </span></span></p>
FIGURE 3. Fossilized bone fragments for the Vrabchov dol. 1 in Bone histology reveals the first record of titanosaur (Dinosauria: Sauropoda) from the Late Cretaceous of Bulgaria
FIGURE 3. Fossilized bone fragments for the Vrabchov dol. 1, Multiple views of specimen U.S., K21586, an undetermined long bone diaphyseal fragment; 2. Specimen NMNHS FR-16, possibly a partial diaphysis of undetermined long bone. Scale bar equals 3 cm.
Figure 1 in Small forest fragments and their importance for conservation of tree communities in Atlantic Semideciduous Forest
Figure 1. Species accumulation curve designed by Bootstrap estimator for the nine sites of seasonal semideciduous forest in southeastern Brazil. Gray lines: Species with DAP <5.0 cm. Black lines: Species with DAP> 5.0 cm. Dashed line: standard deviation.
FIGURE 5 in When roads cross streams: fish assemblage responses to fluvial fragmentation in lowland Amazonian streams
FIGURE 5 | ANOVA results for assemblage structure in northeastern Amazonian streams among stream reach groups. A. Taxonomic structure; B. Functional structure. D: Downstream reaches from impoundments; I: Impounded reaches; U: Upstream reaches from impoundments.
FIGURE 4 in When roads cross streams: fish assemblage responses to fluvial fragmentation in lowland Amazonian streams
FIGURE 4 | Relative contribution of turnover and nestedness component to total beta diversity obtained after averaging pairwise dissimilarities (Sørensen index) between stream reaches at each stream. D: Downstream reaches from impoundments; I: Impounded reaches; U: Upstream reaches from impoundments.
Fig. 6 in Crepuscular and nocturnal hawkmoths (Lepidoptera: Sphingidae) from a fragment of Atlantic rainforest in the state of São Paulo, southeastern Brazil
Fig. 6. Individual-based rarefaction curves, with 95% confidence intervals, of the samplings at the Serra do Japi Biological Reserve (this study; solid line) and at the Boraceia Biological Station (Duarte et al. 2008; dashed line).
Fig. 3 in Crepuscular and nocturnal hawkmoths (Lepidoptera: Sphingidae) from a fragment of Atlantic rainforest in the state of São Paulo, southeastern Brazil
Fig. 3. Fluctuation of richness (A) and relative abundance (B) of the subfamilies during the sampling period.
Fig. 1 in Crepuscular and nocturnal hawkmoths (Lepidoptera: Sphingidae) from a fragment of Atlantic rainforest in the state of São Paulo, southeastern Brazil
Fig. 1. Location of the Serra do Japi Biological Reserve. (A) Brazil with detail showing the state of São Paulo. (B) State of São Paulo with detail of the municipality of Jundiaí. (C) Municipality of Jundiaí and the Serra do Japi Biological Reserve.
Supplementary material 1 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Morphometric data :
Figure 9 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 9 Boxplots showing shell heights on Potamolithus spp. Horizontal Bar, median; vertical bar, whiskers with minimal and maximum observations. 1 P. ribeirensis 2 Potamolithus sp. 1 3 P. karsticus 4 Potamolithus sp. 2 5 Potamolithus sp. 3 6 Potamolithus sp. 4 7 Potamolithus sp. 5 8 Potamolithus sp. 6 9 Potamolithus sp. 7 10 P. troglobius 11 Potamolithus aff. troglobius 12 Potamolithus sp. 8 13 Potamolithus sp. 9 14 Potamolithus sp. 10 15 Potamolithus sp. 11 16 Potamolithus sp. 12. Black bars, epigean species; gray bars, troglophilic species; white bars, troglobitic species; circles, outliers; *, extremes.
Figure 8 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 8 Potamolithus sp. 9 A (dorsal view) B (apertural view) C (apical view); Potamolithus sp. 10 D (dorsal view) E (apertural view) F (apical view); Potamolithus sp. 11 G (dorsal view) H (apertural view); Potamolithus sp. 12 I (dorsal view) J (apertural view) K (apical view). Scale bars: 1mm. (Photographs: LBR Fernandes).
Figure 7 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 7 Potamolithus troglobius A (dorsal view) B (apertural view) C (apical view); Potamolithus aff. troglobius D (dorsal view) E (apertural view) F (apical view); Potamolithus sp. 8 G (dorsal view) H (apertural view) I (apical view). Scale bars: 1mm. (Photographs: LBR Fernandes).
Figure 6 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 6 Potamolithus sp. 4 A (dorsal view) B (apertural view) C (apical view); Potamolithus sp. 5 D (dorsal view) E (apertural view) F (apical view); Potamolithus sp. 6 G (dorsal view) H (apertural view); Potamolithus sp. 7 I (dorsal view) J (apertural view) K (apical view). Scale bars: 1 mm. (Photographs: LBR Fernandes).
Figure 5 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 5 Potamolithus karsticus - A (dorsal view) B (apertural view); Potamolithus sp. 2 C (dorsal view) D (apertural view) E (apical view); Potamolithus sp. 3 F (dorsal view) G (apertural view) H (apical view). Scale bars: 1mm. (Photographs: LBR Fernandes).
Figure 4 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 4 Potamolithus ribeirensis - A (dorsal view) B (apertural view); Potamolithus sp. 1 C (dorsal view) D (apertural view) E (apical view). Scale bars: 1mm. (Photographs: LBR Fernandes).
Figure 2 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 2 Landscape (Atlantic Rainforest) (A), Potamolithus sp. 5 in natural habitat, Santana cave (B) and subterranean streams (C, D) from Alto Ribeira karst area, Southeastern Brazil. Photographs: PP Rizzato (A, C, D), A Gambarini (B).
Figure 10 from: Bichuette ME, Trajano E (2018) Diversity of Potamolithus (Littorinimorpha, Truncatelloidea) in a high-diversity spot for troglobites in southeastern Brazil: role of habitat fragmentation in the origin of subterranean fauna, and conservation status. Subterranean Biology 25: 61-88. https://doi.org/10.3897/subtbiol.25.23778
Figure 10 Boxplots showing shell widths on Potamolithus spp. Horizontal Bar, median; vertical bar, whiskers with minimal and maximum observations. 1 P. ribeirensis 2 Potamolithus sp. 1 3 P. karsticus 4 Potamolithus sp. 2 5 Potamolithus sp. 3 6 Potamolithus sp. 4 7 Potamolithus sp. 5 8 Potamolithus sp. 6 9 Potamolithus sp. 7 10 P. troglobius 11 Potamolithus aff. troglobius 12 Potamolithus sp. 8 13 Potamolithus sp. 9 14 Potamolithus sp. 10 15 Potamolithus sp. 11 16 Potamolithus sp. 12. Black bars, epigean species; gray bars, troglophilic species; white bars, troglobitic species; circles, outliers; *, extremes.
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.