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Deep Learning-based Method for Automatic Resolution of GC-MS Data from Complex Samples
<p>气相色谱-质谱;多元曲线分辨率</p>
Figure 1c from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1c - Phylogenetic tree of cytochrome-b sequences of Odocoileini (continuation). This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
Figure 1b from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1b - Phylogenetic tree of cytochrome-b sequences of Odocoileini (continuation). This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
Figure 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 3 - Hind foot bones of Mazama rufina (A) and Pudu puda (B) sensu Hershkovitz (1982). According to Hershkovitz (1982; see also Brooke 1874, 1878), the union of the cuboideonavicular and external and middle cuneiform tarsal bones into a single bone in Pudu is the only osteological characteristic shared by P. puda and P. mephistophiles that consistently separates them from all other living deer, with exception of the genera Elaphodus and Muntiacus.
Figure 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 2 - Overall morphological appearance of "M." pandora (panels A–C) and that of the genus Odocoileus (panels D–F). Notice the grayish pelage and divergent antlers larger than in other species currently classified in Mazama. "M." pandora, panels A and C individuals kept in captivity at the Parque Zoológico del Bicentenario Animaya, Mérida, Yucatán, Mexico (photographs by Luis A. Escobedo-Morales)—provenance unknown; panel B individual kept in captivity in Tekax, Yucatán, Mexico (photograph by Rosa María González Marín)—provenance unknown. Odocoileus virginianus (see proposals by Molina and Molinari 1999 and Molinari 2007); panels D and E Monteredondo, Parque Nacional Chingaza, ca. 47 km (by road) E Bogota, Cundinamarca, Colombia (photographs by Aideé Vargas-Espinoza and Irene Aconcha, respectively); panel F Laguna de Mucubají, Parque Nacional Sierra Nevada, Mérida, Venezuela (photograph by Rodrigo Díaz Lupanow).
Figure 1a from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Figure 1a - Phylogenetic tree of cytochrome-b sequences of Odocoileini. This is a strict consensus topology resulting from the Bayesian inference analysis. Nodal support is indicated at each node, except where the relationship received negligible support. Posterior probabilities (from the Bayesian inference analysis) and bootstrap values (from the maximum-likelihood analysis) are indicated before and after the slashes ("/") at branches of interest (i.e., nodal support for fairly shallow relationships within intraspecific haplogroups are omitted). The scale represents substitutions per site. For each terminal, country of origin and next-largest administrative unit (state, department, province, etc.) are provided (when reported by the team that generated them; see detailed voucher and locality information in supplementary file 1 for sequences that we generated). GenBank accession numbers are indicated for each terminal.
Supplementary data(Jiacha County area) (including Liegang landslide boundary,Yarlung Tsangpo faults locations, and 14C and 10Be sampling locations) (V1)
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FSPPD_Sample_Data
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FIG. 3 in Sampling the depth: New data on the Caecidae (Mollusca, Gastropoda) from northeastern Papua New Guinea
FIG. 3. — Caecum Fleming, 1813 species from deep-water stations from northeastern PNG: A-D, Caecum microannulatum n. sp., holotype MNHN-IM-2000-38948; E, C. microannulatum n. sp., juvenile from type locality; F, C. musorstomi Pizzini, Raines & Vannozzi, 2013 from Stn DW4412, transitional growth stage. Scale bar: 1 mm, details not to scale.
Sample data for tech savvy digital media
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Aperture data from all hair samples
<p>Aperture data to support my PhD thesis</p>
Sample identification data
<p>Dataset to use in a tutorial about sample identification, using the tool Kraken. </p>
Sample data for Permanganate sequencing
<p>Sample datasets for permanganate seq data analysis (human)</p>
Sample data measurement machine and mill VDL Weweler
<p>Sample data measurement machine and mill VDL Weweler</p>
Raw metagenomic data from Early Detection Rapid Response samples collected in Alaska in 2017
<p>In response to the threat of introductions of non-native forest insects, the Early Detection and Rapid Response (EDRR) program in Alaska monitors for arrivals of non-native insects, an effort that is limited by the time required to process samples using morphological methods. We compared conventional methods of processing EDRR traps with metabarcoding methods for processing the same samples. </p> <p>We deployed Lindgren funnel traps at three points of entry in Alaska using standard EDRR methods and the trap samples were later processed using routine sorting and identification based on morphology. The samples were then processed using High Throughput Sequencing (HTS) metabarcoding methods. In three samples bycatch was included and in three samples non-native species were added.</p> <p>This dataset includes all of the raw FASTQ files obtained from HTS sequencing. </p> <p>Complete specimen and occurrence data are available via an Arctos (<a href="https://arctosdb.org/">https://arctosdb.org/</a>) archive at <a href="https://arctos.database.museum/archive/2017_edrr_ngs_test_records">https://arctos.database.museum/archive/2017_edrr_ngs_test_records</a>. Sequence data have been deposited in in the NCBI Sequence Read Archive under BioProject <a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA542936">PRJNA542936</a>. Complete sample data are provided in the file 2017_EDRR_STDP_sample_data.csv.</p>
Data clustering sample 0107
<p>Telegram's contest of data clustering. First sample of data.</p>
Figure. Map of Georgia with main administrative divisions delimited. Shade intensity indicates the richness of mayfly species for respective administrative unit. Dots indicate localities sampled for mayflies prior to this study. in The first annotated checklist of mayflies (Ephemeroptera: Insecta) of Georgia with new distribution data and a new record for the country
Figure. Map of Georgia with main administrative divisions delimited. Shade intensity indicates the richness of mayfly species for respective administrative unit. Dots indicate localities sampled for mayflies prior to this study.
W-RAG sampled data and weak labels
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Sample-specific data from "The Influence of Seasonal Variation in Wild Pig Diet on Impacts to a Subtropical Agroecosystem" published in Ecosphere
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Data from: Integration of 168,000 samples reveals global patterns of the human gut microbiome
<p>The data and code in this archive was used to generate the analyses and figures from the revised version of "Integration of 168,000 samples reveals global patterns of the human gut microbiome." The first version is available as <a href="https://doi.org/10.1101/2023.10.11.560955">a bioRxiv preprint</a>. Code for the text-mining work is <a href="https://github.com/krishnanlab/microbiome-metadata-annotation">available on GitHub</a>.</p> <p> </p>
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.