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1,773 results for “Supplementary data,”
Supplementary data for: Maternal testosterone and offspring birth weight: A Mendelian randomization study
<p><span>Evidence showed maternal androgen levels in both healthy/general population and populations with hyperandrogenic disorders were inversely associated with offspring's birth weight. We aimed to investigate the causal effect of maternal testosterone levels in general population on offspring's birth weight and preterm delivery risk using two-sample Mendelian randomization (MR) method.</span></p> <p><span>We obtained independent genetic instruments from a sex-specific genome wide association study with up to 230,454 females of European descent from UK biobank. Genetic instruments with consistent testosterone effects but no aggregate effect on sex-hormone binding globulin were used to perform the main analysis. Summary-level data of offspring's birth weight with offspring's genotype adjusted was obtained from a study with 210,406 females of European descent. Summary-level data of preterm delivery was obtained from the FinnGen study (6,736 cases and 116,219 controls).</span></p> <p><span>For outcome of offspring's birth weight, the numbers of instruments included in final MR analyses were 123, 128 and 91 respectively. For outcome of preterm delivery, the numbers were 115, 120 and 83 respectively. The present data files show the genetic instruments and their effects on exposures and outcomes. Pleiotropic genetic instruments that excluded in the MR analysis were also provided in the files.</span></p>
Supplementary Data - Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer network
<p><strong>Supplementary data 1</strong>: Peak annotation evaluation between MetDNA1 and KGMN (MetDNA2)</p> <p><strong>Supplementary data 2</strong>: 46 standard mixture (46std_mix) and the knowledge-based metabolic reaction network</p> <p><strong>Supplementary data 3</strong>: KGMN results of 46std_mix data set and validation results</p> <p><strong>Supplementary data 4</strong>: KGMN results of NIST urine data sets and validation results</p> <p><strong>Supplementary data 5</strong>: KGMN results of different biological samples</p> <p><strong>Supplementary data 6</strong>: Recurrent unknowns of NIST urine via repository-mining</p> <p><strong>Supplementary data 7</strong>: Table of adducts, neutral losses, empirical rules in KGMN</p>
Supplementary data and codes for "Secular change of true polar wander over the past billion years"
<p>Python codes for analysis, supplementary tables, and measurement-level paleomagnetic data for "Secular change of true polar wander over the past billion years" published in <em>Science Advances </em>by Fu et al. [Fu et al., Sci. Adv. 8, eabo2753 (2022)].</p>
Supplementary Information and Data
<p><strong>Supporting Information:</strong> Supplementary figures, tables and references</p> <p><strong>File Name: Data S1</strong></p> <p>Description: Detailed consumption-based freight turnover volume associated with international trade from 1995 to 2015</p> <p><strong>File Name: Data S2</strong></p> <p>Description: Annual growth rate of all the regions or countries between 1995 and 2015 (Sheet 1); The structure of freight turnover of all the regions or countries in 2015 (t-km) (Sheet 2); The equivalent distances of all the regions or countries in 2015 (km) (Sheet 3)</p> <p><strong>File Name: Data S3</strong></p> <p>Description: The average distances of regions or countries from 1995 to 2015</p> <p><strong>File Name: Data S4</strong></p> <p>Description: Detailed results for final consumption in weight and the equivalent distances of regions or countries from 1995 to 2015</p> <p><strong>File Name: Data S5</strong></p> <p>Description: Interregional fluxes of transported goods driven by PR China, the United States and the EU-28</p> <p><strong>File Name: Data S6</strong></p> <p>Description: Detailed CO<sub>2</sub> emissions embodied in consumption-based freight transport of all the regions and countries in 2015.</p>
Supplementary data and files for: The importance of contact zones for distinguishing interspecific from intraspecific geographic variation
<p>With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (<em>Lampropeltis triangulum</em>) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species <em>L. triangulum </em>and <em>L. gentilis</em>, we examined a ~700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of <em>L. triangulum</em>, thus providing strong support for a single species in this region (and no support for the recognition of <em>L. gentilis </em>as a distinct species). At a second contact zone between proposed species <em>L. triangulum </em>and <em>L. elapsoides </em>(but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported <em>L. triangulum </em>and <em>L. elapsoides </em>as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.</p>
Supplementary Data for "The phosphorus budget of the silicate Earth based on an updated estimate of P/Nd ratio".
<p>Supplementary data tables for Ma et al. (2022) associated with the paper entitled "The phosphorus budget of the silicate Earth based on an updated estimate of P/Nd ratio".</p>
Supplementary data- Detailed Geogenic Radon Potential Mapping Using Geospatial Analysis of Multiple Geo-variables. A Case Study from a High-Risk Area in SE Ireland.
<p>Supplementary Data: all the data produced and used, statistical analysis, mathematical proofs diagnostic tests, regression models and additional charts and tables</p> <p>Detailed Geogenic Radon Potential Mapping Using Geospatial Analysis of Multiple Geo-variables. A Case Study from a High-Risk Area in SE Ireland. </p>
Hennessy et al-Supplementary file 2-Data
<p>Territorial vocalization data used to draft figures 3 and 5.</p>
Supplementary material 1 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
The supplementary material provides additional detail on methods and data sources used in the case studies and examples that are describe in the main article.
Supplementary material 2 from: Runnel V, Wetzel F, Groom Q, Koch W, Pe'er I, Valland N, Panteri E, Kõljalg U (2016) Summary report and strategy recommendations for EU citizen science gateway for biodiversity data. Research Ideas and Outcomes 2: e11563. https://doi.org/10.3897/rio.2.e11563
EU BON conducted a survey to assess how willing are researchers to recruit volunteers in their work, what are the main effects, motivators and hindrances.
Supplementary material 3 from: Runnel V, Wetzel F, Groom Q, Koch W, Pe'er I, Valland N, Panteri E, Kõljalg U (2016) Summary report and strategy recommendations for EU citizen science gateway for biodiversity data. Research Ideas and Outcomes 2: e11563. https://doi.org/10.3897/rio.2.e11563
Citizen science and biodiversity observations – EU BON best practice cases of initiatives, systems and tools.
Supplementary material 2 from: Senderov V, Georgiev T, Penev L (2016) Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases . Research Ideas and Outcomes 2: e10617. https://doi.org/10.3897/rio.2.e10617
This spreadsheet contains the information about the specimen API's of GBIF, BOLD Systems, iDigBio, and PlutoF. It lists the endpoints and the documentation URLs in the sheet named "APIs". In the sheet named "Mappings" it lists how to map the non-DwC compliant APIs (BOLD and PlutoF) to DwC-terms.
Supplementary material 3 from: Senderov V, Georgiev T, Penev L (2016) Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases . Research Ideas and Outcomes 2: e10617. https://doi.org/10.3897/rio.2.e10617
This archive contains XSLT transformations from EML v. 2.1.1 and v. 2.1.0 to Pensoft data paper format.
Supplementary material 1 from: Dénes A-L, Kolcsár L-P, Török E, Keresztes L (2016) Taxonomic revision of the Carpathian endemic Pedicia (Crunobia) staryi species–group (Diptera, Pediciidae) based on morphology and molecular data. ZooKeys 569: 81-104. https://doi.org/10.3897/zookeys.569.7458
Sampling information : Explanation note: Information for sampling of the five microendemic Carpathian species (Pedicia lobifera, Pedicia staryi, Pedicia apusenica, Pedicia carpianica, Pedicia costobocica, Pedicia roxolanica), containing the name of the species, the date of collection, with localities, mountains, locations and geographic coordinates
Supplementary material 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 5: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae and Bactrocera dorsalis populations. The highest Betweenness-centrality is highlighted in blue.
Supplementary material 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the five successive thresholds used to illustrate Figure 4: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae populations. The Highest Betweenness-centrality is highlighted in blue.
Supplementary material 4 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Comparisons among three different the individual admixture plots: Explanation note: Comparisons among the individual admixture plots of 289 individuals, for K = 3, considering correlated allele frequency, uncorrelated allele frequency, and missing data as recessive homozygotes for the null alleles, respectively.
Supplementary material 3 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 6: Explanation note: Component data are used to illustrate the structure of the subset of the Salaya5 strain and wild populations. The highest Betweenness-centrality is highlighted in blue.
Supplementary material 1 from: Jochum A, Slapnik R, Klussmann-Kolb A, Páll-Gergely B, Kampschulte M, Martels G, Vrabec M, Nesselhauf C, Weigand AM (2015) Groping through the black box of variability: An integrative taxonomic and nomenclatural re-evaluation of Zospeum isselianum Pollonera, 1887 and allied species using new imaging technology (Nano-CT, SEM), conchological, histological and molecular data (Ellobioidea, Carychiidae). Subterranean Biology 16: 123-165. https://doi.org/10.3897/subtbiol.16.5758
List of localities of Zospeum isselianum: Explanation note: List of localities of Zospeum isselianum. A − Austria, BiH − Bosnia and Herzegovina, Cro − Croatia, Slo − Slovenia, Ita − Italy, CBSS − Collection of Croatian Biospeleological Society, CSR SASA – Malacological collection of the Biological Institute of the Centre for Scientific Research of the Slovenian Academy of Sciences and Arts in Ljubljana, SMNH – Malacological collection of the Slovenian Museum of Natural History, LIT – data from literature.
Supplementary material 2 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132
Maximum likelihood model parameters: Explanation note: Model parameters used in the maximum likelihood approach to phylogenetic reconstruction.
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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.