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3,696 results for “Reference”
RefWUG: Diachronic Reference Word Usage Graphs for German
<p>This data collection contains diachronic Word Usage Graphs (WUGs) for German created with reference use sampling. Find a description of the data format, code to process the data and further datasets on the <a href="https://www.ims.uni-stuttgart.de/data/wugs">WUGsite</a>.</p> <p>Please find more information on the provided data in the paper referenced below.</p> <p>Version: 1.1.0, 15.12.2021.</p> <p><strong>Reference</strong></p> <p>Dominik Schlechtweg and Sabine Schulte im Walde. submitted. Clustering Word Usage Graphs: A Flexible Framework to Measure Changes in Contextual Word Meaning.</p>
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
<p><b>Background:</b> Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. </p> <p><b>Results</b>: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers <i>rbcL</i>, <i>trnH-psbA</i>, <i>matK</i>, and one nuclear marker <i>ITS2</i> were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, <i>ITS2</i>, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, <i>rbcL</i> or <i>trnH-psbA</i> can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. </p> <p><strong>Conclusion:</strong> We suggest to use <em>ITS2</em> to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.</p>
MDMcleaner reference database
<p>MDMcleaner reference database used at time of publication.</p> <p>based on:</p> <p>GTDB release r95</p> <p>RefSeq release 203</p> <p>Silva version 138.1</p>
Dataset: Towards a representative reference for MRI-based human axon radius assessment using light microscopy
<p>Dataset for: Towards a representative reference for MRI-based human axon radius assessment using light microscopy</p>
Raw Data for the article: Use of 27G needles improves sensitivity and performance of ATCC anaerobe reference microorganism detection in BacT/Alert system
<p>Effective detection of microbiological contaminations present in medicinal cellular products is a crucial step to ensure patients' safety. In recent decades, several rapid microbiological methods have been developed and validated, but variabilities linked to the use of different resources have led to discordant validation of methods and performance results. Considering this, while developing an in-house BacT/Alert-based method, we evaluated all of the materials used in its validation. Of particular importance, we noticed that the syringe gauge used to inject the samples into the bottles was crucial to obtain robust results. We chose to conduct a comparative test between the BacT/Alert system and the compendial method described in the European Pharmacopoeia, using five dilutions of nine reference microorganism strains and 21G or 27G needles. Our results confirmed that the BacT/Alert system is a valid and faster alternative method to assess sterility of clinical cell therapy products, and that the use of 27G needles increases its sensitivity to detect reference anaerobe microorganisms.</p>
Technology references in foundational accounts of Responsible Research and Innovation
<p>Coding of references to different technology types within foundational accounts of Responsible Research and Innovation: </p> <ul> <li>Von Schomberg, R. (2013). A Vision of Responsible Research and Innovation. <em>Responsible Innovation: Managing the Responsible Emergence of Science and Innovation in Society</em>, 51–74. <a href="https://doi.org/10.1002/9781118551424.ch3">https://doi.org/10.1002/9781118551424.ch3</a></li> <li>Stilgoe, J., Owen, R., & Macnaghten, P. (2013). Developing a framework for responsible innovation. <em>Research Policy</em>, <em>42</em>(9), 1568–1580. <a href="https://doi.org/10.1016/j.respol.2013.05.008">https://doi.org/10.1016/j.respol.2013.05.008</a></li> <li>European Commission. (2012a). <em>Ethical and Regulatory Challenges to Science and Research Policy at the Global Level (KI-NA-25-101-EN-C)</em>. <a href="http://ec.europa.eu/research/science-society/document_library/pdf_06/ethical-and-regulatory-challenges-042012_en.pdf">http://ec.europa.eu/research/science-society/document_library/pdf_06/ethical-and-regulatory-challenges-042012_en.pdf</a></li> <li>European Commission. (2012b). <em>Responsible Research and Innovation—Europe’s ability to respond to societal challenges (KI-31-12-921-EN-C)</em>. <a href="https://ec.europa.eu/research/swafs/pdf/pub_rri/KI0214595ENC.pdf">https://ec.europa.eu/research/swafs/pdf/pub_rri/KI0214595ENC.pdf</a></li> <li>van den Hoven, J. (2013). Value Sensitive Design and Responsible Innovation. In <em>International handbook on responsible innovation. A global resource</em>. John Wiley & Sons Inc.</li> <li>van den Hoven, J. (2017). The Design Turn in Applied Ethics. In J. van den Hoven, S. Miller, & T. Pogge (Eds.), <em>Designing in Ethics</em> (1st ed., pp. 11–31). Cambridge University Press. <a href="https://doi.org/10.1017/9780511844317.002">https://doi.org/10.1017/9780511844317.002</a></li> </ul> <p>Reported in Novation (<a href="http://www.novation.inrs.ca/index.php/novation/article/view/10">link</a>). Methodology and definitions are set out in the Novation article.</p>
Global forest reference set with time series annual change information
<p><strong>Brief introduction of the reference set:</strong></p> <ul> <li>The initial sample points were stratified. The ratio of non-forest, forest and forest change stratum area is about 67:27:6. In order to increase the number of forest and forest change sample points, the ration of forest sample, forest change sample and non-forest sample points is roughly 4:1:1. The information of stratum identifier is provided in this sample set. The study generated 12925 initial sample points which were further reduced to 10339 points (6252 persisting forest sample points, 2049 change sample points and 2038 persisting non-forest sample points). The details are shown in Table 1. </li> </ul> <table> <caption>Table 1. Initial and finial sample size in each stratum</caption> <tbody> <tr> <td><strong>Stratum name</strong></td> <td><strong>Percent area of each stratum</strong></td> <td><strong>Initial sample size</strong></td> <td><strong>Final sample size</strong></td> <td><strong>Eliminated sample size</strong></td> </tr> <tr> <td>Forest</td> <td>27%</td> <td>8332</td> <td>6252</td> <td>1644</td> </tr> <tr> <td>Non-forest</td> <td>67%</td> <td>1892</td> <td>2038</td> <td>207</td> </tr> <tr> <td>Forest change</td> <td>6%</td> <td>2701</td> <td>2049</td> <td>735</td> </tr> <tr> <td>Sum</td> <td>100%</td> <td>12925</td> <td>10339</td> <td>2586</td> </tr> </tbody> </table> <p> </p> <ul> <li>The sample set will be provided in shapefile version. (The eliminated sample points will not be provided.) In this version, the provided attributions are shown in Table 2.</li> </ul> <p> </p> <table> <caption>Table 2. Details of provided attributions in this version</caption> <tbody> <tr> <td><strong>Name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>per_f</td> <td>unchanged forest (0: No 1: Yes)</td> </tr> <tr> <td>per_nonf</td> <td>unchanged non-forest (0: No 1: Yes)</td> </tr> <tr> <td>change</td> <td>forest change (0: No 1: Yes)</td> </tr> <tr> <td>loss</td> <td>forest loss times</td> </tr> <tr> <td>gain</td> <td>forest gain times</td> </tr> <tr> <td>times</td> <td>change times (gain + loss)</td> </tr> <tr> <td>changeinfo</td> <td>year and order of change</td> </tr> <tr> <td>initial_s</td> <td>initial stratum identifier: change/perf (persisting forest)/nonf (persisting non-forest)</td> </tr> </tbody> </table> <p> </p> <ul> <li>This reference set will be updated regularly. Now it's version 1.1 (from 2000 to 2020).</li> </ul> <p> </p> <p><strong>NOTES:</strong></p> <ol> <li>Please be cautious while using the sample points with multiple change times. </li> <li>We encourage people to send us feedback if you found some mistakes while using this sample set via email.</li> <li>Welcome discussions around potential collaborations. 【You can email Jing (guoj15@tsinghua.org.cn).】</li> </ol> <p> </p> <p><strong>Citation:</strong></p> <p>Please cite the dataset including the version number and the following paper when using this data: </p> <p>Jing Guo, Zhiliang Zhu & Peng Gong (2022) A global forest reference set with time series annual change information from 2000 to 2020, International Journal of Remote Sensing, 43:9, 3152-3162, DOI: <a href="https://doi.org/10.1080/01431161.2022.2088256">10.1080/01431161.2022.2088256</a></p>
KPMP Datasets for a Reference Tissue Atlas for the Human Kidney
<p>This is the dataset for the publication of A Reference Tissue Atlas for the Human Kidney from the Kidney Precision Medicine Project (KPMP). KPMP is building a spatially-specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 subjects. We use single-cell/nucleus transcriptomics, subsegmental laser-microdissection transcriptomics and proteomics, near-single-cell proteomics, 3-D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites and pathways. They further show that mRNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.</p>
Fig. 1 in Fossil Ovibos Moschatus (Artiodactyla, Bovidae) From Buryn, With Reference To Muskox Dispersal In The Late Pleistocene Of Ukraine
Fig. 1. Localities with fossil muskox remains on the territory of Ukraine.
Transitioning from environmental genetics to genomics using mitogenome reference databases
<p><span>Species detection using eDNA is revolutionizing the global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon's resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial "barcode" regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon's fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the "PCR-free" environmental genomics methods of the future can best leverage this information.</span></p>
DNA reference database for macroinvertebrates
<p>This repository hosts a ready-to-use database for the study of macroinvertebrate diversity using DNA metabarcoding with the fwhF2/EPTDr2n primer set (Leese et al. 2022).</p> <p>The database was developed from the MIDORI database and completed with some data from the BOLD database.</p> <p>The process of preparation and curation of the database is described below:</p> <p>1. The MIDORI CO1 RAW v247 database was downloaded from the official servers.</p> <p>2. Reference sequences were matched against the fwhF2 forward primer sequences. Non-matching sequences were removed. Bases preceding the forward primer were removed.</p> <p>3. Reference sequences with a length of less than 142 bp were removed. Bases following the position 142 were removed.</p> <p>4. Taxonomy was simplified to keep only 8 ranks: superkingdom, kingdom, phylum, class, order, family, genus and species.</p> <p>5. Taxonomic nomenclature was harmonized using `refdb::refdb_clean_tax_harmonize_nomenclature`</p> <p>6. Extra words were removed from taxonomic names using `refdb::refdb_clean_tax_remove_extra`</p> <p>7. Subspecific information were removed from taxonomic names using `refdb::refdb_clean_tax_remove_subsp`</p> <p>8. Missing taxonomic names were identified and normalized using `refdb::refdb_clean_tax_NA`.</p> <p>9. Hybrids and taxonomic names with qualifiers of uncertainty were converted to NA.</p> <p>10. Duplicates (identical sequences and taxonomy) were removed.</p> <p>11. Sequences with more than ambiguous nucleotides (N) were removed).</p> <p>12. Sequences with low taxonomic precision (above phylum) were removed.</p> <p>13. A random subset of 10 sequences was retained for each taxa.</p> <p>14. For a given taxonomic rank, records with NA values were removed if they were not the only representative of the upper clade.</p> <p>15. For Switzerland: Missing EPT species and IBCH families were searched in BOLD and merged with the reference database. The same filters and cleaning steps (2-14) were then applied.</p> <p> </p>
reference image data (primary views) for an office building near LAX
<p>image data compressed by view and season (months 1-2-3, 4-5-6, 7-8-9, 10-11-12)</p> <p>see 10.5281/zenodo.6322418 for source files</p>
reference radiance model and result data for an office building near LAX
<p>radiance scene files and metric results generated from high quality referece images for an office building near LAX.</p> <p><strong>contents of lci_tempate.tar.gz:</strong></p> <p>ALLSKIES: <br> 4294 sky conditions generated by write_skydefs.py<br> based on LAX.epw, all conditions with solar altitude >= 2 degrees, diffnorm > 5 w/m^2</p> <p>INSGEO/: (scene files that can be made into an instance using setup.sh)<br> EXT.rad INT.rad LIT2.rad baseglz.rad site.rad</p> <p>MATERIAL/:<br> all.mat</p> <p>POINTS/: (reference view locations as sensor points)<br> ref_views.pts</p> <p>RAD/:<br> ROIglz.rad big.rad</p> <p>ROI/: (radiance scene polygons describing zones around each point)<br> o1.rad o2.rad z1.rad z2.rad</p> <p>VIEWS/: (reference views)<br> o1ref.vf o1ref_r.vf o2ref.vf o2ref_r.vf z1ref.vf z1ref_r.vf z2ref.vf z2ref_r.vf</p> <p>refs/: (source weather data and model units)<br> lax.epw lax.wea sky_runorder.txt units.txt</p> <p>reference images generated with run_step.sh</p> <p>2phs images generated with 2phase_run_auto.sh</p> <p><strong>contents of ref_data.tar.gz:</strong></p> <p>refimgs/ref_data_view_*_metric.txt (for each view)</p> <p>columns: month day hour dgp illum ugr ugp dgp_t1 dgp_t2 avglum loggcr logpwgcr</p> <p>data generated with the run_step.sh file in lci_tempate.tar.gz for all sky files</p> <p>metrics computed with run_rayt.sh in lci_tempate.tar.gz</p> <p>scripts require python3.6-3.8 on mac os or linux with the following packages installed: raytraverse v1.2.7</p> <p> </p> <p> </p>
Northern hemispheric atmospheric ethane trends in the upper troposphere and lower stratosphere (2006-2016) with reference to methane and propane
<p>Datasets for northern hemispheric atmospheric ethane, propane and methane (2006-2016) from airborne measurements by IAGOS-CARIBIC project. </p>
Reference Datasets for: SHAFTS (v2022.3): a deep-learning-based Python package for Simultaneous extraction of building Height And FootprinT from Sentinel Imagery
<p>These are reference building height and footprint datasets which consist of 46 cities worldwide and support the development of SHAFTS (https://github.com/LllC-mmd/3DBuildingInfoMap).</p> <p>The snapshot of original reference datasets from 46 cities and related GitHub repository has been created as a zipped file named <strong><em>SHAFTS_220527_snapshot.zip</em></strong>.</p> <p>On 2022.5.27, we added 8 additional cities from ArcGIS Hub when compared with the previous version (https://doi.org/10.5281/zenodo.6370003).</p>
Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome
<p>Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.</p>
A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fishes (Teleostei: Gymnotiformes)
<p>DNA barcoding is a useful tool for identifying species; however, successful barcode-based identification requires a reference library of barcode sequences from accurately identified specimens. Here we present a reference library of <em>co1</em> barcode sequences for the Neotropical electric knifefish order Gymnotiformes (Teleostei: Ostariophysi), a model taxon for studies of tropical diversification and biogeography, genomics, behaviour, and neurobiology. Our library contains barcodes for 167 of the ca. 270 valid species of gymnotiforms derived from geo-referenced museum voucher specimens, and includes sequences from 26 type specimens and 21 specimens from type localities, most of which we collected. To assess the state of gymnotiform barcodes in two main public barcode repositories, GenBank and BOLD, we compared the barcodes in these databases to our reference library. Our analysis shows that a considerable proportion of gymnotiform barcodes in GenBank and BOLD are mis- or unidentified. We encourage taxonomists to develop and publish barcode reference libraries composed of carefully curated barcode sequences.</p>
Juno Stellar Reference Unit (SRU) image data from Juno's G34 Ganymede flyby on 7 June 2021
<p>This is the Juno Stellar Reference Unit (SRU) image data from Juno's G34 Ganymede flyby on 7 June 2021. The image is discussed in the paper, "Surface features of Ganymede revealed in Jupiter-shine by Juno's Stellar Reference Unit," published in AGU Geophysical Research Letters.</p>
Dataset for publication: "Empirical Characterization of Cable Effects on a Reference Lightning Impulse Voltage Divider"
<p>Dataset for publication: "Empirical Characterization of Cable Effects on a Reference Lightning Impulse Voltage Divider". Excel file contains the data for Figures 5 and 6.</p>
Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
<p><span>Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. </span>RNA-Bloom2 is available on GitHub at: <a href="https://github.com/bcgsc/RNA-Bloom">https://github.com/bcgsc/RNA-Bloom</a>.</p> <p><span>We benchmarked the assembly quality and the computational performance of RNA-Bloom2 on simulated data. We prepared two mouse simulated datasets with Trans-NanoSim</span><span> for the cDNA and dRNA sequencing protocols model on experimental ONT data</span><span>. The datasets were simulated </span><span>based on the mouse ENSEMBL annotation for GRCm39.</span><span> To investigate the effect of sequencing depth, we subsampled each dataset to 2, 10, and 18 million reads, resulting in a total of six sets of reads for our benchmarking experiments. Using the simulated data, w</span><span>e showed that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods.</span></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.