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3,172 results for “Publications”
Data of publication A Frequency-Multiplexed Coherent Electro-optic Memory in Rare Earth Doped Nanoparticles
<p>Data corresponding to main text figures of publication : A. Fossati, S. Liu, J. Karlsson, A. Ikesue, A. Tallaire, A. Ferrier, D. Serrano, and P. Goldner, <em>A Frequency-Multiplexed Coherent Electro-Optic Memory in Rare Earth Doped Nanoparticles</em>, Nano Lett. <strong>20</strong>, 7087 (2020).</p>
Planning universal accessibility to public healthcare in sub-Saharan Africa
<p>Replication code and data for the the paper "Planning universal accessibility to public healthcare in sub-Saharan Africa". </p> <p>The tarball contains computer code (in R and javascript) and input data to replicate or update the analysis and the figures, and the result data of baseline and sensitivity analysis model runs. Powerful (or cloud, e.g. Google Earth Engine, RStudio Cloud, or Google Colab) computing facilities are recommended for a successful replication.</p>
Millstätter See seismic and core data for the publication "High-resolution calibration of seismically-induced lacustrine deposits with historical earthquake data in the Eastern Alps (Carinthia, Austria)"
<p>This dataset comprises the core data and the 3.5 kHz seismic data of Millstätter See, a lake in the Eastern European Alps, Austria. Together with a bathymetric dataset (10.5281/zenodo.5875923) and a core/seismic dataset from Wörthersee (10.5281/zenodo.5875576), this is the basis for the publication Daxer et al. "High-resolution calibration of seismically-induced lacustrine deposits with historical earthquake data in the Eastern Alps (Carinthia, Austria)".</p> <p>28 core sections (individual short cores or sections of long cores - see <em>MillstaetterSee_core_data.xlsx</em> for information) were analysed with a multi-sensor core logger (MSCL) and photographed with a smartcube camera image scanner and an ITRAX core scanner. The generated data are available in the folders <em>MSCL.zip</em> and <em>Photos.zip</em>. Some core sections were also analysed with a Malvern Mastersizer 3000 and/or CT scanning. The generated data are provided in the folders <em>Grain Size.zip </em>and<em> CT data MI17-04.zip </em>(as .dcm files).</p> <p>The seismic profiles are provided as .SGY files (<em>Seismic Pinger Data.zip</em>).</p>
Woerthersee seismic and core data for the publication "High-resolution calibration of seismically-induced lacustrine deposits with historical earthquake data in the Eastern Alps (Carinthia, Austria)"
<p>This dataset comprises the core data and the 3.5 kHz seismic data of Wörthersee, a lake in the Eastern European Alps, Austria. Together with a dataset from Millstättersee (core and seismic data: 10.5281/zenodo.5875911; bathymetric data: 10.5281/zenodo.5875923), this is the basis for the publication Daxer et al. "High-resolution calibration of seismically-induced lacustrine deposits with historical earthquake data in the Eastern Alps (Carinthia, Austria)".</p> <p>24 short cores were analysed with a multi-sensor core logger (MSCL) and photographed with a smartcube camera image scanner and an ITRAX core scanner. The generated data are available in the folders <em>MSCL.zip</em> and <em>Photos.zip</em>. Some core sections were also analysed with a Malvern Mastersizer 3000. The generated grain-size data are provided in the folder <em>Grain Size.zip</em>.</p> <p>The seismic profiles are provided as .SGY files (<em>Seismic Pinger Data.zip</em>).</p>
Datasets for the publication "Sedimentation Kinetics of Hydrous Ferric Oxides in Ferruginous, Circumneutral Mine Water"
<p>This file contains datasets that were generated during laboratory-based column sedimentation experiments. The article was published in Environmental Science & Technology (accepted April 8, 2022).</p>
Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health
<p>Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that several closely-related viruses have been discovered and sarbecovirus-host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modeled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2 °C hotter in a fossil-fueled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.</p>
Public BI benchmark - part 2 & results
<p>Originally published on: https://github.com/cwida/public_bi_benchmark </p> <p>Originally compressed with bzip2. Compressed here with gzip.</p> <p>"User generated benchmark derived from the DBTest'18 paper [1] by Tableau. It contains real data and queries from 46 public workbooks in Tableau Public [2].</p> <p>We downloaded 46 of the biggest workbooks and converted the data to <em>.csv</em> files and collected the SQL queries that appear in the Tableau log when the workbooks are visualized. We processed the <em>.csv</em> files and queries with the purpose of making them load and run on different database systems.</p> <p>Each directory is associated with a workbook and contains:</p> <pre><code>samples: a sample of each .csv file (first 20 rows) tables: .sql files containing the schema of each .csv file queries: .sql files containing the queries data-urls.txt: links for downloading the full .csv.bz2 compressed files </code></pre> <p>There are 46 workbooks containing 206 tables (.csv files) with the total size of 41 GB compressed and 386 GB uncompressed.</p> <p>Multiple .csv files may overlap but are not identical. This is because Tableau extracts the same workbook in multiple different ways for different queries."</p>
Public BI benchmark - part 1
<p>Originally published on: https://github.com/cwida/public_bi_benchmark </p> <p>Originally compressed with bzip2. Compressed here with gzip.</p> <p>"User generated benchmark derived from the DBTest'18 paper [1] by Tableau. It contains real data and queries from 46 public workbooks in Tableau Public [2].</p> <p>We downloaded 46 of the biggest workbooks and converted the data to <em>.csv</em> files and collected the SQL queries that appear in the Tableau log when the workbooks are visualized. We processed the <em>.csv</em> files and queries with the purpose of making them load and run on different database systems.</p> <p>Each directory is associated with a workbook and contains:</p> <pre><code>samples: a sample of each .csv file (first 20 rows) tables: .sql files containing the schema of each .csv file queries: .sql files containing the queries data-urls.txt: links for downloading the full .csv.bz2 compressed files </code></pre> <p>There are 46 workbooks containing 206 tables (.csv files) with the total size of 41 GB compressed and 386 GB uncompressed.</p> <p>Multiple .csv files may overlap but are not identical. This is because Tableau extracts the same workbook in multiple different ways for different queries."</p>
JPG images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"
<p>Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing. Each image is presented as a color JPG. Cells hybridizing with the probe for <em>Streptococcus cristatus</em> are shown in cyan; cells hybridizing with the probe for <em>Streptococcus mitis, S. oralis, </em>and <em>S. infantis </em>are shown in red; cells of genus <em>Corynebacterium</em> are shown in magenta; cells of genera <em>Haemophilus </em>and <em>Aggregatibacter </em>are shown in yellow; and cells of genus <em>Porphyromonas</em> are shown in blue.</p> <p>Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for <em>S. cristatus</em>, the <em>S. mitis</em> group, the <em>Streptococcus </em>genus, <em>Corynebacterium</em> genus, and <em>Porphyromonas</em> genus. </p>
TIFF images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"
<p>Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing. Each image is presented as a TIFF file. Cells hybridizing with the probe for <em>Streptococcus cristatus</em> are shown in cyan; cells hybridizing with the probe for <em>Streptococcus mitis, S. oralis, </em>and <em>S. infantis </em>are shown in red; cells of genus <em>Corynebacterium</em> are shown in magenta; cells of genera <em>Haemophilus </em>and <em>Aggregatibacter </em>are shown in yellow; and cells of genus <em>Porphyromonas</em> are shown in blue.</p> <p>Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for <em>S. cristatus</em>, the <em>S. mitis</em> group, the <em>Streptococcus </em>genus, <em>Corynebacterium</em> genus, and <em>Porphyromonas</em> genus. </p>
Unmixed images from the publication "Corncob structures in dental plaque reveal microhabitat taxon specificity"
<p>Images of bacteria in human dental plaque after fluorescence in situ hybridization, hyperspectral imaging with a Zeiss LSM 780 or LSM 880 laser-scanning confocal microscope, and spectral unmixing. Each image is presented as a stack of the individual unmixed fluorophore channels readable using FIJI (ImageJ) with the Image5D plugin. Channels are shown for <em>Streptococcus cristatus</em>; the <em>Streptococcus mitis </em>group including <em>S. oralis </em>and <em>S. infantis</em>; <em>Streptococcus gordonii</em>; <em>Streptococcus </em>genus; <em>Corynebacterium </em>genus; <em>Corynebacterium matruchotii</em>; <em>Porphyromonas </em>genus; and family Pasteurellaceae including genera <em>Haemophilus </em>and <em>Aggregatibacter</em>. A channel for the residual signal after linear unmixing is also included, as well as a transmitted light image (transmitted PMT). </p> <p>Images labeled as "set 1" (probe set 1) include all probes; "set 2" (probe set 2) and "set 3" (probe set 3) include only probes for <em>S. cristatus</em>, the <em>S. mitis</em> group, the <em>Streptococcus </em>genus, <em>Corynebacterium</em> genus, and <em>Porphyromonas</em> genus. </p>
[Stimulus Set] Evoking the N400 event-related potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
<p>During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.</p>
Video - The PTANOIS POSIN project, digital publication
<p>Video presentation of the PTANOIS POSIN project website: description of the project; presentation and description of the digital product</p>
NAPKON Public Use File
<p>Anonymized Public Use File of the National Pandemic Cohort Network (NAPKON), a German cohort studying the epidemiology and clinical course of SARS-CoV-2 infected patients. For more information see https://napkon.de/</p>
LetterSampo CKCC data publication
<p><strong>LetterSampo CKCC Knowledge Graph</strong></p> <p>The documentation of LetterSampo CKCC dataset is available on <a href="https://www.ldf.fi/dataset/ckcc">Linked Data Finland</a> page and explained in more detail on the <a href="https://seco.cs.aalto.fi/projects/rrl/">project page</a>.</p> <p>This dataset is available on a public SPARQL endpoint (https://ldf.fi/ckcc/sparql).</p>
LetterSampo correspSearch data publication
<p><strong>LetterSampo correspSearch Knowledge Graph</strong></p> <p>The documentation of LetterSampo correspSearch dataset is available on <a href="https://www.ldf.fi/dataset/corresp">Linked Data Finland</a> page and explained in more detail on the <a href="https://seco.cs.aalto.fi/projects/rrl/">project page</a>.</p> <p>This dataset is available on a public SPARQL endpoint (https://ldf.fi/corresp/sparql).</p>
The PI-CAI Challenge: Public Training and Development Dataset
<p>This dataset represents the <strong><a href="https://pi-cai.grand-challenge.org/">PI-CAI</a>: Public Training and Development Dataset</strong>. It contains 1500 anonymized prostate biparametric MRI scans from 1476 patients, acquired between 2012-2021, at three centers (Radboud University Medical Center, University Medical Center Groningen, Ziekenhuis Groep Twente) based in The Netherlands.</p> <p>The PI-CAI challenge is an all-new grand challenge that aims to validate the diagnostic performance of artificial intelligence and radiologists at clinically significant prostate cancer (csPCa) detection/diagnosis in MRI, with histopathology and follow-up (≥ 3 years) as the reference standard, in a retrospective setting. The study hypothesizes that state-of-the-art AI algorithms, trained using thousands of patient exams, are non-inferior to radiologists reading bpMRI.</p> <p>Key aspects of the PI-CAI study design have been established in conjunction with an international scientific advisory board of 16 experts in prostate AI, radiology and urology —to unify and standardize present-day guidelines, and to ensure meaningful validation of prostate AI towards clinical translation (<strong><a href="https://www.sciencedirect.com/science/article/pii/S2405456921001607">Reinke et al., 2021</a></strong>).</p>
Supplementary Data: OpenCOVID model output underlaying Figures 1 and 2 of "Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden"
<p>Supplementary data files <strong>Figure_1.xlsx</strong> and <strong>Figure_2.xlsx</strong> contain the model simulation outcomes for Figures 1 and 2 of <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al</em></a> "<strong>Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden</strong>" (2022)</p> <ul> <li><strong>Figure 1</strong>: Peak daily hospital occupancy (number of beds per 100,000 population over the six-month simulation period) for three variant properties; infectivity (relative to Delta), immune evading capacity (%), and severity (relative to Delta)<br> </li> <li><strong>Figure 2</strong>: Percentage of COVID-19 infections and deaths averted by third-dose vaccines for adults and vaccinating 5-11-year-olds with doses one and two.<br> </li> <li>Open access source-codes of the associated plotting functions are published <a href="http://zenodo.org/record/6532404#.Yqw7cezMKdb">here</a> on Zenodo.<br> </li> <li>Open access source-codes for the OpenCOVID model of all analyses as presented in <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al.</em> (2022)</a> are publicly available at <a href="https://github.com/SwissTPH/OpenCOVID/tree/manuscript_december_2021/src">https://github.com/SwissTPH/OpenCOVID/tree/manuscript_december_2021/src</a>.<br> </li> <li>Detailed model descriptions and model equations of individual-based transmission model <strong>OpenCOVID</strong> are described in <a href="https://pubmed.ncbi.nlm.nih.gov/34923396/">Shattock <em>et al</em>. (2022)</a> and <a href="https://www.medrxiv.org/content/10.1101/2021.12.12.21267673v2">Le Rutte, Shattock <em>et al.</em> (2022).</a></li> </ul>
Data for Analyses presented in associated publication: Investigating trends in those who experience menstrual bleeding changes after SARS CoV-2 vaccination
<p>This is the data used for analyses presented in our associated publication (details to be provided later). There are three datasets, because we analyzed by specific, biologically relevant subgroups (pre-menopausal people with predictable menstrual cycles, pre-menopausal people who usually do not menstruate, and post-menopausal people). The data provided here has been cleaned and aggregated as described in the associated publication. Specifically,</p> <ul> <li>here we have only included the variables that are included in our analyses</li> <li>we collapsed specific identities (gender, race, ethnicity) into binarized categories (as used in the publication) in order to reduce the likelihood someone could be re-identified from this de-identified data</li> <li>this dataset also does not include unique identifiers for individuals, but instead has row numbers for each dataset (starting at 1 for each data subset). There are no repeated individuals between datasets, as these are mutually exclusive subgroups</li> <li>Additional information regarding the survey and data processes can be found at https://osf.io/6rvxk/?view_only=f91f1247658f49e3bbf59b2f6cfd3898</li> </ul>
Behavior preferences between medium-large mammals in Atlantic Forest and Cerrado inside a public university of Southeastern Brazil
<p>We studied large and medium-sized mammals in a modified landscape between the Atlantic Forest and a Cerrado transitional zone (Brazil). We used eight camera traps between August 2016 and August 2017, totaling 75840 camera hours or 3,160 camera trap days. The sampling effort was evaluated from a rarefaction curve based on the daily sampling. We conducted comparative univariate and multivariate ordination statistical analyses. We recorded 19 species in 13 families. The most recorded species were S. scrofa and Cerdocyon thous , while the least recorded were Cuniculus paca, Didelphis albiventris and Tamandua tetradactyla. Richness and total records do not differ among day period, month, season, vegetation type, and moon phase. Individually, species abundance nevertheless sometimes showed trends for these factors. S. scrofa dominated all landscapes and periods of the year because it is an opportunist species that rapidly reproduces and lacks natural efficient predators. The presence of this species reduces the dissimilarity of the community, but when it is removed, the dissimilarity of native species increases. The modified landscape studied here is an important area for mammalian fauna owing to high richness; some species in the area are threatened with extinction. The wide temporal sampling effort contributed to a high number of mammal species records, although without spatial variation.</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.