Find research datasets worth reusing

opencc-by-4.0Jun 2020View details →

A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula

This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural Quercus petraea (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.

Data sets for: Diverse slip behavior of the Banyak Islands sub-segment of the Sunda megathrust in Sumatra, Indonesia

Data sets include: DatasetS1, coral measurements taken within the Banyak Islands from 2005 to 2010  DatasetS2, the slip distribution for the 2010 MW 7.8 Banyak Islands earthquake

opencc-by-4.0Jun 2020View details →

Supplementary data (simulated metagenome set 2) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"

Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of closely related Bacteorides strains. The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.

Full-field numerical simulations of temperate ice viscoplastic deformation and dynamic recrystallization [Data set]

This data set corresponds to the scientific article Llorens, M.-G., Griera, A., Bons, P.D., Gomez-Rivas, E., Weikusat, I., Prior, D., Kerch, J. and Lebensohn, R.A. Seismic anisotropy of temperate ice in polar ice sheets. Journal of Geophysical Research: Earth Surface. This data set contains (i) the output files with the crystal orientation and phase data of each simulation presented in the article (run using the open-source software platform ELLE; Bons et al., 2008; Piazolo et al., 2019), and (ii) a code to plot the crystallographic orientation density function (ODF) using the open-source code MTEX (Mainprice et al., 2015). For the visualization of seismic wave velocities the information contained in these output files can be loaded (in radians) to the software package AEH-EBSD Analysis Toolbox (Naus-Thijseen, 2011; Vel et al., 2016). The output files are provided for time steps 50 (shear strain of 1), 100 (shear strain of 2), 200 (shear strain of 4), 300 (shear strain of 6) and 400 (shear strain of 8). Each file has eight columns and multiple rows. Each row stores the output data for an unode of the model, and the model has 256x256 unodes. The first three columns correspond to the three Euler angles (α, β, γ) in degrees, the fourth and fifth column are the x and y coordinates of each unode, the sixth and seventh columns contain attributes not used in these simulations and column eight shows the phase number corresponding to each unode (1 for solid ice and 2 for water). Three simulations are presented and analyzed in this article, and thus their results stored in this data set: Simulation 1: purely solid ice (melt fraction ϕ=0) Simulation 2: ice including 5% water (melt fraction ϕ=5) Simulation 3: ice including 15% water (melt fraction ϕ=15)

Data set of trials perfomed in Pont Saint Martin Data Center, pilot of CATALYST Project

<blockquote> The zip file contains data sets being the input and/or output of the test case exploited in Pont Saint Martin Data Center, as pilot of CATALYST Project (H2020-EE-2016-2017) </blockquote>

Data Set of Interviews with Industry Representatives on Smart Dust

Data Set of Interviews with Industry Representatives on Smart Dust This data set comprises the following documents: <ul> <li>Coding scheme</li> <li>Model development</li> <li>Interview guideline</li> </ul>

Supplementary data (simulated metagenome set 3) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"

opencc-by-4.0Apr 2020View details →

data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)

Data sets and trees for the Rasplus et al. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1 *.phy = Data sets (phylip format) [see Table 2 of the paper for more details]. - mergeR1R2.phy : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads) - mergeR1R2_GCinfmean.phy : loci with GC content inferior or equal to mean GC content - mergeR1R2_GCsupmean.phy : loci with GC content strictly superior to mean GC content - mergeR1R2_LS3.phy : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade") - mergeR1R2_PCA.phy : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach   Fig*.nwk : Trees (newick format) that were obtained for the different data sets. Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees).    Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees. This file can be opened in Mesquite to get reconstruction of ancestral character states

Event/Nonevent Noun Disambiguation Test Set

The dataset is designed to test classifiers’ ability to determine whether a nominal, in a context, has an eventive sense or not. The test dataset contains examples of eventive and non-eventive use of 3 ambiguous English nouns - "publication", "organization" and "construction". There are ~ 150 sentences per noun: ~75 sentences in which the noun has an eventive sense and ~75 sentences in which this is not the case. The examples are taken from internet news sites.

Data set for the article titled hypertension affects the treatment of wet age-related macular degeneration

This is concise data set for the article titled Hypertension affects the treatment of wet age-related macular degeneration

Data set accompanying: Topology of the Warm plasma dispersion relation at the second Harmonic Electron Cyclotron Resonance Layer

The Warm Plasma Dispersion Relation, for waves in the electron cyclotron resonance range of frequencies, can be cast into the form of a bi-quadratic equation for $N_\perp$, where the coefficients are a function of $N_\perp^2$ and an iterative procedure is required to obtain a solution. However, this iterative procedure is not well understood and fails to converge towards a solution at the second harmonic resonance layer. In particular at higher densities where the wave can couple to an electron Bernstein wave. This paper focuses on a solution to the poor convergence of the iterative method, enabling determination of the topology of the dispersion relation around the second harmonic using a fully relativistic code for oblique waves. A feed-forward controller is proposed with the ability to adjust the rotation of a step of $N_\perp^2$ within the complex plane, while also limiting the step-size. It is shown that implementation of the controller stabilizes unstable solutions, while improving overall robustness of the iteration. This allows the evaluation of the coupling between the fast extraordinary mode and electron Bernstein waves at the second harmonic electron cyclotron resonance layer, for non-perpendicularly propagating waves.

Animation of finite-time coherent sets in the Agulhas region

This animation shows finite-time coherent sets that were detected in the Agulhas region with the OPTICS clustering method applied to simulated Lagrangian particles. Clusters are determined based on the first 100 days of trajectory data. The corresponding trajectory data can be found here: https://doi.org/10.5281/zenodo.3899942.

opencc-zeroOct 2020View details →

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SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study

Background: Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. Methods: We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss. Findings: The use of high efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% CrI: 73.1% - 85.7%) and 87% (CrI: 80.0% - 92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. Our results also indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation. Conclusions: Our analysis shows that a COVID-19 outbreak in a hospital's non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures.

Data set, combining epidemiological, genetics, and government stringency data of COVID-19 pandemic.

This data set combines epidemiological, genetics, and government stringency data of COVID-19 pandemics, all from open data sources. The sources are: Our World in Data, Worldometer, GISAID-Nextstrain, and the Oxford COVID-19 Government Response Tracker (OxCGRT). The cut off date of the first version is at the end of June 2020.  The simple data set is provided as an Excel workbook, where the first, "readme" worksheet describes the details of data of all the worksheets in the data set.  This is a working data set, expected to be refreshed over time.  Raw data are not cleaned - this collection is a tool to check various hypotheses regarding possible relations among the various data types. Simple visualisations of data relations are provided in a separate sheet.

Southern Ocean Cloud and Aerosol data set: a compilation of measurements from the 2018 Southern Ocean Ross Sea Marine Ecosystems and Environment voyage

Due to its remote location and extreme weather conditions, atmospheric in situ measurements are rare in the Southern Ocean. As a result, aerosol-cloud interactions in this region are poorly understood and remain a major source of uncertainty in climate models. This, in turn, contributes substantially to persistent biases in climate model simulations, numerical weather prediction models and reanalyses. It has been shown in previous studies that in situ and ground-based remote sensing measurements across the Southern Ocean are critical for complementing satellite data sets due to the importance of boundary layer and low-level cloud processes. These processes are poorly sampled by satellite-based measurements which are typically obscured by near-continuous overlying cloud cover observed in this region. Here we provide a comprehensive set of ship-based aerosol and meteorological observations collected on the TAN1802 voyage of R/V Tangaroa across the Southern Ocean, from Wellington, New Zealand, to the Ross Sea, Antarctica. The voyage was carried out from 8 February to 21 March, 2018. The compiled data set provides here includes measurements from a range of instruments, such as (i) meteorological conditions at the sea surface and profile measurements; (ii) the size and concentration of particles; (iii) trace gases dissolved in the ocean surface such as dimethyl sulfide and carbonyl sulfide; (iv) and remotely sensed observations of low clouds. We encourage the scientific community to use these measurements for further analysis and model evaluation studies, in particular, for studies of Southern Ocean clouds, aerosol and their interaction.

opencc-by-4.0Nov 2020View details →

ImprovBot.ai - The Show Listings: Full Set

ImprovBot.ai The Show Listings: Full Set  ImprovBot was the world's first AI-generated Arts Festival programme, posting online nearly 400 new show listings from 7 to 31 August 2020. These are generated by The Bot, a recurrent neural network reimagining 2,098,140 words of Edinburgh Fringe show listings (2011-2019). This archive makes the complete set of the project's show listings available in a single text-file download. These are listed as: <ol> <li>ImprovBot.ai The Show Listings: Twitter Length Posts</li> <li>ImprovBot.ai The Show Listings: 100 Word Posts</li> </ol> Licence: CC-BY-NC Project members: Melissa Terras, Gavin Inglis, Rudolf Ammann https://improvbot.ai/ https://twitter.com/improvbot_ai https://improvbot.ai/about/how-the-ai-works/ https://improvbot.ai/about/ Another archive is available of ImprovBot illustrations, by Rudolf Ammann, at http://doi.org/10.5281/zenodo.4384718

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Flick SMART multi-catch rodent station and bait station data sets: Council of the city of Sydney, October 2019 to July 2020

Shortly after the enactment of preventative measures aimed at limiting the spread of COVID-19, local governments and public health authorities around the world reported an increased sighting of rats. We combined multi-catch rodent station data, rodent bait stations data, and rodent-related residents' complaints data to explore the effects that social distancing and lockdown measures might have had on the rodent population within the City of Sydney, Australia. We found that rodent captures, activity, and rodent related residents' complaints increased during the COVID-19 related lockdown period, followed by a steep decline post-lockdown. We found no changes in the geographical distribution of any of our indices of rodent abundance. We hypothesize that lockdown measures resulted in an increase in rodent activity driven by a reduction in human-derived food resources. This might have increased the mortality rate triggering a population crash. There is a high chance that the surviving individuals might be rodenticide resistant. It is possible that the onset of COVID-19 might have disrupted commensal rodent populations, with profound implications for the future management of these species. Here we make available multi-catch rodent station data and rodent bait stations data. We do not include rodent-related residents' complaints data due to potential identifier data that could be seen as a breach of private information sharing.

opencc-zeroNov 2020View details →

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Data from: Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: The sister to all other Metazoa (SOM). Here we use published phylogenomic datasets (∼45,000-400,000 characters in size with ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological datasets (∼15-275 characters). We additionally use small exemplar datasets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, i.e. likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, i.e., that genomic-scale datasets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10× in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular datasets (>200,000 characters and up to ∼100 taxa) showing node stability even with ≧100× up-weighting of morphological data. Accordingly, our analyses have three strong messages. A) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined datasets, even when outnumbered thousands of times by morphological data. Morphology therefore should not be counted out a priori. B.) We here quantify for the first time how the stability of the SOM node improves for several genomic datasets when the taxon sampling is increased. C.) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of datasets that should be developed into a new sensitivity analysis tool.

opencc-zeroNov 2020View details →

opencc-by-4.0May 2020View details →

Data set with reference scenarios

Data set with reference scenarios. As it is not possible to include the entire dataset in this report, we only include two Tables on final energy demand. Table 1 shows the Final Energy Demand projections per industrial subsector and EU28 country in the Reference Scenario and Table 2 the Final Energy Demand projections per industrial subsector and EU28 country in the Frozen Efficiency Scenario. The full dataset, including physical production (in ktonnes) and fuel and electricity demand (in TJ) per industrial sub-sector, per fuel type and per EU 28 country is available upon request to the project coordinator.

Data set on Energy Efficiency potentials on top of reference scenarios

As it is not possible to include the entire dataset in this report, we only include the Energy Efficiency potentials for Austria. The full dataset, showing the savings potentials for all EU27 (and UK) countries, is available upon request to the project coordinator.