Find research datasets worth reusing

opencc-by-4.0May 2022View details →

Multi-stakeholder research data management training as a tool to improve the quality, integrity, reliability and reproducibility of research: Quantitative data of the post-course surveys

Data contains doctoral students' and postdoc researchers' (n=168) self-ratings of their RDM competencies before and after the 3 ECTS credits "Basics of Research Data Management" (BRDM) trainings held 2019-2021 in the University of Turku and Åbo Akademi University, Finland. Moreover, data contains respondents' self-reported further learning needs.

opencc-by-4.0Mar 2022View details →

Supplementary input data for accounting for component condition and preventive retirement in power system reliability of supply analyses

<div> <div>This data set contains supplementary data used for case studies on accounting for transformer condition in reliability of supply analyses in the following manuscripts: 1) H. Toftaker, J. Foros, I. B. Sperstad, "Accounting for component condition and preventive retirement in power system reliability of supply analyses", IET Generation, Transmission & Distribution, vol. 5, no. 1, 2023, DOI: 10.1049/gtd2.12761. 2) I. Bjerkebæk, I. B. Sperstad, H. Toftaker, G. Kjølle, "Simulating the Long Term Effect of Asset Management Strategies on Reliability of Supply", pre-print submitted for peer review, 2024. DOI: 10.36227/techrxiv.172107759.95745501/v1.</div> <div> See README.md for details.</div> </div>

opencc-by-4.0Mar 2018View details →

Data and script for Van Berkel et al: Can starlings use a reliable cue of future food deprivation to adaptively modify foraging and fat reserves?

Supporting materials for: Can starlings use a reliable cue of future food deprivation to adaptively modify foraging and fat reserves? Menno van Berkela, Melissa Batesona, Daniel Nettlea and Jonathon Dunna* aCentre for Behaviour and Evolution & Institute of Neuroscience, Newcastle University, Newcastle, UK *Author for correspondence (email: jonathon.dunn@newcastle.ac.uk; telephone: (+44)7730015855; postal address: Institute of Neuroscience, Henry Wellcome Building, The Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH). R script and 3 .csv files.

opencc-by-4.0Oct 2023View details →

Data of "Towards a More Reliable Forecast of Ice Supersaturation: Concept of a One-Moment Ice Cloud Scheme that Avoids Saturation Adjustment"

These are the data used for generating the figures in the ACP article "Towards a More Reliable Forecast of Ice Supersaturation: Concept of a One-Moment Ice Cloud Scheme that Avoids Saturation Adjustment" by Sperber and Gierens. The data sets labeled "Box" have been generated by the stochastic box model, "adj" refers to the parameterisation using saturation adjustment and data labeled "par" originate from the newly developed parameterisation. The label "const" followed by a number refers to simulations with a constant updraught of the speed specified by the number in cm/s. The label "cos" refers to the simulations in which the updraught velocity follows a cosine function in time. "a10" labels simulations with less initial clear sky humidity fluctuations of plus/minus 10% instead of plus/minus 25%. "al0028" labels simulations with a higher deposition rate of 0.0028 1/s instead of 0.0003 1/s. "step10" labels simulations with a longer time step of 10 minutes instead of 1 minute. "Box_const2_rh1.txt" contains data from a simulation similar to "Box_const2.txt" but with an initial mean relative humidity of 100% instead of 110%. "Box_het.txt" contains data from a simulation including heterogeneous nucleation. "Box_slow_nuc.txt" contains data from a simulation where the deposition rate increases over time from zero after nucleation in every air parcel. "Box_upvar.txt" contains data from a simulation, where the updraught velocity in every air parcel varies randomly between 1 cm/s and 3 cm/s and the deposition rate inside the air parcel depends on the updraught velocity at the time of nucleation.   The columns in the "Box" files represent from left to right: 1. Time since the simulation start in s 2. Cloud fraction 3. Mean relative humidity across all air parcels 4. Mean specific humidity across all air parcels 5. Mean specific ice content across all air parcels 6. Mean relative humidity across all cloudy air parcels 7. Mean relative humidity across all clear air parcels 8. Mean equilibrium supersaturation 9. Mean threshold relative humidity for homogeneous nucleation 10. Mean deposition rate across all cloudy air parcels 11. Mean updraught velocity   The columns in the "adj" files represent from left to right: 1. Time since the simulation start in s 2. Cloud fraction 3. Mean relative humidity 4. Mean specific humidity 5. Mean specific ice content 6. In-cloud Humidity 7. Clear sky humidity   The columns in the "par" files represent from left to right: 1. Time since the simulation start in s 2. Cloud fraction 3. Mean relative humidity 4. Mean specific humidity 5. Mean specific ice content 6. In-cloud Humidity 7. Clear sky humidity 8. Obsolete 9. Equilibrium supersaturation

zenodo44/100

Raw frequency data: Thoughts on "Reliable" Learner's Vocabularies for Classical and Literary Chinese

This dataset includes the raw frequency counts (classical_chinese_learners_vocabularies_raw_frequencies.zip) used in the article Thoughts on “Reliable” Learner’s Vocabularies for Classical and Literary Chinese.  Corpus I – Micheal Loewe (1993)’s Early Chinese Texts Corpus II – Official Histories (zhengshi 正史) Corpus III Six Novels (xiaoshuo 小說), as defined in Hsia 1968 The download includes one folder per corpus, structured as follows: <ul> <li>xx_corpus.csv > list of texts and sources / used versions, token and type counts</li> <li>xx_freq_1-1.csv > unigram / character frequencies and counts</li> <li>xx_freq_1-4.csv > 1 to 4 character word frequencies and counts, "words" according to Hanyu da cidian 漢語大詞典 (Luo 1986–1994))</li> <li>xx_freq_2-4.csv > 2 to 4 character words</li> </ul> Additionally, pca_zhengshi_vs_loewe_vs_xiaoshuo.html is an interactive version of the Principal Component Analysis (PCA) presented in the article, texts from the three corpora are represented using the 1.000 most frequent 1–4 character combinations from the dataset.

opencc-by-4.0Nov 2021View details →

zenodo44/100

Data and Code for: 'Stellar Models are Reliable at Low Metallicity: An Asteroseismic Age for the Ancient Very Metal-Poor Star KIC 8144907', Huber et al. 2024.

Data and code to reproduce plots for the paper 'Stellar Models are Reliable at Low Metallicity: An Asteroseismic Age for the Ancient Very Metal-Poor Star KIC 8144907', Huber et al. 2024. Descriptions of the enclosed data files are as follows: <div> <ul> <li>Freqs_best_fit.dat:  Best-fitting GARSTEC model frequencies (Figure 3, right)</li> <li>KIC10006158_spec.txt:  Reduced and normalized HDS spectrum of KIC10006158 (Figure 1)</li> <li>KIC8144907_ps.txt:  Power spectrum of the Kepler light curve of KIC8144907 (Figure 3, left)</li> <li>KIC8144907_spec.txt:  Reduced and normalized HDS spectrum of KIC8144907 (Figure 1)</li> <li>apokasc2.tsv:  APOKASC sample from Pinsonneault+ 2014 (Figure 2)</li> <li>dwarfs.csv:  Asteroseismic sample from Serenelli+ 2017 (Figure 2) </li> <li>freqs.csv:  Data in Table 1</li> <li>hosts.tsv:  Asteroseismic ages from Silva Aguirre+ 2015 (Figure 4) </li> <li>legacy-t1.tsv:  Asteroseismic ages from Silva Aguirre+ 2017 (Figure 4) </li> <li>legacy-t2.tsv:  Asteroseismic ages from Silva Aguirre+ 2017 (Figure 4) </li> <li>li-2020.csv:  Asteroseismic ages from Li+ 2020 (Figure 4) </li> <li>matsuno.txt:  Asteroseismic sample from Matsuno+ 2021 (Figure 2) </li> </ul> </div>

opencc-by-4.0Aug 2024View details →

zenodo44/100

Concentration-, Temperature- and Solvent-Dependent Self-Assembly: Merocyanine Dimerization as a Showcase Example for Obtaining Reliable Thermodynamic Data

Abstract: Mathematical models for the concentration-, temperature- and solvent-dependent analysis of self-assembly equilibria are derived for the most simple case of dimer formation, to highlight the assumptions these models and the thus determined thermodynamic parameters are based on. The three models were applied to UV/Vis absorption data for the dimerization of a highly dipolar merocyanine dye in 1,4-dioxane. Isothermal titration calorimetry (ITC) dilution experiments were performed as an independent reference technique. While the concentration-dependent analysis is according to our studies the most reliable method, also the less time-consuming temperature-dependent evaluation can give accurate results in the present example, despite small thermochromic effects. In contrast, the strong negative solvatochromism of the merocyanine tampers with the results from the solvent-dependent evaluation. Even though the studies presented in this work are limited to the monomer-dimer equilibrium of a dipolar dye, the basic principles can be transferred to other chromophores and different self-assembly models, including those for supramolecular polymerization.

opencc-by-4.0Apr 2023View details →

opencc-by-4.0Nov 2023View details →

Data for Project 'Diagnostic Accuracy, Reliability, and Construct Validity of the German Quick Mild Cognitive Impairment Screen'

Data for Project 'Diagnostic Accuracy, Reliability, and Construct Validity of the German Quick Mild Cognitive Impairment Screen' consisting of (1) the complete data set of all data analyzed for the project 'Diagnostic Accuracy, Reliability, and Construct Validity of the German Quick Mild Cognitive Impairment Screen' ('Data_Brain-IT-Validation-Qmci_for-publication.xlsx'; and (2) a corresponding README file including (a) general information, (b) data and file overview, (c) sharing and access information, (d) methodological information, and (e) data-specific information.

Data and Analysis for "On the Reliability of Coverage-based Fuzzer Benchmarking"

<pre>Data and Analysis for "On the Reliability of Coverage-based Fuzzer Benchmarking" ## Cite </pre> <pre><code>@inproceedings{benchmarking, author = {B{\"o}hme, Marcel and Szekeres, L{\'a}szl{\'o} and Metzman, Jonathan}, title = {On the Reliability of Coverage-based Fuzzer Benchmarking}, year = {2022}, booktitle = {Proceedings of the 44th International Conference on Software Engineering}, series = {ICSE '22}, pages = {1-13}, doi = {10.1145/3510003.3510230} }</code></pre> <pre> ## Data Analysis The Jupyter notebook generating all tables and figures can be found in fuzzbench.manual.ipynb ## Generated Images and Tables The generated data analysis artifacts are also available in this artifact. ## Data All the data is available in the FuzzBench Reports and will be automatically downloaded. * 20 trials of 23 hours with 15 programs and 10 fuzzers. * Experiment name: 2021-02-17-bug-paper * Report: https://www.fuzzbench.com/reports/2021-02-17-bug-paper/index.html * Data: https://www.fuzzbench.com/reports/2021-02-17-bug-paper/data.csv.gz * Fuzzbench Commit: [38e344fef2f1079579391a0d9dcb52319f7051f2](https://github.com/google/fuzzbench/commits/38e344fef2f1079579391a0d9dcb52319f7051f2) * 30 trials of 23 hours with 11 programs and 10 fuzzers. * Experiment name: 2021-08-19-crash-s * Report: https://www.fuzzbench.com/reports/2021-08-19-crash-s/index.html and * Data: https://www.fuzzbench.com/reports/2021-08-19-crash-s/data.csv.gz * Fuzzbench Commit: db192b60815ac87f69ee0f7f3e37aeac71949e1b * 30 trials of 23 hours with 11 programs and 10 fuzzers. * Experiment name: 2021-08-19-crash-s2 * Report: https://www.fuzzbench.com/reports/2021-08-19-crash-s2/index.html and * Data: https://www.fuzzbench.com/reports/2021-08-19-crash-s2/data.csv.gz * Fuzzbench Commit: db192b60815ac87f69ee0f7f3e37aeac71949e1b The deduplicated data can be found in * 2021-02-17-bug-paper-fixed2.csv.gz * 2021-08-19-crash-s-fixed2.csv.gz * 2021-08-19-crash-s2-fixed2.csv.gz ## Reproducibility </pre> <pre><code class="language-bash"># Download the precise version of FuzzBench used for the experiment git clone https://github.com/google/fuzzbench.git cd fuzzbench git checkout <Fuzzbench Commit> # Download the internal config file. curl https://storage.googleapis.com/[experiment-name]/config/experiment.yaml > /tmp/experiment-config.yaml make install-dependencies # Launch the experiment using paramters from the internal config file. PYTHONPATH=. python experiment/reproduce_experiment.py -c /tmp/experiment-config.yaml -e <new_experiment_name></code></pre>

Fig. 6 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 6: ML phylogenetic tree of the genus Polyclinum (sequences abbreviation: Pln) based on COI nucleotide sequences (1560 aligned nucleotide sites; best-fit substitution model GTR+I+G; bootstrap on 100 replicates). Eudistoma and Pseudodistoma species were used as outgroups. The sequence list and species abbreviations are reported in Supplementary table S1. Black dots: bootstrap values ≥ 70 %; red: P. constellatum sequences; blue: P. indicum sequences; yellow background: our sequences.

Fig. 4 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 4: A, C) Colonies of Polyclinum constellatum with different colours photographed and collected in the Heraklion marina (Crete) (A: colony K11 and C: colony K12); B) Transversal section of the colonies, joined only at the surface layer (upper white arrow); D) Zooid extracted from the red-orange colony (K11), with magnification of the 6-lobed anus; E) Zooid extracted from the dark blue colony (K12) with magnification of the 6-lobed anus. Both K11 and K12 have the same COI haplotype (sequence AC number: MT873559).

Fig. 5 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 5: A) Larva of P. constellatum, showing the ocellus, four long narrow ampullae, three adhesive papillae and a group of a few small ventral vesicles (red arrow). am, ampullae; ap, adhesive papillae; oc, ocellus; B) Larva of P. constellatum, red arrow pointing out the calcite crystal in the middle of the body.

Fig. 2 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 2: A) Orange colony of Polyclinum constellatum from Taranto harbour (colony P1); B) Magnification of the oral (arrow pointing put the oral tentacles of different size) and cloacal aperture (asterisk); C) P. constellatum collected in Heraklion (colony K19) with zooids arranged in systems around the cloacal apertures; D) Section of the colony showing the zooids located only around the outer edge (arrow).

Fig. 3 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 3: A) Whole zooid of Polyclinum constellatum, showing a clear division into thorax, abdomen and post-abdomen with a long vascular stolon. ab, abdomen; pa, post-abdomen; th, thorax; vs, vascular stolon; B) Zooid with evident pharynx, rectum, anus and four embryos incubated in the atrial cavity. The funnel-shaped oesophagus, the smooth stomach and the twisted gut loop are visible in the abdomen. The post-abdomen shows the heart at its terminal end, as well as several rounded testicular follicles and the ovary, with the gonoducts running parallel to the rectum. an, anus; e, embryos; gd, gonoducts; gl, gut loop; oe, oesophagus; ov, ovary; h, heart; r, rectum; st, stomach; tf, testicular follicles; C) Magnification of the oral siphon with six pointed lobes (arrows) and six longitudinal muscle bands (indicated with numbers 1-6); D) Branchial sac with 18 rows of stigmata and narrow languets of the dorsal lamina (arrows); E) Magnification of the pharynx, with minute papillae (arrows) at the level of the transverse vessels; F) Magnification of the six-lobed anus (lobes indicated with numbers 1-6).

Fig. 1 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 1: Map of the Mediterranean Sea showing the literature records (black rhombuses) of P. constellatum and the new findings (red dots). performed in a final reaction volume of 25 μl contain- nus was reconstructed with the online software PHYML ing: 1X reaction buffer with 1 mM final concentration of v3.0 (http://www.atgc-montpellier.fr/phyml-sms/) (Guin- MgCl 2 (Takara Bio Inc.), 0.2 mM of each dNTP, 0.3 μM don & Gascuel, 2003), which also includes the automatof each primer and 1.25 Units of PrimeStar HS (Takara ic model selection algorithm SMS (Smart Model Selec- Bio Inc.). Amplification conditions were: 30 cycles with tion). The best-fit substitution model was selected using denaturation for 10 s at 98°C, annealing for 15 s at 46°C the Akaike Information Criterion (AIC). Bootstrap val- or 50°C, extension for 1 min 30 s at 72°C; a final elonga- ues, indicating node reliability, were based on 100 reption step of 5 min at 72°C. licates. The sequence dataset used for this phylogenetic PCRs with the DreamTaq polymerase were performed reconstruction is reported in Supplementary Table S1 and in a final volume of 25 μl containing: 1X reaction buffer was extracted from the phylogenetic dataset published in with 2 mM final concentration of MgCl 2 (Thermo Fish- Tabudravu et al. (2019). It includes representative species er Scientific), 0.2 mM of each dNTP, 0.4 μM of each of of the Polyclinidae family plus Eudistoma and Pseudodithe two primers, and 1.25 Units of DreamTaq polymerase stoma species chosen as outgroups for their morphologi- (Thermo Fisher Scientific). The amplification conditions cal similarities with Polyclinidae. were as follows: an initial denaturation for 3 min at 95°C, then 34 amplification cycles (denaturation for 30 s at 95°C; annealing for 30 s at 46-50°C; extension for 1 min Results 30 s at 72°C) followed by a final elongation step of 5 min at 72°C. Morphological analyses The obtained amplicons were purified with the DNA Clean&Concentrator kit (Zymo Research) and directly The colonies collected in Taranto harbour and Hersequenced according to the Sanger method by Microsynth aklion marina were all morphologically identified as P. AG (Switzerland). The sequence quality check, compar- constellatum based on the following features: colonies isons and alignment were carried out with Geneious ver. without sand in/outside, zooids arranged in systems, 5.5.7.2 (Kearse et al., 2012). The sequences obtained post-abdomen (without vascular stolon) shorter than the were deposited in the GenBank database (see Accession thorax and abdomen combined, pharynx with 16-18 rows numbers MT873559 and OL597608). For comparative of stigmata, more than 15 stigmata per row, and a 6-lobed analyses, homologous sequences of the genus Polycli- anus. These characteristics are in accordance with the key num were searched for in the non-redundant nucleotide of Polyclinum species edited by Kott (1963) and they are database (nr-nt db, on 21st September 2021) of the NCBI also reported in the description of the species made by (National Center for Biotechnology Information) by En- Van Name (1945). trez text search, and by BLASTn (Altschul et al., 1990) using our P. constellatum sequences as the query. Uncorrected pairwise distances were calculated with PAUP 4.0a (Swofford, 2002), while a Maximum Likelihood (ML) phylogenetic tree of the genus Polyclinum ge-

Fig. 1 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 1: Map of the Mediterranean Sea showing the literature records (black rhombuses) of P. constellatum and the new findings (red dots).

opencc-by-4.0Mar 2018View details →

A Meta-Analysis on the Reliability of Comparative Judgement Data

This is the data and R analysis script with the article "A Meta-Analysis on the Reliability of Comparative Judgement"

opencc-by-4.0Jul 2019View details →

Extended data for the paper "Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction"

Extended data for the paper: Reliable generation of native-like decoys limits predictive ability in fragment-based protein structure prediction Authors: Shaun M Kandathil, Mario Garza-Fabre, Simon C Lovell and Julia Handl -------------------------------- Contents of the zip file:   Directory 'ECDFplots': ----------------------     Data corresponding to Figure 3 for all targets, for the bilevel and ILS protocols. Data are available following stages 3 and 4 of the low-resolution protocol. Directory 'ScoreRMSDplots_3archivers': --------------------------------------     Data corresponding to Figures 6 and 9 for all targets. Data corresponding to decoys obtained after low-resolution stages 3 and 4 can be found in subdirectories 'Stage3' and 'Stage4', respectively.

opencc-by-4.0Dec 2022View details →

Data for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae"

Data and code for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae". Preprint available at bioRxiv: https://doi.org/10.1101/2022.09.07.506897.