Find research datasets worth reusing

Dataset related to the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC"

This record contains original data used in the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC" to develop a linear support vector machine (SVM) classifier to predict chromosomal instability.   We retrospectively evaluated the results of plasma NGS analysis performed at our Institution by using the AVENIO ctDNA Expanded Kit, a panel of 77 genes, which detects the major classes of genetic alterations. Binary classification, into “stable” (SCP) or “unstable” (UCP) chromosomal profiles, was initially performed by visual inspection of individual CNV alteration profiles by two independent professionals of our group. Then we decided to implement a support vector machine (SVM) classifier to automatically classify CNV profiles as SCP or UCP, beyond operators’ experience. We considered the segmented log2 ratios (.cns) files provided by the CNV kit software and computed three features (Segments, Size, Chromosomes).  An alteration (“occurrence of instability”) in the CNV profile was defined each time we found a DNA segment of any size with absolute value of the log2 copy ratio exceeding a fixed cut-off. Two different cut-off values on log2 copy ratio were examined: 0.1 and 0.2. Once the cut-off was defined, three features were considered as covariates in the SVM classifier: 1) number of altered segments (Segments), 2) total length of altered regions (Size) and 3) number of affected chromosomes (Chromosomes). The “dataset_0.1.txt” and “dataset_0.2.txt” files are the original data matrices obtained by considering a cut-off of 0.1 and 0.2, respectively, on the absolute value of the log2 copy ratio. Rows represent available samples in our study (n=177). Columns contain the following variables: anonymized sample IDs (Sample), the class, “stable” or “unstable”, as assigned by two independent professionals of our group (Class), the corresponding binary label (Label: 0 for “stable”, 1 for “unstable”), the three features used as covariates in the SVM classifier and computed as described above (Segments, Size, Chromosomes). For the detailed results of our work, please refer to the full article.

Supporting Data to research article

collection of data and code to plot figures shown in the scientific publication  "Subradiance and Superradiant Long Range Excitation Transport among Quantum Emitter Ensembles in a Waveguide"

General dataset of PNAS article " Ca2+ permeation through C-terminal cleaved, but not full-length human Pannexin1 hemichannels, mediates cell death"

This repository contains an extended version of all real-time dye uptake evaluations, Ca2+ signal measurements, microscopic and gel images, and the corresponding statistical analyzes for each graph presented in the associated article.

openmit-licenseMay 2024View details →

Data underlying the article: "Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling"

This repository contains the data underlying the article: “Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling” available as a preprint on ChemRxiv. Main authors: Marina Gorostiola González & Olivier J.M. Béquignon (Leiden University) Senior author: Gerard J.P. van Westen (Leiden University) This analysis was performed using the code available at <a href="https://github.com/CDDLeiden/chembl_variants" target="_blank" rel="noopener">https://github.com/CDDLeiden/chembl_variants</a>

opencc-by-4.0Apr 2024View details →

Dataset related to article 'The Collaborative Seismic Earth Model: Generation 2'

This repository holds 23 earthquake simulations conducted using the second generation of the Collaborative Seismic Earth Model (CSEM2, Noe et al., submitted), serving as benchmark simulations for reproducibility. The simulations are performed with the spectral-element wave propagation solver Salvus (Afanasiev et al., 2019) on event-adapted meshes (Thrastarson et al., 2020). Accompanying waveform data from the stations can be downloaded from public FDSN services and accessed via tools such as the ObsPy mass downloader (Krischer et al., 2015). Information about the earthquakes and receivers is provided in the event files. The source-time function, a filtered heaviside for 50 - 160 s, is included in 'stf.h5' for global simulations and for 20 - 160 s for regional simulations, respectively. The event and waveform information to create Figure 4 in the manuscript are the following: a) <a href="../api/records/11047927/draft/files/GCMT_event_LAKE_TANGANYIKA_REGION_Mag_6.0_2017-2-24-0.h5/content" target="_blank" rel="noopener noreferrer">GCMT_event_LAKE_TANGANYIKA_REGION_Mag_6.0_2017-2-24-0.h5</a>, stf 50 - 160 s b) <a href="../api/records/11047927/draft/files/GCMT_event_CENTRAL_CALIFORNIA_Mag_5.6_2020-6-4-1.h5/content" target="_blank" rel="noopener noreferrer">GCMT_event_CENTRAL_CALIFORNIA_Mag_5.6_2020-6-4-1.h5</a>, stf 20 - 160 s c) <a href="../api/records/11047927/draft/files/GCMT_event_CHILE-ARGENTINA_BORDER_REGION_Mag_5.7_2018-6-21-16.h5/content" target="_blank" rel="noopener noreferrer">GCMT_event_CHILE-ARGENTINA_BORDER_REGION_Mag_5.7_2018-6-21-16.h5</a>, stf 20 - 160 s Simulations for b&c are performed on smaller domains and on regular cubed-sphere meshes.

Data for the article "Stabilizing perpendicular magnetic anisotropy with strong exchange bias in PtMn/Co by magneto-ionics"

Dataset for the article: B. Bednarz et al., “Stabilizing perpendicular magnetic anisotropy with strong exchange bias in PtMn/Co by magneto-ionics,” Appl. Phys. Lett. 124, 232403 (2024). <div> <div><a href="https://doi.org/10.1063/5.0213731" target="_blank" rel="noopener">https://doi.org/10.1063/5.0213731</a></div> </div>

Supplemental material (movies) to article J. Phys. Complex. 5 (2024) 035003

Movie 1: additional description.— The fluid flow’s projection onto the xz plane (that is, the screen plane) corresponds to the planar cellular flow — cf. the stream function given by Eq. (8) of the main text. We emphasize that what we show is the projection of the swimmers’ three-dimensional dynamics onto the xz plane (where the convective cells are visible). The settling parameter is given by Λ = 0.1 for both passive and swimming particles. The other parameters for the run-and-tumble swimmers are v = 0.5 and δτ = 0.1. Movie 2: additional description.— The remarks on projections made in the description of Movie 1 also apply here.

Dataset for Article - a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle

This dataset contains data for analysis on a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle. Dataset contains raw gene expression data, methylation-ELISA data, MSRE data and life history data collected in laboratory conditions using the study system, Callosobruchus maculatus.

Supplementary material of article Mining disaster in Brumadinho (Brazil): social vulnerability from the perspective of the fisherman community

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Data for the Article "Maturity Assessment of Grid-Scale Flexibility and Energy Storage Services Towards a Decarbonized Europe"

This dataset includes the data collected form various stakeholders regarding grid-scale flexibility and energy services as part of the SINNOGENES Project.

Dataset to reproduce the figures of article "Information dynamics of in silico EEG Brain Waves"

Data and code to reproduce results figures.

Raw numerical data and cleavage assay blot for Figures found in the article: "The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord"

In relation to our publication: "The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord" we provide all the individual quantitative observations that underlie the data summarized in the figures and results of our paper. More specifically we provide the data for Fig. 1G, H, I, P, Q; Fig. 2D-G, R-U; Fig. 3E-H; Fig. 4D-F, Q-S; Fig. 5D-G, K-N; R-U; Fig. 6D-F, S-U; Fig. 7G, H, J-T; Fig. 8G-I, M, N, S, X, Y; Fig. 9D-G, R, S; Fig. 10D-Q, K-R; Fig. 11F, G; Fig. S2T-X; Fig. S3G; Fig. S4K, O, P and Fig. S6E-J. In addition we provide a non-annotated and an annotated version of the original, uncropped gel picture shown in Fig. S4A

Trained Potentials for Article "Computationally Efficient Machine-Learned Model for GST Phase Change Materials via Direct and Indirect Learning"

We provide 8 files here to get started using our trained potentials: 1) *.yaml files for each trained potential. These are the outputs of the PACE training process. 2) *.yace files for each trained potential. These are read by LAMMPS to use the trained potential. They can be obtained from the *.yaml files using the command line command: "pace_yaml2yace *.yaml". 3) GST_config.data   --   a starting configuration of GST to be read by LAMMPS. This configuration contains 504 atoms at density 5.85 g/cm^3. 4) sample.inp   --   a sample LAMMPS input file using the trained potentials. This currently uses "ACE-Indir2.yace" to run the starting configuration "GST_config.data" for 10 ps at 1200 K. When run, it outputs a log file "test.log" and a dump file "test.dump". The choice of trained potential can be changed in the "pair_coeff" section.

Supplementary materials to the article "Practices and attitudes toward replication in empirical translation and interpreting studies"

Abstract of the paper: This article presents the results of three studies on practices in and attitudes toward replication in empirical translation and interpreting studies. The first study reports on a survey in which 52 researchers in translation and interpreting with experience in empirical research answered questions about their practices in and attitudes toward replication. The survey data were complemented by a bibliometric study of publications indexed in the Bibliography of Interpreting and Translation (BITRA) (Franco Aixelá 2001–2019) that explicitly stated in the title or abstract that they were derived from a replication. In a second bibliometric study, a conceptual replication of Yeung’s (2017) study on the acceptance of replications in neuroscience journals was conducted by analyzing 131 translation and interpreting journals. The article aims to provide evidence-based arguments for initiating a debate about the need for replication in empirical translation and interpreting studies and its implications for the development of the discipline. Description of the supplementary materials: <ul> <li>Material 1: questionnaire in English</li> <li>Material 2: questionnaire in Spanish</li> <li>Material 3: results of both questionnaires</li> <li>Material 4: corpus of identified replications in Translation and Interpreting Studies (TIS)</li> <li>Material 5: acceptance of replications in TIS journals</li> </ul>

opencc-by-4.0Sep 2024View details →

Codes and data for the article: Biodiversity on the Line: Life Cycle Impact Assessment of Power Lines on Birds and Mammals in Norway

This repository contains all input data required to run the habitat conversion, collision, and electrocution LCIA models and reproduce the results, as well as all output data generated in various formats. The models are described in the paper "Biodiversity on the Line: Life Cycle Impact Assessment of Power Lines on Birds and Mammals in Norway" (https://doi.org/10.1088/2634-4505/ad5bfd). "The files "01_Get_GBIF_points.R, "02_SDMs_maxent.R" describe how to create the species distribution maps. "03_Data_preparation.R", "04_Pylon_cleaning.py" are to prepare and modify the raw data for the analysis. The raw data are not provided, yet links to the sources are provided either in the R codes or the paper. To run the models, run the "05_SHR_modelling.R" and "06_Collision_electrocution_models.R" files. To calculate characterization factors, run the "07_Characterisation_factors.R" file. To export the tables in the Supporting Information 1, run the file "08_Supporting_Information.R". Finally, the file "09_Sensitivity_analysis.R" performs the sensitivity analyses.

Artifact to accompany "An Empirical Examination of Fuzzer Mutator Performance" (ISSTA 2024 article)

This artifact contains scripts and data to supplement the ISSTA 2024 article "An Empirical Examination of Fuzzer Mutator Performance":   Over the past decade, hundreds of fuzzers have been published in top-tier security and software engineering conferences. Fuzzers are used to automatically test programs, ideally creating high-coverage input corpora and finding bugs. Modern "greybox'' fuzzers evolve a corpus of inputs by applying mutations to inputs and then executing those new inputs while collecting coverage. New inputs that are "interesting'' (e.g. reveal new coverage) are saved to the corpus. Given their non-deterministic nature, the impact of each design decision on the fuzzer's performance can be difficult to predict. Some design decisions (e.g. "should the fuzzer perform deterministic mutations of inputs'') are exposed to end-users as configuration flags, but others (e.g. "what kinds of random mutations to apply to inputs?'') are typically baked-in to the fuzzer code itself. This paper describes our over 12.5-CPU-year evaluation of the set of mutation operators employed by the popular AFL++ fuzzer including the havoc phase, splicing and \redqueen, exploring the impact of adjusting some of those unexposed configurations. In this experience paper, we propose a methodology for determining different fuzzers' behavioral diversity with respect to branch coverage and bug detection using rigorous statistical methods. Our key finding is that, across a range of targets, disabling certain mutation operators (some of which were previously "baked-in'' to the fuzzer) resulted in inputs that cover different lines of code and reveal different bugs. A surprising result is disabling certain mutators leads to more diverse coverage and allows the fuzzer to find more bugs faster. We call for researchers to investigate seemingly simple design decisions in fuzzers more thoroughly and encourage fuzzer developers to expose more configuration parameters pertaining to these design decisions to end-users.

Data pertaining to the published article "Detection of pathological contrast enhancement with synthetic brain imaging from quantitative multiparametric MRI" by Donatelli et al., 2024

Data pertaining to the published article "Detection of pathological contrast enhancement with synthetic brain imaging from quantitative multiparametric MRI" by Donatelli et al., 2024. <a href="https://doi.org/10.1111/jon.13201">https://doi.org/10.1111/jon.13201</a>

opencc-by-4.0Aug 2024View details →

Codes for the article: Biodiversity Impacts of Norway's Renewable Electricity Grid

This repository contains the codes required to run the LCIA models and reproduce the results. The models are described in the paper "Biodiversity Impacts of Norway’s Renewable Electricity Grid" (https://doi.org/10.1016/j.jclepro.2024.143096).

Dataset for the NC article: Deep mantle earthquakes linked to CO2 degassing at the Mid-Atlantic Ridge

The obtained earthquake catalogue, picked P- and S-arrivals, and 1-D velocity models in the Mid-Atlantic Ridge in the equatorial Atlantic ocean, using a recent temporary array of seafloor seismometers. Related article: Yu, Z., Singh, S.C., Hamelin, C. et al. Deep mantle earthquakes linked to CO2 degassing at the mid-Atlantic ridge. Nat Commun 16, 563 (2025). https://doi.org/10.1038/s41467-024-55792-9

Artifacts of the Article: "Guidelines for Using Financial Incentives in Software-Engineering Experimentation"

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