Find research datasets worth reusing

Dataset of the Article Evaluating a Framework of Conceptual Modelling Research through a Family of Experiments

Data set of the article "Evaluating a Framework of Conceptual Modelling Research through a Family of Experiments". Contains the results of: -Demographic questionnaire - Agreement and correctness of Paper A - Agreement and correctness of Paper B - Agreement and correctness of Paper C -Satisfaction questionnaire -Procedure and Pros and Cons of the framework

opencc-by-4.0Feb 2023View details →

Datasets and R script to replicate the statistical analyses from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission

Datasets and R script to replicate the statistical analyses from the article entitled " Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission " by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023

opencc-by-4.0Mar 2023View details →

Supplemetary Data for the article: Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons

This is a set of Supplementary materials for the article 'Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons', by Meng et al. Supplementary_Data_I.pdf contains an extensive table spanning 36 pages that lists the top-10 molecular fragments accountable for the spectral bands between 2.761 and 1172.745 μm. To access this table, hyperlinks within the document can be used for navigation. Supplementary_Data_II.pdf comprises a large table that encompasses 10,691 pages, including the top-100 molecular fragments responsible for the spectral bands between 2.761 and 1172.745 μm. Navigation through the hyperlinks enables access to this table. Supplementary_Data_III.csv encompasses the chemical formulas, number of unpaired valence electrons, spin multiplicities, xyz data, and SMILES strings of the PAHs carrying the additional spectra. Supplementary_data_IV.zip includes the input and output datasets along with the ML code. The code script is written in Python 3.7, and is supported by the following libraries: sklearn, json, numpy, and pandas. Supplementary_Information.pdf contains the evidence supporting the choice of the cutoff radius, as well as the figures of the count of the molecules in the dataset, the FI with changing datasets and hyperparameters, of cross-validation, and of UIE bands and emission features of four SH PAHs. Importance of three carbon skeleton fragments for bands in different intervals is also demonstrated.

Dataset related to article "MiR-146a in ALS: Contribution to Early Peripheral Nerve Degeneration and Relevance as Disease Biomarker"

Raw data supporting results of the study mentioned at title

The simulated outputs analyzed in the article: "Understanding the influences of ocean waves on Arctic sea ice simulation: a modeling study with an atmosphere-ocean-wave-sea ice coupled model"

In Ice-mass_[experiment] files, they include daily-averaged sea ice concentration and sea ice mass/area budgets. In Flux_[experiment] files, they include daily-averaged net ice surface flux, net shortwave/longwave radiation at the ice surface, latent/sensible heat flux at the ice surface, conductive heat flux at the top ice layer, and ice-ocean heat flux.

supplementary atherial of article Pleistocene aquatic refuges support the east-west breakage of the Neotropical catfish Trichomycterinae (Siluriformes: Trichomycteridae) and high diversity in the Magdalena, Guiana, and Paraná-Paraguay basins

Figure S1. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to the branch consistency index (BPP); Figure S2. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to age for clades, as well as the margin of error demonstrated in node bars; Figure S3. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Maximum Likelihood with values above each branch correspond to the branch consistency index (ML bootstrap); Table S1: Sequences used in the present study with their respective locations, references, haplotypes, and clades according to the phylogenetic tree in figure 2; Table S2: Type locality of the species nominally allocated to Trichomycterus and of the type species of the nine genera of Trichomycterinae. Type species in asterisk.; Table S3A: Table with percentages of K2P pairwise genetic distances between the subclades of Trichomycterus sensu stricto. Values in diagonal (below, dark grey) correspond to the genetic distance between clades by category. Values above (above, blue) refer to the respective standard errors. Bold values on the diagonal refer to the intraclade distance (1 to 31, as referenced in Table S1 and S3C); Table S3B: Genetic divergence range, by category, and occurrence within subclades. genera and subfamily; Table S3C: List of Alphabetical clade code and respective genus/species and numerical subclade code with respective species.

Repositiry for the article: "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain Mbebi & Zoran Nikoloski

This is the repository for the manuscript "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain J. Mbebi & Zoran Nikoloski. Organisation <ol> <li>The folder Codes contains the following R scripts with the K-folds cross-validation option to learn the hyperparameters:</li> </ol> <ul> <li>Mixed_L1L21_GRN.R which computes L1L21-solution</li> <li>Mixed_L1L21G_GRN.R which computes L1L21G-solution</li> <li>Mixed_L2L21_GRN.R which computes L2L21-solution</li> <li>Mixed_L2L21G_GRN.R which computes L2L21G-solution</li> <li>L1L21_Dream5_Scerevisiae_example_run.R is an example run using the L1L21-solution with S. cerevisiae data (Network 4 in DREAM5 challenge) All files needed to successfully run "L1L21_Dream5_Scerevisiae_example_run" are locaded in the folder Codes.</li> </ul> 2. The folder Figures contains all figures in the manuscript. 3. The folder Inferred-networks contains all network objects for each dataset and each inference methods in the comparative analysis. Dependencies and required packages The following packages are required for the contending approaches in the comparative analysis: "devtools", "foreach", "plyr", "glmnet" and "randomForest". GENIE3 The GENIE3 package can be installed from: <a href="http://bioconductor.org/packages/release/bioc/html/GENIE3.html">http://bioconductor.org/packages/release/bioc/html/GENIE3.html</a> TIGRESS The TIGRESS repository can be obtained from: <a href="https://github.com/jpvert/tigress">https://github.com/jpvert/tigress</a> ENNET The ENNET repository can be obtained from: <a href="https://github.com/slawekj/ennet">https://github.com/slawekj/ennet</a> PLSNET The Matlab source code of PLSNET can be obtained from: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17</a> PORTIA The PORTIA repository can be obtained from: <a href="https://github.com/AntoinePassemiers/PORTIA">https://github.com/AntoinePassemiers/PORTIA</a> D3GRN The Matlab source code of D3GRN can be obtained from: <a href="https://github.com/chenxofhit/D3GRN">https://github.com/chenxofhit/D3GRN</a> Fused-LASSO The fused-LASSO repository can be obtained from: <a href="https://github.com/omranian/inference-of-GRN-using-Fused-LASSO">https://github.com/omranian/inference-of-GRN-using-Fused-LASSO</a> ANOVerence Because of some technical issues (e.g code's accessibility: <a href="http://www2.bio.ifi.lmu.de/%CB%9Ckueffner/anova.tar.gz">http://www2.bio.ifi.lmu.de/&tilde;kueffner/anova.tar.gz</a>), we were not able to reproduce ANOVerence results and used the inferred network from DREAM5 challenge instead. 4. Although the codes here were tested on Fedora 29 (Workstation Edition) using R (version 4.2.2), they can run under any Linux or Windows OS distributions, as long as all the required packages are compatible with the desired R version.

Data for article "Waterborne virus transport and risk assessment in Lake Geneva under climate change"

Radiation_2019_Aigle contains the daily global radiation measurement data at Station Aigle for the year of 2019. Radiation_yearly contains the historical yearly mean global radiation measurement data at Station Aigle. Virus concentration_measurement contains sewage virus measurement data. Code_and_simulation_files contain files used for hydrodynamic and water quality simulations as well as risk assessment.

Results of article : "Prospective European District Heating Scenarios based on Geographical Analysis"

Results of the paper "Prospective European District Heating scenarios based on geographical analysis". Three scenarios are generated : Ambitious, Circular, and Conservative. For each scenario, there is a gpkg file and an excel file. The gpkg file is the whole dataset of inputs and results, each row being a European city. The excel summarizes the results for each EU27+UK country.

Data set related to the article: "The Role of BPIFB4 in Immune System and Cardiovascular Disease: The Lesson from Centenarians."

Abstract: Recent discoveries have shed light on the participation of the immune system in the physio pathology of the car- diovascular system underpinning the importance of keeping the balance of the first to preserve the latter. Aging, along with other risk factors, can challenge such balance triggering the onset of cardiovascular diseases. Among several mediators ensuring the proper cross-talk between the two systems, bactericidal/permeability- increasing fold-containing family B member 4 (BPIFB4) has been shown to have a pivotal role, also by sustaining important signals such as eNOS and PKC-alpha. In addition, the Longevity-associated variant (LAV), which is an haplotype allele in BPIFB4 characterized by 4 missense polymorphisms, enriched in homozygosity in Long Living Individuals (LLIs), has been shown to be efficient, if admin- istered systemically through gene therapy, in improving many aspects of cardiovascular diseases (CVDs). This occurs mainly through a fine immune system remodeling across: 1) a M2 macrophage polarizing effect, 2) a favorable redistri- bution of the circulating monocyte cell subsets and 3) the reduction of T-cell activation. Furthermore, LAV-BPIFB4 treat- ment induced a desirable recovery of the inflammatory balance by mitigating the pro-inflammatory factor levels and enhancing the anti-inflammatory boost through a mechanism that is partially dependent on SDF-1/CXCR4 axis. Importantly, the remarkable effects of LAV-BPIFB4 treatment, which translates in increased BPIFB4 circulating levels, mirror what occurs in long-living individuals (LLIs) in whom the high circulating levels of BPIFB4 are protective from age-related and CVDs and emphasize the reason why LLIs are considered a model of successful aging. Here, we review the mechanisms by which LAV-BPIFB4 exerts its immunomodulatory activity in improving the cardiovascular-immune system dialogue that might strengthen its role as a key mediator in CVDs.

raw characterization data for the article "Synthesis of Propargyl Silanes from Terminal Alkynes via a Migratory Sonogashira Reaction"

Raw NMR, IR and MS  data  for the article "Synthesis of Propargyl Silanes from Terminal Alkynes via a Mi-gratory Sonogashira Reaction" published in Chemical Communications, DOI:  <a href="https://doi.org/10.1039/D3CC01847D">https://doi.org/10.1039/D3CC01847D</a> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification"

Data needed to reproduce the figures of <a href="https://arxiv.org/abs/2305.05881">https://arxiv.org/abs/2305.05881</a> and a simple code example of a quantum-convex-classical neural network used to train a sine versus cosine classification problem.

Ptatin2D : dataset for run simulations presented in the article Slab pull driven South China Sea opening implies a Mesozoic Proto South China Sea

Overview of pTatin2D pTatin2D is a software package designed for studying long time-scale processes relevant to geodynamics. The original motivation for this development was to provide the community with an open-source toolkit capable of studying high-resolution, two-dimensional models of lithospheric deformation. Functionality <ul> <li>mixed finite elements (Q2-P1_disc) for the Stokes problem</li> <li>material points for tracking Lagrangian state and history variables</li> <li>energy equation solved with Q1 elements + SUPG</li> <li>ALE formulations (with a variety of remeshing solutions)</li> <li>extensible rheology components (currently supports: iso-viscous, Frank-Kamenetskii, Arrhenius, power-law, von Mises, Drucker Prager)</li> <li>full support for spatio-temporal Dirichlet and non-zero Neumann boundary conditions</li> <li>coupling with landscape evolution models</li> <li>full support for Newton and Picard non-linear solvers</li> <li>massively parallel implementation</li> </ul> pTatin2D leverages functionality from <a href="http://www.mcs.anl.gov/petsc">PETSc</a> Requirements <ul> <li>PETSc (only support for version 3.2)</li> </ul>

raw data for the article "Copper(I)-BOX Catalyzed Asymmetric 3-Component Reaction for the Synthesis of Trifluoromethylated Propargylic Ethers and Anilines"

Raw NMR, HPLC, IR and MS  data  for the article "Copper(I)-BOX Catalyzed Asymmetric 3-Component Reaction for the Synthesis of Trifluoromethylated Propargylic Ethers and Anilines" published in Angewandte Chemie, DOI:  <a href="https://doi.org/10.1002/anie.202305776">https://doi.org/10.1002/anie.202305776</a>  The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

Dataset for the article "Polarizable Embedding without Artificial Boundary Polarization"

This dataset contains additional material related to the article: "Polarizable Embedding without Artificial Boundary Polarization". A preprint is freely available at https://doi.org/10.26434/chemrxiv-2023-fc0gk. See readme.md for further description.

Raw data for the article "Synthesis of Trifluoromethylated Alkenes: Hypervalent Iodine Meets High-Valent Copper"

Raw NMR, IR and MS  data  for the article "Synthesis of Trifluoromethylated Alkenes: Hypervalent Iodine Meets High-Valent Copper" published in Angewandte Chemie, DOI:  <a href="https://doi.org/10.1002/anie.202306128">https://doi.org/10.1002/anie.202306128</a> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

Raw data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization"

Raw NMR, HPLC and MS  data  for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization" published in Angewandte Chemie, DOI:  <a href="https://doi.org/10.1002/anie.202306036">https://doi.org/10.1002/anie.202306036</a>  The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

opencc-zeroJun 2023View details →

Dataset for: Do you Cite What you Tweet? Investigating the relationship between tweeting and citing research articles

This dataset was used for the work "Do you cite what you tweet? Investigating the relationship between tweeting and citing research articles", submitted to the Quantitative Science Studies Journal. The accompanying R script was used for the logistic regression model in the paper.

Datasets for the article "Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light"

The datasets include: - Circular dichroism (CD) spectra (Figure 3B). - Nano differential scanning fluorimetry (DSF) melting curves (Figure 3C). - Size-exclusion chromatography (SEC) elution profiles (Figure 3D). - Deconvoluted mass spectra (MS) (Figure 4). - Microscale thermophoresis (MST) binding curves (Figure 5A). - Yeast surface display (YSD) binding curves (Figure 5C) - UV/Visible spectra (Figure S6) - Dose-response curves derived from Western blots (WB) (Figure S12C). For more information, please read: Pham, P.N.; Zahradnik, J.; Kolarova, L.; Schneider, B.; Fuertes, G. Regulation Of IL-24/IL-20R2 Complex Formation Using Photocaged Tyrosines and UV Light. Front. Mol. Biosci. 2023, 10. doi: <a href="http://doi.org/10.3389/fmolb.2023.1214235">https://doi.org/10.3389/fmolb.2023.1214235</a>