Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Randomly Distributed Crab Burrows Enhance Groundwater Flow and Salt Transport in Creek-Marsh Systems

This dataset contains SUTRA input file and training image that used in our research paper "Randomly Distributed Crab Burrows Enhance Groundwater Flow and Salt Transport in Creek-Marsh Systems".

Data for GECCO2023 Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness"

Data for Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness" <ul> <li>instances.tar.xz contains 𝜌mnk-landscape instances</li> <li>metrics.csv contains the (C)PLOS-net metric-values</li> <li>performance.csv contains the performance of the different algorithms on each instance</li> <li>merged.csv contains the merged data from the 2 csv files above</li> </ul> Reference Arnaud Liefooghe, Gabriela Ochoa, Sébastien Verel, and Bilel Derbel. 2023. Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness. In Genetic and Evolutionary Computation Conference (GECCO ’23), July 15–19, 2023, Lisbon, Portugal. ACM, New York, NY, USA, 9 pages. <a href="https://doi.org/10.1145/3583131.3590474">https://doi.org/10.1145/3583131.3590474</a> Abstract The structure of local optima in multi-objective combinatorial optimization and their impact on algorithm performance are not yet properly understood. In this paper, we are interested in the representation of multi-objective landscapes and their multi-modality. More specifically, we revise and extend the network of Pareto local optimal solutions (PLOS-net), inspired by the well-established local optima network from single-objective optimization. We first define a compressed PLOS-net which allows us to enhance its perception while preserving the important notion of connectedness between local optima. We then study an alternative visualization of the (compressed) PLOS-net that focuses on good-quality solutions, improves the distinction between connected components in the network, and generalizes well to landscapes with more than 2 objectives. We finally define a number of network metrics that characterize the PLOS-net, some of them being strongly correlated with search performance. We visualize and experiment with small-size multi-objective nk-landscapes, and we disclose the effect of PLOS-net metrics against well-established multi-objective local search and evolutionary algorithms.

opencc-by-4.0Jun 2023View details →

Data for "Optically Enhanced Solid-State 1H NMR Spectroscopy"

Raw 1H NMR and photo-CIDNP-enhanced NMR data for "Optically Enhanced Solid-State 1H NMR Spectroscopy". A Mathematica notebook for data processing is also included.

opencc-by-4.0Jun 2023View details →

Ojeok-san Enhances Platinum Sensitivity in Ovarian Cancer by Regulating Adipocyte Paracrine IGF1 Secretion

Figure 1 Adipocytes promote platinum drug resistance in OvCa cells (A-B) The effects of Adipo-CM treatment on cell viability and apoptosis level were detected by CCK-8 and flow cytometry. (C) The expression of proliferation-related and apoptosis-related proteins was detected by western blot. (D) The IC50 values of different concentrations of cisplatin and carboplatin treatment on OvCa cells were detected by CCK-8. * p<0.05.   Figure 2 Adipocytes promote OvCa resistance to platinum drugs through paracrine secretion of IGF1 (A) The expression of IGF1 in HPAd cells was detected by western blot. (B) The concentration of IGF1 in culture media of HPAd cells was detected by ELISA. (C-D) The effects of different treatments on SKOV3 cell viability and apoptosis level were detected by CCK-8 and flow cytometry. (E) The expression of proliferation-related and apoptosis-related proteins was detected by western blot. (F) The IC50 values of different concentrations of cisplatin and carboplatin treatment on SKOV3 cells were detected by CCK-8. *VS oe-NC+DMSO, #VS oe-IGF1+DMSO, * p<0.05.   Figure 3 OJS inhibits adipocyte paracrine secretion of IGF1 to regulate OvCa progression (A-B) The expression of IGF1 in HPAd cells and cell culture supernatant was detected by western blot and ELISA, respectively. (C-D) The effects of different treatments on SKOV3 cell viability and apoptosis level were detected by CCK-8 and flow cytometry. (E) The expression of proliferation-related and apoptosis-related proteins was detected by western blot. (F) The IC50 values of different concentrations of cisplatin and carboplatin treatment on SKOV3 cells were detected by CCK-8. *VS Adipo-CM, #VS Adipo-CM2, p<0.05.   Figure 4 OJS enhances the anticancer activity of cisplatin in SKOV3 and HPAd xenograft models (A-C) Tumor growth under different treatments. (D) The effects of OJS and cisplatin on the damage and morphological changes of major organs in mice were detected by H&E staining. (E) The expression of proliferation-related and apoptosis-related proteins was detected by IHC. *VS control, #VS cisplatin, p<0.05.

opencc-zeroJun 2023View details →

Pesticide exposure enhances dominance patterns in a zooplankton community

Exposure to pesticides can profoundly alter community dynamics. It is expected that dominance patterns will be enhanced or reduced depending on whether the dominant species is less or more sensitive to the pesticide than the subdominant species. Community dynamics are, however, also determined by processes linked to population growth as well as competition at carrying capacity. Here, we used a mesocosm experiment to quantify the effect of chlorpyrifos exposure on the population dynamics of four cladoceran species (Daphnia magna, D. pulicaria, D. galeata and Scapholeberis mucronata) in mixed cultures, testing for direct effects of chlorpyrifos and indirect effects mediated by interactions with other species on timing of population growth and dominance at carrying capacity. We also quantified whether the pesticide-induced changes in community dynamics affect top-down control of phytoplankton. By adding a treatment in which we used different genotype combinations of each species, we also tested to what extent genetic composition affects community responses to pesticide exposure. Immobilization tests showed that D. magna is the least sensitive to chlorpyrifos of the tested species. Chlorpyrifos exposure first led to a reduction in the abundance of D. galeata to the benefit of D. pulicaria, and subsequently to a reduction in densities of D. pulicaria to the benefit of D. magna. This resulted in D. magna being more dominant in the pesticide than in the control treatment by the end of the experiment. There was no effect of genotypic differences on community patterns, and top-down control of phytoplankton was high in all treatments. Our results suggest that in this community dominance patterns are enhanced in line with the observed among-species differences in sensitivity to the pesticide. Our results also show that the development of the community in the pesticide treatment is a complex interaction between direct and indirect effects of the pesticide.

opencc-zeroJun 2023View details →

Sample programs of an eco-redox model for the article: Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity

Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition, and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn lead to increased energy use efficiency. Furthermore, the mutualistic division of labor and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and co-evolution of life and Earth.

opencc-by-4.0Jun 2023View details →

MGD+: An Enhanced Music Genre Dataset with Success-based Networks

This dataset is built by using data from Spotify. It provides a daily chart of the 200 most streamed songs for each country and territory it is present, as well as an aggregated global chart.  Considering that countries behave differently when it comes to musical tastes, we use chart data from global and regional markets from January 2017 to March 2022 (downloaded from CSV files), considering 68 distinct markets. We also provide information about the hit songs and artists present in the charts, such as all collaborating artists within a song (since the charts only provide the main ones) and their respective genres, which is the core of this work. MGD+ also provides data about musical collaboration, as we build collaboration networks based on artist partnerships in hit songs. Therefore, this dataset contains: <ul> <li>Genre Networks: Success-based genre collaboration networks</li> <li>Artist Networks: Success-based artist collaboration networks</li> <li>Artists: Some artist data</li> <li>Hit Songs: Hit Song data and features</li> <li>Charts: Enhanced data from Spotify Daily Top 200 Charts</li> </ul>

Enhancing Microservice Reusability in MSA through the Reusable Microservices Framework: Development, Validation, and Evaluation

The data of the paper: Enhancing Microservice Reusability in MSA  through the Reusable Microservices Framework: Development, Validation, and Evaluation

opencc-by-4.0Dec 2022View details →

Computational 3D resolution enhancement for optical coherence tomography with a narrowband visible light source

This repository contains the code and data underlying the publication "Computational 3D resolution enhancement for optical coherence tomography with a narrowband visible light source" in Biomedical Optics Express 14, 3532-3554 (2023) (doi.org/10.1364/BOE.487345). The reader is free to use the scripts and data in this depository, as long as the manuscript is correctly cited in their work. For further questions, please contact the corresponding author.  Description of the code and datasets Table 1 describes all the Matlab and Python scripts in this depository. Table 2 describes the datasets. The input datasets are the phase corrected datasets, as the raw data is large in size and phase correction using a coverslip as reference is rather straightforward. Processed datasets are also added to the repository to allow for running only a limited number of scripts, or to obtain for example the aberration corrected data without the need to use python. Note that the simulation input data (input_simulations_pointscatters_SLDshape_98zf_noise75.mat) is generated with random noise, so if this is overwritten de results may slightly vary. Also the aberration correction is done with random apertures, so the processed aberration corrected data (exp_pointscat_image_MIAA_ISAM_CAO.mat and exp_leaf_image_MIAA_ISAM_CAO.mat) will also slightly change if the aberration correction script is run anew. The current processed datasets are used as basis for the figures in the publication. For details on the implementation we refer to the publication. <table> <caption>Table 1: The Matlab and Python scripts with their description</caption> <tbody> <tr> <td>Script name</td> <td>Description</td> </tr> <tr> <td>MIAA_ISAM_processing.m</td> <td>This scripts performs the DFT, RFIAA and MIAA processing of the phase-corrected data that can be loaded from the datasets. Afterwards it also applies ISAM on the DFT and MIAA data and plots the results in a figure (via the scripts plot_figure3, plot_figure5 and plot_simulationdatafigure).</td> </tr> <tr> <td>resolution_analysis_figure4.m</td> <td>This figure loads the data from the point scatterers (absolute amplitude data), seeks the point scatterrers and fits them to obtain the resolution data. Finally it plots figure 4 of the publication.</td> </tr> <tr> <td>fiaa_oct_c1.m, oct_iaa_c1.m, rec_fiaa_oct_c1.m, rfiaa_oct_c1.m </td> <td>These four functions are used to apply fast IAA and MIAA. See script MIAA_ISAM_processing.m for their usage.</td> </tr> <tr> <td>viridis.m, morgenstemning.m</td> <td>These scripts define the colormaps for the figures.</td> </tr> <tr> <td>plot_figure3.m, plot_figure5.m, plot_simulationdatafigure.m</td> <td>These scripts are used to plot the figures 3 and 5 and a figure with simulation data. These scripts are executed at the end of script MIAA_ISAM_processing.m.</td> </tr> <tr> <td>Python script: computational_adaptive_optics_script.py</td> <td>Python script that applied computational adaptive optics to obtain the data for figure 6 of the manuscript.</td> </tr> <tr> <td>Python script: zernike_functions2.py</td> <td>Python script that gives the values and carthesian derrivatives of the Zernike polynomials.</td> </tr> <tr> <td>figure6_ComputationalAdaptiveOptics.m</td> <td>Script that loads the CAO data that was saved in Python, analyzes the resolution, and plots figure 6.</td> </tr> <tr> <td>Python script: OCTsimulations_3D_script2.py</td> <td>Python script simulates OCT data, adds noise and saves it as .mat file for use in the matlab script above.</td> </tr> <tr> <td>Python script: OCTsimulations2.py</td> <td>Module that contains a python class that can be used to simulate 3D OCT datasets based on a Gaussian beam.</td> </tr> <tr> <td>Matlab toolbox DIPimage 2.9.zip</td> <td>Dipimage is used in the scripts. The toolbox can be downloaded online or this zip can be used.</td> </tr> </tbody> </table> <table> <caption>The datasets in this Zenodo repository</caption> <tbody> <tr> <td>Name</td> <td>Description</td> </tr> <tr> <td>input_leafdisc_phasecorrected.mat</td> <td>Phase corrected input image of the leaf disc (used in figure 5).</td> </tr> <tr> <td>input_TiO2gelatin_004_phasecorrected.mat</td> <td>Phase corrected input image of the TiO2 in gelatin sample.</td> </tr> <tr> <td>input_simulations_pointscatters_SLDshape_98zf_noise75</td> <td>Input simulation data that, once processed, is used in figure 4.</td> </tr> <tr> <td> exp_pointscat_image_DFT.mat exp_pointscat_image_DFT_ISAM.mat exp_pointscat_image_RFIAA.mat exp_pointscat_image_MIAA_ISAM.mat exp_pointscat_image_MIAA_ISAM_CAO.mat </td> <td>Processed experimental amplitude data for the TiO2 point scattering sample with respectively DFT, DFT+ISAM, RFIAA, MIAA+ISAM and MIAA+ISAM+CAO. These datasets are used for fitting in figure 4 (except for CAO), and MIAA_ISAM and MIAA_ISAM_CAO are used for figure 6.</td> </tr> <tr> <td> simu_pointscat_image_DFT.mat simu_pointscat_image_RFIAA.mat simu_pointscat_image_DFT_ISAM.mat simu_pointscat_image_MIAA_ISAM.mat </td> <td>Processed amplitude data from the simulation dataset, which is used in the script for figure 4 for the resolution analysis.</td> </tr> <tr> <td> exp_leaf_image_MIAA_ISAM.mat exp_leaf_image_MIAA_ISAM_CAO.mat </td> <td>Processed amplitude data from the leaf sample, with and without aberration correction which is used to produce figure 6.</td> </tr> <tr> <td> exp_leaf_zernike_coefficients_CAO_normal_wmaf.mat exp_pointscat_zernike_coefficients_CAO_normal_wmaf.mat </td> <td>Estimated Zernike coefficients and the weighted moving average of them that is used for the computational aberration correction. Some of this data is plotted in Figure 6 of the manuscript.</td> </tr> <tr> <td>input_zernike_modes.mat</td> <td>The reference Zernike modes corresponding to the data that is loaded to give the modes the proper name.</td> </tr> <tr> <td> exp_pointscat_MIAA_ISAM_complex.mat exp_leaf_MIAA_ISAM_complex </td> <td>Complex MIAA+ISAM processed data that is used as input for the computational aberration correction. </td> </tr> </tbody> </table>

opencc-zeroJul 2023View details →

Enhancing algebraic equation solving in upper elementary and middle school students using an algebra balance model

This study investigates the effectiveness of Level I, the first seven lessons, of the Hands-On Equations balance model in improving the equation-solving skills of upper elementary and middle school students. Fourth-grade (n = 123) and eighth-grade (n = 105) students from eleven classes in the United States participated in this study. A pretest-to-posttest design was used to evaluate the performance of the students on six algebraic equations, including three equations with the unknown on both sides of the equal sign. The students were provided with a six-question pretest prior to classroom instruction on the system, a posttest following Lesson 6 using the manipulatives, and a posttest following Lesson 7 without the manipulatives. Students were allowed 15 minutes for each of the tests. Each question answered correctly was given 1 point, regardless of the difficulty level of the question. Although the question paper had a field to enter the check for each problem, only the value for x was used to determine if the problem was answered correctly. The study sought to measure the effect of the program on the 4th grade, 8th grade rural, and 8th grade suburban groups. It also sought to compare the 4th grade results to an 8th grade benchmark. The data set includes the testing instrument, the pre- and post-testing data for each class, as well as an item analysis for the three groups.

Functional dissection of human cardiac enhancers and non-coding de novo variants in congenital heart disease

This is the CHD MPRA motif analysis input file. Please see the detail in : https://github.com/pulab/CHD_DNVs/tree/main/MPRA-Enhancer/CHD_MPRA_project/CHD_MPRA_library

opencc-zeroJul 2023View details →

Data for: The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling

Mutations in the tyrosine phosphatase SHP2 are associated with various human diseases. Most of these mutations increase the basal catalytic activity of SHP2 by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, several other disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, molecular dynamics simulations, and cellular assays. We show that, while several of these mutants alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also alters ligand-binding specificity. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

opencc-zeroJul 2023View details →

Data for: Russian honey bee genotype identification through enhanced marker panel set

Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as novel loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.

Enhancing stock price data analysis through variants of principal component analysis

The dataset used in the research titled "Enhancing stock price data analysis through variants of principal component analysis". It includes the daily closing prices of top 100 stocks in S&P500 from 29th March 2020 to 28th March 2023.

Discovery of enhanced lattice dynamics in a single-layered hybrid perovskite

This repository presents the raw data for the paper "Discovery of enhanced lattice dynamics in a single-layered hybrid perovskite", published as an open-access article in Science Advances at <a href="https://www.science.org/doi/10.1126/sciadv.adg4417">https://www.science.org/doi/10.1126/sciadv.adg4417</a>. Data presented in the Supplementary Materials will be provided upon request. For such requests or general questions regarding the paper, please contact Zhuquan Zhang (<a href="mailto:zhuquan@mit.edu">zhuquan@mit.edu</a>), Keith Nelson (<a href="mailto:kanelson@mit.edu">kanelson@mit.edu</a>), or Edoardo Baldini (<a href="mailto:edoardo.baldini@austin.utexas.edu">edoardo.baldini@austin.utexas.edu</a>).

opencc-by-4.0Oct 2022View details →

Data supplement for "Molecular motors enhance microtubule lattice plasticity" Lecompte, William; John, Karin

This dataset contains the data and source files for figures 2 (a-e), 3(a-d), 4(b,c,e) and Supplementary figures 5, 7(a-e), 8 and 9(a-c) in the following publication:    W. Lecompte and K. John   "Molecular motors enhance microtubule lattice plasticity"   published in 2023 in PRX Life (ArXiv https://arxiv.org/abs/2209.09161)   Please follow the instructions given in 'Readme.txt'.

Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction

Supplementary data 1 - Reconstructed  genome-scale metabolic networks from MAGs and Hosts Supplementary data 2 - Plant growth-promoting traits among members of the minimal community   Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an in-silico approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

Data & R Code for "Enhanced long-term memory and increased mushroom body plasticity in Heliconius butterflies"

This ZIP file contains the data and R code used to analyse it for the paper "Enhanced long-term memory and increased mushroom body plasticity in Heliconius butterflies". Behavioural and neuroanatomical data are in separate folders.

Human genome assemblies enhanced by LOCLA

This is a data repository for the genome assemblies of three human samples enhanced by LOCLA (DOI: 10.5281/zenodo.8280853 ). LOCLA is a novel genome assembly optimization tool, LOCLA, that iteratively improves the quality of an assembly by locating sequencing reads on partially assembled scaffolds and thus enable gap filling and further scaffolding.  The three human genome assemblies and the assembly statistics are compressed into one single zip file. File names are explained as follows: <ol> <li>LLD0021C_locla.fasta : Whole genome assembly of a Taiwanese male individual generated by LOCLA</li> <li>LLD0021C_locla_quality.txt : Assembly statistics of LLD0021C_locla.fasta</li> <li>chm13_locla.fasta : Whole genome assembly of the CHM13 cell line generated by LOCLA</li> <li>chm13_locla_quality.txt : Assembly statistics of chm13_locla.fasta</li> <li>hg002_gma_locla.fasta : Whole genome assembly of the HG002 sample generated by LOCLA </li> <li>hg002_gma_locla_quality.txt : Assembly statistics of hg002_gma_locla.fasta</li> </ol>

Enhanced Gas Adsorption Kinetics in Supraparticle-based MOF Materials

This is the raw data for the manuscript: Enhanced Gas Adsorption Kinetics in Supraparticle-based MOF Materials, publlished in Advanced Materials. A read me file containing all descriptions can be found in the main folder of the zip file All data are sorted according to their appearance in the figures of the main manuscript