Find research datasets worth reusing

Supporting data for 'Feedback-based active reset of a spin qubit in silicon'

Underlying data sets of paper 'Feedback-based active reset of a spin qubit in silicon'.

Dataset for the paper "Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites", 2023, ACS Catalysis, DOI:10.1021/acscatal.3c00356

The data in this spreadsheet was used to produce the figures in the paper Authors:Mengjun Gong, Asad Mehmood, Basit Ali, Kyung-Wan Nam and Anthony Kucernak Title:Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites Journal:ACS Catalysis DOI:10.1021/acscatal.3c00356 Please cite the above reference if you wish to use this data DOI of data:10.5281/zenodo.7879881

opennotspecifiedOct 2022View details →

Figure 2 in Quantification of underwater calling and foraging activities in the African clawed frog Xenopus laevis

Figure 2. Variations of A) Vocal activity, B) Foraging activity as estimated as the number of animals captured in food baited traps and C) sex ratio of captures (number of males/ total number of individuals), during the study period, according to date and lunar cycle with points for observed values, and 95% confidence interval around the mean estimated from the best model.

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Common Blackbird weights, activity, fatty acid oxidation rates, and metabolic rates

Seasonal migration is a physiologically-demanding endeavor that animals prepare for by finding and storing energy. Species and populations vary in their tendencies to migrate, and the energetic demands of migration likely determine the degree and type of preparation that different animals undergo. Birds fuel their migratory flight using stored fat. Previous work has suggested that in addition to being energetically-dense, certain lipids like polyunsaturated fatty acids (PUFAs) may be particularly efficient fuels that are preferentially mobilized for flight or serve may additional functions, such as modulating membrane fluidity or stimulating gene expression as ligands, during long-distance migratory flight. Using a series of behavioral and metabolic experiments in a common garden setting of Common Blackbirds (Turdus merula) populations that range from being fully-migratory to partially-migratory to sedentary, we asked how migratory restlessness (Zugunruhe), weight gain, and oxidation of stearic acid (18:0), oleic acid (18:1n-9), linoleic acid (18:2n-6), and alpha linolenic acid (18:3n-3; ALA) varied with migratory mode and season. We found no population-level differences in the timing of Zugunruhe. However, before migration, a greater proportion of individuals from fully-migratory populations exhibited weight gain and migratory restlessness, as well as increased oxidation of PUFAs. After Zugunruhe, only individuals from migratory populations showed reduced PUFA oxidation. All populations showed increased oxidation of saturated fat after Zugunruhe. Our results demonstrate that certain migratory traits, like the timing of Zugunruhe based on local environmental conditions, are more similar across populations, while others, like lipid oxidation, can vary at the population-level.

opencc-zeroMay 2023View details →

data for Pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella

Contains the results of the MCMC sampling (i.e. fluxes) as well as the simulated MS measurements.

opencc-zeroMay 2023View details →

dryad32/100

Data for: Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevant GAL metabolic genes. We quantified the dose-dependent induction of the GAL1 gene encoding the central galactokinase enzyme, and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity of GAL1 induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such as Saccharomyces uvarum, contain a hyperactive GAL3 promoter, sustaining highly sensitive GAL1 expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such as S. cerevisiae Y12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such as S. cerevisiae DBVPG6044, contain an interrupted GAL3 gene, causing extremely reluctant galactose consumption, which however still is improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.

opencc-by-4.0May 2023View details →

Data from: Feeding and water temperature modulate the activity of gut microbiota in greater amberjack juveniles (Seriola dumerili)

Illumina (MiSeq v3) sequencing data for gut microbiota profiling in greater amberjack (Seriola dumerili) juveniles reared at three different water temperatures and sampled along a day cycle.

opencc-by-4.0Feb 2023View details →

Dataset: Activation of skeletal muscle is controlled by a dual-filament mechano-sensing mechanism

Steady-state and dynamic calcium dependence of force and <P2> for RLC/TNC probes in skeletal muscle. Dataset for article 10.1073/pnas.2302837120

opencc-by-4.0Mar 2023View details →

A PETase enzyme synthesised in the chloroplast of the microalga Chlamydomonas reinhardtii is active against PET and polystyrene

The list contains: 1) raw data for chromatographies: HiprepSPHP and SEC 2) raw data for UV-vis Spectrum 3) raw data for all MS/MS spectra manuscript + supplementary 4) raw data for AFM  5) report data from HPLC

opencc-by-4.0May 2023View details →

Matlab code for " Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex"

Here are the data and code supporting the findings of the paper, 'Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex.'

opencc-by-4.0May 2023View details →

Adsorbed polymer conjugates to adaptively inhibit blood coagulation activation by medical membranes

Dataset to the manuscript 'Adsorbed polymer conjugates to adaptively inhibit blood coagulation activation by medical membranes' Tina Helmecke, Dominik Hahn, André Ruland, Mikhail V. Tsurkan, Manfred F. Maitz, Carsten Werner

openJun 2023View details →

IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)

This repository contains the scRNA-Seq data (including TCR-Seq and BCR-Seq data) set used in the manuscript titled "IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)". This dataset is generated from 10x cell ranger software. In the study, we have 10 PBMC samples, from 5 MIS-C children at paired time points. T1 stands for admission time and T3 follow-up time, about 1 month post hospital discharge.

Tracking and blocking interdependencies of cellular BRAF-MEK oncokinase activities

The selective targeting of mutated kinases in cancer therapies has the potential to improve the therapeutic success and thereby the survival of patients. In the case of melanoma, the constitutively active MAP kinase pathway is targeted by combinatorial inhibition of BRAF and MEK activities. These MAPK pathway players may display patient-specific differences in the onco-kinase mutation spectrum, which needs to be considered for the design of more efficient personalized therapies. Here, we extend a bioluminescence-based kinase conformation biosensor (KinCon) to allow for live-cell tracking of interconnected kinase activity states. First, we show that common MEK1 patient mutations promote a structural rearrangement of the kinase to an opened and active conformation. This effect was reversible by binding of MEK inhibitors to mutated MEK1, as shown in biosensor assays and molecular dynamics simulations. Second, we implement a novel application of the KinCon technology for tracking the simultaneous, vertical targeting of the two functionally linked kinases BRAF and MEK1. Thus, we demonstrate that, in the presence of constitutively active BRAF-V600E, specific inhibitors of both kinases are efficient in driving MEK1 into a closed, inactive conformation state. We compare current melanoma treatments and show that combinations of BRAFi and MEKi displayed a more pronounced structural change of the drug sensor than the respective single agents, thereby identifying synergistic effects among these drug combinations. In summary, we depict the extension of the KinCon biosensor technology to systematically validate, anticipate, and personalize tailored drug arrangements using a multiplexed setup.

Auditory cortex single unit population activity during natural sound presentation -- dataset

Overview High-density multi-channel neurophysiology data were collected from primary (A1) and secondary (PEG) fields of auditory cortex of passively listening ferrets during presentation of a large natural sound library. Single unit spikes were sorted using Kilosort. This dataset includes spike times for 849 A1 units and 398 PEG units. Stimulus waveforms were transformed to log-spaced spectrograms for analysis (18 channels, 10 ms time bins). Data set includes raw sound waveforms as well and high resolution (1000 samples/sec) single-trial spike data. The authors request that any publication using this data cite the following work: https://www.biorxiv.org/content/10.1101/2022.06.10.495698v2 Version 1.1 is updated with more examples and documentation. It also includes a less-processed version of the spike data that permits reconstruction of the experimental sequence used at each recording site and single-trial responses to the repeated validation stimuli. Data format/description Preprocessed neural data are aggregated in two main files. All recordings were performed during presentation of the same natural sound library to passively listening  animals. During each experiments, stimuli were presented in a random order, and repeated validation stimuli were interleaved throughout the experiment. In the main files, data have been aligned to the same order by stimulus and averaged across repeated presentations (for the validation stimuli, which were presented 20 times during each experiment). The averaged validation data make up the first 27 seconds of each recoding block. <ul> <li>A1_NAT4_ozgf.fs100.ch18.tgz - data from 849 A1 single units and log spectrogram of stimuli aligned with spike times.  Data are aggregated across 64- or 128-channel recordings from 22 sites in 4 animals.</li> <li>PEG_NAT4_ozgf.fs100.ch18.tgz - data from 398 PEG single units and log spectrogram of stimuli aligned with spike times. Data are aggregated across 64-channel recordings from 12 sites in 2 animals.</li> </ul> Raw sound files (44100/s sampling, wav format) and spike times (1K/s sampling, in the original experimental order) are also provided in separate files. Summary data of model performance from the paper are also included. <ul> <li>wav.zip - raw wav files. As of version 2 of this repository, the wav files have been truncated to the 1-sec duration that was used in the experiments</li> <li>A1_single_sites.zip, PEG_single_sites.zip - collections of files, one per recording site, with spike times stored in the actual order of data collection (including interleaved repeated validation stimuli). These spikes have been binned at 100 Hz and sorted to have matched order across all sites in the processed files (A1_NAT4_ozgf.fs100.ch18.tgz, PEG_NAT4_ozgf.fs100.ch18.tgz, respectively).</li> <li>A1_pred_correlation.csv, PEG_pred_correation.csv - Comma-separated value file containing cross-validated prediction accuracy for each A1, PEG unit for each of the five exemplar models. The "sig_auditory" column is true for all units classified as having significant auditory responses, as classified in the publication.</li> </ul> Example scripts Python scripts included with this dataset demonstrate how to load the neural data and perform a CNN model fit. Running the scripts requires the NEMS0 python library, which is available open source at <a href="http://github.com/lbhb/NEMS0">https://github.com/lbhb/NEMS0</a>. Quick install Create and activate a new conda environment: <blockquote> conda create -n NEMS0 python=3.7 conda activate NEMS0 </blockquote> Download NEMS0: <blockquote> git clone https://github.com/lbhb/NEMS0 </blockquote> Install NEMS0: <blockquote> pip install -e NEMS0 </blockquote> Detailed instructions for installing NEMS0 are available in the Github repository (https://github.com/lbhb/NEMS0). Demo scripts Once NEMS0 is installed and the data are downloaded, move to the directory where the data and demo scripts are stored and run them in a NEMS0 environment. <ul> <li>pop_cnn_load.py - Load the A1 data and compare predictions for two neurons (Fig 3) by two population models (stage 1 fit complete). Illustrates how to load the data using Python.</li> <li>pop_cnn_fit.py - Load  a pre-fit A1 population model (stage 1) and complete stage 2 fit (refinement) for a single neuron. Illustrates use of NEMS0 for CNN model fitting.</li> <li>single_trial_demo.py - Script demonstrating how to load the single trial data for a repeated validation stimulus from one A1 neuron. Also how to compute the average population PSTH for a single validation stimulus at 1000 sec-1 sampling. Unzip A1_single_sites.zip in the director containing this script first in order for it to run correctly.</li> </ul> Funding Data collection, software development and processing were supported by funding from the NIH (R01DC014950, R01EB028155).

CMAUP: a database of collective molecular activities of useful plants

ABSTRACT: Contains information about ingredients, targets, plant-ingredient associations, and ingredient-target associations, along with relevant activity values and references. The dataset has undergone cleaning and preprocessing to ensure data quality and consistency. Instructions: Data were cleaned and duplicates were removed. Inspiration: This dataset uploaded to U-BRITE for  "DRG_DEPOT" summer 2023 team project. Acknowledgements: Xian Zeng, Peng Zhang, Yali Wang, Chu Qin, Shangying Chen, Weidong He, Lin Tao, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen CMAUP: a database of collective molecular activities of useful plants. <a href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky965/5144144">Nucleic Acids Research</a> 2019; 47(D1): D1118-D1127; PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30357356">30357356</a>; DOI: <a href="https://doi.org/10.1093/nar/gky965">doi.org/10.1093/nar/gky965</a> U-BRITE last update data: 06/15/2023

Replication Package for ESEC/FSE 2023 Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects?"

This replication package can be used for replicating results in the paper. It contains 1) a dataset of 290,255 repositories; and 2) Python scripts for training and interpreting models. The GitHub repository of the paper is available at <a href="https://github.com/mcxwx123/Sustainable_projects">https://github.com/mcxwx123/Sustainable_projects</a>. We recommend manually setup the required environment in a commodity Linux machine with at least 1 CPU Core, 8GB Memory and 100GB empty storage space. We conduct development and execute all our experiments on a Ubuntu 20.04 server with two Intel Xeon Gold CPUs, 320GB memory, and 36TB RAID 5 Storage. We use GHTorrent to restore historical states of 290,255 repositories with more than 57 commits, 4 PRs, 1 issue, 1 fork and 2 stars. The raw data of repositories (collected in their first 1,3,5 months(s)) are stored in `Replication Package/data/prodata_1.pkl`, `Replication Package/data/prodata_3.pkl`, and `Replication Package/data/prodata_5.pkl`. The contribution of features resulting from LIME model is stored in `Replication Package/data/limeres_m3_t2_k1.pkl`. `Replication Package/data/X_test_m3_t2_k1.pkl` and `Replication Package/data/y_test_m3_t2_k1.pkl` store the test dataset for the LIME model. You can run `Replication Package/fitdata.py` to get the results in Table 3 and 4, run `Replication Package/draw_compare_variable.py` to get Figure 2 and run `Replication Package/allvari_statistics.py` to get Table 5. In `Replication Package/Variable_comparison_with_different_parameter.pdf`, we show the LIME results under different parameters. In `Replication Package/sample_pros.csv`, we also provide the list of randomly selected repositories in Section 3.1.   The explanations for collecting the variables, the examples of variable effects on project sustainability, and the hyperparameter setting of the machine learning models are provided in the README.md file.

data for "Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel"

Data S1 for Manuscript Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel.

opencc-by-4.0Jul 2023View details →

Arctic Eddy activity as revealed by FESOM2

High resolution FESOM2 results used for Arctic Ocean eddy activity study, with Figure 1-5 featured in the article and Figure S1-10 included in the supplementary material.

dryad32/100

Renewable energies and biodiversity: impact of ground-mounted solar photovoltaic sites on bat activity

<ol> <li>Renewable energy is growing at a rapid pace globally, but as yet there has been little research on the effects of ground-mounted solar photovoltaic (PV) developments on bats, many species of which are threatened or protected.</li> <li>We conducted a paired study at 19 ground-mounted solar PV developments in southwest England. We used static detectors to record bat echolocation calls from boundaries (i.e., hedgerows) and central locations (open areas) at fields with solar PV development, and simultaneously at matched sites without solar PV developments (control fields). We used generalized linear mixed-effect models to assess how solar PV developments and boundary habitat affected bat activity and species richness.</li> <li>The activity of six of eight species/species groups analysed was negatively affected by solar PV panels, suggesting that loss and/or fragmentation of foraging/commuting habitat is caused by ground-mounted solar PV panels. Pipistrellus pipistrellus and Nyctalus spp. activity was lower at solar PV sites regardless of the habitat type considered. Negative impacts of solar PV panels at field boundaries were apparent for the activity of Myotis spp. and Eptesicus serotinus, and in open fields for Pipistrellus pygmaeus and Plecotus spp.</li> <li>Bat species richness was greater along field boundaries compared with open fields, but there was no effect of solar PV panels on species richness.</li> <li> Policy Implications: Ground-mounted solar PV developments have a significant negative effect on bat activity, and should be considered in appropriate planning legislation and policy. Solar PV developments should be screened in Environmental Impact Assessments for ecological impacts, and appropriate mitigation (e.g., maintaining boundaries, planting vegetation to network with surrounding foraging habitat) and monitoring should be implemented to highlight potential negative effects.</li> </ol>

opencc-zeroJul 2023View details →