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10,735 results for “dependence”
Supporting transcriptomic data and code for: "Rapid and dose-dependent Natural Killer (NK) cell modulation and cytokine correlations after human rVSV-ZEBOV Ebolavirus vaccination"
<p>The counts_NK.csv file contains gene expression data (counts) for genes in the Ion Ampliseq human Gene expression kit panel. Data were obtained from whole blood RNA. Subjects were vaccinated with a high dose of the rVSV-ZEBOV vaccine against Ebola virus disease in the Geneva clinical trial.</p> <p>The Descriptive_Table_NK_2.csv contains descriptive data of the subjects for differential expression analysis.</p> <p>The NK_analysis_code.R file contains the code used for analysis.</p>
Closed-loop auditory stimulation targeting alpha and theta oscillations during REM sleep induces phase-dependent power and frequency changes
<p>This repository contains raw data, sleep scoring, and data to create the figures for the paper:</p> <p><strong>"Closed-loop auditory stimulation targeting alpha and theta oscillations during REM sleep induces phase-dependent power and frequency changes"</strong></p> <p>by Valeria Jaramillo, Henry Hebron, Sara Wong, Giuseppe Atzori, Ullrich Bartsch, Derk-Jan Dijk*, Ines R. Violante* (* contributed equally).</p> <p>Journal article has been published in SLEEP and can be found here: <a href="https://doi.org/10.1093/sleep/zsae193">https://doi.org/10.1093/sleep/zsae193</a></p> <p>Code can be found here: <a href="https://gitlab.surrey.ac.uk/nemo/RSN">https://gitlab.surrey.ac.uk/nemo/RSN</a></p> <p>Please cite as indicated under 'Citation' on this page.</p> <p>More information on the datafiles can be found in the README.</p>
Dataset for Rate and Pressure Dependence of Dilatancy and Fault Strength in Partially-Drained Laboratory Fault Zones
<p>The datasets for Affinito et al., 2024 manuscript. Each experiment is was collected on a 24-bit recorder and 16 channels for hydromechanical data. The purpose of these experiments was to document the transition in fault drainage state as a fuction of shearing rate. Samples were prepared from cores collected at the US-DOE Utah FORGE well 16A.</p>
Weekly plots of Great Britain's half-hourly electrical system weather dependent generation, net imports and overall demand from 2008-11-10
<p>Plots that show the electrical system transition of Great Britain, they were created to form the individual frames for a video of the transition.</p>
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
<p>Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. <em>et al.</em> Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. <em>Nat Neurosci</em> (2024). https://doi.org/10.1038/s41593-024-01773-6</p>
Size-dependent effects of oxo-degradable plastic contamination on soil quality and Zea mays L. performance
<p><span>Agricultural plastic mulch films represent a significant source of microplastic contamination in soils, raising concerns about soil health and food security. Oxo-degradable plastics (ODPs) have emerged as a potentially more eco-friendly alternative to conventional plastic mulch films, however, uncertainty remains around the degradation rate of ODPs in soil and their impacts on soil quality and crop health. Using a controlled mesocosm experiment, we evaluated the behaviour and impact of different concentrations of oxo-biodegradable macro- (>10 mm) or micro-plastic (<5 mm) (0.01, 0.1, 1, and 10% w/w) on the performance of <em>Zea mays</em> L. grown in an agricultural soil over a 6-week period. Contrary to expectation, no major fragmentation or degradation of ODP was observed during the experimental period, however, FTIR revealed the formation of carbonyl groups indicative of oxidation. Overall, our results showed that typical levels of plastic contamination (0.01% w/w) had very little effect on soil physicochemical properties, microbial activity or plant performance. However, higher levels of plastic contamination resulted in significant changes in soil pH, EC, NO<sub>3</sub><sup>-</sup>, bulk density, and soil moisture. At extreme plastic loading rates (10% Can you write w/w), both micro- and macro-sized ODPs caused significant reductions in plant height and foliar chlorophyll content, with microplastic treatments showing consistently greater effects than macroplastics. None of the plastic loading rates had an effect on shoot and root biomass or soil NH<sub>4</sub><sup>+</sup> and P concentrations or microbial community structure in comparison to the unamended controls. Our findings indicate that at realistic field concentrations, ODPs are likely to have little effect on agroecosystem functioning but that they may persist in soil for long periods of time leading to their progressive accumulation in agricultural soils if used over repeated cropping cycles. Further research is needed to evaluate the longer-term impacts of ODPs on soil quality and crop health under field conditions.</span></p>
TMEM206 contributes to cancer hallmark functions in colorectal cancer cells and is regulated by p53 in a p21-dependent manner
<p><span>Acid-induced ion flux plays a role in pathologies where tissue acidification is prevalent, including cancer. In 2019, TMEM206 was identified as the molecular component of acid-induced chloride flux. Localizing to the plasma membrane, TMEM206 contributes to cellular processes like acid-induced cell death. Since over 50% of human cancers carry loss of function mutations in the p53 gene, we aimed to analyze how TMEM206 is regulated by p53 and its role in cancer hallmark function and acid-induced cell death in HCT116 colorectal cancer (CRC) cells. We generated p53-deficient HCT116 cells and assessed TMEM206-mediated Cl<sup>-</sup> currents and transcriptional regulation using the patch-clamp and a dual-luciferase reporter assay, respectively. To investigate the contribution of TMEM206 to cancer hallmark functions we performed migration and metabolic activity assays. The role of TMEM206 in p53-mediated acid-induced cell death has been assessed with cell death assays. TMEM206 mRNA level is significantly elevated in human primary CRC tumors. TMEM206 knockout increased acid-induced cell death and reduced proliferation and migration, indicating a role for TMEM206 in these cancer hallmark functions. Furthermore, we observed increased TMEM206 mRNA levels and currents in HCT116 p53 knockout cells. This phenotype can be rescued by transient overexpression of p53, but not by overexpression of dysfunctional p53. In addition, our data suggests that TMEM206 may mediate cancer hallmark functions within p53-associated pathways. TMEM206 promoter activity is not altered by p53 overexpression. Conversely, knockout of p21, a major target gene of p53, increased TMEM206-mediated currents suggesting expression control of TMEM206 by p21 downstream signaling. Our results show that in colorectal cancer cells, TMEM206 expression is elevated, contributes to cancer hallmark functions and its regulation is dependent on p53 through a p21-dependent mechanism.</span></p>
A Nu Supersymmetric Anomaly-free Atlas: anomaly-free, flavour-dependent U(1) charge assignments for the Minimally Supersymmetric Standard Model plus three Standard Model-singlet superfields
<p>We present lists of anomaly-free charge assignments up to a maximum magnitude charge Qmax=10 for the chiral fermionic content of the MSSM plus 3 right-handed neutrinos. </p> <p>Due to the large number of solutions, we compress the list into the file MSSMnuRcharges_Qmax10.gz. Please note that the unzipped file is approximately 130GB in size. We additionally include a smaller file, MSSMnuRcharges_Qmax4, containing the subset of anomaly-free charge assignments up to a maximum magnitude charge Qmax=4.</p> <p>The files searchU1MSSM.cpp and searchU1MSSM.h contain C++ files (in the 2014 standard) to produce the solutions. runsearch.sh is a bash script that compiles the programs and then runs it for a sample set of inputs.</p> <p>We provide Mathematica notebooks Analytic_solution_generator.nb and Analytic_Checks.nb which respectively provide the parametrisation of the analytic solution and checks thereof.</p> <p>The files beginning 'filter' contain example programs that read in each line in the solution list, apply a filter and print only the solutions satisfying the conditions of that filter. runfilter.sh is a bash script that compiles the filters and then runs a single filter as an example.</p> <p>These data and programs are based on this paper: https://arxiv.org/abs/2107.07926.</p>
Dataset: Time-dependent source apportionment of submicron organic aerosol for a rural site in an alpine valley using a rolling positive matrix factorisation (PMF) window
<p>Uploaded igor pxp files are the data to generate all figures of the results from our publication in Atmospheric Chemistry and Physics with the name of <em>"Time dependent source apportionment of submicron organic aerosol for a rural site in an alpine valley using a rolling PMF window"</em> by Chen et al. (2021).</p> <p>This study deployed a novel and advanced source apportionment technique on a dataset measured in Magadino. Rolling PMF allows retrieving more realistic, time-dependent and detailed information of the organic aerosol sources. This work highlights the strength of the rolling PMF mechanism by comparing it with the results derived from conventional seasonal PMF. Overall, this comprehensive interpretation of chemical speciation monitor (ACSM) data could be a role model for similar analyses.</p>
Cyclin-Dependent Kinase-Like 5 (CDKL5); A Target Enabling Package
<p>The protein kinase CDKL5 is best known for harbouring loss of function mutations that cause a variant of Rett syndrome, CDKL5 deficiency disorder, that predisposes to seizures and mental retardation. Recent kinome-wide screening has identified CDKL5 as a therapeutic target to ameliorate acute kidney injury, which is a common complication of hospitalisation that can lead to chronic kidney disease. There are currently no proven treatments. We prepared recombinant proteins for the kinase domains of CDKL1, CDKL2, CDKL3 and CDKL5 and solved the structures of these kinases in complex with identified inhibitors at resolutions from 1.5 to 2.4 Å. Overall, the structures capture the kinases with both active and inactive conformations and provide a model to explain the effects of CDKL5 mutation. An <em>in vitro</em> kinase assay showed the importance of a C-terminal αJ helix for the activity of CDKL2 and CDKL3, but not CDKL1 and CDKL5. Functional analyses of the single orthologue in C. elegans CDKL-1 also suggested that CDKL proteins can limit cilia length, which could potentially contribute to the neurological defects in CDKL5 deficiency syndrome. AST-487 and ASC67 present inhibitors of CDKL5 that could be developed for treating acute kidney injury. However, future work is needed to improve selectivity in this drug development.</p>
Sparsification of AP firing in adult-born hippocampal granule cells via voltage-dependent alpha5-GABAA receptors
<p>The ZIP file consists of folders, containing RAW data used for analysis and used to prepare the Figures 1-6 of the paper published in Cell Reports 2021, with the title mentioned above.</p> <p>All recordings were made from acute hippocampal brain slices, obtained from adult C57BL6 mice. Whole-cell voltage-clamp and current-clamp recordings of mature and adult-born young hippocampal granule cells were performed as outlined in methods and recordings were digitized using a power1401 interface from CED (Cambridge Electronic Design, UK), and saved to file using the CFS library support from CED. The contents of the different files is described in File_Description.pdf.</p>
Protection from radiation-induced neuroanatomical deficits by CCL2-deficiency is dependent on sex
<p>This project investigated the impact of Ccl2 genotype status (+/+, +/-, -/-) on the brain structure changes induced by cranial radiation. Mn-enhanced MR images were acquired at P14, P23, P42, P63 and P98. Radiation (7-Gy) was delivered on P16 to the whole head, with a lead shield used to limit dose to the rest of the body. Further details are available in the manuscript.</p> <p>For the image processing, the registration was accomplished using the pydpiper toolkit (version 2.0.9), available on GitHub (https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.9). A two-level registration was used. Key elements of that registration output are provided in this data posting.</p>
Age-dependent extreme event exposure - data accompanying journal publication
<p>This data set contains the essential files used as input for the analysis, intermediate files produced during the analysis, and the key output fields. The code of the analysis is available here: https://github.com/VUB-HYDR/2021_Thiery_etal_Science</p> <p> </p> <p>Input fields:</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/isimip.zip">isimip.zip</a>: Postprocessed ISIMIP2b simulation output. This data set is very similar to the data presented in Lange et al. (2020 Earth's Future) but includes selected additional impact models and scenarios (notably RCP8.5). This data set also includes the gridded population data.</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/GMT_50pc_manualoutput_4pathways.xlsx">GMT_50pc_manualoutput_4pathways.xlsx</a>: Global mean temperature anomaly trajectories from the IPCC SR15</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/wcde_data.xlsx">wcde_data.xlsx</a>: postprocessed cohort size data originally obtained from the Wittgenstein Centre Human Capital Data Explorer.</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/WPP2019_MORT_F16_1_LIFE_EXPECTANCY_BY_AGE_BOTH_SEXES.xlsx">WPP2019_MORT_F16_1_LIFE_EXPECTANCY_BY_AGE_BOTH_SEXES.xlsx</a>: Postprocessed life expectancy data originally obtained from the UNited Nations World Population Programme</p> <p> </p> <p>Intermediate files *only use if you're interested in reproducing the results*:</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/workspaces.zip">workspaces.zip</a>: Postprocessed ISIMIP2b simulation output. These matlab workspaces contain data on land area annually exposed to extreme events which is stored in a format designed to speed up the analysis.</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_isimip.mat">mw_isimip.mat</a>: ISIMIP2 simulations metadata (e.g. model, gcm and rcp name per simulation)</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_countries.mat">mw_countries.mat</a>: information on the countries used in the analysis (e.g. border polygon coordinates)</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_exposure.mat">mw_exposure.mat</a>: age-dependent exposure computed from the ISIMIP and population data</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_exposure_pic.mat">mw_exposure_pic.mat</a>: pre-industrial control age-dependent exposure computed from the ISIMIP and population data</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_exposure_pic_coldwaves.mat">mw_exposure_pic_coldwaves.mat</a>: pre-industrial control age-dependent exposure to coldwaves computed from the ISIMIP and population data</p> <p> </p> <p> </p> <p>Output of the analysis:</p> <p>- <a href="https://zenodo.org/api/files/9b674428-38e0-4395-a1c0-61b23e9ce3dc/mw_output.mat">mw_output.mat</a>: Matlab workspace containing all variables produced during the analysis presented in thepaper. Use this file if you wish to look up certain numbers or want to use the study results for further analysis.</p> <p> </p> <p> </p>
Supplementary material for "Productivity drives the dynamics of a red kite source population that depends on immigration"
<p>Data files, code and custom functions for all analyses and figures presented in the paper. The seven data files are provided in csv format (CMRJuvRing.csv, CMRJuvDraht.csv, CMRAdDraht.csv, CMRAdSat.csv, RingRecoveries.csv, Bruten.csv, Condition.csv). The code file (RedKiteCode.txt) and the function file (Custom_functions.txt) are space delineated text files. The code file is written for R, but some models are run in JAGS from R. The code file also contains descriptions of the data files and code for data management.</p> <p> </p>
Soybean dependence on biotic pollination decreases with latitude - Data and Computer code
<p>Release of Datasets and R scripts needed to reproduce the analyses and figures published in the article <em>'Soybean dependence on biotic pollination decreases with latitude'</em>, published in Agriculture, Ecosystems & Environment, Volume 347, 1 May 2023, 108376. <a href="https://doi.org/10.1016/j.agee.2023.108376">https://doi.org/10.1016/j.agee.2023.108376</a></p> <p><strong>Highlights</strong></p> <ul> <li>In the absence of pollinators, soybean yield decreases between 0 and ~50%.</li> <li>Variation in pollinator dependence (PD) was found to be structured latitudinally.</li> <li>PD decreases at high latitudes due to an apparently higher incidence of autogamy.</li> <li>Temperature and photoperiod could play an important role in determining PD.</li> <li>Changes in cleistogamy and androsterility might explain the reported trends.</li> </ul> <p><strong>Abstract</strong></p> <p>Identifying large-scale patterns of variation in pollinator dependence (PD) in crops is important from both basic and applied perspectives. Evidence from wild plants indicates that this variation can be structured latitudinally. Individuals from populations at high latitudes may be more selfed and less dependent on pollinators due to higher environmental instability and overall lower temperatures, environmental conditions that may affect pollinator availability. However, whether this pattern is similarly present in crops remains unknown. Soybean (Glycine max), one of the most important crops globally, is partially self-pollinated and autogamous, exhibiting large variation in the extent of PD (from a 0 to ~50% decrease in yield in the absence of animal pollination). We examined latitudinal variation in soybean's PD using data from 28 independent studies distributed along a wide latitudinal gradient (4-43 degrees). We estimated PD by comparing yields between open pollinated and pollinator-excluded plants. In the absence of pollinators, soybean yield was found to decrease by an average of ~30%. However, PD decreases abruptly at high latitudes, suggesting a relative increase in autogamous seed production. Pollinator supplementation does not seem to increase seed production at any latitude. We propose that latitudinal variation in PD in soybean may be driven by temperature and photoperiod affecting the expression of cleistogamy and androsterility. Therefore, an adaptive mating response to an unpredictable pollinator environment apparently common in wild plants can also be imprinted in highly domesticated and genetically-modified crops.</p> <p><strong>Content</strong></p> <p>The dataset consists of two files</p> <p>1 - <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5Bdata%5D%20Cunha%20et%20al.%20MS_soybean.xlsx">[data] Cunha et al. MS_soybean.xlsx</a> is an excel file with two sheets, <strong>data</strong> and <strong>data_map</strong>. These sheets contain the data used in the models defined in the R script <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5BR%20script%5D%20Cunha%20et%20al.%20MS_soybean.R">[R script] Cunha et al. MS_soybean.R</a>.</p> <ul> <li> <p>1.1 The <strong>data</strong> sheet contains the variables:</p> <ul> <li>Value = log_ratios</li> <li>Lat = latitude in decimal degrees</li> <li>Variable = yield component</li> <li>Treatment = treatment type for comparing pollinator dependence</li> <li>Reference_Data_owner = study ID where the data was obtained</li> <li>Site = site within the study where each field experiment was performed</li> </ul> </li> <li> <p>1.2 The <strong>data_map</strong> sheet contains information used for plotting the geographical distribution of the used studies:</p> <ul> <li>Reference_Data_owner = study ID where the data was obtained</li> <li>Country = country where the study was performed</li> <li>Province = province where the study was performed</li> <li>Locality/Farm = locality where the study was performed</li> <li>Lat = latitude in decimal degrees</li> <li>Long = longitude in decimal degrees</li> </ul> </li> </ul> <p>2 - <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5Bdata%5D%20Cunha%20et%20al.%20MS_soybean%20%5Bdate_photoperiod%5D.csv">[data] Cunha et al. MS_soybean [date_photoperiod].csv</a> is a comma-separated file that contains the information used in the R script <a href="https://github.com/NERC-CEH/Soybean-dependence-on-biotic-pollination-decreases-with-latitude/blob/main/%5BR%20script%5D%20Cunha%20et%20al.%20AGEE%20-%20gee_temp_ts_extract.R">[R script] Cunha et al. AGEE - gee_temp_ts_extract.R</a> and produces Figure S2.</p> <ul> <li> <p>2.1 The dataset contains the following variables:</p> <ul> <li>study_ID = study ID number where the data was obtained</li> <li>study_ref = study ID where the data was obtained</li> <li>latitude = latitude in decimal degrees</li> <li>longitude = longitude in decimal degrees</li> <li>date1 = date of the sowing or flowering when the experiment was done</li> <li>date2 = a second date, when available, of the sowing or flowering when the experiment was done</li> <li>event = if the date was related to the sowing of seeds or flowering of soybean.</li> </ul> </li> </ul>
Automatically Reproducing Timing-Dependent Flaky-Test Failures
<p>This artifact contains the source code for FlakeRake, a tool for automatically reproducing timing-dependent flaky-test failures. It also includes raw and processed results produced in the evaluation of FlakeRake</p> <p> </p> <p>Contents:</p> <p> </p> <p>Timing-related APIs that FlakeRake considers adding sleeps at: timing-related-apis</p> <p>Anonymized code for FlakeRake (not runnable in its anonymized state, but included for reference; we will publicly release the non-anonymized code under an open source license pending double-blind review): flakerake.tgz</p> <p>Failure messages extracted from the FlakeFlagger dataset: 10k_reruns_failures_by_test.csv.gz </p> <p>Output from running isolated reruns on each flaky test in the FlakeFlager dataset: 10k_isolated_reruns_all_results.csv.gz (all test results summarized into a CSV), 10k_isolated_reruns_failures_by_test.csv.gz (CSV including just test failures, including failure messages), 10k_isolated_reruns_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven)</p> <p>Output from running the FlakeFlagger replication study (non-isolated 10k reruns):flakeFlaggerReplResults.csv.gz (all test results summarized into a CSV), 10k_reruns_failures_by_test.csv.gz (CSV including just failures, including failure messages), flakeFlaggerRepl_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven - this file is markedly larger than the 10k isolated reruns results because we ran *all* tests in this experiment, whereas the 10k isolated rerun experiment only re-ran the tests that were known to be flaky from the FlakeFlagger dataset).</p> <p>Output from running FlakeRake on each flaky test in the FlakeFlagger dataset:</p> <p>For bisection mode: results-bis.tgz</p> <p>For one-by-one mode: results-obo.tgz</p> <p>Scripts used to execute FlakeRake using an HPC cluster: execution-scripts.tgz<br> Scripts used to execute rerun experiments using an HPC cluster: flakeFlaggerReplScripts.tgz<br> Scripts used to parse the "raw" maven test result XML files in this artifact into the CSV files contained in this artifact: parseSurefireXMLs.tgz </p> <p>Output from running FlakeRake in “reproduction” mode, attempting to reproduce each of the failures that matched the FlakeFlagger dataset (collected for bisection mode only): results-repro-bis.tgz</p> <p>Analysis of timing-dependent API calls in the failure inducing configurations that matched FlakeFlagger failures: bis-sleepyline.cause-to-matched-fail-configs-found.csv</p>
Data related to the article "Frequency-dependent impedance of nanocapacitors from electrode charge fluctuations as a probe of electrolyte dynamics"
<p>Contains input files and data used to generate the figures of the article:</p> <p>Frequency-dependent impedance of nanocapacitors from electrode charge fluctuations as a probe of electrolyte dynamics<br> (Giovanni Pireddu and Benjamin Rotenberg)</p> <p>arXiv: https://arxiv.org/abs/2206.13322</p> <p>The folder EXAMPLE_INPUT_FILES contains typical <a href="https://doi.org/10.21105/joss.02373">MetalWalls</a> (<a href="https://gitlab.com/ampere2/metalwalls">repository</a>) input files used to perform the simulations.</p> <p>The folder DATA_FIGURES contains the processed data used to plot all the figures of the paper (see below).<br> </p> <p>The 'd*' labels are used in the directory or file names to refer to the following interelectrode distances considered:<br> - 'd1' corresponds to 2.51 nm;<br> - 'd2' corresponds to 4.94 nm;<br> - 'd3' corresponds to 9.76 nm;<br> - 'd4' corresponds to 19.42 nm;</p> <p><br> Figure 1:<br> - 'Fig1_Continuum.dat': <br> - Capacitance calculated considering a continuum approximation<br> - 'Fig1_DDS.dat':<br> - Capacitance calculated considering the DDS model (three capacitors in series)<br> - 'Fig1_MD.dat':<br> - Capacitance calculated from MD simulations. Includes the capacitance of the empty capacitor.</p> <p>Figure 2:<br> Panel A<br> - 'Fig2_QACFd*.dat':<br> - Time autocorrelation function of the electrode charge fluctuations<br> Panel B<br> - 'Fig2_Qrampd*.dat':<br> - Charge profile upon a step in voltage (0 to 1 V)<br> - 'Fig2_Vramp.dat':<br> - Voltage ramp related to the charging profiles<br> Panel C<br> - 'Fig2_QACFNormd*.dat':<br> - Normalized charge autocorrelation function<br> -'Fig2_QrampNormd*.dat'<br> - Normalized charge profile</p> <p>Figure 3:<br> - 'Fig3_MDd*.dat':<br> - Real and imaginary parts of impedance as estimated from MD simulations<br> - 'Fig3_ECd*.dat'<br> - Real and imaginary parts of impedance as calculated from the equivalent circuit models</p> <p>Figure 4:<br> - 'Fig4_MDd*.dat':<br> - Magnitude of admittance as estimated from MD simulations<br> - 'Fig4_Debyed*.dat':<br> - Magnitude of admittance as calculated from the Debye relaxation model<br> Inset<br> - 'Fig4_MDTau.dat':<br> - Relaxation time estimated from MD simulations<br> - 'Fig4_TauFit.dat':<br> - Fit of the relaxation time</p>
Concentration-, Temperature- and Solvent-Dependent Self-Assembly: Merocyanine Dimerization as a Showcase Example for Obtaining Reliable Thermodynamic Data
<p><strong>Abstract:</strong> 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.</p>
Temperature-Dependent THz Properties and Emission of Organic Crystal BNA
<p>This dataset is accompanying the paper "Temperature-Dependent THz Properties and Emission of Organic Crystal BNA"</p> <p><strong>General data acquisition:</strong></p> <p>The data was acquired with a modified Menlo Tera K-15 THz-TDS, consisting of a photoconductive emitter/receiver and four off-axis-parabolic mirrors (OAP). The second and third OAP, focusing and collecting the THz, are with a longer focus length to have enough space for the cryostat (Janis ST-100), which is equipped with 3 mm z-cut quartz windows for entry and exit of the THz beam. The delay line offers delays up to 1600 ps but the range was restricted to cut out the reflections from the z-cut quartz windows. Instead of averaging with Menlo’s own software ScanControl, each single trace is read out. 10 000 traces are saved for each unique measurement condition (crystal orientation, temperature) and saved in a single HDF-5 file. HDF-5 is an efficient (binary), cross-platform data format and can be read easily by i.e. Python or Matlab.</p> <p> </p> <p><strong>The structure is as follows:</strong></p> <p><strong>raw_data </strong></p> <p>The folder raw_data contains four folders. The folder “dark” contains a single file since this is independent of crystal orientation and temperature of the cryostat. For this measurement, the THz beam was blocked but all electronics, selected delay range etc. kept the same, to measure the noise-floor of the system.</p> <p>The folder reference was captured with the cryostat incl. windows, vacuum and crystal holder in place. Even though there should be no change in the transfer function by changing the temperature (due to the large aperture of the crystal holder), we still recorded reference traces for each temperature.</p> <p>The folder “BNA_orientation_001” contains the data with the organic crystal BNA in vertical orientation (<001>).</p> <p>The folder “BNA_orientation_100” contains the data with the organic crystal BNA in horizontal orientation (<100>).</p> <p><strong>averaged_corrected_data</strong></p> <p>The folder “averaged_corrected_data” reduces the large amount of raw data due to averaging. The program “Correct@TDS” (developed in the group of Dr. Romain Peretti, Terahertz Photonics Group @ IEMN - CNRS (UMR 8520), publication in preparation), is used to fit specific correction parameters for the delay, dilatation, amplitude noise and periodic sampling. The mean data is saved for each temperature in a text file called “mean.txt”. The other output of “Correct@TDS” is diagnostic information about the correction parameters and about the standard deviation in frequency- and time-domain.</p> <p><strong>extracted_n_alpha</strong></p> <p>The folder “extracted_n_alpha” contains the refractive index, absorption coefficient and more in a single HDF-5 file, extracted by the program phoeniks (<a href="https://github.com/TimVog/phoeniks">https://github.com/TimVog/phoeniks</a>), which is developed in our group. All results for the paper are saved in the internal folder structure of the HDF-5 file (for crystal orientation and temperature).</p> <p>The folder “nelly” shows the extraction of n and alpha done with Nelly [1] (<a href="https://github.com/YaleTHz/nelly">https://github.com/YaleTHz/nelly</a>) for the vertical orientation, which was used for the supplementary document.</p> <p> </p> <p>[1] Nelly: A User-Friendly and Open-Source Implementation of Tree-Based Complex Refractive Index Analysis for Terahertz Spectroscopy</p> <p>Uriel Tayvah, Jacob A. Spies, Jens Neu, and Charles A. Schmuttenmaer</p> <p>Analytical Chemistry 2021 93 (32), 11243-11250</p> <p>DOI: 10.1021/acs.analchem.1c02132</p> <p> </p>
Dataset to: Novel aerosol diluter – Size dependent characterization down to 1 nm particle size
<p>Dataset to: Lampimäki et al. Novel aerosol diluter – Size dependent characterization down to 1 nm particle size. Journal of Aerosol Science 172 (2023) 106180, doi: <a href="https://doi.org/10.1016/j.jaerosci.2023.106180">https://doi.org/10.1016/j.jaerosci.2023.106180</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.