Find research datasets worth reusing

W-band dataset with I/Q measurement for an AMT manuscript

The dataset contains 3 min of I/Q measurements from the W-band radar operated by TU Delft in Cabauw, the Netherlands. The data file has a binary format. The dataset was used in a publication which is currently in preparation. The archive contains the pdf file (IQ_Format.pdf) with the description of the data file content.

Accompanying data set for the manuscript "REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention"

This data set contains all experimental and theoretical data included in the manuscript " REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention", namely: RESTRICT_model: MATLAB script for completing calculations in the RESTRICT theoretical model. Figure 2: <ul> <li>Raw data from theoretical model showing contributions of individual model components, Kaff = 0.3</li> <li>Normalized data from theoretical model showing contributions of individual model components, Kaff = 0.3</li> <li>Experimental NRTI Drug Screen 180 nt TTCA 500 nM dNTP</li> </ul> Figure 3: <ul> <li>Experiment-dNTP-Concentration-Screen</li> <li>Theory-dNTP-Concentration-Screen</li> <li>Experiment-Template-Length-Screen</li> <li>Theory-Template-Length-Screen</li> <li>Experiment-Sequence-Screen</li> <li>Theory-Sequence-Screen</li> </ul> Figure 4: <ul> <li>Experimental-NRTI-Drug-Screen-90nt-TCAA-only</li> <li>Theory-TCAA90-Kaff=0point2</li> <li>Experimental-NRTI-Drug-Screen-GGCA-only</li> <li>Theory-GGCA180-Kaff=0point2</li> </ul> Figure 5: <ul> <li>GGCA-vs-TTCA-Specificity-Analysis</li> </ul>

SNMR-PP measurement - Horstwalde 2020

This data set contains raw and processed data of a prepolarized surface nuclear magnetic resonance (SNMR-PP) experiment over a water basin, which uses an alternative excitation mechanism. Different receiver loop configurations (circular - circ, figure-of-eight - foe) were installed on a fixed platform and measurements were carried out at different basin water level heights. Please unzip the archive files "data_set.zip.00*" with e.g. 7-zip (or any other zipping tool) to find a folder structure and the corresponding README file.

Fast measurement of angular velocity in air-driven flat rotors with periodical features - Supplementary Data

Supplementary Movie and  data files used for generating Figure 4 in the main text. The files are compressed pickled pandas Dataframes and can be read with: <pre><code class="language-python">import pandas as pd df = pd.read_pickle('/folder/file.xz', compression='xz')</code></pre> Along with those files there are .txt files containing the physical information of each experiment.

Groundwater and surface water quantity and quality measurement results for groundwater dependent ecosystem in Kazu leja, Latvia in 2019 and 2020

Groundwater and surface water quantity and quality measurement results and methodology of the investigations of the groundwater dependant ecosystem in Kazu leja, Latvia in 2019 and 2020 is presented. The data comprises: <ol> <li>Methodology</li> <li>Measurement site data [2_observation_sites.csv]</li> <li>Field and laboratory measurement results [3_field_and_lab_results.csv]</li> <li>Measurement uncertainty [4_measurement_uncertainity.csv]</li> <li>Automated water level, temperature, and electrical conductivity measurements [5_level_temperature_electricConductivity_loggers.csv]</li> </ol>

opencc-zeroAug 2021View details →

Beyond species richness and community composition: Using plant functional diversity to measure restoration success in jarrah forest

Aim: The importance of restoring ecosystem functions to native systems that have been degraded, damaged or destroyed is increasingly recognised. Yet few studies have measured the effect of restoration efforts on ecosystem functioning or the functional diversity (FD) that underpins it. Here we assessed change in FD of restored assemblages one to 25 years after the onset of post-mine restoration. Location: Northern Jarrah (Eucalyptus marginata Donn ex Sm.) Forest bioregion of south-western Australia. Methods: Functional richness, evenness, divergence and dispersion were derived from five plant functional traits relevant to community reassembly. Effects of three explanatory variables (i.e., age, year restoration was initiated, and time since fire) on six response variables (i.e., four FD indices, species richness, and compositional similarity to nearby reference forest) were analysed using linear mixed models for a dataset with repeated measures of plots through time (n= 810 plots), and linear models for a sub-set of one-time measures of different aged assemblages (i.e., space-for-time approach; n= 490 plots). Results: Functional evenness and functional dispersion increased with age, while functional divergence and functional richness decreased with age. Functional dispersion increased with time since fire, while functional richness decreased with time since fire. Species richness decreased with age, but at 25-years, species richness was comparable to that observed in reference forest. In contrast, similarity showed no relationship with age of restored forest, and at 25-years, similarity of restored forest to reference was low compared with similarity of reference forest to itself. Three of four FD indices had not reached those of reference jarrah forest 25-years after restoration had been initiated. Conclusions: Reassembly of FD suggests importance of environmental filtering and high functional redundancy. A longer time frame may be needed to assess FD of restored assemblages, and in the meantime, species richness is not an adequate surrogate of FD.

opencc-zeroAug 2021View details →

Yards, block groups, and vegetation cover measures

Residential yards are a significant component of urban socio-ecological systems; residential land covers 11% of the United States and is often the dominant land use within urban areas. Residential yards also play an important role in the sustainability of urban socio-ecological systems, affecting biogeochemical cycles, water, and the climate via individual- and household-level behaviors. Vegetation, such as trees and grasses, are unevenly distributed across front and back yards, and we sought to understand how similar yards are to each other when compared to their neighboring yards and neighborhoods using aerial imagery. There are many ways to measure yard similarity, and we compared several measures to account for different definitions of 'neighborness'. We examined the spatial autocorrelation of several yard vegetation characteristics in both front and backyards in Boston, MA, USA. Our study area included 1,027 Census block groups (sub-neighborhood areas) and 175,576 parcels with matched front-backyard pairings (n = 351,152 yards in total) across Boston's metropolitan area. This data package contains 1) 351,152 yard spatially-referenced yard polygons with five measures of vegetation summarized, 2) the containing block groups, and 3) and *.R script that replicates the analyses reported in Locke, D. H., Ossola, A., Minor, E., & Lin, B. B. (2021). Spatial contagion structures urban vegetation from parcel to landscape. People and Nature, 00, 1–15. <a href="https://doi.org/10.1002/pan3.10254">https://doi.org/10.1002/pan3.10254</a>

opencc-by-4.0Feb 2021View details →

Dinoponera measurements

Measurements of females and males made during the taxonomic revision of Dinoponera Roger (Hymenoptera: Formicidae: Ponerinae) species (Dias & Lattke, 2021). All measurements are expressed in millimeters.

WiFi RSS measurements in Tampere University multi-building campus, 2017

This package contains two Wi-Fi RSSI Datasets, namely TIE1 and SAH1. <ul> <li>TIE1 was collected in the Tietotalo building from Tampere University during the period of August-December 2017 and it is composed of four files: <ul> <li>TIE1_training_rss.csv - Radio map or reference dataset as a matrix with 10633 reference samples (rows) and 613 APs (columns) </li> <li>TIE1_training_coordinates.csv - Ground truth location of the 10633 reference samples (rows) as X,Y,Z and floor being the coordinates in a local system</li> <li>TIE1_test_rss.csv - Operational fingerprints as a matrix with 50 evaluation samples (rows) and 613 APs (columns) </li> <li>TIE1_test_coordinates.csv - Ground truth location of the 50 evaluation samples (rows) as X,Y,Z and floor being the coordinates in a local system</li> </ul> </li> <li>SAH1 was collected in the Sahkotalo building from Tampere University during the period of October-December 2017 and it is composed of four files: <ul> <li>SAH1_training_rss.csv - Radio map or reference dataset as a matrix with 9291 reference samples (rows) and 775 APs (columns) </li> <li>SAH1_training_coordinates.csv - Ground truth location of the 9291 reference samples (rows) as X,Y,Z and floor being the coordinates in a local system</li> <li>SAH1_test_rss.csv - Operational fingerprints as a matrix with 156 evaluation samples (rows) and 775 APs (columns) </li> <li>SAH1_test_coordinates.csv - Ground truth location of the 156 evaluation samples (rows) as X,Y,Z and floor being the coordinates in a local system</li> </ul> </li> </ul> Additional considerations: <ul> <li>All the RSSI values are stored are they were registered with a regular smartphone. In order to generate the fingerprint vectors, the non-detected APs where filled with the default bogus value +100dBm. i.e., the value +100dBm in the training and test rss files indicates that the AP was not detected. Generally, this default bogus value has been replaced with a low RSSI value in experiments, such as -100dBm, -110dBm, -150dBm or -200dBm.</li> <li>The coordinates X,Y,Z are expressed in meters in a local coordinate system. Additionally, the sequential floor identifier is also provided.</li> </ul> Please cite the source at Zenodo when using any of these two datasets: <blockquote> Lohan, E.S; Torres-Sospedra, J.; Gonzalez, A.; "WiFi RSS measurements in Tampere University multi-building campus, 2017", Zenodo, 2021. https://zenodo.org/record/5174851 https://www.doi.org/10.5281/zenodo.5174851 </blockquote>

opencc-zeroAug 2021View details →

Hardware perceptron and ReLU measurements and results

Recently, in-memory analog computing through memristive crossbar arrays attracted a lot of attention due to its efficient power consumption, area, and computing throughput. Using this computing method, different types of neural networks can be implemented for different applications. In such neural networks, memristors represent the synapses. However, in previous work, digital processors have been used to implement the activation functions or neurons. Implementing neurons using analog-based hardware further improves the power consumption, area, and throughput by removing unnecessary data conversions and communication. In this study, we designed a ReLU activation function and built a fully hardware-based two-layer fully connected perceptron using memristive arrays, and verified the operation by classifying downsampled MNIST images. We measured the DC and AC characteristics of our designed ReLU, forming, set, and reset behavior of the memristive arrays, and the perceptron behavior during training and inference in the classification task. We also studied the non-idealities related to both the ReLU design and memristors which is significantly critical in future integrated designs. Moreover, the downsampled 8*8 MNIST images that we generated from the original MNIST dataset are included in the data which can be used in future studies with the limited size of the network.

Raw data for "Measurement of the coherent beam properties at the CoSAXS beamline"

One dataset for each measurment presented in the article.

𝛅11B and B/Ca measurements of the modern and fossil Porites corals from the east coast Hainan Island in the northern South China Sea

This datasets contain the 𝛅11B and B/Ca determinations of three modern Porites corals and four ancient Porites collected from the east coast of Hainan Island in the northern South China Sea. The measurements of skeletal boron isotopes were carried out with a MC-ICP-MS, and the B/Ca was determined by ICP-MS.

Direct measurement of oxygen mass transport at the nanoscale

Dataset for article "Direct measurement of oxygen mass transport at the nanoscale". It contains: -  secondary ion mass spectrometry (SIMS) data for 18O concentration in thin films of lanthanum chromite (epitaxial and nanocrystalline); - atom probe tomography (APT) data for 18O fraction in thin films of nanocrystalline lanthanum chromite - top view transmission electron microscopy (TEM) data for nanocrystalline films of lanthanum chromite

Time series of the longitudinal gradient of Venus's brightness temperature measured by Akatsuki LIR

The files contain the time series of the longitudinal gradient of Venusian cloud's brightness temperature measured by LIR onboard JAXA's Venus orbiter Akatsuki. The data were derived and analyzed in the paper "Planetary-Scale Waves Seen in Thermal Infrared Images of Venusian Cloud Top" by Kajiwara et al. The filename represents the latitude for each time series (For example, "10N" means 10 degrees north, and "EQ" means the equator). In all files, the first column gives the approximate elapsed time in days from 18 May 2017: the exact dates are given in the paper.  The second column gives the longitudinal gradient of the brightness temperature in unit of K/degree.

opencc-by-4.0Dec 2020View details →

Global daily Aerosol Optical Depth measurements from Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA's Aqua and Terra satellites

This repository contains input MODIS AOD data prepared for “Subways and Urban Air Polution” by Gendron-Carrier, Gonzalez-Navarro, Polloni and Turner (American Economic Journal: Applied Economics, <a href="https://doi.org/10.1257/app.20180168">https://doi.org/10.1257/app.20180168</a>). The main replication archive is available at <a href="https://doi.org/10.3886/E126401V1">https://doi.org/10.3886/E126401V1</a> . Description of input MODIS AOD data The Moderate Resolution Imaging Spectroradiometers aboard the Terra and Aqua earth-observing satellites provide daily measures of the aerosol optical depth of the atmosphere at a 3km spatial resolution everywhere in the world. Data is available in ‘granules’ which describe five minutes of satellite time. These granules are available, more or less continuously, from February 24, 2000 for the Terra satellite and from July 4, 2002 for Aqua. During September of 2018, we downloaded all available granules for Terra and Aqua until August 31, 2018 and subsequently consolidated them into daily rasters describing global AOD. In August 2020, we processed additional Terra data. This archive therefore contains daily rasters for Aqua (from 2002-07-04 to 2018-08-31) and Terra (from 2000-02-24 to 2020-07-31). We note that February 2005 data are missing for the Aqua satellite.   We use source products MOD04_3K (<a href="https://doi.org/10.5067/MODIS/MOD04_L2.006">https://doi.org/10.5067/MODIS/MOD04_L2.006</a>) and MYD04_3K (<a href="https://doi.org/10.5067/MODIS/MYD04_L2.006">https://doi.org/10.5067/MODIS/MYD04_L2.006</a>). The product files are stored in Hierarchical Data Format (HDF) and we use the "Optical Depth Land And Ocean" layer, which is stored as a Scientific Data Set (SDS) within the HDF file, as our measure of aerosol optical depth. The "Optical Depth Land And Ocean" dataset contains only the AOD retrievals of high quality. We convert all HDF formatted granules to GIS compatible formats using the HDF-EOS To GeoTIFF Conversion Tool (HEG) provided by NASA’s Earth Observing System Program. We consolidate GeoTIFF granules into a global raster for each day using ArcGIS. First, we keep only AOD values that do contain information. The missing value is -9999 in AOD retrievals. Second, we create a raster catalog with all the granules for a given day and calculate the average AOD value using the Raster Catalog to Raster Dataset tool. The code used to accomplish this is included for reference purposes in “dofiles/old_work” of the main replication archive at <a href="https://doi.org/10.3886/E126401V1">https://doi.org/10.3886/E126401V1</a>.

opencc-zeroSep 2021View details →

Measuring phylogenetic information of incomplete sequence data

Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the Effective Sequence Length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification.

opencc-by-4.0Sep 2021View details →

Fault trace data and supplementary table and figures of "Fault trace corrugation and segmentation as a measure of fault structural maturity"

Fault trace data and supplementary information to the paper "Fault trace corrugation and segmentation as a measure of fault structural maturity" by Manighetti I., Mercier A., and de Barros L., Sept. 2021

opencc-by-4.0Sep 2021View details →

Measured and modeled data of the thermo-radiative and hydrological exhanges of a lawn in a residential area (FluxSAP 2012 campaign)

The dataset includes wind, soil water content and soil temperature data measured in a private home garden collected during the FluxSAP campaign in Nantes in 2012. It also includes equivalent data modeled by the surface model for natural soils and vegetation called ISBA for four sensitivity experiments corresponding to different model configurations.

opencc-zeroSep 2021View details →

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features.Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary 'hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data, and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence), or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.