Find research datasets worth reusing

Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan by a new analysis method for distributed acoustic sensing data using a seafloor cable and seismic interferometry"

Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan, derived from distributed acoustic sensing data collected using a seafloor cable with seismic interferometry", by Shun Fukushima, Masanao Shinohara, Kiwamu Nishida, Akiko Takeo, Tomoaki Yamada, and Kiyoshi Yomogida  For more information, please contact Shun Fukushima (s-fuku@eri.u-tokyo.ac.jp)

opencc-zeroJan 2022View details →

Data from: Research and exploratory analysis driven - time-data visualization (read-tv) software

read-tv The main paper is about, read-tv, open-source software for longitudinal data visualization. We uploaded sample use case surgical flow disruption data to highlight read-tv's capabilities. We scrubbed the data of protected health information, and uploaded it as a single CSV file. A description of the original data is described below. Data source Surgical workflow disruptions, defined as "deviations from the natural progression of an operation thereby potentially compromising the efficiency or safety of care", provide a window on the systems of work through which it is possible to analyze mismatches between the work demands and the ability of the people to deliver the work. They have been shown to be sensitive to different intraoperative technologies, surgical errors, surgical experience, room layout, checklist implementation and the effectiveness of the supporting team. The significance of flow disruptions lies in their ability to provide a hitherto unavailable perspective on the quality and efficiency of the system. This allows for a systematic, quantitative and replicable assessment of risks in surgical systems, evaluation of interventions to address them, and assessment of the role that technology plays in exacerbation or mitigation. In 2014, Drs Catchpole and Anger were awarded NIBIB R03 EB017447 to investigate flow disruptions in Robotic Surgery which has resulted in the detailed, multi-level analysis of over 4,000 flow disruptions. Direct observation of 89 RAS (robitic assisted surgery) cases, found a mean of 9.62 flow disruptions per hour, which varies across different surgical phases, predominantly caused by coordination, communication, equipment, and training problems.

opencc-by-4.0Jan 2022View details →

Nanopore MinION Run Metrics and genomic DNA fragment size analysis data from automated phenol-chloroform extractions (RBI LabDroid Maholo)

Nanopore MinION run MinKNOW statistical metrics output, Agilent Femto Pulse and Tape Station gDNA fragment size analysis reports of genomic DNA isolated from automated RBI LabDroid Maholo organic extractions.

opencc-by-4.0Jan 2022View details →

Data and analysis scripts for "Impact of grid spacing, convective parameterization and cloud microphysics in ICON simulations of a warm conveyor belt"

The data relates to the analysis of "Impact of grid spacing, convective parameterization and cloud microphysics in ICON simulations of a warm conveyor belt" and is in support and reference to the work titled as the same for a research article authored by Choudhary and Voigt. The file 'data.zip' contains different directories named as per the computations related to particular analysis as mentioned below: <table> <tbody> <tr> <td> Directory names and content inside 'data.zip' </td> </tr> <tr> <td> Name of directory </td> <td> Content </td> </tr> <tr> <td> trajectories  </td> <td> Output from run of LAGRANTO tool on regridded ICON simulations* (the input data is not provided here). The output contains computations of 'warm conveyor belt (WCB)' trajectories and different variables traced along them which are stored in different files named as outtrace1.nc and so on. The subdirectories are named as per the resolution, convection and cloud microphysics parametrization used in model setup, for e.g. '0.025convon/1m' corresponds to 2.5 km resolution with parametrized convection and 1-moment cloud microphysics. The file with name ending with 'box' corresponds to different subclasses of trajectory as described in the work.  </td> </tr> <tr> <td> dhr </td> <td> diabatic heating rate, traced along WCB and binned in pressure levels (for 1-moment cloud microphysics) </td> </tr> <tr> <td> dynamical variables </td> <td> av- absolute vorticity, pv- potential vorticity and w- vertical wind traced along WCB and binned in pressure levels (for 1-moment cloud microphysics) </td> </tr> <tr> <td> statistics </td> <td> statistics (different statistical computation of WCB parcels ascent for 1- and 2- moment cloud microphysics, details described in work) </td> </tr> <tr> <td> theta_e </td> <td> equivalent potential temperature for 2.5 km explicit convection simulation (.pkl file) for 2016.09.22 12UTC, 2016.09.23 12UTC and 2016.09.24 12UTC in files numbered 1, 2 and 3 respectively. </td> </tr> <tr> <td> ipv </td> <td> same as above but for isentropic potential vorticity </td> </tr> <tr> <td> mslp </td> <td> mslp.nc- same as above but for mean sea level pressure field  </td> </tr> <tr> <td> cyclone_track </td> <td> File name with convention 'nawdexnwp-5km-mis-0001_vladiana_cyclonepressure.nc' corresponds to file containing central mean sea level pressure of cyclone Vladiana during the simulation period for 5 km resolution with parametrized convection and 1-moment cloud microphysics.  coord_1m.npy- the coordinate/ location of cyclone Vladiana based on central mean sea level pressure  </td> </tr> <tr> <td> pte </td> <td> Pressure tendency equation (PTE) analysis. Subdirectories are named after different resolutions of simulation with 1-moment cloud microphysics and parametrized convection (except for 10, 5 and 2.5 km where convection is explicit). Further, the .npy files are named as per the different vertically integrated tendency terms of PTE equation they represent, as mentioned below: dp_dt: surface pressure dfi_dt: geopotential (upper boundary of integral) i_diab_res: diabatic heating (including residual) i_itt: virtual temperature i_tadv: temperature advection i_vmt: vertical motions </td> </tr> </tbody> </table>   *Note: The original ICON simulations which are not part of this dataset were carried out by Prof. Aiko Voigt (University of Vienna) at the Mistral High Performance Computing system of the German Climate Computing Center (DKRZ) in Hamburg, Germany. The primary data of the ICON simulations (run scripts, namelists, scripts for lateral boundary data) are published at KITopen of Karlsruhe Institute of Technology, https://doi.org/10.5445/IR/1000123695. Note that the KITopen dataset includes all simulations of \cite{svchd20}, from which a subset is analyzed here.   The file 'scripts.zip' contains two directories which is related with analysis presented in the work: 'plotting_scripts' includes script for creating different plots/ figures showcased in the work  'processing_scripts' includes computations for producing different quantities/ data that are named as described above in the table for  'data.zip'

opencc-zeroFeb 2022View details →

Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians

The dental system of ceratopsids is among the most specialized structure in Dinosauria, and includes high angled wear surfaces, split tooth roots, and multiple teeth in each tooth family. However, the early evolution of this unique dental system is generally poorly understood due to a lack of knowledge of the dental morphology and development in early-diverging ceratopsians. Here we study the dental system of three of the earliest-diverging Chinese ceratopsians: Yinlong and Hualianceratops from the early Late Jurassic of Xinjiang, and Chaoyangsaurus from the Late Jurassic of Liaoning. By using micro-computed tomographic analyses, our study has revealed significant new information regarding the dental system of these early ceratopsians, including no more than five replacement teeth in each jaw quadrant; at most one generation of replacement teeth in each alveolus; nearly full resorption of the functional tooth root during tooth replacement; and occlusion with low-angled, concave wear facets that differs significantly from the shearing occlusal system seen in ceratopsids. Yinlong displays an increase in the number of maxillary tooth alveoli and a decrease in the number of replacement teeth during ontogeny as well as the retention of remnants of functional teeth in the largest individual. Early-diverging ceratopsians thus display a relatively slow tooth replacement rate compared to late-diverging ceratopsians. Combined with paleobotany and palaeoenvironment data, Yinlong likely uses gastroliths to triturate foodstuffs, and the difference in diet strategy might have influenced the pattern of tooth replacement in later-diverging ceratopsians.

Mycobacterium tuberculosis complex NGS made easy: data analysis step-by-step (datasets)

Datasets used in the workshop "Mycobacterium tuberculosis complex NGS made easy: data analysis step-by-step". A capacity development initiative by TB-CAPT, PanACEA and Seq&Treat.

Raw Data for the article: A Radioactive-Free Method for the Thorough Analysis of the Kinetics of Cell Cytotoxicity

The cytotoxic activity of T cells and Natural Killer cells is usually measured with the chromium release assay (CRA), which involves the use of 51Chromium (51Cr), a radioactive substance dangerous to the operator and expensive to handle and dismiss. The accuracy of the measurements depends on how well the target cells incorporate 51Cr during labelling which, in turn, depends on cellular division. Due to bystander metabolism, the target cells spontaneously release 51Cr, producing a high background noise. Alternative radioactive-free methods have been developed. Here, we compare a bioluminescence (BLI)-based and a carboxyfluorescein succinimidyl ester (CFSE)-based cytotoxicity assay to the standard radioactive CRA. In the first assay, the target cells stably express the enzyme luciferase, and vitality is measured by photon emission upon the addition of the substrate d-luciferin. In the second one, the target cells are labelled with CFSE, and the signal is detected by Flow Cytometry. We used these two protocols to measure cytotoxicity induced by treatment with NK cells. The cytotoxicity of NK cells was determined by adding increasing doses of human NK cells. The results obtained with the BLI method were consistent with those obtained with the CRA- or CFSE-based assays 4 hours after adding the NK cells. Most importantly, with the BLI assay, the kinetic of NK cells' killing was thoroughly traced with multiple time point measurements, in contrast with the single time point measurement the other two methods allow, which unveiled additional information on NK cell killing pathways.

Raw Data for the article: miRNA expression analysis in the human heart: Undifferentiated progenitors vs. bioptic tissues-Implications for proliferation and ageing

In developed countries, cardiovascular diseases are currently the first cause of death. Cardiospheres (CSs) and cardiosphere-derived cells (CDCs) have been found to have the ability to regenerate the myocardium after myocardial infarction (MI). In recent years, much effort has been made to gain insight into the human heart repair mechanisms, in which miRNAs have been shown to play an important role. In this regard, to elucidate the involvement of miRNAs, we evaluated the miRNA expression profile across human heart biopsy, CSs and CDCs using microarray and next-generation sequencing (NGS) technologies. We identified several miRNAs more represented in the progenitors, where some of them can be responsible for the proliferation or the maintenance of an undifferentiated state, while others have been found to be downregulated in the undifferentiated progenitors compared with the biopsies. Moreover, we also found a correlation between downregulated miRNAs in CSs/CDCs and patient age (eg miR-490) and an inverse correlation among miRNAs upregulated in CSs/CDCs (eg miR-31).

Raw Data for the article: Patient-Specific Analysis of Ascending Thoracic Aortic Aneurysm with the Living Heart Human Model

In ascending thoracic aortic aneurysms (ATAAs), aneurysm kinematics are driven by ventricular traction occurring every heartbeat, increasing the stress level of dilated aortic wall. Aortic elongation due to heart motion and aortic length are emerging as potential indicators of adverse events in ATAAs; however, simulation of ATAA that takes into account the cardiac mechanics is technically challenging. The objective of this study was to adapt the realistic Living Heart Human Model (LHHM) to the anatomy and physiology of a patient with ATAA to assess the role of cardiac motion on aortic wall stress distribution. Patient-specific segmentation and material parameter estimation were done using preoperative computed tomography angiography (CTA) and ex vivo biaxial testing of the harvested tissue collected during surgery. The lumped-parameter model of systemic circulation implemented in the LHHM was refined using clinical and echocardiographic data. The results showed that the longitudinal stress was highest in the major curvature of the aneurysm, with specific aortic quadrants having stress levels change from tensile to compressive in a transmural direction. This study revealed the key role of heart motion that stretches the aortic root and increases ATAA wall tension. The ATAA LHHM is a realistic cardiovascular platform where patient-specific information can be easily integrated to assess the aneurysm biomechanics and potentially support the clinical management of patients with ATAAs.

Sample ERA5 Climate Reanalysis Data for UW Geospatial Data Analysis Course

Used for Module 09: https://uwgda-jupyterbook.readthedocs.io/en/latest/modules/09_NDarrays_xarray_ERA5/ Generated using Copernicus Climate Change Service information [2022] Original license: https://cds.climate.copernicus.eu/api/v2/terms/static/licence-to-use-copernicus-products.pdf

opencc-zeroMar 2022View details →

Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Research in the biological sciences is hampered by the Linnean shortfall, which describes the number of hidden species that are suspected of existing without formal species description. Using machine learning and species delimitation methods, we built a predictive model that incorporates some 5.0 × 105 data points for 117 species traits, 3.3 × 106 occurrence records, and 9.1 × 105 gene sequences from 4,310 recognized species of mammals. Delimitation results suggest that there are hundreds of undescribed species in class Mammalia. Predictive modeling indicates that most of these hid- den species will be found in small-bodied taxa with large ranges characterized by high variability in temperature and precipitation. As demonstrated by a quantitative analysis of the literature, such taxa have long been the focus of taxonomic research. This analysis supports taxonomic hypotheses regarding where undescribed diversity is likely to be found and highlights the need for investment in taxonomic research to overcome the Linnean shortfall.

opencc-by-4.0Jan 2019View details →

Dance Your Ph.D. 2018 Physics FINALIST: Dark energy and dark matter via probabilistic data analysis

Dark matter (dancer in black mask; brings dancers together) and dark energy (dancer in black mask; pulls dancers apart) are the mysterious constituents of the universe that determine the evolution of the largest structures, clusters of galaxies (dancers in tie dye), and I (dancer in gold mask) want to learn about them them by analyzing a huge set of 3D galaxy positions. The telescope (dancer in silver mask) gives me 2D images of galaxies with no distances, so I have to estimate galaxy locations with "redshift," which is correlated with distance. The exciting telescopes of the next decades will build large samples of galaxies by taking lots of superficial color data that's not informative enough to determine the redshift. One thing that tells us about dark matter and dark energy is the redshift distribution (dancer in red stripes) -- I can still learn about dark energy and dark matter if I can figure out how many galaxies have each redshift. Since I don't actually know the redshifts of any galaxies, I consider the probability of redshift (dancers in white shirts) for each galaxy based on its limited color data. However, the redshift probabilities are biased by prior beliefs (dancer in gray scarf) about physics that are transmitted by the way we derive the probabilities from the galaxy colors. If unaccounted for, the prior beliefs could cause us to draw the wrong conclusions about dark matter and dark energy, meaning we won't learn anything from all this amazing telescope data we're going to have. For my thesis, I developed a method that puts the prior beliefs in their proper place and lets the data guide the inference of the redshift distribution, using an approach called Bayesian statistics. I audition many possible redshift distributions and check how likely each is to have caused the observed galaxy colors, with the redshift probabilities as the judges; this procedure is called Markov chain Monte Carlo (MCMC) sampling, and it leads to an ensemble of possible redshift distributions each with an associated probability of having produced the observed galaxy colors. By doing the math carefully and correctly, we will learn more about dark matter and dark energy even with the coarsest data!

opencc-by-4.0Mar 2022View details →

Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia - additional data

Sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this study, we performed whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina short-read sequencing to describe the circulation of the virus lineage in Armenia. This dataset contains Nextstrain configuration files, the auspice JSON file, BEAST output logs, and trees files, and resulting log and tree files as well as R scripts and data files used in phylogenetic and functional analyses.

opencc-by-4.0Jul 2021View details →

Data and script for binomial GLMs in "Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications." (Pratt & Guengerich)

This submission contains data and R-script that enable to reproduce the binomial generalized linear models in the paper “Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications” by Lauren V. Pratt & Anna Guengerich. Please cite the above paper if you use the files included in this Zenodo record in your work.

opencc-zeroApr 2022View details →

R script with data for vegetation and macropod scat analysis

Fire and herbivores alter vegetation structure and function. Future fire activity is predicted to increase, and quantifying changes in vegetation communities arising from post-fire herbivory is needed to better manage natural environments. We investigated the effects of post-fire herbivory on understory plant communities in a coastal eucalypt forest in south-eastern Australia. We quantified herbivore activity, understory plant diversity, and dominant plant morphology following a wildfire in 2017 using two sizes of exclosures. Statistical analysis incorporated the effect of exclusion treatments, time since fire (TSF), and the effect of a previous prescribed burn. Exclusion treatments altered herbivore activity, but TSF did not. Herbivory reduced plant species richness, diversity and evenness and promoted the dominance of the most abundant plants within the understory. Increasing TSF reduced community diversity and evenness and influenced morphological changes to the dominant understory plant species, increasing size and dead material while decreasing abundance. We found the legacy effects of a previous prescribed burn had no effect on herbivores or vegetation within our study. Foraging by large herbivores resulted in a depauperate vegetation community. As post-fire herbivory can alter vegetation communities, we postulate that management burning practices may exacerbate herbivore impacts. Future fire management strategies to minimise herbivore-mediated alterations to understory vegetation could include aggregating management burns into larger fire sizes or linking fire management with herbivore management. Restricting herbivore access following fire (planned or otherwise) can encourage a more diverse and species-rich understory plant community. Future research should aim to determine how vegetation change from post-fire herbivory contributes to future fire risk.

Videographic Data for Pore Formation and Melt Pool Analysis of Laser Welded Al-Cu Joints using Synchrotron Radiation

The published data include video recordings of synchrotron radiation during a laser beam welding process in aluminium-copper joints. The recordings show the phase boundaries of the materials and are suitable for an analysis with regard to material mixing and pore formation. The experiments were conducted with the high energy beamline P07 (EH4) of Petra 3 at Deutsches Elektronen Synchrotron DESY in Hamburg, Germany. General parameters: Photon energy of synchrotron beam: 37,7 keV Scintillator material: CdWO4 Frame rate: 1000 Hz Specific parameters used for videos: HV185: Cu-ETP (top) to Al99.5 (bottom); wavelengths of laser beam source: 1030 nm; laser beam diameter: 117 µm; laser power: 1000 W; feed rate: 50 mm/s HV186: Cu-ETP (top) to Al99.5 (bottom); wavelengths of laser beam source: 1030 nm; laser beam diameter: 117 µm; laser power: 1500 W; feed rate: 100 mm/s HV192: Al99.5 (top) to CuSn6 (bottom);  wavelengths of laser beam source: 1070 nm; laser beam diameter: 34 µm; laser power: 750 W; feed rate: 50 mm/s HV196: Cu-ETP (top) to Al99.5 (bottom); wavelengths of laser beam source: 1070 nm; laser beam diameter: 34 µm; laser power: 750 W; feed rate: 50 mm/s

opencc-zeroApr 2022View details →

Data from: Morphometric analysis of Skiagia-plexus acritarchs from the early Cambrian of North Greenland

The Cambrian evolutionary radiations are marked by spectacular biotic turnovers and the establishment of increasingly tiered food chains. At their base are primary producers, which in the Cambrian fossil record are chiefly represented among organic-walled microfossils. The majority of these microfossil remains have traditionally been attributed to an informal category of incertae sedis called "acritarchs", based entirely on form taxonomy. Acritarch form-taxa have been intensely used for biostratigraphy, and in large-scale studies of phytoplankton diversity. However, both prospects have been challenged by cases of taxonomic inconsistencies and over-splitting arising from the large phenotypic plasticity seen among these microfossils. The acritarch form-genus Skiagia stands as an ideal case-study to explore these taxonomic challenges, since it encompasses a number of form-species widely used in lower Cambrian biostratigraphy. Moreover, subtle morphological differences among Skiagia species were suggested to underlie key evolutionary innovations towards complex reproduction strategies. Here we apply a multivariate morphometric approach to investigate the morphological variation of Skiagia-plexus acritarchs using an assemblage sourced from the Buen Formation (Cambrian Series 2, Stage 3–4) of North Greenland. Our analysis showed that the specific-level classification of Skiagia discretizes a continuous spectrum of morphologies. While these findings bring important taxonomic and biostratigraphic hurdles to light, the unequal frequency distribution of life cycle stages among Skiagia species suggests that certain elements of phytoplankton paleobiology are nonetheless captured by Skiagia form-taxonomy. These results demonstrate the value of using morphometric tools to explore acritarch phenotypic plasticity and its potential ontogenetic and paleoecological drivers in Cambrian ecosystems.

EZ publication: source code, profiling, analysis and simulation data

Data of the PIConGPU simulations as used in the publication: EZ: An Efficient, Charge Conserving Current Deposition Algorithm for Electromagnetic Particle-In-Cell Simulations Data overview: <ul> <li>picongpu_source.zip:  <ul> <li>source code forked from the PIConGPU mainline version 0.7.0-dev</li> <li>used input set `share/picongpu/examples/PaperThermal`</li> </ul> </li> <li>runs_charge_conservation.zip: <ul> <li>output including hdf5 dumps to validate charge conservation property for the PaperThermal setup (warm plasma)</li> </ul> </li> <li>runs_performance.zip: <ul> <li>simulation timings output for Spock CPU, Spock GPU and Summit GPU runs</li> </ul> </li> <li>runs_profiling.zip: <ul> <li>profile data for Spock GPU and Summit GPU runs</li> </ul> </li> <li>runs_singleParticleTest.zip: <ul> <li>output including hdf5 dumps to validate charge conservation property for the single particle test</li> </ul> </li> <li>analysis_scripts.zip:  <ul> <li>jupyter notebooks for setup and analysis of PaperThermal setup</li> <li>python script to plot charge conservation from hdf5 simulation output over time</li> <li>bash script for statistical analysis of performance runs</li> </ul> </li> </ul>

Exploratory Landscape Analysis Feature Data of Recombinations and noiseless BBOB Instances 1-15

Data presented in the paper 'Increasing Diversity of Benchmark Functions Sets by Affine Recombination' which was submitted to PPSN 2022.

Sídliště z mladší doby bronzové v Březnici (Česko): data pro depoziční analýzu – The Late Bronze Age site in Březnice (Czechia): data for deposition analysis

Nálezy z archeologického výzkumu v Březnici (okr. Tábor) v letech 2005-2009 a 2019. Výzkum provedl O. Chvojka (Archeologický ústav FF JU v Českých Budějovicích). Data zahrnují údaje o keramice a dal&scaron;ích nálezech použitých k depoziční analýze sídli&scaron;tních objektů mlad&scaron;í doby bronzové, zejména tzv. žlabů. Výsledky analýzy jsou publikovány v Chvojka et al. 2021. Popis databáze je obsažen v přiloženém PDF souboru. Podpořeno Grantovou agenturou ČR (18-10747S). Finds from the archaeological excavations in Březnice (Tábor district, South Bohemia, Czech Republic) in 2005-2009 and 2019. The fieldwork was directed by O. Chvojka (Institute of Archaeology, South Bohemian University in České Budějovice). Data concern the pottery fragments and other finds (daub, loom weights) used for the analysis of deposition processes in the Late Bronze Age settlement features. Based on this material, a model of house biography and the concept of closing rituals were formulated (see Chvojka et al. 2021). These models suggest an interpretation for the so-called trenches, specific sunken features filled with an unusually rich content of secondary-burnt pottery and other finds. Details of the database are given in the attached PDF file. Supported by the Czech Sceince Foundation (18-10747S). <ul> <li>Chvojka, O. – Kuna, M. – Men&scaron;ík, P. et al. 2021: Rituály ukončení a obnovy. Sídli&scaron;tě mlad&scaron;í doby bronzové v Březnici u Bechyně – Rituals of termination and renewal. The Late Bronze Age settlement in Březnice near Bechyně. České Budějovice – Praha – Plzeň. ISBN 978-80-7394-899-3; ISBN 978-80-7581-039-7;  ISBN 978-80-261-1083-5.</li> </ul>