Find research datasets worth reusing

publicMay 2025View details →

Data and code from: River network connectivity reductions dominate declines in the richness of plateau fish species under climate change in the upper Yangtze River Basin

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publicApr 2025View details →

Data from: Wildfires induce a reduction in body size and morphological variation of an insular endemic insect

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publicSep 2024View details →

Data from: Heatwaves exacerbate pollen limitation through reductions in pollen production and pollen vigour

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publicMay 2025View details →

Data from: A village doctor-led mobile health intervention for cardiovascular risk reduction in rural China: cluster randomised controlled trial

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opencc-by-4.0Jan 2020View details →

Data reduction for in situ synchrotron tomography experiments

This dataset corresponds to a series of phase-enhanced tomographic images recorded during a monotonic mechanical tensile test with a polymer material. Tomographic measurements were performed at the PSICHE beamline, SOLEIL synchrotron. The reconstructed voxel size is 1.3 µm. The reconstruction was performed with pyHST (filtered back-projection) using the paganin filter with a propagation distance of 15 pixels. Each tomography measurement consists of 1000 radiographs of 1024×2048 pixels acquired over 180°. The binary reconstructed volumes are therefore 1024×2048×2048 voxels encoded with a dynamic range of 32 bits (floating-point). The 44 measurements taken during the mechanical test represent a volume of 700 GB. The reduction strategy used is based on a thresholding of the specimen in each volume and a zeroing of the voxels outside the sample. In the preserved voxels, the binary representation of each value is truncated to have a precision of the order of the experimental uncertainties: the insignificant least significant bits are replaced by 0s which, combined with a transposition of the order of the bits just before compression (bit shuffling), makes it possible to drastically increase the compressibility of the data. The data is arranged in an HDF5 container using block access with on-the-fly compression/decompression. The total size of the dataset is thus reduced with a reduction ratio of 16:1 using Zstandard level 1. The mask used as well as even smaller volumes (pixel binning 2×2 and 4×4, dynamic range reduction on 4 or 8 bits) are added to allow fast access to very small data if needed, in the same fashion as the thumbnail used in some 2D image formats. The footprint of the reduced version as described is 47 GB. The format is self-described and contains additional metadata.

opencc-zeroMay 2021View details →

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

<ol> <li>Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the preservation process alters the degree to which metazoan parasites are detectable in fluid-preserved fish specimens when using visual parasite detection techniques.</li> <li>We randomly assigned fish of three species (Gadus chalcogrammus, Thaleichthys pacificus, Parophrys vetulus) to two treatments. In the first treatment, fish were preserved according to the standard procedures used in ichthyological collections. Immediately after the fluid-preservation process was complete, we performed parasitological dissection on those specimens. The second treatment was a control, in which fish were dissected without being subjected to the fluid-preservation process. We compared parasite abundance between the two treatments.</li> <li>Across 298 fish individuals and 59 host–parasite pairs, we found few differences between treatments, with 24 of 27 host–parasite pairs equally abundant between the two treatments. Of these, one pair was significantly more abundant in the preservation treatment than in the control group, and two pairs were significantly less abundant in the preservation treatment than in the control group.</li> <li>Our data suggest that the fluid-preservation process does not have a substantial effect on the detectability of metazoan parasites. This study addresses only the effects of the fixation and preservation process; long-term experiments are needed to address whether parasite detectability remains unchanged in the months, years, and decades of storage following preservation. If so, ecologists will be able to reconstruct novel, long-term datasets on parasite diversity and abundance over the past century or more using fluid-preserved specimens from natural history collections.</li> </ol>

opencc-by-4.0Aug 2020View details →

CO2 Reduction Tafel Dataset for Bayesian Data Analysis

This dataset contains 344 different digitized and tagged Tafel slope datasets from the CO2 reduction literature. We re-analyze this data with a Bayesian data analysis procedure that estimates a Tafel slope and yields distributional uncertainty information about its value. We are releasing this dataset along with our study to facilitate re-analyzing and refitting our data using different models and approaches.

opencc-zeroMay 2020View details →

Data from: Biosynthesis of the redox coenzyme F420 in Thermomicrobia involves reduction by standalone nitroreductase superfamily enzymes.

Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for long that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that PEP is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase superfamily (NTR), converts dehydro-F420 into saturated F420. Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in-vitro assays that standalone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum. These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in E. coli in the future.

opencc-by-4.0Dec 2020View details →

Scripts and data for "The adequacy of time-series reduction for renewable energy systems"

This upload provides the scripts and data used for the computations in the aforementioned working paper. To run these files, you will need to adjust the directory in the files 'testTimeSeries.jl' and 'calli.bat' to your local directory. The subfolder 'reduceTimeSeries' contains all data and the script 'reduceTimeSeries.jl' to reduce the full time-series. Reduction using the 'Gerbaulet' method unfortunately requires a GAMS installation. The results of the reduction are already provided in the folder 'output'. The subfolder 'testTimeSeries' contains all data and the script 'testTimeSeries.jl' to test the reduced time-series with a capacity expansion model. The 'comment' and ‘source’ columns in the AnyMOD.jl input files provide further documentation on the used input parameters. The labels 'lowDem' and 'newDem' relate to what was referred to conventional demand and demand with sector integration in the paper, respectively.

opencc-by-4.0Sep 2024View details →

Data and code for: "Large reductions in tropical bird abundance attributable to heat extreme intensification "

Data and code necessary to reproduce results of paper: Large reductions in tropical bird abundance attributable to heat extreme intensification By Maximilan Kotz, Tatsuya Amanon and James Watson. Please contact maximilian.kotz@bsc.es / maxkotz@pik-potsdam.de for questions.

opencc-by-4.0Nov 2023View details →

STAVER: A Standardized Benchmark Dataset-Based Algorithm for Effective Variation Reduction in Large-Scale DIA-MS Data

This project focuses on developing and applying STAVER, an innovative DIA algorithm designed to eliminate non-biological noise and variability from the large-scale DIA-MS study dataset analyses. STAVER is a flexible framework that utilizes prior knowledge regarding peptide separation coordinates (RT) and fragment ion intensities from the standard benchmark datasets, which effectively mitigates non-biological noise potential during library searches, enhancing spectrum identifications and protein quantification accuracy. Furthermore, the robustness and broad applicability of STAVER were validated in multiple large-scale DIA datasets from different platforms and laboratories, demonstrating significantly improved precision and reproducibility of protein quantification. It facilitates the comparative and integrative analysis of DIA datasets across different platforms and laboratories, enhancing the consistency and reliability of findings in clinical research. The project aims to promote the adoption of hybrid library search and improve the sensitivity and quality of DIA proteomics data through the open-source STAVER software package.

opencc-by-4.0Nov 2023View details →

Data from: Importance of Site Diversity and Connectivity in Electrochemical CO reduction on Cu

Microkinetic Modeling<ul><li>Contains raw ipynb files to generate graphs used in this work</li></ul>EC-Lab Potentiosat Data<ul><li>Contains potentiostat I-V data, organized in folder by date of acquisition</li></ul>Mass flow and product quantification<ul><li>Mass flow measurements, gas chromatography, and nuclear magnetic resonance spectroscopy</li></ul>Overview of all experiments<ul><li>Spreadsheets listing all experiments</li></ul>Cell Design<ul><li>Files for the 1 cm2 gas diffusion electrodes used in this work.</li></ul>

opencc-by-4.0Apr 2024View details →

Data required for "Redefining awn development in rice through the breeding history of Japanese awn reduction"

The study challenges the conventional understanding of awn loss as a  domestication syndrome, showing instead that many awned varieties continued to be widely grown in Japan until the early twentieth century and that selection for awn reduction was active at that time, demonstrating that awn loss is not a domestication syndrome but “a trait that emerged during crop improvement”. Although selection for awnless mutants was carried out independently using different types of awned cultivars in the early twentieth century in Japan, awn loss was caused by the mutation in OsEPFL1. This suggests that a single mutant haplotype of OsEPFL1 was conserved in the genomes of different cultivars and subsequently selected within each line to meet the demand for awnless varieties. The study also conducts phylogenetic analyses of EPFL1 in 48 grass plants, revealing its unique involvement in awn formation in rice while potentially playing a different role in the domestication of other grass plants. Finally, an attempt is made to isolate an awn-forming gene that has not been identified from the awned rice cultivar “Omachi”, which is still cultivated in Japan. The results presented in this paper provide a new perspective on domestication against the conventional understanding of awn development, shedding light on its potential as a useful organ for breeding to mitigate environmental stress.

opencc-by-4.0Nov 2021View details →

Cost reductions in renewables can substantially erode the value of carbon capture and storage in mitigation pathways: supporting data

This provides supporting data for the paper, Cost reductions in renewables can substantially erode the value of carbon capture and storage in mitigation pathways, published in One Earth. The full paper can be accessed at the following DOI: https://doi.org/10.1016/j.oneear.2021.10.024, published on the 19th November 2021.

opencc-zeroJan 2022View details →

Data from: Ultra-wideband and polarization-independent RCS reduction based on polarization conversion metasurface

We proposed an ultra-wideband polarization conversion metasurface (PCM). Because it is an anisotropic structure with a pair of mutually perpendicular symmetric axes u and v, and the phase difference between the reflection coefficients under u- and v-polarized incidences is close to 180° in an ultra-wide frequency range from 9.5 to 29.5 GHz, it can realize ultra-wideband circular polarization (CP) maintaining reflection and make its co-polarized reflection coefficient under CP incidence close to 1.0 in the ultra-wide band 9.2-29.7 GHz. In addition, when its unit cell structure is rotated by an angle ψ, almost ±2ψ Pancharatnam-Berry (PB) phase will be generated in co-polarized reflection coefficient under CP incidence. Thus, based on the proposed PCM, an ultra-wideband Pancharatnam-Berry (PB) 2-dit coding metasurface is conveniently proposed. The simulation and experimental results show that the coding metasurface can achieve more than 10 dB radar cross section (RCS) reduction in the ultra-wide frequency band 8.7-29.3 GHz with a relative bandwidth of 108.4% under normal incidence with arbitrary polarizations, in addition, when the incident angle is increased to 30°, the RCS reduction performance can be kept well. In this data file, the simulation results obtained by commercial software Ansys HFSS and measurement results are listed.

opencc-by-4.0Mar 2022View details →

Pathogen reduction data when applying high pressure processing to milk/colostrum and ready-to-eat foods

Introduction This dataset was built by members of the EFSA Working Group on high pressure processing (HPP) of food during the preparatory work on the BIOHAZ Scientific Opinion on the efficacy and safety of high pressure processing of food (EFSA-Q-2020-00380) (<a href="https://doi.org/10.2903/j.efsa.2022.7128">https://doi.org/10.2903/j.efsa.2022.7128</a>). It was used to answer to the following Terms of Reference (ToR) of the mandate: ToR2. To assess the efficacy of HPP when applied to raw milk and raw colostrum from ruminants, and in particular: a. To recommend minimum requirements as regards time and pressure of the HPP, and other factors if relevant, for the control of Mycobacterium spp., Brucella spp., Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing Escherichia coli (STEC), to achieve an equivalent efficacy to that of thermal pasteurisation.   ToR3. To assess the efficacy of HPP when applied to foods known to cause human listeriosis and in particular: a. To recommend minimum requirements as regards time and pressure of the HPP, and other factors if relevant, to reduce significantly L. monocytogenes levels (e.g. by a certain log reduction), and assuming that the parameters influencing the growth of L. monocytogenes remain unchanged (e.g. shelf-life and storage conditions); b. To assess the efficacy on other relevant pathogens when applying the minimum requirements identified in a. A literature search was conducted to retrieve studies reporting on pathogen-specific parameters when treating milk/colostrum and ready-to-eat foods with HPP. A modelling approach was used to fit the derived log10 reductions (logR) at specific pressure-holding time combinations. More information can be found in the Scientific Opinion. Description Two MS-Excel files contain the extracted data. One file consists of the data used for answering ToR2 and contains data on HPP inactivation of Mycobacterium bovis, L. monocytogenes, Salmonella spp., STEC, Campylobacter spp., and Staphylococcus aureus in milk and colostrum from ruminants. The other file was used for answering ToR3 and contains data on HPP inactivation of L. monocytogenes, Salmonella spp. and E. coli in three types of RTE food categories: category “cooked meat products”,  category “smoked and gravad fish” and category “soft or semi-soft and fresh cheese”. Both files contain metadata related to product characteristics (e.g. the food matrix and composition), contamination characteristics (e.g. pathogen/strain used for inoculation, inoculation level, medium used for enumeration), HPP treatment characteristics (e.g. target pressure, time), and outcome (e.g. log10 reduction).

opencc-by-4.0Jun 2024View details →

Data supporting "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose"

Data supporting our New Phytologist publication: "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose". The file present the data produced during long-term (three consecutive years 2019-2021) field observations and short-term girdling manipulation of top-crown shoots in three mature Betula pendula trees as details of our manuscript. Values of leaf gas-exchange, environmental variables, leaf water and nitrogen status, and concentrations of sucrose, hexoses (glucose and fructose), starch, total sugar, and total non-structural carbohydrate in leaves are listed.

opencc-by-4.0Jun 2024View details →

Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes"

Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes" Supplementary Data 1: The information of the genomes we used in our analyses. The “DsrAB” sheet included the information of DsrAB-containing genomes and denoted whether DsrC, DsrM, DsrK, DsrJ, DsrO, DsrP genes were present. The other sheets included the information of the representative genus-level genomes which comprised DsrAB. These genomes were used to reconstruct genus-level phylogenies to compare tree topologies within phylum. See the “Note” sheet for more details. Supplementary Data 2: The raw data of Ka/Ks values of each gene pair estimated by KaKs_calculator v2.0 with MA method. Supplementary Data 3: the information of the COGs of iron-reducers and SRMs, respectively. Supplementary Data 4: fasta files used for tree reconstruction, including Dsr-related proteins and concatenated sequences for phylogenomic trees. The folder names indicated their analytical purposes. Supplementary Data 5: tree files used in our analyses, including Dsr trees, genetic distance-based trees and dated phylogenetic trees. The folder names indicated their analytical purposes.

opencc-zeroJun 2024View details →

Data from: Extreme mitochondrial reduction in a novel group of free-living metamonads

Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway through lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.