Find research datasets worth reusing

opencc-by-4.0Oct 2019View details →

Drainage reorganisation and species evolution: model sensitivity analysis data

Data description: <ul> <li>‘trial_factor_values.csv’: The factor values for experiment trials were generated using a quasi-random Sobol sequence (Sobol, 1967). The table field, ‘initial_landscape_id’ is the identifier for unique combinations of the following factor values that controlled the landscape elevation in the initial conditions phase of the model: initial elevation seed, \(U\), \(K\), and \(k_d\). The factors, \(U\), \(K\), \(k_d\), \(P_m\), and allopatric wait time varied logarithmically. The values of these factors in the file are the exponent of base 10.</li> <li>‘trial_response_values_initial_conditions_phase.csv’: Topographic relief at steady state along with the model time to initial steady state are the trial model responses included in the file. Values are listed for each initial landscape ID rather than trial because many trials had the same combinations of the factors that controlled the topography of the initial landscape. </li> <li>‘trial_response_values_perturb_phase_base_level_fall_scenario.csv’ and ‘trial_response_values_perturb_phase_fault_throw_scenario.csv’: Model responses of the perturb phase for base level fall and fault throw scenario along with the initial landscape ID, species count values, and the model time back to steady state.</li> <li>The files beginning with `sobol`: the sensitivity analysis results output by the software, ‘SALib’ (Herman and Usher, 2017). ‘S1’, ‘S2’, and ‘ST’ in the file name indicates if the file contains data of the Sobol first, second, or total order effect, respectively.</li> </ul>

Dataset of "Cobalt and nickel doped WSe2 as efficient electrocatalysts for water splitting and as cathodes in hydrogen evolution reaction PEM water electrolysis"

Efficient electrocatalysts are crucial for water splitting and fuel cells. Using cheap alternatives that can improve reaction kinetics is essntial for advancing fuel cell technology. Although, tungsten diselinide (WSe2) is promising for electrocatalysis is not fully explored, especially in oxygen evolution and in applications such as polymer electrolyte membrane water electrolyzer. In this work, we used a simple approach to dope WSe2 with cobalt and/or nickel atoms. The doped material was subsequently tested for hydrogen evolution reaction and oxygen evolution reaction. Accordingly, the two electrocatalysts are highly active and stable, affording low overpotentials comparable to those of noble metals. The effective introduction of heteroatoms causes the retention of coordination vacancies, furnishing active catalytic sites that enhanced electrocatalytic performance both in activity and charge transfer. Moreover, both doped materials show excellent performance and stability as cathode electrocatalysts in the polymer electrolyte membrane water electrolyzer with great promise for real-world applications.

opencc-by-4.0Aug 2024View details →

Dataset of "Towards 2D van der Waals Entropy Mixture MX2 (M=Mo,W; X=S,Se,Te) for Hydrogen Evolution Electrocatalysis"

High-entropy alloys have emerged as a class of materials, offering unique properties due to their irregular and randomized arrangement of multiple elements in an ordered lattice. This concept has been extended to two-dimensional (2D) van der Waals materials, including transition metal dichalcogenides (TMD), which exhibit promising applications in electrocatalysis. In this work, we have explored the synthesis of entropy mixture crystals (TMDmix) involved the chemical vapor transport of five individual elements, Mo and W as metal elements, S, Se, and Te as chalcogenide elements, resulting in a crystalline structure with a controlled composition Mo0.56W0.44(S0.33Se0.35Te0.32)2, with an estimated ΔSmix of 0.96R. When observed along the [001] zone axis, STEM HAADF images indicate the presence of the different crystal phases of the 2D TMDs (1T, 2H, and 3R). Our findings demonstrate the potential of the entropy TMDmix materials as catalysts for the hydrogen evolution reaction, as an alternative to noble metal-based catalysts. To maximize the potential of TMDmix, we chose the chemical exfoliation with the resulting material being subdivided into size groups, big and small according to their lateral size. In acidic medium, the lowest overpotential of 127 mV and Tafel slope of 79 mV/dec were obtained for the exfoliated sample with a small lateral size (exf-TMDsmall).

Dataset of "MoO3-xNiMoO4 nanorods synthetized using NiO nanoparticles for hydrogen evolution in anion exchange membrane water electrolysis"

Novel method of Mo-Ni catalyst for hydrogen evolution reaction in anion exchange membrane water electrolysis was used. Complete physico-chemical and electrochemical characterization was done. Prepared material showed enhanced performance when compared to the similar Ni based materials. Physico-chemical characterization showed, that final material is formed by NiMoO4 nanorods coverd on the surface by the layer of the MoO3-x.

opencc-by-4.0Oct 2023View details →

Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species P. antipodarum—a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness—and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum—a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of non-introgression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.

opencc-by-4.0Jun 2024View details →

Dataset of "Structural Development on Ru and RuO2 Electrodes during Oxygen Evolution – an operando soft X-ray Absorption Spectroscopy Approach"

Time resolved in-situ X-ray absorption spectroscopy (XAS) in soft X-ray region was used to characterize polarized interphase on Ru and Ru oxide based electrodes under oxygen evolution reaction (OER) conditions. XAS spectra were used to align the type and population of oxygen-containing species formed at electrodes at anodic potentials with local electronic structure of the OER catalyst. The operando soft XAS data do not identify a single rate limiting process at potentials negative to 1.4 V vs Ag/AgCl. Individual intermediates of the oxygen evolution process coexist at the surface at potentials preceding the actual OER onset. The OER is accompanied with redistribution of the electron density resulting for a start of the catalytic cycle reflecting increased population of oxygen vacancies at the surface. The observed spectral behavior indicates a confinement of the OER to the coordination unsaturated sites (cus) at the surface.

Dataset of "Nickel-cobalt spinel-based oxygen evolution electrode for zinc-air flow battery"

Following dataset provides all measured data that were collected on nickel (Ni) based electrodes for the oxygen evolution reaction. The electrodes were following: nickel (Ni) pristine mesh (PM), catalysed mesh (CM), nickel pristine foam (PF), catalysed foam (CF). Catalyst was NiCo2O4. Firstly, the catalysed electrodes were prepared and characterized by SEM, EDS and XRD. The electrodes were characterized in three different arrangements: in electrolysis non-flow arrangement, in a flow electrolysis cell and in ZAFB according to the manuscript.

Fifty years of firn evolution on Grigoriev ice cap, Tien Shan, Kyrgyzstan

README Grigoriev data Overview The Grigoriev data collection consists of the following files, which are briefly explained further below. From a relatively large number of files and for clarity, we provide mainly those files which have been directly used in the generation of figures contained in Machguth et al. (2024). While the use in figure creation was the main selection criteria, the files have not been truncated to data shown in the figures.  The files contain more information than shown in the figures. A few files have been added for completeness although not used to create figures (see below). The data sets provided in this repository are listed in the following. Most of these tables contain relatively raw data.  The suggested citations are added in brackets. Please also check Table 1 in Machguth et al. (2024) for potential further references. - 1990_GRG_90_H1-BETA.xlsx                                          (Arkhipov et al., 1996; Thompson et al., 1997) - 1990_GRG_90_H1-CHM.xlsx                                           (Arkhipov et al., 1996; Thompson et al., 1997) - 1990_GRG_90_H1-STRAT.xlsx                                            (Arkhipov et al., 1996; Thompson et al., 1997) - 1990_GRG_90_H2-CHM.xlsx                                            (Arkhipov et al., 1996; Thompson et al., 1997) - 1990_GRG_90_H2-STRAT.xlsx                                            (Arkhipov et al., 1996; Thompson et al., 1997) - 1990_H1-H2_2018_Grigoriev_MI-decadal.xlsx                            (Arkhipov et al., 1996; Thompson et al., 1997; Machguth et al., 2024) - 2001_GRG_01_S1-EE.xlsx                                            (Arkhipov et al., 2004; Mikhalenko et al., 2005) - 2001_metals.pdf                                                    (Usubaliev, 2003) - 2003_GRG03-S1-EE_001.xlsx                                            (Mikhalenko et al., 2005; Kutuzov, 2005) - 2003_GRG03-S2-EE 001.xlsx                                            (Mikhalenko et al., 2005; Kutuzov, 2005) - 2003_pits.xlsx                                                    (Mikhalenko et al., 2005; Kutuzov, 2005) - 2003_temperature_density.xlsx                                        (Mikhalenko et al., 2005; Kutuzov, 2005) - 2003_temperature_logger_data.xls                                    (Mikhalenko et al., 2005; Kutuzov, 2005) - 2018_density_stratigraphy_field_and_PSI_by_centimeter.xlsx        (Machguth et al., 2024) - 2018_PSI_dating_20230517.xlsx                                        (Eichler et al., 2020; Machguth et al., 2024) Detailed Information 1990_GRG_90_H1-BETA.xlsx: refers to Core 1 1990 (labelled H1 probably for "Hole 1"). Unknown to what the 1991 data refer, likely a repeat measurement. 1990_GRG_90_H1-CHM.xlsx: Chemistry Core 1 1990. 1990_GRG_90_H1-STRAT.xlsx: Stratigraphic information Core 1 1990 1990_GRG_90_H2-CHM.xlsx: Chemistry Core 2 1990 1990_GRG_90_H2-STRAT.xlsx: Stratigraphic information Core 2 1990 1990_H1-H2_2018_Grigoriev_MI-decadal.xlsx: This table we calculated from the 1990 tables as well as the 2018 data for the purpose of visualizing                                            decadal means in MIs (Fig. 7). Decadal dating of the 1990 cores was done based on the bomb horizon of 1963 (Thompson et al., 1993, 1997),                                             decadal picks from Thompson et al. (1993) and personal communication by Lonnie Thompson (email 19 June 2023). 2001_GRG_01_S1-EE.xlsx: 2001 core, stable water isotope ratios, firn temperatures, percentage of infiltration ice, stratigraphy 2003_GRG03-S1-EE_001.xlsx: 2003 51m and 22.6m cores, 51m core was drilled thermally, 22.6m core mechanically. For the latter similar data as for 2001 2003_GRG03-S2-EE 001.xlsx: 2003 21.3m core. Reduced amount of measured parameters compared to e.g. 2001 core.  2003_pits.xlsx: Stratigraphy and density measured in a series of snow pits in 2003. 2003_temperature_density.xlsx: Density and temperature measured in 2003 22.6m core. Comparison of T_ice at 4440 m a.s.l. to 1962 core (Dikikh, 1965) 2003_temperature_logger_data.xls: Firn temperatures measured through a thermistor chain during 3 days in June 2003. Data from 14 June have been used for Fig. 5. 2018_density_stratigraphy_field_and_PSI_by_centimeter.xlsx: 2018 core stratigraphy and density. This is a somwhat outdated file which shows the data per centimetre.                                                             The file compares the two measurements of density (only the one from the laboratory was used in Machguth et al., 2024).                                                              Also contains visually observed dust layers (not shown in Machguth et al., 2024) 2018_PSI_dating_20230517.xlsx: Complete data from the analysis of the 2018 core. Bibliography Arkhipov, S. M., Mikhalenko, V. N., & Thompson, L. (1996). Struktura i stratigrafiya deyatel’nogo sloya lednika Grigor’eva na Tyan’-Shanye (Structure and stratigraphy of the active layer  of the Griroriev glacier in the Tjan-Shan). Materialy Glyatsiologicheskikh Issledovaniy (Data of Glaciological Studies), 80, 68–83. Arkhipov, S. M., Mikhalenko, V. N., Kunakhovich, M. G., Dikikh, A. N., and Nagornov, O. V.: Termicheskiy reshim, uslovija l’doobrazovanija i akkumulatsija na lednike Grigor’eva (Tyan’- Shan), v 1962–2001 gg. (Thermal regime, types of ice formation and accumulation on the Grigoriev glacier (Tien Shan), 1962–2001), Materialy Glyatsiologicheskikh Issledovaniy (Data of Glaciological Studies), 96, 77–83, 2004. Eichler, A., Kronenberg, M., Brütsch, S., Rüthi, M., Heule, M., Schwikowski, M., et al. (2020). Chernobyl horizon in a Central Asian ice core.  Annual Report 2019 - Laboratory of Environmental Chemistry - PSI, 31. Kutuzov, S. S.: Prostranstvennie izmenenija i stroenie lednikov vnutrennogo Tyan’-Shanya za poslednie 150 let (Spatial changes and structure of the glaciers of the inner Tien Shan over the last 150 years), Master’s thesis, Lomonossov State University, Moskva, 2005. Machguth, H., Eichler, A., Schwikowski, M., Brütsch, S., Mattea, E., Kutuzov, S., et al. (2024). Fifty years of firn evolution on Grigoriev ice cap, Tien Shan, Kyrgyzstan.  The Cryosphere, 18(4), 1633–1646. https://doi.org/10.5194/tc-18-1633-2024 Mikhalenko, V. N., Kutuzov, S. S., Fayzrakhmanov, F. F., Nagornov, . B., Thompson, L. G., Kunakhovich, M. G., Arkhipov, S. M., Dikikh, A. N., and Usubaliev, R.: Sokrashhenie oledenenija Tyan’-Shanja v XIX – nachale XXI vv.: rezul’taty kernovoro burenija i izmerenija temperatury v skvazhinakh (Glacier recession in the Tien Shan from the XIX to the beginning of the XXI century: results from ice core drilling and borehole temperature measurements), Materialy Glyatsiologicheskikh Issledovaniy (Data of Glaciological Studies), 98, 175–182, 2005. Thompson, L. G., Mosley-Thompson, E., Davis, M., Lin, P. N., Yao, T., Dyurgerov, M., & Dal, J. (1993). “Recent warming” ice core evidence from tropical ice cores with emphasis  on Central Asia. Global Planet. Change, 7(1–3), 145–156. https://doi.org/10.1016/0921-8181(93)90046-Q Thompson, L. G., Mikhalenko, V., Mosley-Thompson, E., Durgerov, M., Lin, P. N., Moskalevsky, M., et al. (1997). Ice core records of recent climatic variability: Grigoriev and It-Tish ice caps  in Central Tien Shan, Central Asia. Materialy Glyatsiologicheskikh Issledovaniy (Data of Glaciological Studies), 81, 100–109. Usubaliev, R. A. (2003). Khimitcheskoe zagryaznenie lednikov Tyan’-Shanya (na primere lednika Grigor’eva) (Chemical pollution of Tien Shan glaciers (on the example of Grigoriev Glacier)).  Izvestija Natsional’noy Akademii Nauk Kirgizskoy Respubliki (News of the National Academy of Sciences of the Kyrgyz Republic), 4, 154–160.

opencc-by-4.0Jul 2024View details →

Dataset of "Hydrogen Evolution Reaction Activity in Mo₂TiC₂Tₓ MXene Derived from Mo₂TiAlC₂ MAX Phase: Insights from Compositional Transformations"

MAX phases represent a crucial building block for the synthesis of MXenes, which constitute an intriguing class of materials with significant application potential. This study investigates the catalytic properties of Mo₂TiAlC₂ MAX phase and the corresponding Mo₂TiC₂Tₓ MXene for hydrogen evolution reaction (HER). Characterization by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS) revealed that despite the presence of secondary phases, the HER catalytic activity is primarily influenced by the MAX phase and its derived MXene. Interestingly, the catalytic activity of the MXene improves over time, attributed to the formation of MoO₂ as identified by XPS. This work enhances the understanding of MXene-based materials for electrochemical applications, highlighting crucial structural and chemical transformations that optimize their performance in sustainable energy technologies.3D structure of lanthanum strontium manganite and yttria-stabilized zirconia composites is predicted based on conductivity measurements using Monte Carlo 3D equivalent circuit network approach. Validation experimental impedance spectra; scanning electron micrographs; cross sections of model simulation or prediction (MSP).

opencc-by-4.0Sep 2021View details →

Seasonal evolution of basal conditions within Russell sector, West Greenland, inverted from satellite observations of surface flow

An annual set of model-inferred basal and surface properties of ice flow at Russell Gletcher sector in Western Greenland with half-month temporal resolution. Derived using the Elmer/Ice ice-flow model by inversion of satellite-observed ice surface velocity (10.5281/zenodo.5535532). The details on the data creatoin can be found in 10.5194/tc-15-5675-2021 . Dataset contains 24 independent NetCDF files (one per 2-weeks time step) with: * alpha - inverted be model basal friction coefficient in log10 (log10(MPa m-1 a) * base - basal topography altitude (m) * lithk - ice thickness (m) * orog - surface altitude (m) * strbasemag - magnitude of basal friction tb (MPa) * xvelbase, yvelbase, zvelbase - 3D basal velocity  (m/yr) * xvelmean, yvelmean - vertically average mean horizontal velocity (m/yr) * xvelsurf, yvelsurf, zvelsurf - 3D surface velocity (m/yr) * n - effective pressure (MPa) The additional WinterMeanState NetCDF file (inversion from the mean velocity of january, Febriary, Mars) contains the same set of variables (except the effective pressure), and in addition contains the As Weertman sliding coeffitient. The results have been interpolated from the native unstructured model grid to the regular grid used for the observed velocity (10.5281/zenodo.5535624).

opencc-by-4.0Oct 2022View details →

DisVis-based filtering of contacts from co-evolution data (or other sources)

Dataset described in the manuscript: Improving the Quality of Co-evolution Intermolecular Contact Prediction with DisVisSiri Camee van Keulen, Alexandre M.J.J. Bonvin Details about the data set can be found at:  https://github.com/haddocking/contact-filtering This archive contains in addition all the models generated with HADDOCK.

edi52/100

Seasonal Evolution of Terrigenous Dissolved Organic Matter in the South Atlantic Bight off Georgia in 2014

Six surveys of the central South Atlantic Bight (SAB) off of Georgia were conducted in 2014. The primary objective of the research cruises was to characterize estuary-shelf exchange and the dispersal of freshwater into the coastal ocean around Sapelo Island off the Georgia coast. The surveys, in April, May, July, August, September, and November, were intended to sample shelf conditions under different seasons. Most of the sampling stations were located at the mouth of the estu-aries around Sapelo Island and over the inner and mid-shelf (<60 km offshore). Eighty samples from transects extending across the shelf from the mouths of the Altamaha River and of Sapelo Sound were selected for the analyses of molecular composition using ultrahigh resolution mass spectrometry (Fourier transform ion cyclotron reso-nance mass spectrometry [FT-ICR MS]) and stable carbon iso-topic signatures (delta 13C). This data set includes spectral analysis of the DOM, including spectral slope (275-295nm wavelength), terrigenous peaks from mass spectrometry analysis, and a computed terrigenous index indicating fraction of terrigenous DOM in water samples.

openCC (other)Jan 2020View details →

opencc-by-4.0Jan 2020View details →

Deep splicing plasticity of the human adenovirus type 5 transcriptome as a driver of virus evolution nanopore data 48hpi

Adenovirus infected MRC5 cells direct RNA sequencing of the mRNA using nanopore. From the paper Deep splicing plasticity of the human adenovirus type 5 transcriptome as a driver of virus evolution. Both the uncorrected fastq files and the lordec corrected files together with the normalised illumina data used to correct the nanpore data are here.

opencc-by-4.0Feb 2020View details →

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

General Description Repository with all analyses described our paper: <a href="https://www.nature.com/articles/s41467-020-17408-w">Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution</a>. If you find this work useful for your own analyses, please cite this work.   Abstract The evolution and diversification of Archaea is central to the history of life on Earth. Cultivation-independent approaches have revealed the existence of the DPANN archaea: a radiation of organisms with small cell and genome sizes. Currently, the placement of the various DPANN lineages and in turn the early evolution of metabolism and symbiosis are debated. Here, we reconstructed genomes of a thus far uncharacterized archaeal phylum-level lineage UAP2 (Candidatus Undinarchaeota). Comparative genomics revealed that members of the Undinarchaeota have small estimated genome sizes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of vitamins, amino acids and other metabolites. In contrast to previous indications, our phylogenomic analyses robustly placed the Undinarchaeota as independent lineage between two major and highly supported clans of ‘DPANN’. Furthermore, our work suggests that DPANN archaea have exchanged core genes with their hosts by horizontal gene transfer, adding to the difficulty of placing DPANN in the tree of life (ToL). In several cases, this pattern is sufficiently dominant that known symbiont-host clades can be identified by inferring routes of HGT across the ToL. Together, our findings provide crucial insights into the origins and evolution of DPANN archaea and their hosts. The annotation workflow for archaeal/bacterial genomes that was used for this paper is also available on github (<a href="https://github.com/ndombrowski/Genome_annotations">here</a>) and an updated version that includes the COG search is available on: <a href="https://github.com/ndombrowski/Annotation_worfklow">https://github.com/ndombrowski/Annotation_workflow</a>   Repository Contents 1_Genome_files.tar.gz includes all Undinarchaeota (original name UAP2) metagenome-assembled genomes (MAGs). This includes:  <ol> <li>The original contigs for each UAP2 MAG (fna files)</li> <li>The prokka output for each UAP2 MAG (faa files)</li> <li>A concatenated file of all proteins from each UAP2 MAG and all archaeal reference genomes (364 genomes in total). This folder also includes a list of archaeal genomes investigated.</li> </ol> 2_Phylogenies.tar.gz includes all files for the phylogenetic analyses. This includes the following folders: 1. Files for the concatenated species trees for different taxa sets. These files are related to the following parts of the manuscript: Supplementary Table 6; Figure 1 and Supplementary Figures S8-S58. The folder includes the following: <ul> <li>Folder '1_unaligned_sequences' includes individual protein sequences extract from the different taxa sets.</li> <li>Folder '2_alignments' includes the alignment files generated by MAFFT.</li> <li>Folder '3_alignments_trimmed' includes the alignments trimmed with BMGE.</li> <li>Folder '4_phylogenies' includes the IQ-TREE output for all phylogenies as well as color-annotation file for figtree. Additionally files rooted with minimal ancestor deviation (MAD) rooting (*.rooted) are provided. Note, that for the final figures the *treefile_renamed (i.e. the iqtree file with the full taxa string) were artificially rooted using the DPANN archaea. The numbering corresponds to Supplementary Table S6 of the main manuscript.</li> <li>Folder ' 5_pdfs' includes the PDFs for each tree</li> </ul> 2. Files for single gene trees that includes: <ul> <li>The folder '1_arcogs' includes the unaligned proteins, alignments, trimmed alignments, trees and pdfs for the single gene trees based on the arCOG identifiers. The arCOGs were extract from 12 UAP2 MAGs + 352 archaeal + 3020 bacterial + 100 eukaryotic genomes. ArCOGs were only considered if they occurred in at least 3 UAP2 genomes. Notice, these files were used to investigate UAP2 for HGT events and correspond to the following parts of the manuscript: Figure 4 and Supplementary Tables 4, 5, 20-22. Additionally, the folder 0_parsing includes some information on how to generate count tables for each marker gene.</li> <li>The folder '151_markers' including the proteins, alignments, trimmed alignments, trees and pdfs for evaluating the 151 marker set used for the concatenated species tree. Files were provided for the 127 and 364 taxa set. These files were used as a basis for the concatenated species trees that were used to generated Supplementary Figures S8-S58. Additionally, the trees were used for ranking marker proteins and generating Supplementary Tables 4-5. For the 364 taxa set, the folder also included a subfolder 0_parsing that provides scripts to investigate some statistics for each marker protein, including the average protein length, average alignment length and average bootstrap support.</li> <li>The folder '3_other_individual_trees' includes the proteins, alignments and phylogenies for the 16S_23S, RubisCO and primase analyses. The data was used to generate the following parts of the manuscript: Supplementary Table 11, Supplementary Figures 3-5, 57 and 59.</li> </ul> 3_Scripts.tar.gz includes all files for the phylogenetic analyses. This includes the following folders: 1. The files for the main workflow for the annotations and phylogenies. <ul> <li>This folder includes the workflow to generate annotations for archaeal genomes as well as an example script that was used to generate phylogenies. These analyses were typically run on a in-house bioinformatics cluster with 4x Xeon Gold 6140 2.3 GHz processors using bash, python and perl. The used system runs a Linux operating system, Red Hat Enterprise 7.5.</li> </ul> 2.  A folder providing any required dependencies that include: <ul> <li>any python or perl scripts that were used during this study and/or that are mentioned in the methods section</li> <li>Databases used for the annotations, esp. if these were slightly modified. Notice, changes typically include parsing of the mapping files or modifications of the sequence headers for easier parsing.</li> <li>mapping files needed to link the genome accession ids to the taxonomy string as well as lists of protein IDs used for different phylogenies (i.e. 14 + 48 arCOGs used for protein phylogenies)</li> </ul> 3. R scripts (including all needed input files) used to:  <ul> <li>generate tables and figures for the annotations, i.e. Figure 2 and 3 and Supplementary Tables 7, 8, 9, 12, 13-15 and Supplementary Figures 60, 62-64 . The input folder includes the raw output from the annotation workflow and includes annotations for the 12 UAP2 MAGs as well as 352 archaeal reference genomes.</li> <li>generate tables and figures for the HGT analyses, i.e. Figure 4 and Supplementary Tables S20-22 Here, proteins based on arCOGs were extracted from 364 archaeal, 3020 bacterial and 98 eukaryotic genomes and used to generate single protein phylogenies. The resulting trees were used to investigate horizontal gene transfer events and the necessary scripts are provided in this folder.</li> <li>generate tables and figures for the amino acid identify (AAI) comparisons, i.e. Supplementary Table S3 and Supplementary Figure S2. </li> <li>rank the marker genes for concatenated species trees for the 127 and 364 taxa set. These were used to generate Supplementary Tables S4 and S5.</li> </ul> General comment: In contrast to the previous version, this datasets includes some small additional scripts generated during the revision process of the corresponding manuscript.

opencc-by-4.0Dec 2020View details →

Evolution of software code at the level of fine-grained elements: data files

The data files available here (68GB uncompressed) have been used for studying the evolution of code at the level of fine-grained elements.  The data are associated with the processing of the 89 open source software repositories hosted on GitHub.  Details regarding each individual GitHub project are stored in the repos folder under directories matching the owner and project name used on GitHub.  For example, the files under repos/KDE/kdevelop correspond to the project hosted on https://github.com/KDE/kdevelop.  Data associated with the statistical analysis of the processed repositories are stored in the statistical-analysis folder.  The file project_details.txt contains the data used for selecting the processed projects.

opencc-by-4.0Jun 2021View details →

Alignments used in "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families"

Alignments used in de Vries et al. (2021) "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families" published as (1) a pre-print: https://doi.org/10.1101/2021.05.27.445924 (2) in Plant Journal (in press)

opencc-by-4.0Oct 2016View details →

RDF Representation of RNA Metabolism Evolution data - version 3 (diagrammed in https://zenodo.org/deposit/47641/)

Version 3 (replaces http://doi.org/10.5281/zenodo.50496) Protein complexes involved in RNA Metabolism; individual proteins and their orthologues through a wide range of fungal species spanning much of the kingdom (using yeast as the primary seed for orthology search, and using the EMBL-EBI orthologue database to identify orthologues). For each family of orthologues, the protein domain structure is determined, and then the presence/absence of that domain is evaluated in each of the species. The data is presented in RDF, and is visualized in the form of Heat Maps in http://doi.org/10.5281/zenodo.47641

Simulation of the SLR Space Segment Evolution to Improve the Realization of Terrestrial Reference Frames and Determination of Low-Degree Gravity Field Parameters

These are data obtained from simulation studies of the development of the space segment of the SLR technique. Detailed information can be found in Najder et al. (2025). Najder, J., Sośnica, K., Zajdel, R., & Kur, T. (2025). Simulation of the SLR space segment evolution to improve the realization of terrestrial reference frames and determination of low-degree gravity field parameters. Journal of Geodesy, 99(6), 46. https://doi.org/10.1007/s00190-025-01971-5

opencc-by-4.0Nov 2023View details →

Longitudinal urban form dataset of Midtown Manhattan: Measuring urban form evolution via quantitative descriptions of plots, buildings and streets from 1890 to the present

This dataset contains data described and used in the research article "The impact of urban form on physical change: A quantitative and diachronic analysis of urban form evolution in Midtown Manhattan".  The longitudinal dataset contains urban form data on nearly 17,000 individual plots (parcels) in Midtown Manhattan, documented through four subsequent time frames: 1890, 1920, 1956 and 2021. The data was compiled from historical cartographic resources and open-access geospatial datasets listed in the ReadMe file.  The dataset includes an array of quantitative descriptions of plots, buildings and streets central to the field of urban morphology, and the binary information of physical change (1: change, 0: no change) identified via diachronic comparison of each time frame at the scale of plots.   Acknowledgements The dataset presented in this repository has been generated as part of a PhD research conducted at the University of Melbourne, Faculty of Architecture, Building and Planning and funded by the University of Melbourne - Melbourne Research Scholarship:  Tümtürk, O. (2024). A data-driven investigation on urban form evolution: Methodological and empirical support for unravelling the relation between urban form and spatial dynamics. Unpublished PhD Thesis. The University of Melbourne, Australia.