Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

Supplementary data from: The Holocene fossil record of the slow loris (Nycticebus sp.) in Java (Indonesia)

Supplementary data from: The Holocene fossil record of the slow loris (Nycticebus sp.) in Java (Indonesia) Abstract: Fossil lorises are rare in Southeast Asia. Their taxonomic relationship with extant populations, and the extent to which their distribution and morphology are influenced by changing environmental conditions, remain poorly understood. This study provides a synthesis of Nycticebus occurrences in Holocene Java (Indonesia). A morphometric analysis of a sample of craniodental remains aims to improve our understanding of their taxonomic status. Morphometrics were also used to explore potential size changes during the Holocene. Based on the literature and a review of museum catalogs, a synthesis was compiled of fossil slow loris occurrences in Java. Morphometric data on the mandible and maxilla of 11 fossil lorises were compared with a dataset of extant specimens to assess variation in size and shape. Five Holocene Nycticebus occurrences were identified in eastern Java. All specimens fall in the range of N. javanicus and N. coucang. The specimens from Hoekgrot, Gua Jimbe and Sampung suggest a closer affinity to N. javanicus. The fossils from Gua Jimbe and Hoekgrot gave values close to the largest N. javanicus specimens, but the (presumably older) Song Terus fossil was of average size. The distribution of Nycticebus suggests that it originally occurred throughout the island. The fossils are probably best identified as N. javanicus or N. coucang, but the Neolithic finds from Hoekgrot and Gua Jimbe are presumably N. javanicus. Size variation in Nycticebus was clinal, but although some large specimens were present, no evidence was found for size diminution during the Holocene.

opencc-by-4.0Feb 2023View details →

Supplementary data for paper titled "Examining the Effects of Environmental Knowledge and Health Insurance Coverage on Health Status"

Codebook, raw data, Stata dataset, Stata code, Stata results

opencc-by-4.0Dec 2022View details →

Supplementary Source Data

Supplementary Main Data.

opencc-by-4.0Feb 2023View details →

Supplementary Data for Manuscript : "Application of OSL surface exposure dating with the use of two-dimensional OSL laser scanning instruments and energy-dispersive x-ray spectroscopy'

Contains all supplementary works mentioned in the manuscript.

Supplementary Data for 'The electron-proton bottleneck of photosynthetic oxygen evolution'

Supplementary data for the publication: 'The electron-proton bottleneck of photosynthetic oxygen evolution', Greife et al. Heat_Artefact_Spectrum.xlsx Spectrum assigned to rapid heating by laser-flash excitation of high-activity Photosystem II membrane particles. This spectrum was used for heat artefact correction of the step-scan data set. The first column is the wavenumber in cm-1, the second column the absorption in arbitrary OD units. Log_Averaged_Interferograms.xlsx Averaged time-resolved FTIR interferograms recorded before and after the application of a saturating excitation flash to high activity Photosystem II membrane particles from spinach. In total 10 sequential flashes were applied. The first column is the time in milliseconds. Remaining columns are the mirror positions of the phase-corrected interferograms with the centerburst shifted to the first position. Amplitude is in arbitrary units. Individual columns correspond to individual time courses at the respective mirror positions. Rows corresponds to interferograms at the respective time. The data for each of the 10 flashes is provided in a separate spreadsheet, which is accordingly labeled. The mirror positions were chosen such that after Fourier transformation the wavenumber range of the resulting spectra corresponds to 929.33 cm-1 to 1858.67 cm-1 , with data points equally spaced on a wavenumber axis.

Supplementary data for eEDM study in thesis 'Low energy observables and fine-tuning in the MSSM'

For the eEDM study in Chapter 5 of the thesis 'Low energy observables and fine-tuning in the MSSM' we have created several input sets, one for each run. These can be found as 'input_iter[x].csv' and are used to created a SPheno input file. The code to run all the software is found in the directory 'Spheno_to_eEDM'. A description of this code can be found in the thesis (DOI will follow upon succesful defense). For each iteration we have gathered the relevant output (masses, couplings, mixing matrices, observables, fine-tuning etc) from the different output files. These are stored in csv files, gathered in eEDMdata.tar . One line in the output file corresponds to one line in the original input file, where the directory name (dir_name) in the output file is the same as the index of the input file. This is one data point of the study.

Supplementary data for: Pevonedistat, a Nedd8-activating enzyme inhibitor, in combination with ibrutinib in patients

In a clinical trial to evaluate a NEDD8-activating enzyme inhibitor in treating a mantle cell lymphoma patient, peripheral blood mononuclear cells (PBMCs) were collected from the patient at baseline and after 3 and 24 hours after drug infusion. Then, single-cell RNA-seq was conducted on the collected PBMCs. The pre-processed data was saved as a Seurat object.

opencc-by-4.0Sep 2022View details →

Supplementary data and code for the analysis of S. kudriavzevii fermentations at 12 and 25C.

Data and code for the analysis of  S. kudriavzevii fermentations at 12 and 25C.

openMar 2023View details →

Supplementary data for Yeoman's et al. in review "Waterfowl eggshell refines palaeoenvironmental reconstruction and multi-species niche construction at the Pleistocene-Holocene transition in the Levant"

This upload contains MALDI-TOF mass spectra, averaged from replicates or as single-best spectrum, as .txt files. Data derive from archaeological eggshells samples for the paper "Waterfowl eggshell refines palaeoenvironmental reconstruction and multi-species niche construction at the Pleistocene-Holocene transition in the Levant".  Sample preparation: Eggshell was recovered from multiple contexts at Shubayqa 1 and Shubayqa 6 from flotation samples [screened with 1mm mesh]. A sample of 34 eggshell fragments were selected for preliminary analysis across seven excavation contexts. Samples were processed according to Demarchi et al., (2022). Briefly, 10-30 mg of sample were ground to a powder and treated with bleach (NaOCl 12-15% w/v) for 72 hours. Samples were washed thoroughly and demineralised in 0.6M hydrochloridric acid (HCl) prior to filtration with 3000 Da Nanosep micro-ultrafiltration cells. Sulfide bonds were reduced and alkylated using dithiothreitol (1M, aqueous solution) and iodoacetamide (0.5 M, aqueous solution)  and the samples were digested in trypsin overnight at 37 °C. Following digestion, peptide digests were purified using C18 Zip-tips according to the manufacturer’s directions, prior to spotting. Samples were analysed in triplicate or duplicate by MALDI-MS (Bruker Microflex MALDI-TOF mass spectrometer).

Supplementary data

supplementary data

opencc-by-4.0Dec 2022View details →

Ranunculales supplementary data

Supplementary data for the analysis of Ranunuculales LC-MS/MS files. They are a part of the workflow for the book chapter "Studying plant specialized metabolites using computational metabolomics strategies" for the Methods in Molecular Biology book series.

Supplementary data products for Ha et al. 'Assessing the biogeography of marine giant viruses in four oceanic transects'.

Processed data products for Ha et al., "Assessing the biogeography of marine giant viruses in four oceanic transects".

opennotspecifiedDec 2021View details →

TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices

TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references

opencc-by-4.0Nov 2022View details →

Supplementary data for "BepiColombo mission confirms stagnation region of Venus and reveals its large extent"

Dataset of the data presented in the figures of Persson et al. (2022), Nature Communications, "BepiColombo mission confirms stagnation region of Venus and reveals its large extent". https://doi.org/10.1038/s41467-022-35061-3 Full author team: M. Persson1*, S. Aizawa1, N. André1, S. Barabash2, Y. Saito3, Y. Harada4, D. Heyner5, S. Orsini6, A. Fedorov1, C. Mazelle1, Y. Futaana2, L.Z. Hadid7, M. Volwerk8, G. Collinson9, B. Sanchez-Cano10, A. Barthe1, E. Penou1, S. Yokota11, V. Génot1, J.A. Sauvaud1, D. Delcourt7, M. Fraenz12, R. Modolo13, A. Milillo6, H.-U. Auster5, I. Richter5, J.Z.D. Mieth5, P. Louarn1, C.J. Owen14, T.S. Horbury15, K. Asamura3, S. Matsuda16, H. Nilsson2 M. Wieser2, T. Alberti6, A. Varsani8, V. Mangano6, A. Mura6, H. Lichtenegger8, G. Laky8, H. Jeszenszky8, K. Masunaga3, C. Signoles1, M. Rojo1, G. Murakami3 1Institut de Recherche en Astrophysique et Planétologie, Centre National de la Recherche Scientifique, Université Paul Sabatier - Toulouse III, Centre National d’Etudes Spatiales, Toulouse, France 2Swedish Institute of Space Physics, Kiruna, Sweden 3Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Japan 4Department of Geophysics, Graduate School of Science, Kyoto University, Kyoto, Japan 5Institute for Geophysics and Extraterrestrial Physics, Technische Universität Braunschweig, Braunschweig, Germany 6Institute of Space Astrophysics and Planetology, Istituto Nazionale di Astrofisica, Rome, Italy 7Laboratoire de Physique des Plasmas (LPP), Centre National de la Recherche Scientifique, Observatoire de Paris, Sorbonne Université, Université Paris Saclay, École Polytechnique, Institut Polytechnique de Paris 8Space Research Institute, Austrian Academy of Sciences, Graz, Austria 9National Aeronautic and Space Administration, Goddard Space Flight Center, Greenbelt, Maryland, USA 10School of Physics and Astronomy, University of Leicester, Leicester, UK 11Department of Earth and Space Science, Graduate School of Science, Osaka University, Japan 12Max-Planck-Institute for Solar System Research, Göttingen, Germany 13Laboratoire Atmosphères, Milieux, Observations Spatiales, Institut Pierre Simon Laplace, Université Versailles Saint Quentin en Yvelines, Université Paris-Saclay, Université Pierre Marie Curie, Centre National de la Recherche Scientifique, Guyancourt, France 14Mullard Space Science Laboratory, University College London, Holmbury St. Mary, UK  15Imperial College London, South Kensington Campus, London, UK  16Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan      *Corresponding author. Email: <a href="mailto:moa.persson@irap.omp.eu">moa.persson@irap.omp.eu</a>

Supplementary Data to "Simulation of dendritic-eutectic growth with the phase-field method" by Seiz et al. pt. 2

Data from some additional simulations conducted during the review of the paper. The goal was to test whether the theory delineating the dendritic-eutectic regime from the eutectic regime would also be applicable at lower solidification speeds. I chose the gradient G = 99 K/mm for quicker convergence and a target crossover concentration of c_0 = 0.11 to roughly get a factor of 10 slower crossover velocity compared to the previous simulations. The crossover velocity, following the theory, ended up being V= 8.347 um/s. The grid spacing was increased by a factor of 3 motivated by the classical scaling laws VR^2 = const. (R= dendrite tip radius or lamellar spacing) and approximating sqrt(10) as 3. At first, three test concentrations (c_0 = 0.1, 0.11, 0.12) are considered. If the theory is right, only c_0 = 0.1 should yield dendritic-eutectic growth.   Even after an increase of grid spacing, having more than 5 diffusion lengths between the solidification front and the boundary would have required in excess of 15k cells in the growth direction. Thus I opted to work with a smaller domain for which I later needed to account. I employed a domain of 1200 um (4k cells) in the growth direction, with the moving cutoff at 600 um, and a width of 270 um. This makes for about 2.5 diffusion lengths (l_d = 239.6 um) between the front and the boundary. This did influence the results, as the simulation with c_0 = 0.11 showed dendritic-eutectic growth. Fitting an exponential ansatz for the concentration c(x) = c_inf + dc exp(-x/l_d) (x starting from the dendrite tip) showed that the apparent far-field concentration c_inf=0.108243 was actually within the dendritic-eutectic regime. In order to approximate a simulation for which c_inf = 0.11, the ansatz was employed to solve for c(x_b = 600um) using the actual diffusion length for l_d and observed tip concentration to determine dc. This led to a boundary value of c(x_b) = 0.115, for which another simulation was run. This simulation did show eutectic growth dominating, though the apparent far-field concentration (c_inf = 0.112216) at simulation end did not match the target concentration, likely due to being not converged yet. However, this point does lie within the eutectic regime as predicted by the theory and thus the theory also works at lower velocities once the problem of finite domain sizes is accounted for.   Videos showing the evolution of the four simulations with different boundary concentration are attached, though with somewhat variable time between frames. The videos show a 660 x 270 um view of the simulation, slightly beyond the moving window cutoff. Attached as well is the updated microstructure map (with the new simulations plotted over their apparent far-field concentration) and a plot of the height difference between the maximal observed position of the alpha and theta phase. The latter serves as an easy way to differentiate dominant eutectic from dominant dendritic-eutectic growth, as this difference goes to zero for dominant eutectic growth, but some significant non-zero value for dendritic-eutectic growth.

opencc-by-4.0Nov 2020View details →

Supplementary data to 'Coupling between cohesive element method and Node-to-segment contact algorithm : Implementation and application'

This archive contains the data and the scripts for the simulations presented in the paper Pundir, M., Guillaume,  A. "Coupling between cohesive element  method and Node-to-segment contact algorithm : Implementation and application'" (2020)

Supplementary data to "Small-scale variation prevails in the cell shape patterning of green microalgae belonging to the genus Micrasterias (Zygnematophyceae, Viridiplantae)"

The supplementary data consist of 24 TPS files including the landmark coordinates of 12 Micrasterias datasets (two separate digitisations for each dataset). In addition, the R script used for the analyses described in the paper submitted to "Evolutionary Biology" and the utility file with factors for Procrustes ANOVA are also included.

opencc-by-4.0Dec 2022View details →

Supplementary Data for "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" in GRL.

Supplementary data tables for Ma et al. (2023) associated with the paper entitled "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" published in GRL.

Supplementary Data for "Volcanic phosphorus supply boosted Mesozoic terrestrial biotas in northern China" in Science Bulletin.

Supplementary data tables for Ma et al. (2023) associated with the paper entitled "Volcanic phosphorus supply boosted Mesozoic terrestrial biotas in northern China" published in Sci. Bull.