cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14775700
title: Why does animal home range size decrease with population density? -Repository

description: Data and R code for calculating snowshoe hare home ranges and testing how snowshoe hare home range size is effected by population density. Study takes place over multiple years of the hare population cycle during which some individuals were recieving supplementary food (food add experiment).

Necessary data and script are shared here. All data cleaning steps and project design can be found in the full repository at: https://github.com/jballuffi/HR_PopCycle_SnowshoeHares

To run:

Source all function scripts ('function_...R'), 'ggplot_themes.R', 'packages.R', and 'variables.R' at the start of each script to load necessary packages, functions, and ggplot formating. This is the first line of each script below.

1) run the script: '03-calc_HRarea.R' to calculate home range sizes from cleaned gps data ('all_gps.rds'). If you wish to not look at home range calculations skip to step 2.

2) take the compiled data (compileddata.rds), which home range data (output from step 1) merged with hare density data (densities.rds) and run the script '05-homerange_plots.R' to get figure 1 in paper.

3) run '06-results_density.R' to get results tables and figures.
DOI: 10.5281/zenodo.14900076
title: LS4P-II prototype experiment (GFS/SSiB2) datasets

description: Here is the LS4P-II prototype experiment (GFS/SSiB2) datasets used for the paper " Effect of Rocky Mountain and Tibetan Plateau 1998 Spring Land Temperature on N. American and East Asian Summer Precipitation Anomalies " by Nayak H P and co-authors submitted to Journal of Geophysical Research (JGR) for publication.
DOI: 10.5281/zenodo.14949934
title: Genomic drivers of pyrethroid resistance escalation in the malaria vector Anopheles funestus across Africa
title: Supplementary figures
title: Supplementary tables

description: Additional informations

These data provide additional information related to the manuscript. They include a supplementary material file containing supplementary figures (Fig. S1–S20) and tables (Table S1–S6) cited in the manuscript, as well as a supplementary text detailing aspects of the methodology and presenting additional findings. Furthermore, supplementary Table 7 reports genes overexpressed in a dose-response manner and associated with pyrethroid resistance escalation in Anopheles funestus in Southern Africa. Supplementary Table 8 lists non-synonymous polymorphisms linked to selective sweeps in An. funestus across Africa, while supplementary Table 9 highlights key structural variant-based duplications associated with selective sweeps in An. funestus across the continent.
DOI: 10.5281/zenodo.14998322
title: Dataset to develop the Carbon Dynamic model for agricultural Ponds in "Small ponds as carbon emission and burial hotspots in lowland agricultural landscape"
DOI: 10.5281/zenodo.15009571
title: Discrete Element Method simulation data for granular flow in a wedge shaped hopper

description: Raw data for all the simulations described in the paper "Granular flow in a wedge-shaped hopper with smooth walls and radial gravity: Theory and simulations", Physical Review E, 2025 by Afroz Momin and D. V. Khakhar.
DOI: 10.5281/zenodo.7431680
title: Systemic Synuclein Sampling Study (S4)

description: The Systemic Synuclein Sampling Study (S4) aimed to investigate the levels and distribution of the protein alpha-synuclein and other biomarkers in Parkinson’s disease. S4 data is a rich data set facilitating discovery, validation, and reproducibility in Parkinson’s disease research. The data set was generated through cross-sectional clinical measurements (health and medical history questionnaires administered by a clinic practitioner), brain imaging, and analysis of assays performed on biofluids and tissues. S4 is a cross-sectional study <em>without longitudinal follow-up</em>, meaning that study activities could be completed over a 16-week time period as described in the S4_Clinical Study Protocol. As part of the testing battery, biological samples including DNA, RNA, CSF, plasma, serum, whole blood, saliva, skin, colon tissue, and submandibular gland tissue were collected from participants. These samples are distributed to academic laboratories and industry groups on an ongoing basis for analysis and the resultant data are returned and are distributed to the public when they become available. As new studies are released, an updated version of this data will be posted. <strong>*Note that downloading this entire data set will require ~550 GB of storage space. Individual file sizes are included in the 'manifest.csv' file. More information on the contents of these data can be found in the 'S4_Data_Dictionary.pdf' file, which can either be downloaded on this page once your access request has been approved or here for those interested in reviewing contents of these data prior to applying.</strong>
DOI: 10.5285/0683e320d8634a37aa1d9ef62dd41a0d
title: ESA Soil Moisture Climate Change Initiative (Soil_Moisture_cci): Version 04.7 data collection

description: Soil Moisture data (version 04.7) from the European Space Agency's (ESA) Soil Moisture Climate Change Initiative (CCI) project. This dataset collection contains three surface soil moisture datasets, alongside ancilliary data products. The ACTIVE and PASSIVE products have been created by fusing satellite scatterometer and radiometer soil moisture products respectively. In the case of the ACTIVE product, these have been derived from the AMI-WS and ASCAT satellite instruments and for the PASSIVE product from the satellite instruments SMMR, SSM/I, TMI, AMSR-E, WindSat, AMSR2 and SMOS. The COMBINED product is generated from the Level 2 active and passive instruments..

The homogenized and merged products present a global coverage of surface soil moisture at a spatial resolution of 0.25 degrees. The products are provided as global daily images, in NetCDF-4 classic file format, the PASSIVE and COMBINED products covering the period (yyyy-mm-dd) 1978-11-01 to 2019-12-31 and the ACTIVE product covering 1991-08-05 to 2019-12-31. The soil moisture data for the PASSIVE and the COMBINED product are provided in volumetric units [m3 m-3], while the ACTIVE soil moisture data are expressed in percent of saturation [%]. For information regarding the theoretical and algorithmic base of the datasets, please see the Algorithm Theoretical Baseline Document (ATBD). Other additional documentation and information documentation relating to the datasets can also be found on the CCI Soil Moisture project web site or in the Product Specification Document.

The data set should be cited using the all of the following references:

1. Gruber, A., Scanlon, T., van der Schalie, R., Wagner, W., and Dorigo, W. (2019). Evolution of the ESA CCI Soil Moisture climate data records and their underlying merging methodology, Earth Syst. Sci. Data, 11, 717–739, https://doi.org/10.5194/essd-11-717-2019

2. Dorigo, W.A., Wagner, W., Albergel, C., Albrecht, F., Balsamo, G., Brocca, L., Chung, D., Ertl, M., Forkel, M., Gruber, A., Haas, E., Hamer, D. P. Hirschi, M., Ikonen, J., De Jeu, R. Kidd, R. Lahoz, W., Liu, Y.Y., Miralles, D., Lecomte, P. (2017). ESA CCI Soil Moisture for improved Earth system understanding: State-of-the art and future directions. In Remote Sensing of Environment, 2017, ISSN 0034-4257, https://doi.org/10.1016/j.rse.2017.07.001

3. Gruber, A., Dorigo, W. A., Crow, W., Wagner W. (2017). Triple Collocation-Based Merging of Satellite Soil Moisture Retrievals. IEEE Transactions on Geoscience and Remote Sensing. PP. 1-13. 10.1109/TGRS.2017.2734070
DOI: 10.6084/m9.figshare.25488016
title: <b>Mycelium biomass and community composition impact nutrient concentration in arbuscular mycorrhizal fungi at fine spatial scale</b>

description: 1. We conducted an experiment to quantify the spatial heterogeneity of plant-soil-mycelia nutrients within a gridded 2 × 2 m² quadrat. Hyphal in-growth bags were installed to extract pure AM mycelium. The concentrations of carbon ([C]), nitrogen ([N]), and phosphorus ([P]) in both plant and mycelium tissues were measured. Additionally, the AM fungal community from the extracted hyphae was sequenced to assess AM fungal composition. Values from each row is data for each grid.
DOI: 10.6084/m9.figshare.25725594
title: Datasets and R code for Hwang, B.C., <i>et al.</i> The impact of insect herbivory on biogeochemical cycling in broadleaved forests varies with temperature. <i>Nature Communications</i><b> </b><b>15</b>, 6011 (2024).

description: We established a global network of 74 plots within 40 mature, undisturbed broadleaved forests located across tropical, temperate, and boreal zones to investigate the impact and drivers of insect herbivory on element cycling. Using standardized methods, we analyzed freshly senesced and green leaves from these plots to estimate foliar production and herbivory, carbon, nitrogen, phosphorus and silica concentrations, and stand-level nutrient fluxes as deposited by insect herbivores. We then compared insect-mediated element fluxes to other sources of labile nutrients such as atmospheric deposition and bedrock weathering. We also investigated abiotic (mean annual temperature, evapotranspiration : mean annual precipitation, soil nutrient concentrations) and biotic (foliar biomass production, leaf-level herbivory, foliar nutrient concentrations) factors as potential drivers of these fluxes. All annual data by litter trap (herblat.xls), by plot means (herblatmeans.xls), and code for analysis (herblatcode.R) found in this folder were used for the following manuscript:Hwang, B.C., Giardina, C.P...Metcalfe, D.B<i>.</i> The impact of insect herbivory on biogeochemical cycling in broadleaved forests varies with temperature. <i>Nature Communications</i> <b>15</b>, 6011 (2024). https://doi.org/10.1038/s41467-024-50245-9<br>V.2 Updated figshare title and citation to corresponding article<br>V.3 Edited plot and means data for GURIA, LAGON1, and SAIRME locations
DOI: 10.6084/m9.figshare.28120670
title: A multisensor dataset of south asian post-graduate students working on mental rotation tasks

description: Spatial thinking, in general, and mental rotation, in particular, have seen sustained research attention due to such abilities playing a critical role in STEM learning. The recent development of sensor-based approaches to identify, understand, and measure cognition and affect opens up new possibilities to study such topics. We collected galvanic skin response, electroencephalography, screen recording, facial expressions, manual emotion logging, log, gaze, and self-reports of 38 participants as they solved mental rotation tasks under various conditions, namely, 1. with no time restriction and no feedback, 2. with no time restriction and with feedback and 3. with time restriction and with no feedback, respectively. The availability of such a dataset will help researchers in the spatial thinking community to study interesting questions related to strategy selection, flexibility, affective response, and group differences in mental rotation tasks. Furthermore, the learning analytics community could gain valuable insights into how providing feedback might change learning and engagement during such tasks.
DOI: 10.6084/m9.figshare.28730105
title: Supplementary Material for: Late onset Sub-Retinal Silicone Oil Migration through Optic Disc Coloboma

description: This report describes a case of late onset subretinal silicone oil migration in an eye with congenital optic disc coloboma and its treatment.
A 15-year-old male with a history of left eye congenital optic disc coloboma and amblyopia presented with a third recurrence of retinal detachment (RD) with proliferative vitreoretinopathy (PVR). The patient underwent PPV, subretinal fluid drainage through a peripheral retinotomy, silicone oil tamponade, and endolaser around the coloboma and retinotomy. The retina re-attached successfully. However, 14 months post-operatively examination revealed high intra-ocular pressure (IOP) of 33 mmHg and a submacular bubble of silicone oil was evident. The patient underwent sub macular silicone oil removal.
Here we describe the unique late onset subretinal migration of intravitreal silicone oil following retinal detachment repair in an eye with optic disc coloboma in association with raised IOP. Silicone oil in the presence of optic disc pit may have serious complications requiring clinician awareness, including, retrolaminar and intraventricular migration with potential vision loss and central nervous system toxicity. This case demonstrates potential mechanisms of sub retinal silicone oil migration through the coloboma that serves as a passage and an increased IOP which drives the oil from the vitreous in to the sub retinal space.
DOI: 10.15152/qdb.115
title: QDB archive #115

description: This QDB archive contains data and model(s) from the following publication: Piir, G.; Sild, S.; Roncaglioni, A.; Benfenati, E.; Maran, U. QSAR model for the prediction of bio-concentration factor using aqueous solubility and descriptors considering various electronic effects. SAR QSAR Environ. Res. 2010, 21, 7-8, 711-729.
DOI: 10.15152/qdb.123
title: QDB archive #123

description: This QDB archive contains data and model(s) from the following publication: Saldana, D. A.; Starck, L.; Mougin, P.; Rousseau, B.; Pidol, L.; Jeuland, N.; Creton, B. Flash Point and Cetane Number Predictions for Fuel Compounds Using Quantitative Structure Property Relationship (QSPR) Methods. Energy Fuels 2011, 25, 9, 3900–3908.
DOI: 10.15152/qdb.99
title: QDB archive #99

description: This QDB archive contains data and model(s) from the following publication: Lang, Andrew SID; Bradley, Jean-Claude Abraham descriptor S.
DOI: 10.17632/vzz7xpymxd.1
title: small_toy_dataset_for_PLOM-CON_analysis

description: a small toy dataset for PLOM-CON analysis
DOI: 10.17632/zddtpgzv63.4
title: Liquid based cytology pap smear images for multi-class diagnosis of cervical cancer

description: While a publicly available benchmark dataset provides a base for the development of new algorithms and comparison of results, hospital-based data collected from the real-world clinical setup is also very important in automated AI-based medical research likewise in disease diagnosis or categorization of predicted disease for tissue level staging or any class identification as per standard protocol so that the developed algorithm works with as much accuracy as possible in the regional context. The repository supports research work related to image segmentation and final classification for a complete decision support system. Liquid based cytology is one of the cervical screening tests. The repository consists of total 963 images sub-divided into four sets of images representing the four classes of pre-cancerous and cancerous lesions of cervical cancer as per standards under The Bethesda System. The pap smear images were captured in 40x magnification using Leica ICC50 HD microscope which is collected and prepared using the liquid-based cytology technique from 460 patients. Microscopic investigation of abnormal changes in cell-level enables detection of malignancy or pre-malignant characteristics. This procedure is time-consuming and subject to inter or intra-observer variability which is why computer-assisted diagnosis can improve the overall disease diagnosis time period to proceed with rapid treatment and therapy which can limit late diagnosis of cervical cancer.
DOI: 10.18150/a3hwnt
title: Electrochemical data for hydrogenated titania nanotubes electrodes modified with M13 bacteriophages

description: Szot-Karpińska, K. Electrochemical data for hydrogenated titania nanotubes electrodes modified with M13 bacteriophages. The data shows; differential pulse voltammograms and cyclic voltammetry measured for different concentrations of M13 phage and E.coli bacteria in the presence of 1-1'-ferrocenedimethanol; cyclic voltammograms for different concentrations of M13 phage in phasphate buffer saline.
DOI: 10.18462/iir.icr.2023.0153
title: Experimental assessment and correlation of the liquid density and saturation pressure of trans-1,2-Dichloroethene (R1130(E)).
DOI: 10.22002/d1.20038
title: Distributed acoustic sensing recorded Ridgecrest Earthquake aftershocks

description: This data set is composed of 30-second time windows that encompass the early onset waveforms of 50 high SNR earthquakes recorded by a distributed acoustic sensing array in Ridgecrest, CA
DOI: 10.23696/vdemds23
title: V-Dem Dataset v13
DOI: 10.26050/wdcc/pmmxmcrtdgp122
title: PalMod2 MPI-M MPI-ESM1-2-CR Transient Simulations of the Last Deglaciation with prescribed ice sheets from GLAC-1D reconstructions (r1i1p2f2)

description: Project: PalMod2 - From the last interglacial to the anthropocene - modeling a complete glacial cycle. The PalMod project (https://www.palmod.de/) aims for a better understanding of how slow feedbacks in the Earth system operate. Using the new insights into Earth system dynamics, PalMod will also make projections of the future climate over the next few millennia. The project PalMod is in the second phase and funded by the German Federal Ministry of Education and Research as a Research for Sustainability Initiative. Summary: The transient simulation was performed with the Max Planck Institute for Meteorology Earth System Model version 1.2 in coarse resolution (MPI-ESM-CR). The model includes the spectral atmospheric model ECHAM6.3 at T31 horizontal resolution (approx. 3.75°) and 31 vertical levels, the land surface vegetation model JSBACH3.2, and the primitive equation ocean model MPIOM1.6 with a nominal resolution of 3°. The applied setup was introduced in detail in Kapsch et al. (2021 and 2022). For the experiment, the model was integrated from a glacial state at 26 ka to the year 1950 with prescribed atmospheric greenhouse gas concentrations (Köhler et al., 2017) and insolation (Berger & Loutre, 1991). Ice sheets and surface topographies were prescribed from GLAC-1D (Tarasov et al., 2012) reconstructions. All forcing fields are updated every 10 years of the simulations and initiate changes in the topography, glacier mask, river pathways, ocean bathymetry, and land-sea mask. Meltwater from ice sheets is calculated as the temporal derivative of ice thickness at grid points covered by grounded ice sheets. The derived meltwater is then distributed by the hydrological discharge model and finally released into the ocean as freshwater. The experiment was performed as part of a model ensemble that contains simulations differing in terms of their tuning parameters, parameterizations and bug fixes. The ensemble is described in detail in the Supplementary Material of Kapsch et al. (2022). The current simulation refers to GLAC1D_P2 in Kapsch et al. (2022) and is significantly colder during the glacial than model version P1, indicating a stronger sensitivity to greenhouse gas changes. The glacial cooling over the North Atlantic is more realistic in P2 and P3 than in P1. P2 and P3 are also more sensitive to small changes in the meltwater forcing than P1. The experiment was performed as part of a model ensemble that contains simulations differing in terms of their tuning parameters, parameterizations, bug fixes and forcing. These differences are described according to the CMIP6 nomenclature, where r denotes the realization, i the initialization method, p differences in the physics and f in the forcing. The ensemble is described in detail in the Supplementary Material of Kapsch et al. (2022).
DOI: 10.34740/kaggle/dsv/8668279
title: 🧠 Alzheimer's Disease Dataset 🧠
DOI: 10.4225/08/57590b59a4a08
title: Topographic Wetness Index derived from 1" SRTM DEM-H

description: Topographic Wetness Index (TWI) is calculated as log_e(specific catchment area / slope) and estimates the relative wetness within a catchment.

The TWI product was derived from the partial contributing area product (CA_MFD_PARTIAL), which was computed from the Hydrologically enforced Digital Elevation Model (DEM-H; ANZCW0703014615), and from the percent slope product, which was computed from the Smoothed Digital Elevation Model (DEM-S; ANZCW0703014016). Both DEM-S and DEM-H are based on the 1 arcsecond resolution SRTM data acquired by NASA in February 2000.

Note that the partial contributing area product does not always represent contributing areas larger than about 25 km2 because it was processed on overlapping tiles, not complete catchments. This only impacts TWI values in river channels and does not affect values on the land around the river channels. Since the index is not intended for use in river channels this limitation has no impact on the utility of TWI for spatial modelling.

The TWI data are available in gridded format at 1 arcsecond and 3 arcsecond resolutions.

The 3 arcsecond resolution TWI product was generated from the 1 arcsecond TWI product and masked by the 3” water and ocean mask datasets.
DOI: 10.5281/zenodo.10908290
title: Data for "Generally noise-resilient quantum gates for trapped-ions"

description: Data for Orozco-Ruiz, M., Rehman, W., and Mintert, M. "Generally noise-resilient quantum gates for trapped-ions".
DOI: 10.5281/zenodo.11074554
title: Data for "The Massive and Distant Clusters of WISE Survey. XII. Exploring X-ray AGN in Dynamically Active Massive Galaxy Clusters at z~1"

description: This dataset corresponds to the manuscript titled "The Massive and Distant Clusters of WISE Survey. XII. Exploring X-ray AGN in Dynamically Active Massive Galaxy Clusters at z~1" (DOI: 10.3847/1538-4357/adbae4), accepted for publication in The Astrophysical Journal on February 24, 2025. To replicate the plots and access the catalogs used in the paper, download and extract all the zip folders along with the Jupyter Notebook "madcows_notebook.ipynb" into the same directory. Open the notebook and follow the instructions provided. For any issues, please contact the corresponding author.
DOI: 10.5281/zenodo.11204182
title: Dataset related to the manuscript Wagner and Schepanski (submitted to JAMES, 2024): "Quantifying fire-driven dust emissions using a global aerosol model"

description: This dataset belongs to the manuscript of Wagner and Schepanski (2024) entitled "Quantifying fire-driven dust emissions using a global aerosol model" submitted to the "Journal of Advances in Modeling Earth Systems (JAMES)".

It contains the for the 10 year simulation period 2004-2013 the monthly, seasonal, or yearly averaged fields of the variables (variable name in brackets) that were used to prepare the plots and statements made in the manuscript. These are in detail:



GFAS input data of FRP (frp)

simulated AOD (tau_2d_550nm) and dust AOD (tau_comp_du_550nm)

simulated wind-driven (emi_du_dust) and fire-driven (emi_du_fdust) dust emission fluxes

simulated atmospheric dust concentration (du_all) including the soluble/insoluble coarse (du_ci, du_cs) and accumulation (du_ai, du_as) mode together with vertical atmospheric pressure levels (pfull)


The simulated results are provided for both simulations, the control run without the additional fire-dust emissions and the actual firedust simulation with the new fire-dust emission parameterization.
DOI: 10.5281/zenodo.14628829
title: Model output (ROMS_HH3) of simulating OAE in Halifax Harbour

description: This repository provides model output (HRM3) for analysis in the following article:

Wang B., Laurent A., Pei Q., Sheng J., Atamanchuk D., Fennel K. Maximizing the detectability of Ocean Alkalinity Enhancement (OAE) while minimizing its exposure risks: Insights from a numerical study. preprint