cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9l9r2vs
title: Structure-from-motion derived orthomosaic imagery and digital surface models (DSMs) from the intertidal region at Whale's Tail Marsh, South San Francisco Bay, CA

description: This data release presents digital surface models (DSMs) and orthomosaic images of the Whale's Tail Marsh region of South San Francisco Bay, CA. The data were created using structure-from-motion (SfM) processing of repeat aerial imagery collected from fixed-wing aircraft. The raw images were acquired from an approximate altitude of 427 meters (1,400 feet) above ground level (AGL), using a Hasselblad A6D-100c camera fitted with an HC 80 lens, resulting in a nominal ground-sample-distance (GSD) of 2.5 centimeters per pixel. The acquisition flight lines were designed to provide approximately 50 percent overlap between adjacent flight lines (sidelap), with approximately 70 percent overlap between sequential images along the flight line (forelap). Survey control was established using an onboard camera-synchronized dual-frequency GPS system as well as ground control points (GCPs) distributed throughout the survey area and measured using survey-grade post-processed kinematic (PPK) GPS. Both the data from the onboard GPS and from the GPS used to measure the GCPs were post-processed using a nearby Continuously Operating Reference Station (CORS) operated by the National Geodetic Survey (NGS). Structure-from-motion processing of these data was conducted using a "4D" processing workflow in which imagery from each of the different acquisition dates were co-aligned to increase relative spatial precision between the final data products.
DOI: 10.5067/7kknq5uurm2w
title: SMAP L3 Radar/Radiometer Global Daily 9 km EASE-Grid Soil Moisture, Version 3
DOI: 10.5281/zenodo.10682781
title: The evolvement of ULVZ at LLSVP margins--reference model with B=3.0 and etaC=1.0

description: This tar file is created and uploaded for the submission of the manuscript titled 'The evolution of dense ULVZs originating outside LLSVPs and implications for dynamics at LLSVP margins' to the journal Journal of Geophysical Research-Solid Earth.

This tar file is for the reference model in the manuscript, which employs a buoyancy number B=3.0 and a compositional viscosity eta_C=1.0 for the ULVZ. The collection includes the raw output data from finite-element mantle convection code CitcomS (www.cig.org, modified from the CitcomS-3.3.1 version) for the evolvement of a ULVZ initially beneath a mantle downwelling. All data follow the CitcomS output convention. Files named *coord* are for the coordinate, *.buoy* are for the density anomaly, *comp_nd* are for the compositional fields (LLSVP and ULVZ), *temp* are for the temperature and velocity fields, *visc* are for the viscosity field. The time frame 12000 is the initial condition of this calculation with one stable LLSVP, having already evolved for ~2 Gyrs, at the bottom center of the model domain, as well as a newly emplaced ULVZ near one sidewall beneath a cold downwelling. The calculation is done for another 18000 time steps.
DOI: 10.5281/zenodo.10778206
title: Phylogenomics and the rise of the angiosperms

description: Data repository of

Zuntini, Carruthers et al. 2024 - Phylogenomics and the rise of the angiosperms
DOI: 10.5281/zenodo.11519056
title: Quantum Chemical Data – A Heterodox Approach for Designing Iron Photosensitizers: Pentacyanoferrate Complexes with Monodentate Pyridinium based Acceptor Ligands

description: Simulated ground and excited state properties of [Fe-mpz+] and [Fe-bpy+], as obtained at the B3LYP/def2svp level of theory within water (PCM vs PCM and 10 explicit water molecules). Both complexes were investigated within Franck-Condon region (see directory: FC) as well as within two triplet equilibria (see directories: 3mc and 3mlct).

The folder of each system contains the charge density differences (CDDs) of dipole-allowed transitions contributing to the electronic absorption within the singlet ground state (singlet-singlet transitions: SS and singlet-triplet transitions: ST).

The spin density of the relaxed triplet ground state (see directories: 3mc and 3mlct) and CDDs of spin and dipole allowed triplet-triplet transitions are given. These transitions are correlated to the excited-state absorption signals as investigated by transient absorption spectroscopy.

All fully relaxed equilibrium structures, i.e., S0 (FC) and T1 (3MC and 3MLCT) as well as (approximate) transition state strutures along the 3MLCT-3MC pathways are provided as xyz files within the respective folders.
DOI: 10.5281/zenodo.12739662
title: Global leaf inclination angle (LIA) and nadir leaf projection function (G(0)) products

description: Leaf inclination angle (LIA), the angle between leaf surface normal and zenith directions, is a vital parameter in radiative transfer, rainfall interception, evapotranspiration, photosynthesis, and hydrological processes. In the radiative transfer regime, LIA is generally represented by the leaf projection function (G(θ)), which is defined as the average projection ratio of unit leaf area in the illumination or viewing direction θ.

This dataset (CAS-GLA) includes the first global mean LIA (MLA) and nadir leaf projection function (G(0)) products at the spatial resolutions of 500 m and 0.05 degrees. The products are recorded in GeoTIFF format under the WGS-84 geographic coordinate system. The global 500 m MLA product was generated by gap-filling LIA measurement data using a random forest regressor after a series of preprocessing, such as spatial expansion, LIA upscaling, and sample screening. Cross-validation shows that the predicted MLA presents a medium consistency (r = 0.75, RMSE = 7.15°) with the validation samples. The 500 m MLA product was further upscaled to 0.05 degrees by weighting the MODIS 500 m leaf area index. The G(0) product was derived from the MLA by assuming a single-parameter ellipsoidal leaf angle distribution. The G(0) product agrees moderately with high-resolution reference data (r = 0.62, RMSE = 0.15). Note the global MLA and G(0) products mainly represent the typical state during the growing season from 2001 to 2022. The MLA and G(0) products would enhance our knowledge about global LIA and should greatly facilitate remote sensing retrieval and land surface modeling studies.

In the version 1.1, two quality layers were added to 500 m MLA product to represent the quality of input data and the prediction model. The input data quality was denoted by the proportion of high-quality BRDF inversions for each pixel. The prediction model quality was represented qualitatively for each pixel considering whether the MLA was predicted by extrapolating beyond the range of the training samples. In the 500 m MLA product, the three bands sequentially store MLA, input data quality (scale factor = 0.01), and model quality (1: predictions within the range of samples; 0: predictions out of the range of samples).
DOI: 10.5281/zenodo.13340574
title: Chemical composition data of sedimentary rocks from the Permian-Triassic boundary and Cretaceous oceanic anoxic events

description: Bulk chemical composition data of sedimentary rocks from the Permian-Triassic boundary and Cretaceous oceanic anoxic events. This is a supplementary dataset for “Geochemical variations in sedimentary records of oxygen-depleted marine environments in representative geological periods: New perspectives from a multivariate statistical technique” by Moei Yano et al.
DOI: 10.5281/zenodo.13787997
title: West Pacific Subtropical High modulates regional hydroclimate changes on multiple timescales in central China

description: This is the file about the Holocene speleothem stable carbon isotope and trace element records from Jiuxian cave, central China.
DOI: 10.5281/zenodo.13865443
title: WRF met-data for generative diffusion model post-processing precipitation map
DOI: 10.5281/zenodo.14227821
title: Supplementary data for TransPharmer
DOI: 10.5281/zenodo.14677612
title: Processed Novelty Layers for Climate, Defaunation, Floristic Disruption, and Total Novelty Exposure, from Kerr et al 2025 "Widespread Ecological Novelty Across the Terrestrial Biosphere"

description: The four raster files contain scaled (0-1) novelty values for three novelty drivers (climate, defaunation, floristic disruption) and one combined "total novelty exposure" (unweighted average of the three drivers) from Kerr et al (2025). These make up extended data figures 1 and 3a-c and are used within the analysis for the paper. The rasters are in a 10x10km resolution covering terrestrial cells only, and are projected on an equal area Mollweide projection ("+proj=moll +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"). See Kerr et al (2025, Nature Ecology and Evolution, https://doi.org/10.1038/s41559-025-02662-2) for the full methodological details and underlying open-access data.

In summary, the climate change layer measures the most recent 300-year period for which palaeoclimate is outside the modern range, for temperature and precipitation, using data from CHELSA and CHELSA-TrACE21k. The defaunation layer measures the log loss in body mass and species richness of mammal fauna, using the predicted "present natural" values from the PHYLACINE atlas of mammal macroecology. The floristic disruption layer firstly measures the proportion of non-native alien plants present in GBIF records, assessed using country level checklists from GRIIS, and secondly uses a modified BII (from Newbold et al 2016, accessed at https://zenodo.org/records/6348164), taking the absolute difference from 1. The value used in the final rasters is the unwighted average of the two individual metrics for each layer.

If you use this data in any form, please cite both this dataset and the original publication.
DOI: 10.5281/zenodo.14794347
title: PROFILER02
DOI: 10.5281/zenodo.3890646
title: Global track dataset of monsoon low pressure systems

description: This dataset contains the tracks and intensities of low pressure system (LPS) in the global tropics (35ºS-35ºN), as identified in five atmospheric reanalyses (ERA5, ERA-Interim, JRA55, MERRA2, and CFSR) using the algorithm described in the paper titled Assessing historical variability of South Asian monsoon lows and depressions with an optimized tracking algorithm.  Tracking of LPS was performed using an automated Lagrangian pointwise feature tracker, TempestExtremes (Ullrich & Zarzycki, 2017), with criteria chosen to best match a subjectively analyzed LPS dataset while minimizing disagreement  between four atmospheric reanalyses. A full description of the algorithm and dataset is described in the preprint *(https://doi.org/10.1029/2020JD032977)

 

Files:



Header.txt: contains the names of columns of the LPS dataset files

LPS_Global_ERA5.dat: LPS track file for ERA5, 1979-2019, hourly resolution

LPS_Global_ERA-Interim.dat: LPS track file for ERA-Interim, 1979-2018, six-hourly resolution

LPS_Global_JRA55.dat: LPS track file for JRA55, 1958-2019, six-hourly resolution

LPS_Global_CFSR.dat: LPS track file for CFSR, 1979-2010, six-hourly resolution

LPS_Global_MERRA2.dat: LPS track file for MERRA2, 1980-2019, three-hourly resolution


Extented Data for ERA5:



ERA5 tracks for 1940-2022 are available on https://boos.berkeley.edu in the "Data & Tools" section.


Script:



Run_tempest_lps.sh: TempestExtremes script to track LPS in reanalysis dataset. 


Additionally, four python scripts are available to subset the dataset:



Python_Moist_LPS_heat_low.py: Python script to create two separate files for  moist LPS and heat lows

Python_Low_Depression.py: Python script to create two separate files for monsoon lows and monsoon depressions

Python_Region.py: Python script to create a separate file for a region

Python_Season.py: Python script to create a separate file for a season


 



 


Note: The TempestExtremes software can be obtained from GitHub at https://github.com/ClimateGlobalChange/tempestextremes.

For further details, contact S. Vishnu (vishnuedv@gmail.com) or William R Boos  (billboos@alum.mit.edu).
DOI: 10.5285/b0634651-410d-4531-8100-e1d4e2873d9e
title: Spatial and temporal datasets for mixing of fluids in a dyke-like (slot) geometry investigated using low-temperature laboratory experiments

description: These spatial and temporal image datasets are of mixing fluids in a dyke-like (slot) geometry investigated using low-temperature laboratory experiments which are described in the paper Analogue experiments to investigate magma mixing within dykes (Havard et al., accepted in Bulletin of Volcanology, February 2025). The experiments are low-temperature analogue models of magma mixing within dykes and are dynamically scaled to the natural system. 
Seven unique experiments using seven different miscible fluid pairs, representing two magmas of differing composition, were conducted at the University of Liverpool. The miscible fluid pairs are (and the shortened experiment names are): water and diluted glycerol (ExpW1); water and pure glycerol (ExpW2); water and glycerol mixed with golden syrup (ExpW3); water and pure golden syrup (ExpW4); diluted glycerol and pure glycerol (ExpD1); pure glycerol and diluted golden syrup (ExpG1); pure glycerol and pure golden syrup (ExpG2). The experiment setup consisted of the lower density fluid placed above the higher density fluid in the tank apparatus, then the tank was inverted to initiate the interaction between the fluids. The raw data is a temporal series of photographs (JPGs) collected over the course of each experiment located within the subdirectories “Raw”. The raw data is processed using the scripts accompanying the dataset to show how density and mixing evolves spatially and temporally within the slot. Further details are available in the directory metadata file.
DOI: 10.6084/m9.figshare.25139510
title: <b>Paleocene</b><b> opening of </b><b>Drake </b><b>Passage</b>

description: <b>The South Shetland Islands paleomagnetic data used in the paper "</b><b>The I</b><b>nitial Opening of </b><b>the </b><b>Drake Passage</b><b> Occurred </b><b>during </b><b>ca. 62-59 Ma</b><b>"</b>
DOI: 10.6084/m9.figshare.25907953
title: Observed and synthetic seismic data of the linear array in eastern Tibet and topographic data extracted from a global relief model with 15 arc-second resolution

description: The observed and synthetic seismic data of the linear array in eastern Tibet.
DOI: 10.6084/m9.figshare.27002569
title: <b>Supplementary data for the small RNA expression analysis in </b><b><i>Gossypium hirsutum</i></b><b> empurpled mutant </b><b><i>HS2</i></b>

description: Below is a concise overview of the documents that have been released to complement our publication detailing the study on the expression patterns and regulatory functions of small RNAs in the empurpled mutant of <i>Gossypium hirsutum</i>.<br><b>1.</b><b> </b><b>Assembly.fa</b>The re-constructed transcripts derived from the RNA-seq data of C312 and HS2. These transcripts are used in de novo prediction of miRNAs.<br><b>2.</b><b> </b><b>Novel miRNAs.docx</b>The pre-sequences and secondary structures of novel miRNAs predicted in our study.<br><b>3.</b><b> </b><b>Sequences and expression profiles of siRNAs.xls</b>Sequences of all the siRNAs predicted in our study, as well as their expression levels in each library. The expression levels are calculated using reads per million (RPM).<br><b>4.</b><b> </b><b>DEG_siRNA.xls</b>All the 761 siRNAs that are differentially expressed between C312 and HS2.<br><b>5.</b><b> </b><b>Regulations.xlsx</b>All the sRNA-target regulations predicted in our study. Only differentially expressed miRNAs and siRNAs were assessed. The mRNAs generated during genome annotation (NAU-NBI_v1.1) are used for target prediction.<br><b>6.</b><b> </b><b>DEG_mRNA.xlsx</b>The expression patterns of 892 differentially expressed coding genes between C312 and <i>HS2</i>.<br><b>7.</b><b> </b><b>All expressed miRNAs.xlsx</b>All the miRNAs detected in C312 and <i>HS2</i> by homology search and <i>de novo</i> prediction. Their expression levels are estimated using RPM.<br>
DOI: 10.6084/m9.figshare.27100615
title: <b>Uncovering the Impacts of 2D and 3D Urbanization on Urban Heat Islands in 384 Chinese Cities</b>

description: We assessed the UHI trends at a 1000-m grid level to compare the impacts induced by 2D and 3D urbanization across 384 Chinese cities.
DOI: 10.6084/m9.figshare.28511111.v1
title: physical_constants

description: This is a table of data obtained from Scopus, a repository of metadata for scientific research papers, together with the processing script. The data was obtained as part of research studying the academic use of data regarding physiccal constants. The data here are used to trace academic collaboration patterns in the four decade period from 1970-1910. Columns used in the work are "title" and "abstract" for topic modelling, "affilname", "affiliation_country","affiliation_city" for the geospatial processing. This is done together with "Year".<br>The data still remain the property of Scopus and may only be used for the purposes of reproducing the results herein. They may not be reproduced in any form without the express permission of Scopus. A processing script is provided with the dataset to reproduce the results of this work.
DOI: 10.6084/m9.figshare.28704977
title: Supplementary Material for: Effects of replacing intradialytic parenteral nutrition by oral nutritional supplements and PEPA membrane on nutritional status in maintenance hemodialysis patients with end-stage kidney disease

description: Introduction: In patients receiving hemodialysis, protein-energy wasting may be frequent and is associated with nutritional and metabolic alterations. This study aimed to describe the effects of a new therapeutic strategy i.e., oral nutritional supplements (ONS) associated with a polyester-polyarylate (PEPA) membrane, on nutritional markers in high-risk patients with IDPN history. Methods: Patients, who received individually IDPN (M-6 to M0) then ONS (M0 to M6), were followed over a 12-month period.
Results: There was no change in serum albumin over time. The BMI increased between M-6 and M6. Food intake showed increase between M0 and M3. Quality-of-life score was stable between M0 et M6. None of the adverse events was judged related to ONS, PEPA or research procedure. 
Conclusion: This study focusing on a new therapeutic strategy composed of ONS and PEPA membrane replacing IDPN to maintain nutritional markers in high-risk patients receiving hemodialysis might warrant further research with robust methodology.
DOI: 10.6084/m9.figshare.28714226
title: Supplementary Material for: Transdermal and Powdered Scopolamine-Induced Anisocoria: A Report of Two Cases

description: Introduction
In this case report, we present two cases of sudden-onset anisocoria caused by accidental exposure to scopolamine in two young female patients.
Case presentation
Two patients presented with unilateral anisocoria. One patient experienced unilateral mydriasis accompanied by neurological symptoms from a transdermal scopolamine patch, while the other, exposed to powdered scopolamine, presented with unilateral mydriasis without additional neurological symptoms. Both cases showed gradual resolution of symptoms over several days without intervention. Initially, Adie’s pupil (tonic pupil) was high in the differential diagnosis, but a comprehensive history taking revealed scopolamine exposure as the more likely cause. In the first case, pilocarpine did not result in miosis, while in the second case, pilocarpine initially induced miosis but was followed by a return to mydriasis. Although current literature suggests that mydriasis caused by an anticholinergic substance presents as pupil dilation unresponsive to pilocarpine, our case series shows its inconsistency in clinical presentation.
Conclusion 
This report presents one case of systemic scopolamine toxicity, alongside unilateral mydriasis, adding confusion to the case given the expected bilateral mydriasis in systemic toxicity, and another case of pharmacological anisocoria secondary to exposure to scopolamine with an atypical reaction to pilocarpine. These cases highlight the importance of thorough history taking and the need to consider pharmacological causes in the differential diagnosis of acute anisocoria.
DOI: 10.6084/m9.figshare.28722584
title: Supplementary Material for: Differential Expression of Immune Checkpoints TIM-3, LAG3, TIGIT, and Siglec-7 on Circulating NK Cells: Insights from Healthy Donors compared to Gastric Cancer Patients

description: Due to the multifactorial nature of cancer, the development of reliable immunotherapies poses a significant challenge for medical research. In this context, targeting immune checkpoints holds promising potential. Natural killer (NK) cells are crucial in the primary defense against viral infections, tumor development, and metastasis. The cytotoxic function of NK cells is finely regulated by a complex array of activating and inhibitory receptors, including checkpoint receptors. Malignantly transformed cells can impair NK cell activity by expressing soluble or membrane-bound checkpoint ligands, thereby modulating immune responses to support tumor progression. To investigate this dilemma, we simulated in vitro activation by NK cell co-incubation with K562 cells and analyzed expression of TIM-3, LAG-3, TIGIT and Siglec-7. After that, we analyzed the checkpoint expression on circulating NK cells from 35 healthy donors and compared it to their expression in patients with gastric cancer (n =21) using flow cytometry. In healthy donors, we observed that 25% to 97% of all circulating NK cells expressed TIM-3, TIGIT, and Siglec-7, while only a small fraction of 0.6% expressed LAG-3. Co-incubation of peripheral blood mononuclear cells (PBMCs) from healthy donors with K562 cells resulted in heightened expression levels of TIM-3 and TIGIT on NK cells. Especially targeting the sialic acid-Siglec-7 axis may offer promising therapeutic strategies for various cancer types in the future. Conversely, NK cells in patients with gastric cancer showed an increased LAG-3 and reduced Siglec-7 expression. Our findings suggest the potential of LAG-3 as a next-generation checkpoint molecule, alongside Siglec-7. Especially targeting the sialic acid-Siglec-7 axis may offer promising therapeutic strategies for various cancer types in the future.