cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.g82zwd
title: Occurrence Download

description: A dataset containing 1133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stipa krylovii Roshev."
 ]
}

 The dataset includes 1133 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000017-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25413/sun.28410506
title: Patient-specific clavicle plate design Data

description: The anonymised clavicle data that was used in the research is indicated in the attached spreadsheets. The full data set is shown. The samples used for training is also indicated. The full set of segmented clavicles are also presented in STL form. All results with regards to morphometric analysis, estimation errors and patient specific heatmaps is also presented.
DOI: 10.25413/sun.28410506.v1
title: Patient-specific clavicle plate design Data

description: The anonymised clavicle data that was used in the research is indicated in the attached spreadsheets. The full data set is shown. The samples used for training is also indicated. The full set of segmented clavicles are also presented in STL form. All results with regards to morphometric analysis, estimation errors and patient specific heatmaps is also presented.
DOI: 10.60893/figshare.apr.28306796
title: Supplementary Information

description: This is the supporting information of the article.
DOI: 10.57745/46s4yk
title: ReadMe_CAF_DL_ADULTS.txt

description: :unav
DOI: 10.57745/fcybgo
title: READING_DATA.csv

description: :unav
DOI: 10.57745/io35bh
title: CAF_DATA.csv

description: :unav
DOI: 10.57745/llg8le
title: FILTER_DATA.csv

description: :unav
DOI: 10.57745/uzw48a
title: RAW_DATA.csv

description: :unav
DOI: 10.5281/zenodo.3634639
title: Initial conditions to reproduce figures of the article "On the impact of tides on the transit-timing fits to the TRAPPIST-1 system"

description: The directory includes the initial conditions of the simulations needed to reproduce the figures of the article "On the impact of tides on the transit-timing fits to the TRAPPIST-1 system". 

The simulations were done with Posidonius version v2019.07.30. The information to download and use Posidonius can be found here:https://www.blancocuaresma.com/s/posidonius. That version was only slightly modified to use a maximum timestep size for the IAS15 algorithm. 

The directory includes:



a README giving all the information defining the test directories

test directories with a file called trappist1.json, which can be used to launch Posidonius:posidonius start --silent trappist1.json data_dir/trappist1.bin data_dir/trappist1_history.bin
DOI: 10.5281/zenodo.3634640
title: Initial conditions to reproduce figures of the article "On the impact of tides on the transit-timing fits to the TRAPPIST-1 system"

description: The directory includes the initial conditions of the simulations needed to reproduce the figures of the article "On the impact of tides on the transit-timing fits to the TRAPPIST-1 system". 

The simulations were done with Posidonius version v2019.07.30. The information to download and use Posidonius can be found here:https://www.blancocuaresma.com/s/posidonius. That version was only slightly modified to use a maximum timestep size for the IAS15 algorithm. 

The directory includes:



a README giving all the information defining the test directories

test directories with a file called trappist1.json, which can be used to launch Posidonius:posidonius start --silent trappist1.json data_dir/trappist1.bin data_dir/trappist1_history.bin
DOI: 10.60893/figshare.jap.28322840
title: Supplemantary Material

description: Measured and calculed characteristics of samples.
DOI: 10.60893/figshare.jap.28322840.v1
title: Supplemantary Material

description: Measured and calculed characteristics of samples.
DOI: 10.5281/zenodo.14930768
title: Naphthalene Acetic Acid and Piriformospora indica 1 Synergistically Regulate WOX Gene Expression to 2 Promote Rooting in Woody Ornamentals
DOI: 10.5281/zenodo.14930769
title: Naphthalene Acetic Acid and Piriformospora indica 1 Synergistically Regulate WOX Gene Expression to 2 Promote Rooting in Woody Ornamentals
DOI: 10.15468/dl.uenq66
title: Occurrence Download

description: A dataset containing 1770876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Achillea ligustica All., Achillea macrophylla L., Achillea maritima (L.) Ehrend. & Y.P.Guo, Achillea millefolium L., Achillea nana L., Achillea oxyloba (DC.) Sch.Bip., Achillea pannonica Scheele, Achillea ptarmica L., Achillea ptarmicoides Maxim., Achillea roseoalba Ehrend.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1770876 records from 4502 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000373-250226093636041/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2gdkar
title: Occurrence Download

description: A dataset containing 399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Acer paxii Franch."
 ]
}

 The dataset includes 399 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008320-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13026/53xq-jz70
title: Characterization of Stigmatizing Language in Medical Records

description: Widespread disparities in clinical outcomes exist between different
demographic groups in the United States. A new line of work in medical
sociology has demonstrated physicians often use stigmatizing language in
electronic medical records within certain groups, such as black patients,
which may exacerbate disparities. The first step to addressing the presence of
stigmatizing language in medical records is identifying it and characterizing
its impact. Towards this end, we release a suite of neural and non-neural
classifiers trained in a supervised manner to recognize three types of
stigmatizing language found in discharge notes from the MIMIC-IV dataset. We
also release the set of 5,043 annotations from 4,710 notes (4,259 patients)
used to train and evaluate our models. These resources provide a foundation
for NLP researchers to contribute timely insights to a problem domain brought
to the forefront by recent legislation regarding clinical documentation
transparency.
DOI: 10.1594/pangaea.836841
title: Growth rates and biometric measurements of coccolithophores (Coccolithus pelagicus, Coccolithus braarudii, Emiliania huxleyi) during experiments

description: Coccolithophores, a diverse group of phytoplankton, make important contributions to pelagic calcite production and export, yet the comparative biogeochemical role of species other than the ubiquitous Emiliania huxleyi is poorly understood. Here we examined the relative importance of E. huxleyi and two Coccolithus species (Coccolithus pelagicus and Coccolithus braarudii), in terms of daily calcite production, by culturing E. huxleyi and Coccolithus in parallel, and comparing growth rates and biometrically determined cellular carbon calcite quotas. Biometric measurements of Coccolithus species, and E. huxleyi cell diameters, were performed using polarised light microscopy. Scanning electron microscopy was used for all other biometric measurements of E. huxleyi.
DOI: 10.1594/pangaea.865403
title: Coccosphere geometry measurements from culture experiments on the coccolithophore species Calcidiscus leptoporus, Calcidiscus quadriperforatus and Helicosphaera carteri

description: Coccolithophores are an abundant phytoplankton group that exhibit remarkable diversity in their biology, ecology and calcitic exoskeletons (coccospheres). Their extensive fossil record is a testament to their important biogeochemical role and is a valuable archive of biotic responses to environmental change stretching back over 200 million years. However, to realise the full potential of this archive for (palaeo-)biology and biogeochemistry requires an understanding of the physiological processes that underpin coccosphere architecture. Using culturing experiments on four modern coccolithophore species (Calcidiscus leptoporus, Calcidiscus quadriperforatus, Helicosphaera carteri and Coccolithus braarudii) from three long-lived families, we investigate how coccosphere architecture responds to shifts from exponential (rapid cell division) to stationary (slowed cell division) growth phases as cell physiology reacts to nutrient depletion. These experiments reveal statistical differences in coccosphere size and the number of coccoliths per cell between these two growth phases, specifically that cells in exponential-phase growth are typically smaller with fewer coccoliths, whereas cells experiencing growth-limiting nutrient depletion have larger coccosphere sizes and greater numbers of coccoliths per cell. Although the exact numbers are species-specific, these growth-phase shifts in coccosphere geometry demonstrate that the core physiological responses of cells to nutrient depletion result in increased coccosphere sizes and coccoliths per cell across four different coccolithophore families (Calcidiscaceae, Coccolithaceae, Isochrysidaceae and Helicosphaeraceae), a representative diversity of this phytoplankton group. Building on this, the direct comparison of coccosphere geometries in modern and fossil coccolithophores enables a proxy for growth phase to be developed that can be used to investigate growth responses to environmental change throughout their long evolutionary history. Our data also show that changes in growth rate and coccoliths per cell associated with growth-phase shifts can substantially alter cellular calcite production. Coccosphere geometry is therefore a valuable tool for accessing growth information in the fossil record, providing unprecedented insights into the response of species to environmental change and the potential biogeochemical consequences.
description: Supplement to: Sheward, Rosie M; Poulton, Alex J; Gibbs, Samantha J; Daniels, Chris J; Bown, Paul R (2017): Physiology regulates the relationship between coccosphere geometry and growth phase in coccolithophores. Biogeosciences, 14(6), 1493-1509
DOI: 10.1594/pangaea.97179
title: Documentation of sediment core GeoB8449-3
DOI: 10.21227/fmnm-bn95
title: Experimental database for detecting and diagnosing broken bar defects in a three-phase induction motor.

description: The data set contains electrical and mechanical signals from experiments on three-phase induction motors. The experimental tests were carried out for different mechanical loads on the induction motor axis and different severities of broken bar defects in the motor rotor, including data regarding the rotor without defects. Ten repetitions were performed for each experimental condition.
DOI: 10.25573/data.26405074
title: Testing for allocation strategies and evolutionary tradeoffs in the bivalve shell: supplemental data and code

description: Supplemental Dataset for Edie, SM, Collins, KS, and Jablonski, D. Testing for Allocation Strategies and Evolutionary Tradeoffs in the Bivalve Shell. Contains metadata for specimens analyzed, 3D mesh models for bivalve shells, and R code for reproducing analyses. See README.txt for more details.
DOI: 10.34973/4f3k-1s63
title: Cell type specific information processing in inhibitory and excitatory neurons

description: Sensory neurons reconstruct the world from action potentials (spikes) impinging on them. Recent work argues that the formation of sensory representations are cell-type specific, as excitatory and inhibitory neurons use complementary information available in spike trains to represent sensory stimuli. Here, by measuring the mutual information between synaptic input and spike trains, we show that inhibitory and excitatory neurons in the barrel cortex transfer information differently: excitatory neurons show strong threshold adaptation and a reduction of intracellular information transfer with increasing firing rates. Inhibitory neurons, on the other hand, show threshold behaviour that facilitates broadband information transfer. We propose that cell-type specific intracellular information transfer is the rate-limiting step for neuronal communication across synaptically coupled networks. Ultimately, at high firing rates, the reduction of information transfer by excitatory neurons and its facilitation by inhibitory neurons together provides a mechanism for sparse coding and information compression in cortical networks.
DOI: 10.48529/k739-c548
title: Socioeconomic Survey 2018-2019
title: ETH_2018_ESS_v03_M
DOI: 10.5066/p901f9g0
title: Parameter Estimation, Uncertainty Analysis, and Optimization with the PEST++ Family of codes: Tutorial Jupyter Notebooks

description: A series of Jupyter notebooks documenting a self-guided, interactive curriculum for the PEST++ family of software codes for uncertainty analysis, parameter estimation, and management optimization. For a currently maintained version of these materials, please visit https://github.com/gmdsi/GMDSI_notebooks.
DOI: 10.5281/zenodo.10571292
title: Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean

description: The Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean is a reference dataset for morphological traits from extant coccolithophores (calcifying marine plankton group), including cell-specific data for coccosphere and cell size, coccolith size, number of coccoliths per cell, and morphometric-based cellular calcite estimates. The dataset also includes ancillary information about the sample and taxonomic identification.

The dataset contains observations from 1074 individual coccolithophore cells representing 61 species from 25 genera. Samples were obtained during the Atlantic Meridional Transect (AMT) 14 cruise that sailed between the Faulkland Islands and the UK in 2004. Measurements were taken from scanning electron microscopy (SEM) images, which are archived on Zenodo at doi: 10.5281/zenodo.10571819. A description of the parameters included in the dataset can be found in the file "2. Descriptor- Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean".

Three additional supporting files are included with this dataset:



"3. Coccolith size, coccolith calcite and cellular calcite in collapsed Umbellosphaera coccospheres" contains measurements of coccolith size (CL) and associated coccolith calcite (PIC) for 20 collapsed Umbellosphaera coccospheres. This data was used to derive an adjustment to coccolith length applied to coccolith length measured on intact Umbellosphaera coccosphere measurements to account for the wide variety of coccolith sizes present on individual coccospheres.

"4. Sensitivity of cellular calcite contents to uncertainties in coccolith size, number of coccoliths per cell and shape factors" contains re-calculations of cellular calcite data using uncertainties of ±5-30% on coccolith size (CL) and species-specific shape factor (Ks) and variations of ±2 coccoliths and ±5 coccoliths for the number of coccoliths per cell (CN) for coccospheres of Gephyrocapsa mullerae, Umbilicosphaera hulburtiana, Syracosphaera spp., and Discosphaera tubifera.

"5. Partial coccolith length and coccolith length measurements" contains measurements used to calculate the uncertainty in coccolith length introduced when partial coccolith length is measured.


Extensive description of the methodology related to this dataset can be found in the associated manuscript: Rosie M. Sheward, Alex J. Poulton, Jeremy R. Young, Joost de Vries, Fanny M. Monteiro, Jens O. Herrle. “Cellular morphological trait dataset for extant coccolithophores from the Atlantic Ocean” in review with Scientific Data.

Correspondence should be directed to:

Rosie M. Sheward, sheward@em.uni-frankfurt.de
DOI: 10.5281/zenodo.11472764
title: Latest Eocene to mid-late Oligocene calcareous nannoplankton assemblage relative abundance counts and coccolith size measurements: IODP Site U1553

description: Calcareous nannoplankton are a major group of calcifying marine phytoplankton. Their distribution, productivity and cellular morphological traits are important factors in the role of calcareous nannoplankton in marine ecosystem functions, including the production and export of organic and inorganic carbon. 

Using morphometric and assemblage data collected from latest Eocene to mid-late Oligocene sediments International Ocean Discovery Program (IODP) Site U1553, Campbell Plateau in the high latitude southwestern Pacific Ocean, we reconstructed the size structure and associated biogeochemical traits (size-fractionated and total community particulate organic and inorganic carbon) of the community through the Oligocene to investigate the impact of climate-driven changes in community composition on calcareous nannoplankton biogeochemistry.

 

The datasets presented in this data record are associated with the manuscript:

Sheward, R. M., Herrle, J. O., Fuchs, J., Gibbs, S. J., Bown, P. R. and Eibes, P. M. Biogeochemical traits of a high latitude South Pacific Ocean calcareous nannoplankton community during the Oligocene, to be submitted to Paleoceanograpy and Paleoclimatology in June 2024.

 

This data record contain two primary datasets generated for this study:



assemblage composition (relative coccolith abundance) of the latest Eocene-earliest Oligocene calcareous nannoplankton community

morphometric data for the coccolith size of the ten most common morphogroups in the assemblage in this time interval (Chiasmolithus, Clausicoccus subdistichus, Coccolithus, Cyclicargolithus, Reticulofenestra, Sphenolithus, Discoaster and Zygrhablithus bijugatus).


 

Correspondence should be addressed to: Rosie Sheward (sheward@em.uni-frankfurt.de).
DOI: 10.5281/zenodo.11473074
title: Coccosphere geometry dataset for Eocene and Oligocene calcareous nannoplankton

description: Coccolithophores and other calcareous nannoplankton are a group of calcifying marine phytoplankton that produce calcium carbonate plates (coccoliths) that form a cell covering (the coccosphere). Calcareous nannoplankton have diverse morphological traits, including cell size, coccosphere size, coccolith size and morphology, the arrangement of coccoliths in the coccosphere, and the number of coccoliths per cell.

The Coccosphere geomety dataset for Eocene and Oligocene calcareous nannoplankton contains coccosphere geometry data for the cell diameter (CellD), coccosphere diameter (CD), coccolith length (CL) and number of coccoliths per cell (CN) measured on 2,202 individual, intact fossil coccospheres of early Eocene to late Oligocene age from 9 localities.

 

This data record contains two files:1. Dataset descriptor (.pdf) that describes the contents of the dataset, briefly outlines the materials and methods used to generate the dataset (including references for further information), and suggests potential topics that the dataset can be used for. A list of associated publications, theses, and similar datasets are also provided in this document.

2. The Coccosphere geometry dataset for Eocene and Oligocene calcareous nannoplankton (.xls) contains morphometric data of the coccosphere geometry of n= 2,202 fossil coccospheres alongside site and taxonomic information.

 

Correspondence should be directed to: Rosie Sheward (sheward@em.uni-frankfurt.de).

Funding acknowledgements: Collection of this dataset was made possible by funding awarded to RMS by the Deutsche Forschungsgemeinschaft (reference 447581699) for data collected at Goethe-University Frankfurt from IODP Site U1553 and a Vice Chancellors Studentship from the University of Southampton and a Natural Environment Research Council (NERC) award (reference 1272561) for data collected during her PhD at the University of Southampton. SJG was funded through a Royal Society University Research Fellowship. Additional financial support was provided to RMS and JOH through the VeWA consortium (Past Warm Periods as Natural Analogues of our high-CO2 Climate Future) by the LOEWE programme of the Hessen Ministry of Higher Education, Research and the Arts, Germany. JOH is supported by grants awarded by the State of Hesse (Germany) in the framework of the Initiative for the Development of Scientific and Economic Excellence (LOEWE) the Biodiversity and Climate Centre Frankfurt (BIK-F) grant number R2107 Project PB A, the DAAD-Programm Strategische Partnerschaften of the Goethe-University Frankfurt (grant number UoT6), and the Freunde und Förderer der Goethe-Universität Frankfurt am Main (funding awarded to JOH in 2010).
DOI: 10.5281/zenodo.12155184
title: DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

description: Here, we store the modeled structures generated by DiffModeler for its 4 benchmark datasets: CryoREAD dataset(0-5A resolution, protein-DNA/RNA complex), ModelAngelo dataset(0-5A resolution, most protein complexes, a few protein-RNA complex), intermediate resolution dataset (5-10A resolution, protein complex), low resolution dataset (10-20A resolution, protein complex). For all protein-DNA/RNA complex, the map will be modeled by CryoREAD+DiffModeler.

For each dataset, we keep the modeled structures by DiffModeler, named as [EMD-ID]_DiffModeler.cif; and their corressponding native structures from RCSB are saved as [EMD-ID]_[PDB_ID]_native.cif.

For CryoREAD dataset, it includes 61 targets. For ModelAngelo dataset, it includes 28 targets. For intermediate resolution dataset , it includes 71 targets. For low resolution dataset, it incldues 6 targets.

For intermediate resolution dataset, many maps were run with inaccurate AF2 predicted single-chain structures. We also benchmarked DiffModeler's performance by using native single-chain structures as input. They are saved under "dataset_5_10A_nativechain" folder.

Additionally, we have stored the traced backbone map of the intermediate resolution dataset in the "dataset_5_10A_diffusion_traced_backbone_map" folder. The traced maps are saved as [EMD-ID]_diffusion.mrc. The intermediate reverse diffusion maps of the intermediate resolution dataset are saved in the "dataset_5_10A_reverse_diffusion_maps" folder. Each sub-folder is named according to the corresponding map's [EMD-ID] and contains three intermediate reverse diffusion maps: 20percentile_reverse_diffusion.mrc, 50percentile_reverse_diffusion.mrc, and 80percentile_reverse_diffusion.mrc. A higher percentile indicates a map closer to the end of the reverse diffusion steps.

If you used DiffModeler, please cite: "Wang, Xiao, Han Zhu, Genki Terashi, Manav Taluja, and Daisuke Kihara. "DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model." bioRxiv (2024): 2024-01.".

If you used CryoREAD, please cite: "Xiao Wang, Genki Terashi & Daisuke Kihara. De novo structure modeling for nucleic acids in cryo-EM maps using deep learning. Nature Methods, 2023."
DOI: 10.5281/zenodo.7299473
title: Cycling Data of 64 Cells manufactured by AutoBASS

description: This is the complete dataset for cells made for the publication of https://doi.org/10.1039/D2DD00046F Robotic cell assembly to accelerate battery research, <em><strong>Digital Discovery</strong></em>, 2022, Advance Article by Zhang et al. This dataset goes beyond the inital cycles and tested, wherever possibile, up to 500 cycles at a constant 1C/1D rate. The details of the robot that made the cells can be found at https://github.com/Helge-Stein-Group/AutoBASS and the details of the cycling procedure and chemistry can be found in the article.
DOI: 10.5525/gla.researchdata.1641
title: Direct observation of subunit rotation during DNA strand exchange by serine recombinases