cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7025602
title: Transmission electron microscopy (TEM) image datasets of peptide / protein nanowire morphologies

description: TEM image dataset containing four nanowire morphologies of bio-derived protein nanowires and synthetic peptide nanowires.

The peptide / protein nanowires used in this study were synthesized and imaged by Brian Montz in Prof. Todd Emrick's research group at the Department of Polymer Science and Engineering Department, University of Massachusetts Amherst. 

We acknowledge financial support from the U.S. National Science Foundation, Grant NSF DMREF #1921839 and DMREF #1921871.

Nanowires were classified into either of the four morphologies: bundle, singular, dispersed or network. Each morphology contains 100 images (jpg files).

For the dispersed and network morphologies, because these two morphologies are harder to visually distinguish, we have created manual segmentation labels of the nanowires (included in these two morphology folders as png files). Percolation analysis was done on these manually segmented nanowires to provide quantitative metric on whether the nanowires form a network in the image. 

seg_mask_5_resolutions.zip contains ground truth 2D binary encoding of segmented nanowires at 5 resolutions.

encoders_trained_with_optimized_hyperparameter.zip contains 4 sets of encoders trained with either SimCLR or Barlow-Twins self-supervised methods on either generic TEM images, or generic everyday photographic images (each with 5 replicates with different random seed) with optimized hyperparameters.

Open-access datasets that have been used during self-supervised training.



2021-CEM500K.zip contains 10,000 images that was used as "generic TEM images" to train the encoders with self-supervised methods, these are a random selection from the CEM500k open-access dataset. DOI: 10.7554/eLife.65894

2022-1000-ImageNet.zip contains 1,000 images from the ImageNet1k dataset, each come from a different category. DOI: 10.1007/s11263-015-0816-y


Open-access datasets that our machine learning workflow have been applied to:



2022-AutoDetect-mNP-morphology.zip contains a selected TEM images of nanoparticles categorized in 3 morphologies from the AutoDetect-mNP datasets: DOI: 10.6078/D1WT44 and DOI: 10.6078/D1S12H

2021-TEM virus.zip contains TEM images of 9 types of viruses from the TEM virus dataset. Matuszewski, Damian; Sintorn, Ida-Maria (2021), “TEM virus dataset”, Mendeley Data, V3, DOI: 10.17632/x4dwwfwtw3.3


The official github page of the implementation of the machine learning models is semi-supervised_learning_microscopy_images.

If you use the dataset or the codes in the repository linked above, please cite the following manuscript:

S. Lu, B. Montz, T. Emrick and A. Jayaraman, Digital Discovery, 2022, 1, 816-833 , DOI: 10.1039/D2DD00066K
DOI: 10.12770/f1f085bb-74d5-48b6-aa23-29b037063e52
title: Bio-Argo quality controlled chlorophyll observations from PROVOR floats with ECO-puck sensors

description: This data set contains the Bio-Argo quality controlled chlorophyll-A observations from PROVOR floats with ECO-puck sensors. The quality control procedure applied to chlorophyll-A vertical profiles is described in “Schmechtig Catherine, Claustre Herve, Poteau Antoine, D'Ortenzio Fabrizio (2014). Bio-Argo quality control manual for the Chlorophyll-A concentration. http://dx.doi.org/10.13155/35385”.
DOI: 10.34683/sr2809
title: StoneRounds Case: SR2809
title: Best Disease

description: StoneRounds Case SR2809 was diagnosed with Best Disease likely caused by mutations in the gene: BEST1.
DOI: 10.5517/ccdc.csd.cc2dhfr3
title: CCDC 2219375: Experimental Crystal Structure Determination

description: Related Article: Li-Hong Yan, Pei-Hai Li, Xiao-Ming Li, Sui-Qun Yang, Ke-Chun Liu, Yun Zhang, Bin-Gui Wang, Xin Li|2024|Bioorg.Chem.|143|107073|doi:10.1016/j.bioorg.2023.107073
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dhfs4
title: CCDC 2219376: Experimental Crystal Structure Determination

description: Related Article: Li-Hong Yan, Pei-Hai Li, Xiao-Ming Li, Sui-Qun Yang, Ke-Chun Liu, Yun Zhang, Bin-Gui Wang, Xin Li|2024|Bioorg.Chem.|143|107073|doi:10.1016/j.bioorg.2023.107073
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dhft5
title: CCDC 2219377: Experimental Crystal Structure Determination

description: Related Article: Li-Hong Yan, Pei-Hai Li, Xiao-Ming Li, Sui-Qun Yang, Ke-Chun Liu, Yun Zhang, Bin-Gui Wang, Xin Li|2024|Bioorg.Chem.|143|107073|doi:10.1016/j.bioorg.2023.107073
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dhfv6
title: CCDC 2219378: Experimental Crystal Structure Determination

description: Related Article: Li-Hong Yan, Pei-Hai Li, Xiao-Ming Li, Sui-Qun Yang, Ke-Chun Liu, Yun Zhang, Bin-Gui Wang, Xin Li|2024|Bioorg.Chem.|143|107073|doi:10.1016/j.bioorg.2023.107073
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dhfw7
title: CCDC 2219379: Experimental Crystal Structure Determination

description: Related Article: Li-Hong Yan, Pei-Hai Li, Xiao-Ming Li, Sui-Qun Yang, Ke-Chun Liu, Yun Zhang, Bin-Gui Wang, Xin Li|2024|Bioorg.Chem.|143|107073|doi:10.1016/j.bioorg.2023.107073
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7883604
title: Feature selection for preserving biological trajectories in single-cell data

description: Contains preprocessed single-cell data and metadata for feature selection. Preprocessed adata objects can be accessed using the <em>read_h5ad</em> function in Scanpy. The RPE iterative indirect immunofluorescence imaging dataset (adata_RPE.h5ad) from Ref. (https://doi.org/10.1016/j.cels.2021.10.007) was originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.4525425). The PDAC iterative indirect immunofluorescence imaging datasets (listed below) were originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.7860332). adata_PDAC_BxPC3.h5ad adata_PDAC_CFPAC.h5ad adata_PDAC_HPAC.h5ad adata_PDAC_MiaPaCa.h5ad adata_PDAC_Pa01C.h5ad adata_PDAC_Pa02C.h5ad adata_PDAC_Pa16C.h5ad adata_PDAC_PANC1.h5ad adata_PDAC_UM53.h5ad The CD8+ T cell differentiation dataset (adata_CD8.h5ad) from Ref. (https://doi.org/10.1126/sciimmunol.aaz6894) was originally downloaded from the Gene Expression Omnibus under the accession code GSE131847 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131847).
DOI: 10.5281/zenodo.10105826
title: Feature selection for preserving biological trajectories in single-cell data

description: Contains preprocessed single-cell data and metadata for feature selection. Preprocessed adata objects can be accessed using the read_h5ad function in anndata.

The RPE iterative indirect immunofluorescence imaging dataset (adata_RPE.h5ad) from Ref. (https://doi.org/10.1016/j.cels.2021.10.007) was originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.4525425).
The PDAC iterative indirect immunofluorescence imaging datasets (listed below) were originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.7860332).

adata_PDAC_BxPC3_control.h5ad
adata_PDAC_CFPAC_control.h5ad
adata_PDAC_HPAC_control.h5ad
adata_PDAC_MiaPaCa_control.h5ad
adata_PDAC_Pa01C_control.h5ad
adata_PDAC_Pa02C_control.h5ad
adata_PDAC_Pa16C_control.h5ad
adata_PDAC_PANC1_control.h5ad
adata_PDAC_UM53_control.h5ad
The CD8+ T cell differentiation dataset (adata_CD8.h5ad) from Ref. (https://doi.org/10.1126/sciimmunol.aaz6894) was originally downloaded from the Gene Expression Omnibus under the accession code GSE131847 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131847).
The definitive endoderm differentiation dataset (adata_DE.h5ad) contains multiplexed single-cell RNA sequencing data profiling the differentiation of human embryonic stem cells into the definitive endoderm.
DOI: 10.5281/zenodo.10534873
title: DELVE: Feature selection for preserving biological trajectories in single-cell data

description: Contains preprocessed single-cell data and metadata for feature selection. Preprocessed adata objects can be accessed using the read_h5ad function in anndata. Also contains the source data files for reproducing the Figures and Supplementary Figures referenced in the manuscript.



The RPE iterative indirect immunofluorescence imaging dataset (adata_RPE.h5ad) from Ref. (https://doi.org/10.1016/j.cels.2021.10.007) was originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.4525425).

The PDAC iterative indirect immunofluorescence imaging datasets (listed below) were originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.7860332).



adata_PDAC_BxPC3_control.h5ad

adata_PDAC_CFPAC_control.h5ad

adata_PDAC_HPAC_control.h5ad

adata_PDAC_MiaPaCa_control.h5ad

adata_PDAC_Pa01C_control.h5ad

adata_PDAC_Pa02C_control.h5ad

adata_PDAC_Pa16C_control.h5ad

adata_PDAC_PANC1_control.h5ad

adata_PDAC_UM53_control.h5ad



The CD8+ T cell differentiation dataset (adata_CD8.h5ad) from Ref. (https://doi.org/10.1126/sciimmunol.aaz6894) was originally downloaded from the Gene Expression Omnibus under the accession code GSE131847 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131847).

The definitive endoderm differentiation dataset (adata_DE.h5ad) contains multiplexed single-cell RNA sequencing data profiling the differentiation of human embryonic stem cells into the definitive endoderm.
DOI: 10.5281/zenodo.7883603
title: DELVE: Feature selection for preserving biological trajectories in single-cell data

description: Contains preprocessed single-cell data and metadata for feature selection. Preprocessed adata objects can be accessed using the read_h5ad function in anndata. Also contains the source data files for reproducing the Figures and Supplementary Figures referenced in the manuscript.



The RPE iterative indirect immunofluorescence imaging dataset (adata_RPE.h5ad) from Ref. (https://doi.org/10.1016/j.cels.2021.10.007) was originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.4525425).

The PDAC iterative indirect immunofluorescence imaging datasets (listed below) were originally downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.7860332).



adata_PDAC_BxPC3_control.h5ad

adata_PDAC_CFPAC_control.h5ad

adata_PDAC_HPAC_control.h5ad

adata_PDAC_MiaPaCa_control.h5ad

adata_PDAC_Pa01C_control.h5ad

adata_PDAC_Pa02C_control.h5ad

adata_PDAC_Pa16C_control.h5ad

adata_PDAC_PANC1_control.h5ad

adata_PDAC_UM53_control.h5ad



The CD8+ T cell differentiation dataset (adata_CD8.h5ad) from Ref. (https://doi.org/10.1126/sciimmunol.aaz6894) was originally downloaded from the Gene Expression Omnibus under the accession code GSE131847 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131847).

The definitive endoderm differentiation dataset (adata_DE.h5ad) contains multiplexed single-cell RNA sequencing data profiling the differentiation of human embryonic stem cells into the definitive endoderm.
DOI: 10.34683/sr474
title: StoneRounds Case: SR474
title: AR Stargardt Disease

description: StoneRounds Case SR474 was diagnosed with AR Stargardt Disease likely caused by mutations in the gene: ABCA4.
DOI: 10.60600/yu/vqkzpy/pj9ra5
title: ATS Codebook_posted.docx

description: This is the codebook for the datasets.
DOI: 10.60600/yu/vqkzpy
title: Replication Data for "Does the Alien Tort Statute Make a Difference?"

description: This dataset was produced for the article: Christopher Ewell, Oona A. Hathaway & Ellen Nohle Has the Alien Tort Statute Made a Difference? A Historical, Empirical, and Normative Assessment, Cornell Law Review, Vol. 107, pp. 1205-1317 (2022). It contains coded data on all published cases in which plaintiffs made a claim under the Alien Tort Statute.
DOI: 10.60600/yu/vqkzpy/hogppw
title: Hathaway et al_unpublished ATS cases_posted.xlsx
DOI: 10.60600/yu/vqkzpy/unb5sv
title: Hathaway_Published ATS Cases_posted.xlsx

description: These are the published Alien Tort Statute cases in the dataset.
DOI: 10.5281/zenodo.10534851
title: Data for Single Shot Measurement of Photonic Topological Invariant

description: Experimental data for the manuscript single shot measurement of photonic topological invariant.
DOI: 10.5281/zenodo.10290206
title: InTaVia/source-data: Pre-Release: First release of the source data repo

description: This first release contains:



a first version of the SHACL shapes used for validation

a first version of the GH action for validating turtle files

a first version of the dataset yaml definition

and a first version of the GH action that updates the provenance graph and pushes everything to the triplestore
DOI: 10.3886/e114847
title: Replication data for: Stimulating Local Public Employment: Do General Grants Work?

description: We apply the regression kink design to the Swedish grant system and estimate causal effects of intergovernmental grants on local public employment. Our robust conclusion is that grants do not stimulate local public employment. We find no statistically significant effects on total local public employment, and we can exclude even moderate effects. When disaggregating the total effect by sector, we find that personnel in the traditional welfare sectors are unaffected, a conclusion which applies to both publicly and privately employed in these sectors. The only positive and statistically significant effect of grants is that on administrative personnel.
DOI: 10.3886/e114847v1-145449
title: Replication data for: Stimulating Local Public Employment: Do General Grants Work?

description: We apply the regression kink design to the Swedish grant system and
estimate causal effects of intergovernmental grants on local public
employment. Our robust conclusion is that grants do not stimulate
local public employment. We find no statistically significant effects
on total local public employment, and we can exclude even moderate
effects. When disaggregating the total effect by sector, we find
that personnel in the traditional welfare sectors are unaffected, a
conclusion which applies to both publicly and privately employed
in these sectors. The only positive and statistically significant effect
of grants is that on administrative personnel.
description: Swedish municipalities.
DOI: 10.5519/qd.zagqvvz0
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.3886/a64d-7398
title: Guatemala Threshold - TVET: Final Analysis Report
DOI: 10.3886/j24m-6d23
title: Guatemala Threshold - TVET: Final Analysis Report
DOI: 10.5519/qd.1qsxp9fj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.10534904
title: Data for "Statistical analysis on branching characteristics of positive streamer discharges in N2-O2 mixtures"

description: This dataset consists of files used to produce the data presented in the article "Statistical analysis on branching characteristics of positive streamer discharges in N2-O2 mixtures". This dataset includes: 1) raw experimentel data (stereoscopic and stroboscopic images), and 2) processed image data in .mat file.
DOI: 10.5281/zenodo.10534905
title: Data for "Statistical analysis on branching characteristics of positive streamer discharges in N2-O2 mixtures"

description: This dataset consists of files used to produce the data presented in the article "Statistical analysis on branching characteristics of positive streamer discharges in N2-O2 mixtures". This dataset includes: 1) raw experimentel data (stereoscopic and stroboscopic images), and 2) processed image data in .mat file.
DOI: 10.7298/dmq3-yh66
title: Data from: Low-dose sugammadex reverses moderate rocuronium-induced neuromuscular block in horses
DOI: 10.6084/m9.figshare.24982581
title: <b>Violence Aestheticization in Catholic Paintings</b>

description: There is a relationship between the legitimization of violence and art known as the aestheticization of the image, which is defined as when the aesthetic value of an image takes precedence over and may even annul its cognitive and normative content,
DOI: 10.6084/m9.figshare.24982581.v1
title: <b>Violence Aestheticization in Catholic Paintings</b>

description: There is a relationship between the legitimization of violence and art known as the aestheticization of the image, which is defined as when the aesthetic value of an image takes precedence over and may even annul its cognitive and normative content,
DOI: 10.3886/e197842
title: Tennessee Residencies Landscape: Data and Analysis Files

description: In this study, we explore the results of a survey administered to all programs across Tennessee—supplemented with administrative data on the students enrolled in these programs and their mentors—to map out the presence of the programmatic features that characterize the teacher residency and assess the extent to which these features distinguish programs identified as teacher residencies (using multiple strategies) from all other programs. <b></b>
description: Response Rates: 69.5% of all programs, covering 83.2% of all teachers
description: web-based survey;
DOI: 10.3886/e197842v1
title: Tennessee Residencies Landscape: Data and Analysis Files

description: In this study, we explore the results of a survey administered to all programs across Tennessee—supplemented with administrative data on the students enrolled in these programs and their mentors—to map out the presence of the programmatic features that characterize the teacher residency and assess the extent to which these features distinguish programs identified as teacher residencies (using multiple strategies) from all other programs. <b></b>
description: Response Rates: 69.5% of all programs, covering 83.2% of all teachers
description: web-based survey;
DOI: 10.5676/eum_saf_cm/fcdr_mwi/v004
title: Fundamental Climate Data Record of Microwave Imager Radiances, Edition 4

description: The CM SAF FCDR of Microwave Imager Radiances comprises inter-calibrated brightness
 temperatures (BTRs) from the SMMR, SSM/I and SSMIS radiometers. This 4th edition covers the time period
 from October 1978 to December 2020 including all available data from the SMMR radiometer
 aboard Nimbus–7, the SSM/I radiometers aboard F08, F10, F11, F13, F14, and F15 and the SSMIS
 radiometers aboard F16, F17, and F18. This data record has been extended by two more years of SSMIS data
 in December 2023. This prolongs the end of the covered time period to December 2022.
 The FCDR provides homogenised and inter-calibrated BTRs in a
 user-friendly data format. SMMR, SSM/I and SSMIS data are used for a variety of applications,
 such as analyses of the hydrological cycle and remote sensing of sea ice. The improved
 homogenization and inter-calibration procedure ensure the long term stability of the FCDR for
 climate related applications. All available raw data records have been reprocessed to a common
 standard, starting with the calibration of the raw Earth counts, to ensure a completely
 homogenized data record. The data processing accounts for several known issues with the
 instruments and corrects calibration anomalies due to along-scan inhomogeneity, moonlight
 intrusions, sunlight intrusions, and emissive reflector. Also, an adjustment to the SSMIS
 geolocation has been implemented in order to improve the consistency. Corrections for SMMR are limited
 because the SMMR raw data records were not available. Furthermore, the inter-calibration model
 incorporates a scene dependent inter-satellite bias correction and a non-linearity correction
 to the instrument calibration. The data files contain all available original sensor data
 (SMMR: Pathfinder Level 1b) and metadata to provide a completely traceable climate data
 record. Inter-calibration and Earth incidence angle normalization offsets are available as
 additional layers within the data files in order to keep this information transparent to the
 users. The data record is complemented with radiometer sensitivities, quality flags, surface
 types, and Earth incidence angles.
DOI: 10.6084/m9.figshare.24894926
title: Two new species of <i>Inocybe</i> from Mediterranean Cistaceae heathlands

description: This study explored a heathland region in Portugal, and through morphology, biogeography, and multilocus phylogeny, two new species of Inocybaceae are described. The first species, <i>Inocybe iberilepora</i>, belongs to “<i>I. flocculosa</i> group,” whereas the second species, <i>Inocybe phaeosquamosa</i>, belongs to a relatively isolated and understudied clade, distantly related to <i>I. furfurea</i> and allies. Both species are tied to a west Mediterranean distribution and ecology, associating with the local Cistaceae ecosystems. By characterizing these new species, our research contributes to the understanding of European Funga and enriches the knowledge of the genus <i>Inocybe</i> on a global scale.
DOI: 10.6084/m9.figshare.24894926.v1
title: Two new species of <i>Inocybe</i> from Mediterranean Cistaceae heathlands

description: This study explored a heathland region in Portugal, and through morphology, biogeography, and multilocus phylogeny, two new species of Inocybaceae are described. The first species, <i>Inocybe iberilepora</i>, belongs to “<i>I. flocculosa</i> group,” whereas the second species, <i>Inocybe phaeosquamosa</i>, belongs to a relatively isolated and understudied clade, distantly related to <i>I. furfurea</i> and allies. Both species are tied to a west Mediterranean distribution and ecology, associating with the local Cistaceae ecosystems. By characterizing these new species, our research contributes to the understanding of European Funga and enriches the knowledge of the genus <i>Inocybe</i> on a global scale.