cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10011861
title: From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability

description: Code: https://github.com/srijitseal/BioMorph_Space

Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predict in vitro and in vivo drug effects. However, Cell Painting features are based on image statistics, and are, therefore, often not readily biologically interpretable. In this study, we introduce an approach that maps specific Cell Painting features into the BioMorph space using readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. In summary, BioMorph space offers a more biologically relevant way to interpret cell morphological features from the Cell Painting assays and to generate hypotheses for experimental validation.


 


The following datasets are released:
 


Cell_Health_median_357_profiles_70_labels.csv :
The Cell Heath dataset for CRISPR perturbations. Contains median consensus signatures for the 357 consensus profiles (119 CRISPR perturbations × 3 cell lines) Ref: Way et al.


Cell_Painitng_CRISPR_Perturbations_357_profiles_827_features_scaled.csv:
The Cell Painting dataset for CRISPR perturbations. Contains 827 morphology features (and metadata annotation) for 357 consensus profiles (119 CRISPR perturbations × 3 cell lines). Ref: Way et al.


Cell_Painting_data_658_compounds_827_Features_scaled.csv
The Cell Painting dataset for compound perturbations. Contains 658 structurally unique compounds with 827 Cell Painting features. Ref: Bray et al


Endpoints_9_Mitotox_biological_activities_658_compounds.csv
The biological assay activity labels for compound perturbations. Contains 658 structurally unique compounds with 9 biological activity consensus hit calls. Ref: ToxCast/MoleculeNet


BioMoprh_pvalue_658_compunds_398_BioMorph_terms.csv:
The dataset of standardised BioMorph term p-values. Contains 398 BioMorph terms for the 658 compounds in the biological activity dataset. 

References: 
Way et al. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021;32(9):995-1005.
Bray et al. A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. Gigascience. 2017;6(12):1-5. 
MoleculeNet: Wu et al. MoleculeNet: A benchmark for molecular machine learning. Chem Sci. 2018;9(2):513-530. 
ToxCast: Exploring ToxCast Data | US EPA https://www.epa.gov/chemical-research/exploring-toxcast-data (accessed Jul 9, 2023).
DOI: 10.5281/zenodo.8147309
title: From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability

description: Code: https://github.com/srijitseal/BioMorph_Space

Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predict in vitro and in vivo drug effects. However, Cell Painting features are based on image statistics, and are, therefore, often not readily biologically interpretable. In this study, we introduce an approach that maps specific Cell Painting features into the BioMorph space using readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. In summary, BioMorph space offers a more biologically relevant way to interpret cell morphological features from the Cell Painting assays and to generate hypotheses for experimental validation.


 


The following datasets are released:
 


Cell_Health_median_357_profiles_70_labels.csv :
The Cell Heath dataset for CRISPR perturbations. Contains median consensus signatures for the 357 consensus profiles (119 CRISPR perturbations × 3 cell lines) Ref: Way et al.


Cell_Painitng_CRISPR_Perturbations_357_profiles_827_features_scaled.csv:
The Cell Painting dataset for CRISPR perturbations. Contains 827 morphology features (and metadata annotation) for 357 consensus profiles (119 CRISPR perturbations × 3 cell lines). Ref: Way et al.


Cell_Painting_data_658_compounds_827_Features_scaled.csv
The Cell Painting dataset for compound perturbations. Contains 658 structurally unique compounds with 827 Cell Painting features. Ref: Bray et al


Endpoints_9_Mitotox_biological_activities_658_compounds.csv
The biological assay activity labels for compound perturbations. Contains 658 structurally unique compounds with 9 biological activity consensus hit calls. Ref: ToxCast/MoleculeNet


BioMoprh_pvalue_658_compunds_398_BioMorph_terms.csv:
The dataset of standardised BioMorph term p-values. Contains 398 BioMorph terms for the 658 compounds in the biological activity dataset. 

References: 
Way et al. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021;32(9):995-1005.
Bray et al. A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. Gigascience. 2017;6(12):1-5. 
MoleculeNet: Wu et al. MoleculeNet: A benchmark for molecular machine learning. Chem Sci. 2018;9(2):513-530. 
ToxCast: Exploring ToxCast Data | US EPA https://www.epa.gov/chemical-research/exploring-toxcast-data (accessed Jul 9, 2023).
DOI: 10.5281/zenodo.10431854
title: Data files to support "Extracting interpretable signatures of whole-brain dynamics through systematic comparison"

description: Data files to support "Extracting interpretable signatures of whole-brain dynamics through systematic comparison".

Some data files are processed rsfMRI time series for participants in two open-access neuroimaging studies:



The UCLA Consortium for Neuropsychiatric Phenomics (CNP) LA5c study, available from OpenfMRI with accession number ds000030 at https://openfmri.org/dataset/ds000030/

The Autism Brain Imaging Data Exchange (ABIDE) I/II study (Di Martino et al. 2014, 2017), preprocessed as part of a global classification challenge by Traut et al. (2020) and available at: https://zenodo.org/records/3625740


Corresponding code is here: https://github.com/DynamicsAndNeuralSystems/fMRI_FeaturesDisorders

Preprint URL will be added upon upload.
DOI: 10.5281/zenodo.10431855
title: Data files to support "Extracting interpretable signatures of whole-brain dynamics through systematic comparison"

description: Data files to support "Extracting interpretable signatures of whole-brain dynamics through systematic comparison".

Some data files are processed rsfMRI time series for participants in two open-access neuroimaging studies:



The UCLA Consortium for Neuropsychiatric Phenomics (CNP) LA5c study, available from OpenfMRI with accession number ds000030 at https://openfmri.org/dataset/ds000030/

The Autism Brain Imaging Data Exchange (ABIDE) I/II study (Di Martino et al. 2014, 2017), preprocessed as part of a global classification challenge by Traut et al. (2020) and available at: https://zenodo.org/records/3625740


Corresponding code is here: https://github.com/DynamicsAndNeuralSystems/fMRI_FeaturesDisorders

Preprint URL will be added upon upload.
DOI: 10.5281/zenodo.8008455
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: In situ measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provide sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 368 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data. Furthermore, we carefully evaluate the effectiveness of the new dataset over sites with different degrees of spatial representativeness. The results demonstrate superior overall accuracy compared to in situ measurement, especially in regions with strong spatial heterogeneity while most in situ measurements have poor spatial representativeness and cannot represent the pixel scale. The dataset offers a unique collection of pixel-scale relative ground “truth” with the widest spatial distribution and longest time series. Its ability to capture both spatial and temporal variations of surface albedo at coarse spatial scales makes it an invaluable resource for validating and correcting global surface albedo products.
DOI: 10.5281/zenodo.10484445
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: In situ measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provides sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 416 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data.  Furthermore, we thoroughly assessed the effectiveness of the dataset at sites with different degrees of spatial representativeness. The results demonstrate that using this dataset in validation outperforms the direct comparison between satellite and in situ site measurements over heterogeneous surfaces when in situ measurement footprints are less than satellite pixel size. The dataset offers a unique collection of coarse pixel scale relative ground "truth" with the widest spatial distribution and longest time series. By merging temporal information from ground-based observations and spatial information from high-resolution data, the dataset we provided represents a valuable resource for validating and correcting worldwide surface albedo products over heterogeneous surfaces.
DOI: 10.5281/zenodo.10484626
title: TEC observation and simulation from Mars to Earth

description: 这些差分相位延迟是通过中国火星航天器天问一号的DOR信号获得的。它显示了 CME 和 CIR 通过信号路径时的 TEC 变化。
DOI: 10.5281/zenodo.10484627
title: TEC observation and simulation from Mars to Earth

description: 这些差分相位延迟是通过中国火星航天器天问一号的DOR信号获得的。它显示了 CME 和 CIR 通过信号路径时的 TEC 变化。
DOI: 10.5281/zenodo.10484670
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: In situ measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provides sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 416 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data.  Furthermore, we thoroughly assessed the effectiveness of the dataset at sites with different degrees of spatial representativeness. The results demonstrate that using this dataset in validation outperforms the direct comparison between satellite and in situ site measurements over heterogeneous surfaces when in situ measurement footprints are less than satellite pixel size. The dataset offers a unique collection of coarse pixel scale relative ground "truth" with the widest spatial distribution and longest time series. By merging temporal information from ground-based observations and spatial information from high-resolution data, the dataset we provided represents a valuable resource for validating and correcting worldwide surface albedo products over heterogeneous surfaces.
DOI: 10.5281/zenodo.8008454
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: In situ measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provides sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 416 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data.  Furthermore, we thoroughly assessed the effectiveness of the dataset at sites with different degrees of spatial representativeness. The results demonstrate that using this dataset in validation outperforms the direct comparison between satellite and in situ site measurements over heterogeneous surfaces when in situ measurement footprints are less than satellite pixel size. The dataset offers a unique collection of coarse pixel scale relative ground "truth" with the widest spatial distribution and longest time series. By merging temporal information from ground-based observations and spatial information from high-resolution data, the dataset we provided represents a valuable resource for validating and correcting worldwide surface albedo products over heterogeneous surfaces.
DOI: 10.5281/zenodo.8362151
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: In situ measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provide sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 368 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data. Furthermore, we carefully evaluate the effectiveness of the new dataset over sites with different degrees of spatial representativeness. The results demonstrate superior overall accuracy compared to in situ measurement, especially in regions with strong spatial heterogeneity while most in situ measurements have poor spatial representativeness and cannot represent the pixel scale. The dataset offers a unique collection of pixel-scale relative ground “truth” with the widest spatial distribution and longest time series. Its ability to capture both spatial and temporal variations of surface albedo at coarse spatial scales makes it an invaluable resource for validating and correcting global surface albedo products.
DOI: 10.5281/zenodo.8362185
title: A coarse pixel scale ground "truth" dataset based on the global in situ site measurements from 2000 to 2021.

description: <em>In situ </em>measurements from sparsely distributed networks worldwide are a valuable source of data for validating satellite products. However, the significant differences in spatial scale between in situ and satellite measurements pose a challenge for validation. To address this challenge, we propose a new global coarse pixel-scale ground "truth" dataset which provides sequential pixel scale albedo on a 500 m resolution over the period 2000-2021. The creation of data set is done using ground measurements from 416 sparsely distributed networks worldwide and high-resolution long-term time series data corresponding to site-based data. Furthermore, we thoroughly assessed the effectiveness of the dataset at sites with different degrees of spatial representativeness. The results demonstrate that using this dataset in validation outperforms the direct comparison between satellite and <em>in situ</em> site measurements over heterogeneous surfaces when <em>in situ</em> measurement footprints are less than satellite pixel size. The dataset offers a unique collection of coarse pixel scale relative ground "truth" with the widest spatial distribution and longest time series. By merging temporal information from ground-based observations and spatial information from high-resolution data, the dataset we provided represents a valuable resource for validating and correcting worldwide surface albedo products over heterogeneous surfaces.
DOI: 10.6084/m9.figshare.22591234
title: Data and Appendix

description: The dats is used for the paper named "Spatial Interaction of Regional Economic Development and its Influencing Factors: Evidence from China ", and the appendix is the results not presented in the paper.
DOI: 10.6084/m9.figshare.22591234.v1
title: Data and Appendix

description: The dats is used for the paper named "Spatial Interaction of Regional Economic Development and its Influencing Factors: Evidence from China ", and the appendix is the results not presented in the paper.
DOI: 10.6084/m9.figshare.23792550
title: eQTL_Graphs.robj

description: Robject containing all eQTL graphs.
DOI: 10.6084/m9.figshare.23792550.v1
title: eQTL_Graphs.robj

description: Robject containing all eQTL graphs.
DOI: 10.6084/m9.figshare.24978660
title: Results data (Figures 1 - 6 and Supplementary Data 1)

description: Source data for all the results described in Figures 1 - 6 and Supplementary Figure 1
DOI: 10.6084/m9.figshare.24978660.v1
title: Results data (Figures 1 - 6 and Supplementary Data 1)

description: Source data for all the results described in Figures 1 - 6 and Supplementary Figure 1
DOI: 10.6084/m9.figshare.24979104
title: Electronic Supplementary Data File from Coupled social and ecological change drove the historical extinction of the California grizzly bear (<i>Ursus arctos californicus</i>)

description: Excel data file containing multiple tabs including: historical food quotes, original radiocarbon and stable isotope data for grizzly bears, original stable isotope values for food items and competitors (including from the literature), references for trophic discrimination factors and other tissue conversions, MRPP B-H complete unformatted results, and body size data.
DOI: 10.6084/m9.figshare.24979104.v1
title: Electronic Supplementary Data File from Coupled social and ecological change drove the historical extinction of the California grizzly bear (<i>Ursus arctos californicus</i>)

description: Excel data file containing multiple tabs including: historical food quotes, original radiocarbon and stable isotope data for grizzly bears, original stable isotope values for food items and competitors (including from the literature), references for trophic discrimination factors and other tissue conversions, MRPP B-H complete unformatted results, and body size data.
DOI: 10.57841/casdc.0003338
title: Zbtb10，Zbtb7A与dna 复合物的晶体衍射数据
DOI: 10.5281/zenodo.10485184
title: PERFIL DOS RESPONDENTES
DOI: 10.5281/zenodo.10485185
title: PERFIL DOS RESPONDENTES
DOI: 10.5281/zenodo.10485166
title: Probing laser plasma dynamics using high-order harmonics generation in carbon-containing nanomaterials (2012) Applied Sciences - Data

description: Dataset for Figure 2, and 4a.

 

Publication:

Ganeev, R. A. , Kim, V. V. , Rao, K. S. and Guo, C., Probing laser plasma dynamics usinghigh-order harmonics generation in carbon-containing nanomaterials, Applied Sciences, 2021, Vol. 11, art. no. 2143. https://doi.org/10.3390/app11052143 , open access(published online: 28 February 2021) Q2

 




Files
DOI: 10.5281/zenodo.10485167
title: Probing laser plasma dynamics using high-order harmonics generation in carbon-containing nanomaterials (2012) Applied Sciences - Data

description: Dataset for Figure 2, and 4a.

 

Publication:

Ganeev, R. A. , Kim, V. V. , Rao, K. S. and Guo, C., Probing laser plasma dynamics usinghigh-order harmonics generation in carbon-containing nanomaterials, Applied Sciences, 2021, Vol. 11, art. no. 2143. https://doi.org/10.3390/app11052143 , open access(published online: 28 February 2021) Q2

 




Files
DOI: 10.5281/zenodo.10484996
title: High-Order Harmonics Generation in Atomic and Molecular Zinc Plasmas (2021) Photonics - Data

description: Dataset for Figure 2, 3, and 4.

 

Publication:

Ganeev, R. A., and Kuroda, H. (2021) High-Order Harmonics Generation in Atomic andMolecular Zinc Plasmas,Photonics, 8, art. no.29. https://doi.org/10.3390/photonics8020029 , open access (published online: 25 January 2021) Q2
DOI: 10.5281/zenodo.10484997
title: High-Order Harmonics Generation in Atomic and Molecular Zinc Plasmas (2021) Photonics - Data

description: Dataset for Figure 2, 3, and 4.

 

Publication:

Ganeev, R. A., and Kuroda, H. (2021) High-Order Harmonics Generation in Atomic andMolecular Zinc Plasmas,Photonics, 8, art. no.29. https://doi.org/10.3390/photonics8020029 , open access (published online: 25 January 2021) Q2
DOI: 10.5281/zenodo.10485158
title: MBB-RCS: Modified Black Body with Resonant Cyclotron Scattering - A Magnetar Flare Spectral Model

description: A Table Model for XSPEC: Modified Black Body with Resonant Cyclotron Scattering

This model incorporates modified Planckian emission in the presence of strong magnetic fields (Lyubarsky 2002), as well as the effects of resonant cyclotron scattering (Yamasaki et al. 2020).

The model has two parameters: the effective temperature in keV, and the normalization. The table model covers the energy range from 5 to 300 keV, and the parameter grid of effective temperature consists of 79 values between 1 and 40 keV with increments of 0.5 keV.
DOI: 10.5281/zenodo.10485159
title: MBB-RCS: Modified Black Body with Resonant Cyclotron Scattering - A Magnetar Flare Spectral Model

description: A Table Model for XSPEC: Modified Black Body with Resonant Cyclotron Scattering

This model incorporates modified Planckian emission in the presence of strong magnetic fields (Lyubarsky 2002), as well as the effects of resonant cyclotron scattering (Yamasaki et al. 2020).

The model has two parameters: the effective temperature in keV, and the normalization. The table model covers the energy range from 5 to 300 keV, and the parameter grid of effective temperature consists of 79 values between 1 and 40 keV with increments of 0.5 keV.
DOI: 10.6084/m9.figshare.24979501
title: Additional file 1 of Effect of mixed Mycobacterium tuberculosis infection on rapid molecular diagnostics among patients starting MDR-TB treatment in Uganda

description: Additional file 1.
DOI: 10.6084/m9.figshare.24979501.v1
title: Additional file 1 of Effect of mixed Mycobacterium tuberculosis infection on rapid molecular diagnostics among patients starting MDR-TB treatment in Uganda

description: Additional file 1.