cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10604552
title: Dataset for "Complexity of crack front geometry enhances toughness of brittle solids"

description: This data package supports the publication

'Complexity of crack front geometry enhances toughness of brittle solids'

by Xinyue Wei, Chenzhuo Li, Cían McCarthy, and John M. Kolinski

Nature physics (2024) - https://doi.org/10.1038/s41567-024-02435-x

 

DOI: 10.5281/zenodo.10604552

 

 

The data package includes 

- data for material characterization in 'material_test.xlsx';

- segmented 3D crack data in "segmented_3D_crack_stacks" folder.

 

 

'material_test.xlsx' includes

- shear modulus for Gel1, Gel2, Gel3, Gel4, and PDMS;

- stretch v.s. engineering stress for the five materials.

 

 

'segmented_3D_crack_stacks' includes

- 'sample_info.xlsx': metadata for all the cracks including the critically loaded cracks and the cracks with local 

  propagation in two sheets, with the following information:

- 'crack_name' corresponds to the title of each tif file in the subfolders;

- 'sample' indicates the material and thickness of the samples;

- 'xy_scale_um' and 'z_scale_um' are the resolutions in microns in xyz direction ;

- 's_start' and 's_end' provide the range of the valid slices, with s_end excluded. The first slice is s=0;

- 'tile_s_start' and 'tile_s_end' provide the range of the valid slices of the tile scans. The tile scans 

          are taken for the measurement of strain energy release rate from the far field CTOD. Since the field of 

  view is large enough to cover the K-dominant region of Gel1, tile scan is not taken for Gel1;

- 'remarks' are the comments for the data points (if applicable).

 

- 'critically_loaded_cracks': tif stacks for the binarized 3D cracks that are loaded to critical state. 

   Different materials and sample thicknesses are in separate folders. 

- 'local_propagation': tif stacks for the binarized 3D cracks before critically loaded.
DOI: 10.6084/m9.figshare.25471468
title: EIS analysis_IC2316932

description: A. Mrzygłód, M. Rzonsowska, M. P. García-Armada, B. Dudziec, M. Nowicki<br>Metallodendrimers Unveiled: Investigating the Formation and Unique Features of Double-Decker Silsesquioxane-Based Silylferrocene Dendrimers<br>Inorg. Chem. 2023, 62, 41, 16932–16942<br>metadata for SEM images<br>sample denoted as 1426 - in publication it is G1-DDSQ-Fc8sample denoted as 1427 - in publication it is G2-DDSQ-Fc16
DOI: 10.26300/ee0c-eh83
title: Supplement for Dissertation: Contextual Clay Bodies: Figurine Use and Meaning in Late Bronze Age Cyprus
DOI: 10.6084/m9.figshare.25407637
title: TGA analysis_IC2316932

description: A. Mrzygłód, M. Rzonsowska, M. P. García-Armada, B. Dudziec, M. Nowicki<br>Metallodendrimers Unveiled: Investigating the Formation and Unique Features of Double-Decker Silsesquioxane-Based Silylferrocene Dendrimers<br>Inorg. Chem. 2023, 62, 41, 16932–16942<br>metadata for TGA analysis<br>sample denoted as 1426 - in publication it is G1-DDSQ-Fc8sample denoted as 1427 - in publication it is G2-DDSQ-Fc16
DOI: 10.6084/m9.figshare.25407637.v1
title: TGA analysis

description: A. Mrzygłód, M. Rzonsowska, M. P. García-Armada, B. Dudziec, M. Nowicki<br>Metallodendrimers Unveiled: Investigating the Formation and Unique Features of Double-Decker Silsesquioxane-Based Silylferrocene Dendrimers<br>Inorg. Chem. 2023, 62, 41, 16932–16942<br>metadata for TGA analysis<br>sample denoted as 1426 - in publication it is G1-DDSQ-Fc8sample denoted as 1427 - in publication it is G2-DDSQ-Fc16
DOI: 10.34740/kaggle/dsv/7938344
title: COVID Vaccination in World (updated daily)
DOI: 10.2908/mar_mt_am_csvi
title: Vessels arriving in the main ports by type of vessels - annual data
title: Navires arrivant dans les ports principaux par type des navires - données annuelles
title: Einlaufende Schiffe in den Haupthäfen nach Schiffstyp - jährliche Daten
DOI: 10.2908/mar_tf_qm
title: Einlaufende Schiffe in den Haupthäfen nach Schiffstyp und Schiffsgröße - vierteljährliche Daten
title: Vessels arriving in the main ports by type and size of vessels - quarterly data
title: Navires arrivant dans les ports principaux par type et taille des navires - données trimestrielles
DOI: 10.6084/m9.figshare.25471459
title: Study Data for "Identifying The Impacts of Urbanisation and Extreme Events on River Water Temperatures in a Headwater Catchment

description: Study data supporting results in "Identifying The Impacts of Urbanisation and Extreme Events on River Water Temperatures in a Headwater Catchment".
DOI: 10.6084/m9.figshare.25471459.v1
title: Study Data for "Identifying The Impacts of Urbanisation and Extreme Events on River Water Temperatures in a Headwater Catchment

description: Study data supporting results in "Identifying The Impacts of Urbanisation and Extreme Events on River Water Temperatures in a Headwater Catchment".
DOI: 10.5281/zenodo.10853625
title: Data source for the ReMap REST API

description: Content

This Zenodo contains the ReMap BED files in bgzip format with the TABIX indexes for the 2022, 2020, 2018 and 2015 ReMap releases.

It contains all three data types (all peaks, non-redundant peaks and CRMs), except for 2015 (only all peaks, and non-redundant peaks available). 

Format 

The files formats for BGZIP BED files and TABIX indexes are as follow : 



remap2018_all_macs2_hg38_v1_2.bed.gz

remap2018_all_macs2_hg38_v1_2.bed.gz.tbi




remap2018 : ReMap release number (2015, 2018, 2020 or 2022)

all : data types (all= all peaks, nr= non-redundant peaks, crm=CisRegulatoryModules)

macs2 : peak caller used (always macs2)

hg38 : assembly version (hg19, hg38, mm10 etc..)

v1.2 : version patches


The versioning number (eg. v1.2, v1.0) which varies between ReMap releases have been normalized with symlinks pointing to *latest* files. e.g.



remap2018_all_macs2_hg38_v1_2.bed.gz --> remap2018_all_macs2_hg38_latest.bed.gz


Folder architecture 

The architecture is as follow  : 

.

├── 2015

│   ├── hg19

│   └── hg38

├── 2018

│   ├── hg19

│   └── hg38

├── 2020

│   ├── TAIR10

│   ├── hg19

│   └── hg38

└── 2022

     ├── TAIR10

     ├── dm6

     ├── hg19

     ├── hg38

     ├── mm10

     └── mm39
DOI: 10.5281/zenodo.10853626
title: Data source for the ReMap REST API

description: Content

This Zenodo contains the ReMap BED files in bgzip format with the TABIX indexes for the 2022, 2020, 2018 and 2015 ReMap releases.

It contains all three data types (all peaks, non-redundant peaks and CRMs), except for 2015 (only all peaks, and non-redundant peaks available). 

Format 

The files formats for BGZIP BED files and TABIX indexes are as follow : 



remap2018_all_macs2_hg38_v1_2.bed.gz

remap2018_all_macs2_hg38_v1_2.bed.gz.tbi




remap2018 : ReMap release number (2015, 2018, 2020 or 2022)

all : data types (all= all peaks, nr= non-redundant peaks, crm=CisRegulatoryModules)

macs2 : peak caller used (always macs2)

hg38 : assembly version (hg19, hg38, mm10 etc..)

v1.2 : version patches


The versioning number (eg. v1.2, v1.0) which varies between ReMap releases have been normalized with symlinks pointing to *latest* files. e.g.



remap2018_all_macs2_hg38_v1_2.bed.gz --> remap2018_all_macs2_hg38_latest.bed.gz


Folder architecture 

The architecture is as follow  : 

.

├── 2015

│   ├── hg19

│   └── hg38

├── 2018

│   ├── hg19

│   └── hg38

├── 2020

│   ├── TAIR10

│   ├── hg19

│   └── hg38

└── 2022

     ├── TAIR10

     ├── dm6

     ├── hg19

     ├── hg38

     ├── mm10

     └── mm39
DOI: 10.21227/7b2a-pe59
title: Sparsely-annotated Datasets for ProCNS

description: Weakly-supervised segmentation (WSS) has emerged as a solution to mitigate the conflict between annotation cost and model performance by adopting sparse annotation formats (e.g., point, scribble, block, etc.). Typical approaches attempt to exploit anatomy and topology priors to directly expand sparse annotations into pseudo-labels. However, due to lack of attention to the ambiguous boundaries in medical images and insufficient exploration of sparse supervision, existing approaches tend to generate erroneous and overconfident pseudo proposals in noisy regions, leading to cumulative model error and performance degradation. In this work, we propose a novel WSS approach, named ProCNS, encompassing two synergistic modules devised with the principles of progressive prototype calibration and noise suppression. Specifically, we design a Prototype-based Regional Spatial Affinity (PRSA) loss to maximize the pair-wise affinities between spatial and semantic elements, providing our model of interest with more reliable guidance. The affinities are derived from the input images and the prototype-refined predictions. Meanwhile, we propose an Adaptive Noise Perception and Masking (ANPM) module to obtain more enriched and representative prototype representations, which adaptively identifies and masks noisy regions within the pseudo proposals, reducing potential erroneous interference during prototype computation. Furthermore, we generate specialized soft pseudo-labels for the noisy regions identified by ANPM, providing supplementary supervision. Extensive experiments on three medical image segmentation tasks involving different modalities demonstrate that the proposed framework significantly outperforms representative state-of-the-art methods. Code and data are available at https://github.com/LyxDLiI/ProCNS
DOI: 10.5517/ccdc.csd.cc2fwmrq
title: CCDC 2260884: Experimental Crystal Structure Determination

description: Related Article: Osvaldo Ordoñez, Greggory T. Kent, Megan A. Schuerlein, Guang Wu, Trevor W. Hayton|2023|Organometallics|42|2347|doi:10.1021/acs.organomet.3c00222
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.cc2fwmsr
title: CCDC 2260885: Experimental Crystal Structure Determination

description: Related Article: Osvaldo Ordoñez, Greggory T. Kent, Megan A. Schuerlein, Guang Wu, Trevor W. Hayton|2023|Organometallics|42|2347|doi:10.1021/acs.organomet.3c00222
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.cc2fwmts
title: CCDC 2260886: Experimental Crystal Structure Determination

description: Related Article: Osvaldo Ordoñez, Greggory T. Kent, Megan A. Schuerlein, Guang Wu, Trevor W. Hayton|2023|Organometallics|42|2347|doi:10.1021/acs.organomet.3c00222
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.cc2fwmvt
title: CCDC 2260887: Experimental Crystal Structure Determination

description: Related Article: Osvaldo Ordoñez, Greggory T. Kent, Megan A. Schuerlein, Guang Wu, Trevor W. Hayton|2023|Organometallics|42|2347|doi:10.1021/acs.organomet.3c00222
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.cc2glvwt
title: CCDC 2282247: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glvxv
title: CCDC 2282248: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glvzx
title: CCDC 2282250: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glvyw
title: CCDC 2282249: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glw0z
title: CCDC 2282251: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glw10
title: CCDC 2282252: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glw21
title: CCDC 2282253: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glw32
title: CCDC 2282254: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2glw43
title: CCDC 2282255: Experimental Crystal Structure Determination

description: Related Article: Pavel Kozáček, Libor Dostál, Adam Hochmal, Monika Pascucci, Aleš Růžička, Tomáš Mikysek, Milan Erben|2023|Organometallics|42|2405|doi:10.1021/acs.organomet.3c00332
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.cc2h118w
title: CCDC 2294907: Experimental Crystal Structure Determination

description: Related Article: Lucas Bacheley, Rathies Ravindra, Gérard Guillamot, Phannarath Phansavath, Virginie Ratovelomanana-Vidal|2024|Adv.Synth.Catal.|366|1019|doi:10.1002/adsc.202301294
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.cc2h119x
title: CCDC 2294908: Experimental Crystal Structure Determination

description: Related Article: Lucas Bacheley, Rathies Ravindra, Gérard Guillamot, Phannarath Phansavath, Virginie Ratovelomanana-Vidal|2024|Adv.Synth.Catal.|366|1019|doi:10.1002/adsc.202301294
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.10868605
title: Cre Expression in Control Tissues of the PTF1a Pig

description: Immunohistochemistry (IHC) analysis of the stomach, colon, lung, muscle, and duodenum tissues from PTF1a-Cre pig reveals an absence of Cre protein expression.
DOI: 10.5281/zenodo.10868606
title: Cre Expression in Control Tissues of the PTF1a Pig

description: Immunohistochemistry (IHC) analysis of the stomach, colon, lung, muscle, and duodenum tissues from PTF1a-Cre pig reveals an absence of Cre protein expression.
DOI: 10.6084/m9.figshare.25450378.v8
title: SAMMY-seq 4f human tracks data

description: In this repository is stored the hub used to make the genomic track UCSC session to display and share all the tracks shown into "Biochemical properties of chromatin domains define genome compartmentalization" based on the human genome (fibroblasts).
DOI: 10.48420/24871785
title: Normalised gene expression, miRNA expression and urinary transcriptomic data from Human Kidney Tissue Resource (HKTR)

description: Normalised kidney gene expression data from HKTR (hktr_gene_expression.txt); normalised kidney microRNA expression data from HKTR (hktr_mirna_expression.txt); normalised urinary data from HKTR (urinary-log2-tpm-scaled.rds). The rds file could be read with readRDS function in R.If you use this data, please cite the following paper: Xu, X., Khunsriraksakul, C., Eales, J.M. et al. Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets. Nat Commun 15, 2359 (2024). https://doi.org/10.1038/s41467-024-46132-y
DOI: 10.48420/24871785.v1
title: Normalised gene expression, miRNA expression and urinary transcriptomic data from HKTR

description: Normalised kidney gene expression data from HKTR (hktr_gene_expression.txt); normalised kidney microRNA expression data from HKTR (hktr_mirna_expression.txt); normalised urinary data from HKTR (urinary-log2-tpm-scaled.rds). The rds file could be read with readRDS function in R.
DOI: 10.25345/c5028pq79
title: MassIVE MSV000094398 - Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer
title: In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) gene ataxia telangiectasia mutated (ATM) are common. While poly-ADP-ribose polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues for ATM mutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream H2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPC in vitro and in vivo, and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.
DOI: 10.5281/zenodo.10869006
title: Unveiling Therapeutic Targets and Immunological Insights in Glioblastoma Through Analysis of Glioma-Associated Mesenchymal Stem Cells
title: Additional file 4: Table S4. Results of drug sensitive analysis of the FLNC gene.

description: To analyze the binding affinities and interaction modes between the drug candidates and their targets, we employed the Autodock Vina software [21]. Molecular structures of the candidate drugs and targets of hub genes were retrieved from Pubchem (https://pubchem.ncbi.nlm.nih.gov/) and Protein Data Bank database (http://www.rcsb.org/), respectively. In the analysis of docking, the files for all proteins and molecules were converted to PDBQT format. Water molecules were removed and polar hydrogen atoms were added. The grid box was positioned at the center to encompass the protein domain, allowing for unrestricted movement of molecules.