cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2fzx4h
title: CCDC 2264027: Experimental Crystal Structure Determination

description: Related Article: Richiro Ushimaru, Lide Cha, Shotaro Shimo, Xiaojun Li, Jared C. Paris, Takahiro Mori, Kazunori Miyamoto, Lindsay Coffer, Masanobu Uchiyama, Yisong Guo, Wei-chen Chang, Ikuro Abe|2023|J.Am.Chem.Soc.|145|24210|doi:10.1021/jacs.3c08413
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.cc2g11h2
title: CCDC 2265123: Experimental Crystal Structure Determination

description: Related Article: Raquel Utrera-Melero, Marie Cordier, Florian Massuyeau, Jean-Yves Mevellec, Aydar Rakhmatullin, Charlotte Martineau-Corcos, Camille Latouche, Sandrine Perruchas|2023|Inorg.Chem.|62|18157|doi:10.1021/acs.inorgchem.3c02634
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.8006961
title: Dataset associated with "Emulating subglacial hydrology in ice sheet models with deep learning methods" by Verjans and Robel.

description: See Readme file for descriptions.
DOI: 10.5281/zenodo.8006962
title: Dataset associated with "Emulating subglacial hydrology in ice sheet models with deep learning methods" by Verjans and Robel.

description: See Readme file for descriptions.
DOI: 10.15151/esrf-es-1314536749
title: Diffusion in Unsaturated Swelling Clayey Materials

description: The experiment consist in mapping the swelling and the spatial distribution of the phases (air, water, intact clay and swelled clay) in partially saturated clayey materials. Osmotic technique is used to control the saturation of the sample. The 100 mm3 sample made of Benthonite powder is confined in an Al cell immersed in a controlled concentration PEG solution. The final objective is twofold. First determine the porosity changes triggers by the clay swelling and compare to the theoretical models and the macroscopic mechanical experiments (focusing on the anisotropy and spatial heterogeneity of the swelling process). Second, perform diffusion simulations on the segmented images in order to compare the results with a large set of laboratory experiments performed during the last 3 years, showing orders of magnitude lower diffusion coefficient values for the partially saturated cases compared to the saturated case, and postulated to be the result of multi-scalar air-water heterogeneities
DOI: 10.15151/esrf-es-1317793050
title: SAARLAND BAG: ATOMIC MECHANISMS OF ACTION OF MEMBRANE PROTEINS AND BIOSYNTHETIC ENZYMES

description: Projects are focussed primarily within the framework of the DFG-funded excellence network program in Homburg (Saar) on "Ca2+signals: Molecular Mechanisms und Integrative Functions" at Saarland University and a joint multidisciplinary initiative of the University with the Helmholtz Institute of Pharmaceutical Research Saarland (HIPS) in Saarbrücken on natural bioactive compounds including their interactions with their target proteins. These projects involve the structure determination of membrane proteins and soluble proteins.
DOI: 10.15151/esrf-es-1317817327
title: ITABAG: 3D structures of macromolecules related to human health

description: The ITABAG includes structural biologists from Universities, the National Research Council and Hospital research centres in Italy. The laboratories take advantage of single crystal and small angle X-ray diffraction methods to study the structure-function relationships in various macromolecules. A unifying factor for the vast majority of the macromolecules under study is that they are related to human health, either directly, being human proteins involved in some disease, or indirectly, as proteins expressed by human pathogens and validated as potential pharmacological targets. Other projects investigate basic chemical processes, such as crystal growth, or aim at characterising macromolecules with potential biotechnological applications.
DOI: 10.15151/esrf-es-1318522611
title: IBS BAG

description: The IBS BAG includes in this proposal IBS teams and external groups from CEA-Cadarache (St Paul lez Durance) and IRBA (Brétigny-sur-Orge). We study structure-function relationships of proteins emphasizing in human health, biotechnology and methodology. Most of the projects are a continuation of the MX-2398 proposal and can be grouped into different topics as follows: host-pathogen interaction, new drug targets, fundamental cellular mechanisms, membrane proteins, biotechnological applications and methodology. Some of these projects use integrative approaches (X-ray crystallography, SAXS, NMR (and cryo-EM), together with other biophysical studies) with the aim to fully understand the complexity of the biological macromolecular systems on study.
DOI: 10.15151/esrf-es-1317799869
title: Investigating cellular signaling proteins and complexes using time-resolved serial crystallography.

description: For many years members of the Laboratory of Biomolecular Research have been driving the development of synchrotron based serial crystallography including pioneering static (Nogly et al., 2015 at ESRF, Weinert et al., 2017) and time-resolved experiments (Nogly et al., 2016, Weinert et al., 2019, Skopintsev et al., 2022, Weinert et al., 2023) at SLS and SwissFEL. With the coming upgrade of the SLS and an expected shutdown of 2 years, we are submitting a BAG proposal in order to continue our research projects at the ESRF. Our interests span photoactivation and ligand un-/binding in G protein-coupled receptors, kinase activation, temperature dependence of enzyme activity and multi-domain photosensors. X-ray beam brilliance, experienced beamline staff and the variety of available sample delivery methods make the ID29 beamline an ideal place to conduct the proposed projects. Additionally, the proposed work will improve collaboration between two centers of European X-ray science.
DOI: 10.15151/esrf-es-1394724947
title: Study of the Co in bone and bone marrow samples

description: Study of the Co in bone and bone marrow samples in inhouse (see proposal MD1364)
DOI: 10.21227/n72j-vz37
title: Gait biomarkers dataset

description: The dataset, developed at the National Institute of Neurology and Neurosurgery in Mexico, encapsulates crucial gait biomarkers associated with neurodegenerative diseases. This invaluable compilation serves as a comprehensive resource for understanding and analyzing the distinctive gait patterns exhibited by patients grappling with neurological disorders. By delving into these intricate biomarkers, researchers gain insights into the nuanced manifestations of conditions impacting the nervous system. This dataset not only facilitates a deeper comprehension of neurodegenerative diseases but also opens avenues for innovative diagnostic and therapeutic interventions. Its creation marks a significant stride towards advancing our understanding of these complex conditions, contributing to enhanced patient care and future breakthroughs in neurology.
DOI: 10.48512/xcv8490426
title: Pottery assemblage data from Roman Britain

description: Data analyzed in: Ortman, Scott, Olivia Bulik, Rob Wiseman, José Lobo, Luis Bettencourt and Lisa Lodwick (2023) Transport Costs and Economic Change in Roman Britain. European Journal of Archaeology:1-24 AND Wiseman, Rob, Olivia Bulik, José Lobo, Lisa Lodwick and Scott G. Ortman (2023) The Impact of Transportation on Pottery Industries in Roman Britain. Open Archaeology 9(1).
DOI: 10.5281/zenodo.8420198
title: The GET insertase exhibits conformational plasticity and induces membrane thinning - The Molecular Dynamics Dataset

description: The molecular dynamics simulation systems.


List of files: 



	
SimulationSystems.pdf: List of all simulation systems reported and their compositions
	
ProteinComplex.pdb: The initial model for the hsGet2ΔN-Get1/Get3 complex used in simulations was constructed based on the cryo-EM structure (PDB accession 6SO5). Missing residues (except the terminal ones) were modeled using Modeller.
	
prod.mdp: The GROMACS molecular dynamics parameters (mdp) file used for all simulations
	
toppar.zip: The Charmm36(m) force field parameter and topology set used for all simulations generated by CHARMM-GUI.
	
Compressed  (zip) files containing simulations inputs and trajectories



1-PC.zip
2-1:4_PI:PC.zip
3-1:4_PE:PC.zip
4-1:4_PS:PC.zip
5-1:4_CL:PC.zip
6-1:4_chol:PC.zip
7-1:1:1:1_PC:PI:PS:PE.zip
8-1:1:1:1:1:1_PC:PDPC:PS:PI:PE:chol.zip


Each zip file contains the following files:



	
System_0ns.pdb: The initial configuration used for the simulations generated using CHARMM-GUI and equilibrated following the CHARMM-GUI equilibration protocol
	
index.ndx: GROMACS index file
	
topol.top: GROMACS topology file
	
prod0.tpr, prod1.tpr, prod2.tpr:  GROMACS run topology files (tpr) for each repeat
	
prod0.gro, prod1.gro, prod2.gro: The final configuration after 3 μs production runs for each repeat
	
noW_0ns.pdb: The initial configuration without the water molecules.
	
noW_0.xtc, noW_1.xtc, noW_2.xtc: The 3 μs processed production trajectories. The water molecules were removed, and the trajectories were subsampled at 1 ns intervals.
DOI: 10.5281/zenodo.8420199
title: The GET insertase exhibits conformational plasticity and induces membrane thinning - The Molecular Dynamics Dataset

description: The molecular dynamics simulation systems.


List of files: 



	
SimulationSystems.pdf: List of all simulation systems reported and their compositions
	
ProteinComplex.pdb: The initial model for the hsGet2ΔN-Get1/Get3 complex used in simulations was constructed based on the cryo-EM structure (PDB accession 6SO5). Missing residues (except the terminal ones) were modeled using Modeller.
	
prod.mdp: The GROMACS molecular dynamics parameters (mdp) file used for all simulations
	
toppar.zip: The Charmm36(m) force field parameter and topology set used for all simulations generated by CHARMM-GUI.
	
Compressed  (zip) files containing simulations inputs and trajectories



1-PC.zip
2-1:4_PI:PC.zip
3-1:4_PE:PC.zip
4-1:4_PS:PC.zip
5-1:4_CL:PC.zip
6-1:4_chol:PC.zip
7-1:1:1:1_PC:PI:PS:PE.zip
8-1:1:1:1:1:1_PC:PDPC:PS:PI:PE:chol.zip


Each zip file contains the following files:



	
System_0ns.pdb: The initial configuration used for the simulations generated using CHARMM-GUI and equilibrated following the CHARMM-GUI equilibration protocol
	
index.ndx: GROMACS index file
	
topol.top: GROMACS topology file
	
prod0.tpr, prod1.tpr, prod2.tpr:  GROMACS run topology files (tpr) for each repeat
	
prod0.gro, prod1.gro, prod2.gro: The final configuration after 3 μs production runs for each repeat
	
noW_0ns.pdb: The initial configuration without the water molecules.
	
noW_0.xtc, noW_1.xtc, noW_2.xtc: The 3 μs processed production trajectories. The water molecules were removed, and the trajectories were subsampled at 1 ns intervals.
DOI: 10.5281/zenodo.8434620
title: Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset

description: The molecular dynamics (MD) simulation dataset. The contents:



	
5ire_BIOMT_expanded.pdb: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE) 
	
5ire_Mprotein_BIOMT_expanded.pdb: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE).  The biological assembly shows the dimeric organization of M proteins.
	
0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively. 
	

		
In each zip file, there are 5 directories: wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files:
		

			
toppar: This directory contains all force field topologies and parameters
			
topol.top: GROMACS topology (top) file
			
index.ndx: GROMACS index (ndx) file
			
prod.mdp: GROMACS MD parameters (mdp)  file
			
0, 1, 2, 3, 4, 5, 6, 7, 8, 9: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files: 
			

				
t0.pdb: The pdb file of the starting coordinates
				
prod0.tpr: GROMACS binary run input (tpr) file 
				
prod0.edr: GROMACS energy (edr) file
				
prod0.gro: GROMACS output coordinates and velocities after 1 microsecond of simulation
				
prod0.cpt: GROMACS checkpoint file after 1 microsecond of simulation
				
noW.pdb: The pdb file of the starting coordinates with all water molecules removed
				
noW.xtc:  GROMACS compressed trajectory (xtc) file with all water molecules removed
DOI: 10.5281/zenodo.8268517
title: Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset

description: The molecular dynamics (MD) simulation dataset. The contents:



	
5ire_BIOMT_expanded.pdb: The complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE) 
	
5ire_Mprotein_BIOMT_expanded.pdb: The M proteins extracted from the complete biological assembly of the cryo-EM structure of Zika Virus (PDB ID:5IRE).  The biological assembly shows the dimeric organization of M proteins.
	
0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip contain simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively. 
	

		
In each zip file, there are 5 directories: wt, R253L+F257A, R253L+F257S, K275L+Y278A, K275L+Y278S corresponding to each simulated M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S. In each directory, there are the following files:
		

			
toppar: This directory contains all force field topologies and parameters
			
topol.top: GROMACS topology (top) file
			
index.ndx: GROMACS index (ndx) file
			
prod.mdp: GROMACS MD parameters (mdp)  file
			
0, 1, 2, 3, 4, 5, 6, 7, 8, 9: These directories contain the simulation inputs and outputs for each simulation repeat. In each of these directories, there are the following files: 
			

				
t0.pdb: The pdb file of the starting coordinates
				
prod0.tpr: GROMACS binary run input (tpr) file 
				
prod0.edr: GROMACS energy (edr) file
				
prod0.gro: GROMACS output coordinates and velocities after 1 microsecond of simulation
				
prod0.cpt: GROMACS checkpoint file after 1 microsecond of simulation
				
noW.pdb: The pdb file of the starting coordinates with all water molecules removed
				
noW.xtc:  GROMACS compressed trajectory (xtc) file with all water molecules removed
DOI: 10.5281/zenodo.8268518
title: Zika

description: The dataset for the manuscript.
DOI: 10.5281/zenodo.10141563
title: TERMINOLOGICAL CHARACTERISTICS OF STOP SIGNS WIDELY DISTRIBUTED IN OUR COUNTRY
DOI: 10.5281/zenodo.10141564
title: TERMINOLOGICAL CHARACTERISTICS OF STOP SIGNS WIDELY DISTRIBUTED IN OUR COUNTRY
DOI: 10.4121/fe506b56-0ae0-4b89-9a5d-654b8b222cb0
title: Data underlying publication "De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features"

description: Bulk and single-molecule raw data underlying the publication "<strong><em>De novo</em> fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features</strong>", the research objective of which is the generation and validation of custom-sequence plasmids for the assembly of DNA constructs with extrahelical features for single-molecule experiments. The data include DNA gel images, as well as force-extension tables and fluorescence tracking data acquired using correlative dual-beam optical tweezers and confocal microscopy.
DOI: 10.4121/fe506b56-0ae0-4b89-9a5d-654b8b222cb0.v1
title: Data underlying publication "De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features"

description: Bulk and single-molecule raw data underlying the publication "<strong><em>De novo</em> fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features</strong>", the research objective of which is the generation and validation of custom-sequence plasmids for the assembly of DNA constructs with extrahelical features for single-molecule experiments. The data include DNA gel images, as well as force-extension tables and fluorescence tracking data acquired using correlative dual-beam optical tweezers and confocal microscopy.
DOI: 10.5281/zenodo.10141583
title: NAVIGATING TECHNOLOGICAL CHALLENGES: FOSTERING YOUNG LEARNERS' READING SKILLS
DOI: 10.5281/zenodo.10141582
title: NAVIGATING TECHNOLOGICAL CHALLENGES: FOSTERING YOUNG LEARNERS' READING SKILLS
DOI: 10.6084/m9.figshare.24552181
title: Pdb files for research

description: We compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modeling and then we employ molecular docking techniques with small molecules to analyze OR functionality based on binding energies.
DOI: 10.6084/m9.figshare.24541387
title: Bats ORs and their ancestor ORs

description: We compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modeling and then we employ molecular docking techniques with small molecules to analyze OR functionality based on binding energies.
DOI: 10.6084/m9.figshare.24541387.v1
title: Bats ORs and their ancestor ORs

description: We compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modeling and then we employ molecular docking techniques with small molecules to analyze OR functionality based on binding energies.
DOI: 10.5281/zenodo.10132786
title: Dataset related to article: "Early Age of Onset Is an Independent Predictor for a Worse Response to Neoadjuvant Therapies in Sporadic Rectal Cancer Patients"

description: This record contains raw data related to article: "Early Age of Onset Is an Independent Predictor for a Worse Response to Neoadjuvant Therapies in Sporadic Rectal Cancer Patients"
The incidence of rectal cancer (RC) is increasing in the population aged ≤ 49 (early-onset RC-EORC). EORC patients are more likely to present with locally advanced disease at diagnosis than late-onset RC (LORC; aged ≥ 50) patients. As a consequence, more EORC patients undergo neoadjuvant therapies. The response to treatment in EORC patients is still unknown. This study aims to explore the effect of age of onset on the pathological response to neoadjuvant therapies in sporadic locally advanced RC (LARC) patients. Based on an institutional prospectively maintained database, LARC patients undergoing neoadjuvant therapies and radical surgery between January 2010 and December 2022 were allocated to the EORC and LORC groups. The primary endpoint was the rate of incomplete response (Dworak 0-2). A total of 326 LORC and 79 EORC patients were included. Pre-neoadjuvant tumor features were comparable. A significantly higher rate of incomplete response was observed in EORC patients (49% vs. 35%; p = 0.028). From multivariable analysis, early age of onset, smoking and extramural invasion presented as independent risk factors for a worse response. This study demonstrates that an early age of onset is related to a worse response and calls for different multimodal strategies in this group of patients.
DOI: 10.5281/zenodo.10132787
title: Dataset related to article: "Early Age of Onset Is an Independent Predictor for a Worse Response to Neoadjuvant Therapies in Sporadic Rectal Cancer Patients"

description: This record contains raw data related to article: "Early Age of Onset Is an Independent Predictor for a Worse Response to Neoadjuvant Therapies in Sporadic Rectal Cancer Patients"
The incidence of rectal cancer (RC) is increasing in the population aged ≤ 49 (early-onset RC-EORC). EORC patients are more likely to present with locally advanced disease at diagnosis than late-onset RC (LORC; aged ≥ 50) patients. As a consequence, more EORC patients undergo neoadjuvant therapies. The response to treatment in EORC patients is still unknown. This study aims to explore the effect of age of onset on the pathological response to neoadjuvant therapies in sporadic locally advanced RC (LARC) patients. Based on an institutional prospectively maintained database, LARC patients undergoing neoadjuvant therapies and radical surgery between January 2010 and December 2022 were allocated to the EORC and LORC groups. The primary endpoint was the rate of incomplete response (Dworak 0-2). A total of 326 LORC and 79 EORC patients were included. Pre-neoadjuvant tumor features were comparable. A significantly higher rate of incomplete response was observed in EORC patients (49% vs. 35%; p = 0.028). From multivariable analysis, early age of onset, smoking and extramural invasion presented as independent risk factors for a worse response. This study demonstrates that an early age of onset is related to a worse response and calls for different multimodal strategies in this group of patients.
DOI: 10.5281/zenodo.10141630
title: PHYSIOLOGICAL APPROACH TO PERSONALITY (AS AN EXAMPLE OF ADOLESCENCE AND YOUNG ADULTHOOD)
DOI: 10.5281/zenodo.10141631
title: PHYSIOLOGICAL APPROACH TO PERSONALITY (AS AN EXAMPLE OF ADOLESCENCE AND YOUNG ADULTHOOD)
DOI: 10.6084/m9.figshare.24572677.v1
title: Questionnaire data on sustainability of traditional village buildings

description: Questionnaire data on sustainability of traditional village buildings
DOI: 10.6084/m9.figshare.24288061.v2
title: Raw data:Untargeted Metabolomics Analysis of Vaginal Secretion Reveals Potential Metabolic Biomarkers of Atrophic Vaginitis

description: In this study, we used untargeted metabolomics via liquid chromatography tandem mass spectrometry (LC-MS/MS) to analysis the differences in metabolic profiles of vaginal secretions between senile vaginitis and a healthy group of people. Then we performed target validation by CCK8 assay and Scratch assay for the screened differential metabolites and try to find their relevance to VK2/E6E7 cells.
DOI: 10.6084/m9.figshare.22817234.v1
title: Late Cambrian geomagnetic instability after the onset of inner core nucleation

description: Supplementary Table S1 Summary of the paleomagnetic data from the studied section of the Huayansi Fm at the Jiangshanian GSSP in Zhejiang Province, China. Supplementary Table S2 Rock magnetic data of the 0-9.5 m interval of the studied section at the Jiangshanian GSSP.
DOI: 10.6084/m9.figshare.22817234
title: Late Cambrian geomagnetic instability after the onset of inner core nucleation

description: Supplementary Table S1 Summary of the paleomagnetic data from the studied section of the Huayansi Fm at the Jiangshanian GSSP in Zhejiang Province, China. Supplementary Table S2 Rock magnetic data of the 0-9.5 m interval of the studied section at the Jiangshanian GSSP.
DOI: 10.6084/m9.figshare.23508369
title: Association between vmPFC gray matter volume and smoking initiation in adolescents

description: The source data of brain imaging results and the GWAS results in the paper.
DOI: 10.6084/m9.figshare.23508369.v1
title: Association between vmPFC gray matter volume and smoking initiation in adolescents

description: The source data of brain imaging results and the GWAS results in the paper.