cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22304569.v1
title: data for SUNS2-ANE paper

description: Videos used in the SUNS2-ANE paper (<em>Accurate and Fast Neuron Segmentation Method for One-photon Calcium Imaging Videos Combining Convolutional Neural Networks and Clustering</em>, will be posted to bioRxiv), including the simulated videos used in Figure 2, the motion corrected videos of the Tenaspis dataset that we used, and the cropped quarter-sized videos from the CNMF-E paper. Our manual segmentations of the videos are also included.
DOI: 10.17630/2c041fd5-37cb-4225-bb4e-0b75d4231d21
title: New Frontiers in Strain-Tuning: Apparatus Development, and Tuning of the Nematicity of FeSe Across a Wide Strain Range (Thesis data)

description: The data files are embargoed until 30/05/2021
DOI: 10.17630/464447c9-ac13-4a06-8a1a-e495cfd45f00
title: Heat Capacity Measurements of Sr2RuO4 under Uniaxial Stress (thesis data)

description: Thesis data.
The data files are embargoed until 20/11/2020.
DOI: 10.17630/e3c404a2-7482-4ebe-a2e2-f320e55781a2
title: Data underpinning "Isothiourea-catalysed regioselective acylative kinetic resolution of axially chiral biaryl diols"
DOI: 10.17630/4dc98a72-4ffe-4f96-813f-fae5b089f768
title: Application of modified xantphos ligands in homogeneous catalysis and photochemistry (thesis data)
DOI: 10.17630/3fbfe834-d0e1-4e21-96f2-7afcf1c261ba
title: Data underpinning:  Organic polariton lasing and the weak- to strong-coupling crossover
DOI: 10.17630/67d9e97f-9374-4912-8861-ff2ab67072de
title: Kinetic stabilization of 1D surface states near twin boundaries in noncentrosymmetric BiPd (dataset)
DOI: 10.17630/259affa7-75ae-495f-8d2a-7d9742d3ef13
title: Computational data for "Artificial Metalloenzymes as Catalysts for Oxidative Lignin Degradation"

description: Data and metadata for the MD simulations included in the paper
M. V. Doble, A. G. Jarvis, A. C. C. Ward, J. D. Colburn, J. P. Götze, M. Bühl, P. C. J. Kamer, "Artificial Metalloenzymes as Catalysts for Oxidative Lignin Degradation", ACS Sustainable Chem. Eng.
DOI: 10.17630/998faf40-3b86-466f-af09-288dd106606c
title: Non-obstructive intracellular nanolasers (dataset)
DOI: 10.5281/zenodo.10068949
title: Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.

description: This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the SCAN_IDR pipeline with AlphaFold2-Multimer.
It contains two archives: 

scanidr_data_repository_corr6J08.tar dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,
923_elm_cases_repository.tar.gz dedicated to the analysis of 923 complexes from the ELM database.
These data can be used to rerun specific sections of the pipeline and scripts provided in: https://github.com/i2bc/SCAN_IDR
Dataset of 42 non redundant complexes
The first archive scanidr_data_repository_corr6J08.tar contains 3 compressed directories and a README file detailing their contents :

the initial raw sequence and alignment data for every chain        -> DIRECTORY fasta_msa/
the input and output data of every Alphafold run for every complex   -> DIRECTORY af2_runs/
the native reference structures    -> DIRECTORY ref_capri_curated/
The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <index>_<pdbcode>.
The models in this archive were generated using AlphaFold2-Multimer v2.2
Dataset of 923 complexes selected from the ELM database
The second archive 923_elm_cases_repository.tar.gz contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.
Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein.  
The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:

the table describing ELM entries -> FILE Table_923ELM_uid_delimitations_info_for_archive.txt
the initial raw sequence and multiple sequence alignment (MSA) data for every chain        -> DIRECTORY fasta_msa/
the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY af2_elm_coali_inputs/
the best model of every AF2 protocol for every complex according to the AF2   -> DIRECTORY af2_elm_models/
the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY elm_cut_models/
the reference structures used for the evaluation of the models   -> DIRECTORY ref_capri_curated/
The models in this archive were generated using AlphaFold2-Multimer v2.3
description: In the version 1.1.0, in the scanidr_data_repository_corr6J08.tar archive, a correction has been made to case 36_6J08. The correct isoform Q3KP22-3 has been used for this case, instead of the previously incorrectly used Q3KP22-1.
DOI: 10.5281/zenodo.7838023
title: Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.

description: This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the SCAN_IDR pipeline with AlphaFold2-Multimer.
It contains two archives: 

scanidr_data_repository_corr6J08.tar dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,
923_elm_cases_repository.tar.gz dedicated to the analysis of 923 complexes from the ELM database.
These data can be used to rerun specific sections of the pipeline and scripts provided in: https://github.com/i2bc/SCAN_IDR
Dataset of 42 non redundant complexes
The first archive scanidr_data_repository_corr6J08.tar contains 3 compressed directories and a README file detailing their contents :

the initial raw sequence and alignment data for every chain        -> DIRECTORY fasta_msa/
the input and output data of every Alphafold run for every complex   -> DIRECTORY af2_runs/
the native reference structures    -> DIRECTORY ref_capri_curated/
The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <index>_<pdbcode>.
The models in this archive were generated using AlphaFold2-Multimer v2.2
Dataset of 923 complexes selected from the ELM database
The second archive 923_elm_cases_repository.tar.gz contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.
Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein.  
The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:

the table describing ELM entries -> FILE Table_923ELM_uid_delimitations_info_for_archive.txt
the initial raw sequence and multiple sequence alignment (MSA) data for every chain        -> DIRECTORY fasta_msa/
the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY af2_elm_coali_inputs/
the best model of every AF2 protocol for every complex according to the AF2   -> DIRECTORY af2_elm_models/
the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY elm_cut_models/
the reference structures used for the evaluation of the models   -> DIRECTORY ref_capri_curated/
The models in this archive were generated using AlphaFold2-Multimer v2.3
description: In the version 1.1.0, in the scanidr_data_repository_corr6J08.tar archive, a correction has been made to case 36_6J08. The correct isoform Q3KP22-3 has been used for this case, instead of the previously incorrectly used Q3KP22-1.
DOI: 10.5281/zenodo.7838024
title: Dataset of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.

description: This archive contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins. The archive contains 3 directories and a README file detailing their contents : the initial raw sequence and alignment data for every chain -&gt; DIRECTORY <strong>fasta_msa/</strong> the input and output data of every Alphafold run for every complex -&gt; DIRECTORY <strong>af2_runs/</strong> the native reference structures -&gt; DIRECTORY <strong>ref_capri_curated/</strong> The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <em>&lt;index&gt;_&lt;pdbcode&gt;</em>. <br> These data can be used to rerun specific sections of the pipeline and scripts provided in: https://github.com/i2bc/SCAN_IDR
DOI: 10.17630/1d32912f-ef4d-4f0f-aaa3-a5d82d3a4f48
title: Analysing the Relation Between Structure and Aggregation Induced Emission (AIE) Properties of Iridium(III) Complexes through Modification of Non-Chromophoric Ancillary Ligands (dataset)
DOI: 10.6084/m9.figshare.24494725
title: Genetic background modulates the effect of glucocorticoids on proliferation, differentiation, and myelin formation of oligodendrocyte lineage cells.

description: This dataset contains immunocytochemical data from mouse primary oligodendrocytes (OLs). We obtained the cells from two inbred mouse strains, C57BL/6NCrl and DBA/2NCrl. These cells were cultured under three distinct conditions: 1) in naïve conditions, 2) with a short 2-hour exposure to 20 μM corticosterone (CORT), or 3) continuously exposed to 50 μM dexamethasone (DEX) until they were fixed at several different time points.For each culture condition, we used investigated the number of proliferating oligodendrocyte progenitor cells (OPCs, Ki67/OLIG2 double-positive cells), pre-myelinating OLs (MAG/OLIG2 double-positive cells), mature OLs (MBP/OLIG2 double-positive cells), the area covered by MBP, and the number of apoptotic cells (CC3 positive cells). Additionally, we conducted Sholl analysis to examine cell morphology under each of these conditions.
DOI: 10.6084/m9.figshare.24494725.v1
title: Genetic background modulates the effect of glucocorticoids on proliferation, differentiation, and myelin formation of oligodendrocyte lineage cells.

description: This dataset contains immunocytochemical data from mouse primary oligodendrocytes (OLs). We obtained the cells from two inbred mouse strains, C57BL/6NCrl and DBA/2NCrl. These cells were cultured under three distinct conditions: 1) in naïve conditions, 2) with a short 2-hour exposure to 20 μM corticosterone (CORT), or 3) continuously exposed to 50 μM dexamethasone (DEX) until they were fixed at several different time points.For each culture condition, we used investigated the number of proliferating oligodendrocyte progenitor cells (OPCs, Ki67/OLIG2 double-positive cells), pre-myelinating OLs (MAG/OLIG2 double-positive cells), mature OLs (MBP/OLIG2 double-positive cells), the area covered by MBP, and the number of apoptotic cells (CC3 positive cells). Additionally, we conducted Sholl analysis to examine cell morphology under each of these conditions.
DOI: 10.17630/1b2fa689-d709-4276-8161-ea7918c17716
title: Preconcentration Techniques for Trace Explosive Sensing (dataset)

description: Science of the Total Environment dataset
DOI: 10.6084/m9.figshare.10298720
title: U-Pb dating of detrital zircons from basal Post Paleoproterozoic metasediments in the Subpolar and Polar Urals: evidence for a Cryogenian, not Mesoproterozoic age

description: In the last ten years, U-Pb ages of detrital zircons has been obtained from Precambrian metasediments of some regions of Timan and the northern part of the Urals, which lie at the base of the visible Post Paleoproterozoic section of the Timan-Ural region. However, the basal status of these stratons remains unproven due to the lack of their relationship with the underlying formations. This article presents the first U-Pb-dating of detrital zircons from terrigenous metasediments of the Puyva suite (Subpolar Urals) and the Miniseyshor suite (Polar Urals) which reliably represents the basis of the Mesoneoproterozoic of the Timan-Northern Urals. The maximum age of deposition (MAD) detrital zircon the onset of sediment deposition is about 870 Ma for the Puyva suite and 660 Ma for the Nyarovey series, which corresponds to the Cryogenian. Therefore, the widespread opinion that the Puyva suite and the Nyrovey series are Mesoproterozoic in age is incorrect. Theis geochronological information integrated with MADs from other Precambrian complexes of the Timan- Urals region, suggests that the Timanian passive continental margin probably formed Tonian-Cryogenian.
DOI: 10.6084/m9.figshare.10298720.v1
title: U-Pb dating of detrital zircons from basal Post Paleoproterozoic metasediments in the Subpolar and Polar Urals: evidence for a Cryogenian, not Mesoproterozoic age

description: In the last ten years, U-Pb ages of detrital zircons has been obtained from Precambrian metasediments of some regions of Timan and the northern part of the Urals, which lie at the base of the visible Post Paleoproterozoic section of the Timan-Ural region. However, the basal status of these stratons remains unproven due to the lack of their relationship with the underlying formations. This article presents the first U-Pb-dating of detrital zircons from terrigenous metasediments of the Puyva suite (Subpolar Urals) and the Miniseyshor suite (Polar Urals) which reliably represents the basis of the Mesoneoproterozoic of the Timan-Northern Urals. The maximum age of deposition (MAD) detrital zircon the onset of sediment deposition is about 870 Ma for the Puyva suite and 660 Ma for the Nyarovey series, which corresponds to the Cryogenian. Therefore, the widespread opinion that the Puyva suite and the Nyrovey series are Mesoproterozoic in age is incorrect. Theis geochronological information integrated with MADs from other Precambrian complexes of the Timan- Urals region, suggests that the Timanian passive continental margin probably formed Tonian-Cryogenian.
DOI: 10.6084/m9.figshare.10329308
title: An A<sub>1</sub>-type granite that borders A<sub>2</sub>-type: insights from the geochemical characteristics of the Zongyang A-type granite in the Lower Yangtze River Belt, China

description: Mesozoic A-type granites are widely distributed in the Lower Yangtze River Belt (LYRB) in China, but their petrogenesis and geodynamic settings are unresolved. Here, we describe geochronological and geochemical study of granites from the Zongyang area of the LYRB. Zircon LA-ICPMS U-Pb dating indicates the granites were emplaced at ca. 127 Ma. They have geochemical characteristics similar to those of A-type granites, with high total-alkali (10.5–10.7 wt.%), HFSEs (Zr + Nb + Ce + Y = 890–1011 ppm), high Ga/Al ratios (10,000 × Ga/Al = 3.19–3.25), and high whole-rock zircon saturation temperatures (850°C–900°C). In discrimination diagrams, samples plot in the A<sub>1</sub>-type granite field but close to the A<sub>1</sub>–A<sub>2</sub> boundary. A representative whole-rock sample yielded an <i>I</i><sub>Sr</sub> ratio of 0.7066 and an ε<sub>Nd</sub>(t) value of – 5.3, with zircon ε<sub>Hf</sub>(t) and δ<sup>18</sup>O values of – 0.2 to – 4.3 and 5.95‰–6.79‰, respectively, all higher than those of depleted mantle, indicating the enriched nature of source materials. Apatites in the granite display mantle-origin characteristics. Incompatible element ratios (Y/Nb, Y/Ta, Nb/U and Ce/Pb) also support the enriched mantle source, and suggest that the source had experienced metasomatism, or the existence of crustal input during magmatic processes. Significant depletions in Ba, Sr, P, Ti, and Eu in the granites indicate fractional crystallization of feldspar and some accessory minerals. We conclude that the Zongyang granite were formed through fractional crystallization of oceanic island basalt (OIB)-like basic magmas derived from the lithospheric mantle. They are classified as A<sub>1</sub> but their borderline A<sub>2</sub> nature is most likely due to metasomatism by slab-derived fluids or melts, possibly involving crustal materials. Our results, together with those of previous studies, indicate that LYRB A-type granites, are the products of partial melting of the mantle or lower continental crust in an extensional setting, caused by slab rollback during the subduction of the Paleo-Pacific Plate.
DOI: 10.6084/m9.figshare.10329308.v1
title: An A<sub>1</sub>-type granite that borders A<sub>2</sub>-type: insights from the geochemical characteristics of the Zongyang A-type granite in the Lower Yangtze River Belt, China

description: Mesozoic A-type granites are widely distributed in the Lower Yangtze River Belt (LYRB) in China, but their petrogenesis and geodynamic settings are unresolved. Here, we describe geochronological and geochemical study of granites from the Zongyang area of the LYRB. Zircon LA-ICPMS U-Pb dating indicates the granites were emplaced at ca. 127 Ma. They have geochemical characteristics similar to those of A-type granites, with high total-alkali (10.5–10.7 wt.%), HFSEs (Zr + Nb + Ce + Y = 890–1011 ppm), high Ga/Al ratios (10,000 × Ga/Al = 3.19–3.25), and high whole-rock zircon saturation temperatures (850°C–900°C). In discrimination diagrams, samples plot in the A<sub>1</sub>-type granite field but close to the A<sub>1</sub>–A<sub>2</sub> boundary. A representative whole-rock sample yielded an <i>I</i><sub>Sr</sub> ratio of 0.7066 and an ε<sub>Nd</sub>(t) value of – 5.3, with zircon ε<sub>Hf</sub>(t) and δ<sup>18</sup>O values of – 0.2 to – 4.3 and 5.95‰–6.79‰, respectively, all higher than those of depleted mantle, indicating the enriched nature of source materials. Apatites in the granite display mantle-origin characteristics. Incompatible element ratios (Y/Nb, Y/Ta, Nb/U and Ce/Pb) also support the enriched mantle source, and suggest that the source had experienced metasomatism, or the existence of crustal input during magmatic processes. Significant depletions in Ba, Sr, P, Ti, and Eu in the granites indicate fractional crystallization of feldspar and some accessory minerals. We conclude that the Zongyang granite were formed through fractional crystallization of oceanic island basalt (OIB)-like basic magmas derived from the lithospheric mantle. They are classified as A<sub>1</sub> but their borderline A<sub>2</sub> nature is most likely due to metasomatism by slab-derived fluids or melts, possibly involving crustal materials. Our results, together with those of previous studies, indicate that LYRB A-type granites, are the products of partial melting of the mantle or lower continental crust in an extensional setting, caused by slab rollback during the subduction of the Paleo-Pacific Plate.
DOI: 10.6084/m9.figshare.9981419
title: Detrital zircon provenance and palaeogeographic implications of the Ediacaran Shigu Group in the Zhongza Terrane, SW China

description: The palaeogeographic positions of South China in the Rodinia and Gondwana supercontinents have long been controversial. We report petrological, detrital zircon U-Pb geochronological, trace element geochemical and Lu-Hf isotopic compositions for metasedimentary rocks from the Shigu Group in the Zhongza Terrane, SW China. The Shigu Group has been regarded as the Precambrian basement of the Zhongza Terrane, and comprises mainly a suite of medium-/low-grade metamorphosed terrigenous clastic rocks. The youngest zircon age population of two metasedimentary rock samples from the bottom Shigu Group yields a weighted average age of 633 ± 9 Ma, indicative of a late Neoproterozoic (ca. 630 Ma) maximum deposition age. The youngest detrital zircon age of a metasedimentary rock from the upper Shigu Group is 597 ± 7 Ma, it may suggesting a considerably later deposition. Detrital zircon age distribution patterns of the Shigu Group metasedimentary rocks are similar to those of coeval sedimentary rocks in the western Yangtze Block. According to Hf isotope compositions and zircon morphology, the Neoproterozoic Shigu Group detritus may have sourced from Neoproterozoic magmatic rocks in the western Yangtze Block, whilst the pre-Neoproterozoic zircons might originate from recycling of the underlying metasedimentary rocks. Our results indicate that the basement of the Zhongza Terrane was a continuation of the Yangtze Block, which implies that Precambrian Yangtze basement rocks were present beyond the current boundary of the Block. In the late Neoproterozoic (ca. 630–570 Ma), the western Yangtze Block may have been facing the Proto-Tethys and received detritus mainly from the local Neoproterozoic magmatic rocks. During the late Neoproterozoic-earliest Palaeozoic (ca. 570–520 Ma), the seaway closure between the Yangtze (incl. Zhongza) Block and northern India likely created new pathways for delivery of the earliest Neoproterozoic and Pan-African detrital zircons into the lowermost Palaeozoic sequences in South China.
DOI: 10.6084/m9.figshare.9981419.v1
title: Detrital zircon provenance and palaeogeographic implications of the Ediacaran Shigu Group in the Zhongza Terrane, SW China

description: The palaeogeographic positions of South China in the Rodinia and Gondwana supercontinents have long been controversial. We report petrological, detrital zircon U-Pb geochronological, trace element geochemical and Lu-Hf isotopic compositions for metasedimentary rocks from the Shigu Group in the Zhongza Terrane, SW China. The Shigu Group has been regarded as the Precambrian basement of the Zhongza Terrane, and comprises mainly a suite of medium-/low-grade metamorphosed terrigenous clastic rocks. The youngest zircon age population of two metasedimentary rock samples from the bottom Shigu Group yields a weighted average age of 633 ± 9 Ma, indicative of a late Neoproterozoic (ca. 630 Ma) maximum deposition age. The youngest detrital zircon age of a metasedimentary rock from the upper Shigu Group is 597 ± 7 Ma, it may suggesting a considerably later deposition. Detrital zircon age distribution patterns of the Shigu Group metasedimentary rocks are similar to those of coeval sedimentary rocks in the western Yangtze Block. According to Hf isotope compositions and zircon morphology, the Neoproterozoic Shigu Group detritus may have sourced from Neoproterozoic magmatic rocks in the western Yangtze Block, whilst the pre-Neoproterozoic zircons might originate from recycling of the underlying metasedimentary rocks. Our results indicate that the basement of the Zhongza Terrane was a continuation of the Yangtze Block, which implies that Precambrian Yangtze basement rocks were present beyond the current boundary of the Block. In the late Neoproterozoic (ca. 630–570 Ma), the western Yangtze Block may have been facing the Proto-Tethys and received detritus mainly from the local Neoproterozoic magmatic rocks. During the late Neoproterozoic-earliest Palaeozoic (ca. 570–520 Ma), the seaway closure between the Yangtze (incl. Zhongza) Block and northern India likely created new pathways for delivery of the earliest Neoproterozoic and Pan-African detrital zircons into the lowermost Palaeozoic sequences in South China.