cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2gqgd2
title: CCDC 2285704: Experimental Crystal Structure Determination

description: Related Article: Christoph Helling, Yannick Schulte, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gqgk7
title: CCDC 2285709: Experimental Crystal Structure Determination

description: Related Article: Christoph Helling, Yannick Schulte, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gqgsg
title: CCDC 2285716: Experimental Crystal Structure Determination

description: Related Article: Christoph Helling, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gqh4v
title: CCDC 2285727: Experimental Crystal Structure Determination

description: Related Article: Christoph Helling, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gqj5x
title: CCDC 2285759: Experimental Crystal Structure Determination

description: Related Article: Christoph Helling, Roland Schoch, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gr7gy
title: CCDC 2286450: Experimental Crystal Structure Determination

description: Related Article: Kristina Helbig, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gr8bv
title: CCDC 2286477: Experimental Crystal Structure Determination

description: Related Article: Meik Blanke, Dominik Naglav, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gr8cw
title: CCDC 2286478: Experimental Crystal Structure Determination

description: Related Article: Meik Blanke, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gvxz7
title: CCDC 2290000: Experimental Crystal Structure Determination

description: Related Article: Bin Li, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gvy4f
title: CCDC 2290005: Experimental Crystal Structure Determination

description: Related Article: Bin Li, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gvy6h
title: CCDC 2290007: Experimental Crystal Structure Determination

description: Related Article: Bin Li, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.cc2gvyhs
title: CCDC 2290016: Experimental Crystal Structure Determination

description: Related Article: Bin Li, Christoph Wölper, Stephan Schulz|2023|CSD Communication|||
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.10560276
title: Classification of research publications based on data from OpenAlex

description: This data set contains an algorithmic classification of research publications based on data from OpenAlex. The classification is based on the OpenAlex snapshot released on November 21, 2023.

To build the classification, we used the so-called extended direct citation approach in combination with the Leiden algorithm. The source code of our software is available here. The classification covers the 71 million journal articles, proceedings papers, preprints, and book chapters in OpenAlex that were published between 2000 and 2023 and that are connected to each other by citation links. Based on 1715 million citation links, we built a three-level hierarchical classification. Each publication was assigned to a cluster at each of the three levels of the classification. Clusters consist of publications that are relatively strongly connected by citation links and that can therefore be expected to be topically related. At each level of the classification, a publication was assigned to only one cluster, which means clusters do not overlap.

The classification consists of 4521 micro clusters at the lowest (most granular) level, 917 meso clusters at the middle level, and 20 macro clusters at the highest (least granular) level. We also algorithmically linked each cluster in the classification to one or more of the following five broad main fields: biomedical and health sciences, life and earth sciences, mathematics and computer science, physical sciences and engineering, and social sciences and humanities.

We used the Updated GPT 3.5 Turbo large language model, developed by OpenAI, to label the 4521 micro clusters at the lowest level in the classification. The source code of our software can be found here.

See this blog post for more information about the classification.

 

The classification, including the labels of the micro clusters, is available in the following tab-delimited files.

 

clustering.tsv



work_id

doi

macro_cluster_id

meso_cluster_id

micro_cluster_id


 

main_field.tsv



main_field_id

main_field


 

macro_cluster.tsv



macro_cluster_id

macro_cluster

n_works


 

macro_cluster_main_field.tsv



macro_cluster_id

main_field_seq

main_field_id

weight

is_primary_main_field


 

meso_cluster.tsv



meso_cluster_id

meso_cluster

parent_macro_cluster_id

n_works


 

meso_cluster_main_field.tsv



meso_cluster_id

main_field_seq

main_field_id

weight

is_primary_main_field


 

meso_cluster_source.tsv



meso_cluster_id

source_seq

source_id

n_works


 

micro_cluster.tsv



micro_cluster_id

micro_cluster

short_label

long_label

keywords

summary

wikipedia_url

parent_macro_cluster_id

parent_meso_cluster_id

n_works


 

micro_cluster_main_field.tsv



micro_cluster_id

main_field_seq

main_field_id

weight

is_primary_main_field


 

micro_cluster_keyword.tsv



micro_cluster_id

keyword_seq

keyword


 

micro_cluster_source.tsv



micro_cluster_id

source_seq

source_id

n_works
DOI: 10.25345/c5804xw48
title: MassIVE MSV000093915 - Large-scale map of RNA binding protein interactomes across the mRNA life-cycle
title: Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) in diverse ribonucleoprotein complexes (RNPs) during distinct life-cycle stages for their processing and maturation. While substantial attention has focused on understanding RNA regulation by assigning proteins, particularly RBPs, to specific RNA substrates, there has been considerably less exploration leveraging protein-protein interaction (PPI) methodologies to identify and study the role of proteins in mRNA life-cycle stages. To address this gap, we generated an RNA-aware RBP-centric PPI map across the mRNA life-cycle by immunopurification (IP-MS) of ~100 endogenous RBPs across the life-cycle in the presence or absence of RNase, augmented by size exclusion chromatography (SEC-MS). Aside from confirming 8,700 known and discovering 20,359 novel interactions between 1125 proteins, we determined that 73% of our IP interactions are regulated by the presence of RNA. Our PPI data enables us to link proteins to life-cycle stage functions, highlighting that nearly half of the proteins participate in at least two distinct stages. We show that one of the most highly interconnected proteins, ERH, engages in multiple RNA processes, including via interactions with nuclear speckles and mRNA export machinery. We also demonstrate that the spliceosomal protein SNRNP200 participates in distinct stress granule-associated RNPs and occupies different RNA target regions in the cytoplasm during stress. Our comprehensive RBP-focused PPI network is a novel resource for identifying multi-stage RBPs and exploring RBP complexes in RNA maturation.
DOI: 10.6073/pasta/4a0b715104849d98320fcc34e7cd63a4
title: Spartina alterniflora marsh vegetation data along the Georgia coast used in the Belowground Ecosystem Resiliency Model version 2.0

description: Study plots (1-m2) were established in eight Spartina alterniflora-dominated marshes (7 on Sapelo Island, Georgia, and 1 on Skidaway Island, Georgia). At three sites, plots were sampled once each during May, July, August, September, and October of 2016. At all sites, plots were sampled once each during June, August, and November of 2021, February, May, August, and November of 2022, and February of 2023. One long-term (quarterly 2013 to 2023) GCE LTER sampling site is also included. Nine replicate plots were placed in vegetated marsh along transects that spanned 3 Landsat-8 and -9 pixel footprints, with 3 plots per pixel footprint. In each plot, measurements included plant biomass, plant species, stem density, and height. Aboveground biomass was calculated using allometric relationships between plant height and mass from plant clipping studies. During these surveys, destructive core sampling was also performed in the proximity of the plots (n = 1 per plot) to measure above and below ground biomass. Chlorophyll, foliar N, and Leaf Area Index measurements were taken in the proximity of the plots.

This dataset reflects an update to the "PLT-GCED-2106" dataset (doi: 10.6073/pasta/03f4f78c6498aecca34faf4339591129). This project also utilized data from the "PLT-GCEM-1610" dataset doi: 10.6073/pasta/9746c71b35e9f8c544ea12c601c33949). Those data utilized in this project are duplicated here for completeness.
DOI: 10.5281/zenodo.10497813
title: Histone Post Translational Modifications (LC-MS) Data

description: RAW MS data were manually analysed using the open-source Skyline software. The relative abundance of a given PTM was calculated by dividing its MS1 intensity (area under the curve) by the sum of the MS1 intensities of all modified and unmodified peptides sharing the same sequence.
DOI: 10.5281/zenodo.10497814
title: Histone Post Translational Modifications (LC-MS) Data

description: RAW MS data were manually analysed using the open-source Skyline software. The relative abundance of a given PTM was calculated by dividing its MS1 intensity (area under the curve) by the sum of the MS1 intensities of all modified and unmodified peptides sharing the same sequence.
DOI: 10.25345/c5474729t
title: MassIVE MSV000093916 - FGFR inhibition blocks NF-kappaB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma
title: This study explored the response to FGFR inhibition in FGFR2-fusion+ intrahepatic cholangiocarcinoma. We conducted phosphoproteomics experiments in a patient-derived FGFR2-driven ICC cell line model upon FGFR inhibition. Samples were treated with the FGFR inhibitor, Futibatinib/TAS120 (75 nM) for 4 or 24 hours or with DMSO vehicle. The experiments were done using an Orbitrap Fusion Lumos mass spectrometer. Multiplexing was achieved using either TMT10/11 reagents and the SPS-MS3 method. Basic pH reversed-phase chromatography (bRPLC) was used for off-line pre-fractionation; 12 fractions were analyzed for proteome mappings (PMID: 26700037) and 24 fractions plus a phosphotyrosine-enriched sample for phosphoproteome mappings (PMID: 31606085). Phosphoproteome mappings were done using both HCD fragmentation with Orbitrap fragment ion detection and CID fragmentation with ion trap fragment ion detection (PMID: 29487189, PMID: 31606085). Labeling scheme: 126: DMSO-1, ICC13-7 cells were treated with DMSO, replicate 1 127n: Futibatinib(TAS120)-4h-1, ICC13-7 cells were treated with Futibatinib (TAS120) for 4h, replicate 1 127c: Futibatinib(TAS120)-24h-1, ICC13-7 cells were treated with Futibatinib (TAS120) for 24h, replicate 1 128n: DMSO-2, ICC13-7 cells were treated with DMSO, replicate 2 128c: Futibatinib(TAS120)-4h-2, ICC13-7 cells were treated with Futibatinib (TAS120) for 4h, replicate 2 129n: Futibatinib(TAS120)-24h-2, ICC13-7 cells were treated with Futibatinib (TAS120) for 24h, replicate 2
DOI: 10.7924/r4mp57d4n
title: Data from: Relationships among stress, perceived stress, trauma, PTSD, and misophonia

description: The relationship between misophonia, stress, and traumatic stress has not been well characterized scientifically. This study aimed to explore the relationships among misophonia, stress, lifetime traumatic events, and traumatic stress. A community sample of adults with self-reported misophonia (N = 143) completed structured diagnostic interviews and psychometrically validated self-report measures. Significant positive correlations were observed among perceived stress, traumatic stress, and misophonia severity. However, multivariate analyses revealed that perceived stress significantly predicted misophonia severity, over and above traumatic stress symptoms. The number of adverse life events was not associated with misophonia severity. Among symptom clusters of post-traumatic stress disorder, only hyperarousal was associated with misophonia severity. These findings suggest that transdiagnostic processes related to stress, such as perceived stress and hyperarousal, may be important phenotypic features and possible treatment targets for adults with misophonia.
DOI: 10.13020/nrt0-h049
title: Numerical simulation setup for single mineral dissolution in a single pore channel

description: We conducted pore-scale numerical simulations for single mineral dissolution for two-dimensional and three-dimensional systems using OpenFOAM. We explored the effects of flow rates on mineral dissolution dynamics.
description: These are C++ script files for OpenFOAM to perform flow and reactive transport with rock dissolution. The files run on OpenFOAM with a dbsFoam solver which is part of porousMedia4Foam. The domain construction in the case folder requires funkySetFields, a module of swak4Foam.
DOI: 10.6084/m9.figshare.24837090
title: Supplemental Tables for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"

description: Supplemental Tables for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"Alicia M. Healey*<sup>2</sup>, Kristina N. Fenner*<sup>1</sup>, Colleen T. O’Dell<sup>1</sup>, B. Paige Lawrence<sup>1,2</sup>Affiliations:Departments of <sup>1</sup>Environmental Medicine and <sup>2</sup>Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USASupplemental Table S1Supplemental Table S2Supplemental Table S3Supplemental Table S4Supplemental Table S5Supplemental Table S6
DOI: 10.6084/m9.figshare.24836799
title: Supplemental Figures for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"

description: Supplemental Figures for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"Alicia M. Healey*<sup>2</sup>, Kristina N. Fenner*<sup>1</sup>, Colleen T. O’Dell<sup>1</sup>, B. Paige Lawrence<sup>1,2</sup>Affiliations:Departments of <sup>1</sup>Environmental Medicine and <sup>2</sup>Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USASupplemental Fig S1Supplemental Fig S2
DOI: 10.6084/m9.figshare.24836799.v1
title: Supplemental Figures for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"

description: Supplemental Figures for paper titled: "Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection"Alicia M. Healey*<sup>2</sup>, Kristina N. Fenner*<sup>1</sup>, Colleen T. O’Dell<sup>1</sup>, B. Paige Lawrence<sup>1,2</sup>Affiliations:Departments of <sup>1</sup>Environmental Medicine and <sup>2</sup>Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USASupplemental Fig S1Supplemental Fig S2
DOI: 10.34740/kaggle/dsv/7473671
title: Public Opinion Russia Ukraine War (Updated Daily)
DOI: 10.26183/nwyn-bt05
title: Making Canterbury-Bankstown a dementia-friendly community

description: Older members of the South Western Sydney community called for the region to be more dementia-friendly. To address this, Canterbury-Bankstown Council formed a Dementia Alliance with Western Sydney University researchers, and people who have dementia. This alliance will empower people with dementia, and their informal caregivers, to identify strategies that will support ageing in place. This particular project will engage with the diverse community of Canterbury-Bankstown to understand how dementia is perceived, and deliver educational workshops to the local community and businesses to increase awareness about dementia.
The survey questionnaire contains 49-items and is based on the dementia attitudes and beliefs survey implemented in a previous Australian study of a dementia-friendly community.
DOI: 10.6084/m9.figshare.24796884
title: Data represented in Fig 1A, B, C, E

description: <b>These files correspond to data in figures 1A, B, C, and E:</b>Fig1A_Cyp1a1 expressionFig1B_Body Weight_DataFig1C_Viral_Load_DataFig1E_MHV1_specific_IgG_ELISA_Data
DOI: 10.6084/m9.figshare.24796884.v1
title: Data represented in Fig 1A, B, C, E

description: <b>These files correspond to data in figures 1A, B, C, and E:</b>Fig1A_Cyp1a1 expressionFig1B_Body Weight_DataFig1C_Viral_Load_DataFig1E_MHV1_specific_IgG_ELISA_Data
DOI: 10.6084/m9.figshare.24796860
title: Day 14 Spleen Myeloid

description: Day 14 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796860.v1
title: Day 14 Spleen Myeloid

description: Day 14 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796854
title: Day 10 Spleen Myeloid

description: Day 10 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796854.v1
title: Day 10 Spleen Myeloid

description: Day 10 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796845
title: Day 8 Spleen Myeloid

description: Day 8 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796845.v1
title: Day 8 Spleen Myeloid

description: Day 8 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.
DOI: 10.6084/m9.figshare.24796833.v1
title: Day 6 Spleen Myeloid

description: Day 6 Spleen Myeloid FCS Files.These are FCS files that correspond to data in figure S1.Compensation controls and FMOs accompany all samples provided as FCS files. All odd numbered FCS files are from TCDD-treated mice and all even numbered FCS files are from Vehicle-treated mice.