cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0999999.09fu
title: SH0999999.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.21950282
title: KG-Hi-BKF Benchmark for Biomedical Knowledge Fusion

description: The KG-Hi-BKF benchmark datasets for the biomedical knowledge integration task, which is proposed in our SIGIR'2023 paper: "HiPrompt: Few-Shot Biomedical Knowledge Fusion via Hierarchy-Oriented Prompting". <br> There are two datasets: SDKG-DzHi repoDB-DzHi <br> Under each dataset, the files are organized as follows: ent_attr_KG.json ent_attr_Hi.json rel_trip_KG.csv hypo_hyper_pair_Hi.csv ent_links.csv zero_shot/ |-- test_ent_links.csv one_shot/ |-- support_ent_links.csv |-- test_ent_links.csv <br> where `ent_attr*.json` denotes entity attribute files, `rel_trip_KG.csv` denotes knowledge graph relational triples, `hypo_hyper_pair_Hi.csv` denotes hierarchy hyponym-hypernym term pairs, and `ent_links.csv` denotes all aligned entity-term pairs. The two subfolders `zero_shot/` and `one_shot/` provide the support&test split used in the paper. <br> If you use the datasets, please cite our paper ```BibTex @inproceedings{lu23HiPrompt,<br> title = {HiPrompt: Few-Shot Biomedical Knowledge Fusion via Hierarchy-Oriented Prompting},<br> author = {Lu, Jiaying and Shen, Jiaming and Xiong, Bo and Ma, Wengjing and Staab Steffen and Yang, Carl},<br> year = {2023},<br> month = {Apr.},<br> Series = {SIGIR 2023},<br> Booktitle = {46th International ACM SIGIR Conference on Research and Development in Information Retrieval - Short Paper},<br> } ```
DOI: 10.6084/m9.figshare.22541605.v2
title: DIPY_EVAC+_test_data

description: The data is for the EVAC+ model in dipy
DOI: 10.5517/ccdc.csd.cc281lzx
title: CCDC 2086919: Experimental Crystal Structure Determination

description: Related Article: Min Zhou, Jet Tsien, Ryan Dykstra, Jonathan M. E. Hughes, Byron K. Peters, Rohan R. Merchant, Osvaldo Gutierrez, Tian Qin|2023|Nature Chemistry|15|550|doi:10.1038/s41557-023-01150-z
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.cc281m0z
title: CCDC 2086920: Experimental Crystal Structure Determination

description: Related Article: Min Zhou, Jet Tsien, Ryan Dykstra, Jonathan M. E. Hughes, Byron K. Peters, Rohan R. Merchant, Osvaldo Gutierrez, Tian Qin|2023|Nature Chemistry|15|550|doi:10.1038/s41557-023-01150-z
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.cc2bx99w
title: CCDC 2172148: Experimental Crystal Structure Determination

description: Related Article: Min Zhou, Jet Tsien, Ryan Dykstra, Jonathan M. E. Hughes, Byron K. Peters, Rohan R. Merchant, Osvaldo Gutierrez, Tian Qin|2023|Nature Chemistry|15|550|doi:10.1038/s41557-023-01150-z
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.cc2bx9bx
title: CCDC 2172149: Experimental Crystal Structure Determination

description: Related Article: Min Zhou, Jet Tsien, Ryan Dykstra, Jonathan M. E. Hughes, Byron K. Peters, Rohan R. Merchant, Osvaldo Gutierrez, Tian Qin|2023|Nature Chemistry|15|550|doi:10.1038/s41557-023-01150-z
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.7268029
title: PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

description: The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7<sup>-/-</sup> cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.
description: Updated version. Date: 2023-04-05.
DOI: 10.5281/zenodo.7268030
title: PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

description: The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7<sup>-/-</sup> cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.
DOI: 10.5281/zenodo.7803294
title: PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

description: The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation, Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7<sup>-/-</sup> cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.
description: Updated version. Date: 2023-04-05.
DOI: 10.7278/s50d-gkhb-mjxc
title: Supplementary material for dissertation’s data collection on the Qassimi Arabic stress system and output frequency of Qassimi Arabic phonological processes
DOI: 10.6084/m9.figshare.22564264
title: Supplementary Material – Floristic inventory of Myrtaceae of Parque Nacional do Iguaçu, Paraná, Brazil

description: <strong>Appendix S1 – List of collectors of Myrtaceae specimens from ParNa Iguaçu.</strong> <br> <strong>This Supplementary Material is part of the Original Paper published at Rodriguesia - DOI: http://dx.doi.org/10.1590/2175-7860202374026</strong>
DOI: 10.6084/m9.figshare.22564264.v1
title: Supplementary Material – Floristic inventory of Myrtaceae of Parque Nacional do Iguaçu, Paraná, Brazil

description: <strong>Appendix S1 – List of collectors of Myrtaceae specimens from ParNa Iguaçu.</strong> <br> <strong>This Supplementary Material is part of the Original Paper published at Rodriguesia - DOI: http://dx.doi.org/10.1590/2175-7860202374026</strong>
DOI: 10.13020/9wm7-x981
title: Structural and chemical characterization data for Ir and Ru metal/metal-oxide thin films showing strain dependence of metal oxidation

description: In this work, the authors uncover a previously unexplored effect of substrate imposed epitaxial strain on the formation energy of a crystalline epitaxial metal oxide thin film, thereby revealing an additional tuning knob to engineer synthesis of oxide thin films of hard-to-oxidize metals.
description: The files contain the source data for characterizations performed on the Ir/IrO2 and Ru/RuO2 thin films grown in this work. The characterization techniques for which raw files have been provided include X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM), Energy Dispersive X-ray Spectroscopy line scans and electrical transport measurements. Any additional information can be requested from the corresponding author.
DOI: 10.6084/m9.figshare.19666314.v1
title: Data and Code for Shin et al., Neuron (2023)

description: MATLAB data and code needed to reproduce all main and supplemental results in "Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamacortical visual system," Neuron (April 05 2023). <br> All code tested in Matlab 2019b, 2020b, 2021a, and 2022a. <br> Note: please add "matfiles" folder as a path in main figure folder before running code for supplementary figures.
DOI: 10.6084/m9.figshare.19666314
title: Data and Code for "Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamocortical visual system," Shin et al., Neuron, Volume 111, Issue 7, 5 April 2023

description: MATLAB data and code needed to reproduce all main and supplemental results in "Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamacortical visual system," Shin et al., Neuron, Volume 111, Issue 7, 5 April 2023, Pages 1076-1085.e8 <br> All code tested in Matlab 2019b, 2020b, 2021a, and 2022a. <br> Note: please add "matfiles" folder as a path in main figure folder before running code for supplementary figures.
DOI: 10.6084/m9.figshare.19666314.v2
title: Data and Code for "Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamocortical visual system," Shin et al., Neuron, Volume 111, Issue 7, 5 April 2023, Pages 1076-1085.e8

description: MATLAB data and code needed to reproduce all main and supplemental results in "Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamacortical visual system," Shin et al., Neuron, Volume 111, Issue 7, 5 April 2023, Pages 1076-1085.e8 <br> All code tested in Matlab 2019b, 2020b, 2021a, and 2022a. <br> Note: please add "matfiles" folder as a path in main figure folder before running code for supplementary figures.
DOI: 10.25345/c5bk17055
title: MassIVE MSV000091649 - Systematic characterization of 21 post-translational modification using synthetic peptides
title: The data presented in this study in the - context of the ProteoemTools project - is based on the synthesis of about 5000 synthetic peptides carrying 21 different post-translational modifications to systematically characterize their chromatographic and mass spectrometric properties using multimodal LC-MS/MS.
DOI: 10.6084/m9.figshare.16415802
title: Data and Model Checkpoints for "Weakly Supervised Concept Map Generation through Task-Guided Graph Translation"

description: Data and model checkpoints for paper "Weakly Supervised Concept Map Generation through Task-Guided Graph Translation" by Jiaying Lu, Xiangjue Dong, and Carl Yang. The paper has been accepted by IEEE Transactions on Knowledge and Data Engineering (TKDE). <br> `GT-D2G-*.tar.gz` are model checkpoints for GT-D2G variants. These models are trained by `seed=27`. `nyt/dblp/yelp.*.win5.pickle.gz` are initial graphs generated by NLP pipelines. `glove.840B.restaurant.400d.vec.gz` is the pre-trained embedding for the Yelp dataset. <br> For more instructions, please refer to our GitHub repo.
DOI: 10.6084/m9.figshare.16415802.v1
title: GT-D2G Data

description: Data for paper "Weakly Supervised Concept Map Generation through Task-Guided Graph Translation" by Jiaying Lu, Xiangjue Dong and Carl Yang.<br>`GT-D2G-*.tar.gz` are model checkpoints for GT-D2G variants. These models are trained by `seed=27`.<br>`nyt/dblp/yelp.*.win5.pickle.gz` are initial graphs generated by NLP pipelines.<br>`glove.840B.restaurant.400d.vec.gz` is the pretrained embedding for Yelp dataset.
DOI: 10.5281/zenodo.7803607
title: Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software: - Apêndice B

description: Este documento é um apêndice do artigo Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software e busca definir a interação entre os fatores e os efeitos da rotatividade em DDS.
DOI: 10.5281/zenodo.7803606
title: Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software: - Apêndice B

description: Este documento é um apêndice do artigo Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software e busca definir a interação entre os fatores e os efeitos da rotatividade em DDS.
DOI: 10.6084/m9.figshare.22494541
title: Zebrafish reconstructed trees

description: Object containing all single-cell lineage trees built for this dataset provided by Hu, Lelek, Spanjaard et al. (Nature Genetics 2022). <br> Please cite the original publication: https://www.nature.com/articles/s41588-022-01129-5
DOI: 10.6084/m9.figshare.22564390
title: adhd2022

description: GWAS summary statistics on ADHD2022
DOI: 10.6084/m9.figshare.22494529
title: Zebrafish heart regeneration

description: Single cell RNA seq of uninjured and injured (wnt-inhibited and non-inhibited) zebrafish hearts accompanied by CRISPR-based lineage tracing obtained by Hu, Lelek, Spanjaard et al. (Nature Genetics 2022).<br> Cell type annotation and cell type color are obtained by the authors. The data was pre-processed to obtain an scvi latent space representation. Growth rates were evaluated using cell cycle marker genes typically used in single cell and the GSEA Hallmark apoptosis geneset and provided in the given adata file. <br> Please cite the original publication: https://www.nature.com/articles/s41588-022-01129-5
DOI: 10.5281/zenodo.7802117
title: Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software - Apêndice A

description: O documento é um apêndice do artigo Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software, que aborda os artigos selecionados para uma revisão sistemática da Literatura sobre o tema abodado. Também faz referência a tabela de causa e efeito entre os fatores e efeitos encontrados a partir da leitura dos artigos selecionados na RSL.
DOI: 10.5281/zenodo.7802116
title: Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software - Apêndice A

description: O documento é um apêndice do artigo Fatores e efeitos relacionados a rotatividade em Projetos com Desenvolvimento Distribuídos de Software, que aborda os artigos selecionados para uma revisão sistemática da Literatura sobre o tema abodado. Também faz referência a tabela de causa e efeito entre os fatores e efeitos encontrados a partir da leitura dos artigos selecionados na RSL.
DOI: 10.6084/m9.figshare.22564402
title: bip2021_noUKBB

description: GWAS summary statistics from the Psychiatric Genomics Consortium (PGC)
DOI: 10.5281/zenodo.7803611
title: A computationally efficient statistically downscaled 100 m resolution Greenland product from the regional climate model MAR: accompanying dataset

description: Dataset containing surface temperature and surface mass balance datasets generated from the MAR regional climate model over Greenland over two test areas using statistical downscaling tools from 6 km to 100m. The abstract of the accompanying submitted paper follows: The Greenland Ice Sheet (GrIS) has been contributing directly to sea level rise and this contribution is projected to accelerate over next decades. A crucial tool for studying the evolution surface mass loss (e.g., surface mass balance, SMB) consists of regional climate models (RCMs) which can provide current estimates and future projections of sea level rise associated with such losses. However, one of the main limitations of RCMs is the relatively coarse horizontal spatial resolution at which outputs are currently generated. Here, we report results concerning the statistical downscaling of the SMB modeled by the Modèle Atmosphérique Régional (MAR) RCM from the original spatial resolution of 6 km to 100 m building on the relationship between elevation and mass losses in Greenland. To this goal, we developed a geospatial framework that allows the parallelization of the downscaling process, a crucial aspect to increase the computational efficiency of the algorithm. The results obtained in the case of the SMB, assessed through the comparison of the modeled outputs with in-situ SMB measurements, show a considerable improvement in the case of the downscaled product with respect to the original, coarse output. In the case of the downscaled MAR product, the coefficient of determination (R<sup>2</sup>) increases from 0.868 for the original MAR output to 0.935 for the downscaled product. Moreover, the value of the slope and intercept of the linear regression fitting modeled and measured SMB values shifts from 0.865 for the original MAR to 1.015 for the downscaled product in the case of the intercept and from the value -235mm (original) to -57 mm (downscaled) in the case of the slope, considerably improving upon results previously published in the literature.
DOI: 10.5281/zenodo.7803610
title: A computationally efficient statistically downscaled 100 m resolution Greenland product from the regional climate model MAR: accompanying dataset

description: Dataset containing surface temperature and surface mass balance datasets generated from the MAR regional climate model over Greenland over two test areas using statistical downscaling tools from 6 km to 100m. The abstract of the accompanying submitted paper follows: The Greenland Ice Sheet (GrIS) has been contributing directly to sea level rise and this contribution is projected to accelerate over next decades. A crucial tool for studying the evolution surface mass loss (e.g., surface mass balance, SMB) consists of regional climate models (RCMs) which can provide current estimates and future projections of sea level rise associated with such losses. However, one of the main limitations of RCMs is the relatively coarse horizontal spatial resolution at which outputs are currently generated. Here, we report results concerning the statistical downscaling of the SMB modeled by the Modèle Atmosphérique Régional (MAR) RCM from the original spatial resolution of 6 km to 100 m building on the relationship between elevation and mass losses in Greenland. To this goal, we developed a geospatial framework that allows the parallelization of the downscaling process, a crucial aspect to increase the computational efficiency of the algorithm. The results obtained in the case of the SMB, assessed through the comparison of the modeled outputs with in-situ SMB measurements, show a considerable improvement in the case of the downscaled product with respect to the original, coarse output. In the case of the downscaled MAR product, the coefficient of determination (R<sup>2</sup>) increases from 0.868 for the original MAR output to 0.935 for the downscaled product. Moreover, the value of the slope and intercept of the linear regression fitting modeled and measured SMB values shifts from 0.865 for the original MAR to 1.015 for the downscaled product in the case of the intercept and from the value -235mm (original) to -57 mm (downscaled) in the case of the slope, considerably improving upon results previously published in the literature.
DOI: 10.6084/m9.figshare.22308463.v4
title: Mapeamento Detalhado WIT - Fatores de Atração, Permanência e Evasão (Santos e Marczak, 2023)

description: Aqui encontram-se os dados completos e detalhados do Mapeamento Sistemático da Literatura realizado dos artigos disponíveis nos Anais do <em>Women in Information Technology</em> (WIT), dos anos de 2016 a 2022. Os dados referem-se aos fatores que motivam a atração, permanência e o abandono de mulheres nas áreas da Computação, objetivo do trabalho submetido ao WIT 2023, elaborado pelas autoras Nayara Dias dos Santos e Sabrina Marczak.