cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8123677
title: Dataset: Simulation-based parameter optimization for fetal brain MRI super-resolution reconstruction

description: This dataset contains the data used in the paper de Dumast, P., Sanchez, T., Lajous, H., Bach Cuadra, M. (2023). Simulation-Based Parameter Optimization for Fetal Brain MRI Super-Resolution Reconstruction. MICCAI 2023. LNCS, vol 14226. Springer, Cham. https://doi.org/10.1007/978-3-031-43990-2_32 A preprint can also be found on arXiv. If you found this dataset useful or used it in your research, please cite this reference. This paper studied the impact of the regularization parameter \(\alpha \) on the super-resolution reconstruction of fetal brain magnetic resonance (MR) images. It used simulated T2-weighted data MR images generated using FaBiAN v2.0, a Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates fast spin echo (FSE) sequences of the developing fetal brain throughout gestation. The dataset contains the raw simulated data, the corresponding ground truths as well as corresponding super-resolution (SR) reconstructions using MIALSRTK and NiftyMIC with varying regularization parameters \(\alpha \). Copyright (c) - All rights reserved. Medical Image Analysis Laboratory - Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland & CIBM Center for Biomedical Imaging. 2023.
description: This work is supported by the Swiss National Science Foundation through grants 182602 and 141283, and by the Eranet Neuron MULTIFACT project (SNSF 31NE30 203977). We acknowledge access to the facilities and expertise of the CIBM Center for Biomedical Imaging, a Swiss research center of excellence founded and supported by CHUV, UNIL, EPFL, UNIGE and HUG.
description: {"references": ["Lajous, H., et al. (2021). Medical-Image-Analysis-Laboratory/FaBiAN: FaBiAN. Zenodo. https://doi.org/10.5281/zenodo.5471094", "Lajous, H., et al. (2022). A Fetal Brain magnetic resonance Acquisition Numerical phantom (FaBiAN). Sci Rep 12, 8682. https://doi.org/10.1038/s41598-022-10335-4", "Tourbier, S., et al. (2015). An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization. NeuroImage, 118, 584-597. https://doi.org/10.1016/j.neuroimage.2015.06.018", "Tourbier, S., et al. (2023). Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit: MIAL Super-Resolution Toolkit v2.1.0 (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.7612119", "Ebner, M., et al. (2020). An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. NeuroImage, 206, 116324. https://doi.org/10.1016/j.neuroimage.2019.116324"]}
DOI: 10.6084/m9.figshare.24242767
title: Supplementary Data

description: sum_orthologue_transcript_counts.py - python script to sum read counts and TPM values after using kallisto to pseudoalign RNA-Seq reads to the pantranscriptome reference.CS_plus_1to1_orthologues_cds.fasta - pantranscriptome reference containing transcripts from the Chinese Spring RefSeq v1.1 high-confidence annotation and transcripts from genes from the pangenome cultivars that exist in a 1-to-1 relationship with a Chinese Spring gene.CS_1to1_orthologue_pairs.tsv - Genes in a 1-to-1 relationship with a Chinese Spring, determined using OrthoFinder with proteins from Chinese Spring and the nine chromosome-level genome assemblies from the wheat pangenome project (Walkowiak et al., 2020).RefSeqv1.1_hc_triad_ids.tsv - Gene IDs of each triad identified by Ramírez-González et al., 2018.accessions_with_chr1D_introgression.tsv - Table showing which accessions from He et al. (2022) contain the chr1D introgression.He_et_al_expression_matrix_CS_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the Chinese Spring RefSeq v.1.1 high-confidence transcripts.He_et_al_expression_matrix_pantranscriptome_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the pantranscriptome reference and processed using sum_orthologue_transcript_counts.py
DOI: 10.6084/m9.figshare.24242767.v1
title: Supplementary Data

description: sum_orthologue_transcript_counts.py - python script to sum read counts and TPM values after using kallisto to pseudoalign RNA-Seq reads to the pantranscriptome reference.CS_plus_1to1_orthologues_cds.fasta - pantranscriptome reference containing transcripts from the Chinese Spring RefSeq v1.1 high-confidence annotation and transcripts from genes from the pangenome cultivars that exist in a 1-to-1 relationship with a Chinese Spring gene.CS_1to1_orthologue_pairs.tsv - Genes in a 1-to-1 relationship with a Chinese Spring, determined using OrthoFinder with proteins from Chinese Spring and the nine chromosome-level genome assemblies from the wheat pangenome project (Walkowiak et al., 2020).RefSeqv1.1_hc_triad_ids.tsv - Gene IDs of each triad identified by Ramírez-González et al., 2018.accessions_with_chr1D_introgression.tsv - Table showing which accessions from He et al. (2022) contain the chr1D introgression.He_et_al_expression_matrix_CS_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the Chinese Spring RefSeq v.1.1 high-confidence transcripts.He_et_al_expression_matrix_pantranscriptome_reference.tsv - expression matrix generated by pseuoaligning the RNA-Seq data from He et al. (2022) to the pantranscriptome reference and processed using sum_orthologue_transcript_counts.py
DOI: 10.6084/m9.figshare.24052273
title: The politics of social media: Utilizing political candidates’ Instagram posts to teach political argumentation and visual argument analysis

description: Analysis of political and visual arguments is a key exercise traditionally included in undergraduate argumentation courses. This activity teaches students how to identify and analyze political candidate arguments presented on visual social media platforms, demonstrating how argumentation theory applies to social media campaigns. In the exercise, students identify an active political candidate’s Instagram account and select a recent post for analysis, focusing primarily on evaluating the visual arguments created within the post. After the analysis, students present their findings to the class, including evidence of the most compelling visual arguments identified. This activity incorporates the use of a familiar visual medium to help students connect wargumentation theories and concepts with relevant social media messages they may encounter in their daily lives. It also capitalizes on students’ existing use of popular visual social media to introduce basic argumentation theory, political communication practices, and visual argument analysis techniques. This single-class activity is useful in undergraduate communication courses related to argumentation, political communication, and social media messaging. Relevant courses can include argumentation and advocacy, political argumentation, or visual argument analysis units of any course. For example, this activity can be successfully deployed in an Introduction to Political Communication course’s unit on the use of visual media during political campaigns. The learning objectives of this activity are: (1) to analyze visual arguments as they appear on social media and (2) to identify specific elements of strong and weak political arguments on a visually dominant social media platform.
DOI: 10.6084/m9.figshare.24052273.v1
title: The politics of social media: Utilizing political candidates’ Instagram posts to teach political argumentation and visual argument analysis

description: Analysis of political and visual arguments is a key exercise traditionally included in undergraduate argumentation courses. This activity teaches students how to identify and analyze political candidate arguments presented on visual social media platforms, demonstrating how argumentation theory applies to social media campaigns. In the exercise, students identify an active political candidate’s Instagram account and select a recent post for analysis, focusing primarily on evaluating the visual arguments created within the post. After the analysis, students present their findings to the class, including evidence of the most compelling visual arguments identified. This activity incorporates the use of a familiar visual medium to help students connect wargumentation theories and concepts with relevant social media messages they may encounter in their daily lives. It also capitalizes on students’ existing use of popular visual social media to introduce basic argumentation theory, political communication practices, and visual argument analysis techniques. This single-class activity is useful in undergraduate communication courses related to argumentation, political communication, and social media messaging. Relevant courses can include argumentation and advocacy, political argumentation, or visual argument analysis units of any course. For example, this activity can be successfully deployed in an Introduction to Political Communication course’s unit on the use of visual media during political campaigns. The learning objectives of this activity are: (1) to analyze visual arguments as they appear on social media and (2) to identify specific elements of strong and weak political arguments on a visually dominant social media platform.
DOI: 10.21227/scn8-ch25
title: Simulated Action YGAR Hard Level

description: Our video action dataset is generated using a 3D simulation program developed in Unity. Each data sample consists of a video capturing a human performing various actions. Our initial set of actions comprises a total of 10 different yoga poses: camel, chair, child's pose, lord of the dance, lotus, thunderbolt, triangle, upward dog, warrior II, and warrior III. Within each of these 10 yoga poses, there are four variations, some exhibiting more pronounced differences than others. This results in a total of 40 action types within our dataset.We opted for this set of actions as our initial dataset because each pose is distinct and has a well-defined ending position. This characteristic allows us to employ image classification techniques to compare both traditional modeling architectures and deep learning approaches.
DOI: 10.5517/ccdc.csd.cc2g7jfp
title: CCDC 2271352: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jgq
title: CCDC 2271353: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jhr
title: CCDC 2271354: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jjs
title: CCDC 2271355: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jkt
title: CCDC 2271356: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jlv
title: CCDC 2271357: Experimental Crystal Structure Determination

description: Related Article: Saral Baweja, Peter Lönnecke, Evamarie Hey-Hawkins|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.cc2g7jt2
title: CCDC 2271364: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7jv3
title: CCDC 2271365: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7jw4
title: CCDC 2271366: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7jx5
title: CCDC 2271367: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7jy6
title: CCDC 2271368: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7jz7
title: CCDC 2271369: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7k09
title: CCDC 2271370: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7k1b
title: CCDC 2271371: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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.cc2g7k2c
title: CCDC 2271372: Experimental Crystal Structure Determination

description: Related Article: Yannick Stöferle, Peter Chen|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: 10.6084/m9.figshare.21608310
title: Graph based embedding learning of trajectory data for transportation mode recognition by fusing sequence and dependency relations.rar

description: Graph based embedding learning of trajectory data for transportation mode recognition by fusing sequence and dependency relations.
DOI: 10.6084/m9.figshare.24242935
title: All data used in the study entitled "Songbirds avoid the oxidative stress costs of high blood glucose levels"

description: Chronically high blood glucose levels (hyperglycaemia) can compromise healthy ageing and lifespan at the individual level. Elevated oxidative stress can play a central role in hyperglycaemia-induced pathologies. Nevertheless, the lifespan of birds shows no species-level association with blood glucose. This suggests that the potential pathologies of high blood glucose levels can be avoided by adaptations in oxidative physiology at the macroevolutionary scale. However, this hypothesis remains unexplored. Here, we examined this hypothesis using comparative analyses controlled for phylogeny, allometry and fecundity based on data from 51 songbird species (681 individuals with blood glucose and 1021 individuals with oxidative state data). We measured blood glucose at baseline and after stress stimulus and computed glucose stress reactivity as the magnitude of change between the two time points. We also measured three parameters of non-enzymatic antioxidants (uric acid, total antioxidants and glutathione) and a marker of oxidative lipid damage (malondialdehyde). We found no clear evidence for blood glucose concentration being correlated with either antioxidant or lipid damage levels at the macroevolutionary scale, as opposed to the hypothesis postulating that high blood glucose levels entail oxidative costs. The only exception was the moderate evidence for species with a stronger stress-induced increase in blood glucose concentration evolving moderately lower investment into antioxidant defence (uric acid and glutathione). Neither baseline nor stress-induced glucose levels were associated with oxidative physiology. Our findings support the hypothesis that birds evolved adaptations preventing the (glyc)oxidative costs of high blood glucose observed at the within-species level. Such adaptations may explain the decoupled evolution of glycaemia and lifespan in birds and possibly the paradoxical combination of long lifespan and high blood glucose levels relative to mammals.
DOI: 10.6084/m9.figshare.24242935.v1
title: All data used in the study entitled "Songbirds avoid the oxidative stress costs of high blood glucose levels"

description: Chronically high blood glucose levels (hyperglycaemia) can compromise healthy ageing and lifespan at the individual level. Elevated oxidative stress can play a central role in hyperglycaemia-induced pathologies. Nevertheless, the lifespan of birds shows no species-level association with blood glucose. This suggests that the potential pathologies of high blood glucose levels can be avoided by adaptations in oxidative physiology at the macroevolutionary scale. However, this hypothesis remains unexplored. Here, we examined this hypothesis using comparative analyses controlled for phylogeny, allometry and fecundity based on data from 51 songbird species (681 individuals with blood glucose and 1021 individuals with oxidative state data). We measured blood glucose at baseline and after stress stimulus and computed glucose stress reactivity as the magnitude of change between the two time points. We also measured three parameters of non-enzymatic antioxidants (uric acid, total antioxidants and glutathione) and a marker of oxidative lipid damage (malondialdehyde). We found no clear evidence for blood glucose concentration being correlated with either antioxidant or lipid damage levels at the macroevolutionary scale, as opposed to the hypothesis postulating that high blood glucose levels entail oxidative costs. The only exception was the moderate evidence for species with a stronger stress-induced increase in blood glucose concentration evolving moderately lower investment into antioxidant defence (uric acid and glutathione). Neither baseline nor stress-induced glucose levels were associated with oxidative physiology. Our findings support the hypothesis that birds evolved adaptations preventing the (glyc)oxidative costs of high blood glucose observed at the within-species level. Such adaptations may explain the decoupled evolution of glycaemia and lifespan in birds and possibly the paradoxical combination of long lifespan and high blood glucose levels relative to mammals.
DOI: 10.21223/1fjz5g
title: Dataset for: Field Evaluation and Nutritional Analysis of Phureja Collection Native Potatoes in Junin, 2006

description: An assessment was conducted on 202 varieties belonging to the Phureja potato collection. The evaluation took place in Huancayo during the 2006 growing season. Additionally, nutritional analyses were performed on micronutrients, vitamin C, carotenoids, and polyphenols.
DOI: 10.6084/m9.figshare.24242956
title: Spatial analysis of Asian protected areas for transboundary conservation

description: This is a data related to the spatial proximity of protected areas across borderlands in Asian countries, developed by Vignesh et al (under review)