cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23912193.v2
title: Retinal regeneration after injury induced by gamma-ray irradiation during early embryogenesis in medaka, <i>Oryzias latipes</i>

description: Zebrafish, a small fish model, exhibits a multipotent ability for retinal regeneration after damage throughout its lifetime. Compared with zebrafish, birds and mammals exhibit such a regenerative capacity only during the embryonic period, and this capacity decreases with age. In medaka, another small fish model that has also been used extensively in biological research, the retina’s inner nuclear layer (INL) failed to regenerate after injury in the hatchling at eight days postfertilization (dpf). We characterized the regenerative process of the embryonic retina when the retinal injury occurred during the early embryonic period in medaka. We employed a 10 Gy dose of gamma-ray irradiation to initiate retinal injury in medaka embryos at 3 dpf and performed histopathological analyses up to 21 dpf. One day after irradiation, numerous apoptotic neurons were observed in the INL; however, these neurons were rarely observed in the ciliary marginal zone and the photoreceptor layer. Numerous pyknotic cells were clustered in the irradiated retina until two days after irradiation. These disappeared four days after irradiation, but the abnormal bridging structures between the INL and ganglion cell layer (GCL) were present until 11 days after irradiation, and the neural layers were completely regenerated 18 days after irradiation. After gamma-ray irradiation, the spindle-like Müller glial cells in the INL became rounder but did not lose their ability to express SOX2. Irradiated retina at 3 dpf of medaka embryos could be completely regenerated at 18 days after irradiation (21 dpf), although the abnormal layer structures bridging the INL and GCL were transiently formed in the retinas of all the irradiated embryos. Four days after irradiation, embryonic medaka Müller glia were reduced in number but maintained SOX2 expression as in nonirradiated embryos. This finding contrasts with previous reports that 8 dpf medaka larvae could not fully regenerate damaged retinas because of loss of SOX2 expression.
DOI: 10.5281/zenodo.8377695
title: Movement-driven modeling reveals new patterns in disease transmission networks

description: Interactions between individuals of different species are highly relevant in the potential transmission of shared pathogens in multi-host systems. In recent decades, several technologies to study pathogen transmission have been developed, such as proximity loggers, GPS tracking devices, and/or camera traps. Despite the diversity of methods aimed at detecting contacts, the analysis of transmission risk is often reduced to contact rates and the probability of transmission given contact. However, the latter process is continuous over time and unique for each contact, and it is influenced by the characteristics of the contact and the pathogen's relationship with both the host and the environment. In this study, we utilized a movement-based model that decomposes transmission into contact formation, contact duration, and host characteristics, assigning a unique transmission risk to each contact. We aimed to assess whether this more comprehensive approach reveals disease transmission dynamics that are not detected with more traditional approaches. The model was built from GPS data from two management systems in Spain where animal tuberculosis (TB) circulates: a national park, and an area with extensive free-range pigs and cattle farms. In addition, we assessed the effect of the GPS device sampling rate on the performance of the model. Considering the specific conditions under which each contact occurs (i.e., whether the contact is direct or indirect, its duration, the hosts characteristics, the environmental conditions, etc.) resulted in the identification of different transmission dynamics compared to a model based solely on contact rates. This indicates that not taking these conditions into account may result in misidentifying the key species in disease transmission. The different transmission dynamics identified between both management systems highlight the need to analyze each system independently. We found that temporal intervals greater than 30 minutes in the GPS tracking data resulted in missed interactions, and intervals greater than 2 hours may be insufficient in interaction studies for epidemiological purposes. This study describes a clear and repeatable methodology to study pathogen transmission from GPS data, and provides further insights to understand how TB is maintained in multi-host systems under different management scenarios in Mediterranean environments.
DOI: 10.35077/ace-bag-kit
title: Whole brain raw fMOST images from mouse: AIBS_746222364

description: Raw fMOST image files from mouse specimens from the Hongkui Zeng lab at Allen Institute for Brain Science
description: DATASET METADATA:
 title:'Whole brain raw fMOST images from mouse: AIBS_746222364',
 GeneralModality:'cell morphology',
 Technique:'fMOST'
 SPECIMEN METADATA:
 LocalID:'AIBS_746222364',
 Species:'mouse',
 NCBITaxonomy:'NCBI:txid10090',
 OrganName:'Brain',
 Locations:'Whole brain'
 INSTRUMENT METADATA:
 MicroscopeType:'fMOST'
 IMAGE METADATA:
 Gbytes:'6149.196975972',
 Files:'46338.0'
DOI: 10.5517/ccdc.csd.cc2fvkb6
title: CCDC 2259848: Experimental Crystal Structure Determination

description: Related Article: Saswat Ranjan Bhoi, Chhanda Debnath, Shikha Gandhi|2024|Chem.Commun.|60|428|doi:10.1039/D3CC05023H
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.cc2fvmmk
title: CCDC 2259919: Experimental Crystal Structure Determination

description: Related Article: Jiang Jiang, Zi-Wei Li, Zhi-Zhuan Zhang, Bin Tan, Zhao-Feng Wu, Xiao-Ying Huang|2024|Dalton Trans.|53|706|doi:10.1039/D3DT03363E
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.cc2fz0p4
title: CCDC 2263176: Experimental Crystal Structure Determination

description: Related Article: Farzaneh Saeedifard, Colton J. Breyer, Thomas Chi Cao, Jayniel M. Kamdar, Jake Kerkhof, Diane K. Smith, Andrew L. Cooksy, Arnold L. Rheingold, Curtis E. Moore, Douglas B. Grotjahn|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.cc2g12m7
title: CCDC 2265158: Experimental Crystal Structure Determination

description: Related Article: Barbara Modec, Nina Podjed|2024|Inorg.Chem.Commun.|159|111831|doi:10.1016/j.inoche.2023.111831
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.cc2dp7hv
title: CCDC 2224947: Experimental Crystal Structure Determination

description: Related Article: Shuang Yu, Jun Ying, Aixiang Tian, Mengle Yang, Xiuli Wang|2023|Inorg.Chem.|62|21336|doi:10.1021/acs.inorgchem.3c03413
description: Related Article: Shuang Yu, Jun Ying, Aixiang Tian, mengle yang, Xiuli Wang|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.cc2g1smy
title: CCDC 2265840: Experimental Crystal Structure Determination

description: Related Article: Vindhya Hegde, C.O. Sreekala, Naveen V. Kulkarni, Jomon Mathew|2024|J.Photochem.Photobiol.A:Chem.|449|115389|doi:10.1016/j.jphotochem.2023.115389
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.cc2dp7x8
title: CCDC 2224960: Experimental Crystal Structure Determination

description: Related Article: Shuang Yu, Jun Ying, Aixiang Tian, Mengle Yang, Xiuli Wang|2023|Inorg.Chem.|62|21336|doi:10.1021/acs.inorgchem.3c03413
description: Related Article: Shuang Yu, Jun Ying, Aixiang Tian, mengle yang, Xiuli Wang|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.cc2gjz44
title: CCDC 2280426: Experimental Crystal Structure Determination

description: Related Article: Jing Qi, Xiyan Wang, Gan Wang, Srinivas Reddy Dubbaka, Patrick O'Neill, Hwee Ting Ang, Jie Wu|2024|Green Chemistry|26|306|doi:10.1039/D3GC04010K
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.cc2gl6hs
title: CCDC 2281615: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2gl6jt
title: CCDC 2281616: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2gl6kv
title: CCDC 2281617: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2gl6lw
title: CCDC 2281618: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2gl6mx
title: CCDC 2281619: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2gl6ny
title: CCDC 2281620: Experimental Crystal Structure Determination

description: Related Article: Anna Schannong Manvell, Rouven Pfleger, Niels Andreas Bonde, Matteo Briganti, Carlo Andrea Mattei, Theis Brock Nannestad, Høgni Weihe, Annie K. Powell, Jacques Ollivier, Jesper Bendix, Mauro Perfetti|2024|Chemical Science|15|113|doi:10.1039/D3SC03928E
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.cc2glb4k
title: CCDC 2281728: Experimental Crystal Structure Determination

description: Related Article: Hiroki Shigehisa|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.cc2gt7cx
title: CCDC 2288369: Experimental Crystal Structure Determination

description: Related Article: Li Zhang|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.cc2fp3r0
title: CCDC 2254622: Experimental Crystal Structure Determination

description: Related Article: Dexin Wang, Yanshu Liu, Guanjie Chen, Fangfang Gao, Guanyun Zhang, Guo Wang, Chen-Ho Tung, Yifeng Wang|2023|Inorg.Chem.|62|21074|doi:10.1021/acs.inorgchem.3c02876
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.cc2gvh50
title: CCDC 2289572: Experimental Crystal Structure Determination

description: Related Article: YUAN CHEN|2023|CSD Communication|||
description: Related Article: Yuan Chen, Rui-jun Peng, Xue-jing Zhang, Ming Yan|2023|Org.Chem.Front.|11|176|doi:10.1039/D3QO01607B
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.10394145
title: Research data and code supporting "A non-FRET DNA reporter that changes fluorescence color upon nuclease digestion"

description: Raw research data and code supporting: Hong, Soonwoo et al. A non-FRET DNA reporter that changes fluorescence color upon nuclease digestion. Nat. Nanotechnol. (2024)
DOI: 10.5281/zenodo.10394146
title: Research data and code supporting "A non-FRET DNA reporter that changes fluorescence color upon nuclease digestion"

description: Raw research data and code supporting: Hong, Soonwoo et al. A non-FRET DNA reporter that changes fluorescence color upon nuclease digestion. Nat. Nanotechnol. (2024)
DOI: 10.5281/zenodo.8089374
title: Supplementary data to Daly, Aoife, 2024. Timber supply through time – Copenhagen waterfronts under scrutiny. Dendrochronologia 126164. https://doi.org/10.1016/j.dendro.2024.126164

description: Supplementary tree-ring data (averages for oak, pine and spruce) associated with the article:

Daly, Aoife, 2024. Timber supply through time – Copenhagen waterfronts under scrutiny. Dendrochronologia, 2024, 126164, https://doi.org/10.1016/j.dendro.2024.126164
DOI: 10.5281/zenodo.8089375
title: Supplementary data to Daly, Aoife, 2024. Timber supply through time – Copenhagen waterfronts under scrutiny. Dendrochronologia 126164. https://doi.org/10.1016/j.dendro.2024.126164

description: Supplementary tree-ring data (averages for oak, pine and spruce) associated with the article:

Daly, Aoife, 2024. Timber supply through time – Copenhagen waterfronts under scrutiny. Dendrochronologia, 2024, 126164, https://doi.org/10.1016/j.dendro.2024.126164
DOI: 10.57745/i4zarv
title: 231020_vdt.csv

description: Earthworm community dataset
DOI: 10.57745/nwvuwl
title: 231020_vdt_readme.txt

description: explanation of column names
DOI: 10.57745/penrby
title: 231020_vdt_readme.csv

description: explanation of column colum names
DOI: 10.57745/td1meb
title: 231020_vdt.tab

description: Earthworm community dataset
DOI: 10.25345/c57m04b1h
title: MassIVE MSV000093799 - Ceramide-GPR64 signaling drives Ewing sarcoma
title: Ewing sarcoma is a cancer of bone and soft tissue in children and young adults primarily driven by the EWS-FLI1 fusion oncoprotein, which has been undruggable. Here, we report that Ewing sarcoma depends on secreted SMPD1, a ceramide-generating enzyme, and ceramide. We identify GPR64/ADGRG2 as the ceramide receptor, mediating critical growth signaling in Ewing sarcoma. We show that ceramide induces the cleavage of the C-terminal intracellular domain of GPR64, which translocates to the nucleus and restrains the protein levels of RIF1 in a manner dependent on SPOP, a substrate adaptor of the Cullin3-RING E3 ubiquitin ligase. We demonstrate that both SMPD1 and GPR64 are transcriptional targets of EWS-FLI1, indicating that SMPD1 and GPR64 are EWS-FLI1-driven cytokine-receptor dependencies. These results reveal the SMPD1-ceramide-GPR64 pathway which drives Ewing sarcoma growth and is amenable to therapeutic intervention.
DOI: 10.5281/zenodo.10471552
title: Datasets used in "Global LHC constraints on electroweak-inos with SModelS v2.3"

description: Input SLHA and SModelS output (.smodels and .py) files from the paper "Global LHC constraints on electroweak-inos with SModelS v2.3". The datasets comprises 18247 electroweak-ino scan points and can be used to reproduce results in sections 4 and 5, and in appendix B.



ewino_slhaFiles.tar.gz : input SLHA files including mass spectra, decay tables and cross sections.

ewino_smodels_mmg10.tar.gz : SModelS outputs with a minmassgap of 10 GeV (value used for the results presented in the main text, used for Figures 12-21). All the 18247 scan points present in the directory were obtained using this minmassgap.

ewino_smodels_mmg05.tar.gz : SModelS outputs with a minmassgap of 5 GeV (value used in appendix B, used for Figures 23 and 24). All the 18247 scan points present in the directory were obtained using this minmassgap.

ewino_smodels_mmg15.tar.gz : SModelS outputs with a minmassgap of 15 GeV (value used in appendix B, used for Figures 23 and 24). Only the points with a mass difference between the next-to-lightest neutralino and the lightest neutralino, or the next-to-lightest neutralino and the lightest chargino, or the lightest chargino and the lightest neutralino comprised between 10 and 15 GeV were computed using this minmassgap. This corresponds to 1732 scan points, which are listed in the summary.txt present in the compressed directory. The results for the remaining points were obtained using a minmassgap of 10 GeV.

ewino_smodels_mmg20.tar.gz : SModelS outputs with a minmassgap of 20 GeV (value used in appendix B, used for Figures 23 and 24). Only the points with a mass difference between the next-to-lightest neutralino and the lightest neutralino, or the next-to-lightest neutralino and the lightest chargino, or the lightest chargino and the lightest neutralino comprised between 15 and 20 GeV were computed using this minmassgap. This corresponds to 870 scan points, which are listed in the summary.txt present in the compressed directory. The results for the remaining points were obtained using a minmassgap of 15 or 10 GeV (depending on the mass difference condition mentioned in the previous paragraph).

combinability_matrix.py: python dictionnary modelling the combinability matrix (Figure 11).
description: MMA is supported by the French Agence Nationale de la Recherche (ANR) under grant ANR-21-CE31-0023 (PRCI SLDNP). SN is supported by the Austrian Science Fund (FWF) under grant number I 5767-N. TP is supported by the Initiatives de Recherche à Grenoble Alpes (IRGA) ANR-15-IDEX-02 project no. G7H-IRG21B26 (APM@LHC). AL is supported by FAPESP grant no. 2018/25225-9 and 2021/01089-1. The work presented here was, moreover, supported in part by the IN2P3 master project “Théorie – BSMGA”.