cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5996855
title: Research data and code for Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants

description: # Research data repository ## Introduction This repository contains the research data, scripts and codes to process the simulation and generate the figures in research article: <br> <em>"Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants"</em> This work uses the discrete 3D mesh of the thorax of a newborn that is available at: http://doi.org/10.5281/zenodo.4916863 This article has been submitted and publied in Journal of Biophotonics:<br> - DOI: 10.1002/jbio.202200041<br> - Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041 ## Article status [X] Submitted <br> [X] Under review <br> [X] Corrections <br> [X] Published<br> <br> ## Content - Folder "data": This folder needs to be unzipped and contains the raw data from the simulation, as well as some processed data needed to generate the figures. This folder contains all the data necessary to generate the figures. However some intermediate data files (the Photon Hitting Density values interpolated on the elements of the mesh) are not given here because the files are too big. These can be created using the convertPHD2element script.<br> - Folder "function": This folder needs to be unzipped and contains some functions that are used by the scripts to process data or generate the figures<br> - Matlab .m files: The .m files are scripts that are used to generate the figures (generateFigX.m) or to process the data computeYYY.m. The description of each script and function is given in the comment section at the beginning of each file. ## Licence<br> This data is published under the creative common CC-BY licence. You are free to use this data as long as you cite this dataset and the article (when DOI available) ## Digital Object Identifier<br> DOI: 10.5281/zenodo.5996855 ## Authors<br> Simulation: Andrea Pacheco<br> Article writing: Andrea Pacheco<br> Data processing and figure generation: Andrea Pacheco and Baptiste Jayet<br> Conceptualisation, investigation, review and editing: Emilie Krite Svanberg, Hamid Dehghani and Eugene Dempsey<br> Project supervision: Stefan Andersson-Engels ## Funding<br> The research leading to these results was funded by Science Fundation Ireland project no. SFI/15/RP/2828
description: This work was funded by Science Foundation Ireland project no. SFI/15/RP/2828
description: {"references": ["Pacheco et. al (2021), Newborn thorax mesh with DOI: 10.5281/zenodo.4916863"]}
DOI: 10.5281/zenodo.5996854
title: Research data and code for Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants

description: # Research data repository ## Introduction This repository contains the research data, scripts and codes to process the simulation and generate the figures in research article: <br> <em>"Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants"</em> This work uses the discrete 3D mesh of the thorax of a newborn that is available at: http://doi.org/10.5281/zenodo.4916863 This article has been submitted and publied in Journal of Biophotonics:<br> - DOI: 10.1002/jbio.202200041<br> - Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041 ## Article status [X] Submitted <br> [X] Under review <br> [X] Corrections <br> [X] Published<br> <br> ## Content - Folder "data": This folder needs to be unzipped and contains the raw data from the simulation, as well as some processed data needed to generate the figures. This folder contains all the data necessary to generate the figures. However some intermediate data files (the Photon Hitting Density values interpolated on the elements of the mesh) are not given here because the files are too big. These can be created using the convertPHD2element script.<br> - Folder "function": This folder needs to be unzipped and contains some functions that are used by the scripts to process data or generate the figures<br> - Matlab .m files: The .m files are scripts that are used to generate the figures (generateFigX.m) or to process the data computeYYY.m. The description of each script and function is given in the comment section at the beginning of each file. ## Licence<br> This data is published under the creative common CC-BY licence. You are free to use this data as long as you cite this dataset and the article (when DOI available) ## Digital Object Identifier<br> DOI: 10.5281/zenodo.5996855 ## Authors<br> Simulation: Andrea Pacheco<br> Article writing: Andrea Pacheco<br> Data processing and figure generation: Andrea Pacheco and Baptiste Jayet<br> Conceptualisation, investigation, review and editing: Emilie Krite Svanberg, Hamid Dehghani and Eugene Dempsey<br> Project supervision: Stefan Andersson-Engels ## Funding<br> The research leading to these results was funded by Science Fundation Ireland project no. SFI/15/RP/2828
description: This work was funded by Science Foundation Ireland project no. SFI/15/RP/2828
description: {"references": ["Pacheco et. al (2021), Newborn thorax mesh with DOI: 10.5281/zenodo.4916863"]}
DOI: 10.5281/zenodo.6418451
title: RegEl Database: text-mined regulatory elements from the literature and their associations to genes and disease

description: <pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre> # RegEl PubMed Database This database contains the annotations generated by running [HunFlair](https://github.com/flairNLP/flair/blob/master/resources/docs/HUNFLAIR.md) models trained on the [RegEl corpus](https://zenodo.org/record/5776679) over &gt;20M PubMed abstracts. By pairing these annotations with the one provided by PubTator this generates a large text mining database of regulatory elements associated with genes (normalized to NCBI Gene ids) and disease (normalized to either MeSH or OMIM). The tables composing the database are: * abstracts.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - text = text of the given sentence * gene.db and disease.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - etype = entity type (enhancer, promoter, TFBS)<br> - ann_text = mention of the regulatory element as found in the abstract<br> - start = position (# character) in which the mention begins<br> - end = position (# characters) in which the mention ends<br> - score = model's confidence<br> - cui = gene or disease identifier<br> - cui_symbol = official symbol of cui (if available)
DOI: 10.5281/zenodo.6418367
title: RegEl Database: text-mined regulatory elements from the literature and their associations to genes and disease

description: <pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre> # RegEl PubMed Database This database contains the annotations generated by running [HunFlair](https://github.com/flairNLP/flair/blob/master/resources/docs/HUNFLAIR.md) models trained on the [RegEl corpus](https://zenodo.org/record/5776679) over &gt;20M PubMed abstracts. By pairing these annotations with the one provided by PubTator this generates a large text mining database of regulatory elements associated with genes (normalized to NCBI Gene ids) and disease (normalized to either MeSH or OMIM). The tables composing the database are: * abstracts.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - text = text of the given sentence * gene.db and disease.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - etype = entity type (enhancer, promoter, TFBS)<br> - ann_text = mention of the regulatory element as found in the abstract<br> - start = position (# character) in which the mention begins<br> - end = position (# characters) in which the mention ends<br> - score = model's confidence<br> - cui = gene or disease identifier<br> - cui_symbol = official symbol of cui (if available)
DOI: 10.48428/adattar/pcabdh
title: Unexpected_CLT

description: dataset
DOI: 10.5281/zenodo.5776679
title: RegEl corpus: Identifying DNA regulatory elements in the scientific literature

description: <pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre>
DOI: 10.5281/zenodo.5776678
title: RegEl corpus: Identifying DNA regulatory elements in the scientific literature

description: <pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre>
DOI: 10.5281/zenodo.7373015
title: Data for 'Fatty acid capped, metal oxo clusters as smallest conceivable nanocrystal prototypes'

description: The <em>.pxp</em> documents contain the experimental data of the figures in the manuscript and they can be opened/edited with the software IGOR Pro 8.0 or higher. Figure 3: Experimental PDF of zirconium oxo clusters with different capping ligands. The C-C, Zr-O, and Zr-Zr distances are assigned. We make a distinction between the Zr-Zr distances within one Zr6 cluster and the Zr-Zr distances that are characteristic for the dimer Figure 4: PDF refinement of the Zr12-acetate cluster with various models, derived from the reported crystal structure. 4 The best fit is obtained when including the oxygen and carbon atoms from the acetate ligands. The refined parameters are given in Table S1 Figure 5: PDF refinement for Zr12-butanoate and Zr12-octanoate using the Zr12-acetate structure model. PDF refinement of Zr6- methylbutanoate using the Zr6-acetate structure model. Finally, the PDF refinement of Zr12-oleate using the Zr12-propionate structure model, with or without background correction in reciprocal space. If applied in the refinement, the exponentially dampening sine wave is shown (orange dotted lines). The refined parameters are given in Table S3. Figure 6: FTIR spectra of Zr12-acetate, -propionate, -hexanoate, -oleate and Zr6-methylheptanoate. The weak band at 1750 cm-1 in the spectrum of Zr12-acetate is assigned to a small amount of acetic acid that is not involved in hydrogen bonding of any kind. 71<br> An ester impurity is ruled out because of the absence of any signal around 4 ppm in NMR, (see Figure S10). Figure 7: (A) NMR spectra in CDCl3 of Zr12-acetate, -propionate, -hexanoate, -oleate and Zr6-methylheptanoate. (B) DOSY of the Zr12-acetate cluster with one faster diffusing species and a set of three resonances pertaining to a slowly diffusing species (the cluster) Figure 8: ESI-HR-MS analysis of the dimeric Zr12-butanoate cluster and of the monomeric Zr6-methylbutanoate cluster. Both the ex- perimental and simulated spectra are shown. Figure 10: (A) PDF fit for Hf12-acetate, Hf6-methylbutanoate and Hf12-oleate clusters with exponentially dampening sine wave con- tribution. The refined parameters are indicated in Table S9. (B) FTIR spectra of the hafnium oxo clusters synthesized via bottom up. Figure 11: Catalytic esterification of oleic acid with ethanol, catalyzed by either Zr12-oleate (green) or ZrO2 nanoparticles (gray). In both cases, 10 mol% Zr, with respect to the carboxylic acid substrate, was added.
description: Grants: NCCR molecular systems engineering (182895) SNF Eccelenza funding scheme (194172)
DOI: 10.5281/zenodo.7373014
title: Data for 'Fatty acid capped, metal oxo clusters as smallest conceivable nanocrystal prototypes'

description: The <em>.pxp</em> documents contain the experimental data of the figures in the manuscript and they can be opened/edited with the software IGOR Pro 8.0 or higher. Figure 3: Experimental PDF of zirconium oxo clusters with different capping ligands. The C-C, Zr-O, and Zr-Zr distances are assigned. We make a distinction between the Zr-Zr distances within one Zr6 cluster and the Zr-Zr distances that are characteristic for the dimer Figure 4: PDF refinement of the Zr12-acetate cluster with various models, derived from the reported crystal structure. 4 The best fit is obtained when including the oxygen and carbon atoms from the acetate ligands. The refined parameters are given in Table S1 Figure 5: PDF refinement for Zr12-butanoate and Zr12-octanoate using the Zr12-acetate structure model. PDF refinement of Zr6- methylbutanoate using the Zr6-acetate structure model. Finally, the PDF refinement of Zr12-oleate using the Zr12-propionate structure model, with or without background correction in reciprocal space. If applied in the refinement, the exponentially dampening sine wave is shown (orange dotted lines). The refined parameters are given in Table S3. Figure 6: FTIR spectra of Zr12-acetate, -propionate, -hexanoate, -oleate and Zr6-methylheptanoate. The weak band at 1750 cm-1 in the spectrum of Zr12-acetate is assigned to a small amount of acetic acid that is not involved in hydrogen bonding of any kind. 71<br> An ester impurity is ruled out because of the absence of any signal around 4 ppm in NMR, (see Figure S10). Figure 7: (A) NMR spectra in CDCl3 of Zr12-acetate, -propionate, -hexanoate, -oleate and Zr6-methylheptanoate. (B) DOSY of the Zr12-acetate cluster with one faster diffusing species and a set of three resonances pertaining to a slowly diffusing species (the cluster) Figure 8: ESI-HR-MS analysis of the dimeric Zr12-butanoate cluster and of the monomeric Zr6-methylbutanoate cluster. Both the ex- perimental and simulated spectra are shown. Figure 10: (A) PDF fit for Hf12-acetate, Hf6-methylbutanoate and Hf12-oleate clusters with exponentially dampening sine wave con- tribution. The refined parameters are indicated in Table S9. (B) FTIR spectra of the hafnium oxo clusters synthesized via bottom up. Figure 11: Catalytic esterification of oleic acid with ethanol, catalyzed by either Zr12-oleate (green) or ZrO2 nanoparticles (gray). In both cases, 10 mol% Zr, with respect to the carboxylic acid substrate, was added.
description: Grants: NCCR molecular systems engineering (182895) SNF Eccelenza funding scheme (194172)
DOI: 10.6084/m9.figshare.21631910
title: ADV-2M ADCP-RBR.zip

description: 1.velocity and sediemnt concentration fluctuation measured by ADV 2.velocity and acoustic backscatter measured by ADCP 3.Sea pressure and turbidity measured by RBR
DOI: 10.6084/m9.figshare.21631910.v1
title: ADV-2M ADCP-RBR.zip

description: 1.velocity and sediemnt concentration fluctuation measured by ADV 2.velocity and acoustic backscatter measured by ADCP 3.Sea pressure and turbidity measured by RBR
DOI: 10.23729/2570b353-187a-488b-ac78-f8687f58a4f2
title: Bog Iron Nodules

description: The images are of freshwater lake iron concentrations (or nodules) that have been historically mined for their iron content, now just scientific curiosities. GTK is investigating whether they may be able to be used for recording environmental changes in Finnish lakes since the last Ice Age (preserving at least 100,000 years of Earth history). Data was used in the MineHeritage project (https://mineheritage-project.eu/) Juankoski leaflet, included in the preview dataset. Preview dataset found at https://doi.org/10.23729/0cb57bd7-1726-4efc-87f4-fc77b7e2adec . To obtain data, please contact fairdata-pas@gtk.fi .
DOI: 10.6084/m9.figshare.21632012
title: Klasse A

description: Klasse A
DOI: 10.6084/m9.figshare.21632012.v1
title: Klasse A

description: Klasse A
DOI: 10.25573/data.21411690
title: Investigating the Past and Future of the Greek-speaking Minorities of Southern Italy: Greko (Calabria)

description: Greko Case Study - June 2019 <br> This case study was completed in June 2019 as part of the Sustaining Minoritized Languages in Europe (SMiLE) Collaborative Research Awards, a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411690.v2
title: Investigating the Past and Future of the Greek-speaking Minorities of Southern Italy: Greko (Calabria)

description: Greko Case Study - June 2019 <br> This case study was completed in June 2019 as part of the Sustaining Minoritized Languages in Europe (SMiLE) Collaborative Research Awards, a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411690.v1
title: Greko Case Study - June 2019

description: This case study was completed in June 2019 as part of the Sustaining Minoritized Languages in Europe (SMiLE) Collaborative Research Awards, a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative.
DOI: 10.25573/data.21411705.v3
title: Measuring Effectiveness: A Study on Changes in Minority Language Use and Perception due to Revitalisation Efforts, with Evidence from North Frisian

description: North Frisian Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411705
title: Measuring Effectiveness: A Study on Changes in Minority Language Use and Perception due to Revitalisation Efforts, with Evidence from North Frisian

description: North Frisian Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411705.v2
title: Measuring Effectiveness:A Study on Changes in Minority Language Use andPerception due to Revitalisation Efforts, with Evidence from North Frisian

description: This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative.
DOI: 10.25573/data.21411699
title: Language, Economics, and the Politics of Transmission: Language Revitalization as Community Building in Occitania

description: Occitan Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411699.v2
title: Language, Economics, and the Politics of Transmission: Language Revitalization as Community Building in Occitania

description: Occitan Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411699.v1
title: Occitan Case Study - June 2019

description: This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative.
DOI: 10.25573/data.21411696
title: An nasc idir an teanga agus an pobal i gCorca Dhuibhne/The Intersection of Language and Community in Corca Dhuibhne

description: Oidhreacht Chorca Dhuibhne (Irish) Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411696.v2
title: An nasc idir an teanga agus an pobal i gCorca Dhuibhne/The Intersection of Language and Community in Corca Dhuibhne

description: Oidhreacht Chorca Dhuibhne (Irish) Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21411696.v1
title: Oidhreacht Chorca Dhuibhne (Irish) Case Study - June 2019

description: This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative.
DOI: 10.25573/data.21401244
title: Investigating the past and future of the Greek-speaking minorities of Southern Italy: Griko (Apulia)

description: Griko Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile
DOI: 10.25573/data.21401244.v2
title: Investigating the past and future of the Greek-speaking minorities of Southern Italy: Griko (Apulia)

description: Griko Case Study - June 2019 <br> This study was completed in June 2019 as part of a Collaborative Research Award from Sustaining Minoritized Languages in Europe (SMiLE), a project of the Smithsonian Center for Folklife and Cultural Heritage’s Language Vitality Initiative. <br> Link to the collection of case studies: https://doi.org/10.25573/data.c.6280911 <br> More information on the SMiLE project website: https://folklife.si.edu/smile