cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12731497.v1
title: Additional file 12 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 12: Dataset S6. Modification of centroid coordinates of cells in an Arabidopsis seed section for analysis with SR-Tesseler software.
DOI: 10.21942/uva.12568559
title: Corpus data for Early English modals

description: This dataset contains corpus material analysed for the PhD dissertation <i>Early English modals: Form, function, and analogy </i>by Sune Gregersen<i>. </i>The research project was carried out at the University of Amsterdam from 2015 to 2019 under the supervision of Prof. Olga Fischer.<br>The dissertation contains four interconnected studies on the development of the modals in Old English (<i>c.</i> AD 800–1100) and Middle English (<i>c.</i> AD 1100–1500). The corpus material in this dataset was used for these four studies. The data were gathered from a number of electronic corpora and repositories of Old and Middle English as well as historical and contemporary Danish texts.<br>The files in this dataset are organized into five folders. One of these (corpus) contains metadata. The remaining four folders (impersonal-modals, dare, can-may, mot) contain one or more files with concordances used for the four main chapters of the dissertation. The files are available in .xlsx and .csv format. For details about the analytical categories and information about the selection of material, please refer to the published dissertation.<br>
DOI: 10.21942/uva.12568559.v1
title: Corpus data for Early English modals

description: This dataset contains corpus material analysed for the PhD dissertation <i>Early English modals: Form, function, and analogy </i>by Sune Gregersen<i>. </i>The research project was carried out at the University of Amsterdam from 2015 to 2019 under the supervision of Prof. Olga Fischer.<br>The dissertation contains four interconnected studies on the development of the modals in Old English (<i>c.</i> AD 800–1100) and Middle English (<i>c.</i> AD 1100–1500). The corpus material in this dataset was used for these four studies. The data were gathered from a number of electronic corpora and repositories of Old and Middle English as well as historical and contemporary Danish texts.<br>The files in this dataset are organized into five folders. One of these (corpus) contains metadata. The remaining four folders (impersonal-modals, dare, can-may, mot) contain one or more files with concordances used for the four main chapters of the dissertation. The files are available in .xlsx and .csv format. For details about the analytical categories and information about the selection of material, please refer to the published dissertation.<br>
DOI: 10.5281/zenodo.4133350
title: A case study of wind farm effects using two wake parameterizations in WRF (V3.7) in the presence of low level jets

description: This repository contains necessary files for reproducing the simulations using WRF in Larsén and Fischereit (2020) - all included in the zipped file. The first group of files are the Namelists, which include the following files namelist.wps. namelist.input.NWF for simulations with no farms namelist.input.Fitch for simulations with farms using the default Fitch scheme for farm wakes namelist.input.EWP for simulations with farms using the EWP scheme for farm wakes The second group of files are the turbine files that need to be specified when simulating the farm wakes. In connection with Fitch scheme, the files are Windturbines.txt and Wind-turbine-*.tbl. In connection with EWP scheme, the files are *.turbine and all_farms_corr_2017.real. The turbine files are downloaded from https://www.wasp.dk/dataandtools#power-curves Finally, the geo_em.d0*.nc files and the table files for running WRF (Vtable.ERA5, METGRID.TBL, VEGPARM.TBL, LANDUSE.TBL, MPTABLE.TBL).
description: This study is supported by the Danish ForskEL/EUDP project "Large Scale Offshore Wake Impact on Danish Power System" (PSO-12521, EUDP 64017-0017)
DOI: 10.5281/zenodo.4118220
title: Research data for "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining"

description: This dataset supports the paper: "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining", available at the following DOI: 10.1039/d0sc03287e. The cleaned-up, coarse-grained, and re-scaled structures are provided here in both XYZ and CIF format. The data presented in the journal publication is also included; namely, MDS coordinates, T densities, and A-site heterogeneities for each structure in the dataset. T densities -- defined as: metals per unit volume (nm-3) -- are calculated using the re-scaled structures.
DOI: 10.5281/zenodo.4118219
title: Research data for "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining"

description: This dataset supports the paper: "Understanding the geometric diversity of inorganic and hybrid frameworks through structural coarse-graining", available at the following DOI: 10.1039/d0sc03287e. The cleaned-up, coarse-grained, and re-scaled structures are provided here in both XYZ and CIF format. The data presented in the journal publication is also included; namely, MDS coordinates, T densities, and A-site heterogeneities for each structure in the dataset. T densities -- defined as: metals per unit volume (nm-3) -- are calculated using the re-scaled structures.
DOI: 10.5281/zenodo.4131246
title: SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

description: Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitable for discovery-driven analyses of glycoproteomes. Therefore, we devised SugarPy, a glycan database independent Python module, and validated it on the glycoproteome of human breast milk. We further demonstrated its applicability by analyzing glycoproteomes with uncommon glycans stemming from the green algae <em>Chlamydomonas reinhardtii </em>and the archaeon <em>Haloferax volcanii</em>. SugarPy also facilitated the novel characterization of glycoproteins from the red alga <em>Cyanidioschyzon merolae</em>. Provided here are, for each species: input files (mzML) SugarPy result files In addition, for <em>Homo sapiens</em> and <em>Chlamydomonas reinhardtii</em>, the following is included: SugarQb result files pGlyco result files MSFragger-Glyco result files Furthermore, a SugarPy example_data folder is provided that can be used with the SugarPy example scripts. The source code for SugarPy can be found on GitHub: https://github.com/SugarPy/SugarPy
DOI: 10.5281/zenodo.4126117
title: 1D and 2D NMR spectra of coffee from 27 countries

description: 715 green coffee samples were gathered by Almacafé S.A. (Bogotá, Colombia) between 2012 and 2014 from 27 different countries and analyzed at the Nuclear Magnetic Resonance (NMR) laboratory at Universidad del Valle (Cali, Colombia). Over 1000 methanolic coffee extracts were prepared and a total of 4563 spectra were acquired in fully automatic mode using a 400MHz NMR spectrometer (Bruker Biospin, Germany). The dataset spans the variance that could be expected for an industrial application of origin monitoring, including samples from different harvest time, collected over several years and processed by at least two distinct operators. The resulting 1D and 2D spectra can be used to develop and evaluate feature extraction methods, multivariate algorithms and automation monitoring techniques, as a dataset for teaching, or as a reference for new studies on similar samples and approach.
DOI: 10.5281/zenodo.4131245
title: SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

description: Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitable for discovery-driven analyses of glycoproteomes. Therefore, we devised SugarPy, a glycan database independent Python module, and validated it on the glycoproteome of human breast milk. We further demonstrated its applicability by analyzing glycoproteomes with uncommon glycans stemming from the green algae <em>Chlamydomonas reinhardtii </em>and the archaeon <em>Haloferax volcanii</em>. SugarPy also facilitated the novel characterization of glycoproteins from the red alga <em>Cyanidioschyzon merolae</em>. Provided here are, for each species: input files (mzML) SugarPy result files In addition, for <em>Homo sapiens</em> and <em>Chlamydomonas reinhardtii</em>, the following is included: SugarQb result files pGlyco result files MSFragger-Glyco result files Furthermore, a SugarPy example_data folder is provided that can be used with the SugarPy example scripts. The source code for SugarPy can be found on GitHub: https://github.com/SugarPy/SugarPy
DOI: 10.5281/zenodo.4130999
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Richard Pyle, https://orcid.org/0000-0003-0768-1286. Claims were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.6084/m9.figshare.13142777
title: The unprecedented outbreak of dengue in Singapore, a dataset of geographical dengue clusters covering the nationwide lockdown period in 2020

description: Dengue, a mosquito-transmitted viral disease, has posed a public health challenge to Singaporean residents over the years. In 2020, Singapore has been experiencing an unprecedented dengue outbreak. We collect a dataset of geographical dengue clusters reported by the National Environment Agency (NEA) from 15 Feb to 9 July in 2020, covering the nationwide lockdown period from 7 April to 1 June for controlling the pandemics of COVID-19. NEA regularly updates the dengue clusters where each infected person is tagged to one cluster based on his/her most probably infection location (residential apartment or workplace address). Each cluster is further matched to fine-grained spatial units termed as subzones with an average coverage of only about 1.35 km<sup>2</sup>. Such dengue cluster dataset helps reveal not only the dengue transmission pattern, but also the effects of lockdown on dengue spreading dynamics to a certain extent. The resulting data records are released in simple formats for easy access to facilitate studies on dengue epidemics.
DOI: 10.5281/zenodo.4118190
title: Dataset: Relativistic EOM-CCSD for core-excited and core-ionized state energiesbased on the 4-component Dirac-Coulomb(-Gaunt) Hamiltonian

description: This dataset collects the unprocessed (= outputs from calculations) and processed (jupyter notebooks) results discussed in the paper titled "Relativistic EOM-CCSD for core-excited and core-ionized state energies based on the 4-component Dirac-Coulomb(-Gaunt) Hamiltonian", by Loïc Halbert, Marta Lopez Vidal, Avijit Shee, Sonia Coriani and Andre Severo Pereira Gomes. It also contains the figures used in the manuscript.
description: ASPG and LH acknowledge support from PIA ANR project CaPPA (ANR-11-LABX-0005-01), the Franco-German project CompRIXS (Agence nationale de la recherche ANR-19-CE29-0019, Deutsche Forschungsgemeinschaft JA 2329/6-1), I-SITE ULNE projects OVER-SEE and MESONM International Associated Laboratory (LAI) (ANR-16-IDEX-0004), the French Ministry of Higher Education and Research, region Hautsde France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, and the French national supercomputing facilities (grants DARI A0050801859, A0070801859). MLV and SC acknowledge support from DTU Chemistry (start-up Ph.D. grant).MLV acknowledges support from COST (CM1405)
DOI: 10.6084/m9.figshare.13142774
title: High Coral Bycatch in Bottom-set Gillnet Coastal Fisheries Reveals Rich Coral Habitats in Southern Portugal_data.xlsx

description: Bottom-contact fisheries are unquestionably one of the main threats to the ecological integrity and functioning of deep-sea and circalittoral ecosystems, notably cold-water corals (CWC) and coral gardens. Lessons from the destructive impact of bottom trawling highlight the urgent need to understand how fisheries affect these vulnerable marine ecosystems. At the same time, the impact of other fishing gear and Small-Scale Fisheries (SSF) remains sparsely known despite anecdotal evidence suggesting their impact may be significant. This study aims to provide baseline information on coral bycatch by bottom-set gillnets used by artisanal fisheries in Sagres (Algarve, southwestern Portugal), thereby contributing to understand the impact of the activity but also the diversity and abundance of corals in this region. Coral bycatch frequency and species composition were quantified over two fishing seasons (summer-autumn and spring) for 42 days. The relationship with fishing effort was characterized according to métiers (n=6). The results showed that 85% of the gillnet deployments caught corals. The maximum number of coral specimens per net was observed in a deployment targeting Lophius budegassa (n=144). In total, 4,326 coral fragments and colonies of 23 different species were captured (fishing depth range of 57-510m, mean 139±8m). The most affected species were Eunicella verrucosa (32%), Paramuricea grayi (29%), Dendrophyllia cornigera (12%) and Dendrophyllia ramea (6%). The variables found to significantly influence the amount of corals caught were the target species, net length, depth and mesh size. The 22 species of corals caught as bycatch belong to Orders Alcyonacea (80%), Scleractinia (18%), Zoantharia (1%) and Antipatharia (1%), corresponding to around 13% of the coral species known for the Portuguese mainland coast. These results show that the impact of artisanal fisheries on circalittoral coral gardens and CWC is potentially greater than previously appreciated, which underscores the need for new conservation measures and alternative fishing practices. Measures such as closure of fishing areas, frequent monitoring onboard of fishing vessels or the development of encounter protocols in national waters is a good course of action. This study highlights the rich coral gardens of Sagres and how artisanal fisheries can pose significant threat to corals habitats in certain areas.
DOI: 10.6084/m9.figshare.13142774.v2
title: High Coral Bycatch in Bottom-set Gillnet Coastal Fisheries Reveals Rich Coral Habitats in Southern Portugal_data.xlsx

description: Bottom-contact fisheries are unquestionably one of the main threats to the ecological integrity and functioning of deep-sea and circalittoral ecosystems, notably cold-water corals (CWC) and coral gardens. Lessons from the destructive impact of bottom trawling highlight the urgent need to understand how fisheries affect these vulnerable marine ecosystems. At the same time, the impact of other fishing gear and Small-Scale Fisheries (SSF) remains sparsely known despite anecdotal evidence suggesting their impact may be significant. This study aims to provide baseline information on coral bycatch by bottom-set gillnets used by artisanal fisheries in Sagres (Algarve, southwestern Portugal), thereby contributing to understand the impact of the activity but also the diversity and abundance of corals in this region. Coral bycatch frequency and species composition were quantified over two fishing seasons (summer-autumn and spring) for 42 days. The relationship with fishing effort was characterized according to métiers (n=6). The results showed that 85% of the gillnet deployments caught corals. The maximum number of coral specimens per net was observed in a deployment targeting Lophius budegassa (n=144). In total, 4,326 coral fragments and colonies of 23 different species were captured (fishing depth range of 57-510m, mean 139±8m). The most affected species were Eunicella verrucosa (32%), Paramuricea grayi (29%), Dendrophyllia cornigera (12%) and Dendrophyllia ramea (6%). The variables found to significantly influence the amount of corals caught were the target species, net length, depth and mesh size. The 22 species of corals caught as bycatch belong to Orders Alcyonacea (80%), Scleractinia (18%), Zoantharia (1%) and Antipatharia (1%), corresponding to around 13% of the coral species known for the Portuguese mainland coast. These results show that the impact of artisanal fisheries on circalittoral coral gardens and CWC is potentially greater than previously appreciated, which underscores the need for new conservation measures and alternative fishing practices. Measures such as closure of fishing areas, frequent monitoring onboard of fishing vessels or the development of encounter protocols in national waters is a good course of action. This study highlights the rich coral gardens of Sagres and how artisanal fisheries can pose significant threat to corals habitats in certain areas.
DOI: 10.6084/m9.figshare.13142774.v1
title: High Coral Bycatch in Bottom-set Gillnet Coastal Fisheries Reveals Rich Coral Habitats in Southern Portugal_data.xlsx

description: Bottom-contact fisheries are unquestionably one of the main threats to the ecological integrity and functioning of deep-sea and circalittoral ecosystems, notably cold-water corals (CWC) and coral gardens. Lessons from the destructive impact of bottom trawling highlight the urgent need to understand how fisheries affect these vulnerable marine ecosystems. At the same time, the impact of other fishing gear and Small-Scale Fisheries (SSF) remains sparsely known despite anecdotal evidence suggesting their impact may be significant. This study aims to provide baseline information on coral bycatch by bottom-set gillnets used by artisanal fisheries in Sagres (Algarve, southwestern Portugal), thereby contributing to understand the impact of the activity but also the diversity and abundance of corals in this region. Coral bycatch frequency and species composition were quantified over two fishing seasons (summer-autumn and spring) for 42 days. The relationship with fishing effort was characterized according to métiers (n=6). The results showed that 85% of the gillnet deployments caught corals. The maximum number of coral specimens per net was observed in a deployment targeting Lophius budegassa (n=144). In total, 4,326 coral fragments and colonies of 23 different species were captured (fishing depth range of 57-510m, mean 139±8m). The most affected species were Eunicella verrucosa (32%), Paramuricea grayi (29%), Dendrophyllia cornigera (12%) and Dendrophyllia ramea (6%). The variables found to significantly influence the amount of corals caught were the target species, net length, depth and mesh size. The 22 species of corals caught as bycatch belong to Orders Alcyonacea (80%), Scleractinia (18%), Zoantharia (1%) and Antipatharia (1%), corresponding to around 13% of the coral species known for the Portuguese mainland coast. These results show that the impact of artisanal fisheries on circalittoral coral gardens and CWC is potentially greater than previously appreciated, which underscores the need for new conservation measures and alternative fishing practices. Measures such as closure of fishing areas, frequent monitoring onboard of fishing vessels or the development of encounter protocols in national waters is a good course of action. This study highlights the rich coral gardens of Sagres and how artisanal fisheries can pose significant threat to corals habitats in certain areas.
DOI: 10.5281/zenodo.4114109
title: Slip model and dataset - A stochastic view of the 2020 Elazig Mw 6.8 earthquake (Turkey)

description: This repository contains files describing the slip model and data published in "A stochastic view of the 2020 Elazig Mw 6.8 earthquake (Turkey)" by T. Ragon et al. The slip model has been inferred with a Bayesian approach (AlTar), assuming a complex fault geometry with triangular subfaults and layered crustal structure, and accounting for epistemic uncertainties.<br> The slip model and dataset are extensively described in the publication. Description of the files:<br> &gt; Slip model<br> - elazig_sigma_dip.dat : Standard deviation of the slip in the along-strike direction<br> - elazig_sigma_stk.dat : Standard deviation of the slip in the along-dio direction<br> - elazig_slip.dat : Total slip amplitude <br> - elazig_slip_dip.dat : Slip amplitude in the along-dip direction<br> - elazig_slip_stk.dat : Slip amplitude in the along-strike direction <br> - elazig_slipdir.dat : Vectors for the rake<br> &gt; Data<br> - elazig_A116_data_rect.dat : downsampled surface displacement for the Sentinel 1A asc. interferogram<br> - elazig_A182_data_rect.dat : downsampled surface displacement for the ALOS 2 asc. interferogram<br> - elazig_A182_po_data_rect.dat : downsampled surface displacement for the ALOS 2 pixel offset ascending track<br> - elazig_D077_data_rect.dat : downsampled surface displacement for the ALOS 2 dsc. interferogram<br> - elazig_D077_po_data_rect.dat : downsampled surface displacement for the ALOS 2 pixel offset descending track<br> - elazig_D123_data_rect.dat : downsampled surface displacement for the Sentinel 1A dsc. interferogram<br> - elazig_gps_data.dat : GPS data The format of all *slip* and *sigma* files at the exception of 'elazig_slipcenterll.dat' and 'elazig_slipdir.dat' is as follow:<br> &gt; -Z[ slip amplitude ] # [subault index 1] [subfault index 2] 9999999 # [ strike slip amplitude] [dip slip amplitude] 0.0 <br> [longitude] [latitude] [depth of point 1]<br> [longitude] [latitude] [depth of point 2]<br> [longitude] [latitude] [depth of point 3] The format of all inteferograms and PO files is as follow:<br> &gt; -Z[surface displacement in the LOS or azimuth direction]<br> [lon] [lat for NW corner]<br> [lon] [lat for NE corner]<br> [lon] [lat for SE corner]<br> [lon] [lat for SW corner]<br> [lon] [lat for NW corner]