cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26050/wdcc/pmmxmchtd
title: PalMod2 MPI-M MPI-ESM1-2-CR-CH4 transient-deglaciation-prescribed-glac1d-methane

description: Project: PalMod2 - From the last interglacial to the anthropocene - modeling a complete glacial cycle. The PalMod project (https://www.palmod.de/) aims for a better understanding of how slow feedbacks in the Earth system operate. Using the new insights into Earth system dynamics, PalMod will also make projections of the future climate over the next few millennia. The project PalMod is in the second phase. Summary: For transient-deglaciation-prescribed-glac1d-methane (r1i1p1f1): The transient experiment was performed with the Max Planck Institute for Meteorology Earth System Model version 1.2 in coarse resolution (MPI-ESM-CR). The model includes the spectral atmospheric model ECHAM6.3 at T31 horizontal resolution (approx. 3.75°) and 31 vertical levels, the land surface vegetation model JSBACH3.2, and the primitive equation ocean model MPIOM1.6 with a nominal resolution of 3°. The model has been extended with a full methane cycle, including a simplified atmospheric chemistry, as described in Kleinen et al. (2020), Kleinen et al. (2021) and Kleinen et al. (2022). For the experiment, the model was integrated from a glacial state at 23 ka to the year 1950 with prescribed atmospheric greenhouse gas concentrations (Köhler et al., 2017) and insolation (Berger & Loutre, 1991). Ice sheets and surface topographies were prescribed from GLAC-1D (Tarasov et al., 2012) reconstructions. All forcing fields are updated every 10 years of the simulations and initiate changes in the topography, glacier mask, river pathways, ocean bathymetry, and land-sea mask. For transient-deglaciation-prescribed-glac1d-methane (r1i1p1f2): This experiment is derived from the r1i1p1f1 experiment. It is branched off at 18 ka BP, and starting at 15.2 ka BP, meltwater from the Laurentide ice sheet was removed from the system and stored. The accumulated meltwater was released over a period of 1200 years starting at 12.8 ka BP. This induced a collapse of the AMOC, leading to climatic conditions very similar to the Younger Dryas cold period seen in climate reconstructions. After the end of the meltwater release, the circulation recovered quickly and climatic conditions converged with the r1i1p1f1 experiment. Important: Please be aware that due to CMORization constraints data set time values concerning to "Before Present(BP)" time got a year offset (+25001). Means for example year range 2001 to 25000 model time is equal to 23000 to 1 BP.
DOI: 10.4121/e32a9868-c5ea-43d3-8969-b1908662b2b2
title: Simulation data and code underlying the publication: Free-vortex models for wind turbine wakes under yaw misalignment – a validation study on far-wake effects

description: Code and simulation results for a validation study comparing three free-vortex wake models for wind turbine control optimisation.<br>The free-vortex wake models for simulating the wind turbine wake are provided as Julia code. The associated data is presented in the publication demonstrating the validation of the models for predicting downwind dynamics of wind turbine wakes under yaw misalignment.<br>Model code and simulation data supporting the paper "Free-vortex models for wind turbine wakes under yaw misalignment – a validation study on far-wake effects"
DOI: 10.5067/aura/mls/data1502
title: MLS/Aura L1 Radiances from Digital Autocorrelators V005
DOI: 10.5281/zenodo.4073035
title: Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1

description: The tables in this dataset associate metabarcoding sequencing files generated by Genoscope (i.e. fastq.gz files with informative filename structures; with sequencing file pairs associated to unique 'readset' identifiers; housed on their FTP server at www.genoscope.cns.fr/sadc/tarapacific/METABARCODING; with the 'METAB' sequence strategy identifier as part of the sequencing file name) with their associated 'sample-id_source' identifier; as detailed in the 'TARA-PACIFIC_samples-provenance' file part of the 'Tara Pacific samples provenance and environmental context' Zenodo publication (DOI: 10.5281/zenodo.4068292) part of the 'tarapacific' Zenodo community). The main purpose of these tables is to act as a reference to identify samples (i.e., with a single 'sample-id_source') for which sequencing replication exists, per primer set (i.e., more than one set of fastq.gz sequencing files were generated, pre primer set). In the case of replication, these tables classify the replication into three classes color coded as green (same DNA extraction, same PCR, same sequencing run, different sequencing lane), yellow (same DNA extraction, same PCR, different sequencing run) and red (different DNA extraction and/or different PCR). It should be noted that in the vast majority of cases a 'sample-id_source' associates to only one readset per primer set. For a full description of the dataset, please see the included README.
description: Special thanks to the Tara Ocean Foundation, the R/V Tara crew and the Tara Pacific Expedition Participants (https://doi.org/10.5281/zenodo.3777760). We are keen to thank the commitment of the following institutions for their financial and scientific support that made this unique Tara Pacific Expedition possible: CNRS, PSL, CSM, EPHE, Genoscope, CEA, Inserm, Université Côte d'Azur, ANR, agnès b., UNESCO-IOC, the Veolia Foundation, the Prince Albert II de Monaco Foundation, Région Bretagne, Billerudkorsnas, AmerisourceBergen Company, Lorient Agglomération, Oceans by Disney, L'Oréal, Biotherm, France Collectivités, Fonds Français pour l'Environnement Mondial (FFEM), Etienne Bourgois, and the Tara Ocean Foundation teams. Tara Pacific would not exist without the continuous support of the participating institutes. The authors also particularly thank Serge Planes, Denis Allemand, and the Tara Pacific consortium.
description: {"references": ["Pesant et al., 2020. Tara Pacific samples provenance and environmental context - version 1 (Version version 1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4068293"]}
DOI: 10.5281/zenodo.6511406
title: TARA Pacific Bleaching Prevalence of Sampling Sites (Islands)

description: <strong>Summary</strong> To obtain a proxy for the stress level of collected corals, we checked for previous occurrences of bleaching events at sampled reef sites by matching island GPS coordinates to the Reef Check dataset (reefcheck.org) obtained from Sully et al (2019). For each Tara Pacific island coordinate, we determined the Reef Check site that was closest (in terms of distance in km); we only considered Reef Check data that was within a 10 km circumference. We further determined short- and long-term climate variables that are known to affect coral stress resilience for all <em>Tara</em> Pacific collection sites that are available from Lombard et al (2022). These data allow to assess if corals from a given site were exposed higher/lower prevalence of thermal stress events and bleaching prior to sampling (over previous years). <strong>References</strong> Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. <em>Nature Communications</em> <strong>10</strong>, 1264 (2019). Fabien Lombard, Guillaume Bourdin, Stephane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar, Megan Clampitt, Pascal Conan, Ophélie Da Silva, Celine Dimier, Eric Douville, Amanda Elineau, Jonathan Fin, J. Michel Flores, Jean François Ghiglione, Benjamin C.C. Hume, Laetitia Jalabert, Seth G. John, Rachel L. Kelly, Ilan Koren, Yajuan Lin, Dominique Marie, Ryan McMinds, Zoé Mériguet, Nicolas Metzl, David A. Paz-García, Maria Luiza Pedrotti, Julie Poulain, Mireille Pujo-Pay, Josephine Ras, Gilles Reverdin, Sarah Romac, Eric Röttinger, Assaf Vardi, Christian R. Voolstra, Clémentine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Colomban de Vargas, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Emmanuel Boss, Gaby Gorsky. Open science resources from the Tara Pacific expedition across the surface ocean and coral reef ecosystems. <em>Submitted</em> (2022)
DOI: 10.5281/zenodo.6619313
title: Output data and namelist - README file of "Evolution of squall line variability and error growth in an ensemble of LES'

description: See README.txt
description: Currently, the README file is also available at: https://irods-web.zdv.uni-mainz.de/irods-rest/rest/fileContents/zdv/project/m2_jgu-w2w/w2w-a1/EG_HT_2022_squall_line_var/README.txt?ticket=tfKfvC272uyo1WC https://tinyurl.com/groot-tost-22
DOI: 10.5281/zenodo.7324981
title: Functional annotation of the reference transcriptome of Dinophysis ovum strain DoSS3195

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.
description: Funded by NOAA/ECOHAB: NA19NOS4780182-722372-712683
DOI: 10.5281/zenodo.7325007
title: Functional annotation of the reference transcriptome of Dinophysis acuminata strain DAVA01

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.
description: Funded by NOAA/ECOHAB: NA19NOS4780182-722372-712683
DOI: 10.5281/zenodo.7325017
title: Functional annotation of the reference transcriptome of Mesodinium rubrum strain MBL-DK2009

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.
description: Funded by NOAA/ECOHAB: NA19NOS4780182-722372-712683
DOI: 10.5281/zenodo.7325044
title: Functional annotation of the reference transcriptome of Teleaulax amphioxeia

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.
description: Funded by NOAA/ECOHAB: NA19NOS4780182-722372-712683
DOI: 10.5281/zenodo.7589824
title: SP2 measurement error of BC mixing state and radiative forcing evaluation

description: The first version of dataset.
DOI: 10.5281/zenodo.7629669
title: Dataset of "Divergent convective outflow in large eddy simulations "

description: See README.txt See download_all_simulations.sh
DOI: 10.5281/zenodo.7887565
title: LegacyClimate 1.0: a dataset of pollen-based climate reconstructions from 2594 Northern Hemisphere sites covering the last 30 kyr and beyond

description: This repository consists of code to run the climate reconstruction from fossil pollen data for an example site based on the R-rioja package. The input data includes harmonized open-access modern and fossil pollen datasets so that customized reconstructions can be easily established. Supplement to: Herzschuh, U., Böhmer, T., Li, C., Chevalier, M., Dallmeyer, A., Cao, X., Bigelow, N. H., Nazarova, L., Novenko, E. Y., Park, J., Peyron, O., Rudaya, N. A., Schlütz, F., Shumilovskikh, L. S., Tarasov, P. E., Wang, Y., Wen, R., Xu, Q., and Zheng, Z.: LegacyClimate 1.0: A dataset of pollen-based climate reconstructions from 2594 Northern Hemisphere sites covering the late Quaternary, Earth Syst. Sci. Data Discuss. [preprint], https://doi.org/10.5194/essd-2022-38, in review, 2022.
DOI: 10.6084/m9.figshare.21185362
title: A new EEG database for the cognitive assessment of motor imagery during walking with a lower-limb exoskeleton. DECODED: a EUROBENCH subproject

description: Check the Scientific Data paper once published
DOI: 10.18430/m37mmz
title: X-ray diffraction data for the crystal Structure of Acetyl-coenzyme A synthetase from Legionella pneumophila Philadelphia 1 in complex with ethyl-AMP (7MMZ)
DOI: 10.3886/e183721v4
title: Investigating the Prevalence of Gastrointestinal Symptomology Following Receipt of the COVID-19 Vaccine

description: The coronavirus disease of 2019 (COVID-19) pandemic presented novel and devastating conditions for both the general and high-risk populations. SARS-CoV-2 is known to affect the respiratory tract, however studies have reveals that changes in gastrointestinal (GI) symptomology are also a prevalent side effect. Although the COVID-19 vaccine has been able to alleviate some of the tumultuous circumstances, there is limited research on the lesser-known side effects experienced following receipt of the COVID-19 vaccination.<br>This study investigated the association between the COVID-19 vaccination and, when applicable, the contraction of acute COVID-19 infection, and resulting onset and/or changes in GI symptomology. The focus of the study was on both the general population and on those previously diagnosed with GI disorders, such as Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD), the latter defined as a special needs population.<br>Through a short, anonymous survey, 215 participants were assessed for acute onset of GI issues and/or worsening of pre-existing GI issues following the receipt of one or more COVID-19 vaccine doses and, when it occurred, following contraction of a COVID-19 infection. Participants were requested to report demographic variables as well as descriptive statistics regarding side effects experienced post-COVID-19 vaccination and post-COVID-19 infection, when applicable. All analyses were performed using SAS version 9.4 and ANOVA was conducted for each survey item to assess for statistically significant differences between the groups, indicated by an omnibus p-value less than 0.05.<br>The resulting database demonstrates the prevalence of side effects following receipt of the COVID-19 vaccination to gain an understanding of how both the general and high-risk populations are being affected by the COVID-19 vaccine and booster doses.
description: Response Rates: Inclusion criteria: having received at least one COVID-19 vaccination<br>Exclusion criteria: not having received at least one COVID-19 vaccination
description: Convenience sampling to collect de-identified survey data from participants who had received at least one COVID-19 vaccination
description: web-based survey;
DOI: 10.5281/zenodo.7325034
title: Functional annotation of the reference transcriptome of Mesodinium rubrum strain JAMR

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.
description: Funded by NOAA/ECOHAB: NA19NOS4780182-722372-712683
DOI: 10.5281/zenodo.7945369
title: Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs"

description: Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs" (https://doi.org/10.5281/zenodo.7927968), recommended by PCI Evol Biol (https://evolbiol.peercommunityin.org/articles/rec?id=651)
DOI: 10.15148/3db37fdf-46b1-4e7a-bd86-ca4fb93307e1
title: Forest biomass loss by fire 2020-2022 in France

description: We estimated the loss of biomass in the forests during the fire season over the period 2020-2022. This estimate is based on a fine resolution method from BAMTs fire polygon, tree height from Schwartz et al. (2022) and NFI data. In comparison, we extracted biomass data based on tree heights calculated by Potapov, from ESA CCI Biomass data and from the GFED framework by Van wees et al. (2022)
DOI: 10.5281/zenodo.7378956
title: Electronic invoicing: an analysis of its implementation in micro and small businesses in Lima, Peru.

description: he implementation of electronic taxation systems helps every company to be able to control, verify and simplify its tax operations. It allows them to manage all their obligations in a faster and more efficient way.<br> To find out, from the accountants' perspective, what attitudes, practices and compliance with tax obligations are being carried out as a result of the implementation of electronic invoicing. Likewise, to note the benefits it has brought to MYPES during COVID-19 in Peru.<br> Applied research with a quantitative and non-experimental approach. The sample consisted of 384 accountants who manage taxation in their respective companies in Metropolitan Lima, to whom a questionnaire was applied as a data collection instrument.<br> The sample indicates that the use of an electronic emission system helps to combat tax evasion (9.6%), cumbersome tax audits (38.8%), informality (9.4), falsification of payment vouchers (8.9), loss and deterioration of payment vouchers (9.1%), informality (8.3%). They also consider that the use of this type of system has facilitated processes (96.6%), reduced costs (96.4%), reduced paper (96.9%) and made administrative and accounting operations much faster (97.4%).<br> It is evident that the sample is in favour of the implementation with an electronic tax system in their business. This new system would be a promising means to help businesses voluntarily comply with their tax obligations. In turn, it generates a positive effect on tax collection and compliance levels.<br> Keywords: Electronic system, tax obligations, electronic vouchers, electronic invoicing, taxes.
DOI: 10.5281/zenodo.7324781
title: Dataset to train, validate and reconstruct POC over the global ocean for 2009-2013 based on PlankTOM12

description: The distribution of in situ UVP5 measurements over the period 2009-2013 was used to create synthetic data by sampling a global biogeochemical ocean model PlankTOM12 at UVP5 time and location. The synthetic data set is used to train, validate and test Machine Learning methods to reconstruct particulate organic carbon concentration. These data are part of publication at the GMD.
DOI: 10.5281/zenodo.7728616
title: ChronoLoess Database

description: ChronoLoess database files
description: SK was supported by the DFG Heisenberg programme in 2023 (project id: 505822867)
DOI: 10.5281/zenodo.7741131
title: Model data and code supporting "Updated Isoprene and Terpene Emission Factors for the Interactive BVOC Emission Scheme (iBVOC) in the United Kingdom Earth System Model (UKESM1.0) "

description: Model data and analysis code supporting the Geoscientific Model Development manuscript "Updated Isoprene and Terpene Emission Factors for the Interactive BVOC Emission Scheme (iBVOC) in the United Kingdom Earth System Model (UKESM1.0) "
DOI: 10.6084/m9.figshare.21295352
title: Curated and harmonized gut microbiome 16S rRNA amplicon sequences, metadata, and OTU tables from dietary fiber intervention studies in humans

description: Data associated with the <em>Scientific Data </em>Data Descriptor " Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans". Please see the Data Descriptor for an detailed description.
DOI: 10.1285/i20356609v14i1p396
title: Contemporary Urban Commons. Rebuilding the Analytical Framework

description: The article contributes to the understanding of contemporary urban commons by developing a renewed analytical framework which approaches them as dynamic configurations. By investigating different types of urban commons in Italy, the article disentangles the notion of urban commons along two axes that take into account their relationship with both local institutions and the surrounding environment. The combination of these two axes produces four possible configurations that allow to grasp the complexity of urban commons, accounting for their multifaceted and at times controversial nature. Moreover, this article identifies three functions that urban commons can perform in the contemporary European cities: as resilient spaces, as reclaimed spaces incorporated into capitalistic models of urban development, or contentious and transformative spaces that combine social reproduction with anti-capitalistic politics. The article is based on qualitative research and participant observation grounded on extensive fieldwork in various urban commons across Italy between 2016 and 2019.