cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17250347
title: Dataset 1: Genomic assemblies and annotations of Coffea species and subgenomes

description: This dataset contains filtered genome assemblies and corresponding GFF3 annotation files for Coffea species. The original assemblies and annotations were obtained from public repositories:

Coffea arabica ET-39 – NCBI: GCF_036785885.1Coffea arabica Caturra – NCBI: GCA_003713225.1Coffea arabica Bourbon – NCBI: GCA_030873655.1Coffea arabica Gesha – Zenodo: https://zenodo.org/records/10059814Coffea arabica Typica – Figshare: https://figshare.com/articles/dataset/b_A_chromosome-level_genome_assembly_of_b_b_Coffea_arabica_b_b_L_var_Kona_Typica_b/28425329/2Coffea eugenioides CCC68 – NCBI: GCA_003713205.1Coffea humblotiana – NCBI: GCA_023065735.1Coffea canephora – NCBI: GCA_900059795.1

After obtaining the assemblies from public repositories, filters were applied to retain only chromosomes and contigs ≥500 kb for all species and cultivars. For Coffea arabica (cultivars Gesha, Caturra, Bourbon, ET-39, and Typica), the assemblies were additionally separated into subgenomes. The corresponding GFF3 annotation files were also filtered to match the retained chromosomes/contigs. Subsequently, the filtered GFF3 files were processed with the AGAT toolkit to generate new longest isoform GFF3 annotation files. Using these longest GFF3 files together with the filtered genomes, protein and CDS sequences were extracted in AGAT. For Coffea arabica Bourbon and Coffea humblotiana, no GFF3 annotations were available, but their genome assemblies were filtered in the same way as for the other species.



Genome file extension = .fasta | Annotation file extension = .gff3 | Protein file extension = .faa | CDS file extension = .fna 

Scripts used for AGAT processing are available at: https://github.com/daisysotero/Coffea-analyses-2025

sgC = canephora-derived subgenome | sgE = eugenioides-derived subgenome
DOI: 10.5281/zenodo.18506530
title: Evolutionary History of LRRK2 and PRKN in Leprosy and Parkinson's Disease
DOI: 10.5281/zenodo.18506529
title: Evolutionary History of LRRK2 and PRKN in Leprosy and Parkinson's Disease
DOI: 10.5281/zenodo.17251360
title: Dataset 2: Genomic assemblies and annotations of Coffea species and subgenomes

description: This dataset contains genome assemblies and corresponding annotation files for various Coffea species. The genomic data were retrieved from public repositories and underwent standardization and validation to ensure consistency across files. Genome assemblies were filtered to retain chromosomes and contigs ≥500 kb. For Coffea arabica, assemblies were further separated into subgenomes derived from Coffea canephora and Coffea eugenioides. Filtered GFF3 files matching these sequences were processed with the AGAT toolkit to generate longest isoform annotations, which were then used together with the filtered genomes to extract protein and CDS sequences.

Scripts used for AGAT processing are available at: https://github.com/daisysotero/Coffea-analyses-2025

*Genome file extension = *_500kb.fasta | Annotation file extension = *_500kb.gff3 | Protein file extension = *_500kb_prot.fasta | sgCC or sgC = canephora-derived subgenome | sgEE or sgE = eugenioides-derived subgenome
DOI: 10.5281/zenodo.17251359
title: Dataset 2: Genomic assemblies and annotations of Coffea species and subgenomes

description: This dataset contains genome assemblies and corresponding annotation files for various Coffea species. The genomic data were retrieved from public repositories and underwent standardization and validation to ensure consistency across files. Genome assemblies were filtered to retain chromosomes and contigs ≥500 kb. For Coffea arabica, assemblies were further separated into subgenomes derived from Coffea canephora and Coffea eugenioides. Filtered GFF3 files matching these sequences were processed with the AGAT toolkit to generate longest isoform annotations, which were then used together with the filtered genomes to extract protein and CDS sequences.

Scripts used for AGAT processing are available at: https://github.com/daisysotero/Coffea-analyses-2025

*Genome file extension = *_500kb.fasta | Annotation file extension = *_500kb.gff3 | Protein file extension = *_500kb_prot.fasta | sgCC or sgC = canephora-derived subgenome | sgEE or sgE = eugenioides-derived subgenome
DOI: 10.17190/amf/3004318
title: AmeriFlux CA-PB1 Polar Bear 1 - Peat Plateau

description: This is the AmeriFlux version of the carbon flux data for the site CA-PB1 Polar Bear 1 - Peat Plateau. Site Description - Ontario Ministry of Environment and Climate Change's Environmental Monitoring and Reporting Branch has established five carbon flux monitoring towers in Ontario’s Far North as part of its Climate Change Modelling and Monitoring program. These long term monitoring stations measure carbon exchange and a suite of soil and meteorological parameters over peatland ecosystems to better understand carbon cycling in Ontario’s Far North. Information produced by these monitoring stations will assist the province in land use planning and the development of climate change adaptation strategies.
DOI: 10.25824/redu/cqiqxo
title: Avaliação subjetiva do diagnóstico do defeito ósseo peri-implantar: gabarito, respostas dos avaliadores e aleatorização dos volumes de imagem na avaliação inicial e reavaliação

description: Na Aba 1 da planilha do Excel encontra-se o gabarito, que apresenta a numeração das costelas catalogadas na coluna 1 e a indicação da presença ou ausência de defeito ósseo peri-implantar na coluna 2, sendo 1 correspondente à presença de defeito e 0 à ausência. Na coluna 3, é informada a utilização da ferramenta de redução de artefatos metálicos (MAR), em que 1 indica “sim” e 0 indica “não”. Na coluna 4, consta a localização do implante adjacente em relação ao campo de visão (FOV): endo corresponde à endomassa, ou seja, dois implantes dentro do campo de visão; e exo corresponde à exomassa, isto é, apenas um implante dentro do campo de visão da TCFC. Na coluna de aleatorização, estão listados os volumes que foram renomeados para serem enviados aos avaliadores. Na Aba 2, são apresentadas as mesmas informações da Aba 1, porém organizadas de acordo com a ordem da aleatorização e na sequência em que os volumes foram avaliados pelos avaliadores. Na Aba 3, as colunas 1 a 5 apresentam o gabarito da avaliação. Nas colunas correspondentes aos avaliadores, estão registradas as respostas dos cinco avaliadores do estudo. As avaliações foram realizadas por meio de uma escala de cinco pontos, na qual: 1 = ausência de defeito ósseo peri-implantar; 2 = provável ausência; 3 = incerteza; 4 = provável presença; 5 = presença de defeito ósseo peri-implantar. Cada costela foi avaliada considerando os seguintes fatores: face do implante (mesial, distal, vestibular ou lingual), presença ou ausência do defeito, uso da ferramenta MAR e posição do implante adjacente. Na Aba 4, encontra-se a planilha do gabarito da reavaliação já aleatorizada, na qual 30% da amostra foi selecionada para nova avaliação, com o objetivo de calcular o coeficiente kappa intraexaminador. Os volumes de imagem foram aleatorizados e encaminhados aos avaliadores para análise. A coluna 6 (aleatorização inicial) corresponde aos volumes de imagem correspondente utilizados na avaliação inicial. Na última aba, observa-se que as colunas 1 e 2 correspondem aos volumes dos exames da avaliação inicial e da reavaliação, respectivamente. A coluna 3 indica as faces avaliadas em cada exame, ou seja, cada exame foi analisado nas quatro faces: mesial, distal, vestibular e lingual. Nas colunas seguintes, estão registradas as respostas de cada avaliador, obtidas por meio da escala de cinco pontos, para cada exame, tanto na avaliação inicial quanto na reavaliação.
DOI: 10.15468/dl.avucqv
title: Occurrence Download

description: A dataset containing 266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hanguana malayana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 266 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016517-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18505612
title: Can't even afford to die.

description: Abstract

Public housing enforcement systems frequently present resident debt as a static financial obligation resulting from tenant noncompliance. This paper demonstrates that, in practice, public housing arrears function as a dynamic, self-reinforcing debt mechanism driven by repayment agreement defaults, payment reallocation rules, and balance re-aging procedures.

Through socio-technical analysis, this paper documents how residents who consistently pay rent and make substantial arrears payments can nonetheless experience balance regeneration, wherein near-zero arrears are reinstated to prior principal amounts following technical default triggers.

The result is not resolution but perpetual indebtedness, sustained through administrative design rather than financial necessity. This paper further argues that such mechanisms produce predictable human outcomes: exhaustion, financial depletion, health deterioration, and ultimately disposability, while maintaining institutional plausibility and legal defensibility.
DOI: 10.5281/zenodo.18505613
title: Can't even afford to die.

description: Abstract

Public housing enforcement systems frequently present resident debt as a static financial obligation resulting from tenant noncompliance. This paper demonstrates that, in practice, public housing arrears function as a dynamic, self-reinforcing debt mechanism driven by repayment agreement defaults, payment reallocation rules, and balance re-aging procedures.

Through socio-technical analysis, this paper documents how residents who consistently pay rent and make substantial arrears payments can nonetheless experience balance regeneration, wherein near-zero arrears are reinstated to prior principal amounts following technical default triggers.

The result is not resolution but perpetual indebtedness, sustained through administrative design rather than financial necessity. This paper further argues that such mechanisms produce predictable human outcomes: exhaustion, financial depletion, health deterioration, and ultimately disposability, while maintaining institutional plausibility and legal defensibility.
DOI: 10.60532/scp.2021-22.w1-2.v1
title: German Social Cohesion Panel 2021-2022 - Wave 1-2
title: SCP 2021-22 W1-2
title: Dataset and Documentation

description: The Research Institute Social Cohesion (RISC) and the Socio-Economic Panel (SOEP) at the German Institute for Economic Research (DIW Berlin) are conducting a panel study as part of their research cooperation. This involves surveying individuals in Germany in their household context on aspects of social cohesion, social inequality and social conflict. The dataset "German Social Cohesion Panel 2021-2022 - Wave 1-2"  includes survey data and generated indicators of the first and second panel wave. It contains responses from household anchor persons drawn from population registers and from adult household members who were named by the anchor persons and subsequently interviewed.
description: Self-administered questionnaire: Paper
description: Self-administered questionnaire: Web-based
description: Individuals in private households in Germany
description: The anchor persons were drawn from population registers using a two-stage sampling procedure. Eastern Germans were disproportionately drawn into the sample. All adult household members named by the anchor persons were subsequently invited to participate in the survey.
DOI: 10.6084/m9.figshare.31281856
title: data for proton precipitations

description: The dataset provides the data corresponding to the figures in the article.
DOI: 10.6084/m9.figshare.31281856.v1
title: data for proton precipitations

description: The dataset provides the data corresponding to the figures in the article.
DOI: 10.15468/dl.8wm89x
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kishinouyepenaeopsis amicus"
 ]
}

 The dataset includes 31 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016521-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.udvv7a
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Helmholtzia glaberrima",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 102 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016522-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.71853/c91h-4125
title: AMBER MD package compatible residue library and PDB structure for publication: &#34;Anticoagulant Potential of Modified Sulfated Exopolysaccharides from Deep-Sea Bacteria: Toward Non-Animal Heparin Alternatives&#34;

description: <p>AMBER MD package compatible residue library for a small molecule and the PDB structure of the oligosaccharide used in the publication https://doi.org/10.3390/polysaccharides6020054</p>
DOI: 10.17190/amf/3004317
title: AmeriFlux BR-Ji3 Ji-Paraná/RO - Reserva Biológica do Jaru (RBJ)

description: This is the AmeriFlux version of the carbon flux data for the site BR-Ji3 Ji-Paraná/RO - Reserva Biológica do Jaru (RBJ). Site Description - The BR-Ji3, RBJ tower (LBA Network) is deployed in a primary forest in the Reserva Biologica do Jaru, management to ICMBio, at 130 km of Ji-Paraná city, in the road to Vale do Paraíso.
DOI: 10.5167/uzh-290785
title: Tritomaria scitula (Taylor) Jørg.
DOI: 10.5167/uzh-290788
title: Southbya nigrella (De Not.) Henriq.
DOI: 10.5167/uzh-290793
title: Odontoschisma francisci (Hook.) L.Söderstr. & Váňa
DOI: 10.5167/uzh-290792
title: Porella baueri (Schiffn.) C.E.O.Jensen
DOI: 10.5167/uzh-290796
title: Lejeunea lamacerina (Steph.) Schiffn. subsp. lamacerina
DOI: 10.5281/zenodo.18506611
title: Intensivkapazitäten und COVID-19-Intensivbettenbelegung in Deutschland

description: Der Datensatz "Intensivkapazitäten und COVID-19-Intensivbettenbelegung in Deutschland" des Robert Koch-Instituts dokumentiert die tägliche intensivmedizinische Versorgungslage seit der COVID-19-Pandemie. Basierend auf Meldungen aller intensivbettenführenden Krankenhäuser in Deutschland erfasst das DIVI-Intensivregister Echtzeitdaten zu belegten und freien Intensivbetten. Die Erhebung differenziert nach Altersgruppen, Regionen und Versorgungsstufen. COVID-19-Fälle auf Intensivstationen werden gesondert ausgewiesen. Die Daten stehen aggregiert auf Bundes-, Landes- und Kreisebene zur Verfügung. Damit bildet der Datensatz eine Grundlage für die Überwachung von Kapazitäten, die Koordination von Behandlungskapazitäten und politische Entscheidungsprozesse während der Pandemie und darüber hinaus.
DOI: 10.5281/zenodo.18506525
title: Supplementary
DOI: 10.5281/zenodo.18506524
title: Supplementary
DOI: 10.15468/dl.z3u7n9
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.2_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Elanus caeruleus",
 "Year is 2022"
 ]
}

 The dataset includes 128 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016524-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13120955
title: Global inventory of submarine mud volcanoes

description: A comprehensive global inventory of submarine mud volcanoes  with their spatial locations and morphometric characteristics.
DOI: 10.5281/zenodo.13120956
title: Global inventory of submarine mud volcanoes

description: A comprehensive global inventory of submarine mud volcanoes  with their spatial locations and morphometric characteristics.
DOI: 10.5281/zenodo.18506607
title: BO'LAJAK BOSHLANG'ICH SINF O'QITUVCHILARIDA MUSTAQIL TA'LIM ORQALI KREATIV VA TANQIDIY TAFAKKURNI SHAKLLANTIRISH
DOI: 10.5281/zenodo.18506608
title: BO'LAJAK BOSHLANG'ICH SINF O'QITUVCHILARIDA MUSTAQIL TA'LIM ORQALI KREATIV VA TANQIDIY TAFAKKURNI SHAKLLANTIRISH
DOI: 10.17044/scilifelab.20514192.v4
title: COI reference sequences from BOLD DB

description: Dataset descriptionThis item contains COI (mitochondrial cytochrome oxidase subunit I) sequences collected from the BOLD database. The fasta file bold_clustered_cleaned.fasta.gz has record ids that can be queried in the Public Data Portal and each fasta header contains the taxonomic ranks + the BIN ID assigned to the record. The taxonomic information for each record is also given in the tab-separated file bold_info_filtered.tsv.gz.<br>The file bold_clustered.sintax.fasta.gz is directly compatible with the SINTAX algorithm in vsearch while files bold_clustered.assignTaxonomy.fasta.gz and bold_clustered.addSpecies.fasta.gz are directly compatible with the assignTaxonomy and addSpecies functions from DADA2, respectively. The dataset was last created on December 16, 2022<br><b>NOTE: We have noticed that the gzipped files in this upload have been compressed twice for some reason. A quick fix is to unzip any file with a ".gz" extension, then rename the unzipped file by adding the ".gz" extension back. Then running the unzipping once again. Sorry for the inconvenience.</b><b>Methods</b>The code used to generate this dataset consists of a snakemake workflow wrapped into a python package that can be installed with conda (`conda install -c bioconda coidb`). Firstly sequence and taxonomic information for records in the BOLD database is downloaded from the GBIF Hosted Datasets. This data is then filtered to only keep records annotated as 'COI-5P' and assigned to a BIN ID. The taxonomic information is parsed in order to assign species names and resolve higher level ranks for each BIN ID. Sequences are processed to remove gap characters and leading and trailing `N`s. After this, any sequences with remaining non-standard characters are removed. Sequences are then clustered at 100% identity using vsearch (Rognes _et al._ 2016). This clustering is done separately for sequences assigned to each BIN ID.<br>For more information, see https://github.com/biodiversitydata-se/coidb
DOI: 10.60905/1me5n0
title: Piden severa investigaci��n para hechos de la UdeA

description: &lt;p&gt; El art��culo comparte la resoluci��n expedida por el Colegio de profesores de la universidad donde condenan los hechos sucedidos y llaman en��rgicamente a una investigaci��n minuciosa. A este pedido se sum�� la Asociaci��n de Ex Estudiantes de Derecho. Hay rechazo a la violencia y disputas entre organismos de representaci��n estudiantil. Guillermo Calder��n, presidente de la Asociaci��n de Ex Alumnos de la Facultad de Derecho, rechaza las declaraciones de Carlos Gaviria D��az, calific��ndolo de oportunista y de respaldar los deplorables episodios.&lt;/p&gt;
description: CONTEXTO DE LA NOTICIA: "Se normaliza el orden p��blico en el pa��s, universitarios regresan a presentar ex��menes, Nixon se re��ne
frecuentemente con l��deres Rusos, Violentos disturbios en Chile y huelga de estudiantes, enfrentamientos en C��rdoba entre militares y el EPL,
estrategia de desarrollo del grupo Andino.
"
DOI: 10.5167/uzh-290791
title: Ptilidium pulcherrimum (Weber) Vain.
DOI: 10.5167/uzh-290789
title: Saccobasis polita (Nees) H.Buch
DOI: 10.6084/m9.figshare.28227788
title: Thermoproteotal <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution

description: This dataset contains supplementary data for the analyses presented in:Xiao-Xi Chen, Yan-Ni Qu, Yang-Zhi Rao, Ze-Wei Li, Qi-Jun Xie, Yuan-Qi Zhang, Paul N. Evans, Wen-Jun Li, Yu-Xian Li*, Zheng-Shuang Hua*. Thermoproteotal <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution (under review)<b>Dataset contents:</b><b>1_29_RMAGs_53markers_tree_file</b>: Phylogenomic tree of 29 reconstructed <i>mcr</i>-containing archaeal MAGs based on 53 concatenated archaeal marker genes, in Newick format.<b>2_Bathyarchaeia_tree_file</b>: Phylogenetic tree showing relationships among Bathyarchaeia orders.<b>3_</b><b><i>mcrABG</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>mcrABG</i> genes.<b>4_</b><b><i>mtrABCDEFGH</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>mtrABCDEFGH</i> genes.<b>5_</b><b><i>cdhABCDE</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>cdhABCDE</i> genes.<b>6_</b><b><i>mtaA</i></b><b>_tree_file</b>: Phylogenetic tree of <i>mtaA</i> genes.
DOI: 10.6084/m9.figshare.28227788.v3
title: Thermoproteotal <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution

description: This dataset contains supplementary data for the analyses presented in:Xiao-Xi Chen, Yan-Ni Qu, Yang-Zhi Rao, Ze-Wei Li, Qi-Jun Xie, Yuan-Qi Zhang, Paul N. Evans, Wen-Jun Li, Yu-Xian Li*, Zheng-Shuang Hua*. Thermoproteotal <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution (under review)<b>Dataset contents:</b><b>1_29_RMAGs_53markers_tree_file</b>: Phylogenomic tree of 29 reconstructed <i>mcr</i>-containing archaeal MAGs based on 53 concatenated archaeal marker genes, in Newick format.<b>2_Bathyarchaeia_tree_file</b>: Phylogenetic tree showing relationships among Bathyarchaeia orders.<b>3_</b><b><i>mcrABG</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>mcrABG</i> genes.<b>4_</b><b><i>mtrABCDEFGH</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>mtrABCDEFGH</i> genes.<b>5_</b><b><i>cdhABCDE</i></b><b>_tree_file</b>: Phylogenetic tree of concatenated <i>cdhABCDE</i> genes.<b>6_</b><b><i>mtaA</i></b><b>_tree_file</b>: Phylogenetic tree of <i>mtaA</i> genes.
DOI: 10.6084/m9.figshare.28227788.v2
title: Non-traditional <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution

description: This dataset contains supplementary data for the analyses presented in:Xiao-Xi Chen, Yan-Ni Qu, Yang-Zhi Rao, Ze-Wei Li, Qi-Jun Xie, Yuan-Qi Zhang, Paul N. Evans, Wen-Jun Li, Yu-Xian Li*, Zheng-Shuang Hua*. Non-traditional <i>mcr</i>-containing archaea dominate the methane metabolism in geothermal springs: insights from genomics and evolution (under review)<b>Dataset contents:</b><b>1_29_RMAGs_53markers.treefile</b>: Phylogenomic tree of 29 reconstructed <i>mcr</i>-containing archaeal MAGs based on 53 concatenated archaeal marker genes, in Newick format.<b>2_</b><b><i>cdhABCDE</i></b><b>.treefile</b>: Phylogenetic tree of concatenated <i>cdhABCDE</i> genes, in Newick format.<b>3_</b><b><i>mtrABCDEFGH</i></b><b>.treefile</b>: Phylogenetic tree of concatenated <i>mtrABCDEFGH</i> genes, in Newick format.<b>4_Bathyarchaeia.treefile</b>: Phylogenetic tree showing relationships among Bathyarchaeia orders, in Newick format.<b>5_</b><b><i>mcrABG</i></b><b>.treefile</b>: Phylogenetic tree of concatenated <i>mcrABG</i> genes, in Newick format.<b>6_</b><b><i>mtaA</i></b><b>.treefile</b>: Phylogenetic tree of <i>mtaA</i> genes, in Newick format.<b>SZTDM_202302_bins_159.fa</b>: <i>mcr</i>-containing Bathyarchaeia MAG.<b>SZTDM_202308_bins_85.fa</b>: <i>mcr</i>-containing Bathyarchaeia MAG.<b>SZTDM_202401_bins_71.fa</b>: <i>mcr</i>-containing Bathyarchaeia MAG.
DOI: 10.5281/zenodo.18506570
title: Frameshift mutations  in the first coding exon of BCOR, a ncPRC1.1 component, do not result in its functional knockout in lymphoma cell lines