cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10034597
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 2016

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 2016.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.48579/pro/6iqn7i/vh83y4
title: 3103M629463-20150914.tab

description: :unav
DOI: 10.5281/zenodo.10034598
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 2016

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 2016.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.48579/pro/6iqn7i/iwcmt2
title: 3110F650652-20150908.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/ewq8p7
title: 3076M645231-20150914.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/nqnkrs
title: 4016M979175-20150908.tab

description: :unav
DOI: 10.5281/zenodo.10034236
title: Multifaceted quality assessment of gene repertoire annotation with OMArk

description: Dataset associated to the OMArk paper.
Contain eight archives:
Supplementary_Tables
The Supplementary Table files referred to in the paper
OMAmerDB:
The OMAmer database constructed using the whole dataset of the OMA database (November 2022 Release) and used in the paper. An OMAmer database is necessary to run OMArk.
Simulation:Proteomes with artificially introduced errors, contaminants or depleted completeness, used to assess OMArk's performance. The archive contains the generated proteomes (Simulated_Data) and their OMArk quality assessments (omark). They also contains the OMAmer results (OMAmerResults) that were used to run OMArk and BUSCO completeness assessments (BUSCO).
*Note that for storage efficiency, only the non-redundant part of the data (added errors, added contamination, random fraction of proteomes) are stored there. The full modified proteome can be regenerated from these data and the source proteomes.
Reference Proteomes:
The UniProt Reference Proteomes (Proteomes) (2021_04) and their proteome quality assesment results according to OMArk. The archive contains the source proteome FASTA (Source folder),  OMAmer results for these proteomes (omamer folder) , OMArk results (omark folder), and BUSCO completeness assesments (BUSCO folder). It also contains a subfolder that contains part of the Contamination detection experiment (Contamination folder).
Ensembl_Metazoa_AssemblyChange.Contains Ensembl Metazoa proteomes with version change between version 52 and 54 as well as their quality assesment resuls for both version. The archive contains the source proteomes FASTA (Source folder), a Splice file that group together all proteins coded by the same gene (Splice folder), omamer results for the proteomes (omamer folder) and the omark results (omark folder)
MissingGenesBLASTContains sequences of HOGs considered as missing in the Human proteome, that was used to look for sequences in the human genome.
Ensembl_NCBI_Results
Contains OMArk and BUSCO results for Ensembl and NCBI proteomes. These results were then used to evaluate OMArk biais due to source of proteomes in the OMA database.
NotebooksJupyter Notebooks that were used to perform the analysis described in the paper
DOI: 10.5281/zenodo.6462026
title: Multifaceted quality assessment of gene repertoire annotation with OMArk

description: Dataset associated to the OMArk paper.
Contain eight archives:
Supplementary_Tables
The Supplementary Table files referred to in the paper
OMAmerDB:
The OMAmer database constructed using the whole dataset of the OMA database (November 2022 Release) and used in the paper. An OMAmer database is necessary to run OMArk.
Simulation:Proteomes with artificially introduced errors, contaminants or depleted completeness, used to assess OMArk's performance. The archive contains the generated proteomes (Simulated_Data) and their OMArk quality assessments (omark). They also contains the OMAmer results (OMAmerResults) that were used to run OMArk and BUSCO completeness assessments (BUSCO).
*Note that for storage efficiency, only the non-redundant part of the data (added errors, added contamination, random fraction of proteomes) are stored there. The full modified proteome can be regenerated from these data and the source proteomes.
Reference Proteomes:
The UniProt Reference Proteomes (Proteomes) (2021_04) and their proteome quality assesment results according to OMArk. The archive contains the source proteome FASTA (Source folder),  OMAmer results for these proteomes (omamer folder) , OMArk results (omark folder), and BUSCO completeness assesments (BUSCO folder). It also contains a subfolder that contains part of the Contamination detection experiment (Contamination folder).
Ensembl_Metazoa_AssemblyChange.Contains Ensembl Metazoa proteomes with version change between version 52 and 54 as well as their quality assesment resuls for both version. The archive contains the source proteomes FASTA (Source folder), a Splice file that group together all proteins coded by the same gene (Splice folder), omamer results for the proteomes (omamer folder) and the omark results (omark folder)
MissingGenesBLASTContains sequences of HOGs considered as missing in the Human proteome, that was used to look for sequences in the human genome.
Ensembl_NCBI_Results
Contains OMArk and BUSCO results for Ensembl and NCBI proteomes. These results were then used to evaluate OMArk biais due to source of proteomes in the OMA database.
NotebooksJupyter Notebooks that were used to perform the analysis described in the paper
DOI: 10.5281/zenodo.6462027
title: Assessing the many aspects of protein-coding gene annotation quality with OMArk

description: Dataset associated to the OMArk paper. Contain four archives: SuppTables The Supplementary Table files referred to in the paper OMAmerDB: The OMAmer database constructed using the whole dataset of the OMA database (December 2021 Release) and used in the paper. An OMAmer database is necessary to run OMArk. Simulation:<br> Proteomes with artificially introduced errors, contaminants or depleted completeness, used to assess OMArk's performance. The archive contains the generated proteomes (Simulated_Data*) and their OMArk quality assessments (OMArk_Results). They also contains the OMAmer results (OMAmer_Placements) that were used to run OMArk and BUSCO completeness assessments (BUSCO_Results). *Note that for storage efficiency, only the non-redundant part of the data (added errors, added contamination, random fraction of proteomes) are stored there. The full modified proteome can be regenerated from these data and the source proteomes. Reference Proteomes: The UniProt Reference Proteomes (Proteomes) (2021_04) and their proteome quality assesment results according to OMArk. The archive also contains the OMAmer results (OMAmerResults) that were used to run OMArk (OMArk_Results), and BUSCO completeness assesments (BUSCO_Results).
DOI: 10.5281/zenodo.7359861
title: Multifaceted quality assessment of gene repertoire annotation with OMArk

description: Dataset associated to the OMArk paper. Contain five archives: Supplementary_Tables The Supplementary Table files referred to in the paper OMAmerDB: The OMAmer database constructed using the whole dataset of the OMA database (December 2021 Release) and used in the paper. An OMAmer database is necessary to run OMArk. Simulation:<br> Proteomes with artificially introduced errors, contaminants or depleted completeness, used to assess OMArk's performance. The archive contains the generated proteomes (Simulated_Data) and their OMArk quality assessments (omark). They also contains the OMAmer results (OMAmerResults) that were used to run OMArk and BUSCO completeness assessments (BUSCO). *Note that for storage efficiency, only the non-redundant part of the data (added errors, added contamination, random fraction of proteomes) are stored there. The full modified proteome can be regenerated from these data and the source proteomes. Reference Proteomes: The UniProt Reference Proteomes (Proteomes) (2021_04) and their proteome quality assesment results according to OMArk. The archive contains the source proteome FASTA (Source folder), OMAmer results for these proteomes (omamer folder) , OMArk results (omark folder), and BUSCO completeness assesments (BUSCO folder). It also contains a subfolder that contains part of the Contamination detection experiment (Contamination folder). Ensembl_Metazoa_AssemblyChange.<br> <br> Contains Ensembl Metazoa proteomes with version change between version 52 and 54 as well as their quality assesment resuls for both version. The archive contains the source proteomes FASTA (Source folder), a Splice file that group together all proteins coded by the same gene (Splice folder), omamer results for the proteomes (omamer folder) and the omark results (omark folder) Notebooks <br> Jupyter Notebooks that were used to perform the analysis described in the paper<br> <br>
DOI: 10.48579/pro/6iqn7i/iborl7
title: 3113M603689-20150919.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/otzajl
title: 4026M118013-20150908.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/qsluqg
title: 4016F603567-20150922.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/l4xqm2
title: 3114M650790-20150919.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/ufizvb
title: 3094F980957-20150925.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/iail20
title: 3103F628965-20151105.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/izd0c8
title: 4018F984747-20150914.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/zslyag
title: 3080F453724-20151104.tab

description: :unav
DOI: 10.5281/zenodo.10031957
title: Parcellating the parcellation issue - a proof of concept for reproducible analyses using Neurolibre

description: Dataset provided for NeuroLibre preprint.
 Author repo: https://github.com/pbellec/editorial_parcellation 
NeuroLibre fork:https://github.com/roboneurolibre/editorial_parcellation For details, please visit the corresponding NeuroLibre technical screening.  

https://neurolibre.org
DOI: 10.48579/pro/6iqn7i/hiekzf
title: 3063F984734-20151104.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/jf7e9l
title: 3010M643814-20151105.tab

description: :unav
DOI: 10.5281/zenodo.10031958
title: Parcellating the parcellation issue - a proof of concept for reproducible analyses using Neurolibre

description: Dataset provided for NeuroLibre preprint.
 Author repo: https://github.com/pbellec/editorial_parcellation 
NeuroLibre fork:https://github.com/roboneurolibre/editorial_parcellation For details, please visit the corresponding NeuroLibre technical screening.  

https://neurolibre.org
DOI: 10.48579/pro/6iqn7i/dccg5k
title: 3120M117668-20151105.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/zefy5d
title: 3095F454126-20151104.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/aktdki
title: 3091M985139-20151104.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/nlogtq
title: 3113F605453-20151104.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/efuztn
title: 8060M644936-20151104.tab

description: :unav
DOI: 10.6084/m9.figshare.24088257
title: data and materials

description: a research depicting the development of Monkey King Algorithm and the empirical evidence of its validity in enhancing the ability to parse for sentence comprehension<br>
DOI: 10.6084/m9.figshare.24088257.v1
title: data and materials

description: a research depicting the development of Monkey King Algorithm and the empirical evidence of its validity in enhancing the ability to parse for sentence comprehension<br>
DOI: 10.48579/pro/6iqn7i/p6nj61
title: 3080M979019-20151105.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/igq1vu
title: 3096M605079-20151006_depthtemp.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/wuevzw
title: 3096M605079-20151006_acc.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/mtteqz
title: 3012F985103-20151007_depthtemp.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/qrelek
title: S0196-3065M453910-20151006acc.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/dcri6k
title: 8060F644643-20151006_acc.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/mhib6y
title: 3012F985103-20151007_acc.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/xrzkpl
title: 8060F644643-20151006_depthtemp.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/admuhx
title: S0196-3065M453910-20151006depthtemp.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/wiuxpz
title: 3065F628212-20151013_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/ic1ubk
title: 3062F605430-20151005_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/cwrelt
title: 3060F984776-20151005_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/epolny
title: 3024M117967-20151007_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/paslhs
title: 3010F453730-20151006_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/oirxjv
title: 3063M629227-20151005_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/rq7hjh
title: 3095M454055-20151007_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/jpmyf7
title: 3118F979025-20151006_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/wp3itw
title: 3096F460065-20151011_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/tyeqre
title: 3091F9848042-20151011_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/mbh6wg
title: 3082M979672-20151011_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/mtdnbt
title: 3104M604759-20151005_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/katqqm
title: 3076M645231-20150914_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/oq83ga
title: 3114M650790-20150919_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/nvusxq
title: 3110F650652-20150908_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/bo3zn8
title: 3094F980957-20150925_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/h76tnl
title: 3113M603689-2015919_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/acdzmp
title: 3103M629463-20150914_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/akod7e
title: 4016M979175-20150908_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/gmxqn5
title: 4018F984747-20150914_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/izyaey
title: 4016F603567-20150922_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/rgeq5t
title: 3120F117592-20150914_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/he3hil
title: 4026M118013-20150908_1.tab

description: :unav
DOI: 10.48579/pro/6iqn7i/5guaxq
title: wacu65_pygmées2015_cc_ACC_Part1.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/hv2ypm
title: wacu65_pygmées2015_cc_ACC_Part2.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/xle1kv
title: Readme.txt

description: :unav
DOI: 10.48579/pro/6iqn7i/ugdflh
title: Deployment_LP_2014.csv

description: :unav
DOI: 10.48579/pro/6iqn7i/gbchgy
title: Deployment_LP_2015.csv

description: :unav
DOI: 10.48579/pro/6iqn7i
title: Bio-logging data of Little penguin, Phillip Island, Australia

description: This is a data repository of long-term Little penguin (Eudyptula minor) monitoring project in Phillip Island, Australia. The raw bio-logging data (time series data including, depth, temperature, GPS position, and acceleration) were recorded during the breeding season.
DOI: 10.3886/e192055v1-142544
title: Data and Code for: Is There A VA Advantage? Evidence from Dually Eligible Veterans

description: We study public vs. private provision of health care for veterans aged 65 and older who may receive care provided by the US Department of Veterans Affairs (VA) and in private hospitals financed by Medicare. Utilizing the ambulance design of Doyle et al. (2015), we find that the VA reduces 28-day mortality by 46% (4.5 percentage points) and that these survival gains are persistent. The VA also reduces 28-day spending by 21% and delivers strikingly different reported services relative to private hospitals. We find suggestive evidence of complementarities between continuity of care, health IT, and integrated care.
DOI: 10.18167/dvn1/nb0qmx
title: Deciphering how plant pathogenic bacteria disperse and meet: molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity

description: Raw data for Pruvost et al., 2019, Evolutionary Applications, Deciphering how plant pathogenic bacteria disperse and meet: molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity
DOI: 10.5281/zenodo.10034622
title: RouteRideCheck_711-Downtown Station To Eastwood Meadows_Spring 2023

description: This data set contains ride check data for Route 711 for March, 2023. The ride check data set contains fields for Stop ID, Stop Name, Stop Seq ID, Day of Week, Date, Arrive, Passenger On, Passenger Off, Passenger Load, Passenger Miles, Interstop Distance, Bus, Lat., Long. The data set was requested from and given by the Regional Transit System of Gainesville, Florida.
DOI: 10.5281/zenodo.10034621
title: RouteRideCheck_711-Downtown Station To Eastwood Meadows_Spring 2023

description: This data set contains ride check data for Route 711 for March, 2023. The ride check data set contains fields for Stop ID, Stop Name, Stop Seq ID, Day of Week, Date, Arrive, Passenger On, Passenger Off, Passenger Load, Passenger Miles, Interstop Distance, Bus, Lat., Long. The data set was requested from and given by the Regional Transit System of Gainesville, Florida.
DOI: 10.5281/zenodo.10023862
title: Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia

description: Transcriptome analysis by single cell sequencing provides valuable information on intratumor heterogeneity and developmental stages of acute myeloid leukemia (AML) as well as interactions of tumor cells with the microenvironment. However, it has been hardly applied to the subgroup of cases with translocations of the mixed lineage leukemia (MLL) gene for which the enhancer of mRNA decapping 4 (EDC4) gene was recently identified as a novel fusion partner (MLL-EDC4). In our study published in Blood Advances (Schuster et al., 2023; https://doi.org/10.1182/bloodadvances.2022009096), we compared different MLL translocations by single cell RNA sequencing of cells derived from peripheral blood or bone marrow. The MLL-EDC4 positive cells almost exclusively showed a transcriptional profile of hematopoietic progenitor cells while leukemic cells of MLL-MLLT3 and MLL-ELL fusions exhibited a more differentiated phenotype. The MLL-EDC4 progenitor state was characterized by the upregulation of key transcriptional regulators in AML (RUNX1, SOX4, HOPX), target genes of MYC and interferon signaling as well as other genes known to play a critical role in hematopoiesis or leukemic stem cell activation (CDK6, FLT3, NPM1). Here, the scRNA-seq dataset of our study is provided. It contains six scRNA-seq read count matrices of the AML samples with MLL fusions as described in the table scRNA-seq_samples.xlsx. Further details are given in the publication associated with this dataset.
DOI: 10.5281/zenodo.7832875
title: Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia

description: Transcriptome analysis by single cell sequencing provides valuable information on intratumor heterogeneity and developmental stages of acute myeloid leukemia (AML) as well as interactions of tumor cells with the microenvironment. However, it has been hardly applied to the subgroup of cases with translocations of the mixed lineage leukemia (MLL) gene for which the enhancer of mRNA decapping 4 (EDC4) gene was recently identified as a novel fusion partner (MLL-EDC4). In our study published in Blood Advances (Schuster et al., 2023; https://doi.org/10.1182/bloodadvances.2022009096), we compared different MLL translocations by single cell RNA sequencing of cells derived from peripheral blood or bone marrow. The MLL-EDC4 positive cells almost exclusively showed a transcriptional profile of hematopoietic progenitor cells while leukemic cells of MLL-MLLT3 and MLL-ELL fusions exhibited a more differentiated phenotype. The MLL-EDC4 progenitor state was characterized by the upregulation of key transcriptional regulators in AML (RUNX1, SOX4, HOPX), target genes of MYC and interferon signaling as well as other genes known to play a critical role in hematopoiesis or leukemic stem cell activation (CDK6, FLT3, NPM1). Here, the scRNA-seq dataset of our study is provided. It contains six scRNA-seq read count matrices of the AML samples with MLL fusions as described in the table scRNA-seq_samples.xlsx. Further details are given in the publication associated with this dataset.
DOI: 10.5281/zenodo.7832876
title: Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia

description: The data set contains four scRNA-seq read count matrices of AML samples with MLL fusion.
DOI: 10.18167/dvn1/ehwigr
title: Raw data for Cuénin et al., in press, Journal of Heredity, Great genetic diversity but high selfing rates and short-distance gene flow characterise populations of a tree (Foetidia; Lecythidaceae) in the fragmented tropical dry forest of the Mascarene Islands

description: Raw data for Cuénin et al. in press Journal of Heredity Great genetic diversity but high selfing rates and short-distance gene flow characterise populations of a tree (Foetidia; Lecythidaceae) in the fragmented tropical dry forest of the Mascarene Islands
DOI: 10.18167/dvn1/nmkvh9
title: Déterminants paysagers et humains de la régulation écologique de la mineuse du mil au Sénégal

description: Jeux de données (indicateurs paysagers, observations agronomiques et entomologiques, enquêtes sur les pratiques culturales) pour étudier la régulation écologique du mil au Sénégal
DOI: 10.5281/zenodo.10034630
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 2017

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 2017.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.5281/zenodo.10034629
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 2017

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 2017.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.21223/ftzhdx/kwbwmy
title: 02_Material_list.txt

description: :unav
DOI: 10.21223/ftzhdx/lwlwfe
title: 03_Data_Dictionary.txt

description: :unav