cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.71687/00010830
title: Sundhedsforvaltningens Visitationssystem (1982-2009)

description: Elektronisk register vedrørende visitation.

bl.a.

- registrering/opdatering af institution stam oplysninger

- fremfinding af ledige institutioner pr. type

- at tilknytte en bestemt institutions forskellige servicetyper samt tilhørende service, og fremvise alle de servicetyper og service, der er tilknyttet institutionen

- at oprette/opdaterer serviceoplysninger (grundoplysninger)

- at oprette/opdatere personale oplysninger til institution

- at oprette/opdaterer stillingstyper og stillingstypenavn , samt evt. deres ophørsdato

- at opdaterer detail oplysninger vedr. boligspecifikation

- at ajourføre oplysninger på den enkelte bolig og de pladser der tilhører boligen

- at håndtere søgekriterier ved bolig/pladssøgning

- at opdaterer typenr/-navn, samt at kunne angive hvad der kan tilknyttes den enkelt type vha . (j/n) felter til flg.: ventesag-opholdssag-åbningsdage-bolig-pladser-ejendomboligspecifikation

- at oprette/opdaterer visitationsteam/anvisningsudvalg, herunder adresseoplysninger, tlf/fax, samt andre relevante oplysninger

Indeholder:
Person- og institutionsoplysninger.
DOI: 10.15468/dl.cwednb
title: Occurrence Download

description: A dataset containing 256 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Utricularia muelleri Kamienski"
 ]
}

 The dataset includes 256 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021564-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2r3t4
title: Occurrence Download

description: A dataset containing 609102 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode(1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000)) AS eeaCellCode, speciesKey, species, establishmentMeans, degreeOfEstablishment, pathway, COUNT(*) AS occurrences,COUNT(DISTINCT recordedBy) AS distinctObservers FROM occurrence WHERE (GBIF_Within('POLYGON((4.08997 49.82741, 4.90937 49.82741, 4.90937 50.19738,4.08997 50.19738, 4.08997 49.82741))', decimalLatitude, decimalLongitude) = True OR GBIF_Within('POLYGON((5.39117 50.79687, 5.80176 50.79687, 5.80176 51.09087, 5.39117 51.09087, 5.39117 50.79687))', decimalLatitude, decimalLongitude) = True) AND occurrenceStatus = 'PRESENT' AND hasCoordinate = TRUE AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND NOT ARRAY_CONTAINS (issue, 'COORDINATE_INVALID') AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH') AND "year" IS NOT NULL AND classKey = 212 GROUP BY "year", eeaCellCode, speciesKey, species, establishmentMeans, degreeOfEstablishment, pathway ORDER BY "year" DESC, eeaCellCode ASC, speciesKey ASC

 The dataset's 609102 records were derived from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021547-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25403/upresearchdata.26533681
title: Western Cape special schools learner communication needs

description: This excel sheet contains the responses of teachers from special schools in the Western Cape to a questionnaire regarding the communication support needs and types of support provided to learners with complex communication needs. The study underlying this dataset is entitled “A survey of learners with complex communication needs (CCN) in the foundation phase of selected special schools in the Western Cape province of South Africa”<strong> </strong>and the main aim of the study was to determine the prevalence of learners with CCN in the foundation phase at selected special schools in the Western Cape province of South Africa. Sub-aims of the study were to:
Describe their concomitant difficulties in other functional areas;Describe the communication methods they use in classDescribe communication support for learners with CCN including the following: Aided AAC provision; Therapeutic support; Documentation of communication support in the Individual Education Development Plan (IEDP) and/or Individual Support Plan (ISP); andTo describe teacher training in AAC.
<br>
A non-experimental quantitative survey research design was used in this study. An online questionnaire was developed and populated onto the QualtricsXM software. A combination of purposive and comprehensive sampling were used in this study. The link to the electronic questionnaire was distributed to foundation phase teachers at 17 special schools in the Western Cape schools whose principals gave permission for distribution. The responses from 56 teachers were analysed using descriptive statistics.
The principles of the 37 special schools selected for the study were approached and permission was obtained from 17 schools to recruit teachers meeting the selection criteria to participate in the study. Prospective respondents were provided with a detailed information letter and consent was obtained by means of an electronic consent form included as the first part of the online questionnaire. The letters with embedded links to the consent form and survey was sent to the liaisons of schools to distribute amongst teachers. The survey was closed after 56 days and all responses were downloaded and imported into a Microsoft Excel spreadsheet for analysis.
DOI: 10.25403/upresearchdata.26533681.v1
title: Western Cape special schools learner communication needs

description: This excel sheet contains the responses of teachers from special schools in the Western Cape to a questionnaire regarding the communication support needs and types of support provided to learners with complex communication needs. The study underlying this dataset is entitled “A survey of learners with complex communication needs (CCN) in the foundation phase of selected special schools in the Western Cape province of South Africa”<strong> </strong>and the main aim of the study was to determine the prevalence of learners with CCN in the foundation phase at selected special schools in the Western Cape province of South Africa. Sub-aims of the study were to:
Describe their concomitant difficulties in other functional areas;Describe the communication methods they use in classDescribe communication support for learners with CCN including the following: Aided AAC provision; Therapeutic support; Documentation of communication support in the Individual Education Development Plan (IEDP) and/or Individual Support Plan (ISP); andTo describe teacher training in AAC.
<br>
A non-experimental quantitative survey research design was used in this study. An online questionnaire was developed and populated onto the QualtricsXM software. A combination of purposive and comprehensive sampling were used in this study. The link to the electronic questionnaire was distributed to foundation phase teachers at 17 special schools in the Western Cape schools whose principals gave permission for distribution. The responses from 56 teachers were analysed using descriptive statistics.
The principles of the 37 special schools selected for the study were approached and permission was obtained from 17 schools to recruit teachers meeting the selection criteria to participate in the study. Prospective respondents were provided with a detailed information letter and consent was obtained by means of an electronic consent form included as the first part of the online questionnaire. The letters with embedded links to the consent form and survey was sent to the liaisons of schools to distribute amongst teachers. The survey was closed after 56 days and all responses were downloaded and imported into a Microsoft Excel spreadsheet for analysis.
DOI: 10.15468/dl.quvy9r
title: Occurrence Download

description: A dataset containing 6331 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "TaxonKey is Ips typographus (C.Linnaeus, 1758)"
 ]
}

 The dataset includes 6331 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021565-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.agrh2d
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Utricularia biloba R.Br."
 ]
}

 The dataset includes 148 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021566-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12570843
title: Progressive degradation of acetylated wood by the brown rot fungi Coniophora puteana and Rhodonia placenta

description: This dataset contains measurement data from the following publication: Belt, T.; Awais, M. (2025) Progressive degradation of acetylated wood by the brown rot fungi Coniophora puteana and Rhodonia placenta. Wood Science and Technology 59:13. https://doi.org/10.1007/s00226-024-01620-8. The experimental methods are described in brief below; further details can be found in the publication.

Scots pine sapwood samples were acetylated in neat acetic anhydride to 9% or 18% weight percent gain (WPG) or left untreated to act as reference. The samples were exposed to brown rot decay in a stacked-sample decay test conducted in test tubes. Each replicate tube received 6 reference or acetylated samples stacked on top of each other (sample positions 1-6 from top to bottom) over nutrient agar inoculated with Coniophora puteana (N = 7) or Rhodonia placenta (N = 5). The different wood-fungus combinations were incubated for different durations until the visible fungal mycelium reached the top of the topmost block in one replicate tube. The samples were weighed before modification, after modification, at the end of the decay test, and after the decay test to determine their WPG, moisture content at the end of the decay test, and mass loss due to decay. After decay, 15 samples from every wood-fungus combination were selected for acetyl content measurement and FTIR spectroscopy.

Acetyl contents were measured on powdered samples by saponification followed by HPLC quantification of the liberated acetic acid. FTIR spectra were measured in the 400-4000 cm-1 spectral range in triplicate on powdered samples using an ATR accessory. For further analysis, the spectra were cut to 800-1800 cm-1 range, baseline corrected (third degree polynomial subtraction), smoothed (Savitzky-Golay procedure with a second-order polynomial and a 15-point window), and normalised (unit vector normalisation).

The "Mass data and acetyl content.csv" -file gives the sample identifiers (ID, sample type, test fungus, tube number, sample position) and measured mass data of all samples, and the acetyl contents of the selected samples. Masses minit, mmod, mwet, and mdec are the initial unmodified dry mass, the modified dry mass, the decaying wet mass, and the decayed dry mass, respectively. Acetyl contents (%) are given on a decayed wood basis.

The “Unprocessed FTIR spectra_reference”, “Unprocessed FTIR spectra_9%”, and “Unprocessed FTIR spectra_18%” -files contain the unprocessed FTIR spectra of the reference, 9% WPG and 18% WPG samples (see the "Mass data and acetyl content.csv" -file for sample identifiers). The “Preprocessed FTIR spectra_reference”, “Preprocessed FTIR spectra_9%”, and “Preprocessed FTIR spectra_18%” -files in turn contain the preprocessed FTIR spectra of reference, 9% WPG and 18% WPG samples.
DOI: 10.5281/zenodo.12570844
title: Progressive degradation of acetylated wood by the brown rot fungi Coniophora puteana and Rhodonia placenta

description: This dataset contains measurement data from the following publication: Belt, T.; Awais, M. (2025) Progressive degradation of acetylated wood by the brown rot fungi Coniophora puteana and Rhodonia placenta. Wood Science and Technology 59:13. https://doi.org/10.1007/s00226-024-01620-8. The experimental methods are described in brief below; further details can be found in the publication.

Scots pine sapwood samples were acetylated in neat acetic anhydride to 9% or 18% weight percent gain (WPG) or left untreated to act as reference. The samples were exposed to brown rot decay in a stacked-sample decay test conducted in test tubes. Each replicate tube received 6 reference or acetylated samples stacked on top of each other (sample positions 1-6 from top to bottom) over nutrient agar inoculated with Coniophora puteana (N = 7) or Rhodonia placenta (N = 5). The different wood-fungus combinations were incubated for different durations until the visible fungal mycelium reached the top of the topmost block in one replicate tube. The samples were weighed before modification, after modification, at the end of the decay test, and after the decay test to determine their WPG, moisture content at the end of the decay test, and mass loss due to decay. After decay, 15 samples from every wood-fungus combination were selected for acetyl content measurement and FTIR spectroscopy.

Acetyl contents were measured on powdered samples by saponification followed by HPLC quantification of the liberated acetic acid. FTIR spectra were measured in the 400-4000 cm-1 spectral range in triplicate on powdered samples using an ATR accessory. For further analysis, the spectra were cut to 800-1800 cm-1 range, baseline corrected (third degree polynomial subtraction), smoothed (Savitzky-Golay procedure with a second-order polynomial and a 15-point window), and normalised (unit vector normalisation).

The "Mass data and acetyl content.csv" -file gives the sample identifiers (ID, sample type, test fungus, tube number, sample position) and measured mass data of all samples, and the acetyl contents of the selected samples. Masses minit, mmod, mwet, and mdec are the initial unmodified dry mass, the modified dry mass, the decaying wet mass, and the decayed dry mass, respectively. Acetyl contents (%) are given on a decayed wood basis.

The “Unprocessed FTIR spectra_reference”, “Unprocessed FTIR spectra_9%”, and “Unprocessed FTIR spectra_18%” -files contain the unprocessed FTIR spectra of the reference, 9% WPG and 18% WPG samples (see the "Mass data and acetyl content.csv" -file for sample identifiers). The “Preprocessed FTIR spectra_reference”, “Preprocessed FTIR spectra_9%”, and “Preprocessed FTIR spectra_18%” -files in turn contain the preprocessed FTIR spectra of reference, 9% WPG and 18% WPG samples.
DOI: 10.5281/zenodo.14170410
title: An updated genome annotation file for the Bicyclus anynana genome GCF_947172395.1_ilBicAnyn1.1

description: The reference genome and annotation for GCF_947172395.1_ilBicAnyn1.1 was downloaded from NCBI RefSeq in August 2023, and updated by incorporating the results of an RNA sequencing investigation into full-length transcripts expressed during metamorphosis, analysing five timepoints during progression from a late larval stage through to the final mature pupal stage. To identify and quantify novel transcript splicing compared to the reference genome, the sample-level alignment bam files were analysed using espresso (version 1.4), increasing the –read_num_cutoff setting to 4 to require a minimum of 4 perfect reads to call de novo detected candidate splice junctions. This procedure in espresso produced an updated unified annotation based on the transcripts detected in all samples. This was subsequently merged with the existing annotation using stringtie (version 2.1.7), generating new unique identifiers beginning with a prefix “BIGESP”.
DOI: 10.5281/zenodo.10463234
title: EAT example applications

description: These are example applications for the Ensemble and Assimilation Tool (EAT).

Instructions for running these examples can be found in the contained README.md.

This updated version uses Jupyter notebooks for all three applications.
DOI: 10.5281/zenodo.10934097
title: EAT example applications

description: These are example applications for the Ensemble and Assimilation Tool (EAT).

Instructions for running these examples can be found in the contained README.md.

This updated version uses Jupyter notebooks for all three applications. It requires EAT version 0.9.8.
DOI: 10.5281/zenodo.11111361
title: EAT example applications

description: These are example applications for the Ensemble and Assimilation Tool (EAT).

Instructions for running these examples can be found in the contained README.md.

This updated version uses Jupyter notebooks for all three applications. It requires EAT version 1.0.
DOI: 10.5281/zenodo.10307315
title: EAT example applications

description: These are example applications for the Ensemble and Assimilation Tool (EAT).

Instructions for running these examples can be found in the contained README.md.

This updated version uses Jupyter notebooks for all three applications. It requires EAT version 1.1 or higher.
DOI: 10.5281/zenodo.14185039
title: EAT example applications

description: These are example applications for the Ensemble and Assimilation Tool (EAT).

Instructions for running these examples can be found in the contained README.md.

This updated version uses Jupyter notebooks for all three applications. It requires EAT version 1.1 or higher.
DOI: 10.5281/zenodo.10672635
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.10698987
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.