cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17599459
title: Dataset of flows and nutrient inputs to the Albufera Coastal Lagoon (Valencia, Spain) during hydrological year 2023-2024

description: Anthropogenic eutrophication, caused by human inputs of nitrogen (N) and phosphorus (P), is a global problem that leads to excessive organic production in aquatic ecosystems. Despite concerted efforts to address specific sources of pollution, diffuse pollution remains an issue. The Albufera of Valencia, a Mediterranean coastal lagoon, has been hypertrophic since the 1970s due to the impact of agricultural, urban and industrial activities. This study provides updated data (October 2023 to September 2024) through monthly sampling of 18 primary irrigation channels (representing 75% of the inflow) and the lagoon, as well as supplementary sampling of Wastewater Treatment Plants (WWTPs) and supply channels. A quantitative analysis of hydrology and water quality was conducted, with nutrient loads and contributions by hydrological sector from WWTPs and rice fields being estimated. The total inflow (265.27 hm³) was deemed acceptable; however, human management had a significant impact on the volume. Overa channel constituted the primary source of flow (29.98%) and was a significant contributor of Total Phosphorus (TP) (15.09 t) and Total Nitrogen (TN) (681.36 t). The southern agricultural sector contributed the majority of the TN (49.17%) and 26.07% of the TP, while the north, influenced by WWTPs, supplied 33.96% of the TP. Poyo stream exhibited an abnormally high TN load (28.62 t) from a contaminated aquifer. The rice fields located in the north and west have been observed to assimilate nutrients during irrigation. In the Albufera lagoon, a strong correlation was observed between phycocyanin (PC) and the total TP load (R² = 0.84). With the exception of "red water" periods, total TN exhibited a significant correlation with chlorophyll-a and carotenoids (Car), thereby suggesting co-limitation. The study corroborates the hypothesis that the Albufera's "poor" trophic status is the result of ongoing diffuse pressure from agriculture, urbanisation and industry. The findings emphasise the necessity for transparent water governance and integrated water quantity/quality management for ecosystem recovery
DOI: 10.5281/zenodo.17599460
title: Dataset of flows and nutrient inputs to the Albufera Coastal Lagoon (Valencia, Spain) during hydrological year 2023-2024

description: Anthropogenic eutrophication, caused by human inputs of nitrogen (N) and phosphorus (P), is a global problem that leads to excessive organic production in aquatic ecosystems. Despite concerted efforts to address specific sources of pollution, diffuse pollution remains an issue. The Albufera of Valencia, a Mediterranean coastal lagoon, has been hypertrophic since the 1970s due to the impact of agricultural, urban and industrial activities. This study provides updated data (October 2023 to September 2024) through monthly sampling of 18 primary irrigation channels (representing 75% of the inflow) and the lagoon, as well as supplementary sampling of Wastewater Treatment Plants (WWTPs) and supply channels. A quantitative analysis of hydrology and water quality was conducted, with nutrient loads and contributions by hydrological sector from WWTPs and rice fields being estimated. The total inflow (265.27 hm³) was deemed acceptable; however, human management had a significant impact on the volume. Overa channel constituted the primary source of flow (29.98%) and was a significant contributor of Total Phosphorus (TP) (15.09 t) and Total Nitrogen (TN) (681.36 t). The southern agricultural sector contributed the majority of the TN (49.17%) and 26.07% of the TP, while the north, influenced by WWTPs, supplied 33.96% of the TP. Poyo stream exhibited an abnormally high TN load (28.62 t) from a contaminated aquifer. The rice fields located in the north and west have been observed to assimilate nutrients during irrigation. In the Albufera lagoon, a strong correlation was observed between phycocyanin (PC) and the total TP load (R² = 0.84). With the exception of "red water" periods, total TN exhibited a significant correlation with chlorophyll-a and carotenoids (Car), thereby suggesting co-limitation. The study corroborates the hypothesis that the Albufera's "poor" trophic status is the result of ongoing diffuse pressure from agriculture, urbanisation and industry. The findings emphasise the necessity for transparent water governance and integrated water quantity/quality management for ecosystem recovery
DOI: 10.5281/zenodo.17588857
title: Datasets of High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform

description: Datasets of High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform. 

Figure 3 was produced using the file 1uM_243_400mM_b-Xyl_1.txt. 

Figure 4 was produced  using the files 25nM_243_100mM_bGalA.txt and 1uM_243_400mM_b-Xyl_1.txt

Figure 5 was produced using the files 25nM_243_100mM_bGalA.txt; 1uM_243_400mM_b-Gal_1.txt and 1uM_243_400mM_b-Xyl_1.txt

Table 1 was produced using all the files

Table 2 was produced using 25nM_243_100mM_bGalA.txt; 10uM_243_400mM_b-Gal_1 and 1uM_243_400mM_b-Xyl_1
DOI: 10.5281/zenodo.17588856
title: Datasets of High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform

description: Datasets of High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform. 

Figure 3 was produced using the file 1uM_243_400mM_b-Xyl_1.txt. 

Figure 4 was produced  using the files 25nM_243_100mM_bGalA.txt and 1uM_243_400mM_b-Xyl_1.txt

Figure 5 was produced using the files 25nM_243_100mM_bGalA.txt; 1uM_243_400mM_b-Gal_1.txt and 1uM_243_400mM_b-Xyl_1.txt

Table 1 was produced using all the files

Table 2 was produced using 25nM_243_100mM_bGalA.txt; 10uM_243_400mM_b-Gal_1 and 1uM_243_400mM_b-Xyl_1
DOI: 10.15468/dl.q68aew
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((132.7157 38.38558,114.53158 48.89827,94.92683 35.26017,111.4061 8.55223,138.39816 18.49668,132.7157 38.38558))",
 "TaxonKey is Maackia hupehensis"
 ]
}

 The dataset includes 132 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030685-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5284/1137441
title: Data from Archaeological Investigations at Agard Street, Derby, Derbyshire, June-July 2022

description: This collection includes the site records, digital photographs and CAD files from the evaluation, watching brief and excavation carried out by Archaeological Research Services Ltd at Agard Street, Derby between June and July 2022.
DOI: 10.15468/dl.wfp3jb
title: Occurrence Download

description: A dataset containing 1207 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((77.28647 7.50685,78.29867 7.23692,79.85975 9.82022,81.05204 11.74318,82.06643 15.99467,77.20398 12.05126,74.26323 13.15155,72.92063 13.74172,77.28647 7.50685))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Butea monosperma"
 ]
}

 The dataset includes 1207 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030686-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13718376
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.sdgaec
title: Occurrence Download

description: A dataset containing 6292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((162.74015 41.94613,135.17992 52.31679,117.56405 49.0493,122.96246 36.12153,131.06008 22.76756,139.01563 31.5755,162.74015 41.94613))",
 "TaxonKey is Castanea crenata"
 ]
}

 The dataset includes 6292 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030687-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17599663
title: Supplementary Information: Deep-sea benthic foraminiferal response to the Late Lutetian Thermal Maximum at Demerara Rise (ODP Site 1260, equatorial western Atlantic)

description: For this study, we combined published with new data from ODP Site 1260 to understand the biotic response to the Late Lutetian Thermal Maximum. This supplementary material includes four tables and a document. Table S1 includes the age model used in this study, S2 has the data from the quantitative analysis of benthic foraminifera associations, S3 has the quantitative and semi-quantitative analysis of other components of the samples, and S4 has the analysis of the preservation of the benthic foraminifera. The document include information about the statistical analyses, including supplementary figures to support the interpretation in the manuscript.
DOI: 10.5281/zenodo.16941244
title: Supplementary Information: Deep-sea benthic foraminiferal response to the Late Lutetian Thermal Maximum at Demerara Rise (ODP Site 1260, equatorial western Atlantic)

description: For this study, we combined published with new data from ODP Site 1260 to understand the biotic response to the Late Lutetian Thermal Maximum. This supplementary material includes four tables and a document. Table S1 includes the age model used in this study, S2 has the data from the quantitative analysis of benthic foraminifera associations, S3 has the quantitative and semi-quantitative analysis of other components of the samples, and S4 has the analysis of the preservation of the benthic foraminifera. The document include information about the statistical analyses, including supplementary figures to support the interpretation in the manuscript.
DOI: 10.15468/dl.4fabwe
title: Occurrence Download

description: A dataset containing 2327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Felis silvestris",
 "Year 2024-2025"
 ]
}

 The dataset includes 2327 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030688-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30609155
title: Additional Files for Transcript-Centric Gene Fusion Validation Pipeline

description: <b>Supplementary Data for: A WGS-Independent Framework for Gene Fusion Validation in Long-Read RNA-Seq Data</b><br><b>Description</b><br>This repository contains the supplementary materials, datasets, and performance metrics associated with the research article: <b>"A WGS-Independent Framework for Gene Fusion Validation in Long-Read RNA-Seq Data."</b><b>Study Overview:</b> Accurate validation of gene fusions from long-read RNA sequencing (RNA-Seq) data is a critical challenge in cancer genomics, often hampered by high false-positive rates and a reliance on matched whole-genome sequencing (WGS) data. This study introduces a novel, WGS-independent validation pipeline that utilizes transcript-centric evidence (full-length spanning reads, supplementary alignments, and realigned soft-clips) and a Random Forest machine learning classifier to automate fusion validation.<b>Contents of this Repository:</b> The following files are provided to support the reproducibility and benchmarking of the reported results:<b>Additional file 1: Evaluation of Random Forest Hyperparameters using 10-Fold Cross-Validation.</b>A visualization of the hyperparameter tuning process, showing performance metrics (Accuracy, AUC-PR, etc.) across various model configurations (number of trees, tree depth, etc.) used to select the optimal Random Forest model.<b>Additional file 2: Validated gene fusions in cancer cell lines.</b>A comprehensive dataset listing all gene fusions validated by the pipeline across the five cancer cell lines analyzed (MCF7, A549, K562, HCT116, HepG2). This includes both known fusions (e.g., <i>BCAS4-BCAS3</i>) and novel discoveries (e.g., <i>MOV10-RHOC</i>).<b>Additional file 3: Merged Reference Database of Known Gene Fusions.</b>A consolidated reference dataset combining gene fusion entries from the COSMIC and FusionGDB databases. This file served as the external knowledge base for cross-referencing fusion candidates and establishing the ground truth labels for the machine learning model.<b>Additional file 4: Example summary of random forest output.</b>A representative output table generated by the pipeline for the MCF7 cell line, showing the probability scores, read support metrics, and final classifications for fusion candidates.<b>Methodology:</b> The data was generated using a custom R-based pipeline that integrates <i>Samtools</i> and <i>Minimap2</i> for alignment processing and <i>tidymodels</i> for machine learning. The initial candidate list was generated using LongGF on long-read RNA-Seq data from the Singapore Nanopore Expression Project (SG-NEx).<b>Code Availability:</b> The source code for the validation pipeline and the Singularity recipe for reproducibility are available on GitHub:https://github.com/iisomineaamos/fusion-validation-pipeline
DOI: 10.6084/m9.figshare.30609155.v1
title: Additional Files for Transcript-Centric Gene Fusion Validation Pipeline

description: <b>Supplementary Data for: A WGS-Independent Framework for Gene Fusion Validation in Long-Read RNA-Seq Data</b><br><b>Description</b><br>This repository contains the supplementary materials, datasets, and performance metrics associated with the research article: <b>"A WGS-Independent Framework for Gene Fusion Validation in Long-Read RNA-Seq Data."</b><b>Study Overview:</b> Accurate validation of gene fusions from long-read RNA sequencing (RNA-Seq) data is a critical challenge in cancer genomics, often hampered by high false-positive rates and a reliance on matched whole-genome sequencing (WGS) data. This study introduces a novel, WGS-independent validation pipeline that utilizes transcript-centric evidence (full-length spanning reads, supplementary alignments, and realigned soft-clips) and a Random Forest machine learning classifier to automate fusion validation.<b>Contents of this Repository:</b> The following files are provided to support the reproducibility and benchmarking of the reported results:<b>Additional file 1: Evaluation of Random Forest Hyperparameters using 10-Fold Cross-Validation.</b>A visualization of the hyperparameter tuning process, showing performance metrics (Accuracy, AUC-PR, etc.) across various model configurations (number of trees, tree depth, etc.) used to select the optimal Random Forest model.<b>Additional file 2: Validated gene fusions in cancer cell lines.</b>A comprehensive dataset listing all gene fusions validated by the pipeline across the five cancer cell lines analyzed (MCF7, A549, K562, HCT116, HepG2). This includes both known fusions (e.g., <i>BCAS4-BCAS3</i>) and novel discoveries (e.g., <i>MOV10-RHOC</i>).<b>Additional file 3: Merged Reference Database of Known Gene Fusions.</b>A consolidated reference dataset combining gene fusion entries from the COSMIC and FusionGDB databases. This file served as the external knowledge base for cross-referencing fusion candidates and establishing the ground truth labels for the machine learning model.<b>Additional file 4: Example summary of random forest output.</b>A representative output table generated by the pipeline for the MCF7 cell line, showing the probability scores, read support metrics, and final classifications for fusion candidates.<b>Methodology:</b> The data was generated using a custom R-based pipeline that integrates <i>Samtools</i> and <i>Minimap2</i> for alignment processing and <i>tidymodels</i> for machine learning. The initial candidate list was generated using LongGF on long-read RNA-Seq data from the Singapore Nanopore Expression Project (SG-NEx).<b>Code Availability:</b> The source code for the validation pipeline and the Singularity recipe for reproducibility are available on GitHub:https://github.com/iisomineaamos/fusion-validation-pipeline
DOI: 10.5281/zenodo.17599671
title: Research data results
DOI: 10.5281/zenodo.17599670
title: Research data results
DOI: 10.5281/zenodo.15727028
title: Behavioral and Hematological Effects of Postnatal Darbepoetin in a Rat Model of ASD

description: This dataset accompanies the manuscript "Therapeutic Timing Limitations of Postnatal Darbepoetin in a Valproic Acid Rat Model of Autism Spectrum Disorder" accepted for publication in PLOS ONE.The dataset includes raw behavioral data from three-chamber social interaction tests and Morris Water Maze with reversal learning, hematological measurements (hemoglobin and hematocrit), and complete statistical analyses.The data support an analysis of the therapeutic potential and timing limitations of EPO analogues in a preclinical model of ASD. All files are provided in accessible formats (Excel) with comprehensive documentation for transparency, replication, and reuse. Full methodological details and results are described in the associated manuscript.

This update includes changes during the manuscript's revision process: hematocrit measurements (in addition to hemoglobin), P28 hematological data for the VPA group, and reformatted statistical outputs matching the manuscript's supplementary files.
DOI: 10.5281/zenodo.17597016
title: Behavioral and Hematological Effects of Postnatal Darbepoetin in a Rat Model of ASD

description: This dataset accompanies the manuscript "Therapeutic Timing Limitations of Postnatal Darbepoetin in a Valproic Acid Rat Model of Autism Spectrum Disorder" accepted for publication in PLOS ONE.The dataset includes raw behavioral data from three-chamber social interaction tests and Morris Water Maze with reversal learning, hematological measurements (hemoglobin and hematocrit), and complete statistical analyses.The data support an analysis of the therapeutic potential and timing limitations of EPO analogues in a preclinical model of ASD. All files are provided in accessible formats (Excel) with comprehensive documentation for transparency, replication, and reuse. Full methodological details and results are described in the associated manuscript.

This update includes changes during the manuscript's revision process: hematocrit measurements (in addition to hemoglobin), P28 hematological data for the VPA group, and reformatted statistical outputs matching the manuscript's supplementary files.
DOI: 10.15468/dl.n9j744
title: Occurrence Download

description: A dataset containing 4003 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((139.79898 24.95682,123.74581 47.40285,91.63947 45.55603,87.94581 24.38857,103.14661 14.44412,126.87121 19.27428,139.79898 24.95682))",
 "TaxonKey is Castanea mollissima"
 ]
}

 The dataset includes 4003 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030691-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bfmdsq
title: Occurrence Download

description: A dataset containing 3301276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eucalyptus brandiana, Eucalyptus cloeziana, Eucalyptus microcorys, Populus nigra, Rhododendron molle, Rubia yunnanensis, Setaria viridis, Solanum ochranthum, Triadica sebifera, Tubocapsicum anomalum, Corymbia maculata, Poacynum pictum, Boechera falcata, Amaranthus retroflexus, Cichorium intybus, Elaeis oleifera, Geum urbanum, Glycine max, Kirengeshoma palmata, Macadamia integrifolia, Oryza rufipogon, Poa annua, Rhododendron delavayi, Solanum torvum, Tagetes erecta, Xanthium orientale, Ficus simplicissima, Aralia elata, Erigeron bonariensis, Myrica gale, Simmondsia chinensis, Viola odorata, Populus deltoides, Alcea rosea, Antiaris toxicaria, Phanera championii, Conyza sumatrensis, Eucalyptus paniculata, Firmiana major, Luffa acutangula, Lysimachia maritima, Mangifera indica, Pistacia vera, Populus lasiocarpa, Rhododendron vialii, Dryas octopetala, Abrus pulchellus, Actinidia eriantha, Actinidia latifolia, Actinidia rufa)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3301276 records from 5828 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030674-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13837552
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.17688066
title: Certificate (HarvardX – Online Learning)
DOI: 10.5281/zenodo.17688067
title: Certificate (HarvardX – Online Learning)
DOI: 10.15468/dl.eruq5m
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((113.63536 -8.03849,115.03133 -8.03849,115.03133 -7.48042,113.63536 -7.48042,113.63536 -8.03849))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bubalus bubalis",
 "Year 2010-2025"
 ]
}

 The dataset includes 31 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003961-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xez83d
title: Occurrence Download

description: A dataset containing 52665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Ursidae"
 ]
}

 The dataset includes 52665 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003951-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hsje4y
title: Occurrence Download

description: A dataset containing 180495 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "GadmGid is IND.16.5_1",
 "HasCoordinate is true"
 ]
}

 The dataset includes 180495 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003943-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17688115
title: Supplementary Table 1

description: This dataset contains the Specimen IDs, the species names of each specimen, and the original measurement values for On.Ar and H.Ar.
DOI: 10.5281/zenodo.17688116
title: Supplementary Table 1

description: This dataset contains the Specimen IDs, the species names of each specimen, and the original measurement values for On.Ar and H.Ar.
DOI: 10.6084/m9.figshare.30686624
title: Supplementary Information 2 Assay Methods & Results FINAL

description: The paper displays an exemplification of antiorganotrophism (tissue reduction) in vivo utilising ovine materials obtained from adult ewes. Ovine plasma was subjected to a bioassay-guided fractionation utilising a rat organometric assay that was conducted according to a standardised method over four days with intraperitoneal dosing. Organ shrinkage was readily provoked in what is a relatively crude assay in vivo. In cell culture experiments, shrinkage of rat bone marrow stem cells could be readily demonstrated using neat plasma from ovary-intact sheep, with such activity lacking in plasma from ovariectomised sheep