cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3706747_d3
title: MOESM2 of Assessing histone demethylase inhibitors in cells: lessons learned

description: Additional file 2: Table S1. KDMs and mutant KDMs for which assays are reported including histone mark assessed.
DOI: 10.6084/m9.figshare.c.3706753_d4.v1
title: Additional file 4: of Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

description: Common dysregulated miRNAs between human UPJ (urine) and mouse partial UUO (kidney tissue). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3706768_d2
title: Additional file 2: of Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

description: Gene Ontology terms significantly differentially regulated in sequential life history transitions (Blast2GO, FDR
DOI: 10.6084/m9.figshare.c.3706768_d4.v1
title: Additional file 4: of Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

description: Leading edge analysis results for protein, carbohydrate, and fatty acid metabolism pathways. Worksheet 1: Change in gene expression in multiple protein metabolism pathways, as determined by leading edge analysis in GSEA. Shows those genes that are shared in more than one protein metabolism pathway (as denoted by X), not all genes in all pathways; Worksheet 2: Change in gene expression in multiple carbohydrate and fatty acid metabolism pathways, as determined by leading edge analysis in GSEA. Shows those genes that are shared in more than one protein metabolism pathway (as denoted by X), not all genes in all pathways. (XLSX 48Â kb)
DOI: 10.15468/dl.6hxuwr
title: Occurrence Download

description: A dataset containing 614 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cantherhines macrocerus (Hollard, 1853)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 614 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038356-241126133413365/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.c.3706768_d4
title: Additional file 4: of Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

description: Leading edge analysis results for protein, carbohydrate, and fatty acid metabolism pathways. Worksheet 1: Change in gene expression in multiple protein metabolism pathways, as determined by leading edge analysis in GSEA. Shows those genes that are shared in more than one protein metabolism pathway (as denoted by X), not all genes in all pathways; Worksheet 2: Change in gene expression in multiple carbohydrate and fatty acid metabolism pathways, as determined by leading edge analysis in GSEA. Shows those genes that are shared in more than one protein metabolism pathway (as denoted by X), not all genes in all pathways. (XLSX 48Â kb)
DOI: 10.6084/m9.figshare.c.3706747_d8.v1
title: MOESM7 of Assessing histone demethylase inhibitors in cells: lessons learned

description: Additional file 7: Table S3. Effect of Doxorubicin, Paclitaxel and Staurosporine on KDM activity measured in in vitro KDM assay.
DOI: 10.6084/m9.figshare.c.3706768_d6.v1
title: Additional file 6: of Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

description: Transcripts with potential orthologs in humans and not in D. melanogaster or C. elegans. (TXT 44Â kb)
DOI: 10.6084/m9.figshare.c.3706747_d8
title: MOESM7 of Assessing histone demethylase inhibitors in cells: lessons learned

description: Additional file 7: Table S3. Effect of Doxorubicin, Paclitaxel and Staurosporine on KDM activity measured in in vitro KDM assay.
DOI: 10.6084/m9.figshare.c.3706768_d6
title: Additional file 6: of Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system

description: Transcripts with potential orthologs in humans and not in D. melanogaster or C. elegans. (TXT 44Â kb)
DOI: 10.5281/zenodo.14511331
title: Queer Food Futures: Ethical Intersections of Artificial Intelligence, Queer Theory, and Global Food Systems

description: This article interrogates the evolving intersections between artificial intelligence (AI), queer ethics, and global food systems through a multidisciplinary and critical theoretical lens. As AI technologies increasingly permeate the agricultural, culinary, and gastronomic spheres, their role as both disruptors and facilitators of traditional food hierarchies necessitates nuanced ethical exploration. Drawing from posthumanist ethics (Braidotti, 2013), queer ecologies (Mortimer-Sandilands & Erickson, 2010), and intersectional analyses of food justice (Crenshaw, 1989), this paper reconfigures the human-machine-food nexus, foregrounding marginalized perspectives in the techno-ecological assemblage.
DOI: 10.5281/zenodo.14511332
title: Queer Food Futures: Ethical Intersections of Artificial Intelligence, Queer Theory, and Global Food Systems

description: This article interrogates the evolving intersections between artificial intelligence (AI), queer ethics, and global food systems through a multidisciplinary and critical theoretical lens. As AI technologies increasingly permeate the agricultural, culinary, and gastronomic spheres, their role as both disruptors and facilitators of traditional food hierarchies necessitates nuanced ethical exploration. Drawing from posthumanist ethics (Braidotti, 2013), queer ecologies (Mortimer-Sandilands & Erickson, 2010), and intersectional analyses of food justice (Crenshaw, 1989), this paper reconfigures the human-machine-food nexus, foregrounding marginalized perspectives in the techno-ecological assemblage.
DOI: 10.6084/m9.figshare.c.3706792_d3
title: Additional file 3: Table S1. of A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality

description: Sequences of primers used for studies of GhLPAAT expression. Table S2. Sequences of primers of GhLPAATs to identify single nucleotide polymorphic markers (SNPs) based on single strand conformation polymporphism (SSCP). Table S3. Domain analysis and annotation. Table S4. Oil and protein quantitative trait loci (QTL). Table S5. Identification of putative sequence variation (SNPs) by SOAPsnp in NMGA-062 vs. NMGA-105 database. L indicates SNP only exists in long fiber length line NMGA-062 (fiber length, 32.58 mm) when compared with the sequenced genome sequence of TM-1. S indicates SNP only exists in short fiber length line NMGA-105 (fiber length, 27.06 mm) when compared with the sequenced genome sequence of TM-1. L/S indicates SNP exists in the two lines. Table S6. Identification of putative SNPs by SOAPsnp in Xuzhou 142 vs. Xuzhou 142 fl database. WT indicates SNP only exists in Xuzhou 142 when compared with the sequenced genome sequence of TM-1. fl indicates SNP only exists in Xuzhou 142 fl when compared with the sequenced genome sequence of TM-1. WT/fl indicates SNP exists in the two lines. The polymorphic SSCP marker is shown in red color. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3706795_d2.v1
title: Additional file 2: of A rapid review of the rate of attrition from the health workforce

description: SoWMy Dataset for Attrition. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3706795_d2
title: Additional file 2: of A rapid review of the rate of attrition from the health workforce

description: SoWMy Dataset for Attrition. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.28050632
title: Supplementary Material for: Real-life nationwide outcomes of bronchoscopic lung volume reduction with endobronchial valves in severe COPD

description: Introduction:
Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death globally, characterized by airflow limitation and lung hyperinflation due to emphysema. Bronchoscopic lung volume reduction (BLVR) with endobronchial valves offers a minimally invasive treatment option for emphysema, aiming to reduce lung hyperinflation, thereby improving lung function and exercise tolerance.

Methods:
This study evaluated the efficacy of BLVR in a real-life nationwide setting using comprehensive Danish registries. The study population included patients who underwent BLVR between January 1, 2013, and December 31, 2021. We assessed clinical outcomes, including Forced Expiratory Volume in 1 second (FEV1), Medical Research Council (MRC) dyspnea score, and the rates of exacerbations and pneumonia before and after the procedure. A control cohort of matched COPD patients was also analyzed.

Results:
Following BLVR, a significant increase in FEV1, similar to the improvements reported in randomized controlled trials was observed. Additionally, the proportion of patients classified as GOLD stage IV decreased from 71.3% to 60.6% after BLVR. The incidence rate ratio for severe exacerbations significantly dropped to 0.56 (95% CI 0.47-0.67, p&lt;0.01) after BLVR. No significant changes were observed in the rates of moderate and severe pneumonia, and mortality rates did not differ significantly from those in the matched control cohort.

Conclusion:
This study demonstrates the real-life efficacy of BLVR using endobronchial valves, highlighting a significant improvement in FEV1 and a reduction in severe COPD exacerbations. The procedure did not increase pneumonia rates or affect mortality, supporting continued use of BLVR for managing patients with COPD.
DOI: 10.6084/m9.figshare.28050632.v1
title: Supplementary Material for: Real-life nationwide outcomes of bronchoscopic lung volume reduction with endobronchial valves in severe COPD

description: Introduction:
Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death globally, characterized by airflow limitation and lung hyperinflation due to emphysema. Bronchoscopic lung volume reduction (BLVR) with endobronchial valves offers a minimally invasive treatment option for emphysema, aiming to reduce lung hyperinflation, thereby improving lung function and exercise tolerance.

Methods:
This study evaluated the efficacy of BLVR in a real-life nationwide setting using comprehensive Danish registries. The study population included patients who underwent BLVR between January 1, 2013, and December 31, 2021. We assessed clinical outcomes, including Forced Expiratory Volume in 1 second (FEV1), Medical Research Council (MRC) dyspnea score, and the rates of exacerbations and pneumonia before and after the procedure. A control cohort of matched COPD patients was also analyzed.

Results:
Following BLVR, a significant increase in FEV1, similar to the improvements reported in randomized controlled trials was observed. Additionally, the proportion of patients classified as GOLD stage IV decreased from 71.3% to 60.6% after BLVR. The incidence rate ratio for severe exacerbations significantly dropped to 0.56 (95% CI 0.47-0.67, p&lt;0.01) after BLVR. No significant changes were observed in the rates of moderate and severe pneumonia, and mortality rates did not differ significantly from those in the matched control cohort.

Conclusion:
This study demonstrates the real-life efficacy of BLVR using endobronchial valves, highlighting a significant improvement in FEV1 and a reduction in severe COPD exacerbations. The procedure did not increase pneumonia rates or affect mortality, supporting continued use of BLVR for managing patients with COPD.
DOI: 10.15468/dl.34r7vn
title: Occurrence Download

description: A dataset containing 611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cantherhines pullus (Ranzani, 1842)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 611 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038357-241126133413365/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.c.3708112_d1.v1
title: Additional file 1: of Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use

description: Relative abundances of bacterial groups in each sample. (XLSX 316 kb)
DOI: 10.6084/m9.figshare.c.3708112_d1
title: Additional file 1: of Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use

description: Relative abundances of bacterial groups in each sample. (XLSX 316 kb)
DOI: 10.6084/m9.figshare.c.3708112_d2.v1
title: Additional file 2: of Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use

description: R script for the main analysis. (R 4 kb)
DOI: 10.6084/m9.figshare.c.3708112_d2
title: Additional file 2: of Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use

description: R script for the main analysis. (R 4 kb)
DOI: 10.15468/dl.mbyrhj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Canthigaster jamestyleri Moura & Castro, 2002",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038358-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3708169_d10.v1
title: Additional file 9: of Normalization and microbial differential abundance strategies depend upon data characteristics

description: Code adapted from McMurdie and Holmes [18] to include additional methods. This code is the basis for Figs. 4 and 5.
DOI: 10.6084/m9.figshare.c.3708169_d10
title: Additional file 9: of Normalization and microbial differential abundance strategies depend upon data characteristics

description: Code adapted from McMurdie and Holmes [18] to include additional methods. This code is the basis for Figs. 4 and 5.
DOI: 10.15468/dl.eah4m7
title: Occurrence Download

description: A dataset containing 1637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Canthigaster rostrata (Bloch, 1786)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1637 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038359-241126133413365/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.c.3709237_d1
title: Additional file 1: Table S1. of SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

description: Sensitivity and specificity of our approach to discriminate non-target sequences. (XLSX 34 kb)ďťż
DOI: 10.6084/m9.figshare.c.3709237_d2
title: Additional file 2: Table S2. of SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

description: List of taxa confirmed from contigs of E. coli SAGs and no template control. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.c.3709270_d2.v1
title: Additional file 11: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: sheet a Summary statistics of filtering steps (using cutadapt v.1.8.1 and ConDeTri v.2.2) performed on raw Illumina sequencing data of three different tissue types (putative venom glands, pharyngeal lobes, and posterior body wall) analyzed in G. tridactyla. Transcriptome libraries were constructed for a single individual (SR21, putative venom glands; SR23, pharyngeal lobes; and SR25, posterior body wall), and based on pooled samples comprising RNA of three individuals (SR22, putative venom glands; SR24, pharyngeal lobes; and SR26, posterior body wall). Abbreviations: PE, paired-end reads; SR, single reads. sheet b Summary statistics of IDBA-tran v.1.1.1 assemblies performed on processed Illumina sequencing data originating from G. tridactyla. Assemblies were done for three different tissue types of a single individual (SR21, putative venom glands; SR23, pharyngeal lobes; and SR25, posterior body wall), and for Illumina sequencing data of three pooled individuals (SR22, putative venom glands; SR24, pharyngeal lobes; and SR26, posterior body wall). In addition, the filtered reads of single and pooled libraries were merged (SR21 + SR22, putative venom glands; SR23 + SR24, pharyngeal lobes; SR25 + SR26, posterior body wall) to perform comparative expression studies by mapping them against GLTx reference sequences. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3709231_d8
title: Additional file 8: of Improving disclosure of medical error through educational program as a first step toward patient safety

description: Participantâ  s Response to medical errors. Description of data: Raw data of participantâ  s response to medical errors (3 clinical cases with different severity of error outcome), satisfaction and change after the education program. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3709270_d2
title: Additional file 11: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: sheet a Summary statistics of filtering steps (using cutadapt v.1.8.1 and ConDeTri v.2.2) performed on raw Illumina sequencing data of three different tissue types (putative venom glands, pharyngeal lobes, and posterior body wall) analyzed in G. tridactyla. Transcriptome libraries were constructed for a single individual (SR21, putative venom glands; SR23, pharyngeal lobes; and SR25, posterior body wall), and based on pooled samples comprising RNA of three individuals (SR22, putative venom glands; SR24, pharyngeal lobes; and SR26, posterior body wall). Abbreviations: PE, paired-end reads; SR, single reads. sheet b Summary statistics of IDBA-tran v.1.1.1 assemblies performed on processed Illumina sequencing data originating from G. tridactyla. Assemblies were done for three different tissue types of a single individual (SR21, putative venom glands; SR23, pharyngeal lobes; and SR25, posterior body wall), and for Illumina sequencing data of three pooled individuals (SR22, putative venom glands; SR24, pharyngeal lobes; and SR26, posterior body wall). In addition, the filtered reads of single and pooled libraries were merged (SR21 + SR22, putative venom glands; SR23 + SR24, pharyngeal lobes; SR25 + SR26, posterior body wall) to perform comparative expression studies by mapping them against GLTx reference sequences. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3709270_d3.v1
title: Additional file 12: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Set of primers used to analyze the molecular organization of the GLTx gene. sheet a Primer used to amplify GLTx fragments before cloning into the pGEMÂŽ -T Vector (pGEMÂŽ-T Vector System I, Promega Corporation, Madison, WI). sheet b Primer used for primer walking (Cons_clone_5A, 6A, and 7). sheet c Primer used to analyze the intron-exon-structure in genomic DNA of G. tridactyla. GW, Genome walking. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3709270_d3
title: Additional file 12: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Set of primers used to analyze the molecular organization of the GLTx gene. sheet a Primer used to amplify GLTx fragments before cloning into the pGEMÂŽ -T Vector (pGEMÂŽ-T Vector System I, Promega Corporation, Madison, WI). sheet b Primer used for primer walking (Cons_clone_5A, 6A, and 7). sheet c Primer used to analyze the intron-exon-structure in genomic DNA of G. tridactyla. GW, Genome walking. (XLSX 14 kb)
DOI: 10.15468/dl.jy8n6t
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Capros aper (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 625 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038360-241126133413365/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.c.3709306_d1
title: Additional file 10: Simulated Dataset 2. of ProteoModlR for functional proteomic analysis

description: Normalization_dataset_no_error. The file contains a simulated datasets with identical intensity values for all peptides in all conditions. This dataset is provided as a reference to evaluate the accuracy of normalization strategies. (CSV 4 kb)
DOI: 10.6084/m9.figshare.c.3709270_d9.v1
title: Additional file 5: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: MS-MS best hits of the 150Â kDa fractions (sheet a and b) of G. tridactyla venom. Spectra were searched against a pooled-tissue transcriptomic sequence database of the pharyngeal lobes (SR23, single specimen and merged SR23â  +â  SR24, pooled multiple specimen) with ProteinPilot v.5.0. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3709270_d10.v1
title: Additional file 6: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Alignment comprising a 746Â bp gene fragment of 52 GLTx clones and three GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318). The alignment was used for the maximum likelihood analysis shown in Fig.Â 1b. (TXT 42 kb)
DOI: 10.6084/m9.figshare.c.3709270_d9
title: Additional file 5: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: MS-MS best hits of the 150Â kDa fractions (sheet a and b) of G. tridactyla venom. Spectra were searched against a pooled-tissue transcriptomic sequence database of the pharyngeal lobes (SR23, single specimen and merged SR23â  +â  SR24, pooled multiple specimen) with ProteinPilot v.5.0. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3709270_d11.v1
title: Additional file 7: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Alignment of amplicons generated in genomic DNA of G. tridactyla. Sanger sequences revealed an intron-exon-structure for the GLTx gene (see Additional file 4: Figure S2). (TXT 68 kb)
DOI: 10.6084/m9.figshare.c.3709270_d10
title: Additional file 6: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Alignment comprising a 746Â bp gene fragment of 52 GLTx clones and three GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318). The alignment was used for the maximum likelihood analysis shown in Fig.Â 1b. (TXT 42 kb)