cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.smnq9e
title: Occurrence Download

description: A dataset containing 490 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((128.1495 -3.721335, 128.2744 -3.721335, 128.2744 -3.616112, 128.1495 -3.616112, 128.1495 -3.721335))",
 "Year is greater than or equal to 2013",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 490 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002436-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25rruu
title: Occurrence Download

description: A dataset containing 69598 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gorsachius melanolophus (Raffles, 1822)"
 ]
}

 The dataset includes 69598 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002432-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dk7zhr
title: Occurrence Download

description: A dataset containing 389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Russian Federation",
 "GadmGid is one of (RUS.18_1, RUS.9_1, RUS.83_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Rattus norvegicus (Berkenhout, 1769), Ondatra zibethicus (Linnaeus, 1766), Nyctereutes procyonoides (Gray, 1834), Neogale Gray, 1865, Mus musculus Linnaeus, 1758, Canis familiaris Linnaeus, 1758, Apodemus agrarius (Pallas, 1771), Phasianus colchicus Linnaeus, 1758, Pseudorasbora parva (Temminck & Schlegel, 1846), Perccottus glenii Dybowski, 1877, Carassius gibelio (Bloch, 1782), Carassius auratus (Linnaeus, 1758), Polygraphus proximus Blandford, 1894, Leptinotarsa decemlineata (Say, 1824), Harmonia axyridis (Pallas, 1773), Diaspidiotus perniciosus (Comstock, 1881))"
 ]
}

 The dataset includes 389 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002438-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3mh2br
title: Occurrence Download

description: A dataset containing 69598 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gorsachius melanolophus (Raffles, 1822)"
 ]
}

 The dataset includes 69598 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002435-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2se8g
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DEU.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Pacifastacus leniusculus (Dana, 1852)",
 "Year 2019-2024"
 ]
}

 The dataset includes 136 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002448-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gknx25
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Loxodonta cyclotis (Matschie, 1900)"
 ]
}

 The dataset includes 710 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002439-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/6ee17a0b-2d29-485c-9e1e-1f56648ddefc
title: Data underlying the publication: "Nature-based mitigation of shoreline erosion risks in tidal marshes created by managed realignment vs. sediment nourishment"

description: We aimed to improve our current understanding of the development of sediment strength and erosion resistance under a high flow velocity in restored and created tidal marshes, and of how this development is affected by tidal inundation, sediment characteristics, and vegetation. We compared sediment strength and erosion resistance at a managed realignment site (since 2015) and at a sediment nourishment site combined with brushwood groynes (since 2018). At both these sites, we selected locations with differences in tidal inundation duration, sediment grain size, and vegetation presence or absence, to test the effect of these factors on sediment strength and erosion resistance. This dataset contains all data of these two sites.
DOI: 10.4121/6ee17a0b-2d29-485c-9e1e-1f56648ddefc.v1
title: Data underlying the publication: "Nature-based mitigation of shoreline erosion risks in tidal marshes created by managed realignment vs. sediment nourishment"

description: We aimed to improve our current understanding of the development of sediment strength and erosion resistance under a high flow velocity in restored and created tidal marshes, and of how this development is affected by tidal inundation, sediment characteristics, and vegetation. We compared sediment strength and erosion resistance at a managed realignment site (since 2015) and at a sediment nourishment site combined with brushwood groynes (since 2018). At both these sites, we selected locations with differences in tidal inundation duration, sediment grain size, and vegetation presence or absence, to test the effect of these factors on sediment strength and erosion resistance. This dataset contains all data of these two sites.
DOI: 10.15468/dl.zwszft
title: Occurrence Download

description: A dataset containing 995 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is China",
 "TaxonKey is Gymnaconitum gymnandrum (Maxim.) Wei Wang & Z.D.Chen"
 ]
}

 The dataset includes 995 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010325-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvajac
title: Occurrence Download

description: A dataset containing 69119 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oenanthe fistulosa L."
 ]
}

 The dataset includes 69119 records from 621 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010324-241107131044228/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.27678792
title: Raw data files

description: Transcriptome analysis of AoNmd5 in nematode-trapping fungus Arthrobotrys oligospora
DOI: 10.6084/m9.figshare.27678540
title: Metadata spreadsheet

description: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoNmd5 were involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.
DOI: 10.6084/m9.figshare.27678567
title: Processed data files

description: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoNmd5 were involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.
DOI: 10.15468/dl.7gzss6
title: Occurrence Download

description: A dataset containing 2287 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oenanthe fluviatilis (Bab.) Coleman"
 ]
}

 The dataset includes 2287 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010326-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tztqdp
title: Occurrence Download

description: A dataset containing 2171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichosurus vulpecula (Kerr, 1792)",
 "Country is New Zealand",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 2171 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010327-241107131044228/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.27231701
title: Targeting AGAT gene expression – a drug screening approach for the treatment of GAMT deficiency

description: Targeting the enzyme L-Arginine:glycine amidinotransferase (AGAT) to reduce the formation of guanidinoacetate (GAA) in patients with guanidinoacetate methyltransferase (GAMT) deficiency, we attempted to identify drugs for repurposing that reduce the expression of AGAT via transcriptional inhibition. The authors applied a HeLa cell line stably expressing AGAT promoter and firefly luciferase reporter for high-content screening and secondary screening. For further assessment, the authors integrated Nanoluc luciferase as a reporter into the endogenous AGAT gene in HAP1 cell lines and used the human immortalized cell line RH30 as model of GAMT deficiency. Screening 6,000 drugs and drug-like compounds, the authors identified 43 and 34 high-score candidates as inhibitors and inducers of AGAT promoter-reporter expression, respectively. After further deselection considering dose response, drug toxicity, topical formulations, price, and accessibility, the authors assessed seven candidates and found none of them demonstrating efficacy in HAP1 and RH30 cells and warranting further assessment. The selection of the test models is crucial for screening of gene repressor drugs. Almost all drugs with an impact on gene expression had off-target effects. It is unlikely to find drugs that are selective inhibitors of AGAT expression, rendering pharmacological AGAT gene repression a risky approach for the treatment of GAMT deficiency.
DOI: 10.6084/m9.figshare.27231701.v1
title: Targeting AGAT gene expression – a drug screening approach for the treatment of GAMT deficiency

description: Targeting the enzyme L-Arginine:glycine amidinotransferase (AGAT) to reduce the formation of guanidinoacetate (GAA) in patients with guanidinoacetate methyltransferase (GAMT) deficiency, we attempted to identify drugs for repurposing that reduce the expression of AGAT via transcriptional inhibition. The authors applied a HeLa cell line stably expressing AGAT promoter and firefly luciferase reporter for high-content screening and secondary screening. For further assessment, the authors integrated Nanoluc luciferase as a reporter into the endogenous AGAT gene in HAP1 cell lines and used the human immortalized cell line RH30 as model of GAMT deficiency. Screening 6,000 drugs and drug-like compounds, the authors identified 43 and 34 high-score candidates as inhibitors and inducers of AGAT promoter-reporter expression, respectively. After further deselection considering dose response, drug toxicity, topical formulations, price, and accessibility, the authors assessed seven candidates and found none of them demonstrating efficacy in HAP1 and RH30 cells and warranting further assessment. The selection of the test models is crucial for screening of gene repressor drugs. Almost all drugs with an impact on gene expression had off-target effects. It is unlikely to find drugs that are selective inhibitors of AGAT expression, rendering pharmacological AGAT gene repression a risky approach for the treatment of GAMT deficiency.
DOI: 10.6084/m9.figshare.27124515
title: A real-world pharmacovigilance study using disproportionality analysis of United States Food and Drug Administration Adverse Event Reporting System events for vinca alkaloids: comparing vinorelbine and Vincristine

description: Vinca alkaloids are widely used in cancer treatment for their ability to target microtubule dynamics. While their efficacy in treating certain cancers is well-established, the full spectrum of their adverse event profiles remains an area of ongoing research. We analyzed AEs related to vinorelbine and vincristine using a retrospective case/non-case approach with data from the FDA Adverse Event Reporting System (FAERS). We applied various algorithms to detect AE signals: the reporting odds ratio (ROR) and proportional reporting ratio (PRR) measured disproportionality and association strength; the Bayesian confidence propagation neural network (BCPNN) calculated the Information Component (IC) for associations against background rates; and the multi-item gamma Poisson shrinker (MGPS) yielded empirical Bayes geometric mean (EBGM) values, accounting for reporting variability. Both medications significantly involve the blood and lymphatic systems, with vinorelbine reporting 401 cases in this System Organ Class (SOC), exhibiting a ROR of 17.4, PRR of 12.4, IC of 3.63, and EBGM of 12.38. An intersection analysis of Preferred Terms (PTs) has uncovered previously unreported AEs shared by both drugs, including posterior reversible encephalopathy syndrome and inappropriate antidiuretic hormone secretion. This analysis highlights the need for ongoing research of the risks associated with vinorelbine and vincristine.
DOI: 10.6084/m9.figshare.27124515.v2
title: A real-world pharmacovigilance study using disproportionality analysis of United States Food and Drug Administration Adverse Event Reporting System events for vinca alkaloids: comparing vinorelbine and Vincristine

description: Vinca alkaloids are widely used in cancer treatment for their ability to target microtubule dynamics. While their efficacy in treating certain cancers is well-established, the full spectrum of their adverse event profiles remains an area of ongoing research. We analyzed AEs related to vinorelbine and vincristine using a retrospective case/non-case approach with data from the FDA Adverse Event Reporting System (FAERS). We applied various algorithms to detect AE signals: the reporting odds ratio (ROR) and proportional reporting ratio (PRR) measured disproportionality and association strength; the Bayesian confidence propagation neural network (BCPNN) calculated the Information Component (IC) for associations against background rates; and the multi-item gamma Poisson shrinker (MGPS) yielded empirical Bayes geometric mean (EBGM) values, accounting for reporting variability. Both medications significantly involve the blood and lymphatic systems, with vinorelbine reporting 401 cases in this System Organ Class (SOC), exhibiting a ROR of 17.4, PRR of 12.4, IC of 3.63, and EBGM of 12.38. An intersection analysis of Preferred Terms (PTs) has uncovered previously unreported AEs shared by both drugs, including posterior reversible encephalopathy syndrome and inappropriate antidiuretic hormone secretion. This analysis highlights the need for ongoing research of the risks associated with vinorelbine and vincristine.
DOI: 10.6084/m9.figshare.27124515.v1
title: A real-world pharmacovigilance study using disproportionality analysis of united states food and drug administration adverse event reporting system events for vinca alkaloids: comparing vinorelbine and Vincristine

description: Vinca alkaloids are widely used in cancer treatment for their ability to target microtubule dynamics. While their efficacy in treating certain cancers is well-established, the full spectrum of their adverse event profiles remains an area of ongoing research. We analyzed AEs related to vinorelbine and vincristine using a retrospective case/non-case approach with data from the FDA Adverse Event Reporting System (FAERS). We applied various algorithms to detect AE signals: the reporting odds ratio (ROR) and proportional reporting ratio (PRR) measured disproportionality and association strength; the Bayesian confidence propagation neural network (BCPNN) calculated the Information Component (IC) for associations against background rates; and the multi-item gamma Poisson shrinker (MGPS) yielded empirical Bayes geometric mean (EBGM) values, accounting for reporting variability. Both medications significantly involve the blood and lymphatic systems, with vinorelbine reporting 401 cases in this System Organ Class (SOC), exhibiting a ROR of 17.4, PRR of 12.4, IC of 3.63, and EBGM of 12.38. An intersection analysis of Preferred Terms (PTs) has uncovered previously unreported AEs shared by both drugs, including posterior reversible encephalopathy syndrome and inappropriate antidiuretic hormone secretion. This analysis highlights the need for ongoing research of the risks associated with vinorelbine and vincristine.
DOI: 10.15468/dl.ma67pv
title: Occurrence Download

description: A dataset containing 8172 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oenanthe javanica (Blume) DC."
 ]
}

 The dataset includes 8172 records from 215 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010328-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14097665
title: geophis_sartorii_spades_01.fasta.gz
DOI: 10.5281/zenodo.14097666
title: geophis_sartorii_spades_01.fasta.gz
DOI: 10.15468/dl.t9wyz6
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Iguana iguana (Linnaeus, 1758)",
 "Year 1000-2000"
 ]
}

 The dataset includes 129 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010329-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ez27vt
title: Occurrence Download

description: A dataset containing 1525 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Boana albomarginata (Spix, 1824))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1525 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010330-241107131044228/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.27678552
title: Results of the Study on Climate Change and Its Impacts on Flooding and Seasonal Flow in the Kaligandaki River Basin, Nepal

description: These datasets were generated in a study assessing the impacts of climate change on seasonal flow and flood characteristics in the Kaligandaki River Basin of Nepal, South Asia.
DOI: 10.5281/zenodo.14097784
title: Supplementary Files (Figures and Tables)

description: Supplementary files for publication: 

Figure S1: Stacked barplots of the mean relative abundances of the most abundant phyla. The x-axis labels refer to soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA), Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed). 

Figure S2: Ordination showing the first two axes of the Principal Coordinates Analysis (PCO). a. total microbial community, b. virulence factors. Light grey symbols represent total microbial community or VFs with the symbol size representing their abundance (number of sequence reads). Symbol codes refer to: soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA), Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed).

Figure S3: Procrustes analysis comparing putative pathogens versus a. total microbial community, b. antibiotic resistance genes (ARGs) and c. virulence factor (Vfs) composition (arrowbase indicates the corresponding positions of the samples in the total microbial community or ARGs or VFs ordination (de Voogd et al. 2019) while arrowheads indicate the corresponding positions of the samples in the putative pathogens ordination). While d. represents the procrustes analysis comparing total microbial community versus a. ARGs (in this case: arrowbase indicates the corresponding positions of the samples in ARGs ordination while arrowheads indicate the corresponding positions of the samples in the total microbial community ordination). Symbol codes refer to: soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA),  Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed).

Tables S1-S11.
DOI: 10.5281/zenodo.14097785
title: Supplementary Files (Figures and Tables)

description: Supplementary files for publication: 

Figure S1: Stacked barplots of the mean relative abundances of the most abundant phyla. The x-axis labels refer to soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA), Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed). 

Figure S2: Ordination showing the first two axes of the Principal Coordinates Analysis (PCO). a. total microbial community, b. virulence factors. Light grey symbols represent total microbial community or VFs with the symbol size representing their abundance (number of sequence reads). Symbol codes refer to: soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA), Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed).

Figure S3: Procrustes analysis comparing putative pathogens versus a. total microbial community, b. antibiotic resistance genes (ARGs) and c. virulence factor (Vfs) composition (arrowbase indicates the corresponding positions of the samples in the total microbial community or ARGs or VFs ordination (de Voogd et al. 2019) while arrowheads indicate the corresponding positions of the samples in the putative pathogens ordination). While d. represents the procrustes analysis comparing total microbial community versus a. ARGs (in this case: arrowbase indicates the corresponding positions of the samples in ARGs ordination while arrowheads indicate the corresponding positions of the samples in the total microbial community ordination). Symbol codes refer to: soft coral (CrS), hard coral (CrH), sea cucumber (SeC), flatworm (Flt), chiton (Cht), algae (Alg), the sponges Ptilocaulis sp. (SpT), Aaptos lobata (SpA),  Cinachyrella sp. (SpC), and Paratetilla sp. (SpP), seawater (Wat), and sediment (Sed).

Tables S1-S11.
DOI: 10.25345/c56h4d279
title: MassIVE MSV000096388 - HDAC8_SAHA_PCI-34051_HDX-MS_Luo
title: This dataset contains the HDX-MS raw mass spectra data in the article 'Integrating native MS, HDX-MS, and MD simulations to uncover the dynamic inhibition mechanism and distant structural changes of PCI-34051 on HDAC8'.
DOI: 10.15468/dl.hajnzu
title: Occurrence Download

description: A dataset containing 700 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hemitriccus kaempferi (Zimmer, 1953))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 700 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010334-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.