cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25981450.v9
title: 2020-2021 Changjiang estuary dissloved oxygen isotopic compositions, gas ratios and MATLAB scripts

description: Understanding the complex processes that lead to oxygen depletion is challenging. The nonlinear relationship between dissolved oxygen (DO) isotopic composition (δ<sup>18</sup>O ) and its concentration makes δ<sup>18</sup>O a unique tracer for studying O2 cycling in oxygen depletion zones. Based on the DO δ<sup>18</sup>O compositions from four cruises conducted from summer 2020 to spring 2021 in the Changjiang Estuary, we identified a dynamic northern oxygen depletion zone (NODZ) with seasonally varying DO δ<sup>18</sup>O values, and a relatively stable southern oxygen depletion zone (SODZ). To quantify the contributions of low oxygen water mixing and respiration to oxygen depletion, we conducted a Monte-Carlo mixing experiment involving high salinity and low oxygen water (HSLO) and mixed layer water (MLW). Our findings indicated that HSLO mixing contributed to 59% to 100% of oxygen deficit in oxygen depletion zones, with SODZ exhibiting a HSLO mixing contribution of more than 78%. Respiration contributed to the remaining oxygen deficit, with water column respiration consuming approximately 1.5 times more oxygen than sediment oxygen consumption. In the NODZ, oxygen depletion was further enhanced by water column stratification, respiration and seafloor topography. Overall, the influx of HSLO was a key trigger for oxygen depletion in the Changjiang Estuary. The spatial and temporal variations of the two oxygen depletion zones were closely linked to the intrusion and retreat of HSLO from summer to autumn. Our findings highlight the importance of utilizing DO δ<sup>18</sup>O to differentiate and quantify biological and physical processes in coastal oxygen depletion zones.File description：Table S1: Data for this study, including latitude and longitude, sampling depth, temperature, salinity, δO<sub>2</sub>/Ar,δ<sup>18</sup>O,[O<sub>2</sub>],[O<sub>2</sub>]/[O<sub>2</sub>]<sub>sat</sub>, densityTable S3: The results of Monte-Carlo mixing experiments in all samples beneath mixed layer: the fraction of HSLO in different water masses, [O<sub>2</sub>] and δ<sup>18</sup>O after mixing from Monte-Carlo mixing experiment. Oxygen depletion caused by mixing and total oxygen depletion. The contribution of mixing and respiration to oxygen deficit. The apparent respiration fractionation factor and the proportion of WCR and SOC to oxygen deficit as well as the observed salinity, [O<sub>2</sub>] and δ<sup>18</sup>O beneath the mixed layerThe text file contains the MATLAB code for the Monte Carlo mixing experiments. It demonstrates the computational process of the Monte Carlo method using July as an example.<br>
DOI: 10.15468/dl.ykv43u
title: Occurrence Download

description: A dataset containing 1808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dieffenbachia seguine (Jacq.) Schott)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1808 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000437-250226211154957/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nyjrkb
title: Occurrence Download

description: A dataset containing 166 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macaca mulatta mulatta"
 ]
}

 The dataset includes 166 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000421-250226211518916/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.26520670
title: Data package for Size control and oscillations of active droplets in synthetic cells

description: Supporting datasets for each figure
DOI: 10.6084/m9.figshare.26520670.v1
title: Data package for Size control and oscillations of active droplets in synthetic cells

description: Supporting datasets for each figure
DOI: 10.6084/m9.figshare.26396422
title: Structures of TGF-β with betaglycan and the signaling receptors reveal the mechanism whereby betaglycan potentiates receptor complex assembly and signaling

description: Cryo-EM maps with models and X-ray crystallography data with models for TGF-β in complex with betaglycan and other signalling receptors
DOI: 10.6084/m9.figshare.26396422.v1
title: Structures of TGF-β with betaglycan and the signaling receptors reveal the mechanism whereby betaglycan potentiates receptor complex assembly and signaling

description: Cryo-EM maps with models and X-ray crystallography data with models for TGF-β in complex with betaglycan and other signalling receptors
DOI: 10.5287/bodleian:y095g0n9g
title: Data for PloS One resilience paper

description: Data in excel format underpinning Plos One research paper about cognitive resilience on the Whitehall II imaging sub-study
DOI: 10.15468/dl.6m2hkp
title: Occurrence Download

description: A dataset containing 955 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salix babylonica L."
 ]
}

 The dataset includes 955 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000423-250226211518916/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.26318410
title: Interpreting mammalian evolutionary constraint at synonymous sites in light of the unwanted transcript hypothesis

description: Source data for the analysis carried out in this manuscript, as an RData object
DOI: 10.6084/m9.figshare.26318410.v1
title: Interpreting mammalian evolutionary constraint at synonymous sites in light of the unwanted transcript hypothesis

description: Source data for the analysis carried out in this manuscript, as an RData object
DOI: 10.6084/m9.figshare.28187936
title: Constructing a global human epidemic database using open-source digital biosurveillance

description: Here we present a subset of data from Ginkgo Biosecurity's Human Epidemic Database (HED), which consists of outbreak data collected from official, open-source surveillance reports. This provided dataset includes 1,044 epidemic events with onset between 2015 and 2020, covering more 230 countries and territories and 120 pathogens.

The methodology to collate these data have been described in a manuscript submitted for publication, ‘Constructing a global human epidemic database using open-source digital biosurveillance’.

Datasets included:
- HED_data repository.csv - Event-level data repository with epidemics starting in 2015 to 2020.
- HED_pathogens_supplement.csv - A list of pathogens and their associated grouping within our epidemic event scoring framework. This pathogen/grouping list is not comprehensive but rather a sampling of the pathogens scored.
- HED_metadata.csv - Meta data describing columns in ‘HED_complete data repository.csv’
DOI: 10.6084/m9.figshare.27242145
title: Direct conversion of various phosphate sources to a versatile P-X reagent [TBA][PO2X2] via redox-neutral halogenation

description: Direct conversion of various phosphate sources to a versatile 
P-X reagent [TBA][PO2X2] via redox-neutral halogenation (Supporting source data)
DOI: 10.6084/m9.figshare.27242145.v1
title: Direct conversion of various phosphate sources to a versatile P-X reagent [TBA][PO2X2] via redox-neutral halogenation

description: Direct conversion of various phosphate sources to a versatile 
P-X reagent [TBA][PO2X2] via redox-neutral halogenation (Supporting source data)
DOI: 10.15468/dl.xq3dsm
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Citrus ×limon (L.) Osbeck"
 ]
}

 The dataset includes 306 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000424-250226211518916/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.27179964
title: A high-quality chromosome-level genome assembly of Pacific white shrimp (Penaeus vannamei)

description: we sequenced the genome of the Pacific white shrimp using PacBio and Hi-C technologies, resulting in a 1.7Gb genome assembly with a Contig N50 of 57.65Kb and a Scaffold N50 of 605Kb. BUSCO analysis revealed that the genome assembly exhibited a gene coverage of 84.6%, which is considered high among crustacean reference genomes. In total, 907,237,377 bp of repetitive sequences (accounting for 50.48% of the assembled genome) and 22,923 protein-coding genes were identified. Utilizing Hi-C technology, we anchored 14,604 contigs onto 44 chromosomes, yielding a chromosome-level genome assembly with a contig N50 of 42,894,961 bp. In summary, our high-quality genome assembly provides valuable reference genomic resources for the improvement and breeding of elite cultivars of the Pacific white shrimp.
DOI: 10.6084/m9.figshare.27871998
title: High electrostrain in lead-free piezoceramic from chemopiezoelectric effect

description: Source Data of Figures in main article.
DOI: 10.6084/m9.figshare.27871998.v1
title: High electrostrain in lead-free piezoceramic from chemopiezoelectric effect

description: Source Data of Figures in main article.
DOI: 10.5281/zenodo.14909537
title: Raw data of SARS-CoV-2 samples collected in Sicily in July and November 2021.
title: CovidTGI: a tool to investigate the Temporal Genetic Instability of SARS-CoV-2 variants

description: Next Generation Sequencing (NGS) DNAseq data of Sars-CoV-2 coming from swab samples.
DOI: 10.5281/zenodo.14909538
title: Raw data of SARS-CoV-2 samples collected in Sicily in July and November 2021.
title: CovidTGI: a tool to investigate the Temporal Genetic Instability of SARS-CoV-2 variants

description: Next Generation Sequencing (NGS) DNAseq data of Sars-CoV-2 coming from swab samples.
DOI: 10.15468/dl.q3sztd
title: Occurrence Download

description: A dataset containing 987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Digera muricata (L.) Mart.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 987 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000425-250226211518916/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.86ftyv
title: Occurrence Download

description: A dataset containing 1129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is one of (China, Chinese Taipei)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Solenopsis invicta Buren, 1972, Rhynchophorus ferrugineus (A.G.Olivier, 1791), Phenacoccus solenopsis Tinsley, 1898, Oracella acuta (Lobdell, 1930), Matsucoccus matsumurae (Kuwana, 1905), Liriomyza sativae Blanchard, 1938, Leptinotarsa decemlineata (Say, 1824), Hyphantria cunea (Drury, 1773), Dendroctonus valens LeConte, 1859, Cydia pomonella (Linnaeus, 1758), Lissorhoptrus oryzophilus Kuschel, 1952, Tuta absoluta (Meyrick, 1917), Spodoptera frugiperda J.E.Smith, 1797)"
 ]
}

 The dataset includes 1129 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000426-250226211518916/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fc4u54
title: Occurrence Download

description: A dataset containing 305 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Camera trap database of Tiger from Rajaji National Park, Uttarakhand"
 ]
}

 The dataset includes 305 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000438-250226211154957/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14280723
title: Nasal vs. oral BREATHing WIn Strategies in healthy individuals during cardiorespiratory Exercise testing (BreathWISE)

description: Background: Nasal and oral exclusive breathing modes have benefits and drawbacks during submaximal exercise. It is less known whether these responses would extend to anaerobic work performed at high intensity. The purpose of this study is to find the most efficient mode of breathing during different phases of a maximal exercise at cardiopulmonary exercise test (CPET).

Methods: Healthy subjects were recruited to perform 4 maximal CPETs (standard conditions (STD), exclusively nasal breathing (eNAS), exclusively oral breathing (eOR), partial nasal breathing (pNAS) with just one blocked nostril) using the same ramp protocol on an electronically braked cycle ergometer. Before the exercise a standard spirometry was executed in the same order.

Results: Twelve healthy subjects (28.6±5.2 y, 50% males) performed the 4 CPETs within one month. Variables were analysed at rest, at anaerobic threshold (AT), at intermediate exercise steps, and at peak. Compared to STD, eOR, and pNAS conditions, eNAS was associated with a significant lower peakVO2, peakVCO2, peak ventilation, respiratory rate, VE/VCO2 slope, respiratory exchange ratio, and workload (p<0.05 for all). Moreover, peak inspiration and peak expiration time were augmented, while forced expiratory volume and vital capacity at rest were reduced. On opposite, only minor differences were detected at rest or AT. eNAS breathing Borg scale was higher in all phases of the exercise.

Conclusions: In young healthy subjects, an exclusively nasal respiration induces significant impairment on peak exercise capacity at CPET due to ventilatory limitation, with only minor effects on metabolic parameters at rest and in submaximal effort.
DOI: 10.5281/zenodo.14280724
title: Nasal vs. oral BREATHing WIn Strategies in healthy individuals during cardiorespiratory Exercise testing (BreathWISE)

description: Background: Nasal and oral exclusive breathing modes have benefits and drawbacks during submaximal exercise. It is less known whether these responses would extend to anaerobic work performed at high intensity. The purpose of this study is to find the most efficient mode of breathing during different phases of a maximal exercise at cardiopulmonary exercise test (CPET).

Methods: Healthy subjects were recruited to perform 4 maximal CPETs (standard conditions (STD), exclusively nasal breathing (eNAS), exclusively oral breathing (eOR), partial nasal breathing (pNAS) with just one blocked nostril) using the same ramp protocol on an electronically braked cycle ergometer. Before the exercise a standard spirometry was executed in the same order.

Results: Twelve healthy subjects (28.6±5.2 y, 50% males) performed the 4 CPETs within one month. Variables were analysed at rest, at anaerobic threshold (AT), at intermediate exercise steps, and at peak. Compared to STD, eOR, and pNAS conditions, eNAS was associated with a significant lower peakVO2, peakVCO2, peak ventilation, respiratory rate, VE/VCO2 slope, respiratory exchange ratio, and workload (p<0.05 for all). Moreover, peak inspiration and peak expiration time were augmented, while forced expiratory volume and vital capacity at rest were reduced. On opposite, only minor differences were detected at rest or AT. eNAS breathing Borg scale was higher in all phases of the exercise.

Conclusions: In young healthy subjects, an exclusively nasal respiration induces significant impairment on peak exercise capacity at CPET due to ventilatory limitation, with only minor effects on metabolic parameters at rest and in submaximal effort.
DOI: 10.15468/dl.8a7mzm
title: Occurrence Download

description: A dataset containing 1015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Digitalis lanata Ehrh.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1015 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000428-250226211518916/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5287/bodleian:pzme0pzak
title: Municipal evidence for cities of Roman Sicily

description: Data was gathered from published epigraphic evidence according to a set of categories and criteria agreed in the EMIRE programme of UMR8210 ANHIMA of the CNRS, during 2007-2008 Spreadsheet of attestations of evidence for municipal institutions and administration in the coloniae and municipia of Sicily in the first three centuries AD.
DOI: 10.15468/dl.favam9
title: Occurrence Download

description: A dataset listing the 209 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Kenya",
 "DatasetKey is one of (EOD – eBird Observation Dataset, A Bird Atlas of Kenya, VectorBase (Bioinformatics Resource for Invertebrate Vectors of Human Pathogens), NRM-Mammals, Kenya Bird Map (Full protocol and Adhoc records), International Barcode of Life project (iBOL), CABI Africa Invasive and Alien Species data, Academy of Natural Sciences of Philadelphia Ornithology Collection, UJ Nature Education Centre - the Lepidoptera Collection, Fish species occurrences in the rivers of the Lake Victoria Basin Kenya, digitized from the Ichthyology specimen collection at the National Museums of Kenya, Occurrence data of dragonflies available at the National Museums of Kenya's Natural History Collection, Invertebrates Zoology Section.)",
 "Geometry POLYGON((34.66548 0.07851,34.83142 0.08251,34.83142 0.28148,34.66988 0.28164,34.63149 0.21606,34.66548 0.07851))",
 "IucnRedListCategory is one of (EX, EW, CR, EN, NT, VU, NE, LC, DD)",
 "PublishingOrg is one of (e2e717bf-551a-4917-bdc9-4fa0f342c530, d8d6c888-92e7-4036-9808-fb3812be61e1, 6ba9a8cc-513a-4a51-bf93-6f5de8040a96, dd862d06-e6e9-4ab9-bc86-c875cc148c1f, 29817330-5d61-11d8-b9b2-b8a03c50a862, fd515d3a-b237-42de-bba6-760008580da5, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 97a3ce10-3e54-11d9-8439-b8a03c50a862, b3bf3a83-1f68-4541-a03f-330d30d567f5)",
 "Year 1980-2025"
 ]
}

 The dataset's 209 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000422-250226211518916/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qr5san
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Macaca mulatta mulatta"
 ]
}

 The dataset includes 62 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000440-250226211154957/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcj6a3
title: Occurrence Download

description: A dataset containing 203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Kalidium cuspidatum (Ung.-Sternb.) Grubov"
 ]
}

 The dataset includes 203 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000429-250226211518916/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6k9rs2
title: Occurrence Download

description: A dataset containing 880141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carassius auratus (Linnaeus, 1758), Carassius carassius (Linnaeus, 1758), Ctenopharyngodon idella (Valenciennes, 1844), Cyprinus carpio Linnaeus, 1758, Esox lucius Linnaeus, 1758, Macrobrachium rosenbergii (De Man, 1879))",
 "HasCoordinate is true",
 "DecimalLatitude is less than 60",
 "DecimalLatitude is greater than -56",
 "DecimalLongitude is less than 180",
 "DecimalLongitude is greater than -145"
 ]
}

 The dataset includes 880141 records from 1141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000433-250226211154957/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14887338
title: Data and code for "Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD"

description: Purpose

Single nucleotide polymorphisms (SNPs), the most common form of genomic variation, play key roles in micro-evolution and adaptation. In Drosophila melanogaster, many SNPs have been associated to phenotypes through association studies, yet functional validation remains challenging and experimental evidence for functional impact rare.

Here, we present FlyCADD, an impact prediction tool that integrates high-quality D. melanogaster genome annotations into a single score reflecting the predicted impact of a SNP. FlyCADD can be applied to distinguish causal from neutral variants, 1) for variant ranking and prioritization of SNPs for functional studies, 2) to improve genome-editing experimental design or evaluation and 3) to enhance interpretation of naturally occuring SNPs, thereby improving our understanding of genotype-phenotype relationships. 

Dataset content

We provide FlyCADD impact prediction scores readily available, both as precomputed scores for all possible single nucleotide variants on the D. melanogaster reference genome and through a locally executable pipeline for scoring novel variants of interest. If you want the FlyCADD scores to your SNPs of interest, they can often be found in the precomputed FlyCADD score files without the need to run the pipeline. If you have any questions, feel free to contact j.beets@vu.nl.

This repository provides:



        Precomputed FlyCADD scores for all possible SNPs on the D. melanogaster reference genome Release 6 (.csv files)

        A locally executable FlyCADD pipeline for scoring novel variants, including the trained logistic regression model files, annotation files and scripts (Python)

        166-way multi-species alignment file underlying FlyCADD (.maf file)

        Reconstructed ancestral sequence underlying FlyCADD (.fasta files)

        Derived and simulated variants used for model training and testing FlyCADD (.vcf files)

        FlyCADD scores at all codon positions of unique transcripts in D. melanogaster (.txt files)


Additional resources

The full pipeline of FlyCADD development is available on GitHub (https://github.com/JuliaBeets/FlyCADD/). For any additional information regarding the collection and generation of data please contact us.