cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24032337
title: Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs

description: Single-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impacting phenotypic traits. In this study, we utilised reduced representation bisulphite sequencing (RRBS) to analyse DNA methylation in muscle tissue samples collected from 140 Yorkshire pigs. Additionally, we assessed SNPs using the Porcine 50K chip, examined 17 fatty acid traits, and conducted epigenome-wide association studies (EWAS) and genome-wide association studies (GWAS). Our investigation revealed numerous associations between DNA methylation and fatty acid traits, including C16:0, C18:0, C20:3n-3, and C22:6n-3. Notably, a substantial portion of these associations was specifically identified by EWAS and not GWAS. Subsequently, we performed GWAS to identify meQTLs using methylation levels of significant CpGs from the EWAS as traits. The results revealed the predominance of trans-meQTLs; however, we also discovered a cis-meQTL on SSC12. Finally, we reported a crucial CpG site (SSC12:3735523) and its cis-meQTL on SSC12, which are located in close proximity to the FASN gene. Our findings contribute to the identification of CpG sites and their cis-meQTLs associated with fatty acid traits, utilising comprehensive genome and methylome data. Moreover, our study provides novel insights into the molecular mechanisms underlying fatty acid traits in pigs.
DOI: 10.6084/m9.figshare.24032337.v1
title: Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs

description: Single-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impacting phenotypic traits. In this study, we utilised reduced representation bisulphite sequencing (RRBS) to analyse DNA methylation in muscle tissue samples collected from 140 Yorkshire pigs. Additionally, we assessed SNPs using the Porcine 50K chip, examined 17 fatty acid traits, and conducted epigenome-wide association studies (EWAS) and genome-wide association studies (GWAS). Our investigation revealed numerous associations between DNA methylation and fatty acid traits, including C16:0, C18:0, C20:3n-3, and C22:6n-3. Notably, a substantial portion of these associations was specifically identified by EWAS and not GWAS. Subsequently, we performed GWAS to identify meQTLs using methylation levels of significant CpGs from the EWAS as traits. The results revealed the predominance of trans-meQTLs; however, we also discovered a cis-meQTL on SSC12. Finally, we reported a crucial CpG site (SSC12:3735523) and its cis-meQTL on SSC12, which are located in close proximity to the FASN gene. Our findings contribute to the identification of CpG sites and their cis-meQTLs associated with fatty acid traits, utilising comprehensive genome and methylome data. Moreover, our study provides novel insights into the molecular mechanisms underlying fatty acid traits in pigs.
DOI: 10.6084/m9.figshare.21804943
title: Genetic background of semen parameters in Italian Simmental bulls

description: The aim of this study was to estimate genetic parameters and investigate the genomic background of scrotal circumference and semen parameters in the Italian Simmental bulls. Scrotal circumference, number of normal spermatozoa, ejaculate volume, spermatozoa motility, and total spermatozoa were measured on 622 bulls, of which 603 had genotypes for 42,141 SNP. Variance components of scrotal circumference were estimated with an animal model that included the fixed effects of birth year, animal age, and measurement method, and the random effects of day of measurement and animal. In the model for the other traits, the scrotal circumference was added as a covariate to account for its influence on the semen parameters. A genome-wide association study was carried out using the ssGBLUP-approach. Heritabilities ranged from 0.07 ± 0.05 (spermatozoa motility) to 0.50 ± 0.14 (scrotal circumference). A total of 13 SNP passed the Bonferroni correction threshold and the number of significantly associated markers ranged from 1 (ejaculate volume and spermatozoa motility) to 5 (total spermatozoa). Genes already associated with reproduction parameters were retrieved close to the significant SNP. Results of the present study gave preliminary insights about the genetic determinism of semen quality in Italian Simmental bulls.HighlightsLow to moderate heritabilities were estimated for semen traits.Few markers were associated with the phenotypes, suggesting their polygenic determinism.Candidate genes already associated in literature with sperm traits were found. Low to moderate heritabilities were estimated for semen traits. Few markers were associated with the phenotypes, suggesting their polygenic determinism. Candidate genes already associated in literature with sperm traits were found.
DOI: 10.6084/m9.figshare.21804943.v2
title: Genetic background of semen parameters in Italian Simmental bulls

description: The aim of this study was to estimate genetic parameters and investigate the genomic background of scrotal circumference and semen parameters in the Italian Simmental bulls. Scrotal circumference, number of normal spermatozoa, ejaculate volume, spermatozoa motility, and total spermatozoa were measured on 622 bulls, of which 603 had genotypes for 42,141 SNP. Variance components of scrotal circumference were estimated with an animal model that included the fixed effects of birth year, animal age, and measurement method, and the random effects of day of measurement and animal. In the model for the other traits, the scrotal circumference was added as a covariate to account for its influence on the semen parameters. A genome-wide association study was carried out using the ssGBLUP-approach. Heritabilities ranged from 0.07 ± 0.05 (spermatozoa motility) to 0.50 ± 0.14 (scrotal circumference). A total of 13 SNP passed the Bonferroni correction threshold and the number of significantly associated markers ranged from 1 (ejaculate volume and spermatozoa motility) to 5 (total spermatozoa). Genes already associated with reproduction parameters were retrieved close to the significant SNP. Results of the present study gave preliminary insights about the genetic determinism of semen quality in Italian Simmental bulls.HighlightsLow to moderate heritabilities were estimated for semen traits.Few markers were associated with the phenotypes, suggesting their polygenic determinism.Candidate genes already associated in literature with sperm traits were found. Low to moderate heritabilities were estimated for semen traits. Few markers were associated with the phenotypes, suggesting their polygenic determinism. Candidate genes already associated in literature with sperm traits were found.
DOI: 10.6084/m9.figshare.21804943.v1
title: Genetic background of semen parameters in Italian Simmental bulls

description: The aim of this study was to estimate genetic parameters and investigate the genomic background of scrotal circumference and semen parameters in the Italian Simmental bulls. Scrotal circumference, number of normal spermatozoa, ejaculate volume, spermatozoa motility, and total spermatozoa were measured on 622 bulls, of which 603 had genotypes for 42,141 SNP. Variance components of scrotal circumference were estimated with an animal model that included the fixed effects of birth year, animal age, and measurement method, and the random effects of day of measurement and animal. In the model for the other traits, the scrotal circumference was added as a covariate to account for its influence on the semen parameters. A genome-wide association study was carried out using the ssGBLUP-approach. Heritabilities ranged from 0.07 ± 0.05 (spermatozoa motility) to 0.50 ± 0.14 (scrotal circumference). A total of 13 SNP passed the Bonferroni correction threshold and the number of significantly associated markers ranged from 1 (ejaculate volume and spermatozoa motility) to 5 (total spermatozoa). Genes already associated with reproduction parameters were retrieved close to the significant SNP. Results of the present study gave preliminary insights about the genetic determinism of semen quality in Italian Simmental bulls.HighlightsLow to moderate heritabilities were estimated for semen traits.Few markers were associated with the phenotypes, suggesting their polygenic determinism.Candidate genes already associated in literature with sperm traits were found. Low to moderate heritabilities were estimated for semen traits. Few markers were associated with the phenotypes, suggesting their polygenic determinism. Candidate genes already associated in literature with sperm traits were found.
DOI: 10.6084/m9.figshare.24204399
title: Assessing major genes allele frequencies and the genetic diversity of the native Aosta cattle female population

description: The Aosta cattle breeds have a key role in the economy of the Aosta Valley. In addition to the meat and milk production these autochthonous breeds are important for their cultural value, and for their role in the maintenance of the mountain environment. The knowledge of their genetic makeup represents a fundamental asset to managing the reproduction of the population in order to maintain the existing genetic diversity and, as a possible input, to apply genomic selection in a small population. A total of 3195 Aosta cows were genotyped with the GeneSeek Genomic Profiler® (GGP) Bovine 100K by Neogen in the framework of the DUALBREEDING-2 project. The Aosta Black-Chestnut and Chestnut-Herèn resulted to be a unique population. The Aosta female population had shorter ROH than bulls and shared ROH_islands that harbour adaptative and functional genes. Allele frequencies of major genes highlight the possibility for selection for both milk and meat quality variants and that the Aosta cattle population is free from the known Mendelian inheritance diseases found in cosmopolitan breeds (e.g. BLAD, CVM, HCD). The autochthonous Aosta cattle breeds are free from the Mendelian inheritance disease variants found in cosmopolitan cattle.Allele frequencies revealed the effort in selection for variants related to cheese yield and a viable selection for variants related to meat quality.The use of genomic information in Aosta cattle can help maintain the biodiversity of these local breeds and their peculiarities. The autochthonous Aosta cattle breeds are free from the Mendelian inheritance disease variants found in cosmopolitan cattle. Allele frequencies revealed the effort in selection for variants related to cheese yield and a viable selection for variants related to meat quality. The use of genomic information in Aosta cattle can help maintain the biodiversity of these local breeds and their peculiarities.
DOI: 10.6084/m9.figshare.24204399.v1
title: Assessing major genes allele frequencies and the genetic diversity of the native Aosta cattle female population

description: The Aosta cattle breeds have a key role in the economy of the Aosta Valley. In addition to the meat and milk production these autochthonous breeds are important for their cultural value, and for their role in the maintenance of the mountain environment. The knowledge of their genetic makeup represents a fundamental asset to managing the reproduction of the population in order to maintain the existing genetic diversity and, as a possible input, to apply genomic selection in a small population. A total of 3195 Aosta cows were genotyped with the GeneSeek Genomic Profiler® (GGP) Bovine 100K by Neogen in the framework of the DUALBREEDING-2 project. The Aosta Black-Chestnut and Chestnut-Herèn resulted to be a unique population. The Aosta female population had shorter ROH than bulls and shared ROH_islands that harbour adaptative and functional genes. Allele frequencies of major genes highlight the possibility for selection for both milk and meat quality variants and that the Aosta cattle population is free from the known Mendelian inheritance diseases found in cosmopolitan breeds (e.g. BLAD, CVM, HCD). The autochthonous Aosta cattle breeds are free from the Mendelian inheritance disease variants found in cosmopolitan cattle.Allele frequencies revealed the effort in selection for variants related to cheese yield and a viable selection for variants related to meat quality.The use of genomic information in Aosta cattle can help maintain the biodiversity of these local breeds and their peculiarities. The autochthonous Aosta cattle breeds are free from the Mendelian inheritance disease variants found in cosmopolitan cattle. Allele frequencies revealed the effort in selection for variants related to cheese yield and a viable selection for variants related to meat quality. The use of genomic information in Aosta cattle can help maintain the biodiversity of these local breeds and their peculiarities.
DOI: 10.15468/dl.28cq3c
title: Occurrence Download

description: A dataset listing the 17369 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((119.58483 19.95066,118.39874 15.55726,119.28514 13.10545,120.78262 10.14523,119.63839 7.27887,120.17397 3.68134,119.41705 1.10723,118.27591 -1.97582,118.23497 -3.96066,116.16471 -6.34903,114.49934 -7.16739,114.32699 -8.43587,115.67227 -9.68291,117.95291 -10.72275,121.24207 -11.84168,124.57701 -11.96147,128.62265 -9.57238,130.46148 -7.83039,132.13112 -4.52347,129.99612 2.41832,128.82022 8.69088,126.17798 13.73557,125.77395 17.76563,119.58483 19.95066))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Magnoliopsida, Liliopsida)"
 ]
}

 The dataset's 17369 records were derived from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048878-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14030799
title: Dataset of the paper: A new species of mantellid frog of the genus Guibemantis from south-eastern Madagascar

description: Dataset of the paper: A new species of mantellid frog of the genus Guibemantis from south-eastern Madagascar

Carl R. Hutter, Zo F. Andriampenomanana, Edmund W. Basham, Frank Glaw, Matteo D. Masotti, Shea M. Lambert, Miguel Vences

Zootaxa 5647 (3): 260–274

https://doi.org/10.11646/zootaxa.5647.3.3

 

Contains:

Original call recording of the new species, guibemantis sioka

Maximum likelihood tree in Newick format

Fasta file of alignment used for analysis (mitochondrial 16S rRNA gene fragment)
DOI: 10.5281/zenodo.14030800
title: Dataset of the paper: A new species of mantellid frog of the genus Guibemantis from south-eastern Madagascar

description: Dataset of the paper: A new species of mantellid frog of the genus Guibemantis from south-eastern Madagascar

Carl R. Hutter, Zo F. Andriampenomanana, Edmund W. Basham, Frank Glaw, Matteo D. Masotti, Shea M. Lambert, Miguel Vences

Zootaxa 5647 (3): 260–274

https://doi.org/10.11646/zootaxa.5647.3.3

 

Contains:

Original call recording of the new species, guibemantis sioka

Maximum likelihood tree in Newick format

Fasta file of alignment used for analysis (mitochondrial 16S rRNA gene fragment)
DOI: 10.5281/zenodo.15675353
title: Dataset "Inferential online measurement of 3D fractal dimension of spray fluidized bed agglomerates"

description: The archive contains all data files necessary for replication of the findings reported in Men et al. "Inferential online measurement of 3D fractal dimension of spray fluidized bed agglomerates" (DOI: to be added).
DOI: 10.5281/zenodo.15675354
title: Dataset "Inferential online measurement of 3D fractal dimension of spray fluidized bed agglomerates"

description: The archive contains all data files necessary for replication of the findings reported in Men et al. "Inferential online measurement of 3D fractal dimension of spray fluidized bed agglomerates" (DOI: to be added).
DOI: 10.57701/suf.vvl.2010.1-0
title: Vollendete Versichertenleben 2010
title: SUF
title: VVL

description: Scientific Use File Vollendete Versichertenleben (SUF.VVL):Grundlage des Verlaufsdatensatzes SUF.VVL ist die Rentenzugangsstatistik (§ 6 RSVwV, SK90) verknüpft mit Daten im Format der Versichertenkontenstichprobe (§ 1 RSVwV Abs. 2, SK79). Die Grundgesamtheit bildet der Versichertenrentenzugang eingeschränkt auf Alters- und Erwerbsminderungsrenten sowie definierte Meldegründe (insbesondere erstmaliger Rentenbezug). Die Größe der Zufallsstichprobe beträgt 25% Prozent.Berichtet wird neben demographischen Angaben über wichtige rentenrechtliche Sachverhalte wie beispielsweise Rentenhöhe, Komponenten des Rentenzahlbetrages, Entgeltpunkte sowie angerechnete versicherungsrechtliche Zeiten. Die Verlaufsdaten beschreiben die soziale Erwerbssituation während des Versichertenlebens, aber auch Sachverhalte wie beispielsweise Krankheit, Arbeitslosigkeit, Kindererziehung und Entgelt monatsgenau. Die monatlichen Angaben sind dabei lebenszeitbezogen (Januar des 14. bis Dezember des 65. Lebensjahres) als Querschnitt organisiert.
DOI: 10.5281/zenodo.13321603
title: iNaturalist: iNat images from GBIF (100 per taxon) (deprecated)

description: http://www.inaturalist.org/ is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world. Images and data published on EOL originate from iNaturalist Research Grade observations.
- 100 images per taxon
- without any image scoring considered
DOI: 10.5281/zenodo.13321604
title: iNaturalist: iNat images from GBIF (100 per taxon) (deprecated)

description: http://www.inaturalist.org/ is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world. Images and data published on EOL originate from iNaturalist Research Grade observations.
- 100 images per taxon
- without any image scoring considered
DOI: 10.15468/dl.7rxmru
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Haloxylon ammodendron (C.A.Mey.) Bunge ex Fenzl"
 ]
}

 The dataset includes 431 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048883-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15675142
title: MS1 feature library-based virtual match-between-runs quantification improves site-specific glycan identification and occupancy ratio analysis

description: Glycosylation changes are closely related to various diseases including cancer.  The quantitative analysis of site-specific glycans at proteomics scale remains challenging due to low glycopeptide spectra interpretation. Here, we present GlyPep-Quant, a tool for sensitive quantification and identification of site-specific glycans. Using a well-trained machine learning model, GlyPep-Quant quantified 25.1%-178.9% more site-specific glycans without missing values than pGlycoQuant, MSFragger-Glyco, and Skyline. To utilize identified information from previous large-scale dataset, an MS1 feature library-based “virtual match-between-runs” quantification scheme was developed, enabling over 8-fold more site-specific glycan identification/quantification than conventional MS2-based methods. Enhanced  coverage prompted the development of a glycoproteomic biomarker discovery method, involving calculation of site-specific glycan abundances ratios at the same glycosylation site, minimizing individual expression and experimental condition variability. Two pairs of site-specific glycan ratios on sites P01011-N127 and P08185-N96, were selected as high-performance biomarkers to classify gastric cancer (GC) from healthy controls (AUC >0.95). Moreover, the two ratios performed well in distinguishing GC using an independent cohort by the library-based quantification strategy with diagnostic accuracy up to 85%. GlyPep-Quant is poised for broader glycoproteomic applications.
DOI: 10.5066/p14tehat
title: Diamondback terrapins and their potential diet isotope values and associated metadata collected 2018-2021 in St. Joseph Bay, Florida

description: These datasets contain the carbon and nitrogen stable isotope data from diamondback terrapin epidermis tissue and a variety of sampled prey items.
DOI: 10.5281/zenodo.15675141
title: MS1 feature library-based virtual match-between-runs quantification improves site-specific glycan identification and occupancy ratio analysis

description: Glycosylation changes are closely related to various diseases including cancer.  The quantitative analysis of site-specific glycans at proteomics scale remains challenging due to low glycopeptide spectra interpretation. Here, we present GlyPep-Quant, a tool for sensitive quantification and identification of site-specific glycans. Using a well-trained machine learning model, GlyPep-Quant quantified 25.1%-178.9% more site-specific glycans without missing values than pGlycoQuant, MSFragger-Glyco, and Skyline. To utilize identified information from previous large-scale dataset, an MS1 feature library-based “virtual match-between-runs” quantification scheme was developed, enabling over 8-fold more site-specific glycan identification/quantification than conventional MS2-based methods. Enhanced  coverage prompted the development of a glycoproteomic biomarker discovery method, involving calculation of site-specific glycan abundances ratios at the same glycosylation site, minimizing individual expression and experimental condition variability. Two pairs of site-specific glycan ratios on sites P01011-N127 and P08185-N96, were selected as high-performance biomarkers to classify gastric cancer (GC) from healthy controls (AUC >0.95). Moreover, the two ratios performed well in distinguishing GC using an independent cohort by the library-based quantification strategy with diagnostic accuracy up to 85%. GlyPep-Quant is poised for broader glycoproteomic applications.
DOI: 10.5281/zenodo.15675401
title: RINEX high-rate and HAS products: Days 223–228 of 2024
DOI: 10.5281/zenodo.15675402
title: RINEX high-rate and HAS products: Days 223–228 of 2024