cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13370729
title: Carbon storage response to land use/land cover changes and SSP-RCP scenarios simulation: A case study in Yunnan Province, China
DOI: 10.5281/zenodo.13370994
title: Carbon storage response to land use/land cover changes and SSP-RCP scenarios simulation: A case study in Yunnan Province, China
DOI: 10.15468/dl.w7639v
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Brachyarthrum limitatum Fieber, 1858",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 82 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089248-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h957f3
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Anyphaena alboirrorata Simon, 1878",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 80 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089250-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vtn9wq
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Haplochromis guiarti (Pellegrin, 1904))",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 85 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089249-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4pnnbt
title: Occurrence Download

description: A dataset containing 171829 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Sicalis flaveola (Linnaeus, 1766)"
 ]
}

 The dataset includes 171829 records from 337 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089166-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aac6ss
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Haplochromis victorianus (Pellegrin, 1904))",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089252-240626123714530/datasets/export for details.
DOI: 10.15468/dl.erdznr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Spiroctenus lusitanus Franganillo, 1920",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089253-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ycyptg
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Hypseloecus visci (Puton, 1888)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 64 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089251-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcqgzy
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Haplochromis argenteus Regan, 1922)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 157 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089254-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmubj2
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Heterocordylus genistae (Scopoli, 1763)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 138 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089255-240626123714530/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.16815570
title: Additional file 8 of A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

description: Additional file 8: Table S7 QKI5 motif nearby TF motif and QKI5 co-IP mass spectrometry (MS) data
DOI: 10.6084/m9.figshare.16815567.v1
title: Additional file 7 of A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

description: Additional file 7: Table S6 QKI5 transcriptionally regulated genes
DOI: 10.6084/m9.figshare.16815552
title: Additional file 2 of A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

description: Additional file 2: Table S1 RBP&TFs library and hematopoiesis-related RBPs
DOI: 10.6084/m9.figshare.16815540.v1
title: Additional file 10 of A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

description: Additional file 10: Table S9 Sequencing datasets
DOI: 10.5525/gla.researchdata.1593
title: Data for 'Two-Photon Interference LiDAR Imaging' - Updated February 2024

description: Data used in the manuscript. Full details are included in the readme file.
DOI: 10.6084/m9.figshare.14196627.v1
title: Additional file 2 of Integrative proteomic and lipidomic analysis of Kaili Sour Soup-mediated attenuation of high-fat diet-induced nonalcoholic fatty liver disease in a rat model

description: Additional file 2: Figure S2. Lipid species identified by lipidomic analysis.
DOI: 10.6084/m9.figshare.14196627
title: Additional file 2 of Integrative proteomic and lipidomic analysis of Kaili Sour Soup-mediated attenuation of high-fat diet-induced nonalcoholic fatty liver disease in a rat model

description: Additional file 2: Figure S2. Lipid species identified by lipidomic analysis.
DOI: 10.6084/m9.figshare.7380797.v1
title: An agp file indicating how contigs are scaffolded

description: An agp file indicating how contigs are scaffolded
DOI: 10.6084/m9.figshare.7380863
title: Additional file 3: of Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

description: The predicted tRNA 3D structures. (RAR 539 kb)
DOI: 10.6084/m9.figshare.7380863.v1
title: Additional file 3: of Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

description: The predicted tRNA 3D structures. (RAR 539 kb)
DOI: 10.6084/m9.figshare.14724643
title: Supplementary Files S7 De-novo repeat libraries: Excel factsheet with description and fasta files. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.16815555
title: Additional file 3 of A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

description: Additional file 3: Table S2 Sub-nuclear distribution of RBPs and TFs in 3 cell lines (THP-1, K562, 293T)
DOI: 10.6084/m9.figshare.23633902
title: Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package

description: Epimutations are rare alterations of the normal DNA methylation pattern at specific loci, which can lead to rare diseases. Methylation microarrays enable genome-wide epimutation detection, but technical limitations prevent their use in clinical settings: methods applied to rare diseases’ data cannot be easily incorporated to standard analyses pipelines, while epimutation methods implemented in R packages (<i>ramr</i>) have not been validated for rare diseases. We have developed <i>epimutacions</i>, a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/epimutacions.html). <i>epimutacions</i> implements two previously reported methods and four new statistical approaches to detect epimutations, along with functions to annotate and visualize epimutations. Additionally, we have developed an user-friendly Shiny app to facilitate epimutations detection (https://github.com/isglobal-brge/epimutacionsShiny) to non-bioinformatician users. We first compared the performance of <i>epimutacions</i> and <i>ramr</i> packages using three public datasets with experimentally validated epimutations. Methods in <i>epimutacions</i> had a high performance at low sample sizes and outperformed methods in <i>ramr</i>. Second, we used two general population children cohorts (INMA and HELIX) to determine the technical and biological factors that affect epimutations detection, providing guidelines on how designing the experiments or preprocessing the data. In these cohorts, most epimutations did not correlate with detectable regional gene expression changes. Finally, we exemplified how <i>epimutacions</i> can be used in a clinical context. We run <i>epimutacions</i> in a cohort of children with autism disorder and identified novel recurrent epimutations in candidate genes for autism. Overall, we present <i>epimutacions</i> a new Bioconductor package for incorporating epimutations detection to rare disease diagnosis and provide guidelines for the design and data analyses.
DOI: 10.6084/m9.figshare.14724649
title: Supplementary Files S3 It contains the annotation of full-length ERVs made by LTRharvest/LTRdigest. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.11588/data/xkfwi4
title: Right thoughts, right words, right actions? The EU‘s application of the Cyber Diplomacy Toolbox [data]

description: This dataset is the first to address the application of the EU's cyber diplomacy toolbox (CDT) by EU institutions/actors since 2017 until the end of May 2023. Based on this, the related research paper highlights trends, patterns, and anomalies in previous usage that can be identified and analysed in the respective political context. The publication is complemented by insights from the European Repository of Cyber Incidents (EuRepoC) to evaluate the intended impact of the measures in a more detailed manner.
DOI: 10.6084/m9.figshare.14724661
title: Supplementary Files S4 Annotation for intact LINE retrotransposons and DNA transposons. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.14724664
title: Supplementary Files S2 It contains the annotation of full-length ERVs made by RetroTector. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.14724667
title: Supplementary Files S6 MaxQuant output and XML file with parameters used for the analysis. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.16815702
title: Additional file 2 of Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants

description: Additional file 2: Table S1. In vitro binding and neutralizing activity of RBD-specific mAbs.
DOI: 10.5281/zenodo.7714021
title: Personality in chronic headaches: A systematic review with meta-analysis

description: Dataset refers to a systematic review on the personality traits associated to Chronic Headache (CH) compared to healthy controls and to a quantitative meta-analysis with the studies using the same instrument to assess personality traits. Thirteen studies were included in the systematic review but only three studies were deeply explored in a meta-analysis since the only ones using a common instrument to assess personality dimensions. According to the results of the meta-analysis, different subtypes of CH patients scored higher than healthy controls on Hypochondriasis and Hysteria scales highlighting that these personality traits are common across CH categories. The systematic review showed higher levels of depressive and anxious personality dimensions and pain catastrophizing in CH compared to healthy controls. Moreover, frequent-chronic forms and Medication Overuse Headache were the most symptomatic and frail categories showing higher levels of dysfunctional personality traits and psychopathological symptoms