cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13633136.v1
title: Additional file 2 of Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

description: Additional file 2: Table S1. Molecular subtyping in gastric cancer cell lines. Table S2. Categories of isoform identified. Table S3. Correlation between predicted transcriptome (Iso-seq) with promoter activity (proActiv) at different gene lengths. Table S4. Correlation coefficient between Iso-seq and proActiv. Table S5. List of unique peptides in Iso-seq sequences and not found in Gencode v32, validated from mass spectrometer data. Table S6. Down-regulated promoter (tumor vs normal). Table S7. Up-regulated promoter (tumor vs normal). Table S8. Gene-specific outer/inner primers used for RLM-RACE.
DOI: 10.6084/m9.figshare.13633167
title: Additional file 1 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 1: Table S1. Relative electrolyte leakage (REL) of 492 populations subjected to − 30 °C treatment.
DOI: 10.6084/m9.figshare.13633170
title: Additional file 2 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 2: Table S2. Lethal temperature of 50% (LT50) in 100 populations of ‘Ruby-3’ × ‘Kuilv’ male.
DOI: 10.6084/m9.figshare.13633176.v1
title: Additional file 4 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 4: Table S4. Significant GO classifications associated with differentially expressed genes.
DOI: 10.6084/m9.figshare.13633179
title: Additional file 5 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 5: Table S5. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.13633179.v1
title: Additional file 5 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 5: Table S5. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.13633167.v1
title: Additional file 1 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 1: Table S1. Relative electrolyte leakage (REL) of 492 populations subjected to − 30 °C treatment.
DOI: 10.6084/m9.figshare.13633170.v1
title: Additional file 2 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 2: Table S2. Lethal temperature of 50% (LT50) in 100 populations of ‘Ruby-3’ × ‘Kuilv’ male.
DOI: 10.6084/m9.figshare.9963206
title: Metadata record for: Morphometrics of eight Chinese cavefish species

description: This dataset contains key characteristics about the data described in the Data Descriptor Morphometrics of eight Chinese cavefish species. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 <br> <br>

 Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9963206.v1
title: Metadata record for: Morphometrics of eight Chinese cavefish species

description: This dataset contains key characteristics about the data described in the Data Descriptor Morphometrics of eight Chinese cavefish species. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 <br> <br>

 <br>
DOI: 10.6084/m9.figshare.9963206.v2
title: Metadata record for: Morphometrics of eight Chinese cavefish species

description: This dataset contains key characteristics about the data described in the Data Descriptor Morphometrics of eight Chinese cavefish species. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format 
 <br> <br>

 Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.13633173
title: Additional file 3 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 3: Table S3. Significant KEGG pathways associated with differentially expressed genes.
DOI: 10.6084/m9.figshare.13633173.v1
title: Additional file 3 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 3: Table S3. Significant KEGG pathways associated with differentially expressed genes.
DOI: 10.6084/m9.figshare.13633176
title: Additional file 4 of BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

description: Additional file 4: Table S4. Significant GO classifications associated with differentially expressed genes.
DOI: 10.6084/m9.figshare.25144220
title: Geo-referenced microsatellite data from <i>Triturus cristatus</i> in Luxembourg (1068 samples)

description: Microsatellite genotypes (15 loci) and geographical locations of 1068 samples from the northern crested newt (<i>Triturus cristatus</i>) in Luxembourg. Provided coordinates are based on the Luxembourg 1930 (EPSG: 2169) projection. The data were analysed in the context of the article: "Spatial prioritisation for crested newt conservation in Luxembourg: insights from population genetics and species distribution modelling".A subset of these samples from southwestern Luxembourg (N=897) was previously published here: https://doi.org/10.6084/m9.figshare.23966898.v1
DOI: 10.6084/m9.figshare.7866071
title: Overexpression of salt-induced protein (salT) delays leaf senescence in rice

description: Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions.
DOI: 10.6084/m9.figshare.7866071.v1
title: Overexpression of salt-induced protein (salT) delays leaf senescence in rice

description: Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions.
DOI: 10.6084/m9.figshare.9963524
title: Syntheses, structures and properties of two mononuclear copper(I) complexes with <i>N</i>-heterocyclic ligands

description: Two mononuclear Cu(I) complexes, [Cu(PBO)(PPh<sub>3</sub>)<sub>2</sub>]·PF<sub>6</sub>·CH<sub>2</sub>Cl<sub>2</sub> (<b>1</b>) and [Cu(PBM)(PPh<sub>3</sub>)<sub>2</sub>]·PF<sub>6</sub> (<b>2</b>) (PBO = 2-(2′-pyridyl)benzoxazole, PBM = 2-(2′-pyridyl)benzimidazole, PPh<sub>3</sub> = triphenylphosphine), have been synthesized and characterized by elemental analyses, IR, single crystal X-ray diffraction, fluorescence spectroscopy, and cyclic voltammetry. The structural analysis revealed that in <b>1</b> and <b>2</b>, the Cu(I) ions are four-coordinate and the coordination geometry around the Cu(I) is distorted tetrahedral. Photoluminescent investigation shows that <b>1</b> and <b>2</b> exhibit distinct tunable green (523 nm)-to-yellow (557 nm) photoluminescence by varying the <i>N</i>-heterocyclic ligands. Electrochemical properties of <b>1</b> and <b>2</b> have been investigated by cyclic voltammetry. The results suggest the frontier molecular orbits and the HOMO-LUMO energy gaps of these cuprous complexes are effectively adjusted through the introduction of different <i>N</i>-heterocyclic ligands.
DOI: 10.6084/m9.figshare.9963524.v1
title: Syntheses, structures and properties of two mononuclear copper(I) complexes with <i>N</i>-heterocyclic ligands

description: Two mononuclear Cu(I) complexes, [Cu(PBO)(PPh<sub>3</sub>)<sub>2</sub>]·PF<sub>6</sub>·CH<sub>2</sub>Cl<sub>2</sub> (<b>1</b>) and [Cu(PBM)(PPh<sub>3</sub>)<sub>2</sub>]·PF<sub>6</sub> (<b>2</b>) (PBO = 2-(2′-pyridyl)benzoxazole, PBM = 2-(2′-pyridyl)benzimidazole, PPh<sub>3</sub> = triphenylphosphine), have been synthesized and characterized by elemental analyses, IR, single crystal X-ray diffraction, fluorescence spectroscopy, and cyclic voltammetry. The structural analysis revealed that in <b>1</b> and <b>2</b>, the Cu(I) ions are four-coordinate and the coordination geometry around the Cu(I) is distorted tetrahedral. Photoluminescent investigation shows that <b>1</b> and <b>2</b> exhibit distinct tunable green (523 nm)-to-yellow (557 nm) photoluminescence by varying the <i>N</i>-heterocyclic ligands. Electrochemical properties of <b>1</b> and <b>2</b> have been investigated by cyclic voltammetry. The results suggest the frontier molecular orbits and the HOMO-LUMO energy gaps of these cuprous complexes are effectively adjusted through the introduction of different <i>N</i>-heterocyclic ligands.
DOI: 10.6084/m9.figshare.5244934
title: Additional file 3 of Genome-wide DNA methylation profile analysis identifies differentially methylated loci associated with ankylosis spondylitis

description: Presenting significantly differentially methylated CpG sites between AS patients and healthy controls. (XLSX 167 kb)
DOI: 10.6084/m9.figshare.6817799
title: Additional file 3: of Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer

description: Table S1. List of differential expression genes in vitamin C treated and control T24 cells. (XLSX 224Â kb)
DOI: 10.6084/m9.figshare.6817799.v1
title: Additional file 3: of Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer

description: Table S1. List of differential expression genes in vitamin C treated and control T24 cells. (XLSX 224Â kb)
DOI: 10.6084/m9.figshare.5244937
title: Additional file 4 of Genome-wide DNA methylation profile analysis identifies differentially methylated loci associated with ankylosis spondylitis

description: Presents genome-wide DNA methylation microarray data. (CSV 244140 kb)
DOI: 10.6084/m9.figshare.25144226
title: PCR.PTML-Project Supporting Information

description: The characterization of DNA sequence variants (variant calling) from ancient samples (aDNA) is a topic of major interest in modern science. However, there are important theoretical and experimental problems to be overcome like the low number of reliable samples, the possibility of contamination, <i>etc</i>. On the other hand, the main concern during the extraction ancient of DNA (aDNA) is to prevent contamination with modern materials. Consequently, it is crucial to be able to differentiate modern from ancient sequences in aDNA variant calling. In this context, computational techniques may play an important role. Most methods reported use alignment-dependent algorithms relying on limited samples. More recently Artificial Intelligence / Machine Learning (AI/ML) methods have been proposed as an alternative. However, almost all of them focus on the analysis of Mammoth, Neanderthal, or other Demographic aDNA problems and omit the study of aDNA paleo-microobiomes. In this work, we report by the first time the PCR.PTML methodology based on the combination of experimental Polymerase Chain Reaction (PCR) metagenomic analysis of aDNA sequences with the Perturbation Theory (PT) and Machine Learning (ML) predictive modeling. Firstly, we reported the extraction and PCR analysis of a new set of putative microbiome 16S aDNA sequences from Miocene fossil amber. Next, we developed a variant calling PTML model able to discriminate 16S aDNA sequences of Miocene bacteria from modern bacteria sequences with more that 80% of specificity and sensitivity in training and validation series. We used both Linear Discriminant Analysis (LDA) and Artificial Neural Networks (ANN) algorithms for variant calling exploration of 100000 combinations of query and reference sequences to seek model.
DOI: 10.6084/m9.figshare.25144226.v1
title: PCR.PTML-Project Supporting Information

description: The characterization of DNA sequence variants (variant calling) from ancient samples (aDNA) is a topic of major interest in modern science. However, there are important theoretical and experimental problems to be overcome like the low number of reliable samples, the possibility of contamination, <i>etc</i>. On the other hand, the main concern during the extraction ancient of DNA (aDNA) is to prevent contamination with modern materials. Consequently, it is crucial to be able to differentiate modern from ancient sequences in aDNA variant calling. In this context, computational techniques may play an important role. Most methods reported use alignment-dependent algorithms relying on limited samples. More recently Artificial Intelligence / Machine Learning (AI/ML) methods have been proposed as an alternative. However, almost all of them focus on the analysis of Mammoth, Neanderthal, or other Demographic aDNA problems and omit the study of aDNA paleo-microobiomes. In this work, we report by the first time the PCR.PTML methodology based on the combination of experimental Polymerase Chain Reaction (PCR) metagenomic analysis of aDNA sequences with the Perturbation Theory (PT) and Machine Learning (ML) predictive modeling. Firstly, we reported the extraction and PCR analysis of a new set of putative microbiome 16S aDNA sequences from Miocene fossil amber. Next, we developed a variant calling PTML model able to discriminate 16S aDNA sequences of Miocene bacteria from modern bacteria sequences with more that 80% of specificity and sensitivity in training and validation series. We used both Linear Discriminant Analysis (LDA) and Artificial Neural Networks (ANN) algorithms for variant calling exploration of 100000 combinations of query and reference sequences to seek model.
DOI: 10.6084/m9.figshare.7866407
title: The annotation, molecular markers, and transcription factor of Platanus acerifolia transcriptome

description: Annotation, molecular markers, and transcription factor output files of Platanus acerifolia transcriptome<br>
DOI: 10.6084/m9.figshare.13633238
title: Additional file 6 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 6. The spearman’s rank correlation coefficients between gene intrinsic properties (gene age, zinc finger divergence time or SDR values) and expression level (TPM) in 7 mammals (related to Fig. 5).
DOI: 10.6084/m9.figshare.13633247
title: Additional file 9 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 9. The protein-protein interaction network of human KZFPs and the expression of baits and preys in each sample.
DOI: 10.6084/m9.figshare.6817811.v1
title: Additional file 4: of Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer

description: Table S2. KEGG_PATHWAY analysis of 1172 differential expression genes in Fig.Â 6b. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.6817811
title: Additional file 4: of Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer

description: Table S2. KEGG_PATHWAY analysis of 1172 differential expression genes in Fig.Â 6b. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.13633226
title: Additional file 2 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 2. Percentage of each disorder grade of KRAB domains and other chordata-specific domains in each of the 64 species (related to Fig. 1).
DOI: 10.6084/m9.figshare.13633238.v1
title: Additional file 6 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 6. The spearman’s rank correlation coefficients between gene intrinsic properties (gene age, zinc finger divergence time or SDR values) and expression level (TPM) in 7 mammals (related to Fig. 5).
DOI: 10.6084/m9.figshare.13633220
title: Additional file 10 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 10. The number of PCGs and KZFP genes in each evolutionary age grade in 7 mammals.
DOI: 10.6084/m9.figshare.13633220.v1
title: Additional file 10 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 10. The number of PCGs and KZFP genes in each evolutionary age grade in 7 mammals.
DOI: 10.6084/m9.figshare.13633229
title: Additional file 3 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 3. The annotation information and SDR values of KZFPs in 7 mammals (related to Fig. 2 and Figure S2 in Additional file 1).
DOI: 10.6084/m9.figshare.13633232.v1
title: Additional file 4 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 4. The annotation information and SDR values of PCGs in 7 mammals (related to Fig. 2 and Figure S2 in Additional file 1).
DOI: 10.6084/m9.figshare.13633235.v1
title: Additional file 5 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 5. The number and percentage of expressed KZFPs (related to Figs. 3 and 4 and Figure S3 in Additional file 1).
DOI: 10.6084/m9.figshare.13633229.v1
title: Additional file 3 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 3. The annotation information and SDR values of KZFPs in 7 mammals (related to Fig. 2 and Figure S2 in Additional file 1).
DOI: 10.6084/m9.figshare.13633241
title: Additional file 7 of Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics

description: Additional file 7. The expression z-score of KZFPs in 7 representative mammals (related to Figure S4 & S5 in Additional file 1).
DOI: 10.15468/dl.spjd5r
title: Occurrence Download

description: A dataset containing 151 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 Hilara platyura Loew, 1873",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 151 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085243-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qf8eu
title: Occurrence Download

description: A dataset containing 196 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 Diabrotica undecimpunctata Jacoby, 1879",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 196 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085244-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrtyx3
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Litoria castanea (Steindachner, 1867))",
 "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 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085245-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k7gkjj
title: Occurrence Download

description: A dataset containing 42 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 Hilara discoidalis Lundbeck, 1910",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 42 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085246-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8wjf4
title: Occurrence Download

description: A dataset containing 196 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 Diabrotica undecimpunctata Jacoby, 1879",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 196 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085248-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.