cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4uys32
title: Occurrence Download

description: A dataset containing 2375 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 Tropinota squalida (Scopoli, 1763)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 2375 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089380-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyngzq
title: Occurrence Download

description: A dataset containing 35629 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macromitrium Brid."
 ]
}

 The dataset includes 35629 records from 255 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089374-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5c3c98
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Labeobarbus platystomus (Pappenheim, 1914))",
 "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/0089381-240626123714530/datasets/export for details.
DOI: 10.15468/dl.v5j79c
title: Occurrence Download

description: A dataset containing 1515 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 Onthophagus landolti Harold, 1880",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1515 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089383-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrd75b
title: Occurrence Download

description: A dataset containing 22037 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calotropis procera (Aiton) W.T.Aiton"
 ]
}

 The dataset includes 22037 records from 384 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089384-240626123714530/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.20488455.v1
title: Additional file 6 of Systematic transcriptome profiling of pyroptosis related signature for predicting prognosis and immune landscape in lower grade glioma

description: Additional file 6: Table S5. Drug or small molecule compounds predicted using L1000FWD and CMap tools.
DOI: 10.6084/m9.figshare.20488469.v1
title: Additional file 11 of A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

description: Additional file 11: Table S11. qPCR primer and probe sequence information.
DOI: 10.6084/m9.figshare.16818851.v2
title: Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

description: DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs was identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (&gt;90%) of cGCPs was tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlights the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, the early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalogue of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.
DOI: 10.6084/m9.figshare.16818851.v1
title: Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

description: DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs were identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (&gt;90%) of cGCPs were tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlighted the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalog of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.
DOI: 10.6084/m9.figshare.20488458
title: Additional file 7 of Systematic transcriptome profiling of pyroptosis related signature for predicting prognosis and immune landscape in lower grade glioma

description: Additional file 7: Table S6. RiskScore values for glioma cell lines predicted based on signature genes expression.
DOI: 10.5281/zenodo.10624841
title: craterocephalus_stercusmuscarum_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10624842
title: craterocephalus_stercusmuscarum_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.6857438
title: Decreased serum PON1 arylesterase activity in familial hypercholesterolemia patients with a mutated LDLR gene

description: Abstract Paraoxonase 1 (PON1) is a serum enzyme associated with high density lipoprotein (HDL) regulation through its paraoxonase and arylesterase activity. PON1 inhibits the oxidation of HDL and low density lipoprotein (LDL), and is involved in the pathogenesis of a variety of diseases including atherosclerosis. Conversely, mutations in the low density lipoprotein receptor (LDLR) result in failure of receptor mediated endocytosis of LDL leading to its elevated plasma levels and onset of familial hypercholesterolemia (FH). In the current study we investigated the role of PON1 polymorphisms rs662; c.575A &gt; G (p.Gln192Arg) and rs854560; c.163T &gt; A (p.Leu55Met) in a large family having FH patients harboring a functional mutation in LDLR. Genotypes were revealed by RFLP, followed by confirmation through Sanger sequencing. PON1 activity was measure by spectrophotometry. Our results show significantly reduced serum paraoxonase and arylesterase activities in FH patients compared with the healthy individuals of the family (p &lt; 0.05). PON1 QQ192 genotype showed a significantly higher association with FH (p=0.0002). PON1 Q192 isoform was associated with reduced serum paraoxonase activity by in silico analysis and PON1 R192 exhibited higher serum paraoxonase and arylesterase activity than the other polymorphs. Our results highlight that the combination of LDLR mutations and PON1 MMQQ genotypes may lead to severe cardiac events.
DOI: 10.6084/m9.figshare.16818836.v2
title: Circular RNA erythrocyte membrane protein band 4.1 assuages ultraviolet irradiation-induced apoptosis of lens epithelial cells by stimulating 5’-bisphosphate nucleotidase 1 in a miR-24-3p-dependent manner

description: Apoptosis of lens epithelial cells contributed to the formation of age-related cataract (ARC), and previous data revealed that circular RNA (circRNA) was responsible for the underneath mechanism. The study was organized to explore the role of circular RNA erythrocyte membrane protein band 4.1 (circ_EPB41) in ultraviolet (UV) irradiation-induced apoptosis of lens epithelial cells. SRA01/04 cells were irradiated with UV to mimic the ARC cell model. The RNA levels of circ_EPB41, microRNA-24-3p (miR-24-3p), and 3ʹ(2ʹ), 5ʹ-bisphosphate nucleotidase 1 (BPNT1) were detected by quantitative real-time polymerase chain reaction. Protein expression was checked by western blot. 5-Ethynyl-29-deoxyuridine, 3-(4,5-Dimethylthazol-2-yl)-2,5-diphenyltetrazolium bromide and DNA content quantitation assays were performed to investigate cell proliferation. Flow cytometry was conducted to analyze cell apoptosis. Dual-luciferase reporter assay was implemented to confirm the interaction among circ_EPB41, miR-24-3p, and BPNT1. Our data showed that circ_EPB41 and BPNT1 expression were downregulated in ARC tissues and UV-irradiated SRA01/04 cells as compared with normal anterior lens capsules and untreated SRA01/04 cells. Circ_EPB41 overexpression ameliorated the effects of UV irradiation on the proliferation and apoptosis of SRA01/04 cells. Besides, miR-24-3p, a target miRNA of circ_EPB41, attenuated circ_EPB41 introduction-mediated proliferation, and apoptosis of UV-irradiated SRA01/04 cells. MiR-24-3p regulated UV irradiation-induced effects by targeting BPNT1. Importantly, it was found that circ_EPB41 stimulated BPNT1 production by miR-24-3p. Taken together, the enforced expression of circ_EPB41 ameliorated UV irradiation-induced apoptosis of lens epithelial cells by miR-24-3p/BPNT1 pathway, providing us with a potential target for the therapy of UV-caused ARC.
DOI: 10.6084/m9.figshare.6857414.v1
title: Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

description: Abstract Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.
DOI: 10.6084/m9.figshare.20488496.v1
title: Additional file 8 of A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

description: Additional file 8: Table S8. Significant KEGG pathways and GO terms associated with growth traits. (P &lt; 0.05).
DOI: 10.6084/m9.figshare.24159024.v1
title: Myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes

description: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and fibromyalgia have overlapping neurologic symptoms particularly disabling fatigue. This has given rise to the question whether they are distinct central nervous system (CNS) entities or is one an extension of the other. To investigate this, we used unbiased quantitative mass spectrometry-based proteomics to examine the most proximal fluid to the brain, cerebrospinal fluid (CSF). This was to ascertain if the proteome profile of one was the same or different from the other. We examined two separate groups of ME/CFS, one with (<i>n</i> = 15) and one without (<i>n</i> = 15) fibromyalgia. We quantified a total of 2083 proteins using immunoaffinity depletion, tandem mass tag isobaric labelling and offline two-dimensional liquid chromatography coupled to tandem mass spectrometry, including 1789 that were quantified in all the CSF samples. ANOVA analysis did not yield any proteins with an adjusted <i>p</i> value &lt;.05. This supports the notion that ME/CFS and fibromyalgia as currently defined are not distinct entities.Key messageME/CFS and fibromyalgia as currently defined are not distinct entities.Unbiased quantitative mass spectrometry-based proteomics can be used to discover cerebrospinal fluid proteins that are biomarkers for a condition such as we are studying. ME/CFS and fibromyalgia as currently defined are not distinct entities. Unbiased quantitative mass spectrometry-based proteomics can be used to discover cerebrospinal fluid proteins that are biomarkers for a condition such as we are studying.
DOI: 10.6084/m9.figshare.6857414
title: Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

description: Abstract Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.
DOI: 10.6084/m9.figshare.22586062.v1
title: Characterization of the complete mitochondrial genome of the nematode-trapping fungus <i>Drechslerella dactyloides</i>

description: The complete mitochondrial genome of <i>Drechslerella dactyloides</i> was characterized in this study. This mitogenome is a closed circular molecule of 246860 bp in length with a GC content of 26.16%, including 87 predicted protein-coding genes, 29 transfer RNA genes, and two rRNA gens. Phylogenetic analyses based on concatenated amino acid sequences at 14 conserved mitochondrial protein-coding genes showed that <i>D. dactyloides</i> was closely related to <i>Dactylellina haptotyla</i>.
DOI: 10.6084/m9.figshare.16815713.v1
title: Additional file 2 of Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

description: Additional file 2 Table S2. Analysis and distribution of the conserved motifs in S. bicolor trihelix proteins. (XLS 22 kb)
DOI: 10.6084/m9.figshare.16815710.v1
title: Additional file 1 of Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

description: Additional file 1 Table S1. List of the 40 SbTH genes identified in this study. (XLS 143 kb)
DOI: 10.6084/m9.figshare.16815716
title: Additional file 3 of Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

description: Additional file 3 Table S3. Seven pairs of segmental duplicated S. bicolor trihelix genes. (XLS 22 kb)
DOI: 10.6084/m9.figshare.24137973.v1
title: Optimising CNN-based GPS Data Interpretation for Hiking Map Generation

description: In this context, we are sharing the data related to our article. We have made available the datasets used for training, the data employed to generate predictions in the test environment, the outcomes of our experiments, and the code that facilitated the evaluation of the data.
DOI: 10.6084/m9.figshare.24137973
title: Optimising CNN-based GPS Data Interpretation for Hiking Map Generation

description: In this context, we are sharing the data related to our article. We have made available the datasets used for training, the data employed to generate predictions in the test environment, the outcomes of our experiments, and the code that facilitated the evaluation of the data.
DOI: 10.6084/m9.figshare.25152698
title: Deep Neural Network Architectures for Advanced Hiking Map Generation

description: In this context, we are sharing the data related to our article. We have made available the datasets used for training, the data employed to generate predictions in the test environment, the outcomes of our experiments, and the code that facilitated the evaluation of the data.
DOI: 10.6084/m9.figshare.23638434
title: Table S2. Quantitative proteomic analysis of PP2A-Tws dependent phosphosites. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: Cells treated with dsRNA targeting Tws, Endos, Gwl or KAN (non-target), or treated with okadaic acid or DMSO were submitted to phosphopeptide enrichment. Products were analyzed by mass spectrometry. Results from 4 technical replicates are shown.
DOI: 10.6084/m9.figshare.23638434.v1
title: Table S2. Quantitative proteomic analysis of PP2A-Tws dependent phosphosites. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: Cells treated with dsRNA targeting Tws, Endos, Gwl or KAN (non-target), or treated with okadaic acid or DMSO were submitted to phosphopeptide enrichment. Products were analyzed by mass spectrometry. Results from 4 technical replicates are shown.
DOI: 10.6084/m9.figshare.23638452
title: Table S3. Quantitative proteomic analysis of Otefin interactors from Drosophila embryos. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: GFP, GFP-OteWT, GFP-OteAA or GFP-OteDD were purified from embryos and purification products were analyzed by mass spectrometry to identify associated proteins. Results of 3 independent biological replicates are shown.
DOI: 10.6084/m9.figshare.23638452.v1
title: Table S3. Quantitative proteomic analysis of Otefin interactors from Drosophila embryos. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: GFP, GFP-OteWT, GFP-OteAA or GFP-OteDD were purified from embryos and purification products were analyzed by mass spectrometry to identify associated proteins. Results of 3 independent biological replicates are shown.
DOI: 10.6084/m9.figshare.23638455
title: Table S1. Quantitative proteomic analysis of Tws interactors from <i>Drosophila</i> embryos. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: GFP, GFP-Tws or Tws-GFP were purified from embryos and purification products were analyzed by mass spectrometry to identify associated proteins. Results of 3 independent biological replicates are shown.
DOI: 10.6084/m9.figshare.23638455.v1
title: Table S1. Quantitative proteomic analysis of Tws interactors from <i>Drosophila</i> embryos. from Identification of PP2A-B55 targets uncovers regulation of Emerin during nuclear envelope reassembly in <i>Drosophila</i>

description: GFP, GFP-Tws or Tws-GFP were purified from embryos and purification products were analyzed by mass spectrometry to identify associated proteins. Results of 3 independent biological replicates are shown.