cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nzq45n
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Réunion",
 "DatasetKey is one of (Données d’observations floristiques agrégées au sein de Mascarine (CBN-CPIE Mascarin) - Données d’observations floristiques acquises par le CBN-CPIE Mascarin, Données du Parc national de la Réunion - Relevé flore vasculaire menacée de La Réunion, Données d’observations floristiques agrégées au sein de Mascarine (CBN-CPIE Mascarin) - Données d’observations floristiques produits par les partenaires externes (hors parc National de La Réunion) agrégées au sein de Mascarine, Données d'occurrences Espèces issues de l'inventaire des ZNIEFF)",
 "TaxonKey is Drypetes caustica (Frapp. ex Cordem.) Airy Shaw",
 "Year 2000-2022"
 ]
}

 The dataset includes 72 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060046-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oiqdmy
title: Occurrence Download

description: A dataset containing 17787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Falco amurensis Radde, 1863",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 17787 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002585-171020152545675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zgzagd
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bolitoglossa yucatana (Peters, 1882)"
 ]
}

 The dataset includes 268 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005128-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wefhxf
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Opuntia palmadora Britton & Rose",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017853-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.66rhvp
title: Occurrence Download

description: A dataset containing 130328 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taxus baccata L."
 ]
}

 The dataset includes 130328 records from 879 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054496-231120084113126/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.7193561.v1
title: Additional file 5: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: The respective numbers of overlapping up-regulated genes in comparative treatment groups. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7193729.v1
title: Additional file 4: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: 184 gene sequences of influenza A (H7N9) virus isolated in chicken downloaded from GISAID. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.20300931
title: Multiway sparse distance weighted discrimination

description: Modern data often take the form of a multiway array. However, most classification methods are designed for vectors, i.e., 1-way arrays. Distance weighted discrimination (DWD) is a popular high-dimensional classification method that has been extended to the multiway context, with dramatic improvements in performance when data have multiway structure. However, the previous implementation of multiway DWD was restricted to classification of matrices, and did not account for sparsity. In this paper, we develop a general framework for multiway classification which is applicable to any number of dimensions and any degree of sparsity. We conducted extensive simulation studies, showing that our model is robust to the degree of sparsity and improves classification accuracy when the data have multiway structure. For our motivating application, magnetic resonance spectroscopy (MRS) was used to measure the abundance of several metabolites across multiple neurological regions and across multiple time points in a mouse model of Friedreich’s ataxia, yielding a four-way data array. Our method reveals a robust and interpretable multi-region metabolomic signal that discriminates the groups of interest. We also successfully apply our method to gene expression time course data for multiple sclerosis treatment. An R implementation is available in the package MultiwayClassification at <b>http://github.com/lockEF/MultiwayClassification</b>.
DOI: 10.6084/m9.figshare.20300931.v1
title: Multiway sparse distance weighted discrimination

description: Modern data often take the form of a multiway array. However, most classification methods are designed for vectors, i.e., 1-way arrays. Distance weighted discrimination (DWD) is a popular high-dimensional classification method that has been extended to the multiway context, with dramatic improvements in performance when data have multiway structure. However, the previous implementation of multiway DWD was restricted to classification of matrices, and did not account for sparsity. In this paper, we develop a general framework for multiway classification which is applicable to any number of dimensions and any degree of sparsity. We conducted extensive simulation studies, showing that our model is robust to the degree of sparsity and improves classification accuracy when the data have multiway structure. For our motivating application, magnetic resonance spectroscopy (MRS) was used to measure the abundance of several metabolites across multiple neurological regions and across multiple time points in a mouse model of Friedreich’s ataxia, yielding a four-way data array. Our method reveals a robust and interpretable multi-region metabolomic signal that discriminates the groups of interest. We also successfully apply our method to gene expression time course data for multiple sclerosis treatment. An R implementation is available in the package MultiwayClassification at <b>http://github.com/lockEF/MultiwayClassification</b>.
DOI: 10.6084/m9.figshare.14526227
title: Additional file 5 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S4. The published bZIP genes of Arabidopsis, rice and tomato used as outgroups for phylogenetic analysis of the PgbZIP gene family.
DOI: 10.6084/m9.figshare.14526233.v1
title: Additional file 7 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S5. Annotation and GO categorization of the 273 PgbZIP transcripts.
DOI: 10.6084/m9.figshare.7193669
title: Additional file 6: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S5. Relative abundance of 1-d-Larvae and 5-d-Larvae at genus level. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7193678.v1
title: Additional file 7: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S6. Relative abundance of female and male at genus level. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7193639.v1
title: Additional file 4: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S3. Numbers OTU that belong to core genera. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.15057976.v1
title: microRNA-26a shuttled by extracellular vesicles secreted from adipose-derived mesenchymal stem cells reduce neuronal damage through KLF9-mediated regulation of TRAF2/KLF2 axis

description: Extracellular vesicles (EVs) are nano-sized vesicles secreted actively by numeorus cells and have fundamental roles in intercellular communication through shuttling functional RNAs. This study sets out to elucidate the role of microRNA-26a (miR-26a) shuttled by EVs derived from adipose-derived mesenchymal stem cells (ASCs) in neuronal damage. After extraction and identification of ASC-derived EVs (ASC-EVs), mouse cortical neuronal cells were selected to establish an in vivo cerebral ischemia/reperfusion mouse model and an in vitro oxygen glucose deprivation/reperfusion (OGD/RP) cell model. The downstream genes of miR-26a were analyzed. The gain- and loss-of function of miR-26a and KLF9 was performed in mouse and cell models. Neuronal cells were subjected to co-culture with ASC-EVs and biological behaviors were detected by flow cytometry, Motic Images Plus, TTC, TUNEL staining, qRT-PCR and western blot analysis. ASC-EVs protected neuronal cells against neuronal damage following cerebral ischemia/reperfusion, which was related to transfer of miR-26a into neuronal cells. In neuronal cells, miR-26a targeted KLF9. KLF9 could suppress the expression of TRAF2 and KLF2 to facilitate neuronal damage. In vitro and in vivo results showed that miR-26a delivered by ASC-EVs inhibited neuronal damage. In summary, ASC-EVs-derived miR-26a can arrest neuronal damage by disrupting the KLF9-meidated suppression on TRAF2/KLF2 axis.
DOI: 10.6084/m9.figshare.7193699.v1
title: Additional file 2: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: The 495 sequence alignments of influenza A (H7N9) isolated in chicken from GISAID. (FAS 1511 kb)
DOI: 10.6084/m9.figshare.7193612
title: Additional file 2: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S2. OTU taxonomy of all samples. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.7193828
title: Additional file 2 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

description: Assignments of transcription factors to biological components. (XLSX 35.2 kb)
DOI: 10.6084/m9.figshare.7193672
title: Additional file 1: of High throughput small RNA and transcriptome sequencing reveal capacitation-related microRNAs and mRNA in boar sperm

description: Raw and collated data. Table S1. Differential expression of mRNAs between fresh and capacitated boar sperm. Table S2. Differential expression of miRNAs between fresh and capacitated boar sperm. Table S3–1. 69 specifically expressed mRNAs in capacitated boar sperm. Table S3–2. 4554 specifically expressed mRNAs in fresh boar sperm. Table S3–3. 434 co-expressed mRNAs in fresh and capacitated boar sperm. Table S4. 49 miRNAs with higher expression level in boar fresh sperm compared to capacitated sperm. (XLSX 818 kb)
DOI: 10.6084/m9.figshare.7193678
title: Additional file 7: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S6. Relative abundance of female and male at genus level. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7193840.v1
title: Additional file 3 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

description: Results of ToppGene analysis of each of the thirty biological components. (XLSX 571 kb)
DOI: 10.6084/m9.figshare.22333150
title: scCPEP

description: scCPEP
DOI: 10.6084/m9.figshare.22333150.v4
title: PredGCN

description: PredGCN
DOI: 10.6084/m9.figshare.15058006
title: Profile of gut microbiota in patients with traumatic thoracic spinal cord injury and its clinical implications: a case-control study in a rehabilitation setting

description: Gut microbiota are the candidate biomarkers for neurogenic bowel dysfunction (NBD) in patients with spinal cord injury (SCI). We aimed to identify the common features between patients with varying degree of thoracic SCI and healthy individuals and subpopulations of microbiota correlated with the serum biomarkers. Twenty-one patients with complete thoracic SCI (CTSCI), 24 with incomplete thoracic SCI (ITSCI), and 24 healthy individuals (HC) were enrolled in this study. Fresh stool samples and clinical data were collected from all participants, and their bowel functions with SCI were assessed. Microbial diversity and composition were analyzed by sequencing the 16S rRNA gene. The features of gut microbiota correlated with the serum biomarkers and their functions were investigated. The mean NBD score of patients with CTSCI was higher than that of patients with ITSCI. Diversity of the gut microbiota in SCI group was reduced, and with an increase in the degree of damage, alpha diversity had decreased gradually. The composition of gut microbiota in patients with SCI was distinct from that in healthy individuals, and CTSCI group exhibited further deviation than ITSCI group compared to healthy individuals. Four serum biomarkers were found to be correlated with most differential genera. Patients with thoracic SCI present gut dysbiosis, which is more pronounced in patients with CTSCI than in those with ITSCI. Therefore, the gut microbiota profile may serve as the signatures for bowel and motor functions in patients with thoracic SCI.
DOI: 10.6084/m9.figshare.15058006.v1
title: Profile of gut microbiota in patients with traumatic thoracic spinal cord injury and its clinical implications: a case-control study in a rehabilitation setting

description: Gut microbiota are the candidate biomarkers for neurogenic bowel dysfunction (NBD) in patients with spinal cord injury (SCI). We aimed to identify the common features between patients with varying degree of thoracic SCI and healthy individuals and subpopulations of microbiota correlated with the serum biomarkers. Twenty-one patients with complete thoracic SCI (CTSCI), 24 with incomplete thoracic SCI (ITSCI), and 24 healthy individuals (HC) were enrolled in this study. Fresh stool samples and clinical data were collected from all participants, and their bowel functions with SCI were assessed. Microbial diversity and composition were analyzed by sequencing the 16S rRNA gene. The features of gut microbiota correlated with the serum biomarkers and their functions were investigated. The mean NBD score of patients with CTSCI was higher than that of patients with ITSCI. Diversity of the gut microbiota in SCI group was reduced, and with an increase in the degree of damage, alpha diversity had decreased gradually. The composition of gut microbiota in patients with SCI was distinct from that in healthy individuals, and CTSCI group exhibited further deviation than ITSCI group compared to healthy individuals. Four serum biomarkers were found to be correlated with most differential genera. Patients with thoracic SCI present gut dysbiosis, which is more pronounced in patients with CTSCI than in those with ITSCI. Therefore, the gut microbiota profile may serve as the signatures for bowel and motor functions in patients with thoracic SCI.
DOI: 10.6084/m9.figshare.20301066
title: DNMT1-mediated demethylation of lncRNA MEG3 promoter suppressed breast cancer progression by repressing Notch1 signaling pathway

description: Breast carcinoma is one of the common causes of cancer-related mortality in women. Maternally expressed gene 3 (MEG3), a lncRNA located at 14q32, can be involved in carcinogenesis. In this study, we discovered that MEG3 was downregulated by CpG hypermethylation within its gene promoter. Functionally, treatment of breast cancer cells with the DNA methylation inhibitor 5-AzadC as well as silencing of DNA methyltransferase-1 (DNMT1) could decrease the abnormal hypermethylation of the MEG3 promoter, reverse MEG3 expression, inhibit cell proliferation and promote cell apoptosis. In addition, we found that MEG3 expression was negatively correlated with DNMT1. Mechanistically, MEG3 knockdown combined with 5-AzadC or sh-DNMT1 treatment restored the expression of Notch1 receptor, leading to the Notch1 pathway activation, and promoted the progression of epithelial mesenchymal transformation (EMT). Finally, the mice tumor model experiments showed that DNMT1 knockdown can increase MEG3 expression and inhibit tumor growth. Collectively, our findings uncovered that DNMT1-mediated MEG3 demethylation leads to MEG3 upregulation, which in turn inhibits the Notch1 pathway and EMT process in breast cancer.
DOI: 10.6084/m9.figshare.20301066.v1
title: DNMT1-mediated demethylation of lncRNA MEG3 promoter suppressed breast cancer progression by repressing Notch1 signaling pathway

description: Breast carcinoma is one of the common causes of cancer-related mortality in women. Maternally expressed gene 3 (MEG3), a lncRNA located at 14q32, can be involved in carcinogenesis. In this study, we discovered that MEG3 was downregulated by CpG hypermethylation within its gene promoter. Functionally, treatment of breast cancer cells with the DNA methylation inhibitor 5-AzadC as well as silencing of DNA methyltransferase-1 (DNMT1) could decrease the abnormal hypermethylation of the MEG3 promoter, reverse MEG3 expression, inhibit cell proliferation and promote cell apoptosis. In addition, we found that MEG3 expression was negatively correlated with DNMT1. Mechanistically, MEG3 knockdown combined with 5-AzadC or sh-DNMT1 treatment restored the expression of Notch1 receptor, leading to the Notch1 pathway activation, and promoted the progression of epithelial mesenchymal transformation (EMT). Finally, the mice tumor model experiments showed that DNMT1 knockdown can increase MEG3 expression and inhibit tumor growth. Collectively, our findings uncovered that DNMT1-mediated MEG3 demethylation leads to MEG3 upregulation, which in turn inhibits the Notch1 pathway and EMT process in breast cancer.
DOI: 10.6084/m9.figshare.15058005
title: Anti-neoplastic characteristics and potential targets of calycosin against bisphenol A-related osteosarcoma: bioinformatics analysis

description: Environmentally, bisphenol A (BPA) is a well-known pollutant caused human health risk, including osteosarcoma (OS). OS, a deadly bone neoplasia, may occur in children and adults. However, the anti-OS pharmacotherapy prescribes limitedly in clinical practice. Interestingly, previous experimental evidences indicate calycosin-exerting potential anti-OS actions. Thus, in this report, we aimed to further characterize and detail the therapeutic targets and molecular mechanisms of calycosin-anti-BPA-related OS by using network pharmacology and molecular docking analyses. In results, the bioinformatics data disclosed all mapped, core targets, biological functions, molecular pathways of calycosin to treat BPA-related OS. The computational analysis using molecular docking indicated that potential binding ability of core targets in calycosin to treat BPA-related OS was identified. Moreover, detailed biological functions and optimal pathways of calycosin-anti-BPA-related OS were revealed, as shown in integrated network maps. Taken together, these network pharmacology and structural biology findings illustrate the core biotargets, pharmacological functions and pathways of calycosin-anti-BPA-related OS. Potentially, these core targets identified by molecular docking may attribute to the potential clinical application of calycosin against BPA-related OS.
DOI: 10.6084/m9.figshare.14526215
title: Additional file 1 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S1. The PgbZIP genes identified in this study and their transcript sequences.
DOI: 10.6084/m9.figshare.14526221.v1
title: Additional file 3 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S3. Sequence alignment of the Jilin ginseng PgbZIP genes to the Korean Ginseng Genome Database.
DOI: 10.6084/m9.figshare.7193879.v1
title: Additional file 2: of Transcriptome analysis of radish sprouts hypocotyls reveals the regulatory role of hydrogen-rich water in anthocyanin biosynthesis under UV-A

description: Table S2. The differentially expressed genes involved in anthocyanin biosynthesis-related signaling pathways. (XLS 131 kb)
DOI: 10.6084/m9.figshare.14526218
title: Additional file 2 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S2. The 62 PgbZIP genes that were spliced into transacripts having full-length ORFs and their putative protein sequences.
DOI: 10.6084/m9.figshare.7193717
title: Additional file 3: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: IDs and names of selected 150 common migratory birds in China. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7193879
title: Additional file 2: of Transcriptome analysis of radish sprouts hypocotyls reveals the regulatory role of hydrogen-rich water in anthocyanin biosynthesis under UV-A

description: Table S2. The differentially expressed genes involved in anthocyanin biosynthesis-related signaling pathways. (XLS 131 kb)
DOI: 10.6084/m9.figshare.7193699
title: Additional file 2: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: The 495 sequence alignments of influenza A (H7N9) isolated in chicken from GISAID. (FAS 1511 kb)
DOI: 10.6084/m9.figshare.7193729
title: Additional file 4: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: 184 gene sequences of influenza A (H7N9) virus isolated in chicken downloaded from GISAID. (XLSX 17 kb)
DOI: 10.25386/genetics.11388195
title: Supplemental Material for Li et al., 2020

description: This is the zipped file for File S1 that contains all the supplementary tables and figures.
DOI: 10.6084/m9.figshare.15058092
title: Additional file 1 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 1. The 92 up-regulated genes
DOI: 10.6084/m9.figshare.15058092.v1
title: Additional file 1 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 1. The 92 up-regulated genes
DOI: 10.6084/m9.figshare.15058107.v1
title: Additional file 6 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 6. The network of hub genes and KEGG interaction
DOI: 10.6084/m9.figshare.7193717.v1
title: Additional file 3: of Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China

description: IDs and names of selected 150 common migratory birds in China. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7193828.v1
title: Additional file 2 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

description: Assignments of transcription factors to biological components. (XLSX 35.2 kb)
DOI: 10.6084/m9.figshare.15058104
title: Additional file 5 of Analysis of immune cell components and immune-related gene expression profiles in peripheral blood of patients with type 1 diabetes mellitus

description: Additional file 5. Distribution of immune cells
DOI: 10.6084/m9.figshare.7193840
title: Additional file 3 of Thirty biologically interpretable clusters of transcription factors distinguish cancer type

description: Results of ToppGene analysis of each of the thirty biological components. (XLSX 571 kb)
DOI: 10.6084/m9.figshare.15058221.v1
title: Additional file 1 of Effect of COVID-19 on epidemiological characteristics of road traffic injuries in Suzhou: a retrospective study

description: Additional file 1.