cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7012037
title: MiR-3606-3p inhibits systemic sclerosis through targeting TGF-β type II receptor

description: Systemic sclerosis (SSc) is a multisystemic fibrotic disease characterized by excessive collagen deposition and extracellular matrix synthesis. Though transforming growth factor-β (TGF-β) plays a fundamental role in the pathogenesis of SSc, the mechanism by which TGF-β signaling acts in SSc remains largely unclear. Here, we showed that TGF-β type II receptor (TGFBR2) was significantly upregulated in both human SSc dermal tissues and primary fibroblasts. In fibroblasts, siRNA-induced knockdown of <i>TGFBR2</i> resulted in a reduction of p-SMAD2/3 levels and reduced production of type I collagen. Additionally, functional experiments revealed that downregulation of <i>TGFBR2</i> yielded an anti-growth effect on fibroblasts through inhibiting cell cycle progression. Further studies showed that miR-3606-3p could directly target the 3′-UTR of <i>TGFBR2</i> and significantly decrease the levels of both TGFBR2 mRNA and protein. Furthermore, SSc dermal tissues and primary fibroblasts contain significantly reduced amounts of miR-3606-3p, and the overexpression of miR-3606-3p in fibroblasts replicates the phenotype of TGFBR2 downregulation. Collectively, our findings demonstrated that increased TGFBR2 could be responsible for the hyperactive TGF-β signaling observed in SSc. Moreover, we identified a pivotal role for miR-3606-3p in SSc, which acts, at least partly, through the attenuation of TGF-β signaling via TGFBR2 repression, suggesting that the regulation of miR-3606-3p/TGFBR2 could be a promising therapeutic target that could improve the treatment strategy for fibrosis.
DOI: 10.6084/m9.figshare.7012052.v1
title: Identification of compound CA-5f as a novel late-stage autophagy inhibitor with potent anti-tumor effect against non-small cell lung cancer

description: Currently, particular focus is placed on the implication of autophagy in a variety of human diseases, including cancer. Discovery of small-molecule modulators of autophagy as well as their potential use as anti-cancer therapeutic agents would be of great significance. To this end, a series of curcumin analogs previously synthesized in our laboratory were screened. Among these compounds, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one (CA-5f) was identified as a potent late-stage macroautophagy/autophagy inhibitor via inhibiting autophagosome-lysosome fusion. We found that CA-5f neither impaired the hydrolytic function nor the quantity of lysosomes. Use of an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic screen in combination with bioinformatics analysis suggested that treatment of human umbilical vein endothelial cells (HUVECs) with CA-5f for 1 h suppressed the levels of cytoskeletal proteins and membrane traffic proteins. Subsequent studies showed that CA-5f exhibited strong cytotoxicity against A549 non-small cell lung cancer (NSCLC) cells, but low cytotoxicity to normal human umbilical vein endothelial cells (HUVECs), by increasing mitochondrial-derived reactive oxygen species (ROS) production. Moreover, CA-5f effectively suppressed the growth of A549 lung cancer xenograft as a single agent with an excellent tolerance in vivo. Results from western blot, immunofluorescence, and TdT-mediated dUTP nick end labeling (TUNEL) assays showed that CA-5f inhibited autophagic flux, induced apoptosis, and did not affect the level of CTSB (cathepsin B) and CTSD (cathepsin D) in vivo, which were consistent with the in vitro data. Collectively, these results demonstrated that CA-5f is a novel late-stage autophagy inhibitor with potential clinical application for NSCLC therapy. <b>Abbreviations</b>: 3-MA, 3-methyladenine; ANXA5, annexin A5; ATG, autophagy related; CA-5f, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one; CQ, chloroquine; CTSB, cathepsin B; CTSD, cathepsin D; DMSO, dimethyl sulfoxide; DNM2, dynamin 2; EBSS, Earle’s balanced salt solution; GFP, green fluorescent protein; HCQ, hydroxyl CQ; HEK293, human embryonic kidney 293; HUVEC, human umbilical vein endothelial cells; LAMP1, lysosomal associated membrane protein 1; LC-MS/MS, liquid chromatography coupled to tandem mass spectrometry; LDH, lactic acid dehydrogenase; LMO7, LIM domain 7; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; NAC, N-acetyl cysteine; MYO1E, myosin IE; NSCLC, non-small cell lung cancer; PARP1, poly(ADP-ribose) polymerase 1; PI, propidium iodide; RFP, red fluorescent protein; ROS, reactive oxygen species; SQSTM1, sequestosome 1; TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling.
DOI: 10.6084/m9.figshare.13294957.v1
title: Additional file 4 of Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

description: Additional file 4:. Protein-coding transcript (cds) and Protein-coding transcript translation (pep) sequences, and GFF (gff) files of antioxidant enzymes in 58 nematodes.
DOI: 10.6084/m9.figshare.12254519.v1
title: Exploring of InDel in bovine <i>PSAP</i> gene and their association with growth traits in different development stages

description: <i>PSAP</i> (prosaposin) is widely expressed in different organs, and plays an important role in fat deposit. Insertion/Deletion (InDel) is a relatively simple and effective DNA marker. However, the association of molecular marker at different stages of animal development has not received enough attention, especially fat deposition related traits. Therefore, eight cattle breeds were used to explore novel InDels variants within bovine <i>PSAP</i> gene, and to evaluate their effects on growth traits in different development stages. Herein, two novel InDels (P5:NC037355.1g.27974439-27974440 ins AGTGTGGTTAATGTCAAC and P8:NC037355.1g.27980734-27980752 del GTCAAAAAATCAGGGGAAAC) within the bovine <i>PSAP</i> gene were found, and their association with growth traits in different development stages were analyzed. Interestingly, the dominant genotype was different in different development stages both in NY cattle and JX cattle for daily gain and body weight. <i>PSAP</i> Gene expression patterns were analyzed in this study, high expression in the middle stage of adipocytes differentiation suggests that it plays a certain role in fat development. It reveals that InDels could affect phenotype in different development stages, which depend on the expression pattern of the host gene and their function in different tissues. These findings could provide a new way for molecular marker studies in bovine breeding and genetics.
DOI: 10.6084/m9.figshare.9108821.v1
title: Additional file 1: of Relationship between ALDH2 genotype and in-stent restenosis in Chinese Han patients after percutaneous coronary intervention

description: Table S1. Clinical information of all patients in this study. (XLSX 90 kb)
DOI: 10.25403/upresearchdata.25150772
title: Best practices, challenges and resources for teaching numeracy to Foundation Phase learners with blindness in South Africa

description: This dataset contains the data generated during a Participatory Reflection and Action (PRA) workshop and focus group held with Foundation Phase teachers who teach at a school for learners with visual impairment in Gauteng. It was collected in December 2022 as part of a masters in Educational Psychology mini dissertation. The data includes photographs of the resources used by the participants to teach numeracy to Foundation Phase learners with blindness; the concept maps generated by the participants in response to the prompt questions; the transcription of the PRA workshop and focus group; and the research journal. The data explores the questions: how are best practices for teaching numeracy to Foundation Phase learners with blindness conceptualised by teachers? Which resources may promote best practices for teaching numeracy to Foundation Phase learners with blindness? Which challenges may inhibit best practices for teaching numeracy to Foundation Phase learners with blindness?
DOI: 10.25403/upresearchdata.25150772.v1
title: Best practices, challenges and resources for teaching numeracy to Foundation Phase learners with blindness in South Africa

description: This dataset contains the data generated during a Participatory Reflection and Action (PRA) workshop and focus group held with Foundation Phase teachers who teach at a school for learners with visual impairment in Gauteng. It was collected in December 2022 as part of a masters in Educational Psychology mini dissertation. The data includes photographs of the resources used by the participants to teach numeracy to Foundation Phase learners with blindness; the concept maps generated by the participants in response to the prompt questions; the transcription of the PRA workshop and focus group; and the research journal. The data explores the questions: how are best practices for teaching numeracy to Foundation Phase learners with blindness conceptualised by teachers? Which resources may promote best practices for teaching numeracy to Foundation Phase learners with blindness? Which challenges may inhibit best practices for teaching numeracy to Foundation Phase learners with blindness?
DOI: 10.6084/m9.figshare.20110659.v1
title: Additional file 3 of Metabolomics and integrated network pharmacology analysis reveal SNKAF decoction suppresses cell proliferation and induced cell apoptisis in hepatocellular carcinoma via PI3K/Akt/P53/FoxO signaling axis

description: Additional file 3: Table S3. Metabolic pathways and corresponding metabolites.
DOI: 10.6084/m9.figshare.6487880
title: Additional file 6: of Diversification and independent domestication of Asian and European pears

description: List of 47 genes in common selective sweeps of both Asian and European groups during domestication from wild to cultivated pears. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.9108917
title: Additional file 2: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Hotspot mutations found in the TCGA dataset. (XLSX 152 kb)
DOI: 10.6084/m9.figshare.12254672.v1
title: Improvement in the Analysis of Vaccine Adverse Event Reporting System Database

description: As a national public health surveillance resource, Vaccine Adverse Event Reporting System (VAERS) is a key component in ensuring the safety of vaccines. Numerous methods have been used to conduct safety studies with the VAERS database. These efforts focus on the downstream statistical analysis of the vaccine and adverse event associations. In this article, we primarily focus on processing the raw data in VAERS before the analysis step, which is also an important part of the signal detection process. Due to the semiannual update in the Medical Dictionary for Regulatory Activities (MedDRA) coding system, adverse event terms that describe the same symptom might change in VAERS; therefore, we identify these terms and combine them to increase the signal detection power. We also consider the uncertainty of the vaccine and adverse event pairs that arise from reports with multiple vaccines. Finally, we discuss four commonly used statistics in assessing the vaccine and adverse event associations, and propose to use the statistics that are robust to the reporting bias in VAERS and adjust for potential confounders of the vaccine and adverse event association to increase signal detection accuracy.
DOI: 10.6084/m9.figshare.6487844
title: Additional file 4: of Diversification and independent domestication of Asian and European pears

description: S-genotyping for different accessions. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.6487880.v1
title: Additional file 6: of Diversification and independent domestication of Asian and European pears

description: List of 47 genes in common selective sweeps of both Asian and European groups during domestication from wild to cultivated pears. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.6487844.v1
title: Additional file 4: of Diversification and independent domestication of Asian and European pears

description: S-genotyping for different accessions. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.6487796.v1
title: Additional file 2: of Diversification and independent domestication of Asian and European pears

description: Summary of sequencing and mapping of 113 pear accessions. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.13294957
title: Additional file 4 of Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

description: Additional file 4:. Protein-coding transcript (cds) and Protein-coding transcript translation (pep) sequences, and GFF (gff) files of antioxidant enzymes in 58 nematodes.
DOI: 10.6084/m9.figshare.23265114
title: Additional file 8 of Breast metastatic tumors in lung can be substituted by lung-derived malignant cells transformed by alternative splicing H19 lncRNA

description: Additional file 8. Data file S1: PCR array plate layout.
DOI: 10.6084/m9.figshare.12254963.v2
title: Modeling and Regionalization of China’s PM<sub>2.5</sub> Using Spatial-Functional Mixture Models

description: Severe air pollution affects billions of people around the world, particularly in developing countries such as China. Effective emission control policies rely primarily on a proper assessment of air pollutants and accurate spatial clustering outcomes. Unfortunately, emission patterns are difficult to observe as they are highly confounded by many meteorological and geographical factors. In this study, we propose a novel approach for modeling and clustering PM2.5 concentrations across China. We model observed concentrations from monitoring stations as spatially dependent functional data and assume latent emission processes originate from a functional mixture model with each component as a spatio-temporal process. Cluster memberships of monitoring stations are modeled as a Markov random field, in which confounding effects are controlled through energy functions. The superior performance of our approach is demonstrated using extensive simulation studies. Our method is effective in dividing China and the Beijing-Tianjin-Hebei region into several regions based on PM2.5 concentrations, suggesting that separate local emission control policies are needed.
DOI: 10.6084/m9.figshare.12254963.v3
title: Modeling and Regionalization of China’s PM<sub>2.5</sub> Using Spatial-Functional Mixture Models

description: <b><i>Abstract–</i>Severe air pollution affects billions of people around the world, particularly in developing countries such as China. Effective emission control policies rely primarily on a proper assessment of air pollutants and accurate spatial clustering outcomes. Unfortunately, emission patterns are difficult to observe as they are highly confounded by many meteorological and geographical factors. In this study, we propose a novel approach for modeling and clustering PM</b>2.5<b>concentrations across China. We model observed concentrations from monitoring stations as spatially dependent functional data and assume latent emission processes originate from a functional mixture model with each component as a spatio-temporal process. Cluster memberships of monitoring stations are modeled as a Markov random field, in which confounding effects are controlled through energy functions. The superior performance of our approach is demonstrated using extensive simulation studies. Our method is effective in dividing China and the Beijing-Tianjin-Hebei region into several regions based on PM</b>2.5<b>concentrations, suggesting that separate local emission control policies are needed. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.</b>
DOI: 10.6084/m9.figshare.23264990
title: Additional file 4 of NPM3 as a novel oncogenic factor and poor prognostic marker contributes to cell proliferation and migration in lung adenocarcinoma

description: Additional file 4: Supplementary Table S1. Primer sequences.
DOI: 10.6084/m9.figshare.6487826.v1
title: Additional file 3: of Diversification and independent domestication of Asian and European pears

description: SNPs and genotype verification by Sanger sequencing. (XLSX 76Â kb)
DOI: 10.6084/m9.figshare.23265002
title: Additional file 8 of NPM3 as a novel oncogenic factor and poor prognostic marker contributes to cell proliferation and migration in lung adenocarcinoma

description: Additional file 8: Supplementary Table S5. The genes negatively associated with NPM3 expression.
DOI: 10.6084/m9.figshare.6487943
title: Additional file 9: of Diversification and independent domestication of Asian and European pears

description: List of domesticated genes within QTL regions and association SNPs. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.9109346.v1
title: Additional file 2: of Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns

description: Table S1. Basic pathways and Cancer-related genes. Table S2. Four patterns of DEGs. Table S3. Key DEGs of sub of KYSE-180 12Gy. Table S4. Disease ontology of 1.5 fold DEGs. Table S5. KEGG of DEGs-obtained. Table S6. Key DEGs of bulk cell. Table S7. qPCR primer sequences of mRNA. Table S8. The enrichment GO analysis of four patterns of DEGs. (XLS 302 kb)
DOI: 10.6084/m9.figshare.23265005.v1
title: Additional file 9 of NPM3 as a novel oncogenic factor and poor prognostic marker contributes to cell proliferation and migration in lung adenocarcinoma

description: Additional file 9: Supplementary Table S6. The KEGG enrichment pathway of genes negativelyassociated with NPM3 expression.
DOI: 10.6084/m9.figshare.23265120.v1
title: Additional file 10 of Breast metastatic tumors in lung can be substituted by lung-derived malignant cells transformed by alternative splicing H19 lncRNA

description: Additional file 10. Data file S2: List of all the expressed long ncRNAs identified by RNA-seq in the exosomes from E-MDC and M-MDC cells.
DOI: 10.6084/m9.figshare.13294960.v1
title: Additional file 5 of Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

description: Additional file 5: Table S5. Transcriptome data information (SRA information and genome alignment summary) for 20 nematodes.
DOI: 10.6084/m9.figshare.20110700
title: Additional file 1 of Assessment of malaria transmission intensity and insecticide resistance mechanisms in three rural areas of the Moyen Ogooué Province of Gabon

description: Additional file 1. Sequence identification of Anopheles sp. using ITS2.
DOI: 10.6084/m9.figshare.20110700.v1
title: Additional file 1 of Assessment of malaria transmission intensity and insecticide resistance mechanisms in three rural areas of the Moyen Ogooué Province of Gabon

description: Additional file 1. Sequence identification of Anopheles sp. using ITS2.
DOI: 10.6084/m9.figshare.12254963.v4
title: Modeling and Regionalization of China’s PM<sub>2.5</sub> Using Spatial-Functional Mixture Models

description: <b><i>Abstract–</i>Severe air pollution affects billions of people around the world, particularly in developing countries such as China. Effective emission control policies rely primarily on a proper assessment of air pollutants and accurate spatial clustering outcomes. Unfortunately, emission patterns are difficult to observe as they are highly confounded by many meteorological and geographical factors. In this study, we propose a novel approach for modeling and clustering PM</b>2.5<b>concentrations across China. We model observed concentrations from monitoring stations as spatially dependent functional data and assume latent emission processes originate from a functional mixture model with each component as a spatio-temporal process. Cluster memberships of monitoring stations are modeled as a Markov random field, in which confounding effects are controlled through energy functions. The superior performance of our approach is demonstrated using extensive simulation studies. Our method is effective in dividing China and the Beijing-Tianjin-Hebei region into several regions based on PM</b>2.5<b>concentrations, suggesting that separate local emission control policies are needed. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.</b>
DOI: 10.6084/m9.figshare.23265005
title: Additional file 9 of NPM3 as a novel oncogenic factor and poor prognostic marker contributes to cell proliferation and migration in lung adenocarcinoma

description: Additional file 9: Supplementary Table S6. The KEGG enrichment pathway of genes negativelyassociated with NPM3 expression.
DOI: 10.6084/m9.figshare.6487796
title: Additional file 2: of Diversification and independent domestication of Asian and European pears

description: Summary of sequencing and mapping of 113 pear accessions. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.6487952.v1
title: Additional file 2: of Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans

description: Logistic regression analysis of eleven candidate genes using tumor expression data derived from TCGA, GSE21032 and GSE46691. Five of eleven candidate genes CCDC115, DNAJC10, RNF149, STYXL1, and ZNF502 that harbored significant associations with aggressive disease traits in TCGA cohort only. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6487943.v1
title: Additional file 9: of Diversification and independent domestication of Asian and European pears

description: List of domesticated genes within QTL regions and association SNPs. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.13294954.v1
title: Additional file 3 of Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

description: Additional file 3: Table S4. Gene information of antioxidant enzymes in reannotation and original gene annotation in 59 nematodes.
DOI: 10.15468/dl.vh9z75
title: Occurrence Download

description: A dataset containing 16946 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON(((5.241862535476685 43.294803095683314,5.241862535476685 43.25493380778211,5.340739488601685 43.25493380778211,5.340739488601685 43.294803095683314,5.241862535476685 43.294803095683314)))"
 ]
}

 The dataset includes 16946 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084644-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2edn7q
title: Occurrence Download

description: A dataset containing 926 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((4.95044 5.32532,50.61642 4.16573,123.10365 24.47145,119.88835 53.99644,45.99542 53.61602,-26.48649 36.39142,-30.11413 12.15095,4.95044 5.32532))",
 "TaxonKey is Calligonum L."
 ]
}

 The dataset includes 926 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0303624-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.662mcb
title: Occurrence Download

description: A dataset containing 114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Pudu puda (Molina, 1782)"
 ]
}

 The dataset includes 114 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240235-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.