cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28089747
title: Correlation analysis of key genes and immune infiltration in visceral adipose tissue and subcutaneous adipose tissue of patients with type 2 diabetes in women

description: Immune cell infiltration into adipose tissue (AT) is a key factor in type 2 diabetes (T2DM). However, research on the impact of fat distribution on immune cells and immune responses in women is still lacking. This study used enrichment, protein–protein interaction network, immune cell infiltration, and correlation analysis to compare the similarities and differences between the transcriptome data of visceral AT (VAT) and subcutprotein-proteinaneous AT (SAT) obtained from the omprehensive database of gene expression in women with non-T2DM and T2DM. DEGs with the same biological function in two types of ATs often exhibited different expression trends. SharedVAT-specific and SAT-specific hub genes were mainly associated with transcription factors, monocyte-macrophage markers, and chemokines, respectively. Immune cells affected by both AT types included monocytes, granulocytes, T and B lymphocytes, and NK cells. VAT affected more immune cells, mainly myeloid cells. Shared hub genes in VAT correlated positively with M1 macrophages, suggesting pro-inflammatory effects, while those in SAT correlated negatively with M1 macrophages and lymphocytes, suggesting anti-inflammatory effects. This study provides a theoretical basis for further understanding the correlation between AT and T2DM in women.
DOI: 10.6084/m9.figshare.28089747.v1
title: Correlation analysis of key genes and immune infiltration in visceral adipose tissue and subcutaneous adipose tissue of patients with type 2 diabetes in women

description: Immune cell infiltration into adipose tissue (AT) is a key factor in type 2 diabetes (T2DM). However, research on the impact of fat distribution on immune cells and immune responses in women is still lacking. This study used enrichment, protein–protein interaction network, immune cell infiltration, and correlation analysis to compare the similarities and differences between the transcriptome data of visceral AT (VAT) and subcutprotein-proteinaneous AT (SAT) obtained from the omprehensive database of gene expression in women with non-T2DM and T2DM. DEGs with the same biological function in two types of ATs often exhibited different expression trends. SharedVAT-specific and SAT-specific hub genes were mainly associated with transcription factors, monocyte-macrophage markers, and chemokines, respectively. Immune cells affected by both AT types included monocytes, granulocytes, T and B lymphocytes, and NK cells. VAT affected more immune cells, mainly myeloid cells. Shared hub genes in VAT correlated positively with M1 macrophages, suggesting pro-inflammatory effects, while those in SAT correlated negatively with M1 macrophages and lymphocytes, suggesting anti-inflammatory effects. This study provides a theoretical basis for further understanding the correlation between AT and T2DM in women.
DOI: 10.6084/m9.figshare.28450878.v1
title: Adipogenic dedifferentiation enhances survival of human umbilical cord-derived mesenchymal stem cells under oxidative stress

description: Mesenchymal stem cells (MSCs) serve as ideal candidates for a broad range of cell-based therapies. However, cell ageing caused by long-term in vitro expansion and poor survival after in vivo delivery greatly limits their success in preclinical and clinical applications. Dedifferentiation represents a potential strategy for enhancing the retention and function of MSCs in hostile environments. In this study, we evaluated the cell phenotype, proliferation, and differentiation potential, as well as the anti-oxidative stress ability of human umbilical cord-derived MSCs (hMSCs) manipulated with adipogenic priming and subsequent dedifferentiation. After an in vitro differentiation and dedifferentiation procedure, the resultant dedifferentiated hMSCs (De-hMSCs) displayed properties similar to their original counterparts, including immunophenotype and mesodermal potential. Upon re-induction, De-hMSCs exhibited a significantly higher adipogenic differentiation capability than unmanipulated hMSCs. Importantly, De-hMSCs showed a significantly enhanced ability to resist tert-butyl hydroperoxide (t-BHP) induced apoptosis compared to undifferentiated hMSCs. Mechanisms involving bcl-2 family proteins and autophagy may contribute to the demonstrated advantages of dedifferentiation-reprogrammed hMSCs. These results indicate that adipogenic dedifferentiation promotes adipogenesis and cell persistence, as well as preserves the stemness of human umbilical cord-derived MSCs that have been committed to the adipocytic lineage. As a unique stem cell population, dedifferentiated MSCs may represent an attractive and promising candidate for MSC-based therapy.
DOI: 10.6084/m9.figshare.28450878
title: Adipogenic dedifferentiation enhances survival of human umbilical cord-derived mesenchymal stem cells under oxidative stress

description: Mesenchymal stem cells (MSCs) serve as ideal candidates for a broad range of cell-based therapies. However, cell ageing caused by long-term in vitro expansion and poor survival after in vivo delivery greatly limits their success in preclinical and clinical applications. Dedifferentiation represents a potential strategy for enhancing the retention and function of MSCs in hostile environments. In this study, we evaluated the cell phenotype, proliferation, and differentiation potential, as well as the anti-oxidative stress ability of human umbilical cord-derived MSCs (hMSCs) manipulated with adipogenic priming and subsequent dedifferentiation. After an in vitro differentiation and dedifferentiation procedure, the resultant dedifferentiated hMSCs (De-hMSCs) displayed properties similar to their original counterparts, including immunophenotype and mesodermal potential. Upon re-induction, De-hMSCs exhibited a significantly higher adipogenic differentiation capability than unmanipulated hMSCs. Importantly, De-hMSCs showed a significantly enhanced ability to resist tert-butyl hydroperoxide (t-BHP) induced apoptosis compared to undifferentiated hMSCs. Mechanisms involving bcl-2 family proteins and autophagy may contribute to the demonstrated advantages of dedifferentiation-reprogrammed hMSCs. These results indicate that adipogenic dedifferentiation promotes adipogenesis and cell persistence, as well as preserves the stemness of human umbilical cord-derived MSCs that have been committed to the adipocytic lineage. As a unique stem cell population, dedifferentiated MSCs may represent an attractive and promising candidate for MSC-based therapy.
DOI: 10.6084/m9.figshare.28227194
title: Bioinformatics analysis identifies key secretory protein-encoding differentially expressed genes in adipose tissue of metabolic syndrome

description: The objective of this study was to identify key secretory protein-encoding differentially expressed genes (SP-DEGs) in adipose tissue in female metabolic syndrome, thus detecting potential targets in treatment. We examined gene expression profiles in 8 women with metabolic syndrome and 7 healthy, normal body weight women. A total of 143 SP-DEGs were screened, including 83 upregulated genes and 60 downregulated genes. GO analyses of these SP-DEGs included proteolysis, angiogenesis, positive regulation of endothelial cell proliferation, immune response, protein processing, positive regulation of neuroblast proliferation, cell adhesion and ER to Golgi vesicle-mediated transport. KEGG pathway analysis of the SP-DEGs were involved in the TGF-beta signalling pathway, cytokine‒cytokine receptor interactions, the hippo signalling pathway, Malaria. Two modules were identified from the PPI network, namely, Module 1 (DNMT1, KDM1A, NCoR1, and E2F1) and Module 2 (IL-7 R, IL-12A, and CSF3). The gene DNMT1 was shared between the network modules and the WGCNA brown module. According to the single-gene GSEA results, DNMT1 was significantly positively correlated with histidine metabolism and phenylalanine metabolism. This study identified 7 key SP-DEGs in adipose tissue. DNMT1 was selected as the central gene in the development of metabolic syndrome and might be a potential therapeutic target.
DOI: 10.6084/m9.figshare.28227194.v1
title: Bioinformatics analysis identifies key secretory protein-encoding differentially expressed genes in adipose tissue of metabolic syndrome

description: The objective of this study was to identify key secretory protein-encoding differentially expressed genes (SP-DEGs) in adipose tissue in female metabolic syndrome, thus detecting potential targets in treatment. We examined gene expression profiles in 8 women with metabolic syndrome and 7 healthy, normal body weight women. A total of 143 SP-DEGs were screened, including 83 upregulated genes and 60 downregulated genes. GO analyses of these SP-DEGs included proteolysis, angiogenesis, positive regulation of endothelial cell proliferation, immune response, protein processing, positive regulation of neuroblast proliferation, cell adhesion and ER to Golgi vesicle-mediated transport. KEGG pathway analysis of the SP-DEGs were involved in the TGF-beta signalling pathway, cytokine‒cytokine receptor interactions, the hippo signalling pathway, Malaria. Two modules were identified from the PPI network, namely, Module 1 (DNMT1, KDM1A, NCoR1, and E2F1) and Module 2 (IL-7 R, IL-12A, and CSF3). The gene DNMT1 was shared between the network modules and the WGCNA brown module. According to the single-gene GSEA results, DNMT1 was significantly positively correlated with histidine metabolism and phenylalanine metabolism. This study identified 7 key SP-DEGs in adipose tissue. DNMT1 was selected as the central gene in the development of metabolic syndrome and might be a potential therapeutic target.
DOI: 10.15468/dl.qfmdnp
title: Occurrence Download

description: A dataset containing 679 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-103.42526 20.28846,-103.41735 20.28719,-103.40873 20.29407,-103.41237 20.3034,-103.4163 20.30765,-103.42315 20.30931,-103.43177 20.30671,-103.44183 20.30582,-103.44916 20.30095,-103.45509 20.30192,-103.4511 20.29628,-103.42526 20.28846))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 679 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048321-251120083545085/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.28433340
title: Effects of alpelisib treatment on murine <i>Pten</i>-deficient lipomas

description:  Phosphatase and tensin homolog (PTEN) hamartoma tumour syndrome (PHTS) is a rare disorder caused by germline mutations in the tumour suppressor gene PTEN, a key negative regulator of phosphatidylinositol 3-kinase (PI3K)/AKT signalling. Children with PHTS often develop lipomas, for which only surgical resection is available as treatment. We investigated the effects of the selective PI3K-inhibitor alpelisib on Pten-deficient lipomas. After incubation with alpelisib or the non-selective PI3K inhibitor wortmannin, we analysed histology, gene expression, and Pi3k pathway in lipoma and control epididymal adipose tissue (epiWAT). Alpelisib increased adipocyte area in lipomas compared to epiWAT. Baseline gene expression showed higher levels of markers for proliferation (<i>Pcna</i>), fibrosis (<i>Tgfb1</i>), and adipogenesis (<i>Pparg</i>) in lipomas, while hormone-sensitive lipase expression was lower than in epiWAT. Following alpelisib incubation, target genes of Pi3k signalling and extracellular matrix factors were reduced. We confirmed Pi3k inhibition through detecting decreased Akt levels compared to control treatment. Human lipoma samples treated with alpelisib showed variable lipolysis responses, suggesting variability in therapeutic outcomes. We established an ex vivo model to study alpelisib effects on Pten-deficient lipomas. These results underscore the therapeutic potential of targeted PI3K inhibition in the treatment of PHTS-associated lipomas, particularly in cases that are inoperable.
DOI: 10.6084/m9.figshare.28433340.v1
title: Effects of alpelisib treatment on murine <i>Pten</i>-deficient lipomas

description:  Phosphatase and tensin homolog (PTEN) hamartoma tumour syndrome (PHTS) is a rare disorder caused by germline mutations in the tumour suppressor gene PTEN, a key negative regulator of phosphatidylinositol 3-kinase (PI3K)/AKT signalling. Children with PHTS often develop lipomas, for which only surgical resection is available as treatment. We investigated the effects of the selective PI3K-inhibitor alpelisib on Pten-deficient lipomas. After incubation with alpelisib or the non-selective PI3K inhibitor wortmannin, we analysed histology, gene expression, and Pi3k pathway in lipoma and control epididymal adipose tissue (epiWAT). Alpelisib increased adipocyte area in lipomas compared to epiWAT. Baseline gene expression showed higher levels of markers for proliferation (<i>Pcna</i>), fibrosis (<i>Tgfb1</i>), and adipogenesis (<i>Pparg</i>) in lipomas, while hormone-sensitive lipase expression was lower than in epiWAT. Following alpelisib incubation, target genes of Pi3k signalling and extracellular matrix factors were reduced. We confirmed Pi3k inhibition through detecting decreased Akt levels compared to control treatment. Human lipoma samples treated with alpelisib showed variable lipolysis responses, suggesting variability in therapeutic outcomes. We established an ex vivo model to study alpelisib effects on Pten-deficient lipomas. These results underscore the therapeutic potential of targeted PI3K inhibition in the treatment of PHTS-associated lipomas, particularly in cases that are inoperable.
DOI: 10.6084/m9.figshare.30484999
title: Adipose tissue explant culture using PDMS flow chambers: an alternative to static explant culture

description: As obesity rates continue to rise, it is important that we can effectively study adipose tissue to understand its physiological contribution in individuals with obesity. Unfortunately, due to the fragility and buoyancy of adipose tissue, culture remains challenging. <i>Ex vivo</i> culture of tissue explants is possible, however after 48 hours explants often display declining viability, increased inflammation, and de-differentiation. Other common approaches include differentiation of preadipocytes and adipocyte isolation by enzymatic dissociation, however these methods are time-consuming and fail to recapitulate the structure and cellular network within adipose tissue. Given these shortcomings, we developed a novel explant culture method using polydimethylsiloxane (PDMS) flow chambers attached to a micro peristaltic pump. This approach reduces air interface while enabling media perfusion, time-resolved measurements of secreted factors, and easy incorporation of treatments. Using our chambers, we assessed viability with resazurin and lactate dehydrogenase (LDH) assays, physiology by measuring glycerol release, architecture by confocal imaging, and retention of adipose gene expression by qPCR. Explants remained viable for over 72 hours. Resazurin reduction was at 84 ± 9% of baseline, and LDH release remained low. Isoproterenol treatment resulted in 2.7 ± 0.5-fold increased glycerol release, while insulin returned release to baseline. Confocal imaging showed preserved architecture, while qPCR of human tissue with insulin and dexamethasone supplementation showed maintained expression of <i>PPARG</i> and <i>FABP4</i> over 72 hours. Overall, our results suggest PDMS flow chambers are a suitable method for adipose explant culture that requires minimal processing, making this system a viable option for translational research.
DOI: 10.6084/m9.figshare.30484999.v1
title: Adipose tissue explant culture using PDMS flow chambers: an alternative to static explant culture

description: As obesity rates continue to rise, it is important that we can effectively study adipose tissue to understand its physiological contribution in individuals with obesity. Unfortunately, due to the fragility and buoyancy of adipose tissue, culture remains challenging. <i>Ex vivo</i> culture of tissue explants is possible, however after 48 hours explants often display declining viability, increased inflammation, and de-differentiation. Other common approaches include differentiation of preadipocytes and adipocyte isolation by enzymatic dissociation, however these methods are time-consuming and fail to recapitulate the structure and cellular network within adipose tissue. Given these shortcomings, we developed a novel explant culture method using polydimethylsiloxane (PDMS) flow chambers attached to a micro peristaltic pump. This approach reduces air interface while enabling media perfusion, time-resolved measurements of secreted factors, and easy incorporation of treatments. Using our chambers, we assessed viability with resazurin and lactate dehydrogenase (LDH) assays, physiology by measuring glycerol release, architecture by confocal imaging, and retention of adipose gene expression by qPCR. Explants remained viable for over 72 hours. Resazurin reduction was at 84 ± 9% of baseline, and LDH release remained low. Isoproterenol treatment resulted in 2.7 ± 0.5-fold increased glycerol release, while insulin returned release to baseline. Confocal imaging showed preserved architecture, while qPCR of human tissue with insulin and dexamethasone supplementation showed maintained expression of <i>PPARG</i> and <i>FABP4</i> over 72 hours. Overall, our results suggest PDMS flow chambers are a suitable method for adipose explant culture that requires minimal processing, making this system a viable option for translational research.
DOI: 10.17026/ar/adp0cp
title: PAN-00178829 - multipartite belt fastening with plate E

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00178829&lt;/p&gt;
description: Modified: 2025-10-23T09:19:41+02:00
DOI: 10.15468/dl.bb7gyd
title: Occurrence Download

description: A dataset containing 25033666 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.occurrencestatus = 'PRESENT'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 25033666 records were derived from 70577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048297-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/lsv5br
title: PAN-00108968 - coin/coin-related, stad, florijn van 28 stuiver

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00108968&lt;/p&gt;
description: Modified: 2025-07-29T10:45:03+02:00
DOI: 10.5281/zenodo.15571709
title: Automatic Classification of Thermal Phases During Steel Oxidation via PCA and Infrared Thermography Time Series

description:  

Contents





Raw Thermograms (/Raw_Thermograms_CSV/):Time-series thermal data (in CSV) from five controlled high-temperature oxidation experiments on AISI 1045 steel.




PCA Results (/PCA_Results_XLSX/):Principal Component Analysis (PCA) outputs (first two components) derived from the flattened thermograms, used as input features for machine learning classification.



A total of 3356 thermographic records were compiled, covering heating, isothermal, and cooling phases.

Methodology

Steel specimens (AISI 1045) were oxidized using a Joule-heating system, with thermal data captured using an Optris PI 1M infrared camera.PCA was applied to the flattened thermal matrices to reduce dimensionality.Five machine learning models (Random Forest, MLP, SVM, KNN, XGBoost) were trained and validated (5-fold CV) for automatic classification of thermal phases.

Purpose

This dataset supports the development of non-invasive phase recognition tools in metallurgical processes using infrared thermography and machine learning, enhancing process monitoring and decision-making.

How to Use



Clone the Repository:

git clone https://github.com/YOUR_USERNAME/Thermal_Phase_Classification_Dataset.git



Explore the Data:


Raw thermograms are organized in /Raw_Thermograms_CSV/.

PCA results for classification are in /PCA_Results_XLSX/.



Note: The scripts used for analysis are available upon request or will be made public after article acceptance.


Data Availability Statement

The dataset will be permanently archived with a DOI via Zenodo upon publication.

Citation

If you use this dataset, please cite:

Chávez-Campos, G. M., Vergara-Hernández, H. J., Téllez-Martínez, J. S., Guevara, E., Díaz-Ibarra, M. A., Morales-Cervantes, A. (2025). Automatic Classification of Thermal Phases During Steel Oxidation via PCA and Infrared Thermography Time Series.

Authors' Contributions

Antony Morales-Cervantes led the data collection. All authors contributed to data analysis and interpretation. All authors approved the final version of the manuscript for publication.

License

This dataset is distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
DOI: 10.15468/dl.whj656
title: Occurrence Download

description: A dataset containing 562 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "TaxonKey is Marsilea quadrifolia"
 ]
}

 The dataset includes 562 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048325-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/7b6ghh
title: PAN-00161202 - terra sigillata bowl type Drag. 37 (SG)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00161202&lt;/p&gt;
description: Modified: 2025-11-06T09:43:25+01:00