cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc25xcr7
title: CCDC 2023269: Experimental Crystal Structure Determination

description: Related Article: Babli K. Jha, Jaggaraju Prudhviraj, Prathama S. Mainkar, Nagender Punna, Srivari Chandrasekhar|2020|RSC Advances|10|38588|doi:10.1039/D0RA08289A
DOI: 10.5517/ccdc.csd.cc265zw8
title: CCDC 2031550: Experimental Crystal Structure Determination

description: Related Article: Antoine Meunier, Michael L. Singleton, Brice Kauffmann, Thierry Granier, Guillaume Lautrette, Yann Ferrand, Ivan Huc|2020|Chemical Science|11|12178|doi:10.1039/D0SC05143H
DOI: 10.34777/055b-xs02
title: MediaParl

description: Mediaparl is a Swiss accented bilingual database containing recordings in both 	French and German as they are spoken in Switzerland. The data were recorded at the Valais Parliament. Valais is a bi-lingual Swiss canton with many local accents and dialects. Therefore, the database contains data with high variability and is suitable to study multilingual, accented and non-native speech recognition as well as language identification and language switch detection.
DOI: 10.6084/m9.figshare.12851264
title: A new human adipocyte model with PTEN haploinsufficiency

description: Few human cell strains are suitable and readily available as <i>in vitro</i> adipocyte models. We used resected lipoma tissue from a patient with germline phosphatase and tensin homolog (PTEN) haploinsufficiency to establish a preadipocyte cell strain termed LipPD1 and aimed to characterize cellular functions and signalling pathway alterations in comparison to the established adipocyte model Simpson-Golabi-Behmel-Syndrome (SGBS) and to primary stromal-vascular fraction cells. We found that both cellular life span and the capacity for adipocyte differentiation as well as adipocyte-specific functions were preserved in LipPD1 and comparable to SGBS adipocytes. Basal and growth factor-stimulated activation of the PI3 K/AKT signalling pathway was increased in LipPD1 preadipocytes, corresponding to reduced PTEN levels in comparison to SGBS cells. Altogether, LipPD1 cells are a novel primary cell model with a defined genetic lesion suitable for the study of adipocyte biology.
DOI: 10.6084/m9.figshare.12851264.v1
title: A new human adipocyte model with PTEN haploinsufficiency

description: Few human cell strains are suitable and readily available as <i>in vitro</i> adipocyte models. We used resected lipoma tissue from a patient with germline phosphatase and tensin homolog (PTEN) haploinsufficiency to establish a preadipocyte cell strain termed LipPD1 and aimed to characterize cellular functions and signalling pathway alterations in comparison to the established adipocyte model Simpson-Golabi-Behmel-Syndrome (SGBS) and to primary stromal-vascular fraction cells. We found that both cellular life span and the capacity for adipocyte differentiation as well as adipocyte-specific functions were preserved in LipPD1 and comparable to SGBS adipocytes. Basal and growth factor-stimulated activation of the PI3 K/AKT signalling pathway was increased in LipPD1 preadipocytes, corresponding to reduced PTEN levels in comparison to SGBS cells. Altogether, LipPD1 cells are a novel primary cell model with a defined genetic lesion suitable for the study of adipocyte biology.
DOI: 10.6084/m9.figshare.13150482
title: Surface-associated lipid droplets: an intermediate site for lipid transport in human adipocytes?

description: Adipose tissue plays a major role in regulating whole-body energy metabolism. While the biochemical processes regulating storage and release of excess energy are well known, the temporal organization of these events is much less defined. In this study, we have characterized the presence of small surface-associated lipid droplets, distinct from the central droplet, in primary human adipocytes. Based on microscopy analyses, we illustrate the distribution of mitochondria, endoplasmic reticulum and lysosomes in the vicinity of these specialized lipid droplets. Ultrastructure analysis confirmed the presence of small droplets in intact adipose tissue. Further, CIDEC, known to bind and regulate lipid droplet expansion, clearly localized at these lipid droplets. Neither acute or prolonged stimulation with insulin or isoprenaline, or pharmacologic intervention to suppress lipid flux, affected the presence of these lipid droplets. Still, phosphorylated perilipin and hormone-sensitive lipase accumulated at these droplets following adrenergic stimuli, which supports metabolic activity at these locations. Altogether, we propose these lipid droplet clusters represent an intermediate site involved in lipid transport in primary adipocytes.
DOI: 10.6084/m9.figshare.12851255
title: Identification of differentially expressed mRNA and the Hub mRNAs modulated by lncRNA <i>Meg3</i> as a competing endogenous RNA in brown adipose tissue of mice on a high-fat diet

description: Obesity is associated with insulin resistance, diabetes, and obesity-related metabolic disorders. Brown adipocytes have emerged as potential targets for the treatment of obesity and obesity-related diseases. However, changes that occur in brown adipose tissue during various stages of high fat diet (HFD)-induced obesity remain poorly understood. The present study aimed to determine the changes occurring in brown adipose tissue during various stages of an HFD by analyzing two microarray expression profiles. A total of 1,337 differentially expressed RNAs (DE RNAs) were identified between the HFD and ND groups, using the limma package in R. The DE RNAs included 1,249 mRNAs, 74 long non coding RNAs (lncRNAs), and 14 pseudogenes. Functional annotation of the DE mRNAs, including GO terms and KEGG pathways were identified using the Database for Annotation, Visualization, and Integrated Discovery. A protein-protein interaction network was constructed using STRING and clusters were obtained through the Molecular Complex Detection plug-in. In the present study, the lncRNA,maternally expressed gene 3 (<i>Meg3</i>), was identified as the DE lncRNA with a significant fold change. The network of <i>Meg3</i> as a ceRNA was constructed, which demonstrated that <i>Meg3</i> modulated five hub DE mRNAs via competitive binding to microRNAs.
DOI: 10.6084/m9.figshare.12851255.v1
title: Identification of differentially expressed mRNA and the Hub mRNAs modulated by lncRNA <i>Meg3</i> as a competing endogenous RNA in brown adipose tissue of mice on a high-fat diet

description: Obesity is associated with insulin resistance, diabetes, and obesity-related metabolic disorders. Brown adipocytes have emerged as potential targets for the treatment of obesity and obesity-related diseases. However, changes that occur in brown adipose tissue during various stages of high fat diet (HFD)-induced obesity remain poorly understood. The present study aimed to determine the changes occurring in brown adipose tissue during various stages of an HFD by analyzing two microarray expression profiles. A total of 1,337 differentially expressed RNAs (DE RNAs) were identified between the HFD and ND groups, using the limma package in R. The DE RNAs included 1,249 mRNAs, 74 long non coding RNAs (lncRNAs), and 14 pseudogenes. Functional annotation of the DE mRNAs, including GO terms and KEGG pathways were identified using the Database for Annotation, Visualization, and Integrated Discovery. A protein-protein interaction network was constructed using STRING and clusters were obtained through the Molecular Complex Detection plug-in. In the present study, the lncRNA,maternally expressed gene 3 (<i>Meg3</i>), was identified as the DE lncRNA with a significant fold change. The network of <i>Meg3</i> as a ceRNA was constructed, which demonstrated that <i>Meg3</i> modulated five hub DE mRNAs via competitive binding to microRNAs.
DOI: 10.6084/m9.figshare.13150482.v1
title: Surface-associated lipid droplets: an intermediate site for lipid transport in human adipocytes?

description: Adipose tissue plays a major role in regulating whole-body energy metabolism. While the biochemical processes regulating storage and release of excess energy are well known, the temporal organization of these events is much less defined. In this study, we have characterized the presence of small surface-associated lipid droplets, distinct from the central droplet, in primary human adipocytes. Based on microscopy analyses, we illustrate the distribution of mitochondria, endoplasmic reticulum and lysosomes in the vicinity of these specialized lipid droplets. Ultrastructure analysis confirmed the presence of small droplets in intact adipose tissue. Further, CIDEC, known to bind and regulate lipid droplet expansion, clearly localized at these lipid droplets. Neither acute or prolonged stimulation with insulin or isoprenaline, or pharmacologic intervention to suppress lipid flux, affected the presence of these lipid droplets. Still, phosphorylated perilipin and hormone-sensitive lipase accumulated at these droplets following adrenergic stimuli, which supports metabolic activity at these locations. Altogether, we propose these lipid droplet clusters represent an intermediate site involved in lipid transport in primary adipocytes.
DOI: 10.6084/m9.figshare.12084423.v1
title: Insulin-induced serine 22 phosphorylation of retinoid X receptor alpha is dispensable for adipogenesis in brown adipocytes

description: Insulin action initiates a series of phosphorylation events regulating cellular differentiation, growth and metabolism. We have previously discovered, in a mass spectrometry-based phosphoproteomic study, that insulin/IGF-1 signalling induces phosphorylation of retinoid x receptor alpha (RXRα) at S22 in mouse brown pre-adipocytes. Here, we show that insulin induces the phosphorylation of RXRα at S22 in both brown precursor and mature adipocytes through a pathway involving ERK, downstream of IRS-1 and −2. We also found that RXRα S22 phosphorylation is promoted by insulin and upon re-feeding in brown adipose tissue <i>in vivo</i>, and that insulin-stimulated S22 phosphorylation of RXRα is dampened by diet-induced obesity. We used <i>Rxra</i> knockout cells re-expressing wild type (WT) or S22A non-phosphorylatable forms of RXRα to further characterize the role of S22 in brown adipocytes. Knockout of <i>Rxra</i> in brown pre-adipocytes resulted in decreased lipid accumulation and adipogenic gene expression during differentiation, and re-expression of <i>Rxra</i>WT alleviated these effects. However, we observed no significant difference in cells re-expressing the <i>Rxra</i>S22A mutant as compared with the cells re-expressing <i>Rxra</i>WT. Furthermore, comparison of gene expression during adipogenesis in the WT and S22A re-expressing cells by RNA sequencing revealed similar transcriptomic profiles. Thus, our data propose a dispensable role for RXRα S22 phosphorylation in adipogenesis and transcription in differentiating brown pre-adipocytes.
DOI: 10.6084/m9.figshare.12851279
title: HuR expression in adipose tissue mediates energy expenditure and acute thermogenesis independent of UCP1 expression

description: The goal of this study was to define the functional role of adipocyte-specific expression of the RNA binding protein Human antigen R (HuR). Mice with an adipocyte-specific deletion of HuR (<i>Adipo-HuR<sup>−/-</sup> </i>) were generated by crossing HuR floxed (<i>HuR<sup>fl/fl</sup> </i>) mice with mice expressing adiponectin-driven cre-recombinase (<i>Adipoq-cre</i>). Our results show that <i>Adipo-HuR<sup>−/-</sup> </i> mice display a lean phenotype compared to wild-type littermate controls. HuR deletion results in a diet-independent reduction in percent body fat composition along with an increase in energy expenditure. Functionally, <i>Adipo-HuR<sup>−/-</sup> </i> mice show a significant impairment in acute adaptive thermogenesis (six hours at 4°C), but uncoupling protein 1 (UCP1) protein expression in brown adipose tissue (BAT) is unchanged compared to control. Pharmacological inhibition of HuR also results in a marked decline in core body temperature following acute cold challenge independent of UCP1 protein expression. Among the 588 HuR-dependent genes in BAT identified by RNA-seq analysis, gene ontology analysis shows a significant enrichment in mediators of calcium transport and signalling, almost all of which are decreased in <i>Adipo-HuR<sup>−/-</sup> </i> mice compared to control. In conclusion, adipocyte expression of HuR plays a central role in metabolic homoeostasis and mediates UCP1-independent thermogenesis in BAT, potentially through post-transcriptional control of intracellular calcium transport.Abbreviations: Adipo-HuR<sup>−/-</sup>: Adipocyte-specific HuR deletion mice; BAT: Brown adipose tissue; HuR: Human antigen R; UCP1: Uncoupling protein 1
DOI: 10.6084/m9.figshare.12084423
title: Insulin-induced serine 22 phosphorylation of retinoid X receptor alpha is dispensable for adipogenesis in brown adipocytes

description: Insulin action initiates a series of phosphorylation events regulating cellular differentiation, growth and metabolism. We have previously discovered, in a mass spectrometry-based phosphoproteomic study, that insulin/IGF-1 signalling induces phosphorylation of retinoid x receptor alpha (RXRα) at S22 in mouse brown pre-adipocytes. Here, we show that insulin induces the phosphorylation of RXRα at S22 in both brown precursor and mature adipocytes through a pathway involving ERK, downstream of IRS-1 and −2. We also found that RXRα S22 phosphorylation is promoted by insulin and upon re-feeding in brown adipose tissue <i>in vivo</i>, and that insulin-stimulated S22 phosphorylation of RXRα is dampened by diet-induced obesity. We used <i>Rxra</i> knockout cells re-expressing wild type (WT) or S22A non-phosphorylatable forms of RXRα to further characterize the role of S22 in brown adipocytes. Knockout of <i>Rxra</i> in brown pre-adipocytes resulted in decreased lipid accumulation and adipogenic gene expression during differentiation, and re-expression of <i>Rxra</i>WT alleviated these effects. However, we observed no significant difference in cells re-expressing the <i>Rxra</i>S22A mutant as compared with the cells re-expressing <i>Rxra</i>WT. Furthermore, comparison of gene expression during adipogenesis in the WT and S22A re-expressing cells by RNA sequencing revealed similar transcriptomic profiles. Thus, our data propose a dispensable role for RXRα S22 phosphorylation in adipogenesis and transcription in differentiating brown pre-adipocytes.
DOI: 10.6084/m9.figshare.12851258.v1
title: The common pathophysiologic threads between Asian Indian diabetic’s ‘Thin Fat Phenotype’ and partial lipodystrophy: the peripheral adipose tissue transcriptomic evidences

description: T2D is a complex disease with poorly understood mechanisms. In Asian Indians, it is associated with “thin fat” phenotype which resembles with partial lipodystrophy. We hypothesized that disturbed expression of lipodystrophy genes might play a role in T2D pathogenesis. Therefore, we attempted to establish a link between these two diseases by studying the overlap between the network of lipodystrophy genes and the differentially expressed genes (DEGs) in the peripheral subcutaneous adipose tissue of Asian Indians diabetics. We found that 16, out of 138 lipodystrophy genes were differentially regulated in diabetics and around 18% overlap between their network and the DEGs; the expression level of lipodystrophy genes showed an association with disease-related intermediate phenotypic traits among diabetics but not in the control group. We also attempted to individualize the diabetic patients based on ±2 fold altered expression of lipodystrophy genes as compared to their average expression in the control group. In conclusion, significant overlap exists between some of the lipodystrophy genes and their network with DEGs in the peripheral adipose tissue in diabetics. They possibly play a role in the pathogenesis of diabetes and individualization of diabetics is possible based on their altered expression in their peripheral adipose tissue.
DOI: 10.6084/m9.figshare.13109490.v1
title: CRISPR/Cas9-mediated gene knockout in human adipose stem/progenitor cells

description: The CRISPR/Cas9 system is a powerful tool to generate a specific loss-of-function phenotype by gene knockout (KO). However, this approach is challenging in primary human cells. In this technical report, we present a reliable protocol to achieve a functional KO in the genome of human adipose stem/progenitor cells (ASCs). Using Sprouty1 (<i>SPRY1</i>) as a model target gene for a CRISPR/Cas9 mediated KO, we particularize the procedure including the selection of the CRISPR/Cas9 target sequences and the employment of appropriate lentiviral vectors to obtain a functional gene KO. The efficiency of CRISPR/Cas9 to mutate the <i>SPRY1</i> gene is determined by a PCR-based mutation detection assay and sequence analysis. Effects on mRNA and protein levels are studied by RT-qPCR and Western blotting. In addition, we demonstrate that CRISPR/Cas9 mediated <i>SPRY1</i> KO and gene silencing by shRNA are similarly effective to deplete the Sprouty1 protein and to inhibit adipogenic differentiation. In summary, we show a reliable approach to achieve a gene KO in human ASCs, which could also apply to other primary cell types. <b>Abbreviations:</b> ASC: Adipogenic Stem/Progenitor Cell; Cas: CRISPR-associated system; CRISPR: Clustered Regularly Interspaced Palindromic Repeat; gDNA: Genomic DNA; GOI: Gene of interest; gRNA: Guide RNA; NHEJ: Non-homologous end joining; Indel: Insertion/Deletion; PAM: Protospacer adjacent motif; sWAT: Subcutaneous white adipose tissue; TIDE: Tracking of indels by decomposition
DOI: 10.6084/m9.figshare.13109490
title: CRISPR/Cas9-mediated gene knockout in human adipose stem/progenitor cells

description: The CRISPR/Cas9 system is a powerful tool to generate a specific loss-of-function phenotype by gene knockout (KO). However, this approach is challenging in primary human cells. In this technical report, we present a reliable protocol to achieve a functional KO in the genome of human adipose stem/progenitor cells (ASCs). Using Sprouty1 (<i>SPRY1</i>) as a model target gene for a CRISPR/Cas9 mediated KO, we particularize the procedure including the selection of the CRISPR/Cas9 target sequences and the employment of appropriate lentiviral vectors to obtain a functional gene KO. The efficiency of CRISPR/Cas9 to mutate the <i>SPRY1</i> gene is determined by a PCR-based mutation detection assay and sequence analysis. Effects on mRNA and protein levels are studied by RT-qPCR and Western blotting. In addition, we demonstrate that CRISPR/Cas9 mediated <i>SPRY1</i> KO and gene silencing by shRNA are similarly effective to deplete the Sprouty1 protein and to inhibit adipogenic differentiation. In summary, we show a reliable approach to achieve a gene KO in human ASCs, which could also apply to other primary cell types. <b>Abbreviations:</b> ASC: Adipogenic Stem/Progenitor Cell; Cas: CRISPR-associated system; CRISPR: Clustered Regularly Interspaced Palindromic Repeat; gDNA: Genomic DNA; GOI: Gene of interest; gRNA: Guide RNA; NHEJ: Non-homologous end joining; Indel: Insertion/Deletion; PAM: Protospacer adjacent motif; sWAT: Subcutaneous white adipose tissue; TIDE: Tracking of indels by decomposition
DOI: 10.6084/m9.figshare.12851258
title: The common pathophysiologic threads between Asian Indian diabetic’s ‘Thin Fat Phenotype’ and partial lipodystrophy: the peripheral adipose tissue transcriptomic evidences

description: T2D is a complex disease with poorly understood mechanisms. In Asian Indians, it is associated with “thin fat” phenotype which resembles with partial lipodystrophy. We hypothesized that disturbed expression of lipodystrophy genes might play a role in T2D pathogenesis. Therefore, we attempted to establish a link between these two diseases by studying the overlap between the network of lipodystrophy genes and the differentially expressed genes (DEGs) in the peripheral subcutaneous adipose tissue of Asian Indians diabetics. We found that 16, out of 138 lipodystrophy genes were differentially regulated in diabetics and around 18% overlap between their network and the DEGs; the expression level of lipodystrophy genes showed an association with disease-related intermediate phenotypic traits among diabetics but not in the control group. We also attempted to individualize the diabetic patients based on ±2 fold altered expression of lipodystrophy genes as compared to their average expression in the control group. In conclusion, significant overlap exists between some of the lipodystrophy genes and their network with DEGs in the peripheral adipose tissue in diabetics. They possibly play a role in the pathogenesis of diabetes and individualization of diabetics is possible based on their altered expression in their peripheral adipose tissue.
DOI: 10.24378/exe.2883
title: Climate-driven variability and trends in plant productivity over recent decades based on three global products (dataset)

description: This is the dataset used for the O'Sullivan et al. (2020) article "Climate-driven variability and trends in plant productivity over recent decades based on three global products" published in Global Biogeochemical Cycles.
description: This data set contains raw model and observation data, processing scripts, and plotting scripts. The raw data includes; TRENDYv6, RS-LUE, FLUXCOM, and FluxNetG GPP fields, GOME-2 SIF fields, and CRUNCEPv8 climate data. The scripts used to process and plot (Figures 1-7) this data are also included.
description: The article associated with this dataset is located in ORE at: http://hdl.handle.net/10871/123733
DOI: 10.5281/zenodo.4288412
title: Dublin Boundary Shapefile

description: A simple boundary of Dublin geometry was extracted from a shapefile dataset created by the Central Statistics Office (CSO) via GeoPandas. Local_Electoral_Areas_-_OSi_National_Statutory_Boundaries-shp.zip https://www.cso.ie/en/census/census2016reports/census2016smallareapopulationstatistics/
DOI: 10.21227/zbsa-ew37
title: raw citrus leaf images

description: The citrus leaf dataset used in this study was obtained from PlantVillage [24], an open access public resource for agriculture-related content. The dataset includes three types of citrus leaves: citrus healthy, citrus HLB (Huanglongbing) general, and citrus HLB serious. The original dataset contains 4577 images of citrus leaves, divided into three categories
DOI: 10.21227/x2ct-y194
title: raw citrus leaf images

description: The citrus leaf dataset used in this study was obtained from PlantVillage [24], an open access public resource for agriculture-related content. The dataset includes three types of citrus leaves: citrus healthy, citrus HLB (Huanglongbing) general, and citrus HLB serious. The original dataset contains 4577 images of citrus leaves, divided into three categories
DOI: 10.25502/sp4n-pc47/d
title: Validation trial of improved yam varieties in Nigeria in 2017

description: The average yam yields of local varieties is less than 25% of the yield of improved released varieties, which range from 30 to 40 tons/ha. Absence of a formal seed system has not encouraged the promotion and adoption of released improved yam varieties. To sensitize farmers on the superiority of improved varieties, seed tubers of selected released varietiesproduced by IITA were planted in comparison with local checks in 80 on-farm validation/demonstration trials in six states of Nigeria - Enugu, Benue, Nasarawa, Federal Capital Territory (FCT), Niger and Oyo. Three improved yam varieties [two Dioscorea rotundata (TDr 89/02665 and TDr 95/19177) and one D. alata (TDa 98/01176)], and one location specific farmers’ best variety were used to quantify the superiority of the improved varieties over the locals.
DOI: 10.21227/amk0-8m93
title: raw citrus leaf images

description: 本研究中使用的柑橘叶数据集来自 PlantVillage [24]，用于以下方面的开放访问公共资源： 与农业有关的内容。数据集包括三种类型柑桔叶片：柑桔健康，柑桔HLB（黄龙病） 一般，柑橘HLB严重。原始数据集包含4577张柑橘叶片图像，分为三部分 分类
DOI: 10.6084/m9.figshare.13280375
title: Dataset

description: This item contains 20 publicly available datasets taken from PROMISE repository.<br>