cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7276517
title: Dataset for puplication: Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing 1H-1H TOCSY NMR

description: Data set used in the publication: <strong>Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing <sup>1</sup>H-<sup>1</sup>H TOCSY NMR. </strong> Abstract: In this work, the dynamic evolution of adipose tissue-derived human MSCs (AT-derived hMSCs) after fourteen days of cultivation, adiobocytes and osteocytes differentiation has been inspected based on 2D NMR TOCSY using machine learning techniques. Multi-class classification in addition to novelty detection of metabolites was established based on the profile of a control hMSCs sample at four days cultivation and successively detect the absence and the abundance of metabolites in differentiated MSCs following a set of <sup>1</sup>H-<sup>1</sup>H TOCSY profiles. The uploaded files are: File: metabolites_names.xlsx contain the names of the used metabolites. File: metabolites.xlsx column 1: metabolite abbreviation column 2: 2D NMR TOCSY horizontal and vertical frequencies of metabolites in the control group at 4 days cultivation (Ct d4) column 3: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of cultivation (Ct d14) column 4: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of differentiation into adipocytes (AT d14) column 5: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after14 days of differentiation into osteocytes (OS d14) column 6: 2D NMR TOCSY horizontal and vertical standard frequencies of all metabolites measured at broadband high resolution 600.13 MHz NMR
DOI: 10.6084/m9.figshare.21065785
title: Supplementary Material for: Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters

description: Introduction: Flame retardants (FRs) are common bodily and environmental pollutants, creating concern about their potential toxicity. We and others have found that the commercial mixture, FireMaster® 550 (FM 550) or its individual brominated (BFR) and organophosphate ester (OPFR) components are potential developmental neurotoxicants. Using Wistar rats, we previously reported developmental exposure to FM 550 or its component classes produced sex- and compound-specific effects on adult socioemotional behaviors. The underlying mechanisms driving the behavioral phenotypes are unknown. Methods: To further mechanistic understanding, here we conducted transcriptomics in parallel with a novel lipidomics approach using cortical tissues from newborn siblings of the rats in the published behavioral study. Inclusion of lipid composition is significant because it is rarely examined in developmental neurotoxicity studies. Pups were gestationally exposed via oral dosing to the dam to FM 550 or the BFR or OPFR components at environmentally relevant doses. Results: The neonatal cortex was highly sexually dimorphic in lipid and transcriptome composition, and males were more significantly impacted by FR exposure. Multiple adverse modes of action for the BFRs and OPFRs on neurodevelopment were identified, with the OPFRs more disruptive than the BFRs via multiple mechanisms including dysregulation of mitochondrial function and disruption of cholinergic and glutamatergic systems. Disrupted mitochondrial function by environmental factors has been linked to higher risk of autism spectrum disorders. Impacted lipid classes included the ceramides, sphingomyelins, and triacylglycerides. Robust ceramide upregulation in the OPFR females could suggest heightened risk of brain metabolic disease. Conclusions: This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern.
DOI: 10.6084/m9.figshare.21065785.v1
title: Supplementary Material for: Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters

description: Introduction: Flame retardants (FRs) are common bodily and environmental pollutants, creating concern about their potential toxicity. We and others have found that the commercial mixture, FireMaster® 550 (FM 550) or its individual brominated (BFR) and organophosphate ester (OPFR) components are potential developmental neurotoxicants. Using Wistar rats, we previously reported developmental exposure to FM 550 or its component classes produced sex- and compound-specific effects on adult socioemotional behaviors. The underlying mechanisms driving the behavioral phenotypes are unknown. Methods: To further mechanistic understanding, here we conducted transcriptomics in parallel with a novel lipidomics approach using cortical tissues from newborn siblings of the rats in the published behavioral study. Inclusion of lipid composition is significant because it is rarely examined in developmental neurotoxicity studies. Pups were gestationally exposed via oral dosing to the dam to FM 550 or the BFR or OPFR components at environmentally relevant doses. Results: The neonatal cortex was highly sexually dimorphic in lipid and transcriptome composition, and males were more significantly impacted by FR exposure. Multiple adverse modes of action for the BFRs and OPFRs on neurodevelopment were identified, with the OPFRs more disruptive than the BFRs via multiple mechanisms including dysregulation of mitochondrial function and disruption of cholinergic and glutamatergic systems. Disrupted mitochondrial function by environmental factors has been linked to higher risk of autism spectrum disorders. Impacted lipid classes included the ceramides, sphingomyelins, and triacylglycerides. Robust ceramide upregulation in the OPFR females could suggest heightened risk of brain metabolic disease. Conclusions: This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern.
DOI: 10.6084/m9.figshare.21617886
title: Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease

description: Datasets for the analysis of "Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease" <br> <strong>RNASeq data:</strong> gene expression quantification (raw) as output from Salmon (https://combine-lab.github.io/salmon/) <strong>Proteomics data: </strong>raw data output from MaxQuant in R file format ".rds" (https://www.maxquant.org/).* <strong>Metadata</strong>: Sample information for RNA ("info_rna_all.rds") and proteomics data ("info.rds") in R file format ".rds" <br> *Proteomics data includes protein expression of samples that were not included in the analysis. Data is provided to enable the reproducibility of normalization procedures (see code) <br> Data, description and code is available on https://github.com/fifdick/alt_rna_prot_coupling_PD <br> <br>