LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Peripheral modulation of antidepressant targets MAO-B and GABAAR by harmol induces mitohormesis and delays aging in preclinical models'.
Answer: Reversible and sub-lethal stresses to the mitochondria elicit a program of compensatory responses that ultimately improve mitochondrial function, a conserved anti-aging mechanism termed mitohormesis. Here, we show that harmol, a member of the beta-carbolines family with anti-depressant properties, improves mitochondrial function and metabolic parameters, and extends healthspan. Treatment with harmol induces a transient mitochondrial depolarization, a strong mitophagy response, and the AMPK compensatory pathway both in cultured C2C12 myotubes and in male mouse liver, brown adipose tissue and muscle, even though harmol crosses poorly the blood-brain barrier. Mechanistically, simultaneous modulation of the targets of harmol monoamine-oxidase B and GABA-A receptor reproduces harmol-induced mitochondrial improvements. Diet-induced pre-diabetic male mice improve their glucose tolerance, liver steatosis and insulin sensitivity after treatment with harmol. Harmol or a combination of monoamine oxidase B and GABA-A receptor modulators extend the lifespan of hermaphrodite Caenorhabditis elegans or female Drosophila melanogaster. Finally, two-year-old male and female mice treated with harmol exhibit delayed frailty onset with improved glycemia, exercise performance and strength. Our results reveal that peripheral targeting of monoamine oxidase B and GABA-A receptor, common antidepressant targets, extends healthspan through mitohormesis.
Question: Write a study description for the study titled 'Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna'.
Answer: Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the Deep Metabolome Annotation (DMA) workflow. Applied to the ecological sentinel species, Daphnia magna, one pooled sample comprising ten distinct genotypes exposed to two environment conditions was systematically physicochemically-separated via solid-phase extraction, liquid- and gas-chromatography prior to extensive mass spectrometric (MS) fragmentation, generating >8000 data files, and supplemented by nuclear magnetic resonance spectroscopy. An extensive Galaxy-based computational approach was built to analyse these data, comprising over 30 tools. DMA generated 8577 polar metabolite and lipid annotations in D. magna, with the data, tools and annotations disseminated freely via public data repositories and a custom web-based interface to ensure reusability and transferability.
Question: Write a study description for the study titled 'Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data (Plasma)'.
Answer: Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets. We present a novel algorithm for the detection of mass traces and their aggregation into features (i.e. all signals caused by the same analyte species) that is computationally efficient and sensitive and that leads to reproducible quantification results. The algorithm is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing, co-elution information, and a support vector machine–based classifier able to identify potential metabolite isotope patterns. The algorithm is not limited to metabolites but is applicable to a wide range of small molecules (e.g. lipidomics, peptidomics), as well as to other separation technologies. We assessed the algorithm's robustness with regard to varying noise levels on synthetic data and then validated the approach on experimental data investigating human plasma samples. We obtained excellent results in a fully automated data-processing pipeline with respect to both accuracy and reproducibility. Relative to state-of-the art algorithms, ours demonstrated increased precision and recall of the method. The algorithm is available as part of the open-source software package OpenMS and runs on all major operating systems. Plasma data is reported in the current study MTBLS234.Simulated data is reported in MTBLS235.
Question: Write a study description for the study titled 'OsTTG1-dependent gene activation confer chilling tolerance in colored rice'.
Answer: Metabolomic analysis of anthocyanin accumulation in colored rice under cold stress
Question: Write a study description for the study titled 'Transcriptomics integrated with metabolomics reveals partial molecular mechanisms of nutritional risk and neurodevelopment in children with congenital heart disease'.
Answer: PURPOSE: To explore molecular mechanisms affecting nutritional risk and neurodevelopment in children with congenital heart disease (CHD) by combining transcriptome and metabolome analysis.METHODS: A total of 26 blood and serum samples from 3 groups of children with CHD (low nutritional risk combined with normal neurodevelopment (group A), low nutritional risk combined with neurodevelopmental disorders (group B) and high nutritional risk combined with normal neurodevelopment (group C)) were analyzed by transcriptome and metabolomics to search for differentially expressed genes (DEGs) and metabolites (DEMs). Functional analysis was conducted for DEGs and DEMs. Further, the joint pathway analysis and correlation analysis of DEGs and DEMs were performed.RESULTS: A total of 362 and 1351 DEGs were detected in group B and C compared to A, respectively. A total of 6 and 7 DEMs were detected in group B and C compared to A in positive mode, respectively. There were 39 and 31 DEMs in group B and C compared to A in negative mode. Transcriptomic analysis indicated that neurodevelopment may be regulated by some genes such as NSUN7, SLC6A8, CXCL1 and LCN8, nutritional risk may be regulated by SLC1A3 and LCN8. Metabolome analysis and joint pathway analysis showed that tryptophan metabolism, linoleic and metabolism and glycerophospholipid metabolism may be related to neurodevelopment, and glycerophospholipid metabolism pathway may be related to nutritional risk.CONCLUSION: By integrating transcriptome and metabolome analyses, this study revealed key genes and metabolites associated with nutritional risk and neurodevelopment in children with CHD, as well as significantly altered pathways. It has important clinical translational significance.
Question: Write a study description for the study titled 'Polyphenolic Profiling of Plants and Edible Mushrooms to Aid Characterizing Polyphenol Oxidase Selectivity'.
Answer: Polyphenol oxidases are important metalloenzymes that catalyze the oxidation of polyphenols. Organisms can contain multiple isoenzymes whose possible different functionality is not understood. Moreover, their substrate preference is still unexplored, and a working hypothesis assumes their specificity is tailored to the substrates naturally present. Polyphenols are a broad molecular class whose presence in an organism is frequently unknown. Therefore, nine different mushrooms and plants were applied to a LC-HRMS-based suspect screening workflow to investigate the polyphenols present. Overall, 401 features were annotated, composed of 221 flavonoids and 180 non-flavonoids. As 64% of the flavonoids were conjugated with a glycone, (semi-)quantification was applied when a reference standard of the aglycone was available. Isomers of hesperetin-O-glucoside were ubiquitous in all investigated samples. Additionally, a targeted LC-MS/MS assay covering 90 polyphenols was applied, showing phenolic acids as prevalent (data not presented within MetaboLights). This study provides new insights into the complex polyphenol profiles of nine mushroom and plant species.
Question: Write a study description for the study titled 'Global metabolomics of fireflies (Coleoptera: Lampyridae) explore metabolic adaptation to fresh water in insects'.
Answer: Aquatic insects are well-adapted to freshwater environments, but metabolic mechanisms of such adaptations, particularly to primary environmental factors (e.g., hypoxia, water pressure, dark light and abundant microbes), are poorly known. Most firefly species (Coleoptera: Lampyridae) are terrestrial, but the larvae of a few species are aquatic. We generated 24 global metabolomic profiles of larvae and adults of Aquatica leii (freshwater) and Lychnuris praetexta (terrestrial) to identify freshwater adaptation-related metabolites (AARMs). We identified 110 differentially abundant metabolites (DAMs) in A. leii (adults vs aquatic larvae) and 183 DAMs in L. praetexta (adults vs terrestrial larvae). Furthermore, 100 DAMs specific to aquatic A. leii larvae were screened as AARMs via interspecific comparisons (A. leii vs L. praetexta), which were primarily involved in antioxidant activity, immune response, energy production and metabolism, and chitin biosynthesis. They were assigned to six categories/superclasses (e.g., lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compound). Finally, ten metabolic pathways shared between KEGG terms specific to aquatic fireflies and enriched by AARMs were screened as aquatic adaptation-related pathways (AARPs). These AARPs were primarily involved in energy metabolism, xenobiotic biodegradation, protection of oxidative/immune damage, oxidative stress response and sense function (e.g., glycine, serine and threonine metabolism, drug metabolism-cytochrome P450 and taste transduction), and certain aspects of morphology (e.g., steroid hormone biosynthesis). These results provide evidence suggesting that abundance changes in metabolomes contribute to freshwater adaptation of fireflies. The metabolites identified here may be vital targets for future work to determine the mechanism of freshwater adaptation in insects.
Question: Write a study description for the study titled 'Spatial metabolomics of in situ, host-microbe interactions (On-tissue MALDI imaging MS/MS assay)'.
Answer: "Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric pressure mass spectrometry imaging (AP-MALDI-MSI) to image host-microbe symbioses and their metabolic interactions. metaFISH aligns and integrates metabolite and fluorescent images at the micrometer-scale for a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts, a variation in metabolic phenotypes in one symbiont type, and novel symbiosis metabolites. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ - a powerful tool for microbiologists across fields.  On-tissue MALDI imaging MS/MS assay protocols and data are reported in the current study MTBLS805. MALDI imaging MS assay protocols and data associated to this study are reported in MTBLS744. UPLC-MS/MS assay protocols and data associated to this study are reported in MTBLS746. MRMS assay protocols and data associated to this study are reported in MTBLS811."
Question: Write a study description for the study titled 'TGF-β uncouples glycolysis and inflammation in macrophages and controls the survival during sepsis'.
Answer: The mechanisms by which macrophage metabolism is regulated and the effects of metabolism on diseases remain largely unknown. We show here that TGF-β regulates the glycolysis of macrophages independently of inflammatory cytokine production, and thus affects the survival in experimental sepsis. Specifically, TGF-β increased expression and activity of phosphofructokinase-1 liver type (PFKL) in macrophages and thus promoted their glycolysis during cell activation, yet paradoxically suppressed the production of proinflammatory cytokines in the same macrophages. The upregulation of glycolysis was mediated by a mTOR-c-MYC dependent pathway, whereas the inhibition of cytokines was ascribed to the activation of SMAD3 and a downregulated activation of the pro-inflammatory transcription factors AP-1, NFkB and STAT1. Importantly, in an LPS-induced endotoxemia and CLP-sepsis models, TGF-β enhancement of macrophage glycolysis led to a decreased survival in mice, which was associated with increased blood coagulation. Analysis of cohorts of patients with sepsis and covid-19 revealed that the expression of PFKL, TGF-β receptor TGFBRI and coagulation factor F13A1 in myeloid cells positively correlated with the progression of the disease. Thus, TGF-β is emerging as a critical cytokine regulating macrophage metabolism and could serve as a therapeutic target in patients with sepsis.
Question: Write a study description for the study titled 'Trans-tissue molecular coordination in high-intensity physical activity'.
Answer: High-intensity physical activity has major impacts in different parts of the body. However, the regulatory coordination between different tissues to support the high physical demands is poorly understood. Here we performed a multi-omics analysis of blood plasma, urine and saliva from a group of firefighters that underwent a 45-minute intense exercise session. The plasma analysis showed signatures of tissue damage and acute repair response. This is accompanied by lipolysis, glycolysis and amino acid degradation towards supplying the high-energetic demands. Concomitantly, the urine analysis showed a strong regulation of the renin-angiotensin system towards excretion of catabolites, reabsorption of nutrients and balance of the body fluids. The saliva showed a decrease in inflammatory molecules and increase in antimicrobial peptides, possibly towards improving the circulatory and respiratory capacity. Overall, our data show signatures of coordinated action between different organs towards supplying the demands of high-intensity physical activity.
Question: Write a study description for the study titled 'Short-Term Clinical Response and Changes in the Fecal Microbiota and Metabolite Levels in Patients with Crohn's Disease After Stem Cell Infusions'.
Answer: Recent studies have shown a close relationship between the gut microbiota and Crohn's disease (CD). This study aimed to determine whether mesenchymal stem cell (MSC) treatment alters the gut microbiota and fecal metabolite pathways and to establish the relationship between the gut microbiota and fecal metabolites. Patients with refractory CD were enrolled and received 8 intravenous infusions of MSCs at a dose of 1.0 × 106 cells/kg. The MSC efficacy and safety were evaluated. Fecal samples were collected, and their microbiomes were analyzed by 16S rDNA sequencing. The fecal metabolites at baseline and after 4 and 8 MSC infusions were identified by liquid chromatography-mass spectrometry (LC--MS). A bioinformatics analysis was conducted using the sequencing data. No serious adverse effects were observed. The clinical symptoms and signs of patients with CD were substantially relieved after 8 MSC infusions, as revealed by changes in weight, the CD activity index (CDAI) score, C-reactive protein (CRP) level, and erythrocyte sedimentation rate (ESR). Endoscopic improvement was observed in 2 patients. A comparison of the gut microbiome after 8 MSC treatments with that at baseline showed that the genus Cetobacterium was significantly enriched. Linoleic acid was depleted after 8 MSC treatments. A possible link between the altered Cetobacterium abundance and linoleic acid metabolite levels was observed in patients with CD who received MSCs. This study enabled an understanding of both the gut microbiota response and bacterial metabolites to obtain more information about host-gut microbiota metabolic interactions in the short-term response to MSC treatment.
Question: Write a study description for the study titled 'Spatiotemporal determination of metabolite activities in the corneal epithelium on a chip'.
Answer: The corneal epithelial barrier maintains the metabolic activities of the ocular surface by regulating membrane transporters and metabolic enzymes responsible for the homeostasis of the eye as well as the pharmacokinetic behavior of drugs. Despite its importance, no established biomimetic in vitro methods are available to perform the spatiotemporal investigation of metabolism and determine the transportation of endogenous and exogenous molecules across the corneal epithelium barrier. This study introduces multiple corneal epitheliums on a chip namely, Corneal Epithelium on a Chip (CEpOC), which enables the spatiotemporal collection as well as analysis of micro-scaled extracellular metabolites from both the apical and basolateral sides of the barriers. Longitudinal samples collected during 48 h period were analyzed using untargeted liquid chromatography-mass spectrometry metabolomics method, and 104 metabolites were annotated. We observed the spatiotemporal secretion of biologically relevant metabolites (i.e., antioxidant, glutathione and uric acid) as well as the depletion of essential nutrients such as amino acids and vitamins mimicking the in vivo molecules trafficking across the human corneal epithelium. Through the shifts of extracellular metabolites and quantitative analysis of mRNA associated with transporters, we were able to investigate the secretion and transportation activities across the polarized barrier in a correlation with the expression of corneal transporters. Thus, CEpOC can provide a non-invasive, simple, yet effectively informative method to determine pharmacokinetics and pharmacodynamics as well as to discover novel biomarkers for drug toxicological and safety tests as advanced experimental model of the human corneal epithelium.
Question: Write a study description for the study titled 'Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry'.
Answer: Untargeted metabolomics aims at obtaining quantitative information on the highest possible number of low-molecular biomolecules present in a biological sample. Rather small changes in mass spectrometric spectrum acquisition parameters may have a significant influence on the detectabilities of metabolites in untargeted global-scale studies by means of high-performance liquid chromatography-mass spectrometry (HPLC-MS). Employing whole cell lysates of human renal proximal tubule cells, we present a systematic global-scale study of the influence of mass spectrometric scan parameters on the number and intensity of metabolites detectable in whole cell lysates. Ion transmission and ion collection efficiencies in an Orbitrap-based mass spectrometer generally depend on the m/z range scanned, which, ideally, requires different instrument settings for the respective mass ranges investigated. Therefore, we split a full scan range of m/z 50-1000 relevant for metabolites into two separate segments (m/z 50-200 and m/z 200-1000), allowing an independent tuning of the ion transmission parameters for both mass ranges. Three different implementations, involving either scanning from m/z 50-1000 in a single scan, or scanning from m/z 50-200 and from m/z 200-1000 in two alternating scans, or performing two separate HPLC-MS runs with m/z 50-200 and m/z 200-1000 scan ranges were critically assessed. The most efficient approach in terms of feature number, which forms the basis for statistical analysis, identification, and for generating biological hypotheses, was the separate analysis of two different mass ranges. This lead to an increase in the number of detectable metabolite features, especially in the higher mass range (m/z greater than 400), by 2.5 (negative mode) to 6-fold (positive mode) as compared to analysis involving a single scan range. Application of the method to metabolite extracts prepared from whole cell lysates of human renal proximal tubule epithelial cells initially yielded up to 13,000 – 69,000 detectable features, which were subjected to rigorous background filtering and quality control in order to obtain reliable metabolite features for subsequent differential quantification.
Question: Write a study description for the study titled 'Study on the Hepatoprotection of Schisandra chinensis Caulis Ploysaccharides in nonalcoholic fatty liver disease in rats based on metabolomics'.
Answer: The aim of this study was to investigate the hepatoprotection of Schisandra chinensis Caulis polysaccharides (SCP) in the nonalcoholic fatty liver disease (NAFLD) induced by high-fat diet (HFD) in rats. A total of 30 Wistar rats were randomly divided into control group (CON), model group (MOD) and Schisandra chinensis caulis polysaccharide (SCP) group. Except for those in CON group, the other rats were fed with high-fat diet for 4 weeks to establish a NAFLD model. From the 5th week, rats in SCP group were given SCP solution (100 mg/kg) by gavage for 6 weeks, and those in CON and MOD groups were given an equal volume of distilled water in the same way. The serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) levels were detected. The small molecular metabolites in the blood of rats were determined by the metabolomics method of ultra-high performance liquid chromatography-quadrupole/electrostatic field orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) combined with multivariate analysis. The enrichment analysis and pathway analysis of the different metabolites were carried out. The therapeutic mechanism of SCP in NAFLD rats was verified by Western blot. The results showed that the levels of AST, ALT, TG, TC and LDL-C in the serum of rats in SCP group were significantly lower, and the levels of HDL-C were significantly higher than those in MOD group. The screening and analysis of the metabolic pathways showed that SCP could alleviate the development of NAFLD by regulating the expression of UDP-glucose pyrophosphorylase (UGP2), UDP-glucose 6-dehydrogenase (UGDH), acetyl CoA carboxylase (ACC) and fatty acid synthase (FAS) in the blood of NAFLD rats. This study may provide a theoretical basis for the development and utilization of SCP.