LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomics Analysis of Limoniastrum monopetalum Extract'.
Answer: Limoniastrum monopetalum is a halophytic plant traditionally used in folk medicine for its purported antioxidant, antimicrobial, and anti-inflammatory properties. However, its chemical composition and bioactive constituents remain insufficiently characterized. In this study, we employed an untargeted metabolomics approach using liquid chromatography–mass spectrometry (LC–MS) to profile the phytochemical landscape of L. monopetalum extract. Data preprocessing and multivariate statistical analyses revealed a diverse metabolic fingerprint consisting of phenolic acids, flavonoids, tannins, and other secondary metabolites. Several compounds with known pharmacological relevance, including gallic acid derivatives, catechins, and flavonol glycosides, were identified and annotated against public metabolite databases. Pathway enrichment analysis further suggested the involvement of phenylpropanoid, flavonoid, and galactose metabolism, highlighting potential mechanisms underlying the plant’s bioactivities. Collectively, these findings provide the first comprehensive metabolomic characterization of L. monopetalum extract, offering a valuable resource for future pharmacological, nutraceutical, and biotechnological applications.
Question: Write a study description for the study titled 'Sarcopenic metabolomic profile reflected a sarcopenic phenotype associated with amino acid and essential fatty acid changes'.
Answer: INTRODUCTION: Although sarcopenia greatly affects health and quality of life in older people, its pathophysiological causes are not fully elucidated. To face this challenge, omics technologies can be used. The metabolome gives a vision of the interaction between the genome and the environment through metabolic networks, thus contributing in clarifying the pathophysiology of the sarcopenic phenotype.OBJECTIVES: The main goal of this study was to compare the plasma metabolome of sarcopenic and non-sarcopenic older people.METHODS: Cross-sectional study of 20 sarcopenic and 21 non-sarcopenic older subjects with available frozen plasma samples. Non-targeted metabolomic study by ultra-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) analysis with later bioinformatics data analysis. Once the significantly different metabolites were identified, the KEGG database was used on them to establish which were the metabolic pathways mainly involved.RESULTS: From 657 features identified, 210 showed significant differences between the study groups, and 30 had a FoldChangeLog2 > 2. The most interesting metabolic pathways found with the KEGG database were the biosynthesis of amino acids, arginine and proline metabolism, the biosynthesis of alkaloids derived from ornithine, linoleic acid metabolism, and the biosynthesis of unsaturated fatty acids.CONCLUSIONS: The study results allowed us to confirm that the concept of 'sarcopenic phenotype' is also witnessed at the plasma metabolite levels. The non-targeted metabolomics study can open a wide view of the sarcopenic features changes at the plasma level, which would be linked to the sarcopenic physiopathological alterations.
Question: Write a study description for the study titled 'Inhibition of glioblastoma cell proliferation and invasion by the choline-kinase inhibitor JAS239 varies with cell type and hypoxia.'.
Answer: BACKGROUND: Elevated choline kinase alpha (ChoK) is observed in most solid tumours including glioblastomas (GBM), yet until recently, inhibitors of ChoK have demonstrated limited efficacy in GBM models. Given that hypoxia is associated with GBM therapy resistance, we hypothesised that tumour hypoxia could be responsible for such limitations. We therefore evaluated in GBM cells, the effect of hypoxia on the function of JAS239, a potent ChoK inhibitor.METHODS: Rodent (F98 and 9L) and human (U-87 MG and U-251 MG) GBM cell lines were subjected to 72 hours of hypoxia conditioning and treated with JAS239 for 24 hours. NMR metabolomic measurements and analyses were performed to evaluate the signalling pathways involved. In addition, cell proliferation, cell cycle progression and cell invasion were measured in cell monolayers and 3D spheroids, with or without JAS239 treatment in normoxic or hypoxic cells to assess how hypoxia affects JAS239 function.RESULTS: Hypoxia and JAS239 treatment led to significant changes in the cellular metabolic pathways, specifically the phospholipid and glycolytic pathways associated with a reduction in cell proliferation via induced cell cycle arrest. Interestingly, JAS239 also impaired GBM invasion. However, JAS239 effects were variable depending on the cell line, reflecting the inherent heterogeneity observed in GBMs.CONCLUSION: Our findings indicate that JAS239 and hypoxia can deregulate cellular metabolism, inhibit proliferation and alter cell invasion. These results may be useful for the design of new therapeutic strategies based on ChoK inhibition that can act on multiple pro-tumorigenic features.
Question: Write a study description for the study titled 'Analysis of human urine reveals metabolic changes related to the development of acute kidney injury following cardiac surgery'.
Answer: In an effort to identify novel biomarkers capable of predicting the development of acute kidney injury (AKI) after cardiac surgery with cardiopulmonary bypass (CPB) use, urine specimens were collected before and at 4 and 24 hours after surgery from 106 patients and analyzed by means of nuclear magnetic resonance (NMR) spectroscopy and machine learning methods.
Question: Write a study description for the study titled 'Small molecule produced by Photorhabdus interferes with ubiquinone biosynthesis in Gram-negative bacteria'.
Answer: We report identification of 3,6-dihydroxy-1,2-benzisoxazole (DHB) in a screen of Photorhabdus and Xenorhabdus, whose symbiotic relationship with eukaryotic nematodes favors secondary metabolites that meet several requirements matching those for clinically useful antibiotics. DHB is produced by Photorhabdus laumondii and is selective against Gram-negative species Escherichia coli, Enterobacter cloacae, Serratia marcescens, Klebsiella pneumoniae, Proteus mirabilis and Acinetobacter baumannii. It is inactive against anaerobic gut bacteria and nontoxic to human cells. Mutants resistant to DHB map to the ubiquinone biosynthesis pathway. DHB binds to 4-hydroxybenzoate octaprenyltransferase (UbiA) and prevents the formation of 4-hydroxy-3-octaprenylbenzoate. Remarkably, DHB itself is prenylated, forming an unusable chimeric product that likely contributes to the toxic effect of this antimicrobial. DHB appears to be both a competitive enzyme inhibitor and a prodrug; this dual mode of action is unusual for an antimicrobial compound.
Question: Write a study description for the study titled 'LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome'.
Answer: Lipid identification is a major bottleneck in high-throughput lipidomics studies. We combined the in silico fragmentation tool MetFrag with LipidMaps lipid-class specific classifiers which calculate probabilities for lipid class assignments. The LipidFrag approach was then applied to MS/MS spectra of lipid extracts of the nematode Caenorhabditis elegans.
Question: Write a study description for the study titled 'Individual variability in human blood metabolites identifies age-related differences (30 persons, whole blood data)'.
Answer: Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and lifestyle factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed nontargeted, quantitative metabolomics analysis in blood of 15 young (29 ± 4 y of age) and 15 elderly (81 ± 7 y of age) individuals. Coefficients of variation (CV = SD/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found 14 blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine, N-acetyl-arginine, N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD+, and NADP+. Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in antioxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson’s coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. Although our CV values are mostly consistent with those CVs previously published, we here report previously unidentified CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4–2.5) are often modified. Compounds having low CV values, such as ATP and glutathione, may be related to various diseases because their concentrations are strictly controlled, and changes in them would compromise health. Thus, human blood is a rich source of information about individual metabolic differences.  Data from three injections of the same sample and three samples prepared from the same donated blood are available under accession number MTBLS263. Blood samples drawn from four volunteers four times within 24 h are available under accession number MTBLS264. Plasma and RBC data from all 30 subjects can be found under MTBLS266 and MTBLS267, respectively.
Question: Write a study description for the study titled 'Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics (Aging mouse liver positive mode)'.
Answer: Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.Aging mouse liver positive mode is reported in MTBLS601.Aging mouse liver negative mode is reported in MTBLS606.Aging fruit fly positive mode is reported in MTBLS612.Aging fruit fly negative mode is reported in MTBLS615.
Question: Write a study description for the study titled 'Proteomic and metabolomic profiling of acute and chronic stress events associated with military exercises.'.
Answer: By characterizing physiological changes that occur in warfighters during simulated combat, we can start to unravel the key biomolecular components that are linked to physical and cognitive performance. Viable field-based sensors for the warfighter must be rapid and noninvasive. In an effort to facilitate this, we applied a multiomics pipeline to characterize the stress response in the saliva of warfighters to correlate biomolecular changes with overall performance and health. In this study, two different stress models were observed - one of chronic stress and one of acute stress. In both models, significant perturbations in the immune, metabolic, and protein manufacturing/processing systems were observed. However, when differentiating between stress models, specific metabolites associated with the 'fight or flight' response and protein folding were seen to be discriminate of the acute stress model.
Question: Write a study description for the study titled 'Olive Oil Authenticity Studies by Target and Non-target LC-QTOF-MS combined with Advanced Chemometric Techniques'.
Answer: Food analysis is continuously requesting the development of more robust, efficient and cost-effective food authentication analytical methodologies to guarantee the safety, quality and traceability of food commodities with respect to legislation and consumer demands. Hence, a novel RP-UHPLC-ESI-QTOF-MS/MS analytical method was developed employing target, suspect and non-target screening strategies coupled to advanced chemometric tools for the investigation of authenticity of extra virgin olive oil (EVOO). The proposed method was successfully applied in real olive oil samples for the identification of markers responsible for its sensory profile. The proposed target analytical method includes the determination of 14 phenolic compounds and demonstrated low limits of detection (LODs) over the range of 0.015 (apigenin) - 0.039 (vanillin) μg/ml and adequate recoveries (96-107%). A suspect list of 60 relevant compounds was compiled and suspect screening was then applied to all the samples. Semi-quantitation of the suspect compounds was performed using the calibration curves of the target compounds having similar structures. Then, a non-target screening workflow was applied with the aim to identify additional compounds, responsible to differentiate EVOOs from defective oils. Robust classification-based models were built using supervised discrimination techniques, PLS-DA and CP-ANNs, for the classification of olive oils into EVOOs or defectives. Variance in Projection (VIP) was calculated to select the most significant features that affect the discrimination. Overall, 51 compounds were identified and suggested as markers; 14, 26 and 11 compounds were identified using target, suspect and non-target screening, respectively. Retrospective analysis was also performed to identify 19 free fatty acids.
Question: Write a study description for the study titled '"Metabolic response to low-level toxicant exposure in a novel renal tubule epithelial cell system"'.
Answer: "Toxicity testing is vital to protect human health from exposure to toxic chemicals in the environment. Furthermore, combining novel cellular models with molecular profiling technologies, such as metabolomics can add new insight into the molecular basis of toxicity and provide a rich source of biomarkers that are urgently required in a 21st Century approach to toxicology. We have used an NMR-based metabolic profiling approach to characterise for the first time the metabolome of the RPTEC/TERT1 cell line, an immortalised non-tumour human renal epithelial cell line that recapitulates phenotypic characteristics that are absent in other in vitro renal cell models. RPTEC/TERT1 cells were cultured with either the dosing vehicle (DMSO) or with exposure to one of six compounds (nifedipine, potassium bromate, monuron, D-mannitol, ochratoxin A and sodium diclofenac), several of which are known to cause renal effects. Aqueous intracellular and culture media metabolites were profiled by 1H NMR spectroscopy at 6, 24 and 72 hours of exposure to a low effect dose (IC10). We defined the metabolome of the RPTEC/TERT1 cell line and used a principal component analysis approach to derive a panel of key metabolites, which were altered by chemical exposure. By considering only major changes (+/- 1.5 fold change from control) across this metabolite panel we were able to show specific alterations to cellular processes associated with chemical treatment. Our findings suggest that metabolic profiling of RPTEC/TERT1 cells can report on the effect of chemical exposure on multiple cellular pathways at low-level exposure, producing different response profiles for the different compounds tested with a greater number of major metabolic effects observed in the toxin treated cells. Importantly, compounds with established links to chronic renal toxicity produced more diverse and severe perturbations to the cellular metabolome than non-toxic compounds in this model. As these changes can be rationalised with the different pharmacological and toxicity profiles of the chemicals it is suggested that metabolic profiling in the RPTEC/TERT1 model would be useful in investigating the mechanism of action of toxins at a low dose."
Question: Write a study description for the study titled 'Distinct lipid signatures are identified in the plasma of rats with chronic inflammation induced by estradiol benzoate and sex hormones'.
Answer: INTRODUCTION: Prostatitis is likely to occur in younger or middle-aged men, while prostate cancer is likely to occur in older men. Although amino acids and lipids as biomarkers of prostate cancer have been examined using prostate cancer cell lines/tissues, no previous studies have evaluated amino acids or lipids as potential chronic prostatitis biomarkers.OBJECTIVES: The study's aim was to identify amino acids and lipids that could serve as potential biomarkers of chronic prostatitis.METHODS: We profiled the amino acids and lipids found in plasma from rats collected in a previous study. In brief, a total of 148 Sprague-Dawley rats (offspring) were dosed with estradiol benzoate (EB) on postnatal days (PNDs) 1, 3 and 5, and subsequently dosed with testosterone (T)/estradiol (E) tubes via subcutaneous implants from PND 90 to 200. Plasma was collected on PNDs 30, 90, 100, 145 and 200. Analysis was conducted with a Xevo TQ-S triple-quadrupole mass spectrometer using a Biocrates AbsoluteIDQ p180 kit.RESULTS: Plasma acylcarnitines [(C2, C16:1, C18, C18:1, C18:1-OH, and C18:2)], glycerophospholipids (lysophosphatidylcholine-acyl, -di-acyl, and -di-acyl acyl-alkyl) and sphingomyelins [SM (OH) C16:1, SM C18:0, SM C18:1, and SM C20:2] significantly increased on PND 145, when chronic inflammation was observed in the dorsolateral prostate of rats dosed with EB, T, and E. No statistical significances of amino acid levels were observed in the EB + T + E group on PND 145.CONCLUSION: Exposure to EB, T, and E altered lipid levels in rat plasma with chronic prostate inflammation. These findings suggest that the identified lipids may be predictive chronic prostatitis biomarkers. The results require confirmation through additional nonclinical and human studies.
Question: Write a study description for the study titled 'Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study.'.
Answer: The use of face masks has become an integral part of public life in the post-pandemic era. However, the understanding of the effect of wearing masks on physiology remains incomplete and is required for informing public health policies. For the first time, we report the effects of wearing FFP2 masks on the metabolic composition of saliva, a proximal matrix to breath, along with cardiopulmonary parameters. Un-induced saliva was collected from young (31.2 ± 6.3 years) healthy volunteers (n = 10) before and after wearing FFP2 (N95) masks for 30 minutes and analyzed using GCMS. The results showed that such short-term mask use did not cause any significant change in heart rate, pulse rate or SpO2. Three independent data normalization approaches were used to analyze the changes in metabolomic signature. The individuality of the overall salivary metabotype was found to be unaffected by mask use. However, a trend of an increase in the salivary abundance of L-fucose, 5-aminovaleric acid, putrescine and phloretic acid was indicated irrespective of the method of data normalization. Quantitative analysis confirmed increases in concentrations of these metabolites in saliva of paired samples amid high inter-individual variability. The results showed that while there was no significant change in measured physiological parameters and individual salivary metabotypes, mask use was associated with correlated changes in these metabolites plausibly originating from altered microbial metabolic activity. These results might also explain the change in odour perception reported to be associated with mask use. Potential implications of these changes on mucosal health and immunity warrants further investigation to evolve more prudent mask use policies.
Question: Write a study description for the study titled 'Adipocyte-specific Zeb1 confers breast cancer progression by triggering the tumor-associated adipose microenvironment remodeling_untargeted metabolites_Lipidomics'.
Answer: Upon penetrating the basement membrane, breast cancer cells directly interact with their surrounding adipose tissue, which forms a unique tumor-associated adipose microenvironment (TAME). However, the underlying mechanism involved in the regulation of lipid metabolic remodeling in the TAME remains elusive. Herein, we identified a Zeb1-orchestrated bidirectional communication between breast cancer cells and their adjacent cancer-associated adipocytes (CAAs). At the molecular level, breast cancer cells, through the secretion of adrenomedullin (AM), induce downregulation of Zeb1 expression to activate the Atgl/Hsl/Scd-depedent lipolysis in CAAs, which subsequently results in the release of palmitoleic acid (POA) into the TAME. In turn, accumulated POA triggers the malignant growth and metastasis of breast cancer cells and their production of AM via an ARA-PDG2-mediated membrane phospholipid replacement mechanism. Importantly, disruption of Zeb1-dependent lipolytic activity and/or membrane phospholipid remodeling within the TAME, severely diminishes the aggressiveness of breast cancer in vitro and in vivo.
Question: Write a study description for the study titled 'Alterations in the metabolic footprint induced by Mayaro virus infection in cell culture'.
Answer: This study focuses metabolic footprinting of Vero cells infected by Mayaro virus. Nuclear magnetic resonance combined with multivariate analytical methods and tools of pattern recognition shows that metabolic changes can be attributed to the effect of Mayaro virus infection. Vero cells infected by Mayaro and incubated for periods of 2h, 6h and 12h show in each period different variations in the levels of several metabolites such as amino acids, organic acids and carbohydrate. These organic compounds are metabolites involved in the pathway of glycolysis, tricarboxylic acid cycle, pentose phosphate pathway, and the oxidation pathway of fatty acids (via the β-oxidation). This study of footprinting analysis demonstrates the effect of the action of virus in the metabolism of the Vero cells, moreover, these analyses indicate intracellular metabolic state, and contributes to the knowledge of the microorganism influence on cellular metabolism.
Question: Write a study description for the study titled 'Exploring the Influence of Psychological Factors on the Comorbidity of Dental Caries and Obesity in Adolescents from the Perspective of the Oral-Gut-Brain Axis'.
Answer: This study explores the impact of psychological factors on the comorbidity of dental caries and obesity in adolescents through the oral-gut-brain axis. An epidemiological survey was conducted on 1,024 students from Beizhen No. 1 Junior High School, with 90 adolescents aged 12–15 included in biosample research. Methods such as 16S rRNA gene sequencing, untargeted metabolomics, and SourceTracker analysis were used. Results showed significant differences in oral and gut microbiota and metabolite concentrations among adolescents with different health statuses, highlighting the roles of the oral-gut and oral-brain axes in disease progression. This study provides new insights into the mechanisms underlying the comorbidity of dental caries and obesity in adolescents and offers theoretical foundations for prevention and treatment strategies.