LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A combined direct infusion/reversed phase chromatography – high resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C- internal standards'.
Answer: We propose a fully automated novel workflow for lipidomics based on flow injection, followed by liquid chromatography-high-resolution mass spectrometry (FI/LC-HRMS). The workflow combined in-depth characterization of the lipidome achieved via reversed-phase LC-HRMS with absolute quantification by using a large number of lipid species-specific and/or retention time (RT)-matched/class-specific calibrants. The lipidome of 13C-labelled yeast (LILY) provided a large panel of cost-effective internal standards (ISTDs) covering triacylglycerols (TG), steryl esters (SE), free fatty acids (FA), diacylglycerols (DG), sterols (ST), ceramides (Cer), hexosyl ceramides (HexCer), phosphatidylglycerols (PG), phosphatidylethanolamines (PE), phosphatidic acids (PA), cardiolipins (CL), phosphatidylinositols (PI), phosphatidylserines (PS), phosphatidylcholines (PC), lysophosphatidylcholines (LPC) and lysophosphatidylethanolamines (LPE). The workflow in combination with the LILY lipid panel enables simultaneous quantification via (1) external multi-point calibration with internal standardization and (2) internal one-point calibration with LILY as a surrogate ISTD, increasing the coverage while keeping the accuracy and throughput high. Extensive measures on quality control allowed us to rank the calibration strategies and to automatically select the calibration strategy of the highest metrological order for the respective lipid species. Overall, the workflow enabled a streamlined analysis, with a limit of detection in the low femtomolar range, and provided validation tools together with absolute concentration values for >350 lipids in human plasma on a species level. Based on the selected standard panel, lipids from 7 classes (LPC, LPE, PC, PE, PI, DG, TG) passed stringent quality filters, which included QC accuracy, a precision and recovery bias of <30% and concentrations within the 99% confidence interval of the international laboratory comparison of SRM 1950, NIST, USA. The quantitative values are independent of common deuterated or non-endogenous ISTDs, thus offering cross-validation of different lipid methods and further standardizing lipidomics.
Question: Write a study description for the study titled 'Tissue, urine and serum NMR metabolomics dataset from a 5/6 nephrectomy rat model of chronic kidney disease'.
Answer: Serum, urine and tissue from a rat model of chronic kidney disease (CKD) were analysed using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics methods, and compared with samples from sham operated rats. Both urine and serum were sampled at multiple timepoints, and the results have been reported elsewhere [1]. The data could be useful to researchers working with human CKD or rat models of the disease. In addition, several different types of NMR spectra were recorded, including 1D NOESY, CPMG, and 2D J-resolved spectra, and the data could be useful for method comparison and algorithm development, both in terms of NMR spectroscopy and multivariate analysis.References:[1] Hanifa MA, Skott M, Maltesen RG, Rasmussen BS, Nielsen S, Frøkiær J, Ring T & Wimmer R. (2019). Tissue, urine and blood metabolite signatures of chronic kidney disease in the 5/6 nephrectomy rat model. Metabolomics 15;112. doi.org/10.1007/s11306-019-1569-3.
Question: Write a study description for the study titled 'N-glycosylation Profiling of Colorectal Cancer Cell Lines Reveals Association of Fucosylation with Differentiation and Caudal Type Homebox 1 (CDX1)/Villin mRNA Expression'.
Answer: Various cancers such as colorectal cancer (CRC) are associated with alterations in protein glycosylation. CRC cell lines are frequently used to study these (glyco)biological changes and their mechanisms. However, differences between CRC cell lines with regard to their glycosylation have hitherto been largely neglected. Here, we comprehensively characterized the N-glycan profiles of 25 different CRC cell lines, derived from primary tumors and metastatic sites, in order to investigate their potential as glycobiological tumor model systems and to reveal glycans associated with cell line phenotypes. We applied an optimized, high-throughput membrane-based enzymatic glycan release for small sample amounts. Released glycans were derivatized to stabilize and differentiate between a2,3- and a2,6-linked N-acetylneuraminic acids, followed by N-glycosylation analysis by MALDI-TOF(/TOF)-MS. Our results showed pronounced differences between the N-glycosylation patterns of CRC cell lines. CRC cell line profiles differed from tissue-derived N-glycan profiles with regard to their high-mannose N-glycan content but showed a large overlap for complex type N-glycans, supporting their use as a glycobiological cancer model system. Importantly, we could show that the high-mannose N-glycans did not only occur as intracellular precursors but were also present at the cell surface. The obtained CRC cell line N-glycan features were not clearly correlated with mRNA expression levels of glycosyltransferases, demonstrating the usefulness of performing the structural analysis of glycans. Finally, correlation of CRC cell line glycosylation features with cancer cell markers and phenotypes revealed an association between highly fucosylated glycans and CDX1 and/or villin mRNA expression that both correlate with cell differentiation. Together, our findings provide new insights into CRC-associated glycan changes and setting the basis for more in-depth experiments on glycan function and regulation.
Question: Write a study description for the study titled 'Calenduloside E produced by Bifidobacterium animalis B960 increases glibenclamide efficacy and alleviates drug-induced adverse effects via the IRS1/PI3K/AKT signaling pathway in a type 2 diabetes model Calenduloside E produced by Bifidobacterium animalis B960 increases glibenclamide efficacy and alleviates drug-induced adverse effects via the IRS1/PI3K/AKT signaling pathway in cell, organ-on-a-chip, and mouse models of type 2 diabetes.'.
Answer: Glibenclamide (GLIB), a type 2 diabetes therapy, has long-term safety concerns. Probiotic–drug coadministration, an emerging adjunctive approach for metabolic diseases, improves therapeutic outcomes and side effects. Here, Bifidobacterium animalis B960 was selected from 71 probiotic strains by HPLC and in vitro cell assays; it effectively maintained GLIB integrity and ameliorated insulin resistance. In vivo, combined B960+GLIB therapy significantly reduced blood glucose, prevented weight gain, improved intestinal homoeostasis and increased beneficial metabolite levels. Moreover, B960 significantly mitigated GLIB-induced side effects, particularly hepatotoxicity and inflammation. B960 activated a 9-enzyme cascade involving IolS and EpsJ, biotransforming oleanolic acid into calenduloside E, which synergized with GLIB by activating the IRS1/PI3K/AKT signaling pathway—upregulating insulin effectors (Irs1, Pik3r1, Akt1, Slc2a4) while suppressing gluconeogenic regulators (Gsk3b, Foxo1, Pck1) and increasing insulin sensitivity and glucose utilization. Proof-of-concept studies utilizing insulin-resistant models and a human-relevant gut–liver organ-on-a-chip platform demonstrated targeted insulin sensitization without compromising GLIB pharmacokinetics. This work offers an efficacy-enhanced and toxicity-reduced T2D therapeutic strategy
Question: Write a study description for the study titled '"A multidimensional 1H NMR lipidomics workflow to address chemical food safety issues"'.
Answer: "INTRODUCTION: Although it is still at a very early stage compared to its mass spectrometry (MS) counterpart, proton nuclear magnetic resonance (NMR) lipidomics is worth being investigated as an original and complementary solution for lipidomics. Dedicated sample preparation protocols and adapted data acquisition methods have to be developed to set up an NMR lipidomics workflow; in particular, the considerable overlap observed for lipid signals on 1D spectra may hamper its applicability.  OBJECTIVES: The study describes the development of a complete proton NMR lipidomics workflow for application to serum fingerprinting. It includes the assessment of fast 2D NMR strategies, which, besides reducing signal overlap by spreading the signals along a second dimension, offer compatibility with the high-throughput requirements of food quality characterization.  METHOD: The robustness of the developed sample preparation protocol is assessed in terms of repeatability and ability to provide informative fingerprints; further, different NMR acquisition schemes—including classical 1D, fast 2D based on non-uniform sampling or ultrafast schemes—are evaluated and compared. Finally, as a proof of concept, the developed workflow is applied to characterize lipid profiles disruption in serum from β-agonists diet fed pigs.  RESULTS: Our results show the ability of the workflow to discriminate efficiently sample groups based on their lipidic profile, while using fast 2D NMR methods in an automated acquisition framework.  CONCLUSION: This work demonstrates the potential of fast multidimensional 1H NMR—suited with an appropriate sample preparation—for lipidomics fingerprinting as well as its applicability to address chemical food safety issues. "
Question: Write a study description for the study titled 'Brown and beige adipose tissue regulate systemic metabolism through a metabolite interorgan signaling axis'.
Answer: Brown and beige adipose tissue are emerging as distinct endocrine organs. These tissues are functionally associated with skeletal muscle, adipose tissue metabolism and systemic energy expenditure, suggesting an interorgan signaling network. Using metabolomics, we identify 3-methyl-2-oxovaleric acid, 5-oxoproline, and β-hydroxyisobutyric acid as small molecule metabokines synthesized in browning adipocytes and secreted via monocarboxylate transporters. 3-methyl-2-oxovaleric acid, 5-oxoproline and β-hydroxyisobutyric acid induce a brown adipocyte-specific phenotype in white adipocytes and mitochondrial oxidative energy metabolism in skeletal myocytes both in vitro and in vivo. 3-methyl-2-oxovaleric acid and 5-oxoproline signal through cAMP-PKA-p38 MAPK and β-hydroxyisobutyric acid via mTOR. In humans, plasma and adipose tissue 3-methyl-2-oxovaleric acid, 5-oxoproline and β-hydroxyisobutyric acid concentrations correlate with markers of adipose browning and inversely associate with body mass index. These metabolites reduce adiposity, increase energy expenditure and improve glucose and insulin homeostasis in mouse models of obesity and diabetes. Our findings identify beige adipose-brown adipose-muscle physiological metabokine crosstalk.
Question: Write a study description for the study titled 'Imaging with Mass Spectrometry of Bacteria on the Exoskeleton of Fungus-Growing Ants'.
Answer: Mass spectrometry imaging is a powerful analytical technique for detecting and determining spatial distributions of molecules within a sample. Typically, mass spectrometry imaging is limited to the analysis of thin tissue sections taken from the middle of a sample. In this work, we present a mass spectrometry imaging method for the detection of compounds produced by bacteria on the outside surface of ant exoskeletons in response to pathogen exposure. Fungus-growing ants have a specialized mutualism with Pseudonocardia, a bacterium that lives on the ants’ exoskeletons and helps protect their fungal garden food source from harmful pathogens. The developed method allows for visualization of bacterial-derived compounds on the ant exoskeleton. This method demonstrates the capability to detect compounds that are specifically localized to the bacterial patch on ant exoskeletons, shows good reproducibility across individual ants, and achieves accurate mass measurements within 5 ppm error when using a high-resolution, accurate-mass mass spectrometer.
Question: Write a study description for the study titled 'Monounsaturated fatty acids in serum triacylglycerols are associated with response to neoadjuvant chemotherapy in breast cancer patients'.
Answer: Changes in cellular lipid metabolism are a common feature in most solid tumors, which occur already in early stages of the tumor progression. However, it remains unclear if the tumor-specific lipid changes can be detected at the level of systemic lipid metabolism. The objective of this study was to perform comprehensive analysis of lipids in breast cancer patient serum samples. Lipidomic profiling using an established analytical platform was performed in two cohorts of breast cancer patients receiving neoadjuvant chemotherapy. The analyses were performed for 142 patients before and after neoadjuvant chemotherapy, and the results before chemotherapy were validated in an independent cohort of 194 patients. The analyses revealed that in general the tumor characteristics are not reflected in the serum samples. However, there was an association of specific triacylglycerols (TGs) in patients' response to chemotherapy. These TGs containing mainly oleic acid (C18:1) were found in lower levels in those patients showing pathologic complete response before receiving chemotherapy. Some of these TGs were also associated with estrogen receptor status and overall or disease-free survival of the patients. The results suggest that the altered serum levels of oleic acid in breast cancer patients are associated with their response to chemotherapy.
Question: Write a study description for the study titled 'Comparative analysis of rhizosphere soil between three plantation types in Karst Rocky Desertification area by widely targeted metabolomics'.
Answer: Understanding the differences in rhizosphere soil microbial metabolites between severely and mildly rocky desertified areas is crucial for developing ecological restoration strategies and land management measures in rocky desertification regions. This study systematically analyzed the differences in rhizosphere soil microbial metabolites of Toona sinensis, Vernicia fordii, and Cornus wilsoniana in severely and mildly rocky desertified areas of Western Hunan using untargeted metabolomics. The results showed that the types and quantities of primary and secondary metabolites in the rhizosphere soil of severely rocky desertified areas were significantly lower than those in mildly rocky desertified areas. Additionally, under severe rocky desertification conditions, 15 common compounds (e.g., 17a-Estradiol, Adenine, all-trans-Retinoic acid) were significantly increased in the rhizosphere soil microbial metabolites of the three tree species. These compounds may provide defense mechanisms for plants to adapt to harsh environments. KEGG metabolic pathway analysis revealed that under severe rocky desertification conditions, Toona sinensis, Vernicia fordii, and Cornus wilsoniana shared six enriched pathways, which play an important role in the biosynthesis of compounds such as phenylpropanoids and unsaturated fatty acids. By revealing the differences in rhizosphere soil microbial metabolites, this study not only deepens the understanding of rocky desertification ecosystems but also provides valuable scientific evidence for ecological restoration and sustainable land management.
Question: Write a study description for the study titled 'Integrated metabolomics and transcriptome revealed the effect of fermented Lycium barbarum residue promoting Ovis aries immunity'.
Answer: Lycium barbarum residue contains abundant bioactive nutrients which can be used as feed supplement. This study investigated the effects of fermented and non-fermented Lycium barbarum residues (RFW and RW) on the meat quality and immunity of sheep (Ovis aries). Fifty-four Tan sheep were randomly divided into control, RFW or RW treatments. Data showed that RFW and RW increased the carcass weight, fat content, ash content and reduced the cooking loss of lamb. RFW performed more significant effects on activating immune-related genes than those of RW. The expression of chemokines and immune-related pathways, such as signaling pathways of interleukin-17 signaling pathway and NOD-like receptor signaling pathway, were elevated in sheep fed RFW. RW increased the diversity in rumen metabolites, especially compositions of lipids, organic acids and organ heterocyclic compounds. RFW affected numerous compounds which are closely correlated with the activation of immune genes. In conclusion, RFW could represent a valuable strategy to improve growth performance and immunity of sheep
Question: Write a study description for the study titled 'Gregarines impact consumption and development but not glucosinolate metabolism in the mustard leaf beetle'.
Answer: Gregarines are usually classified as parasites, but recent studies suggest that they should be viewed on a parasitism-mutualism spectrum and may even be seen as part of the gut microbiota of host insects. As such, they may also impact the consumption of their hosts and/or be involved in the digestion or detoxification of the host's diet. To study such effects of a gregarine species on those traits in its host, the mustard leaf beetle (Phaedon cochleariae) was used. This beetle species feeds on Brassicaceae plants that contain glucosinolates, which form toxic compounds when hydrolyzed by myrosinases. We cleaned host eggs from gametocysts and spores and reinfected half of the larvae with gregarines, to obtain gregarine-free (G-) and gregarine-infected (G+) larvae. Growth and food consumption parameters of these larvae were assessed by rearing individuals on watercress (Nasturtium officinale, Brassicaceae). A potential involvement of gregarines in the glucosinolate metabolism of P. cochleariae larvae was investigated by offering G-and G+ larvae leaf discs of watercress (containing mainly the benzenic 2-phenylethyl glucosinolate and myrosinases) or pea (Pisum sativum, Fabaceae, lacking glucosinolates and myrosinases) treated with the aliphatic 4-pentenyl glucosinolate or the indole 1-methoxy-3-indolylmethyl glucosinolate. Larval and fecal samples were analyzed via UHPLC-QTOF-MS/MS to search for breakdown metabolites. Larval development, body mass, growth rate and efficiency to convert food into body mass were negatively affected by gregarine infection while the pupal mass remained unaffected. The benzenic and aliphatic glucosinolates were conjugated with aspartic acid, while the indole glucosinolate was conjugated with glutamic acid. Gregarine infection did not alter the larvae's ability to metabolize glucosinolates and was independent of plant myrosinases. In summary, some negative effects of gregarines on host performance could be shown, indicating parasitism. Future studies may further disentangle this gregarine-host relationship and investigate the microbiome potentially involved in the glucosinolate metabolism.
Question: Write a study description for the study titled 'Regulation mechanism of gibberellic acid-3 for astaxanthin biosynthesis in heterotrophically growing Chromochloris zofingiensis'.
Answer: Chromochloris zofingiensis has been proved as a potential resource for large-scale astaxanthin production, but little information of phytohormones on growth and astaxanthin accumulation could be obtained. This study explored the impact of gibberellic acid-3 (GA3) on growth and astaxanthin generation in heterotrophically growing C. zofingiensis. On Day 16, the astaxanthin yield in 7.5 L fermenters was 89% higher at 0.34 g/L compared to the control. GA3 changed transcription levels of genes linked to carbon metabolism, lipid metabolism, astaxanthin production and ABC transporters. Genes related to astaxanthin biosynthesis, such as phytoene synthase (PSY), phytoene desaturase (PDS), beta-carotenoid hydroxylase (CHYb) and beta-carotenoid ketolase (BKT), were upregulated under GA3 induction. The relative abundances of metabolites involved in carbon metabolisms, such as glucose-1-phosphate (G1P), glucose-6-phosphate (G6P) and glyceraldehyde-3-phosphate (GAP), were altered. By using GA3 and arginine together, the astaxanthin yield increased by 2.3 times to 0.39 g/L over the control. This research proposed novel feasible approaches for heterotrophic C. zofingiensis high astaxanthin production.
Question: Write a study description for the study titled 'A large-scale metabolomics study to harness chemical diversity and explore biochemical mechanisms in ryegrass (UPLC-MS C1 reverse phase POS and GC-MS FAME assays)'.
Answer: Perennial ryegrass (Lolium perenne) is integral to temperate pastoral agriculture, which contributes most of the milk and meat production worldwide. Chemical profiles and diversity of ryegrass offer several opportunities to harness specific traits and elucidate underlying biological mechanisms for forage improvement. We conducted a large-scale metabolomics study of perennial ryegrass comprising 715 genotypes, representing 118 populations from 21 countries. Liquid/gas chromatography-mass spectrometry based targeted and non-targeted techniques were used to analyse fructan oligosaccharides, lipids, fatty acid methyl esters, polar and semi-polar compounds. Fructan diversity across all genotypes was evaluated, high- and low-sugar groups identified, and fructan accumulation mechanisms explored. Metabolites differentiating the two groups were characterised, modules and pathways they represent deduced, and finally, visualisation and interpretation provided in a biological context. We also demonstrate a workflow for large-scale metabolomics studies from raw data through to statistical and pathway analysis.  UPLC-MS C1 reverse phase POS and GC-MS FAME assays are reported in the current study MTBLS66. UPLC-MS HILIC POS assay is reported in MTBLS62. UPLC-MS HILIC NEG assay is reported in MTBLS63. UPLC-MS C18 reverse phase POS assay is reported in MTBLS64. UPLC-MS C18 reverse phase NEG assay is reported in MTBLS65. UPLC-MS C1 reverse phase NEG assay is reported in MTBLS68. HPLC-MS Hypercarb reverse phase NEG assay is reported in MTBLS529.
Question: Write a study description for the study titled 'Gut microbiota production of trimethyl-5-aminovaleric acid reduces fatty acid oxidation and accelerates cardiac hypertrophy'.
Answer: Numerous studies found intestinal microbiota alterations which are thought to affect the development of various diseases through the production of gut-derived metabolites. However, the specific metabolites and their pathophysiological contribution to cardiac hypertrophy or heart failure progression still remain unclear. N,N,N-trimethyl-5-aminovaleric acid (TMAVA), derived from trimethyllysine through the gut microbiota, was elevated with gradually increased risk of cardiac mortality and transplantation in a prospective heart failure cohort (n=1647). TMAVA treatment aggravated cardiac hypertrophy and dysfunction in high-fat diet-fed mice. Decreased fatty acid oxidation (FAO) is a hallmark of metabolic reprogramming in the diseased heart and contributes to impaired myocardial energetics and contractile dysfunction. Proteomics uncovered that TMAVA disturbed cardiac energy metabolism, leading to inhibition of FAO and myocardial lipid accumulation. TMAVA treatment altered mitochondrial ultrastructure, respiration and FAO and inhibited carnitine metabolism. Mice with γ-butyrobetaine hydroxylase (BBOX) deficiency displayed a similar cardiac hypertrophy phenotype, indicating that TMAVA functions through BBOX. Finally, exogenous carnitine supplementation reversed TMAVA induced cardiac hypertrophy. These data suggest that the gut microbiota-derived TMAVA is a key determinant for the development of cardiac hypertrophy through inhibition of carnitine synthesis and subsequent FAO.