LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'massPix: An R package for annotation and interpretation of mass spectrometry imaging data for lipidomics'.
Answer: Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools. Here we have developed massPix - an R package for analysing and interpreting data from MSI of lipids in tissue. MassPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications. MassPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries. Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering. Mouse cerebellum was analysed using matrix assisted laser desorption ionisation (MALDI) MSI. The resulting MSI dataset forms the test data for massPix.
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 C18 reverse phase POS assay)'.
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 C18 reverse phase POS assay is reported in the current study MTBLS64. UPLC-MS HILIC POS assay is reported in MTBLS62. UPLC-MS HILIC NEG assay is reported in MTBLS63. UPLC-MS C18 reverse phase NEG assay is reported in MTBLS65. UPLC-MS C1 reverse phase POS and GC-MS FAME assays are reported in MTBLS66. 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 'Blood pseudotargeted metabolome of moyamoya disease'.
Answer: We aimed to identify specific metabolomic changes and biomarkers for the differential clinical diagnosis of different subtypes of moyamoya disease (MMD). We conducted an pseudotargeted metabolomics analysis and pseudotargeted metabolomics analysis revealed decreased LPC expression in patients with MMD. LPC 16:1-2 expression was significantly decreased in patients with ischemic MMD while LPC 22:1 expression was significantly reduced in both ischemic and hemorrhagic MMD.
Question: Write a study description for the study titled 'Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats'.
Answer: Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient
Question: Write a study description for the study titled 'Targeted metabolomic analysis in hepatic extracts, serum, and urine of female mice gavaged with TCDD every 4 days for 28 days'.
Answer: TCDD is an environmental contaminant that elicits a number of hepatic effects including fat accumulation, inflammation, and fibrosis that can progress to hepatocellular carcinoma. RNA-Seq and targeted metabolomics were integrated with complementary dioxin response element (DRE) location and aryl hydrocarbon receptor (AhR) ChIP-Seq data to further investigate the hepatotoxicity of TCDD. Our integrative analysis identified changes similar to the Warburg effect observed in cancer cells, including pyruvate kinase isoform switching (PKM1 to PKM2), and an increase in the glutaminase (GLS1) GAC:KGA isoform ratio. Consequently, metabolites are redirected towards the pentose phosphate pathway, serine biosynthesis, and glutaminolysis. We propose that the effects of TCDD on central carbon and amino acid metabolism represents AhR-mediated hepatic metabolic reprogramming in order to increase NADPH production as an oxidative stress counter-measure.
Question: Write a study description for the study titled 'Maternal chromium propionate reprograms the gut-blood-placenta axis to support neonatal immune and metabolic development in dairy calves: a multi-omics insight'.
Answer: In this study, non-targeted metabolomics sequencing was performed on fecal samples from dairy cows to investigate the effect of chromium propionate supplementation on fecal metabolism in periparturient dams
Question: Write a study description for the study titled 'Global analysis of plasma lipidomics reveals altered lipid signatures in patients with osteonecrosis of the femoral head'.
Answer: AIMS: Although studies have made the connection between lipid metabolism disorder and osteonecrosis of the femoral head (ONFH), the characteristics of the circulating lipidome signature of ONFH have not yet been investigated yet and need to be explored.METHODS: We conducted a comprehensive analysis of plasma lipidomics in a clinical human cohort including 32 healthy normal control (NC) subjects and 91 ONFH patients in different subgroups (alcohol-induced [AONFH], steroid-induced, and traumatic ONFH) and stages (stages I/II, stages III/IV), using ultra-high performance liquid chromatography–tandem mass spectrometry.RESULTS: The PLS-DA model indicates that the global plasma lipidome profile differs between the ONFH and NC samples. We identified a signature including 22 common differentially expressed lipids (DELs) in all the three subgroups (VIP > 1, P < 0.05, FC > 1.5 or FC < 0.67, compared with the NC group), and for each of the subtype-specific lipidome profiles, as well as altered lipid biomarkers (FC > 2, P < 0.05, and AUC > 0.7, compared with the NC group) for each subgroup. The AONFH subgroup has the most DELs, and the plasma levels of lipid compounds in the subclass of triacylglycerol increased obviously in the AONFH samples. We identified that 9 stage-positive and 2 stage-negative lipids may function as novel biomarkers that predict the disease progression of ONFH.CONCLUSION: This study provides the first overview, analysis, and understanding of the unique phenotype-related plasma lipidome signature of ONFH. The results will offer insights into the mechanisms underlying lipid metabolism in the pathogenesis and progression of ONFH, and will help to identify novel lipids biomarkers or targets for disease diagnosis and treatment.
Question: Write a study description for the study titled 'Airway Dysbiosis Accelerates Lung Function Decline in Chronic Obstructive Pulmonary Disease (Human UPLC-MS/MS assays)'.
Answer: Progressive decline in lung function is a hallmark of chronic obstructive pulmonary disease (COPD). Although airway dysbiosis occurs in COPD, whether it contributes to disease progression remains unknown. Here, through a longitudinal analysis on 181 COPD individuals from two large cohorts involving four UK clinical centers, we showed that baseline airway dysbiosis, characterized by enrichment of opportunistic pathogenic taxa, was associated with rapid forced expiratory volume in one second (FEV1) decline over two years. Co-presence of Moraxella, Staphylococcus and Stenotrophomonas was associated with an accelerated FEV1 decline by 139.7 mL/year. The dysbiosis was associated with exacerbation-related FEV1 fall and sudden FEV1 fall at clinical stability, two critical events contributing to long-term FEV1 decline. The microbiota association with FEV1 decline was validated in a third, independent cohort in China. Human multi-omics, murine and cellular mechanistic studies showed that chronic airway colonization of Staphylococcus aureus promoted lung function decline through producing homocysteine, which elicited an apoptosis-to-NETosis shift in neutrophils toward persistent inflammation via AKT1-S100A8/A9 axis. Prophylactic and therapeutic depletion of S. aureus via bacteriophage restored lung function in emphysema mice. These results provide a fresh approach to slow COPD progression by targeting the airway microbiome.Linked studies:UPLC-MS/MS assays of human samples are reported in this study.UPLC-MS/MS assays of murine samples are reported in MTBLS6894.UPLC-MS/MS assays of original cohort human samples are reported in MTBLS4017.
Question: Write a study description for the study titled 'Comprehensive High-Resolution Multiple-Reaction Monitoring Mass Spectrometry for Targeted Eicosanoid Assays'.
Answer: Eicosanoids comprise a class of bioactive lipids derived from a unique group of essential fatty acids that mediate a variety of important physiological functions. Owing to the structural diversity of these lipids, their analysis in biological samples is often a major challenge. Advancements in mass spectrometry have been helpful for the characterization and quantification of these molecular lipid species in complex matrices. However, there are technical limitations to this approach, including low-abundant and/or poorly ionizable lipids. Using high-resolution multiple-reaction monitoring (MRM-HR), we were able to develop a targeted bioanalytical method for eicosanoid quantification. For this, we optimized the LC-MS/MS conditions and evaluated several parameters, including linearity, limits of quantification, matrix effects and recovery yields. For validation purposes, we looked at the method’s precision and accuracy. A library of high-resolution fragmentation spectra for eicosanoids was developed. Our comprehensive dataset meets benchmark standards for targeted analysis, having been derived using best-practice workflows and rigorous quality assessments. As such, our method has applications for determining complex eicosanoid profiles in the biomedical field.
Question: Write a study description for the study titled 'Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects'.
Answer: Apples are one of the most commonly consumed fruits and their high polyphenol content is considered one of the most important determinants of their health-promoting activities. Here we studied the nutrikinetics of apple polyphenols by UHPLC-HRMS metabolite fingerprinting, comparing the bioavailability when assumed in a natural or a polyphenol-enriched cloudy apple juice. Twelve men and women participated in an acute single blind controlled crossover study in which they consumed 250 mL of cloudy apple juice (CAJ), Crispy Pink apple variety, or 250 mL of the same juice enriched with 750 mg of an apple polyphenol extract (PAJ). Plasma and whole blood were collected at time 0, 1, 2, 3 and 5 h. Urine was collected at time 0 and 0-2, 2-5, 5-8, and 8-24 h after juice consumption. Faecal samples were collected from each individual during the study for 16S rRNA gene profiling. As many as 110 metabolites were significantly elevated following intake of polyphenol enriched cloudy apple juice, with large inter-individual variations. The comparison of the average area under the curve of circulating metabolites in plasma and in urine of volunteers consuming either the CAJ or the PAJ demonstrated a stable metabotype, suggesting that an increase in the concentration of polyphenols in the fruit do not limit their bioavailability. Faecal bacteria were correlated with specific microbial catabolites derived from apple polyphenols. Human metabolism of apple polyphenols is a co-metabolic process between human encoded activities and those of our resident microbiota. Here we have identified specific blood and urine metabolic biomarkers of apple polyphenol intake and identified putative associations with specific genera of gut bacteria, associations which now need confirmation in specifically designed mechanistic studies.
Question: Write a study description for the study titled 'Large-scale non-targeted serum metabolomics in the Prospective Investigation of the Vasculature in Uppsala Seniors'.
Answer: The Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) is a community-based study where all men and women at age 70 living in Uppsala, Sweden were invited to participate in 2001. The 1,016 participants (50% women) have been extensively phenotyped. In March 2006 a reinvesigation of the cohort at the age of 75 was started. The major measurements performed at age 70 were also repeated at age 75. Here we make publically available all the metabolomics analysis on serum samples from the investigation at age 70. In the final analysis we included samples from 968 individuals.
Question: Write a study description for the study titled 'Metabolic flux analysis of glucose through the glycolytic pathway.'.
Answer: C13 whole-labeled glucose was added into the culture medium of tumor cells to analyze the changes of metabolic flux in glycolytic pathway under metformin treatment or without HK2 knockout, and to analyze the glycolytic link affected by HK2 and metformin treatment.
Question: Write a study description for the study titled 'Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS'.
Answer: Detailed characterization of complex biological surfaces by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) requires instrumentation that is capable of high mass resolving power, mass accuracy and dynamic range. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral performance for MALDI MSI experiments, and often reveals molecular features that are unresolved on lower performance instrumentation. Higher magnetic field strength improves all performance characteristics of FT-ICR; mass resolving power improves linearly, while mass accuracy and dynamic range improve quadratically with magnetic field strength. Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below 100 ppb, and dynamic range per pixel over 500:1 were obtained from the direct analysis of biological tissue sections. Molecular features with m/z differences as small as 1.79 mDa were resolved and identified with high mass accuracy. These features allow for the separation and identification of lipids to the underlying structures of tissues. The unique molecular detail, accuracy, sensitivity and dynamic range combined in a 21T MALDI FT-ICR MSI experiment enable researchers to visualize molecular structures in complex tissues that have remained hidden until now. The instrument described allows for future innovative, such as high-end studies to unravel the complexity of biological, geological and engineered organic material surfaces with an unsurpassed detail.
Question: Write a study description for the study titled 'Sarcosine decreases in sarcopenia and enhances muscle regeneration and adipose thermogenesis by activating ant-inflammatory macrophages (cohort1)'.
Answer: Age-related changes in circulating metabolites significantly influence systemic physiology and may contribute to diseases like sarcopenia. Although metabolic dysregulation is closely linked to sarcopenia, the roles of specific metabolites remain unclear. Here we performed comprehensive plasma metabolomic and lipidomic analyses across two cohorts comprising 1,013 individuals. Our findings revealed the metabolic characteristics of sarcopenia, including a notable decline in plasma sarcosine levels in both aging and sarcopenic individuals. Functional studies showed that sarcosine helps maintain muscle mass homeostasis during aging, promotes adipose thermogenesis and enhances muscle regeneration. These effects may increase energy expenditure and restore metabolic balance to reduce chronic inflammation and improve insulin sensitivity, which are crucial for managing sarcopenia. We demonstrate that sarcosine activated the GCN2 signaling pathway to enhance anti-inflammatory macrophage polarization, promoting adipose thermogenesis and muscle regeneration. This study underscores the potential of sarcosine supplementation as an adjunctive strategy for preventing sarcopenia in older adults.cohort1 is reported in the current study MTBLS12015.cohort2 is reported in MTBLS12036.
Question: Write a study description for the study titled 'Zingerone treats postmenopausal osteoporosis via increased ferroptosis sensitivity by p53-mediated regulation of Sat1 and Gpx4 expression'.
Answer: Zingerone, a component of dried ginger, has known anti-ulcer and bone growth-promoting effects, but its impact on postmenopausal osteoporosis (PO) is unclear. This study investigates the therapeutic potential and underlying mechanisms of zingerone in PO. A concentration-dependent effect identified on osteoclast precursors: at low concentrations, zingerone maintains low ROS levels, enhance proliferation, and facilitates bone remodelling; at high concentrations, it elevates ROS levels, enhances ferroptosis sensitivity, and suppresses osteoclast formation.Zingerone significantly improves bone mass in an ovariectomised mouse model of PO. Metabolomics identifies 869 differential metabolites linked to glutathione and purine metabolism. Transcriptomics highlights pathways including ferroptosis, leukocyte migration, and cell adhesion.In RAW264.7 cells, zingerone modulates p53, enhances ferroptosis sensitivity, increasing ROS and Fe2+, upregulates Sat1, and downregulates Gpx4, suggesting that zingerone may act via p53-mediated ferroptosis, indicating potential clinical utility. Before clinical application, the dose-dependent effects of zingerone on bone remodelling and its underlying mechanisms warrant further investigation.
Question: Write a study description for the study titled 'Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level (Amino acid profiling)'.
Answer: Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. The application of omics technologies - mainly studying nucleic acids - has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans reflect the phenotype of a tumor in a more direct way and thus hold the potential to discover clinically relevant phenotypes and targetable pathways. We compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylome and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.Amino acid profiling is reported in the current study MTBLS9836.Metabolite profiling is reported in MTBLS9830.
Question: Write a study description for the study titled 'Metabolomics Characterization of Human Calcific Aortic Valve Stenosis'.
Answer: BACKGROUND: Calcific aortic valve stenosis (CAVS) is the most prevalent valvular heart disease in developed countries with significant morbidity and mortality. Given the poor understanding of the pathophysiological processes leading to CAVS, we utilized a joint non-targeted metabolomics and targeted lipidomics approach to better characterize the metabolic perturbations involved in its development and progression.METHODS: We collected human aortic valve tissue from 106 patients undergoing aortic valve replacement surgery. Our cohort represented aortic valvular hemodynamics from mild to severe aortic stenosis with varying degrees of valvular calcification.RESULTS: Seventy-two significantly differential (p<0.01) metabolites across different stages of CAVS severity were filtered and identified from the tissue metabolome. Each stage of valvular stenosis was characterized by a distinct metabolic signature. The top three perturbed metabolic pathways in the setting of CAVS involved glycerophospholipid metabolism, linoleic acid metabolism and primary bile acid biosynthesis. The lysophosphatidic acid species (LysoPA) exhibited significant (p<0.05) association with CAVS severity and were also found to select patients with accelerated rate of CAVS progression. Two LysoPA species namely, 18:2 LysoPA and 20:4 LysoPA, exhibited potential to serve as biomarkers of CAVS severity.CONCLUSIONS: The present study reports the largest and most comprehensive metabolomics analysis of human aortic valve stenosis that highlights the dysregulated LysoPA pathway involved in the pathogenesis of CAVS.