LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Comprehensive profiling of semi‐polar phytochemicals in whole wheat grains (Triticum aestivum) using liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry'.
Answer: INTRODUCTION: Wheat (Triticum aestivum) it is one of the most important staple food crops worldwide and represents an important resource for human nutrition. Besides starch, proteins and micronutrients wheat grains accumulate a highly diverse set of phytochemicals.OBJECTIVES: This work aimed at the development and validation of an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains.METHOD: Reversed-phase ultra-high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC/ESI-QTOFMS) was used as analytical platform. For annotation of metabolites accurate mass collision-induced dissociation mass spectra were acquired and interpreted in conjunction with literature data, database queries and analyses of reference compounds.RESULTS: Based on reversed-phase UHPLC/ESI-QTOFMS an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains was developed. For method development the extraction procedure and the chromatographic separation were optimized. Using whole grains of eight wheat cultivars a total of 248 metabolites were annotated and characterized by chromatographic and tandem mass spectral data. Annotated metabolites comprise hydroquinones, hydroxycinnamic acid amides, flavonoids, benzoxazinoids, lignans and other phenolics as well as numerous primary metabolites such as nucleosides, amino acids and derivatives, organic acids, saccharides and B vitamin derivatives. For method validation, recovery rates and matrix effects were determined for ten exogenous model compounds. Repeatability and linearity were assessed for 39 representative endogenous metabolites. In addition, the accuracy of relative quantification was evaluated for six exogenous model compounds.CONCLUSIONS: In conjunction with non-targeted and targeted data analysis strategies the developed analytical workflow was successfully applied to discern differences in the profiles of semi-polar phytochemicals accumulating in whole grains of eight wheat cultivars.
Question: Write a study description for the study titled 'Intestinal TM6SF2 Protects Against Metabolic Dysfunction-associated Steatohepatitis through the Gut-Liver Axis'.
Answer: Transmembrane-6 superfamily member 2 (TM6SF2) regulates hepatic fat metabolism and is closely associated with metabolic dysfunction-associated steatohepatitis (MASH). MASH involves genetic predisposition and gut microbiota alteration, yet the role of host-microbes interaction in disease development remains unclear. Here, we discover that mice with Tm6sf2 specific knockout in intestinal epithelial cells (Tm6sf2ΔIEC) developed MASH, accompanied by impaired intestinal barrier and microbial dysbiosis. Transplanting stools from Tm6sf2ΔIEC mice induce steatohepatitis in recipient germ-free mice, whereas MASH is alleviated in Tm6sf2ΔIEC mice cohoused with wildtype mice. Mechanistically, Tm6sf2-deficient intestinal cells secrete increased free fatty acids by interplaying with fatty acid-binding protein 5 to induce intestinal barrier dysfunction, pathobiont enrichment and elevated lysophosphatidic acid (LPA). LPA is further translocated to the liver, causing lipid accumulation and inflammation. Pharmacological inhibition of LPA receptor suppresses MASH in both Tm6sf2ΔIEC and wildtype mice. Hence, modulating microbiota or blocking metabolite receptor is potential therapeutics against TM6SF2 deficiency-induced MASH.
Question: Write a study description for the study titled 'Untargeted lipidomic profiling of grape highlights the importance of modified lipid species beyond the traditional compound classes'.
Answer: The aim of this paper is to provide a detailed characterisation of grape lipidome. To achieve this objective, it starts by describing a pipeline implemented in R software to allow the semi-automatic annotation of the detected lipid species. It also provides an extensive description of the different properties of each molecule (such as retention time dependencies, mass accuracy, adduct formation and fragmentation patterns), which allowed the annotations to be made more accurately. Most annotated lipids in the grape samples were (lyso)glycerophospholipids and glycerolipids, although a few free fatty acids, hydroxyceramides and sitosterol esters were also observed. The proposed pipeline also allowed the identification of a series of methylated glycerophosphates never previously observed in grapes. The current results highlight the importance of expanding chemical analyses beyond the classical lipid categories.
Question: Write a study description for the study titled 'LC-HRMS-Driven Computational Toolbox to Assess Extraction Protocols Dedicated to Untargeted Analysis: How to Ease Analyzing Pesticide-Contaminated Soils?'.
Answer: Metabolomics is a powerful approach that allows for high throughput analysis and the acquisition of large biochemical data. Nonetheless, it still faces several challenging requirements, such as the development of optimal extraction and analytical methods able to respond to its high qualitative and quantitative requisites. Hence, the objective of the present article is to suggest a LC-HRMS-based untargeted profiling approach aiming to provide performant tools that help assess the performance and the quality of extraction methods. It is applied in a herbicide-contaminated soil metabolomics context. The trifactorial experimental design consists of 150 samples issued from five different extraction protocols, two types of soils, and three contamination conditions (contaminated soils with two different formulated herbicides against uncontaminated soils). Four performance and quality criteria are investigated using adapted LC-HRMS-driven computational tools. First, 861 metabolic features are annotated, and then the width of metabolome coverage and quantitative performance of the five different extraction protocols are assessed in all samples using various optimized configurations of heatmaps as well as van Krevelen diagrams. Then, the reproducibility of LC-HRMS profiles issued from the five extractions is studied by two different approaches: Euclidean distances and relative standard deviations. The two methods are examined and compared. Their advantages and limitations are thus discussed. After, the capacity of the different extractions to discriminate between contaminated and uncontaminated soils will be evaluated using orthogonal projections to latent structures-discriminant analysis. Different data scaling parameters are tested, and the results are explored and discussed. All of the suggested computational and visualization tools are performed using public-access platforms or open-source software. They can be readapted by metabolomics developers and users according to their study contexts and fields of application.
Question: Write a study description for the study titled 'Metabolic Responses of a Model Green Microalga Euglena gracilis to Different Environmental Stresses'.
Answer: Euglena gracilis, a green microalga known as a potential candidate for jet fuel producers and new functional food resources, is highly tolerant to antibiotics, heavy metals and other environmental stresses. Its cells contain many high-value products, including vitamins, amino acids, pigments, unsaturated fatty acids and carbohydrate paramylon as metabolites, which change contents in response to various extracellular environments. However, mechanism insights into the cellular metabolic response of Euglena to different toxic chemicals and adverse environmental stresses were very limited. We extensively investigated the changes of cell biomass, pigments, lipids and paramylon of E. gracilis under several environmental stresses, such as heavy metal CdCl2, antibiotics paromomycin and nutrient deprivation. In addition, global metabolomics by ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was applied to study other metabolites and potential regulatory mechanisms behind the differential accumulation of major high-valued metabolites. This study collects a comprehensive update on the biology of E. gracilis for various metabolic responses to stress conditions, and it will be of great value for Euglena cultivation and high-value [154 mm] [10 mm] Q7 metabolite production.
Question: Write a study description for the study titled 'Clenbuterol exerts antidiabetic activity through metabolic reprogramming of skeletal muscle cells'.
Answer: Activation of the sympathetic nervous system causes pronounced metabolic changes that are mediated by multiple adrenergic receptor subtypes. Systemic treatment with β2-adrenergic receptor agonists results in multiple beneficial metabolic effects, including improved glucose homeostasis. To elucidate the underlying cellular and molecular mechanisms, we chronically treated wild-type mice and several newly developed mutant mouse strains with clenbuterol, a selective β2-adrenergic receptor agonist. Clenbuterol administration caused pronounced improvements in glucose homeostasis and prevented the metabolic deficits in mouse models of β-cell dysfunction and insulin resistance. Studies with skeletal muscle-specific mutant mice demonstrated that these metabolic improvements required activation of skeletal muscle β2-adrenergic receptors and the stimulatory G protein, Gs. Unbiased transcriptomic and metabolomic analyses showed that chronic β2-adrenergic receptor stimulation caused metabolic reprogramming of skeletal muscle characterized by enhanced glucose utilization. These findings strongly suggest that agents targeting skeletal muscle metabolism by modulating β2-adrenergic receptor-dependent signaling pathways may prove beneficial as antidiabetic drugs.
Question: Write a study description for the study titled 'NPC1 regulates the distribution of phosphatidylinositol 4 kinases at Golgi and Lysosome membranes'.
Answer: Cholesterol and phosphoinositides (PI) are two critically important lipids that are found in cellular membranes and dysregulated in many disorders. Therefore, uncovering molecular pathways connecting these essential lipids may offer new therapeutic insights. We report that loss of function of lysosomal Niemann-Pick Type C1 (NPC1) cholesterol transporter, which leads to neurodegenerative NPC disease, initiates a signaling cascade that alters the cholesterol/phosphatidylinositol 4-phosphate (PtdIns4P) countertransport cycle between Golgi-endoplasmic reticulum (ER), as well as lysosome-ER membrane contact sites (MCS). Central to these disruptions is increased recruitment of phosphatidylinositol 4-kinases-PI4KIIα and PI4KIIIβ-which boosts PtdIns4P metabolism at Golgi and lysosomal membranes. Aberrantly increased PtdIns4P levels elevate constitutive anterograde secretion from the Golgi complex, and mTORC1 recruitment to lysosomes. NPC1 disease mutations phenocopy the transporter loss of function and can be rescued by inhibition or knockdown of either key phosphoinositide enzymes or their recruiting partners. In summary, we show that the lysosomal NPC1 cholesterol transporter tunes the molecular content of Golgi and lysosome MCS to regulate intracellular trafficking and growth signaling in health and disease.
Question: Write a study description for the study titled 'Mesenchymal stromal cells secretome restores bioenergetic and redox homeostasis in human proximal tubule cells after ischemic injury'.
Answer: BACKGROUND: Ischemia/reperfusion injury (IRI) is the leading cause of acute kidney injury (AKI). The current standard of care focuses on supporting kidney function, stating the need for more efficient and targeted therapies to enhance repair. Mesenchymal Stromal Cells (MSCs) and their secretome, either as conditioned medium (CM) or extracellular vesicles (EVs), have emerged as promising options for regenerative therapy, however, their full potential in treating AKI remains unknown.METHODS: In this study, we employed an in vitro model of chemically-induced ischemia using antimycin A combined with 2-deoxy-D-glucose to induce ischemic injury in proximal tubule epithelial cells. Afterwards, we evaluated the effects of MSC secretome, CM or EVs obtained from adipose tissue, bone marrow and umbilical cord, on ameliorating the detrimental effects of ischemia. To assess the damage and treatment outcomes, we analyzed cell morphology, mitochondrial health parameters (mitochondrial activity, ATP production, mass and membrane potential) and overall cell metabolism by metabolomics.RESULTS: Our findings show that ischemic injury caused cytoskeletal changes confirmed by disruption of the F-actin network, energetic imbalance as revealed by a 50% decrease in the oxygen consumption rate, increased oxidative stress, mitochondrial dysfunction and reduced cell metabolism. Upon treatment with MSC secretome, the morphological derangements were partly restored and ATP production increased by 40-50%, with umbilical cord-derived EVs being most effective. Furthermore, MSC treatment led to phenotype restoration as indicated by an increase in cell bioenergetics, including increased levels of glycolysis intermediates, as well as an accumulation of antioxidant metabolites.CONCLUSION: Our in vitro model effectively replicated the in vivo-like morphological and molecular changes observed during ischemic injury. Additionally, treatment with MSC secretome ameliorated proximal tubule damage, highlighting its potential as a viable therapeutic option for targeting AKI.
Question: Write a study description for the study titled 'Exposure to environmental hazard pesticide rotenone triggers redox driven system-wide lipidome alterations and metabolic trade-offs linked to Parkinson’s disease'.
Answer: With the global rise in aging populations, the increasing incidence of neurodegenerative diseases underscores concerns about brain health, with pesticides like rotenone, emerging as key environmental hazardous. The precise mechanism by which chronic environmental concentration of rotenone exposure causes Parkinson-like phenotype is not understood. Previous studies showed that rotenone induces depletion of dopaminergic neurons by influencing mitochondrial functions. Mitochondrial dysfunction alters lipid homeostasis; therefore, brain lipids can be potential targets for the early risk assessment and prognosis of Parkinson’s disease (PD). However, the specific lipidome changes and associated biomarkers of chronic rotenone in vivo exposure causing PD are largely unknown. This study investigates the lipid profile disruptions and biomarkers induced by environmentally relevant concentrations of chronic rotenone exposure using the neuro-model Drosophila melanogaster. An untargeted LC-HRAMS-based lipidomics identified that lipid classes, GP, SP, FA and GL were significantly altered. Furthermore, system-wide loss of cross talk of mitochondrial and peroxisome lipids by altering their redox homeostasis causing PD was observed. Additionally, lipid oxidative stress markers, and behavior abnormalities correlated with altered lipids linked to PD. The findings highlight the rotenone induced complex metabolic trade-offs, prioritizing brain’s neural integrity at the expense of peripheral lipid levels, leading to PD.
Question: Write a study description for the study titled '1H-NMR-Based Analysis for Exploring Knee Synovial Fluid Metabolite Changes after Local Cryotherapy in Knee Arthritis Patients'.
Answer: Rehabilitation using cryotherapy has widely been used in inflammatory diseases to relieve pain and decrease the disease activity. The aim of this study was to explore the metabolite changes in inflammatory knee-joint synovial fluids following local cryotherapy treatment (ice or cold CO2). We used proton nuclear magnetic resonance (1H NMR) spectroscopy to assess the metabolite patterns in synovial fluid (SF) in patients with knee arthritis (n = 46) before (D0) and after (D1, 24 h later) two applications of local cryotherapy. Spectra from aqueous samples and organic extracts were obtained with an 11.75 Tesla spectrometer. The metabolite concentrations within the SF were compared between D1 and D0 using multiple comparisons with the application of a false discovery rate (FDR) adjusted at 10% for each metabolite. A total of 32 metabolites/chemical structures were identified including amino acids, organic acids, fatty acids or sugars. Pyruvate, alanine, citrate, threonine was significantly higher at D1 vs D0 (p  0.05). The present study provides new insight into a short-term effect of cold stimulus in synovial fluid from patients with knee arthritis. Our observations suggest that the increased level of metabolites involved in energy metabolism may explain the underlying molecular pathways that mediate the antioxidant and anti-inflammatory capacities of cryotherapy.
Question: Write a study description for the study titled 'The Metabolic Fate of Oxaliplatin in the Biological Milieu Investigated During In Vivo Lung Perfusion Using a Unique Miniaturized Sampling Approach Based on Solid-Phase Microextraction Coupled with Liquid Chromatography-Mass Spectrometry'.
Answer: Adjuvant chemotherapy after pulmonary metastasectomy for colorectal cancer may reduce recurrence and improve survival rates; however, the benefits of this treatment are limited by the significant side effects that accompany it. The development of a novel in vivo lung perfusion (IVLP) platform would permit the localized delivery of high doses of chemotherapeutic drugs to target residual micrometastatic disease. Nonetheless, it is critical to continuously monitor the levels of such drugs during IVLP administration, as lung injury can occur if tissue concentrations are not maintained within the therapeutic window.This paper presents a simple chemical-biopsy approach based on sampling with a small nitinol wire coated with a sorbent of biocompatible morphology and evaluates its applicability for the near-real-time in vivo determination of oxaliplatin (OxPt) in a 72-hour porcine IVLP survival model. To this end, the pigs underwent a 3-hour left lung IVLP with 3 doses of the tested drug (5, 7.5, and 40 mg/L), which were administered to the perfusion circuit reservoir as a bolus after a full perfusion flow had been established. Along with OxPt levels, the biocompatible solid-phase microextraction (SPME) probes were employed to profile other low-molecular-weight compounds to provide spatial and temporal information about the toxicity of chemotherapy or lung injury.The resultant measurements revealed a rather heterogeneous distribution of OxPt (over the course of IVLP) in the two sampled sections of the lung. In most cases, the OxPt concentration in the lung tissue peaked during the 2nd hour of IVLP, with this trend being more evident in the upper section. In turn, OxPt in supernatant samples represented ~25% of the entire drug after the first hour of perfusion, which may be attributable to the binding of OxPt to albumin, its sequestration into erythrocytes, or its rapid nonenzymatic biotransformation. Additionally, the Bio-SPME probes also facilitated the extraction of various endogenous molecules for the purpose of screening biochemical pathways affected during IVLP (i.e., lipid and amino acid metabolism, steroidogenesis, or purine metabolism).Overall, the results of this study demonstrate that the minimally invasive SPME-based sampling approach presented in this work can serve as (pre)clinical and precise bedside medical tool.
Question: Write a study description for the study titled 'Multi-omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer'.
Answer: Endometrial cancer (EC) is one of the most common gynecological cancers. Finding biomarkers of EC can support its diagnosis in a non- or minimally-invasive way. In this work, we integrated metabolomics and proteomics for the analysis of multiple types of biosamples to gain a more comprehensive view on the altered metabolism in EC patients, and to demonstrate the potential of metabolite biomarker-based EC diagnosis. Based on the differential metabolites and proteins between EC patients and controls detected in the endometrial tissue samples, EC related significant pathways, such as amino acid metabolism and nucleotide metabolism, were identified. Then, the significance of the pathways was further demonstrated by metabolomic analysis of urine and intrauterine brushings samples. We also demonstrated the potential of EC diagnosis by metabolite biomarkers in urine or intrauterine brushings samples. This study provides a network explanation of the metabolic changes of EC with the verification by multi-omics and multi-biosamples, and further demonstrates the potential of non- or minimally-invasive biopsy for EC diagnosis in the future.
Question: Write a study description for the study titled 'The Arabidopsis Concert of Metabolic Acclimation to High Light Stress'.
Answer: In plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time-course experiments spanning 2 minutes to 72 hours with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labelling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well-orchestrated mechanisms contributing to high light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. Their accumulation in vacuoles surpasses plastidic levels and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2-oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the TCA cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.