LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A Python-based pipeline for preprocessing LC-MS data for untargeted metabolomics workflows'.
Answer: Preprocessing data in a reproducible and robust way is one of the current challenges in untargeted metabolomics workflows. Data curation in liquid chromatography-mass spectrometry (LC-MS) involves the removal of unwanted features (retention time; m/z pairs) to retain only high-quality data for subsequent analysis and interpretation. The present work introduces a package for the Python programming language for pre-processing LC-MS data for quality control procedures in untargeted metabolomics workflows. It is a versatile strategy that can be customized or fit for purpose according to the specific metabolomics application. It allows performing quality control procedures to ensure accuracy and reliability in LC-MS measurements, and it allows preprocessing metabolomics data to obtain cleaned matrices for subsequent statistical analysis. The capabilities of the package are showcased with pipelines for an LC-MS system suitability check, system conditioning, signal drift evaluation, and data curation. These applications were implemented to preprocess data corresponding to a new suite of plasma candidate plasma reference materials developed by the National Institute of Standards and Technology (NIST; hypertriglyceridemic, diabetic, and African-American plasma pools) to be used in untargeted metabolomics studies. in addition to NIST SRM 1950 – Metabolites in Frozen Human Plasma. The package offers a rapid and reproducible workflow that can be used in an automated or semi-automated fashion, and it is an open and free tool available to all users.
Question: Write a study description for the study titled 'Enterobacter ludwigii protects DSS-induced colitis through choline-mediated immune tolerance'.
Answer: Commensal intestinal bacteria play key roles in regulating cells mediating immune tolerance; however, bacterial strains and related metabolites directly involved in this regulation are largely unknown. Here, using a mouse model of dextran sulfate sodium (DSS)-induced colitis combined with different antibiotic treatment, Enterobacter ludwigii, abundant in microbiota of mice treated with metronidazole, was screened out to have prophylactic and therapeutic effects on DSS-induced colitis with or without the presence of complex intestinal bacteria. E. ludwigii was demonstrated to induce CD103+DC and Treg-mediated immune tolerance for colitis remission using in vitro and in vivo experiments. Moreover, choline, one of E. ludwigii metabolites, was identified to increase DCs’ immune tolerance to promote Treg differentiation. E. ludwigii was found to induce DCs’ immune tolerance ability for Treg differentiation through choline and α7nAChR-mediated RA and TGF-β upregulation, resulting in protecting mice against DSS-induced colitis. This study provides potential therapeutic approaches for IBD.
Question: Write a study description for the study titled 'Illuminating the dark space of neutral glycosphingolipidome by selective enrichment and profiling at multi-structural levels'.
Answer: Glycosphingolipids (GSLs) are essential components of cell membranes, particularly enriched in the nervous system. Altered molecular distributions of GSLs are increasingly associated with human diseases, emphasizing the significance of lipidomic profiling. Traditional GSL analysis methods are hampered by matrix effect from phospholipids and the difficulty in distinguishing structural isomers. Herein, we introduce a highly sensitive workflow that harnesses magnetic TiO2 nanoparticle-based selective enrichment, charge-tagging Paternò–Büchi reaction, and liquid chromatography-tandem mass spectrometry. This approach enables mapping over 300 distinct GSLs in brain tissues by defining sugar types, long chain bases, N-acyl chains, and the locations of desaturation and hydroxylation. Relative quantitation of GSLs across multiple structural levels provides evidence of dysregulated gene and protein expressions of FA2H and CerS2 in human glioma tissue. Based on the structural features of GSLs, our method accurately differentiates human glioma with/without isocitrate dehydrogenase genetic mutation, and normal brain tissue.
Question: Write a study description for the study titled 'Metabolic signatures of Arabidopsis thaliana abiotic stress responses elucidate patterns in stress priming, acclimation, and recovery'.
Answer: Temperature, water and light are 3 abiotic stress factors that have major influences on plant growth, development and reproduction. Plants can be primed by a prior mild stress to enhance their resistance to future stress. We used an untargeted metabolomics approach to examine Arabidopsis thaliana 11-day-old seedling’s abiotic stress responses including heat (with and without priming), cold (with and without priming), water-deficit and high-light before and after a 2-day recovery period. Analysis of the physiological phenotypes showed that seedlings with stress treatment resulted in a reduction in fresh weight, hypocotyl and root length but remained viable. Several stress responsive metabolites were identified, confirmed with reference standards, quantified and clustered. We identified shared and specific stress signatures for cold, heat, water-deficit and high-light treatments. Central metabolism including amino acid metabolism, sugar metabolism, glycolysis, TCA cycle, GABA shunt, glutathione metabolism, purine metabolism and urea cycle were found to undergo changes that are fundamentally different, although some shared commonalities in response to different treatments. Large increases in cysteine abundance and decreases in reduced glutathione were observed following multiple stress treatments highlighting the importance of oxidative stress as a general phenomenon in abiotic stress. Large fold increases in low-turnover amino acids and maltose demonstrate the critical role of protein and starch autolysis in early abiotic stress responses.
Question: Write a study description for the study titled 'Exploring Lipidomic Profiles and Their Correlation with Hormone Receptor and HER2 Status in Breast Cancer'.
Answer: Dysregulated lipid metabolism promotes the progression of various cancers, including breast cancer. This study aimed to explore the lipidomic profiles of breast cancer patients, providing insights into the correlation between lipid compositions and tumor subtypes characterized by hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status. Briefly, 30 breast cancer patients were categorized into four cohorts based on their HR and HER2 status: HR+, HER2 zero (HR+ HER2-0); HR+, HER2 low (HR+ HER2-low); HR+, HER2 pos (HR+ HER2-pos); and HR-, HER2 positive (HR- HER2-pos). Lipidomic profiles were analyzed using high-throughput liquid chromatography-mass spectrometry (LC-MS). Data were processed through principal component analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Random Forest (RF) classification to assess lipidomic variations and significant lipid features among these groups. Profiles of lipids, particularly triglycerides (TG) such as TG (16:0_18:1_18:1) +NH4, were significantly different across the cohorts. PCA and PLS-DA analyses identified unique lipid profiles in the HR+ HER2-pos and HR+ HER2-0 groups, while RF highlighted PIP3(21:2)+NH4 as a crucial lipid feature for accurate patient grouping. Advanced statistical analysis showed significant correlations between lipid carbon chain length and the number of double bonds with the classifications, providing insights into the role of structural lipid properties in tumor biology. Additionally, a clustering heatmap and network analysis indicated significant lipid-lipid interactions. Pathway enrichment analysis showed critical biological pathways, such as the assembly of active LPL and LIPC lipase complexes. In conclusion, the study underscores the importance of lipidomic profiling is crucial in understanding the metabolic alterations associated with different breast cancer subtypes. These findings highlight specific lipid features and interactions that may serve as potential biomarkers for breast cancer classification and target pathways for therapeutic intervention. Furthermore, advanced lipidomic analyses can be integrated to decipher complex biological data, offering a foundation for further research into the role of lipid metabolism in cancer progression.
Question: Write a study description for the study titled 'The maturity in fetal pigs using a multi-fluid metabolomic approach'.
Answer: In mammalian species, the first days after birth are an important period for survival and the rates of mortality before weaning are high. In pigs, the perinatal deaths average 20% of the litter, with important economic and societal consequences. Among the factors influencing piglet survival at birth, the maturity is likely to be one of the most important. Maturity can be defined as the outcome of complex mechanisms of intra-uterine development and maturation occurring during the last month of gestation. Here, we provide new insights on maturity by studying the end of gestation at two different stages (three weeks before term and close to term) in two breeds of pigs that strongly differ in terms of neonatal survival. Since metabolomics is a promising approach for phenotype characterization or biomarker discovery, we provide a complete understanding of the metabolome of the fetuses in late gestation in three fluids (plasma, urine, and amniotic fluid). We found that biological processes related to amino acid and carbohydrate metabolisms are critical for piglet maturity. We also confirmed some previously described metabolites associated with delayed growth. Altogether, our study proposes new routes for a better characterization of piglet maturity at birth.
Question: Write a study description for the study titled 'Rapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida'.
Answer: Members of the genus Candida, such as C. albicans and C. parapsilosis, are important human pathogens. Other members of this genus, previously believed to carry minimal disease risk, are increasingly recognised as important human pathogens, particularly because of variations in susceptibilities to widely used anti-fungal agents. Thus, rapid and accurate identification of clinical Candida isolates is fundamental in ensuring timely and effective treatments are delivered. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has previously been shown to provide a high-throughput platform for the rapid and accurate identification of bacterial and fungal isolates. In comparison to commercially available matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF), REIMS based methods require no preparative steps nor time-consuming cell extractions. Here, we report on the ability of REIMS-based analysis to rapidly and accurately identify 153 clinical Candida isolates to species level. Both handheld bipolar REIMS and high-throughput REIMS platforms showed high levels of species classification accuracy, with 96% and 100% of isolates classified correctly to species level respectively. In addition, significantly different (FDR corrected P value < 0.05) lipids within the 600 to 1000 m/z mass range were identified, which could act as species-specific biomarkers in complex microbial communities.
Question: Write a study description for the study titled 'From grape berries to wines: drought impacts on key secondary metabolites'.
Answer: AIM: We aimed to study the impact of water deficit on the concentration of key flavour and phenolic secondary metabolites of wines.METHODS AND RESULTS: A drought-stress field trial was conducted on Vitis vinifera cv. Merlot and Tocai Friulano for two seasons. Fully irrigated (C) and deficit irrigated (D) grapes were microvinified and the resulting wines were analysed to determine the concentrations of anthocyanins, tannins, and free and glycosidically-bound Volatile Organic Compounds (VOCs). A descriptive sensory test was undertaken on the same wines. Water stressed grapes produced wines with higher concentrations of anthocyanins in Merlot and of free and glycosidically-bound monoterpenes in Tocai Friulano. Both cultivars displayed higher amounts of glycosidically-bound C13-norisoprenoids.CONCLUSIONS: Previously observed drought-induced compositional changes to the grapes were transfered to the wines, with an increase in polyphenols and VOCs. However, the timing and the duration of the water stress in the field only heavily impacted the final wine composition with major metabolic modification when the severe water deficit started early (at approximately 40 days after anthesis) and lasted over the entire season until harvest. SIGNIFICANCE AND IMPACT OF THE STUDY: This study highlights the positive role of a controlled water deficit on the composition of the wines in terms of secondary metabolites.
Question: Write a study description for the study titled 'Physiological and Molecular Dissection of Daily Variance in Exercise Capacity'.
Answer: Physical performance relies on the concerted action of myriad responses, many of which are under circadian clock control. Little is known, however, regarding the time-dependent effect on exercise performance at the molecular level. We found that both mice and humans exhibit daytime variance in exercise capacity between the early and late part of their active phase. The daytime variance in mice was dependent on exercise intensity and relied on the circadian clock proteins PER1/2. High-throughput gene expression and metabolic profiling of skeletal muscle revealed metabolic pathways that are differently activated upon exercise in a daytime-dependent manner. Remarkably, we discovered that ZMP, an endogenous AMPK activator, is induced by exercise in a time-dependent manner to regulate key steps in glycolytic and fatty acid oxidation pathways and potentially enhance exercise capacity. Overall, we propose that time of day is a major modifier of exercise capacity and associated metabolic pathways.
Question: Write a study description for the study titled 'FOXK1 and FOXK2 Promote Cardiomyocyte Proliferation and Heart Regeneration'.
Answer: Promoting the proliferation of endogenous cardiomyocytes represents a promising strategy for treating cardiac injuries. Identifying key factors that regulate cardiomyocyte proliferation can advance the development of novel therapies for heart regeneration. Here we identify that FOXK1 and FOXK2 act as master regulators of cardiomyocyte proliferation and metabolism. The expression of FOXK1 and FOXK2 decreased with postnatal heart development. Cardiomyocyte-specific knockout of Foxk1 or Foxk2 inhibited neonatal heart regeneration after myocardial infarction (MI) injury. Conversely, AAV9-mediated cardiomyocyte-specific overexpression of FOXK1 or FOXK2 prolonged the postnatal proliferative window of cardiomyocytes and enhanced cardiac repair in adult mice by promoting endogenous cardiomyocyte proliferation after MI. Mechanistically, FOXK1 and FOXK2 induce Ccnb1 and Cdk1 transcription and cardiomyocyte cell cycle progression, respectively. Ccnb1 knockdown hindered FOXK1 overexpression-induced cardiomyocyte proliferation, and the same effect was observed when Cdk1 was knocked down in FOXK2 overexpressing cardiomyocytes. Additionally, we further revealed that FOXK1 and FOXK2 induced a metabolic shift toward glycolysis by promoting HIF1α expression in cardiomyocytes, which favors cardiomyocyte proliferation. Our findings identify FOXK1 and FOXK2 as critical triggers of cardiomyocyte proliferation and define these two transcription factors as novel therapeutic targets for myocardial infarction.
Question: Write a study description for the study titled 'Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria'.
Answer: Malaria, caused by Plasmodium species, remains a significant cause of morbidity and mortality globally. Gut bacteria can influence the severity of malaria, but the contribution of specific bacteria to the risk of severe malaria is unknown. Here, multiomics approaches demonstrate specific species of Bacteroides are causally linked to the risk of severe malaria. Plasmodium yoelii hyperparasitemia-resistant mice gavaged with murine-isolated Bacteroides fragilis develop P. yoelii hyperparasitemia. Moreover, Bacteroides are significantly more abundant in Ugandan children with severe malarial anemia than with asymptomatic P. falciparum infection. Human isolates of Bacteroides caccae, Bacteroides uniformis, and Bacteroides ovatus but not Bacteroides thetaiotaomicron caused susceptibility to severe malaria in mice. However, the pathogenic potential of gut Bacteroides towards susceptibility to severe malaria is dependent on additional gut microbiota, indicating a consortium effect in severe malaria. Approaches that target gut Bacteroides may present an opportunity to prevent severe malaria and associated deaths.
Question: Write a study description for the study titled 'Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit (Carotenoids; UPLC-DAD assay)'.
Answer: Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.UPLC-DAD assay of Carotenoids is reported in the current study MTBLS984SPME-GC-MS assay of Volatile organic compounds is reported in MTBLS982UPLC-MS/MS assay of Phenolics is reported in MTBLS898
Question: Write a study description for the study titled 'Metabolomic Analysis of the Metabolome of Fusobacterium mortiferum'.
Answer: We cultured Fusobacterium mortiferum and performed metabolomic identification using BHI broth as a control group.
Question: Write a study description for the study titled 'Targeting the Ceramidase ACER3 Attenuates Cholestasis in Mice by Mitigating Bile Acid Overload via Unsaturated Ceramide-mediated LXRβ Signaling Transduction'.
Answer: In this work, we show that ACER3 expression is upregulated in cholestatic livers and positively correlates with the severity of CLI in patients. Targeting ACER3 increases CER(d18:1/18:1) in the cholestatic liver, which binds to LXRβ and activates its signaling transduction to enhance BA sulfation and restore lipogenesis. These mechanisms mitigate BA overload in hepatocytes and attenuate CLI. Our findings highlight the therapeutic potential of targeting ACER3 and CER(d18:1/18:1) to attenuate CLI.
Question: Write a study description for the study titled 'The natural variance of the Arabidopsis floral secondary metabolites'.
Answer: Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as transcripts, proteins and growth and flowering related phenotypes.