LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Effects of hypoxic preconditioning on neuroblastoma tumour oxygenation and metabolic signature in a chick embryo model'.
Answer: Hypoxia episodes and areas in tumours have been associated with metastatic dissemination and poor prognosis. Given the link between tumour tissue oxygen levels and cellular metabolic activity, we hypothesised that the metabolic profile between metastatic and non-metastatic tumours would reveal potential new biomarkers and signalling cues. We have used a previously established chick embryo model for neuroblastoma growth and metastasis, where the metastatic phenotype can be controlled by neuroblastoma cell hypoxic preconditioning (3 days at 1% O2). We measured, with fibre-optic oxygen sensors, the effects of the hypoxic preconditioning on the tumour oxygenation, within tumours formed by SK-N-AS cells on the chorioallantoic membrane (CAM) of chick embryos. We found that the difference between the metastatic and non-metastatic intratumoural oxygen levels was small (0.35% O2), with a mean below 1.5% O2 for most tumours. The metabolomic profiling, using NMR spectroscopy, of neuroblastoma cells cultured in normoxia or hypoxia for 3 days, and of the tumours formed by these cells showed that the effects of hypoxia in vitro did not compare with in vivo tumours. One notable difference was the high levels of the glycolytic end-products triggered by hypoxia in vitro, but not by hypoxia preconditioning in tumours, likely due to the very high basal levels of these metabolites in tumours compared with cells. In conclusion, we have identified high levels of ketones (3-hydroxybutyrate), lactate and phosphocholine in hypoxic preconditioned tumours, all known to fuel tumour growth, and we herein point to the poor relevance of in vitro metabolomic experiments for cancer research.
Question: Write a study description for the study titled 'Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants'.
Answer: Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system.
Question: Write a study description for the study titled 'Targeting lung microbiota with Lactobacillus aerosolization: a novel strategy to alleviate inflammation and enhance productivity in broilers'.
Answer: Background In large-scale poultry farming, broilers of the same breed, sharing a common genetic background and identical management conditions, nevertheless exhibit considerable individual variation in body weight. Multitudinous stressors can profoundly influence the host microbiota, thereby modulating overall health and growth. This study employed multi-omics approaches to elucidate the underlying factors contributing to the disparities between high- and low-weight broilers and to evaluate the effects of Lactobacillus aerosolization on growth performance and systemic inflammation in these animals.Results This study identified distinct plasma proteomic profiles between high- and low-weight broilers, with the latter exhibiting a systemic inflammatory response. Gut microbiota differences were minimal, and fecal microbiota transplantation did not alter broiler body weight. However, lung microbiota analysis revealed a higher relative abundance of Lactobacillus in high-weight broilers, linked to altered plasma tryptophan metabolism. Aerosolized Lactobacillus reuteri C501, Lacticaseibacillus rhamnosus UA260, and their combination enhanced growth and mitigated LPS-induced inflammation. This intervention increased L-Tryptophan (L-Trp), indoleacrylic acid (IAA), and indole-3-carboxaldehyde (I3C) levels in plasma and bronchoalveolar lavage fluid (BALF). Mechanistic studies showed that IAA and I3C activated the AHR pathway, promoting SOCS3 expression in macrophages, inhibiting JAK2/STAT3 signaling, and alleviating LPS-induced inflammation.Conclusions Aerosolization of Lactobacillus enhances broiler performance and alleviates LPS-induced stress responses. This effect is mediated through the modulation of tryptophan metabolism, which interacts with the AHR/SOCS3 axis to inhibit JAK2/STAT3 signaling, thereby reducing both pulmonary and systemic inflammation. Our findings provide insights into the interaction between poultry production and lung microbiota, establishing Lactobacillus aerosolization as a promising strategy to combat systemic inflammation and improve poultry health and performance.
Question: Write a study description for the study titled 'Distribution of RESV and its metabolite peaks in mouse tissues after oral and skin administration'.
Answer: Resveratrol (RESV) is a plant polyphenol, which is thought to have beneficial metabolic effects in laboratory animals as well as in humans. Following oral administration, RESV is immediately catabolized, resulting in low bioavailability. This study compared RESV metabolites and their tissue distribution after oral uptake and skin absorption. Metabolomic analysis of various mouse tissues revealed that RESV can be absorbed and metabolized through skin. We detected sulfated and glucuronidated RESV metabolites, as well as dihydroresveratrol. These metabolites are thought to have lower pharmacological activity than RESV. Similar quantities of most RESV metabolites were observed 4 h after oral or skin administration, except that glucuronidated RESV metabolites were more abundant in skin after topical RESV application than after oral administration. This result is consistent with our finding of glucuronidated RESV metabolites in cultured skin cells. RESV applied to mouse ears significantly suppressed inflammation in the TPA inflammation model. The skin absorption route could be a complementary, potent way to achieve therapeutic effects with RESV.  RESV (1 mg in 200 µl saline) was orally administered to hairless mice or 1 mg RESV dissolved in ethanol was applied on the dorsal skin of hairless mice. After 4 h mice were sacrificed, metabolites were extracted from the tissues and analyzed by the LC-MS. Peak areas of metabolites were normalized by the peak areas of spiked internal standards (10 nmol 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and piperazine-N,N’-bis(2-ethanesulfonic acid) (PIPES).
Question: Write a study description for the study titled 'FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry - simulated Imaging MS (Imaging simulation assay)'.
Answer: High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites directly from tissues, cell cultures, and agar plates with cellular resolution, but is hampered by the lack of bioinformatics for automated metabolite identification. We developed the first bioinformatics framework for False Discovery Rate (FDR)-controlled metabolite annotation for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM) introducing a Metabolite-Signal Match (MSM) score and a target-decoy FDR-estimate for spatial metabolomics. MALDI-FTICR datasets acquired from normal rat brain were used for the development of spatial metabolomics annotation bioinformatics. This study together with MTBLS313 and MTBLS378 provide the accompanying data for FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.
Question: Write a study description for the study titled 'Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Spatial metabolomics_LCM]'.
Answer: Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
Question: Write a study description for the study titled 'Examination of human osteoarchaeological remains as a feasible source of polar and apolar metabolites to study past conditions'.
Answer: Metabolomics is a modern tool that aids in our understanding of the molecular changes in organisms. Archaeological science is a branch of archaeology that explores different archaeological materials using modern analytical tools. Human osteoarchaeological material are a frequent finding in archaeological contexts and have the potential to offer information about previous human populations, which can be illuminating about our current condition. Using a set of samples comprising different skeletal elements and bone structures, here we explore for the first time the possibility of extracting metabolites from osteoarchaeological material. Here, a protocol for extraction and measurement of extracted polar and less-polar/apolar metabolites by ultra-high performance liquid chromatography hyphenated to high resolution mass spectrometry is presented to measure the molecules separated after a reversed phase and hydrophilic interaction liquid chromatography column. Molecular information was obtained, showing that osteoarchaeological material is a viable source of molecular information for metabolomic studies.
Question: Write a study description for the study titled 'Correlation-based Deconvolution (CorrDec) to generate high quality MS2 spectra from data independent acquisition in multi-sample studies (Chemical standards assay)'.
Answer: Data-independent acquisition mass spectrometry (DIA-MS) is essential for information-rich spectral annotations in untargeted metabolomics. However, the acquired MS2 spectra are highly complex, posing significant annotation challenges. We have developed a correlation-based deconvolution (CorrDec) method that uses ion abundance correlations in multi-sample studies using DIA-MS as an update of our MS-DIAL software. CorrDec is based on the assumption that peak intensities of precursor and fragment ions correlate across samples, and exploits this quantitative information to deconvolute complex DIA spectra. CorrDec clearly improved deconvolution of the original MS-DIAL deconvolution method (MS2Dec) in a dilution series of chemical standards and a 224-sample urinary metabolomics study. The primary advantage of CorrDec over MS2Dec is the ability to discriminate co-eluting low-abundance compounds. CorrDec requires the measurement of multiple samples to successfully deconvolute DIA spectra, and our randomized assessment demonstrated that CorrDec can contribute to studies with as few as 10 unique samples. The presented methodology improves compound annotation and identification in multi-sample studies and will be useful for applications in large cohort studies.Chemical standards assay is reported in the current study MTBLS787.Urine assay is reported in MTBLS816.
Question: Write a study description for the study titled 'Towards a semi-automated metabolic profile analysis of fish blood plasma by 1H NMR'.
Answer: Aquafeed is one of the main costs in aquaculture and major efforts are being made to find sustainable ingredients that could improve production sustainability and efficiency. Our research focused on the inclusion of glycerol in the feed of European seabass (Dicentrarchus labrax), as it is a cheap carbon substrate expected to enter metabo- lism through the glycolytic pathway. The Nuclear Magnetic Resonance (NMR) spectroscopy provides accurate and high-throughput metabolic profiles, allowing quantification and evaluation of the effects of experimental diets in the context of fish nutrition. The aim of the present study was to assess the applicability of the automated on-line profiling routine Bayesil to fish blood plasma and compare with the manual targeted metabolite profiling approach. After a 60-day feeding trial (0%, 2.5%, 5.0% glycerol supplemented diets), fish were sacrificed at 6 h and 24 h after last meal and blood was sampled. Filtered plasma samples were analysed by NMR, followed by two metabolite-profiling approaches: i) an automated spectral profiling provided by the Bayesil platform, and ii) a manual metabolite profiling. Spectra were analysed with the automated Bayesil routine, identifying and quantifying 51 metabolites, in a reproducible, fast and user-independent method. On the other hand, the manual approach only managed to quantify 20 metabolites. However, under supraphysiological concentrations of glycerol, namely in the 5.0% diet, the Bayesil algorithm was not able to properly integrate the glycerol and glycine signals. The Bland-Altman and PLS-DA analysis revealed differences; nonetheless, with the exception of acetic acid, creatinine, formate, glutamine and threonine, all other metabolites presented a low bias and/or a strong correlation coefficient. Overall, it is expected a reasonable tradeoff between the accuracy in metabolite quantification and the increase of variables.The automated Bayesil database may be applied as a useful tool for systematic monitoring of fish plasma profile in aquaculture research and industrial quality control analysis, to generate robust variance-based multivariate statistical models. To our knowledge, this is the first time a NMR-based high-throughput automated routine is evaluated in aquaculture research.
Question: Write a study description for the study titled 'Unraveling the Mechanisms of Propofol-Induced Psychological Dependence: A Multi-Omics Approach Linked to Gut Microbiota in Hippocampal Function'.
Answer: Introduction: Drug abuse is becoming a global public health crisis. According to the United Nations, the number of drug users worldwide has increased dramatically over the past decade, with a surge in the number of drug abusers. The problem was exacerbated by the expanding market for illicit drugs and the increasing availability of synthetic drugs such as fentanyl. Clinical drug abuse is a problem that requires particular attention, and the potential addictive properties of some drugs and their mechanisms of action are currently unknown, which limits the development and implementation of drug addiction intervention strategies.Methods: Eight-week-old C57BL/6J mice were used as study subjects. A mental dependence model was established using the conditional position preference experiment (CPP), and the hippocampal tissues of the model mice were subjected to RNA-seq transcriptome sequencing, LC-MS non-targeted metabolome sequencing and intestinal macro-genome sequencing in order to discover propofol mental dependence signature genes. Correlation analyses of transcriptomics and metabolomics were performed using the Spearman method, and gene-metabolite networks were mapped using Cytoscape software. Real-time fluorescence quantitative PCR and immunoprotein blotting (Western blotting) methods were used to validate the characterized genes.Results: After the conditioned position preference experiment, the conditioned preference scores of the 75 mg/kg propofol and 2 g/kg alcohol groups were significantly higher than those of the control saline group. 152 differential genes and 214 differential metabolites were identified in the 75 mg/kg group. Cluster analysis revealed that changes in the neuroactive ligand receptor pathway were most pronounced. Gut microbiomics assays revealed significant changes in five differential enterobacterial phyla (Campylobacter phylum, Thick-walled phylum, Anaplasma phylum, Actinobacteria phylum, and Chlorella verticillata phylum) in the 75 mg/kg propofol group, which may be related to changes in the differential expression of dopamine.
Question: Write a study description for the study titled 'Gut symbiotic bacteria-derived nicotinic acid regulates Bactrocera dorsalis reproduction'.
Answer: Depletion of gut commensal bacteria significantly reduced nicotinic acid (NA) levels in the hemolymph and ovaries of Bactrocera dorsalis, leading to impaired ovarian development. This inhibition was reversed by exogenous NA supplementation. We identified Enterobacter hormaechei as a key NA-producing gut symbiont. Recolonization with E. hormaechei restored NA levels in both the hemolymph and ovaries, thereby rescuing ovarian development in B. dorsalis.
Question: Write a study description for the study titled 'A microfluidics-based in vitro model of the gastrointestinal human-microbe interface'.
Answer: Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human–microbial crosstalk), which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal human–microbe interface. We demonstrate the ability of HuMiX to recapitulate in vivo transcriptional, metabolic and immunological responses in human intestinal epithelial cells following their co-culture with the commensal Lactobacillus rhamnosus GG (LGG) grown under anaerobic conditions. In addition, we show that the co-culture of human epithelial cells with the obligate anaerobe Bacteroides caccae and LGG results in a transcriptional response, which is distinct from that of a co-culture solely comprising LGG. HuMiX facilitates investigations of host–microbe molecular interactions and provides insights into a range of fundamental research questions linking the gastrointestinal microbiome to human health and disease.
Question: Write a study description for the study titled 'Integrated Metabolomic and Transcriptomic Profiling Reveals Novel Activation-Induced Metabolic Networks in Human T cells'.
Answer: The targeting of metabolic pathways is emerging as an exciting new approach for modulating immune cell function and polarization states. In this study, carbon tracing and systems biology approaches integrating metabolomic and transcriptomic profiling data were used to identify adaptations in human T cell metabolism important for fueling pro-inflammatory T cell function. Results of this study demonstrate that T cell receptor (TCR) stimulation leads to a significant increase in glucose and amino acid metabolism that trigger downstream biosynthetic processes. Specifically, increased expression of several enzymes such as CTPS1, IL4I1, and ASL results in the reprogramming of amino acid metabolism. Additionally, the strength of TCR signaling resulted in different metabolic enzymes utilized by T cells to facilitate similar biochemical endpoints. Furthermore, this study shows that cyclosporine represses the pathways involved in amino acid and glucose metabolism, providing novel insights on the immunosuppressive mechanisms of this drug. To explore the implications of the findings of this study in clinical settings, conventional immunosuppressants were tested in combination with drugs that target metabolic pathways. Results showed that such combinations increased efficacy of conventional immunosuppressants. Overall, the results of this study provide a comprehensive resource for identifying metabolic targets for novel combinatorial regimens in the treatment of intractable immune diseases.
Question: Write a study description for the study titled 'Diagnostic Potential of Plasma IgG N-glycans in Discriminating Thyroid Cancer from Benign Thyroid Nodules and Healthy Controls'.
Answer: BACKGROUND: Novel biomarkers are urgently needed to distinguish between benign and malignant thyroid nodules and detect thyroid cancer in the early stage. The associations between serum IgG N-glycosylation and thyroid cancer risk have been revealed. We aimed to explore the potential of IgG N-glycan traits as biomarkers in the differential diagnosis of thyroid cancer.METHODS: Plasma IgG N-glycome analysis was applied to a discovery cohort followed by independent validation. IgG N-glycan profiles were obtained using a robust quantitative strategy based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. IgG N-glycans were relatively quantified, and classification performance was evaluated based on directly detected and derived glycan traits.RESULTS: Four directly detected glycans were significantly changed in thyroid cancer patients compared to that in non-cancer controls. Derived glycan traits and a classification glycol-panel were generated based on the directly detected glycan traits. In the discovery cohort, derived trait BN (bisecting type neutral N-glycans) and the glyco-panel showed potential in distinguishing between thyroid cancer and non-cancer controls with AUCs of 0.920 and 0.917, respectively. The diagnostic potential was further validated. Derived trait BN and the glycol-panel displayed “accurate” performance (AUC>0.8) in discriminating thyroid cancer from benign thyroid nodules and healthy controls in the validation cohort. Meanwhile, derived trait BN and the glycol-panel also showed diagnostic potential in detecting early-stage thyroid cancer.CONCLUSIONS: IgG N-glycome analysis revealed N-glycomic differences that allow classification of thyroid cancer from non-cancer controls. Our results suggested that derived trait BN and the classification glyco-panel rather than single N-glycans may serve as candidate biomarkers for further validation.