LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer'.
Answer: Lung cancer remains the most common cause of cancer deaths worldwide, yet there is currently a lack of diagnostic noninvasive biomarkers that could guide treatment decisions. Small molecules (<1500 Da) were measured in urine collected from 469 lung cancer patients and 536 population controls using unbiased liquid chromatography-mass spectrometry. Clinical putative diagnostic and prognostic biomarkers were validated by quantitation and normalized to creatinine levels at two different time points and further validated in an independent sample set, which comprises 80 cases and 78 population controls, with similar demographic and clinical characteristics when compared to the training set. Creatine riboside (IUPAC name: 2-{2-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-oxolan-2-yl]-1-methylcarbamimidamido}acetic acid), a novel molecule identified in this study, and N-acetylneuraminic acid (NANA), were each significantly (P <0.00001) elevated in non–small cell lung cancer (NSCLC) and associated with worse prognosis (hazard ratio (HR) =1.81 [P =0.0002], and 1.54 [P =0.025], respectively). Creatine riboside was the strongest classifier of lung cancer status in all and stage I–II cases, important for early detection, and also associated with worse prognosis in stage I–II lung cancer (HR =1.71, P =0.048). All measurements were highly reproducible with intraclass correlation coefficients ranging from 0.82 – 0.99. Both metabolites were significantly (P <0.03) enriched in tumor tissue compared to adjacent non-tumor tissue (N =48), thus revealing their direct association with tumor metabolism. Creatine riboside and NANA may be robust urinary clinical metabolomic markers that are elevated in tumor tissue and associated with early lung cancer diagnosis and worse prognosis.
Question: Write a study description for the study titled 'Disease progression-associated alterations in fecal metabolites in SAMP1/YitFc mice, a Crohn’s disease model'.
Answer: INTRODUCTION: Crohn’s disease (CD) is a chronic, relapsing inflammatory bowel disease affecting the gastrointestinal tract. Although its precise etiology has not been fully elucidated, imbalance of the intestinal microbiota has been known to play a role in CD. Fecal metabolites may be related to the onset and progression of CD.OBJECTIVES: This study aimed to clarify the transition of fecal metabolites associated with disease progression using SAMP1/YitFc mice, mouse models of spontaneous CD.METHODS: Feces from control ICR (n = 6) and SAMP1/YitFc (n = 8) mice at different ages were subjected to 1H nuclear magnetic resonance (NMR) analysis. The obtained NMR spectra were used for multivariate and quantitative analyses.RESULTS: Fecal metabolites, such as short-chain fatty acids, lactate, glucose, xylose, and choline, dramatically fluctuated with disease progression before histological abnormalities associated with CD were apparent in SAMP1/YitFc mice. Unlike that of other metabolites, fecal taurine concentration in SAMP1/YitFc was high regardless of age.CONCLUSION: The fecal metabolites showing characteristic fluctuations may be utilized as potential biomarkers in predicting CD pathology.
Question: Write a study description for the study titled 'Synergistic metabolism of salivary MUC5B in oral commensal bacteria during early biofilm formation'.
Answer: Bacterial metabolism in oral biofilms is comprised of complex networks of nutritional chains and biochemical regulations. These processes involve both intraspecies and interspecies networks as well as interactions with components from host saliva, gingival crevicular fluid, and dietary intake. In a previous paper, a large salivary glycoprotein, mucin MUC5B, was suggested to promote a dental health-related phenotype in the oral type strain of Streptococcus gordonii DL1, by regulating bacterial adhesion and protein expression. In this study, nuclear magnetic resonance-based metabolomics was used to examine the effects on the metabolic output of monospecies compared to dual species early biofilms of two clinical strains of oral commensal bacteria, S. gordonii and Actinomyces naeslundii, in the presence of MUC5B. The presence of S. gordonii increased colonization of A. naeslundii on salivary MUC5B, and both commensals were able to utilize MUC5B as a sole nutrient source during early biofilm formation. The metabolomes suggested that the bacteria were able to release mucin carbohydrates from oligosaccharide side chains as well as amino acids from the protein core. Synergistic effects were also seen in the dual species biofilm metabolome compared to the monospecies, indicating that A. naeslundii and S. gordonii cooperated in the degradation of salivary MUC5B. A better understanding of bacterial interactions and salivary-mediated regulation of early dental biofilm activity is meaningful for understanding oral biofilm physiology and may contribute to the development of future prevention strategies for biofilm-induced oral disease.
Question: Write a study description for the study titled 'Comparison of intestinal microbes and metabolites in active VKH versus acute anterior uveitis associated with ankylosing spondylitis'.
Answer: BACKGROUND: It has been reported that the gut microbiome is involved in the pathogenesis of uveitis, but the specific pathogenic microbes and metabolites in different types of uveitis are still unclear.METHODS: Microbiome and metabolites were detected using 16S ribosomal DNA and LC‒MS/MS (liquid chromatography tandem mass spectrometry) in 45 individuals, including 16 patients with Vogt Koyanagi Harada (VKH), 11 patients with acute anterior uveitis (AAU) and 18 healthy controls.RESULT: The diversity of intestinal microbes among the VKH, AAU and control groups was not significantly different. 13 specific microbes and 38 metabolites were detected in the VKH group, and 7 metabolites (vanillin, erythro-isoleucine, pyrimidine, 1-aminocyclopropanecarboxylic acid, beta-tocopherol, (-)-gallocatechin and N1-methyl-4-pyridone-3-carboxamide) significantly changed only in patients with VKH, which mainly acted on nicotinamide and nicotinamide metabolism and biotin metabolism (p<0.05). Compared with the VKH group, the AAU group had milder intestinal changes. Only 11 specific microbes and 29 metabolites changed in the AAU group, while these metabolites were not specific (p<0.05). These metabolites mainly acted on arachidonic acid metabolism. In addition, 3 microbes and 2 metabolites had the same changes in the VKH and AAU groups (p<0.05). Multiple correlations were found between gut microbes and metabolites in the VKH and AAU groups. 6 microbes (Pediococcus, Pseudomonas, Rhodococcus, Photobacterium, Gardnerella and Lawsonia) and 2 metabolites (pyrimidine and gallocatechin) as biomarkers could effectively distinguish patients with VKH from patients with AAU and healthy individuals, with AUC (area under the curve) values greater than 82%. 4 microbes (Lentilactobacillus, Lachnospiraceae_UCG-010, Cetobacterium, Liquorilactobacillus) could distinguish patients with AAU from patients with VKH and healthy controls with AUC>76%.CONCLUSION: Significant differences in intestinal microbes and metabolites suggest their different roles in the pathogenesis of uveitis entities. Changes in the metabolism of certain B vitamins may be involved in the pathogenesis of VKH.
Question: Write a study description for the study titled 'Untargeted metabolomics reveals alterations in metabolites of lipid metabolism and immune pathways in serum of rats after long term oral administration of Amalaki rasayana'.
Answer: Amalaki rasayana (AR), a traditional preparation is widely used by Ayurvedic physicians for the treatment of inflammatory conditions, cardiovascular diseases, cancer and for rejuvenating aged people. Metabolic alterations induced by Amalaki rasayana intervention are unknown. We aimed to investigate modulations in serum metabolomic profiles following long term oral Amalaki rasayana administration in Wistar rats. A global metabolic profiling was performed of the serum of rats administered with Amalaki rasayana or ghee+honey (GH) for 18 months and control animals which were left untreated. Amalaki rasayana components were identified from AR extract using HR-LCMS analysis. Significant reductions in prostaglandin J2, 11-dehydrothromboxane B2 and higher levels of reduced glutathione and glycitein metabolites were observed in serum of AR administered rats compared to the control groups. Pathway analysis suggest that altered metabolites in AR administered rats are those associated with different biochemical pathways of arachidonic acid metabolism, fatty acid metabolism, leukotriene metabolism, G-protein mediated events, phospholipid metabolism and the immune system. Our study identifies the AR components that induce alterations in lipid metabolism and immune pathways in animals which consume AR for a long period.
Question: Write a study description for the study titled 'Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis'.
Answer: Characterizing the metabolic changes pertaining to hepatocellular carcinoma (HCC) in patients with liver cirrhosis is believed to contribute towards early detection, treatment, and understanding of the molecular mechanisms of HCC. In this study, we compare metabolite levels in sera of 78 HCC cases with 184 cirrhotic controls by using ultra performance liquid chromatography coupled with a hybrid quadrupole time-of-flight mass spectrometry (UPLC-QTOF MS). Following data preprocessing, the most relevant ions in distinguishing HCC cases from patients with cirrhosis are selected by parametric and non-parametric statistical methods. Putative metabolite identifications for these ions are obtained through mass-based database search. Verification of the identities of selected metabolites is conducted by comparing their MS/MS fragmentation patterns and retention time with those from authentic compounds. Quantitation of these metabolites is performed in a subset of the serum samples (10 HCC and 10 cirrhosis) using isotope dilution by selected reaction monitoring (SRM) on triple quadrupole linear ion trap (QqQLIT) and triple quadrupole (QqQ) mass spectrometers. The results of this analysis confirm that metabolites involved in sphingolipid metabolism and phospholipid catabolism such as sphingosine-1-phosphate (S-1-P) and lysophosphatidylcholine (lysoPC 17:0) are up-regulated in sera of HCC vs. those with liver cirrhosis. Down-regulated metabolites include those involved in bile acid biosynthesis (specifically cholesterol metabolism) such as glycochenodeoxycholic acid 3-sulfate (3-sulfo-GCDCA), glycocholic acid (GCA), glycodeoxycholic acid (GDCA), taurocholic acid (TCA), and taurochenodeoxycholate (TCDCA). These results provide useful insights into HCC biomarker discovery utilizing metabolomics as an efficient and cost-effective platform. Our work shows that metabolomic profiling is a promising tool to identify candidate metabolic biomarkers for early detection of HCC cases in high risk population of cirrhotic patients.
Question: Write a study description for the study titled 'Co-exposure of di(2-ethylhexyl) phthalate (DEHP) decreased the submicron plastic stress in soil-plant system'.
Answer: The widespread use of agricultural plastic films has made micro- and nanoplastics (MNPs) and phthalate esters (PAEs) contaminants of emerging concern in agroecosystems. However, the interactive mechanisms underlying their combined pollution in soil-plant systems remain elusive. To fill this gap, this study investigated the interaction between submicron plastics (SMPs, 0.01% and 0.1% w/w) and di(2-ethylhexyl) phthalate (DEHP) in soil-lettuce systems. Contrary to the anticipated synergistic toxicity, DEHP significantly reduced SMP uptake into and by cracked surface cells of lettuce roots (with root concentration factors decreasing by 19%–64%), i.e., DEHP alleviated SMP-induced oxidative stress, as evidenced by reduced levels of reactive oxygen species (–26.8% and –66.7%) and antioxidant enzyme activities (–118% and –128%). Metabolomic profiling revealed that SMP exposure significantly dysregulated multiple metabolic pathways (amino acid, carbohydrate, energy, glycan, lipid, and nucleotide metabolism), while SMP+DEHP co-exposure selectively attenuated these metabolic disturbances, showing enrichment only in glycan biosynthesis/metabolism and suppressing SMP-induced perturbations in other pathways (biosynthesis of secondary metabolites, energy metabolism, and signal transduction). Microbial community analysis showed that high-level SMP exposure significantly diminished bacterial α-diversity and amplicon sequence variant (ASV) richness, whereas DEHP supplementation enhanced those of Myxococcota in the soil, potentially counterbalancing SMP-induced microbial dysbiosis. These findings collectively demonstrate that co-contamination by MNPs and plastic additives may produce antagonistic interactions rather than uniformly synergistic effects, and provide a more comprehensive evaluation of the risks of PAEs and MNPs to food security, human health, and ecological environment.
Question: Write a study description for the study titled 'Untargeted metabolomics of cecal contents from DSS induced colitis mice with and without Veillonella parvula colonization'.
Answer: Cecal contents metabolomics analysis of DSS-induced colitis mice and DSS-induced colitis mice with V. parvula colonization.
Question: Write a study description for the study titled 'Bifidobacterium bifidum-derived nanoparticles attenuate alcoholic liver disease via enhanced hepatic phagocytosis and gastrointestinal homeostasis'.
Answer: Alcohol-associated liver disease (ALD) has limited therapeutic options due to its complex pathogenesis. This study demonstrates the ALD-protective effects of extracellular nanoparticles derived from Bifidobacterium bifidum (BNPs), focusing on the novel concept of gut microbiota-derived nanoparticles (GNPs) in disease pathogenesis. When isolated BNPs were administered in an ALD mouse model, they upregulated Vsig4 receptor expression in liver macrophages, improving phagocytic clearance of harmful GNPs that contained bacterial DNA. GNPs activated liver inflammation via the cGAS-STING pathway, exacerbating ALD and liver fibrosis in Vsig4-deficient mice. BNP treatment suppressed the inflammatory cascade, modulated macrophage polarization, and reduced hepatic steatosis and liver injury, while also restoring the balance of the gut microbiota and enhancing intestinal barrier function. These new insights reveal the role of GNPs in ALD pathogenesis and present targeted microbial nanoparticle postbiotics as potential new therapeutics for treatment of alcohol-associated and other liver diseases.
Question: Write a study description for the study titled 'Transcript variants of long-chain acyl-CoA synthase 1 have distinct roles in sheep lipid metabolism'.
Answer: Mutton has recently been identified to be a consumer favorite, and intermuscular fat is the key factor in determining meat tenderness. Long-chain acyl-CoA synthetase 1 (ACSL1) is a vital subtype of the ACSL family that is involved in the synthesis of lipids from acyl-CoA and the oxidation of fatty acids. The amplification of the ACSL1 gene using rapid amplification of cDNA ends revealed that the alternative polyadenylation (APA) results in two transcripts of the ACSL1 gene. Exon 18 had premature termination, resulting in a shorter CDS region. In this study, the existence of two transcripts of varying lengths translated normally and designated ACSL1-a and ACSL1-b was confirmed. Overexpression of ACSL1-a can promote the synthesis of an intracellular diglyceride, while ACSL1-b can promote triglyceride synthesis. The transfection of ACSL1 shRNA knocks down both the transcripts, the triglyceride content was significantly reduced after differentiation and induction; and lipidome sequencing results exhibited a significant decrease in 14-22 carbon triglyceride metabolites. The results of the present study indicated that the ACSL1 gene played a crucial role in the synthesis of triglycerides. Furthermore, the two transcripts involved in various interactions in the triglyceride synthesis process may be the topic of interest for future research and provide a more theoretical basis for sheep breeding.
Question: Write a study description for the study titled 'A Combined Metabolomic and Proteomic Investigation of the Effects of a Failure to Express Dystrophin in the Mouse Heart'.
Answer: Muscle degeneration in the heart of 1-9 month-old mdx mice (a model for Duchenne muscular dystrophy) has been monitored using metabolomic and proteomic approaches. In both data sets, a pronounced aging trend was detected in control and mdx mice, and this trend was separate from the disease process. In addition, the characteristic increase in taurine associated with dystrophic tissue is correlated with proteins associated with oxidative phosphorylation and mitochondrial metabolism.
Question: Write a study description for the study titled 'Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants'.
Answer: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2′-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites.
Question: Write a study description for the study titled 'Inhibition of glycolysis and mitochondrial respiration promotes radiosensitisation of neuroblastoma and glioma cells'.
Answer: BACKGROUND: Neuroblastoma accounts for 7% of paediatric malignancies but is responsible for 15% of all childhood cancer deaths. Despite rigorous treatment involving chemotherapy, surgery, radiotherapy and immunotherapy, the 5-year overall survival rate of high-risk disease remains < 40%, highlighting the need for improved therapy. Since neuroblastoma cells exhibit aberrant metabolism, we determined whether their sensitivity to radiotherapy could be enhanced by drugs affecting cancer cell metabolism.METHODS: Using a panel of neuroblastoma and glioma cells, we determined the radiosensitising effects of inhibitors of glycolysis (2-DG) and mitochondrial function (metformin). Mechanisms underlying radiosensitisation were determined by metabolomic and bioenergetic profiling, flow cytometry and live cell imaging and by evaluating different treatment schedules.RESULTS: The radiosensitising effects of 2-DG were greatly enhanced by combination with the antidiabetic biguanide, metformin. Metabolomic analysis and cellular bioenergetic profiling revealed this combination to elicit severe disruption of key glycolytic and mitochondrial metabolites, causing significant reductions in ATP generation and enhancing radiosensitivity. Combination treatment induced G2/M arrest that persisted for at least 24 h post-irradiation, promoting apoptotic cell death in a large proportion of cells.CONCLUSION: Our findings demonstrate that the radiosensitising effect of 2-DG was significantly enhanced by its combination with metformin. This clearly demonstrates that dual metabolic targeting has potential to improve clinical outcomes in children with high-risk neuroblastoma by overcoming radioresistance.
Question: Write a study description for the study titled 'Comprehensive analysis of metabolome and transcriptome reveals the mechanism of color formation in different leave of Loropetalum chinense var. rubrum'.
Answer: BACKGROUND: Loropetalum chinense var. rubrum (L. chinense var. rubrum) is a precious, native, coloured-leaf ornamental plant in the Hunan Province. We found a L. chinense var. rubrum tree with 3 different leaf colours: GL (green leaf), ML (mosaic leaf) and PL (purple leaf). The mechanism of leaf coloration in this plant is still unclear. The aim of this study was to identify the metabolites and genes involved in determining the colour composition of L. chinense var. rubrum leaves, using phenotypic/anatomic observations, pigment content detection, and comparative metabolomics and transcriptomics.RESULTS: We observed that the mesophyll cells in PL were purple, those in GL were green and those in ML were a mix of purple-green. The contents of chlorophyll a, b, carotenoids and total chlorophyll in PL and ML were significantly lower than those in GL. While the anthocyanin content in PL and ML was significantly higher than that in GL. The metabolomics results showed that the differences in content of cyanidin 3-O-glucoside, delphinidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, pelargonin and petunidin 3,5-diglucoside in ML, GL and PL were significant. Considering that the trend of anthocyanin content change was consistent with the leaf colour difference, we speculated that these compounds might influence the colour of L. chinense var. rubrum leaves. Finally, using transcriptomics, we identified 9 differentially expressed structural genes (one ANR (ANR1217); four CYP75A (CYP75A1815, CYP75A2846, CYP75A2909 and CYP75A1716); four UFGTs (UFGT1876, UFGT1649, UFGT1839 and UFGT3273) and nine transcription factors (two MYBs (MYB1057 and MYB1211), one MADS-box (MADS1235), two AP2-likes (AP2-like1779 and AP2-like2234), one bZIP (bZIP3720), two WD40s (WD2173 and WD1867) and one bHLH (bHLH1631) that might be related to flavonoid biosynthesis that impacted the appearance of colour in L. chinense var. rubrum leaves.CONCLUSIONS: This study revealed potential molecular mechanisms associated with leaf coloration in L. chinense var. rubrum by analysing differential metabolites and genes related to the anthocyanin biosynthesis pathway. It also provides a reference for research on leaf colour variation in other ornamental plants.