LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers (NMR assay)'.
Answer: A multiplatform comparison of serum of smokers (n=56) and non-smokers (n=57) using NMR spectroscopy and UPLC-MS was carried out to determine perturbed biochemical functions associated with tobacco smoking. This should be helpful for establishing causal relationships between exposure and adverse events. The statistical modelling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modelling adverse biological events using available databases. Perturbation of metabolites involved in COPD, cardiovascular diseases and cancer were identified. Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development which can be applied to next-generation tobacco/ nicotine products for risk assessment.NMR assay is reported in the current study MTBLS374.UPLC-MS assay is reported in MTBLS364.
Question: Write a study description for the study titled 'Pronounced uptake and metabolism of organic substrates by diatoms revealed by pulse-labeling metabolomics'.
Answer: Diatoms contribute as a major group of microalgae to approximately 20% of the global carbon fixation. In the plankton, these algae are exposed to a plethora of metabolites, especially when competing algae are lysed. In line with evidence that these phototrophs can also engage in heterotrophy we asked about the scope of uptake of organic material from lysed competitors. Using labelled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up organic substrates with little bias. The newly developed pulse label / metabolomics analyses revealed not only uptake, but also diverse catabolic and anabolic usage of acquired metabolites. One of the most dominant phytoplankton groups is thus competing with other heterotrophs for organic material, suggesting that a form of absorbotrophy may have substantial impact on organic material fluxes in the oceans. This calls for refinement of our understanding of competition in the plankton.
Question: Write a study description for the study titled 'Gut microflora alleviate immune response during E.coli-induced bladder cystits via AhR/MANF activation'.
Answer: In recent years, with the deepening of research on intestinal microbiota, we found intestinal microbiota plays an important role in host immune regulation and barrier maintenance through cross-talk between the microbiota and the host. New evidence suggests that disruption of the fragile balance within the intestinal microbiota, termed as dysbiosis, may cause tremendous inflammation in both intestine proximal and distant organ. Our previous studies have shown that Bacterial infections of the liver and lungs are accompanied by changes in intestinal flora diversity, and the depletion of intestinal bacteria can aggravate bacterial infection. Though, fecal microbiota transplantation (FMT) from a healthy population has already been associated with the reduction of urinary tract infections which caused by C. difficile. However, the mechanisms by which the intestinal microbiota affects the immune responses in bacterial cystitis (BC) remain poorly characterized.
Question: Write a study description for the study titled 'Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values'.
Answer: BACKGROUND: Lipidomics, the comprehensive measurement of lipids within a biological system or substrate, is an emerging field with significant potential for improving clinical diagnosis and our understanding of health and disease. While lipids diverse biological roles contribute to their clinical utility, the diversity of lipid structure and concentrations prove to make lipidomics analytically challenging. Without internal standards to match each lipid species, researchers often apply individual internal standards to a broad range of related lipids. To aid in standardizing and automating this relative quantitation process, we developed LipidMatch Normalizer (LMN) http://secim.ufl.edu/secim-tools/ which can be used in most open source lipidomics workflows.RESULTS: LMN uses a ranking system (1-3) to assign lipid standards to target analytes. A ranking of 1 signifies that both the lipid class and adduct of the internal standard and target analyte match, while a ranking of 3 signifies that neither the adduct or class match. If multiple internal standards are provided for a lipid class, standards with the closest retention time to the target analyte will be chosen. The user can also signify which lipid classes an internal standard represents, for example indicating that ether-linked phosphatidylcholine can be semi-quantified using phosphatidylcholine. LMN is designed to work with any lipid identification software and feature finding software, and in this study is used to quantify lipids in NIST SRM 1950 human plasma annotated using LipidMatch and MZmine.CONCLUSIONS: LMN can be integrated into an open source workflow which completes all data processing steps including feature finding, annotation, and quantification for LC-MS/MS studies. Using LMN we determined that in certain cases the use of peak height versus peak area, certain adducts, and negative versus positive polarity data can have major effects on the final concentration obtained.
Question: Write a study description for the study titled 'Metabolomics analysis of antibacterial mechanism'.
Answer: Metabolomics, as a high-throughput analytical technique, enables comprehensive analysis of the metabolic changes in microorganisms under different environmental conditions, revealing the molecular basis of their antibacterial mechanisms. This study employs metabolomics analysis to investigate the antibacterial effects and mechanisms of specific natural products against common pathogenic bacteria.
Question: Write a study description for the study titled 'Effects of Centella asiatica extract on antioxidant status and liver metabolome of rotenone-treated rats using GC-MS'.
Answer: The standardized extract of Centella asiatica (ECa233) contains >80% triterpenoids with a ratio of madecassoside to asiaticoside of 1.5(±0.5):1. Hepatoprotective effect of ECa233 has not yet been reported. The aim of this study was to examine the effect of ECa233 on liver metabolome of rotenone-treated rats to better understand the underlying mechanisms of this bioactive substance in liver tissue. Rats were randomly divided into three groups (with six rats/group): sham negative control, rotenone positive control, and the ECa233 test group. Rats in the ECa233 group received 10 mg/kg ECa233 orally for 20 days, followed by 2.5 mg/kg intraperitoneal rotenone injection to induce toxicity before being sacrificed. The liver samples were collected for antioxidant assays and untargeted metabolomic analysis using a GC-MS. Antioxidant tests revealed that ECa233 inhibited lipid peroxidation and increased catalase activities in liver tissue. Orthogonal partial least squares-discriminant analysis clearly showed complete separation between control and rotenone groups, whereas the ECa233 group was located between these two groups and tended to reverse the effects of rotenone treatment. Two candidate markers were identified, pipecolinic acid and Unknown #21. Findings from this study suggested that supplementation of ECa233 protected rat liver against rotenone toxicity. However, further investigations are needed to elucidate the mechanisms involved.
Question: Write a study description for the study titled 'Rabbit plasma metabolomic analysis of Nitroproston: a multi target natural prostaglandin based-drug (Targeted study)'.
Answer: INTRODUCTION: Nitroproston® is a novel multi-target drug bearing natural prostaglandin E2 (PGE2) and nitric oxide (NO)-donating fragments for treatment of inflammatory and obstructive diseases (i.e. asthma and obstructive bronchitis).  OBJECTIVES: To investigate the effects of Nitroproston® administration on plasma metabolomics in vivo.  METHODS: Experimental in vivo study randomly assigning the target drug (treatment group) or a saline solution without the drug (vehicle control group) to 12 rabbits (n=6 in each group). Untargeted (5880 initial features; 1869 negative-4011 positive ion peaks; UPLC-IT-TOF/MS) and 84 targeted moieties (Nitroproston® related metabolites, prostaglandins, steroids, purines, pyrimidines and amino acids; HPLC-QQQ-MS/MS) were measured from plasma at 0, 2, 4, 6, 8, 12, 18, 24, 32 and 60 minutes after administration.  RESULTS: PGE2, 13,14-dihydro-15-keto-PGE2, PGB2, 1,3-GDN and 15-keto-PGE2 increased in the treatment group. Steroids (i.e. cortisone, progesterone), organic acids, 3-oxododecanoic acid, nicotinate D-ribonucleoside, thymidine, the amino acids serine and aspartate, and derivatives pyridinoline, aminoadypic acid and uric acid increased (p0.75) after treatment. Purines (i.e. xanthine, guanine, guanosine), bile acids, acylcarnitines and the amino acids L-tryptophan and L-phenylalanine were decreased. Nitroproston® impacted steroidogenesis, purine metabolism and ammonia recycling pathways, among others.  CONCLUSION: Nitroproston®, a multi action novel drug based on natural prostaglandins, altered metabolites previously implicated as having anti inflammatory or anti-asthma properties (i.e. guanine, adenine, cortisol, cortisone and aspartate). Steroids, purine, urea and ammonia biological cycles were impacted. Mechanisms of action, metabolic pathway interconnections and useful information to further understand the metabolic effects of prostaglandin administration are presented.  The targeted study data is reported in the current study MTBLS728.  The untargeted study data associated with this study is reported in MTBLS727.  Linked Studies: MTBLS727
Question: Write a study description for the study titled 'Environmental impacts on barley grain composition and longevity'.
Answer: To counter projected reductions in yields of the major crop barley, it is essential to elucidate the mechanisms of its resilience. To assist such efforts, we collected grains from plants grown in fields at 12 testing stations, with suitable temperature and precipitation gradients for identifying environmentally induced changes in their protein and metabolite contents. We then subjected the grains to detailed molecular analysis. The results showed that numerous metabolites and at least a quarter of the grain protein content was modulated by the environment, and provided insights into barley seed production under abiotic stress, including alterations in ribosomal proteins, heatshock protein 70 family proteins, inhibitors, storage proteins and lipid droplet formation. Potential positive and negative markers of yield were also identified, including the phenolic compound catechin and storage protein levels, respectively. Complementary analyses of barley seedlings and Arabidopsis seeds, respectively, confirmed the role of the identified proteins in abiotic stress responses and highlighted evolutionarily conserved mechanisms. In addition, accelerated ageing experiments revealed that variations in the environment had stronger effects on seed longevity than the genotype. Finally, seeds with the highest longevity differed from the others in gibberellin contents, H2O2 metabolism and levels of >250 proteins, providing novel targets for improving resilience.
Question: Write a study description for the study titled 'Metabolomics study for investigating the specific role of INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B under chronic endoplasmic reticulum stress in Arabidopsis thaliana'.
Answer: The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This metabolomic dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT), double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A [IRE1A] and INOSITOL-REQUIRING ENZYME 1B [IRE1B]), as well as doubles mutants complemented with either of the WT IRE1 alleles were used as genetic backgrounds in our experimental setup. This allows to distinguish among differentially-overaccumulated metabolites which ones are dependent on IRE1A and/or IRE1B. Also, shoots and roots were harvested separately to determine organ-specific metabolic responses to Tm.
Question: Write a study description for the study titled 'Metabolomic Aspects of Conservative and Resistance-related Elements of Response to Fusarium culmorum in the Grass Family'.
Answer: BACKGROUND: Fusarium head blight (FHB) is a serious fungal disease of crop plants due to substantial yield reduction and production of mycotoxins in the infected grains. The breeding progress in increasing resistance with maintaining a high yield is not possible without a thorough examination of the molecular basis of plant immunity responses.METHODS: LC-MS based metabolomics approaches powered by three-way ANOVA and differentially accumulated metabolites (DAMs) selection, correlation network and functional enrichment were conducted on grains of resistant and susceptible to FHB genotypes of barley and wheat as well as model grass Brachypodium distachyon (Bd) still poorly known at metabolomic level.RESULTS: We selected common and genotype-specific DAMs in response to F. culmorum inoculation. Immunological reaction at metabolomic level was strongly diversified between resistant and susceptible genotypes. DAMs common for all tested species from porphyrins, flavonoids and phenylpropanoids metabolic pathways were highly correlated and reflects conservativeness in FHB response in Poaceae family. Resistant related DAMs belonged to different structural classes including tryptophan derived metabolites, pirimidines, amino acids proline and serine as well as phenylpropanoids and flavonoids. Physiological response to F. culmorum of Bd was close to barley and wheat genotypes however, metabolomic changes were strongly diversified. CONCLUSIONS: Combined targeted and untargeted metabolomics provides comprehensive knowledge about significant elements of plant immunity with potential of being molecular biomarkers of enhance resistance to FHB in grass family. Thorough examination of Bd21 metabolome in juxtaposition with barley and wheat diversified genotypes facilitate their setting as model grass for plant-microbe interaction.
Question: Write a study description for the study titled 'Puerarin Combined with Hericium Erinaceus Insoluble Dietary Fiber Alleviate Obesity Induced by High-fat Diet Through Regulating the Glycerophospholipid Metabolism Pathway Influenced by Gut Microbiota'.
Answer: The combination of HEIDF and Pue holds significant importance in the context of obesity. This synergistic effect not only aids in weight management but may also enhance metabolic health through various mechanisms, including increased satiety and promotion of fat oxidation. Therefore, incorporating these two components into the daily diet could offer effective strategies for the prevention and intervention of obesity and its related diseases.
Question: Write a study description for the study titled 'A synthetic community system for probing microbial interactions driven by exometabolites'.
Answer: Despite that most microorganisms live as part of community, we have modest knowledge about the interactions among microbial community members in nature, and the implications of those interactions for emergent community properties or ecosystem-relevant functions. To facilitate advances in understanding microbial interactions, we describe a straightforward synthetic community system for interrogating the extracellular interactions among microbial community members. The laboratory-scale system physically separates microbial populations within the community, but allows for chemical interactions via a shared media reservoir. Community goods, including small molecules, extracellular enzymes, and antibiotics, can be assayed using sensitive mass spectrometry, and community member outcomes can be assayed, for example, using flow cytometry, biomass measurements, and transcript analyses. The synthetic community design allows for determining the causes and consequences of community diversity and functional outcomes given manipulation of community membership or structure, abiotic stressors, or temporal dynamics. Because it is versatile to accommodate any artificial or environmental microbiome members, scalable to high-throughput capacity, flexible to an array of experimental designs, and accessible to a variety of laboratories because no specialized or costly components are required, this synthetic community system has the potential to practically advance knowledge of microbial interactions within both natural and artificial communities.
Question: Write a study description for the study titled 'Direct on-swab metabolic profiling of vaginal microbiome:host interactions during pregnancy and preterm birth'.
Answer: The pregnancy vaginal microbiome contributes to risk of preterm birth, the primary cause of death in children under 5 years of age. Here we describe direct on-swab metabolic profiling by Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) for sample preparation-free characterisation of the cervicovaginal metabolome in two independent pregnancy cohorts (VMET, n = 160; 455 swabs; VMET II, n = 205; 573 swabs). By integrating metataxonomics and immune profiling data from matched samples, we show that specific metabolome signatures can be used to robustly predict simultaneously both the composition of the vaginal microbiome and host inflammatory status. In these patients, vaginal microbiota instability and innate immune activation, as predicted using DESI-MS, associated with preterm birth, including in women receiving cervical cerclage for preterm birth prevention. These findings highlight direct on-swab metabolic profiling by DESI-MS as an innovative approach for preterm birth risk stratification through rapid assessment of vaginal microbiota-host dynamics.Linked cross omic data sets:Meta-taxonomics data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB11895, PRJEB12577 and PRJEB41427.
Question: Write a study description for the study titled 'Non-targeted in vitro metabolomics for proteome-scale identification of novel enzymes in Escherichia coli'.
Answer: Many yet undiscovered enzymes still limit our understanding of metabolism. Here, we develop a high-throughput mass spectrometry approach to comprehensively profile proteome-scale protein collections for in vitro enzymatic activity. Overexpressed or purified proteins are incubated in a supplemented metabolome extract containing hundreds of biologically relevant candidate substrates, and accumulating or depleting metabolite ions are determined by nontargeted mass spectrometry. Combining chemometrics and database approaches, we established an automated pipeline for unbiased annotation of novel enzyme functions that was demonstrated to achieve 75% predictive accuracy. In a screen of all 1,275 functionally uncharacterized Escherichia coli proteins, this low false-positive rate discovery method identified 241 potential novel enzymes. Twelve of these were experimentally validated to catalyze 29 diverse metabolic reactions, including the long-elusive multispecific cytidine monophosphate nucleosidase PpnN (YgdH) and the two fumarases FumD (YdhZ) and FumE (YggD). Thus, we establish high-throughput nontargeted in vitro metabolomics and the corresponding hypothesis generation pipeline as an approach for proteome-scale enzyme discovery and assign enzymatic functions to about 20% of the so far uncharacterized E. coli proteins.
Question: Write a study description for the study titled 'The glycosyltransferase UGT76B1 modulates N-hydroxy-pipecolic acid homeostasis and plant immunity'.
Answer: The trade-off between growth and defense is a critical aspect of plant immunity. Therefore, the plant immune response needs to be tightly regulated. Salicylic acid (SA) is an important plant hormone regulating defense against biotrophic pathogens. Recently, N-hydroxy-pipecolic acid (NHP) was identified as anotherregulator for plant innate immunity and systemic acquired resistance. Although the biosynthetic pathway leading to NHP formation has already been identified, how NHP is further metabolized was unclear. Here, we present UGT76B1 as a UDP-dependent glycosyltransferase that modifies NHP by catalyzing the formation of 1-O-glucosyl-pipecolic acid (NHP-OGlc) in Arabidopsis thaliana. Analysis of T-DNA and CRISPR knock-out mutant lines of UGT76B1 by targeted and non-targeted UHPLC-HRMS underlined NHP and SA as endogenous substrates of this enzyme in response to Pseudomonas infection and UV treatment. ugt76b1 mutant plants have a dwarf phenotype and constitutive defense response which can be suppressed by loss of function of the NHP biosynthetic enzyme Flavin-dependent monooxygenase 1 (FMO1). This suggests that elevated accumulation of NHP contributes to the enhanced disease resistance in ugt76b1. Externally applied NHP can move to distal tissue in ugt76b1 mutant plants. Although glycosylation is not required for the long-distance movement of NHP during systemic acquired resistance, it is crucial to balance growth and defense.
Question: Write a study description for the study titled 'Metabolomics Analysis Reveals Tissue-Specific Metabolite Compositions in Leaf Blade and Traps of Carnivorous Nepenthes Plants'.
Answer: Nepenthes is a genus of carnivorous plants that evolved a pitfall trap, the pitcher, to catch and digest insect prey to obtain additional nutrients. Each pitcher is part of the whole leaf, together with a leaf blade. These two completely different parts of the same organ were studied separately in a non-targeted metabolomics approach in Nepenthes x ventrata, a robust natural hybrid. The first aim was the analysis and profiling of small (50-1000 m/z) polar and non-polar molecules to find a characteristic metabolite pattern for the particular tissues. Second, the impact of insect feeding on the metabolome of the pitcher and leaf blade was studied. Using UPLC-ESI-qTOF and cheminformatics, about 2000 features (MS/MS events) were detected in the two tissues. They showed a huge chemical diversity, harboring classes of chemical substances that significantly discriminate these tissues. Among the common constituents of N. x ventrata are phenolics, flavonoids and naphthoquinones, namely plumbagin, a characteristic compound for carnivorous Nepenthales, and many yet-unknown compounds. Upon insect feeding, only in pitchers in the polar compounds fraction, small but significant differences could be detected. By further integrating information with cheminformatics approaches, we provide and discuss evidence that the metabolite composition of the tissues can point to their function.