LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Chronic Obstructive Pulmonary Disease (COPD) Biomarker Identification Study: Serum Lipidomics'.
Answer: The overall clinical study used a parallel-group, case-controlled study design in order to identify a biomarker or panel of biomarkers for the differentiation of subjects with mild to moderate COPD (GOLD stage I and II), asymptomatic current smokers, former smokers and never-smokers and to compare physiological measurements and quality of life (QoL) across the study groups. The study was conducted between July 2011 and December 2012, at a single clinical site in London, UK, after approval from a UK National Health Service (NHS) ethics committee (The Black County Ethics Committee) and in strict compliance with International Conference on Harmonisation-Good Clinical Practice (ICH-GCP) guidelines. The study has been registered on ClinicalTrials.gov with identifier NCT01780298. Male and female subjects aged between 41 and 70 years were enrolled with a completed total subject number of 60 per group. During the course of the study, sputum, blood, and nasal samples were collected and a number of physiological and clinical measurements were recorded from a total of 240 subjects. Each subject in each of the 3 control groups, namely the healthy smokers, never-smokers and ex-smokers, were matched to subjects in the COPD group by age (+/-5 years), ethnicity, gender, and all smoking subjects had a smoking history of at least 10 pack-years. The study subject were required to attend the study visits after having eaten a light breakfast. Analyses of lipid species were performed in serum samples from a subset of study subjects including 40 never-smokers, 40 former smokers, 40 smokers, and 40 COPD patients by Zora Biosciences Oy (Espoo, Finland). The data from this analysis are reported here.
Question: Write a study description for the study titled 'Alterations in the oral microbiome and metabolome of methamphetamine addicts'.
Answer: BACKGROUND: Drug addiction can seriously damage human physical and mental health, while detoxification is a long and difficult process. Although studies have reported changes in the oral microbiome of methamphetamine (METH) addicts, the role of the microbiome plays in this process is still unknown. This study aims to explore the function of the microbiome based on analysis of the variations in the oral microbiome and metabolome of METH addicts. We performed the 16S rRNA sequencing analysis based on the oral saliva samples collected from 278 METH addicts and 105 healthy controls (CTL) undergoing detoxification at the detoxification center in Shandong, China. In addition, the untargeted metabolomic profiling was conducted based on 220 samples (170 METH addicts and 50 CTL) to identify the biomarkers and build classifiers for both oral microbiota and metabolites.RESULTS: Compared to the CTL group, alpha diversity was reduced in the group of METH addicts, with significant differences in the microbiota and changes in oral metabolic pathways, including enhanced tryptophan metabolism, lysine biosynthesis, purine metabolism and steroid biosynthesis. Conversely, the metabolic pathways of porphyrin metabolism, glutathione metabolism and pentose phosphate were significantly reduced. It was speculated that four key microbial taxa, i.e., Peptostreptococcus, Gemella, Campylobacter and Aggregatibacter, could be involved in the toxicity and addiction mechanisms of METH by affecting the above metabolic pathways. And, it was found that with the increase of drug use years, the content of tryptamine associated with neuropsychiatric disorders gradually increased. In addition, microbial prediction models were more effective than metabolite-based prediction models in identifying METH addiction.CONCLUSIONS: Our study identified the potential functional connections between the oral microbiome and metabolic profile of METH addicts, providing novel insights into exploring the toxic damage and addiction mechanisms underlying the METH addiction.
Question: Write a study description for the study titled 'Mass spectrometry data on volatile compounds of Polygonum minus Huds. leaf essential oil'.
Answer: Polygonum minus Huds., commonly referred to as kesum, is a traditional medicinal plant in Malaysia known for its unique fragrance attributed to its volatile compounds. The essential oil extracted from P. minus displayed various benefits, comprised of antioxidant, antimicrobial and anticancer properties. Therefore, to identify volatile metabolites associated with such biological activities, we performed untargeted metabolite analysis on the essential oil extracted from P. minus leaf tissue. After the leaf samples were collected from the INBIOSIS experimental plot, a 6-hour hydro-distillation procedure was performed to extract the essential oil, which was then subjected to GC-MS analysis. Thus, this data could provide a reference and benchmark for researchers conducting analyses on volatile compounds in P. minus.
Question: Write a study description for the study titled 'Integrated Metabolomics and Transcriptomics Analyses Reveal Anthocyanin and Carotenoid Biosynthesis Involved in Color Development in Willow Bark'.
Answer: Shrub willow has strong adaptability, large biomass and short rotation period. Colorful willow barks have great ornamental and economic value. To study the color regulation mechanism, metabolomics and transcriptomics were used to analyze the purple, green and red barks. In the positive mode, a total of 1639 metabolites were identified and 1026 metabolites in negative mode. Flavone and flavonol biosynthesis (ko00944), flavonoid biosynthesis (ko00941), were all enriched in the 3 groups G vs P (G/P), G vs R (G/R) and P vs R (P/R). A total of 12 flavone and flavonol biosynthesis metabolites were isolated. A total of 448,839,796 raw reads were obtained with Q30 more than 93.15%. In the G/P, G/R and P/R groups, 27, 28 and 21 genes were enriched in the flavonoid biosynthesis (ko00941). The expression of CHS, ANS, DFR, ANR in the flavonoid biosynthesis pathway was the most in red. The content of canthaxanthin in purple bark was 10x more than green and 6x than red. The integration of metabolites and genes indicated the role of pelargonidin and canthaxanthin in regulating red and purple color pigment. Our research provides a fundamental basis for colorful willow breeding.
Question: Write a study description for the study titled 'Taurine ameliorates oxidative stress of BMSCs and promotes osteogenesis in irradiated jaws'.
Answer: Osteoradionecrosis of the jaw (ORNJ) is a complication after head and neck radiotherapy that severely affects patients’ quality of life. Currently, an overall understanding of microenvironmental factors of ORNJ is still lacking. Here, we reveal the activation of taurine metabolism in irradiated mandibular stromal cells with scRNA-Seq and the decrease of taurine in irradiated bone marrow mesenchymal stromal cells (BMSCs) with metabolomics. Compared to the unirradiated BMSCs, the taurine uptake of irradiated BMSCs increases. The taurine concentration in peripheral blood and jaws of irradiated mice are significantly lower than the unirradiated mice. Supplementation of taurine promotes osteogenic differentiation, decreases oxidative stress and DNA damage of irradiated BMSCs. Oral administration of taurine significantly promotes survival rate of irradiated mice and promotes osteogenesis of irradiated jaws. Our study sheds light on the role of taurine during the recovery of radiation-induced jaw injury, suggesting a potential non-invasive therapeutic means to combat ORNJ.
Question: Write a study description for the study titled 'Quantitative profiling of endocannabinoids in lipoproteins by LC–MS/MS'.
Answer: Endocannabinoids belong to a diverse family of endogenous lipid bioregulators acting as physiological ligands of cannabinoid receptor type 1 and cannabinoid receptor type 2 in the central and peripheral nervous system. They are also present in nmol/l concentrations in human blood plasma; however, their association with possible molecular carriers remains poorly characterized. Here we report on the quantification of 46 endogenous molecular species from five major classes of endocannabinoids and endocannabinoid-related compounds in three lipoprotein fractions of human blood plasma: (VLDL), LDL, HDL, and in the plasma lipoproteinfree fraction. Although sizable quantities of endocannabinoid related molecules are associated with lipoproteins, we identified the lipoprotein-free fraction as a major carrier of endocannabinoids in blood circulation with the exception of 2-acylglycerols, which are markedly abundant in VLDL.
Question: Write a study description for the study titled 'Exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome'.
Answer: The exposome represents a summation of exposures which influence an individual’s health over their lifetime. Understanding the exposome will aid in determining the environmental factors that contribute to disease states. Due to the biological complexity of the exposome and the resulting high dimensionality of the data, it is relatively difficult to predict adverse health outcomes resulting from a summation of environmental exposures. Therefore, accurate and relevant exposome criteria for biological assays is the first step toward addressing the current knowledge gaps for exposome research. This study aims to assess the presence of and health effects from exposure to contaminants in Wisconsin groundwater. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards (i.e., nitrate, atrazine and imidacloprid) and the emerging contaminant, microplastics (i.e., polyethylene fiber). The agricultural chemical mixture of nitrate, atrazine and imidacloprid represent a known and ecologically relevant contaminant because each chemical individually has health risk levels established. Microplastics (MPs) are plastic fragments less than 5 mm in diameter that have been implicated in intestinal toxicity, altered metabolites, and other adverse health outcomes following exposure. In recent years, MPs have increasingly been found in locations where there could be interaction with other environmental contaminants such as pesticides. However, there is limited knowledge regarding the impacts of MPs on health of terrestrial species sources such as poultry. In this study, broilers were exposed to two ternary chemical mixtures or polyethylene microplastics (PE MPs) for 49 days. We observed significant perturbations to the cecal microbiome and metabolome of broiler in all exposure groups. We observed that both ternary mixtures and PE fiber MPs significantly altered the cecal microbiomes as determined by the enrichment of genera, Fournierella, Ruminococcus and an unclassified genus in the family Coriobacteriaceae. Perturbations to cecal microbial activity were also confirmed via modulation of pathways such as the pentose phosphate pathway, Vitamin B metabolism and metabolism of xenobiotics by cytochrome P450. The data presented here will aid in improving current groundwater regulations for agricultural chemical mixtures and microplastics.
Question: Write a study description for the study titled '"Human gut microbes impact host serum metabolome and insulin sensitivity"'.
Answer: "Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus are identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders."
Question: Write a study description for the study titled 'Time-resolved decoding of metabolic signatures of in vitro growth of the hemibiotrophic pathogen Colletotrichum sublineolum'.
Answer: Metabolomics has emerged as a powerful approach to comprehensively interrogate cellular biochemistry. As such, we applied an untargeted liquid chromatography-mass spectrometry metabolomic strategy to elucidate metabolome changes in the anthracnose-causing hemibiotrophic sorghum pathogen, Colletotrichum sublineolum. An in vitro batch culture study model with different carbon sources, glucose, arabinose and rhamnose, were used to support fungal growth over a period of twelve days. Metabolites representing the intracellular and extracellular (secreted) metabolomes were extracted with methanol and subjected to LC-MS analyses. Chemometric modelling revealed a metabolic variation trajectory, comprising three distinct stages that metabolically describe the adaptation of the fungus to diminishing nutrients. Selected marker gene expression indicated stage one (0-3 d.p.i) as corresponding to the early logarithmic phase. Stage two can be interpreted as an intermediate transitionary stage with stage three corresponding to the stationary phase (9-12 d.p.i). Stage one was characterised by up-regulation of endo-metabolites such as ferricrocin, fatty acids and flavone-conjugates, while stage three was characterised by the secretion of phytotoxins, including colletotrichin and colletotric acid. Ultimately, results from our in vitro model reveal previously unknown insights into the dynamic aspects of metabolome reprogramming in the growth phases of Colletotrichum spp as determined by nutrients obtainable from plant cell walls.
Question: Write a study description for the study titled 'Finger sweat analysis enables short interval metabolic biomonitoring in humans'.
Answer: Metabolic biomonitoring in humans is typically based on the sampling of blood, plasma or urine. Although established in the clinical routine, these sampling procedures are often associated with a variety of compliance issues and are impractical for performing time-course studies. The analysis of the minute amounts of sweat sampled from the fingertip enables a solution to thischallenge. Sweat sampling from the fingertip is non-invasive and robust and can be accomplished repeatedly by untrained personnel. This matrix represents a rich source for metabolomic phenotyping, which is exemplified by the detection of roughly 50’000 features per sample. Moreover, the determined limits of detection demonstrate that the ingestion of 200 μg of a xenobiotic may be sufficient for its detection in sweat from the fingertip. The feasibility of short interval sampling of sweat from the fingertips was confirmed in three time-course studies after coffee consumption or ingestion of a caffeine capsule, successfully monitoring all known caffeine metabolites. Fluctuations in the rate of sweat production were accounted for by mathematical modelling to reveal individual rates of caffeine uptake, metabolism and clearance. Biomonitoring using sweat from the fingertip has far reaching implications for personalised medical diagnostics and biomarker discovery.Additional LC-MS data associated with this study can be found with the identifier MTBLS2776.
Question: Write a study description for the study titled 'Limitations to Starch Utilization in Barramundi (Lates calcarifer) as Revealed by NMR-Based Metabolomics'.
Answer: Practical diets for commercial barramundi production rarely contain greater than 10% starch, used mainly as a binding agent during extrusion. Alternative ingredients such as digestible starch have shown some capacity to spare dietary protein catabolism to generate glucose. In the present study, a carnivorous fish species, the Asian seabass (Lates calcarifer) was subjected to two diets with the same digestible energy: Protein (P) - with high protein content (no digestible starch); and Starch (S) - with high digestible (pregelatinized) starch content. The effects of a high starch content diet on hepatic glycogen synthesis as well as the muscle and liver metabolome were studied using a complementary approach of 1H and 2H NMR. The hepatosomatic index was lower for fish fed high starch content diet while the concentration of hepatic glycogen was similar between groups. However, increased glycogen synthesis via the direct pathway was observed in the fish fed high starch content diet which is indicative of increased carbohydrate utilization. Multivariate analysis also showed differences between groups in the metabolome of both tissues. Univariate analysis revealed more variations in liver than in muscle of fish fed high starch content diet. Variations in metabolome were generally in agreement with the increase in the glycogen synthesis through direct pathway, however, this metabolic shift seemed to be insufficient to keep the growth rate as ensured by the diet with high protein content. Although liver glycogen does not make up a substantial quantity of total stored dietary energy in carnivorous fish, it is a key regulatory intermediate in dietary energy utilization.
Question: Write a study description for the study titled 'Androgens drive SLC1A5-dependent metabolic reprogramming in polycystic ovary syndrome-GC-MS analysis of follicular fluid'.
Answer: Polycystic ovary syndrome (PCOS) is the primary cause of female infertility. Growing evidence suggests that dysregulation of amino acid metabolism plays a significant role in the onset and progression of PCOS. However, the underlying mechanism remains unclear. In this study, we conducted targeted metabolite profiling of human follicular fluid (FF) and granulosa cells (GCs). A significant increase in glutamine (Gln) uptake was observed in patients with hyperandrogenic-PCOS (HA-PCOS), mediated by the upregulation of SLC1A5, a specific Gln transporter. We subsequently confirmed that androgen excess primarily activates SLC1A5 expression. Furthermore, Slc1a5 overexpression in female mice induced PCOS-like phenotypes, including hyperandrogenism and abnormal follicle development. Additionally, the pharmacological blockade of SLC1A5 provided reproductive benefits to mice exhibiting PCOS-like symptoms. Mechanistically, we found that elevated flux of Gln-derived α-ketoglutarate (α-KG) enhanced HDAC5 expression and suppressed acetylation on histone 3 lysine residue 14 and lysine residue 56. The reduction in acetylation level correlated with the downregulation of several genes related to folliculogenesis, including CYP19A1, thereby exacerbating androgenic homeostasis imbalance. These findings indicate that androgen-induced aberrant Gln uptake via SLC1A5 is crucial for the development and progression of PCOS, suggesting pharmacological blockade of SLC1A5 as a potential therapeutic strategy for PCOS patients.
Question: Write a study description for the study titled 'Comparative metabolomics analysis of bronchial epithelium during barrier establishment after allergen exposure'.
Answer: BACKGROUND: Several studies have shown a correlation between an altered metabolome and respiratory allergies. The epithelial barrier hypothesis proposes that an epithelial barrier dysfunction can result in allergic diseases development. Der p 1 allergen from house dust mite is a renowned epithelial barrier disruptor and allergy initiator due to its cysteine-protease activity. Here, we compared the metabolic profile of the bronchial epithelium exposed or not to Der p 1 during barrier establishment to understand its active role in allergy development.METHODS: Calu-3 cells were cultivated in air-liquid interface cultures and exposed to either Der p 1 or Ole e 1 allergens during barrier establishment. The comparative metabolomics analysis of apical and basolateral media were performed using liquid chromatography and capillary electrophoresis both coupled to mass spectrometry.RESULTS: We showed that epithelial barrier disruption by Der p 1 was associated with a specific metabolic profile, which was highly dependent on the state of the epithelium at the time of contact. Moreover, an apical-basolateral distribution of the metabolites was also observed, indicating a compartmentalization of the response with differential metabolic patterns. A number of metabolites were changed by Der p 1, mainly related to amino acids metabolism, such as L-arginine, L-kynurenine and L-methionine.CONCLUSION: This work is the first report on the metabolic response in human bronchial epithelial cells associated with cysteine-protease Der p 1 activity, which could contribute to allergy development. Moreover, it supports a reformulated epithelial barrier hypothesis that might help to explain allergies and their increasing prevalence.
Question: Write a study description for the study titled 'ATP-binding Cassette Sub-family C Member 5 (ABCC5) Functions as an Efflux Transporter of Glutamate Conjugates and Analogs'.
Answer: The ubiquitous efflux transporter ATP-binding cassette sub-family C member 5 (ABCC5) is present at high levels in the blood-brain barrier, neurons and glia, but its function is not known. Untargeted metabolomic screens revealed that Abcc5-/- mice accumulate endogenous glutamate conjugates in several tissues, but brain in particular. The abundant neurotransmitter N-acetylaspartylglutamate (NAAG), for example, was over 2-fold higher in Abcc5-/- brain. In line with ABCC5-mediated transport, the metabolites that accumulated in Abcc5-/- tissues were depleted in cultured cells that overexpressed human ABCC5. Using membrane vesicles, we show that ABCC5 not only transports the metabolites detected in our screen, but also a wide range of peptides containing a C-terminal glutamate. Glutamate conjugates are of physiological relevance because they can affect the function of glutamate, the principal excitatory neurotransmitter in the brain. Interestingly, we found that ABCC5 also transports exogenous glutamate analogs, like the classic excitotoxic neurotoxins kainic acid, domoic acid and N-methyl-D-aspartate (NMDA), and the therapeutic glutamate analog ZJ43. Taken together, we have identified ABCC5 as a general glutamate conjugate and analog transporter that can affect the disposition of endogenous metabolites, toxins and drugs.
Question: Write a study description for the study titled 'Lipidomic Changes in the Liver of Beagle Dogs Associated with Toxocara canis Infection'.
Answer: In this study, lipid alterations in Beagle dog’s liver caused by Toxocara canis infection were investigated by using liquid chromatography with tandem mass spectrometry at 12 hours post infection (hpi), 24 hpi and 36 days post infection (dpi). A total of 6 categories and 42 subclasses of lipids were identified, including 173, 64 and 116 differentially abundant lipid species at 12 hpi, 24 hpi and 36 dpi, respectively. Many of the identified lysophospholipids, such as lysophosphatidylglycerol, lysophosphatidyiserine and lysophosphatidylcholine, seem to contribute to the migration and development of T. canis at the early infection stage. Pathway analysis revealed significant alterations of several lipid metabolism pathways, such as B cell receptor signaling pathway, NF-kappa B signaling pathway and C-type lectin receptor signaling pathway at 12 hpi and 24 hpi. Our findings provide the first detailed insight into how T. canis infection causes substantial changes in the composition and abundance of hepatic lipid metabolites with relevance to pathophysiology of toxocariasis in Beagle dogs.