LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season'.
Answer: BACKGROUND: Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown.RESULTS: Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season.CONCLUSIONS: These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.
Question: Write a study description for the study titled 'Metabolomics dataset of PPAR-pan treated rat liver (eicosanoid assay)'.
Answer: This article contains mass spectrometry (MS) data investigating small molecule changes as an effect of a triple peroxisome proliferator-activated receptor (PPAR-pan) agonist GW625019 in the liver as described in the manuscript “PPAR-pan Activation Induces Hepatic Oxidative Stress and Lipidomic Remodelling“ [1]. Samples were analysed using liquid chromatography-mass spectrometry (LC-MS) to measure intact lipids, carnitines and selected aqueous metabolites and eicosanoids. Data files comprise of Excel (Microsoft, WA, USA) spreadsheets of identified metabolites and there area ratio values for total fatty acids, carnitines, aqueous metabolites, and eicosanoids where the intensity of the analytes were normalised to the intensity of the internal standard. In the case of open profiling intact lipid data, the Excel file contains area ratio values of retention time and mass to charge ratio pairs; again, the area ratio values were calculated by normalising to the intensity of the internal standard. It should be noted that several metabolic changes are potentially indirect (secondary, tertiary and ensuing changes).The protocols and data of eicosanoids are included in current study MTBLS278.The protocols and data of the carnitine and targeted aqueous metabolites are reported in the study MTBLS303.
Question: Write a study description for the study titled 'A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients'.
Answer: Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC-MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
Question: Write a study description for the study titled 'Evaluation of significant features discovered from different data acquisition modes in mass spectrometry-based untargeted metabolomics'.
Answer: Despite the growing popularity of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics, no study has yet to systematically compare the performance of different data acquisition modes in the discovery of significantly altered metabolic features, which is an important task of untargeted metabolomics for identifying clinical biomarkers and elucidating disease mechanism in comparative samples. In this work, we performed a comprehensive comparison of three most commonly used data acquisition modes, including full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA), using a metabolomics study of human plasma samples from leukemia patients before and after one-month chemotherapy. After optimization of data processing parameters, we extracted and compared statistically significant metabolic features from the results of each data acquisition mode. We found that most significant features can be consistently found in all three data acquisition modes with similar statistical performance as evaluated by Pearson correlation and receiver operating characteristic (ROC) analysis. Upon comparison, DDA mode consistently generated fewer uniquely found significant features than full-scan and DIA modes. We then manually inspected over 2000 uniquely discovered significant features in each data acquisition mode and showed that these features can be generally categorized into four major types. Many significant features were missed in DDA mode, primarily due to its low capability of detecting or extracting these features from raw LC-MS data. We thus proposed a bioinformatic solution to rescue these missing significant features from the raw DDA data with good reproducibility and accuracy. Overall, our work asserts that data acquisition modes can influence metabolomics results, suggesting room for improvement of data acquisition modes for untargeted metabolomics.
Question: Write a study description for the study titled 'X chromosome dosage drives statin-induced dysglycemia and mitochondrial dysfunction'.
Answer: Statin drugs lower blood cholesterol levels for cardiovascular disease prevention. Women are more likely than men to experience adverse statin effects, particularly new-onset diabetes (NOD) and muscle weakness. Here we find that impaired glucose homeostasis and muscle weakness in statin-treated female mice are associated with reduced levels of the omega-3 fatty acid, docosahexaenoic acid (DHA), impaired redox tone, and reduced mitochondrial respiration. Statin adverse effects are prevented in females by administering fish oil as a source of DHA, by reducing dosage of the X chromosome or the Kdm5c gene, which escapes X chromosome inactivation and is normally expressed at higher levels in females than males. As seen in female mice, we find that women experience more severe reductions than men in DHA levels after statin administration, and that DHA levels are inversely correlated with glucose levels. Furthermore, induced pluripotent stem cells from women who developed NOD exhibit impaired mitochondrial function when treated with statin, whereas cells from men do not. These studies identify X chromosome dosage as a genetic risk factor for statin adverse effects and suggest DHA supplementation as a preventive co-therapy.
Question: Write a study description for the study titled 'Gut Microbiota Regulates Serum Metabolites in Mice with Nonalcoholic Fatty Liver Disease via Gut Metabolites: Mechanisms Involving Branched-Chain Amino Acids and Unsaturated Fatty Acids'.
Answer: In recent years, nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease globally. Studies indicate that the gut-liver axis plays an important role in the occurrence and development of this disease. Our previous studies showed that the gut microbiota and gut metabolites in mice with NAFLD changed significantly, but it is unclear whether these changes influenced the disease process through serum metabolites. We conducted a non-targeted metabolome analysis on serum metabolites and systematically investigated the correlations between serum metabolites, gut microbiota, gut metabolites, and phenotypic index. Additionally, we traced the potential origins of serum metabolites and analyzed host-microbial interactions to elucidate the underlying mechanisms linking changes in serum metabolites with gut microbiota and gut metabolites. The findings suggest that the imbalance of gut pathogenic microbiota, specifically Blautia and Helicobacter, and beneficial microbiota such as Allobaculum, in mice with nonalcoholic fatty liver disease may be an important cause of gut metabolic disorders. This disorder results in a reduction of unsaturated fatty acid contend, particularly a decrease in Eicosapentaenoic Acid (EPA) and Docosahexaenoic Acid (DHA), and an accumulation of branched fatty acids in the serum. Consequently, there is a significant elevation in liver injury indices, potentially exacerbating the progression of nonalcoholic fatty liver disease and obesity in mice. These results suggest that serum metabolites are influenced by gut microbiota and their metabolites, and the variations in serum metabolites provide valuable insights into the relationship between gut microbiota and their metabolites in the context of nonalcoholic fatty liver disease.
Question: Write a study description for the study titled 'Health outcomes of fruit juice and fruity beverage: a comparative analysis of gut microbiota and metabolomics in rats (Metabolomics assay)'.
Answer: BACKGROUND: Evidence on the relationship between food processing and health outcomes has been increasing steadily. Under this context, ultra-processing food, such as sugar-sweetened fruity beverages (SS-FB), is associated with a higher risk of metabolic syndrome. However, whether drinking fruit juice not from concentrate (NFC-FJ), which belongs to minimally processed food, causes poor health or not is controversial. The major goal was to determine the impact of fruit drinks with different processing degrees on health via the interaction of gut microbiota and metabolomics.RESULTS: Significant different trends in metabolic syndrome were found between NFC-FJ and SS-FB in a 4-week experiment. NFC-FJ increased alpha diversity and decreased F/B ratio compared to SS-FB. The modulated bacterial taxa by NFC-FJ increased lipid metabolism as well as decreased insulin resistance and inhibited the dimethyl-L-arginine (ADMA) formation from S-adenosyl-L-methionine (SAM), contributing to a lower risk of metabolic syndrome in rats. However, SS-FB led to a higher risk of metabolic syndrome in rats with increased food intake and weight change. Additionally, SS-FB with the fructose-to-glucose ratio of 1.5 corresponded to an increase in kidney mass and serum C17-sphinganine level, boosting risks for kidney disease. More than 10 times higher flavonoid content in NFC-FJ than SS-FB was caused by processing degrees, which might be partly responsible for the alteration of gut microbiota.CONCLUSIONS: Our results revealed that rich flavonoids in minimally processed fruit juice decreased the risk of metabolic syndrome in rats through the pathway of insulin resistance via gut microbiota alteration, while ultra-processed fruit beverages enhanced the risk of metabolic syndrome. Based on our data, NFC fruit juice should be considered a healthy choice.Metabolomics assay is reported in the current study MTBLS3943.Lipidomics assay is reported in MTBLS4108.
Question: Write a study description for the study titled 'Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure'.
Answer: Respiratory failure and mortality from COVID-19 result from virus- and inflammation-induced lung tissue damage. The intestinal microbiome and associated metabolites are implicated in immune responses to respiratory viral infections, however their impact on progression of severe COVID-19 remains unclear. We prospectively enrolled 71 patients with COVID-19 associated critical illness, collected fecal specimens within 3 days of medical intensive care unit admission, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived metabolites (NCT 04552834). Of the 71 patients, 39 survived and 32 died. Mortality was associated with increased representation of Proteobacteria in the fecal microbiota and decreased concentrations of fecal secondary bile acids and desaminotyrosine (DAT). A microbiome metabolic profile (MMP) that accounts for fecal secondary bile acids and desaminotyrosine concentrations was independently associated with progression of respiratory failure leading to mechanical ventilation. Our findings demonstrate that fecal microbiota composition and microbiota-derived metabolite concentrations can predict the trajectory of respiratory function and death in patients with severe SARS-Cov-2 infection and suggest that the gut-lung axis plays an important role in the recovery from COVID-19.
Question: Write a study description for the study titled 'LCMS analysis of seven apple varieties with a leaking chromatographic column'.
Answer: The experiment contains data from a metabolomics experiment on different apple varieties. Quality Control and Standard Mixture samples are also included. In this study, retention times are extremely variable because of a problem with the chromatographic column.
Question: Write a study description for the study titled 'Effect of Pro-longevity drugs on Lipid profile, link between lipid signalling and longevity'.
Answer: We report the effect of four lifespan modifying drugs and of combinations of these drugs on lipid profile in Caenorhabditis elegans. We investigated drug-drug interactions and identified beneficial drug interactions between drugs selected to target synergistic longevity mechanisms and pathways. We employ ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) to compare the abundance of lipid species in treated and control animals. Adult nematodes were treated with rapamycin, rifampicin, psora-4 and allantoin and combinations of these compounds and the resulting change in lipid profiles, specifically in those of triacylglycerol (TAG), phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were determined. We quantified changes resulting from treatment with the drug combinations relative to untreated controls and relative to animals treated with each constituent single drugs. We further determined the dependence of changes in lipid profiles on genes know to affect lipid metabolism using strains carrying mutations in these pathways. In particular, we determined lipid profiles in genetic model of caloric restriction (eat-2), strain lacking homolog of TGFβ (daf-7) and in strain lacking the SREBP/sbp-1 transcription factor.
Question: Write a study description for the study titled 'Comparative Metabolomic Profiling of Compatible and Incompatible Interactions Between Potato and Phytophthora infestans'.
Answer: Late blight is one of the main biological stresses limiting the potato yield; however, the biochemical mechanisms underlying the infection process of Phytophthora infestans remain unrevealed. In this study, the late blight-resistant potato cultivar Ziyun No.1 (R) and the susceptible cultivar Favorita (S) were inoculated with P. infestans. Untargeted metabolomics was used to study the changes of metabolites in the compatible and incompatible interactions of the two cultivars and the pathogen at 0, 48 and 96 h postinoculation (hpi). A total of 819 metabolites were identified, and the metabolic differences mainly emerged after 48 hpi. There were 198 and 115 differentially expressed metabolites (DEMs) in the compatible and incompatible interactions. These included 147 and 100 upregulated metabolites during the compatible and incompatible interactions, respectively. Among them, 73 metabolites were identified as the P. infestans-responsive DEMs. Furthermore, the comparisons between the two cultivars identified 57 resistance-related metabolites. Resistant potato cultivar had higher levels of salicylic acid and several upstream phenylpropanoid biosynthesis metabolites, triterpenoids and hydroxycinnamic acids and their derivatives, such as sakuranetin, ferulic acid, ganoderic acid Mi, lucidenic acid D2 and caffeoylmalic acid. These metabolites play crucial roles in cell wall thickening and have antibacterial and antifungal activities. This study reports the time-course metabolomic responses of potatoes to P. infestans. The findings reveal the responses involved in the compatible and incompatible interactions of potatoes and P. infestans.
Question: Write a study description for the study titled 'Rapid detection of Staphylococcus aureus and Streptococcus pneumoniae by real-time analysis of volatile metabolites'.
Answer: Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that Secondary Electro-Spray Ionization-High Resolution Mass Spectrometry (SESI-HRMS) can be used as a diagnostic tool for rapid detection of bacterial infections as a supportive system for current state of the art diagnostics. Volatile Organic Compounds (VOCs) produced by growing S. aureus or S. pneumoniae cultures on blood agar plates were detected within minutes and allowed for the distinction of these two bacteria on a species and even strain level within hours. Furthermore, we obtained a fingerprint of clinical patient samples within minutes of measurement and predominantly observed a separation of samples containing living bacteria compared to samples with no bacterial growth. Further development of this technique may reduce the time required for microbiological diagnosis and should help to improve patient’s tailored treatment.
Question: Write a study description for the study titled 'Metabolic Phenotypes of Hypoxic-Ischemic Encephalopathy with Normal vs. Pathologic Magnetic Resonance Imaging Outcomes'.
Answer: Hypoxic-Ischemic Encephalopathy (HIE) is one of the most relevant contributors to neurological disability in term infants. We hypothesized that clinical outcomes of newborns with (HIE) can be associated with changes at plasma metabolic level enabling the detection of brain injury. Plasma samples of a cohort of 55 asphyxiated infants who evolved to moderate/severe HIE were collected between birth and completion of therapeutic hypothermia (TH). Samples were analyzed employing a quantitative gas chromatography-mass spectrometry method for the determination of lactate and pyruvate and an untargeted liquid chromatography-time-of-flight mass spectrometry method for metabolic fingerprinting. Brain injury was assessed employing magnetic resonance imaging (MRI). A critical assessment of the usefulness of lactate, pyruvate, and pyruvate/lactate for outcome prediction was carried out. Besides, metabolic fingerprinting identified a dynamic perturbation of eleven metabolic pathways, including amino acid and purine metabolism, and the steroid hormone biosynthesis, in newborns with pathologic MRI outcomes. Although data suggest the usefulness of lactate and pyruvate monitoring during 72 h for discerning outcomes, only the steroid hormone biosynthesis pathway was significantly altered in early plasma samples (i.e., before the initiation of TH). This study highlights pathways that might potentially be targeted for biomarker discovery or adjuvant therapies to be combined with TH.
Question: Write a study description for the study titled 'Vegetable Signatures Derived from Human Urinary Metabolomic Data in Controlled Feeding Studies'.
Answer: Examination of changes in urinary metabolomic profiles after vegetable ingestion may lead to new methods of assessing plant food intake. To this regard, we developed a proof-of-principle methodology to identify urinary metabolomic signatures for spinach, celery, and onion. Three feeding studies were conducted. In the first study, healthy individuals were fed with spinach, celery, onion, and no vegetables in four separate experiments with pooled urinary samples for metabolite discovery. The same protocol was used to validate the finding at the individual level in the second study and when feeding all three vegetables simultaneously in the third study. An LC-MS-based metabolomics approach was adopted to search for indicative metabolites from urine samples collected during multiple time periods before and after the meal. Consequently, a total of 1, 9, and 3 nonoverlapping urinary metabolites were associated with the intake of spinach, celery, and onion, respectively. The PCA signature of these metabolites followed a similar time cycle pattern, which maximized at approximately 2-4 h after intake. In addition, the metabolite profiles for the same vegetable were consistent across samples, regardless of whether it was consumed individually or in combination. The developed methodology along with the identified urinary metabolomic signatures were potential tools for assessing plant food intake.
Question: Write a study description for the study titled 'Profiles of phenolic secondary metabolites in plants of barley (Hordeum vulgare L.)'.
Answer: Secondary metabolites are frequently involved in mechanisms of the plant tolerance to environmental stresses. Determining metabolic biomarkers for drought tolerance may be a useful implementation in increasing and stabilizing crop plant productivity. The most accurate and fast tool for this purpose is the ultra-high performance liquid chromatography (UHPLC). It enabled a rapid discrimination between samples from plants grown in different water limitation regimes. Multivariate statistical analysis was applied to handle and interpret the complexity of the generated data. UHPLC raw data was mathematically pre-processed to reduce the effects of instrumental factors. The multivariate analysis of variance was used to find the significant changes in the secondary metabolites composition induced by the drought stress. Tests were performed on 9 varieties of spring barley (Hordeum vulgare L.) originating from Europe, North America and Syria. Drought stress was applied at different developmental stages. The UHPLC results suggest that the changes in metabolite profiles are a stage-specific trait and alter in the life cycle. In addition, there is variability in metabolites selected as significant for the reaction to drought depending on sampling time and variety. In parallel, an ion trap mass spectrometer with an electrospray ion source coupled to a high performance liquid chromatography (HPLC) and UV detector was used for qualitative analysis of phenolic compounds and identification of the potential biomarkers.