LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomic Analysis Reveals an Important Role of Sphingosine 1-phosphate in the Development of HFMD due to EV-A71 Infection'.
Answer: Hand, foot, and mouth disease (HFMD) is a serious pediatric infectious disease that causes immeasurable physical and mental health burdens. Currently, there is a lack of information on the mechanisms of HFMD severity and early diagnosis. We performed metabolomic profiling of sera from 84 Enterovirus A71 (EV-A71) infections and 45 control individuals. Targeted metabolomics assays were employed to further validate some of the differential metabolic molecules. We identified significant molecular changes in the sera of HFMD patients compared to healthy controls (HC). A total of 54, 60, 35 and 62 differential metabolites were screened between mild cases and HC, severe cases and HC, severe cases and mild cases, and among the three groups, respectively. These differential metabolites implicated dysregulation of tricarboxylic acid cycle, alanine, aspartate and glutamate metabolism, and valine, leucine and isoleucine biosynthesis. The diagnostic panel based on overlapped differential metabolites could effectively discriminate severe cases from mild cases with an AUC of 0.912 (95% CI: 0.85~0.97) using Logistic regression model. Next, we found the elevation of serum sphingosine 1-phosphate (S1P) level in EV-A71 infection mice, which was similar to clinical observation. Importantly, after blocking the release of S1P by MK571, the clinical symptoms and survival of mice were significantly improved, involving with the reduce of leukocyte infiltration in infected brain tissues. Collectively, our data provided a landscape view of metabolic alterations in EV-A71 infected children, and revealed regulating S1P metabolism was an exploitable therapeutic target against EV-A71 infection.
Question: Write a study description for the study titled 'Identifying metabolic alterations associated with coral growth anomalies using 1H NMR metabolomics'.
Answer: Coral growth anomalies (GAs) are tumor-like protrusions that are detrimental to coral health, impacting both the coral skeleton and soft tissues. These lesions are increasingly found throughout the tropics and are commonly associated with high human population density, yet little is known about the molecular pathology of the disease. Here, we investigate the metabolic impacts of GAs through 1H NMR metabolomics in Porites compressa tissues from a site of high disease prevalence (Coconut Island, Hawaii). We annotated 18 metabolites through complementary 1H and 1H–13C heteronuclear single quantum correlation (HSQC) data that increase confidence in pathway analyses and may bolster future efforts in coral metabolite annotation. Mass of extracted metabolites was elevated in both GA and unaffected (normal tissue from a diseased colony) compared to reference (normal tissue from GA-free colony) samples, potentially indicating elevated metabolic activity in GA-afflicted colonies. Relatively high variation in metabolomic profiles among corals of the same treatment confounded data interpretation, however, analyses of paired GA and unaffected samples identified 73 features that differed between these respective metabolome types. These features were largely annotated as unknowns, but 1-methylnicotinamide and trigonelline were found to be elevated in GA samples, while betaine, glycine and histamine were lower in GA samples. Pathway analyses suggest decreased choline oxidation in GA samples, making this a pathway of interest for future targeted studies. Collectively, our results provide unique insights into GA pathophysiology by showing these lesions alter both the absolute and relative metabolism of affected colonies and by identifying features (metabolites and unknowns) and metabolic pathways of interest in GA pathophysiology going forward.
Question: Write a study description for the study titled 'Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation (Targeted lipidomics assay without inhibition)'.
Answer: During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a lipid-centric multi-omics approach to create a quantitative map of the MK lipidome during maturation and proplatelet formation. Data reveal that MK differentiation is driven by an increased fatty acyl import and de novo lipid synthesis, resulting in an anionic membrane phenotype. Pharmacological perturbation of fatty acid import and phospholipid synthesis blocked membrane remodeling and directly reduced MK polyploidization and proplatelet formation resulting in thrombocytopenia. The anionic lipid shift during megakaryopoiesis was paralleled by lipid-dependent relocalization of the scaffold protein CKIP-1 and recruitment of the kinase CK2α to the plasma membrane, which seems to be essential for sufficient platelet biogenesis. Overall, this study provides a framework to understand how the MK lipidome is altered during maturation and the impact of MK membrane lipid remodeling on MK kinase signaling involved in thrombopoiesis.Targeted lipidomics assay without inhibition are reported in the current assay MTBLS6084Shotgun lipidomics assays without inhibition are reported in MTBLS6082Shotgun lipidomics assays after inhibition with FSG67 and Triacsin C are reported in MTBLS6083
Question: Write a study description for the study titled 'Impact of Diabetic Stress Conditions on Renal Cell Metabolome'.
Answer: Diabetic kidney disease is a major complication in diabetes mellitus, and the most common reason for end-stage renal disease. Patients suffering from diabetes mellitus encounter glomerular damage by basement membrane thickening, and develop albuminuria. Subsequently, albuminuria can deteriorate the tubular function and impair the renal outcome. The impact of diabetic stress conditions on the metabolome was investigated by untargeted gas chromatography-mass spectrometry (GC-MS) analyses. The results were validated by qPCR analyses. In total, four cell lines were tested, representing the glomerulus, proximal nephron tubule, and collecting duct. Both murine and human cell lines were used. In podocytes, proximal tubular and collecting duct cells, high glucose concentrations led to global metabolic alterations in amino acid metabolism and the polyol pathway. Albumin overload led to the further activation of the latter pathway in human proximal tubular cells. In the proximal tubular cells, aldo-keto reductase was concordantly increased by glucose, and partially increased by albumin overload. Here, the combinatorial impact of two stressful agents in diabetes on the metabolome of kidney cells was investigated, revealing effects of glucose and albumin on polyol metabolism in human proximal tubular cells. This study shows the importance of including highly concentrated albumin in in vitro studies for mimicking diabetic kidney disease.
Question: Write a study description for the study titled 'NGT induced mitochondrial dysfunction, led to apoptosis, and changed metabolites associated with oxidized lipids in sperm of Pacific oyster (Crassostrea gigas).'.
Answer: The risk of norgestrel (NGT) exposure in the aquatic environment has been identified, but the toxic effects on invertebrate germ cells are unknown. Therefore, the toxic effects of NGT on oyster sperm were investigated by combining transcriptome and metabolome analysis with histology. Transcriptome sequencing showed that differential genes were significantly enriched in regulation of cellular processes, protein digestion and absorption signaling pathways, and focal adhesion. We found that NGT exposure caused significant decreasing of mitochondrial ATP binding cassette and calcium uptake protein 1, and triggered apoptosis in sperm. Meanwhile, metabolome data showed that most of the differential metabolites were phosphatidylic acid, ammonium phosphatidylacetate and phosphatidylcholine, all of which were one of the main components of cell membrane, indicating that NGT exposure significantly affected the integrity and function of sperm cell membrane. In addition, NGT exposure induced significant changes in oxidized lipid metabolites, which may be related to apoptosis. In conclusion, this study suggests that NGT may induce mitochondrial dysfunction, lead to apoptosis, and significantly change the cell membranes and metabolites associated with oxidized lipids. This study is helpful to reveal the toxic effect of water environment NGT on in vitro fertilization invertebrate germ cells, and provide theoretical basis for formulating relevant environmental protection measures.
Question: Write a study description for the study titled 'Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data (Simulated)'.
Answer: Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets. We present a novel algorithm for the detection of mass traces and their aggregation into features (i.e. all signals caused by the same analyte species) that is computationally efficient and sensitive and that leads to reproducible quantification results. The algorithm is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing, co-elution information, and a support vector machine–based classifier able to identify potential metabolite isotope patterns. The algorithm is not limited to metabolites but is applicable to a wide range of small molecules (e.g. lipidomics, peptidomics), as well as to other separation technologies. We assessed the algorithm's robustness with regard to varying noise levels on synthetic data and then validated the approach on experimental data investigating human plasma samples. We obtained excellent results in a fully automated data-processing pipeline with respect to both accuracy and reproducibility. Relative to state-of-the art algorithms, ours demonstrated increased precision and recall of the method. The algorithm is available as part of the open-source software package OpenMS and runs on all major operating systems.Simulated data is reported in the current study MTBLS235.Plasma data is reported in MTBLS234.
Question: Write a study description for the study titled 'Changes in L-phenylalanine concentration reflect and predict response to anti-PD-1 treatment combined with chemotherapy in patients with non-small cell lung cancer'.
Answer: Chemotherapy combined with checkpoint blockade antibodies targeting programmed cell death protein (PD-1) has achieved remarkable success in non-small cell lung cancer (NSCLC). However, few patients benefit from long-term treatment. Therefore, biomarkers capable of guiding the optimal therapeutic selection and reducing unnecessary toxicity are of pressing importance. In our research, we gathered serial blood samples from two groups of NSCLC patients: 49 patients received a combination of therapies, and 34 patients went under chemotherapy alone. Utilizing non-targeted metabolomic analysis, we examined different metabolites’ disparity. Among the lot, L-phenylalanine emerged as a significant prognostic in the combination treatment of NSCLC patients, interestingly absent in patients under sole chemotherapy. The reduced ratio of L-phenylalanine concentration (two cycles treatment vs. pre-treatment) was associated with improved progression-free survival (hazard ratio [HR] = 1.8000, 95% confidence interval [CI], 0.8566‒3.7820, p < 0.0001) and overall survival (HR = 1.583, 95% CI, 0.7416‒3.3800, p < 0.005). We further recruited two validation cohorts (cohort 1:40 patients and cohort 2:30 patients) to validate the sensitivity and specificity of L-phenylalanine prediction. Our results demonstrate that a model based on L-phenylalanine variations could serve as an early risk-assessment tool for NSCLC patients undergoing treatment, potentially facilitating strategic clinical decision-making.
Question: Write a study description for the study titled 'Symptomatology and Serum Nuclear Magnetic Resonance Metabolomics; Do They Predict Endometriosis in Fertile Women Undergoing Laparoscopic Sterilisation? A Prospective Cross-sectional Study'.
Answer: Endometriosis is a common, chronic inflammatory condition, thought to have a higher incidence in symptomatic women, yet, commonly associated symptoms do not always correlate with the presence or severity of disease and diagnosis requires surgery. We prospectively collected data and assessed symptomology and NMR spectroscopy-based metabolomics of 102 women undergoing laparoscopic sterilisation at a tertiary referral centre in a cross-sectional study. Twelve women were incidentally diagnosed with endometriosis (11.7%). According to the pre-operative questionnaire, presence and absence of many symptoms usually attributed to endometriosis were declared at similar frequencies in women with or without endometriosis. Women with endometriosis reported apparently more persistent heavy periods (50% vs 18.9%), prolonged periods (25% versus 7.8%) and problems conceiving (27.3% versus 9%) than those without endometriosis. NMR could not discern any distinguishable differences in the serum metabolome between those with and without endometriosis. Our paper highlights the complex symptomology experienced by women, regardless of a surgical diagnosis of endometriosis. Previous literature and the current study failed to identify clear, distinguishable symptoms or biomarkers pertinent to surgically confirmed endometriosis in the general population. Therefore, development of effective, non-invasive tests for identifying this heterogenous benign condition, endometriosis, is likely to be challenging.
Question: Write a study description for the study titled 'Headspace volatile organic compounds from bacteria implicated in ventilator-associated pneumonia analysed by TD-GC/MS'.
Answer: Ventilator-associated pneumonia (VAP) is a healthcare-acquired infection arising from the invasion of the lower respiratory tract by opportunistic pathogens in ventilated patients. The current method of diagnosis requires the culture of an airway sample such as bronchoalveolar lavage, which is invasive to obtain and may take up to seven days to identify a causal pathogen, or indeed rule out infection. While awaiting results, patients are administered empirical antibiotics; risks of this approach include lack of effect on the causal pathogen, contribution to the development of antibiotic resistance and downstream effects such as increased length of intensive care stay, cost, morbidity and mortality. Specific biomarkers which could identify causal pathogens in a timely manner are needed as they would allow judicious use of the most appropriate antimicrobial therapy. Volatile organic compound (VOC) analysis in exhaled breath is proposed as an alternative due to its non-invasive nature and its potential to provide rapid diagnosis at the patient's bedside. VOCs in exhaled breath originate from exogenous, endogenous, as well as microbial sources. To identify potential markers, VAP-associated pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were cultured in both artificial sputum medium and nutrient broth, and their headspaces were sampled and analysed for VOCs. Previously reported volatile markers were identified in this study, including indole and 1-undecene, alongside compounds that are novel to this investigation, cyclopentanone and 1-hexanol. We further investigated media components (substrates) to identify those that are essential for indole and cyclopentanone production, with potential implications for understanding microbial metabolism in the lung.
Question: Write a study description for the study titled 'Experiment design beyond gut feeling: statistical tests and power to detect differential metabolites in mass spectrometry data'.
Answer: We use metabolite profiles of the model plant Arabidopsis thaliana measured on an UPLC-ESI/QqTOF-MS as a pilot study to estimate variance levels which then can be used to obtain several statistical parameters (e.g. minimum detectable effect, number of required replicates and error probabilities) which influence the design of a subsequent study.
Question: Write a study description for the study titled 'Metabolite profile of mice hippocampus following Toxoplasma gondii infection'.
Answer: Toxoplasma gondii is a protozoan parasite with a remarkable neuro-tropismneurotropic affinity. We recently showed that T. gondii infection can alter the global metabolism of the cerebral cortex of the mice. However, the impact of this infection on the metabolism of the hippocampus remains unclear. In this study, we compared the metabolomic profiles of mouse hippocampus following acute and chronic infection with T. gondii. Our data provide new insight into the neuropathogenesis of T. gondii infection and reveal new pathways and metabolites that mediate the interplay between T. gondii infection and the mouse hippocampus
Question: Write a study description for the study titled 'Altered metabolome and lipidome profiling in fearful companion dogs'.
Answer: Behavioral dysfunctions in dogs represent one of the main social concerns, since they can endanger animals and human-dog relationship. Together with the trigger stimulus (human, animal, place, scent, auditory stimuli, object), dogs can experience stressful situations, either in multiple settings or unique situations, more often turning into generalized fear. Such a dysfunctional behavior can be associated with genetic susceptibility, environmental factors, traumatic experiences, and medical conditions. The available therapy, based on behavior, environmental management, and neurochemical manipulation through nutrition, supplements, medicines, and pheromones, represent the main stays of the treatments currently accessible. Growing evidence in humans and animals highlight the importance of the gut-brain axis in the modulation of the brain physiology and behavior. Here, taking advantage of the next generation sequencing approach we sought to investigate the potential connection between gut microbiota and generalized fear dogs (n=8), when compared to healthy subjects (n=8), who lived in 16 different families. Then, using targeted LC-MS/MS method, we evaluated the metabolomics signature in the patients. Our results showed differentially abundance analysis in taxa related to Proteobacteria and Firmicutes Phyla, significantly altered in fearful dogs. In addition, metabolome analysis on the blood serum of the same showed significant alterations of molecules associated to GABA and glutamate neurotransmission in the patients, as well as bile acids metabolism. Overall, our preliminary and integrated investigations highlighted an intriguing role for the microbiome-metabolome network, allowing to further unveil the potential pathophysiology of relational issues in companion animals and paving the way for more effective therapeutical approaches. Accordingly, lipids are regarded as main components of the brain structure and facilitate a wide range of neuronal activities, ranging from energy-storing enzyme cofactors, emulsifying agents, vitamins, hormones, intercellular messengers and structural components of cell membranes. So, we investigated the serum lipidome profiles of fearful family dogs using a targeted lipidomic approach. Out of 26 differentially abundant lipids, we identified 17 phosphatidylcholine species increased in the diseased group compared to healthy subjects. Of these, were statistically validated and included in a combination of lipids operating as disease biomarkers. Collectively, our data pave the way for a deeper characterization of the impact of lipid dysregulation upon mood-related dysfunctions in dogs, and for identifying diagnostic biomarkers in the veterinary practice to cope with this neuropsychiatric disorder.
Question: Write a study description for the study titled 'Metabolic alterations in pea leaves during arbuscular mycorrhiza development'.
Answer: Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.
Question: Write a study description for the study titled 'Metabolism links nutrient stress and harmful algal bloom formation'.
Answer: Four species of phytoplankton representing important bloom-forming species from three globally important phyla (Bacillariophyta, Haptophyta, and Ochrophyte) were cultured in this study. These species include the cosmopolitan diatom Chaetoceros affinis CCMP159 (isolated from Great South Bay, NY, USA, 1958), the haptophytes Chrysochromulina polylepis CCMP1757 (isolated from the North Sea 1988) and Gephyrocapsa oceanica RCC1303 (isolated from Arachon Bay, France, Jan 1999), and the raphidophyte Heterosigma akashiwo strain CCMP 2393 (isolated from Rehoboth Bay, Delaware, USA). Cultures were grown under three conditions: nitrogen-stress, phosphorus-stress, and replete conditions. Intracellular metabolites were extracted from cultures and analyzed with targeted and untargeted mass spectrometry-based metabolomics methods.