LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Distinct succinate modifying products are clinically diagnostic and prognostic biomarkers for fumarate hydratase deficient renal cell carcinoma'.
Answer: Germline or somatic loss-of-function of fumarate hydratase (FH) predisposes patients to an aggressive form of renal cell carcinoma (RCC). Since other than tumor resection, there is no effective therapy for FH-deficient RCC, a competent method for early diagnosis and for early detection of recurrent and metastatic disease is an unmet clinical need. Currently, at best, an annual MRI scan is offered, though typically, MRI is used for symptomatic patients only. Therefore, finding specific and sensitive biomarkers suitable for routine and simple screens is crucial for improving the clinical outcome of these patients. Taking advantage of the robust metabolic rewiring that occurs in FH-deficient cells, we performed a large-scale study of plasma metabolomics comparing FH-deficient RCC patients to no-tumor control individuals or to wildtype FH RCC patients. Our results indicated two fumarate-derived metabolites, succinyl-adenosine and succinic-cysteine, to be outstanding plasma biomarkers for early diagnosis, with a positive predictive value of more than 90%. Furthermore, using pre-clinical and biochemical studies, we identified the enzymatic mechanisms by which these biomarkers are produced in and around the tumors.
Question: Write a study description for the study titled 'Long-lasting effects of oral polysaccharides on chemotherapy efficacy via alteration of the gut microbiota in a mouse model'.
Answer: Gemcitabine always has a short-term immune effect, and we consider using oral polysaccharides to lengthen its immune effect by modulating gut microbiotas. To verify this, we built a breast cancer mice model in situ, oral polysaccharides and a low-dose of Gemcitabine were administrated, and we found combined treatment has a certain immune enhancement effect through immunological-related experiments and tumor measurement. Additionally, 16s rRNA sequencing and metabonomics studies found combination treatment increases Butyric Acid and Trptophan and reshapes the gut microbiota.
Question: Write a study description for the study titled 'Excoriation Disorder Is Characterized by Systemic Glutamatergic Dysfunction'.
Answer: Excoriation disorder (ED), also known as neurotic excoriations, is a psychocutaneous disorder characterized by repetitive, compulsive picking of the skin leading to secondary tissue damage. ED carries an estimated prevalence of 1.4%, and is associated with significant social dysfunction, as patients often spend several hours each day performing compulsive behaviors leading to absence from work, school or other social events. Despite the significant impact on quality of life, there is still a lack of understanding of the factors involved in disease precipitation or progression, highlighting a need for identification of novel biomarkers of disease. The study of metabolic alterations, through plasma metabolomics, may lead to a greater understanding of disease pathogenesis, as metabolic alterations have been identified in related conditions such as obsessive-compulsive disorder (OCD) and in animal models of compulsive behavior. However, the metabolomic abnormalities present in ED have yet to be described. The purpose of this study is to perform an untargeted comparative plasma metabolomics analysis on ED patients and healthy controls to characterize the metabolic alterations in ED. Mass spectrometry quantified 76 total metabolites, 20 of which were identified as significantly different between ED and healthy controls, with four being increased and 16 being decreased in ED.
Question: Write a study description for the study titled 'LipidCreator workbench to probe the lipidomic landscape - Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standard'.
Answer: Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.In MTBLS1375, to validate tissue-specific transitions which we generated with LipidCreator, we conducted quantitative lipidomics experiments monitoring 433 lipids in the plasma of 21 healthy Asian human subjects. For a subset of 50 individual lipid levels the concentrations were compared to a recently conducted ring trial monitoring the lipid content of a reference material obtained from a mixed American population (NIST SRM 1950). The rationale behind this was to see if the creation of a list including internal standard and endogenous lipids lead to similar quantitative results as the ring trial experiment.Studies linked to this manuscript include;MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HFMTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTofMTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid ProfilingMTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standardMTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identificationMTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator ProfilingMTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation
Question: Write a study description for the study titled 'Untargeted food chemical safety assessment: A proof-of-concept on two analytical platforms and contamination scenarios of tea (Green tea study)'.
Answer: This study aims at assessing the capability of comparing and combining different instrumental platforms in an untargeted approach with a view of detecting chemical contaminants in food matrices at low levels. A strategy based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) and chemometrics has been applied on two different complex food contamination scenarios, with tea as study product. The first scenario aimed at mimic the presence of a dozen of contaminants at levels just above regulatory limits (i.e. 10 and 30 μg/kg); the second scenario, more complex, aimed at simulate the presence of several different contaminations at levels close to regulatory limits (10 μg/kg) in different samples. This work was carried on two LC-HRMS platforms (with respectively ToF and Orbitrap mass analyzer technologies), and a highly automated data treatment workflow was implemented to deal with data acquired on both platforms. The untargeted approach performed well on all scenarios (even the most complex) and analytical platforms. Performance comparison between LC-HRMS technologies was made possible thanks to a vendor-neutral data treatment process.  Sub-samples of green tea (Bancha type, gross, Japan) were spiked at different levels with a pool of 11 contaminants and then extracted with a generic method and analyzed by LC-HRMS (in both positive and negative ionization modes) on two platforms (respectively Orbitrap and ToF to generate a total of four data sets.  Green tea spiked with contaminants is reported in the current study MTBLS771.  Black tea spiked with contaminants is reported in MTBLS772.  Linked Studies: MTBLS772
Question: Write a study description for the study titled 'LipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation, targeted lipid mediator profiling'.
Answer: Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.In MTBLS1381, to validate the performance and accuracy of the transition lists provided by LipidCreator and their applicabability on other MS platforms, we used the transition lists for targeted profiling of lipid mediators in human platelet material. Platelets were stimulated with 0.01 U/ml thrombin, 1 U/ml thrombin, 1 µg/ml CRP or 5 µg/ml CRP for 5 min. The MS profiling of unstimulated and stimulated platelet material (pellet and supernatant) was performed after HPLC separation on an AB Sciex QTrap 6500 (Applied Biosystems, Darmstadt, Germany) in negative mode. Samples were measured in triplicates, interspersed with blank and standard runs.Studies linked to this manuscript include;MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HFMTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTofMTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid ProfilingMTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standardMTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identificationMTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator ProfilingMTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation
Question: Write a study description for the study titled 'Synovial Fluid Metabolites Differentiate between Septic and Nonseptic Joint Pathologies'.
Answer: Osteoarthritis (OA), osteochondrosis (OC), and synovial sepsis in horses cause loss of function and pain. Reliable biomarkers are required to achieve accurate and rapid diagnosis, with synovial fluid (SF) holding a unique source of biochemical information. Nuclear magnetic resonance (NMR) spectroscopy allows global metabolite analysis of a small volume of SF, with minimal sample preprocessing using a noninvasive and nondestructive method. Equine SF metabolic profiles from both nonseptic joints (OA and OC) and septic joints were analyzed using 1D 1H NMR spectroscopy. Univariate and multivariate statistical analyses were used to identify differential metabolite abundance between groups. Metabolites were annotated via 1H NMR using 1D NMR identification software Chenomx, with identities confirmed using 1D 1H and 2D 1H 13C NMR. Multivariate analysis identified separation between septic and nonseptic groups. Acetate, alanine, citrate, creatine phosphate, creatinine, glucose, glutamate, glutamine, glycine, phenylalanine, pyruvate, and valine were higher in the nonseptic group, while glycylproline was higher in sepsis. Multivariate separation was primarily driven by glucose; however, partial-least-squares discriminant analysis plots with glucose excluded demonstrated the remaining metabolites were still able to discriminate the groups. This study demonstrates that a panel of synovial metabolites can distinguish between septic and nonseptic equine SF, with glucose the principal discriminator.
Question: Write a study description for the study titled 'Bacterial profiles analysed by REIMS using Xevo G2-XS'.
Answer: Rapid evaporative ionisation mass spectrometry (REIMS) has been demonstrated capable of bacterial speciation by differentiation of their metabolic/lipidomic profiles. Previous work has shown the use of hand-held probes [1,2], and this dataset makes use of a robotic sampling probe which allows for high-throughput analysis [3]. This dataset consists of 651 isolates spanning 38 bacterial (564 isolates) and 6 (87 isolates) fungal species. Data are provided as Waters .raw and .mzXML files, with taxonomic and sample culturing information.[1] Strittmatter, N. et al., Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry. Chem. Commun., 2013, 49, 6188-6190. https://doi.org/10.1039/C3CC42015A[2] Strittmatter, N. et al., Characterization and Identification of Clinically Relevant Microorganisms Using Rapid Evaporative Ionization Mass Spectrometry. Anal. Chem., 2014, 86, 6555-6562. https://doi.org/10.1021/ac501075f[3] Bolt, F. et al., Automated High-Throughput Identification and Characterization of Clinically Important Bacteria and Fungi using Rapid Evaporative Ionization Mass Spectrometry. Anal. Chem., 2016, 88, 9419-9426. https://doi.org:10.1021/acs.analchem.6b01016
Question: Write a study description for the study titled 'Resveratrol metabolism in HepG2 (human hepatocytes), HaCaT (human keratinocytes), and C2C12 (mouse myoblasts)'.
Answer: Resveratrol (RESV) is a plant polyphenol, which is thought to have beneficial metabolic effects in laboratory animals as well as in humans. Following oral administration, RESV is immediately catabolized, resulting in low bioavailability. This study compared RESV metabolites and their tissue distribution after oral uptake and skin absorption. Metabolomic analysis of various mouse tissues revealed that RESV can be absorbed and metabolized through skin. We detected sulfated and glucuronidated RESV metabolites, as well as dihydroresveratrol. These metabolites are thought to have lower pharmacological activity than RESV. Similar quantities of most RESV metabolites were observed 4 h after oral or skin administration, except that glucuronidated RESV metabolites were more abundant in skin after topical RESV application than after oral administration. This result is consistent with our finding of glucuronidated RESV metabolites in cultured skin cells. RESV applied to mouse ears significantly suppressed inflammation in the TPA inflammation model. The skin absorption route could be a complementary, potent way to achieve therapeutic effects with RESV.  Cells were treated with 0, 20 or 200 µM RESV for 4 h. After washing with PBS, cells were lysed, and metabolites were extracted and analyzed by LC-MS. Peak areas metabolites were normalized by peak areas of spiked internal standards (10 nmol 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and piperazine-N,N’-bis(2-ethanesulfonic acid) (PIPES). 3 samples for each condition (except for HaCaT 200 µM, 2 samples).
Question: Write a study description for the study titled 'Growth Substrate and Prophage Induction Collectively Influence Metabolite and Lipid Profiles in a Marine Bacterium'.
Answer: Bacterial growth substrates influence a variety of biological functions, including the biosynthesis and regulation of lipid intermediates. The extent of this rewiring is not well understood nor has it been considered in the context of virally-infected cells. Here, we use a one-host-two-temperate phage model system to probe the combined influence of growth substrate and phage infection on host carbon and lipid metabolism. Using untargeted metabolomics and lipidomics, we report the detection of a suite of metabolites and lipid classes for two Sulfitobacter lysogens provided with three growth substrates of differing complexity and nutrient composition (yeast extract/tryptone [complex], glutamate and acetate). Growth medium led to dramatic differences in the detectable intracellular metabolites, with only 15% of 175 measured metabolites showing overlap across the three growth substrates. Between-strain differences were most evident in the cultures grown on acetate, followed by glutamate then complex medium. Lipid distribution profiles were also distinct between cultures grown on different substrates as well as between the two lysogens grown in the same medium. Five phospholipid, three aminolipid and one class of unknown lipid-like features were identified. Most (≥ 94%) of these 75 lipids were quantifiable in all samples. Metabolite and lipid profiles were strongly determined by growth medium composition and modestly by strain type. As fluctuations in availability and form of carbon substrates and nutrients, as well as virus pressure, are common features of natural systems, the influence of these intersecting factors will undoubtedly be imprinted in the metabolome and lipidome of resident bacteria.
Question: Write a study description for the study titled 'Towards improving point-of-care diagnosis of non-malaria febrile illness: a metabolomics approach'.
Answer: Background: Non-malaria febrile illnesses such as bacterial bloodstream infections (BSI) are a leading cause of disease and mortality in the tropics. However, there are no reliable, simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses. We hypothesized that different infectious agents responsible for severe febrile illness would impact on the host metabololome in different ways, and investigated the potential of plasma metabolites for diagnosis of non-malaria febrile illness.  Methodology: We conducted a comprehensive mass-spectrometry based metabolomics analysis of the plasma of 61 children with severe febrile illness from a malaria-endemic rural African setting. Metabolite features characteristic for non-malaria febrile illness, BSI, severe anemia and poor clinical outcome were identified by receiver operating curve analysis.  Principal Findings: The plasma metabolome profile of malaria and non-malaria patients revealed fundamental differences in host response, including a differential activation of the hypothalamic-pituitary-adrenal axis. A simple corticosteroid signature was a good classifier of severe malaria and non-malaria febrile patients (AUC 0.82, 95% CI: 0.70-0.93). Patients with BSI were characterized by upregulated plasma bile metabolites; a signature of two bile metabolites was estimated to have a sensitivity of 98.1% (95% CI: 80.2-100) and a specificity of 82.9% (95% CI: 54.7-99.9) to detect BSI in children younger than 5 years. This BSI signature demonstrates that host metabolites can have a superior diagnostic sensitivity compared to pathogen-detecting tests to identify infections characterized by low pathogen load such as BSI.  Conclusions: This study demonstrates the potential use of plasma metabolites to identify causality in children with severe febrile illness in malaria-endemic settings.
Question: Write a study description for the study titled 'Differential role of sphingomyelin in influenza virus, rhinovirus and SARS-CoV-2 infection of Calu-3 cells'.
Answer: Host cell lipids play a pivotal role in the pathogenesis of respiratory virus infection. However, a direct comparison of the lipidomic profile of influenza virus and rhinovirus infections is lacking. In this study, we first compared the lipid profile of influenza virus and rhinovirus infection in a bronchial epithelial cell line. Most lipid features were downregulated for both influenza virus and rhinovirus, especially for the sphingomyelin features. Pathway analysis showed that sphingolipid metabolism was the most perturbed pathway. Functional study showed that bacterial sphingomyelinase suppressed influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, but promoted rhinovirus replication. These findings suggest that sphingomyelin pathway can be a potential target for antiviral therapy, but should be carefully evaluated as it has opposite effects on different respiratory viruses. Furthermore, the differential effect of sphingomyelinase on rhinovirus and influenza virus may explain the interference between rhinovirus and influenza virus infection.
Question: Write a study description for the study titled 'Assessing the potential of sputtered gold nanolayers in mass spectrometry imaging for metabolomics applications (Brain MALDI-MSI assay)'.
Answer: Mass spectrometry imaging (MSI) is a molecular imaging technique that maps the distribution of molecules in biological tissues with high spatial resolution. The most widely used MSI modality is matrix-assisted laser desorption/ionization (MALDI), mainly due to the large variety of analyte classes amenable for MALDI analysis. However, the organic matrices used in classical MALDI may impact the quality of the molecular images due to limited lateral resolution and strong background noise in the low mass range, hindering its use in metabolomics. Here we present a matrix-free laser desorption/ionization (LDI) technique based on the deposition of gold nanolayers on tissue sections by means of sputter-coating. This gold coating method is quick, fully automated, reproducible, and allows growing highly controlled gold nanolayers, necessary for high quality and high resolution MS image acquisition. The performance of the developed method has been tested through the acquisition of MS images of brain tissues. The obtained spectra showed a high number of MS peaks in the low mass region (m/z below 1000 Da) with few background peaks, demonstrating the ability of the sputtered gold nanolayers of promoting the desorption/ionization of a wide range of metabolites. These results, together with the reliable MS spectrum calibration using gold peaks, make the developed method a valuable alternative for MSI applications.Brain MALDI MS imaging assay is reported in the current study MTBLS588.Liver MALDI MS imaging assay is reported in MTBLS589.
Question: Write a study description for the study titled 'Integrated transcriptomic and metabolomic analyses reveal the mechanism by which quercetin inhibits reflux esophagitis in rats'.
Answer: Quercetin relieves symptoms in mice with reflux esophagitis (RE), but the mechanism is unclear. Quercetin attenuates esophageal mucosal inflammation in RE mice by inhibiting the production of inflammatory factors IL-β and IL-6. In addition, using transcriptomic and metabolomic analyses, we found that metabolites related to bile acid metabolism, such as taurine, taurocholic acid and nicotinamide, were closely associated with RE mice. Quercetin reduced the expression of bile acid-related genes, such as Cd38, Sez6l2 and Nos2, who may be characteristic genes and therapeutic targets for reflux esophagitis.
Question: Write a study description for the study titled 'Targeted plasma metabolomics combined with machine learning for the diagnosis of acute SARS-CoV-2'.
Answer: The routine clinical diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely restricted to real-time reverse transcription polymerase chain reaction (RT-qPCR), and tests that detect SARS-CoV-2 nucleocapsid antigen. Given the diagnostic delay and suboptimal sensitivity associated with these respective methods, alternative diagnostic strategies are needed for acute infection. We studied the use of a clinically validated liquid chromatography triple quadrupole method (LC/MS-MS) for detection of amino acids from plasma specimens. We applied machine learning models to distinguish between SARS-CoV-2-positive and negative samples and analyzed amino acid feature importance. A total of 200 samples were tested, including 70 from individuals with COVID-19, and 130 from negative controls. The top performing model overall allowed discrimination between SARS-CoV-2-positive and negative control samples with an area under the receiver operating characteristic curve (AUC) of 0.96 (95% confidence interval [CI] 0.91, 1.00), overall sensitivity of 0.99 (95%CI 0.92, 1.00), and specificity of 0.92 (95%CI 0.85, 0.95). This approach holds potential as an alternative to existing methods for the rapid and accurate diagnosis of acute SARS-CoV-2 infection.