LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'LipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation - DIA lipid mediator validation'.
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 MTBLS1382, to validate lipid mediator species identified with the Qtrap instrument (https://www.ebi.ac.uk/metabolights/MTBLS1381), the Thermo QEx HF was used to perform high resolution MS full scan (HR-FS) and data independent acquisition (DIA) analyses between 200-400 m/z with a 20 m/z step size. DIA method preparation and data analysis were performed with Skyline. We used LipidCreator as an external tool in Skyline to generate a collision-energy specific transition list for the mediators 12-HETE, 13-HODE, 15-HETE, arachidonic acid (AA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and thromboxane B2 (TXB2) and their deuterated counterparts 12-HETE-d8, 13-HODE-d4, 15-HETE-d8, AA-d8, DHA-d5, EPA-d5 and TXB2-d4, at a normalized collision energy NCE=21. We also used LipidCreator's relative fragment intensity prediction model to generate a custom spectral library for the light and heavy mediators. We transfered both the transition list and the spectral library directly from LipidCreator to Skyline and exported the dot product values after manual fragment peaks review.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 (Black 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 black tea (Keemun type, gross, China) were spiked at 10 µg/kg levels with two different spiking mixes: Three sub-samples were spiked with a pool of 11 contaminants (spiking mix n°1); and Three sub-samples were spiked with 3 others contaminants (malathion, OTA, BPS, spiking mix n°2). Samples were 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.  Black tea spiked with contaminants is reported in the current study MTBLS772.  Green tea spiked with contaminants is reported in MTBLS771.  Linked Studies: MTBLS771
Question: Write a study description for the study titled 'Specific biomarkers for stochastic division patterns and starvation-induced quiescence under limited glucose levels in fission yeast'.
Answer: Glucose as a source of energy is centrally important to our understanding of life. We investigated the cell division-quiescence behavior of the fission yeast Schizosaccharomyces pombe under a wide range of glucose concentrations (0-111 mM). The mode of S. pombe cell division under a microfluidic perfusion system was surprisingly normal under highly diluted glucose concentrations (5.6 mM, 1/20 of the standard medium, within human blood sugar levels). Division became stochastic, accompanied by a curious division-timing inheritance, in 2.2-4.4 mM glucose. A critical transition from division to quiescence occurred within a narrow range of concentrations (2.2-1.7 mM). Under starvation (1.1 mM) conditions, cells were mostly quiescent and only a small population of cells divided. Under fasting (0 mM) conditions, division was immediately arrested with a short chronological lifespan (16 h). When cells were first glucose starved prior to fasting, they possessed a substantially extended lifespan (∼14 days). We employed a quantitative metabolomic approach for S. pombe cell extracts, and identified specific metabolites (e.g. biotin, trehalose, ergothioneine, S-adenosyl methionine and CDP-choline), which increased or decreased at different glucose concentrations, whereas nucleotide triphosphates, such as ATP, maintained high concentrations even under starvation. Under starvation, the level of S-adenosyl methionine increased sharply, accompanied by an increase in methylated amino acids and nucleotides. Under fasting, cells rapidly lost antioxidant and energy compounds, such as glutathione and ATP, but, in fasting cells after starvation, these and other metabolites ensuring longevity remained abundant. Glucose-starved cells became resistant to 40 mM H(2)O(2) as a result of the accumulation of antioxidant compounds.
Question: Write a study description for the study titled 'Integration of metabolomics and transcriptomics reveals major metabolic pathways and potential biomarkers involved in pulmonary tuberculosis and pulmonary tuberculosis-complicated diabetes'.
Answer: Pulmonary tuberculosis (PTB) and diabetes mellitus (DM) are common chronic diseases that threaten human health. Patients with DM are susceptible to PTB, an important factor that aggravates the complications of diabetes. However, the molecular regulatory mechanism underlying the susceptibility of patients with DM to PTB infection remains unknown. Healthy subjects, patients with primary PTB and patients with primary PTB complicated by DM were recruited according to inclusion and exclusion criteria. Peripheral whole blood was collected, and alteration profiles and potential molecular mechanisms were further analyzed using integrated bioinformatics analysis of metabolomics and transcriptomics. In this study, transcriptional data revealed that lipocalin 2 (LCN2), defensin alpha 1 (DEFA1), peptidoglycan recognition protein 1 (PGLYRP1) and integrin subunit alpha 2b (ITGA2B) were significantly upregulated, while chloride intracellular channel 3 (CLIC3) significantly down-regulated in PTB-DM by contrast to HC group. Additionally, the IL-17, PI3K-AKT and PPAR signaling pathways are important for PTB infection and regulation of PTB-complicated diabetes. Metabolomic data showed that glycerophospholipid metabolism, carbon metabolism and fat digestion and absorption processes were enriched in the differential metabolic analysis. Finally, integrated analysis of both metabolomic and transcriptomic data indicated that the NOTCH1/JAK/STAT signaling pathway is important in PTB complicated by DM. In conclusion, PTB infection altered the transcriptional and metabolic profiles of patients with DM. Metabolomic and transcriptomic changes were highly correlated in PTB-infected patients with DM. Peripheral metabolite levels may be used as biomarkers for PTB management in patients with DM.IMPORTANCE: The comorbidity of diabetes mellitus (DM) significantly increases the risk of tuberculosis infection and adverse tuberculosis treatment outcomes. Most previous studies have focused on the relationship between the effect of blood glucose control and the outcome of anti-tuberculosis treatment in pulmonary tuberculosis (PTB)-DM; however, early prediction and the underlying molecular mechanism of susceptibility to PTB infection in patients with DM remain unclear. Here, transcriptome sequencing and untargeted metabolomics were performed to elucidatethe key molecules and signaling pathways involved in PTB infection and the susceptibility of patients with diabetes to PTB. Our findings contribute to the development of vital diagnostic biomarkers for PTB or PTB-DM and provide acomprehensive understanding of molecular regulation during disease progression.
Question: Write a study description for the study titled 'Large-scale non-targeted plasma metabolomics in the Uppsala Longitudinal Study of Adult Men'.
Answer: The Uppsala Longitudinal Study of Adult Men (ULSAM) study is an ongoing, longitudinal, epidemiologic study started in 1970 and based on men born between 1920 and 1924 in Uppsala, Sweden which were invited to participate at age 50 (N=2,841) [PMID: 9484991]; 81.7% (N=2,322) participated. Individuals were reinvestigated at the ages of 60, 70, 77, 82 and 88 years. Information collected includes a medical questionnaire, blood pressure and anthropometric measurements, glucose tolerance test and 24-hour ambulatory blood pressure. Metbaolomics has been performed on plasma samples from age 70. In the final analysis we included samples from 1,138 individuals.
Question: Write a study description for the study titled 'Untargeted LC-HRMS Based-Plasma Metabolomics Reveals 3-O-Methyldopa as a New Biomarker of Poor Prognosis in High-Risk Neuroblastoma'.
Answer: Neuroblastoma (NB) is the most common extracranial malignant tumor in children. Although the survival rate of NB has improved over the years, the outcome of NB still remains poor for over 30% of cases. A more accurate risk stratification remains a key point in the study of NB and the availability of novel prognostic biomarkers of 'high-risk' at diagnosis could help improving patient stratification and predicting outcome. In this paper we show a biomarker discovery approach applied to the plasma of 172 NB patients. Plasma samples from a first cohort of NB patients and age-matched healthy controls were used for untargeted metabolomics analysis based on high-resolution mass spectrometry (HRMS). Differential expression analysis highlighted a number of metabolites annotated with a high degree of identification. Among them, 3-O-methyldopa (3-O-MD) was validated in a second cohort of NB patients using a targeted metabolite profiling approach and its prognostic potential was also analyzed by survival analysis on patients with 3 years follow-up. High expression of 3-O-MD was associated with worse prognosis in the subset of patients with stage M tumor (log-rank p < 0.05) and, among them, it was confirmed as a prognostic factor able to stratify high-risk patients older than 18 months. 3-O-MD might be thus considered as a novel prognostic biomarker of NB eligible to be included at diagnosis among catecholamine metabolite panels in prospective clinical studies. Further studies are warranted to exploit other potential biomarkers highlighted using our approach.
Question: Write a study description for the study titled 'Sexual dimorphism in the gonad lipidome of blue mussels (Mytilus sp.): New insights from a global lipidomics approach'.
Answer: Blue mussels (Mytilus sp.) are an economically important species for European aquaculture. Their importance as a food source is expected to increase in the coming net-zero society due to their low environmental footprint; however, their production is affected by anthropogenic stressors and climate change. During reproduction, lipids are key molecules for mussels as they are the main source of energy on which newly hatched embryos depend in the first days of their development. In this work, blue mussels of different origins are analysed, focusing on the differences in lipid composition between the ovary (BMO) and the testis (BMT). The lipidome of blue mussel gonads (BMG) is studied here by combining traditional lipid profiling methods, such as fatty acid and lipid class analysis, with untargeted liquid chromatography-mass spectrometry (LC-MS) lipidomics. The approach used here enabled the identification of 770 lipid molecules from 23 different lipid classes in BMG. BMT, which consists of billions of spermatocytes, had greater amounts of cell membrane and membrane lipid components such as FA18:0, C20 polyunsaturated fatty acids (PUFA), free sterols (ST), ceramide phosphoethanolamines (CerPE), ceramide aminoethylphosphonates (CAEP), cardiolipins (CL), glycerophosphocholines (PC), glycerophosphoethanolamines (PE) and glycerophosphoserines (PS). In BMO, saturated fatty acids (FA14:0 and FA16:0), monounsaturated fatty acids (MUFA) and other storage components such as C18-PUFA accumulated in triradylglycerolipids (TG) and alkyldiacylglycerols (neutral plasmalogens, TG O-), which, together with terpenes, wax esters and cholesterol esters, make up most of oocytes yolk reserves. BMO also had higher levels of ceramides (Cer) and generally alkyl/alkenyl glycerophospholipids (mainly plasmanyl/plasmenyl PC), suggesting a role for these lipids in vitellogenesis. Non-methylene interrupted dienoic fatty acids (NMID FA), typically found in plasmalogens, were the only membrane-forming PUFA predominantly detected in BMO. The results of this study are of great importance for clarifying the lipid composition of BMG and provide an important basis for future studies on the reproductive physiology of these organisms.
Question: Write a study description for the study titled 'Metabolic reprogramming is an initial step in pancreatic carcinogenesis that can be targeted to inhibit acinar-to-ductal metaplasia'.
Answer: Metabolic reprogramming is a hallmark of cancer and is crucial for cancer progression, making it an attractive therapeutic target. Understanding the role of metabolic reprogramming in cancer initiation could help identify prevention strategies. To address this, we investigated metabolism during acinar-to-ductal metaplasia (ADM), the first step of pancreatic carcinogenesis. Glycolytic markers were elevated in ADM lesions compared to normal tissue from human samples. Comprehensive metabolic assessment in three mouse models with pancreas-specific activation of KRAS, PI3K or MEK1 using Seahorse measurements, NMR metabolome analysis, mass spectrometry, isotope tracing and RNA-seq analysis revealed a switch from oxidative phosphorylation to glycolysis in ADM. Blocking the metabolic switch attenuated ADM formation. Furthermore, mitochondrial metabolism was required for de novo synthesis of serine and glutathione but not for ATP production. MYC mediated the increase in GSH intermediates in ADM, and inhibition of GSH synthesis suppressed ADM development. This study thus identifies metabolic changes and vulnerabilities in the early stages of pancreatic carcinogenesis.
Question: Write a study description for the study titled 'Spatial metabolomics shows contrasting phosphonolipid distributions in tissues of marine bivalves'.
Answer: Lipids are an integral part of cellular membranes, vary between species, and allow cells to alter stiffness, permeability and curvature. Among lipids, phosphonolipids uniquely contain a phosphonate bond between carbon and phosphorous. Despite this distinctive biochemical characteristic, few models explore the biological role of phosphonolipids. A protective function has been inferred based on chemical and biological stability. The function of a tissue ultimately depends on its chemical makeup. Thus if the function of a tissue is known, for example, the barrier function of exposed epithelial cells, the function of an associated metabolite can be inferred. To investigate possible functions of phosphonolipids we analyzed two species of marine mollusks, the blue mussel Mytilus edulis and pacific oyster Crassostrea gigas, and determined the diversity of phosphonolipids and their distribution in different organs. High resolution spatial metabolomics revealed that the lipidome varies significantly between tissues within one organ. Despite their chemical similarity, the heterogeneity of the phosphonolipids within the lipid landscape likely reflects a functional diversity of the tissue. While some phosphonolipids are ubiquitously distributed, others are present almost exclusively in the ciliated epithelial cells. The exclusive localization of certain phosphonolipids in tissues exposed to the environment supports the hypothesis of a protective function in mollusks. This study highlights that the tissue specific distribution of an individual metabolite can be a valuable tool in inferring its function.
Question: Write a study description for the study titled 'Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons'.
Answer: Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and Fv/Fm were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.
Question: Write a study description for the study titled 'Cysteamine-bicalutamide combination therapy corrects proximal tubule phenotype in cystinosis'.
Answer: Nephropathic cystinosis is a severe monogenic kidney disorder caused by mutations in CTNS, encoding the lysosomal transporter cystinosin, resulting in lysosomal cystine accumulation. The sole treatment, cysteamine, slows down the disease progression, but does not correct the established renal proximal tubulopathy. Here, we developed a new therapeutic strategy by applying omics to expand our knowledge on the complexity of the disease and prioritize drug targets in cystinosis. We identified alpha-ketoglutarate as a potential metabolite to bridge cystinosin loss to autophagy, apoptosis and kidney proximal tubule impairment in cystinosis. This insight combined with a drug screen revealed a bicalutamide-cysteamine combination treatment as a novel dual-target pharmacological approach for the phenotypical correction of cystinotic kidney proximal tubule cells, patient-derived kidney tubuloids and cystinotic zebrafish.
Question: Write a study description for the study titled 'A comprehensive metabonomic and transcriptomic analysis reveals how inhibiting glycolysis affects regulatory T cell proliferation'.
Answer: Background: Blocking glycolysis inhibits regulatory T cells (Tregs), which are often hijacked by tumor cells whose survival relies on glycolysis to inhibit antitumor immunity. However, how glycolysis influences Treg proliferation/differentiation remains unclear. Monocarboxylate transporters (MCTs) are key regulatory proteins that affect glycolysis. Methods: To describe the potential mechanism underlying the effect of glycolysis on Treg proliferation and differentiation as well as the role of MCT1 on Treg metabolism, we conducted a comprehensive metabonomic and transcriptomic analysis using omics and molecular biology techniques. Results: Fifteen differential metabolites and 2232 differentially expressed genes (DEGs) were identified, which were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to determine the most widely affected pathways. The results revealed that the adenosine triphosphate-binding cassette (ABC) transporter metabolism pathway was the most differentially activated between these two groups. According to The Cancer Genome Atlas (TCGA) database, the expression of ABC transporter-related genes affects renal clear cell carcinoma prognosis and is closely related to tumor immune cell infiltration. Conclusions: The comprehensive analysis showed that MCT1-induced ABC transporter disorder has important effects on Treg biology. These insights will help to clarify the mechanism of MCT1-induced Treg growth inhibition and emphasize the importance of omics research for deepening the understanding of tumor cell proliferation mechanisms.
Question: Write a study description for the study titled 'Identification of Biomarkers using Metabolomics in Porcine Hemorrhagic Shock'.
Answer: Hemorrhagic shock with injury results in alterations of the metabolic state of an organism, which contribute to organ dysfunction and death. Previous investigations have explored the effects of carbohydrate prefeed in murine models but few in clinically relevant large animal models. We performed carbohydrate prefeed in pigs undergoing simulated polytrauma and hemorrhagic shock with resuscitation to determine if carbohydrate prefeeding if the metabolic response to shock is dependent on fed state. Sixty-four Yorkshire pigs were divided into two experimental groups: fasted and prefed in additon to two Control groups. Experimental animals were subjected to a standardized hemorrhagic shock protocol, including pulmonary contusion and liver crush injury. To determine molecular alterations in response to trauma as a result of prefeeding, liver and muscle biopsies in addition to serum and urine samples were obtained at set timepoints throughout the procedure. The samples were prepared and analyzed by NMR spectroscopy.