LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. ('Sacurine' data set)'.
Answer: Urine metabolomics is widely used for biomarker research in the fields of medicine and toxicology. As a consequence, characterization of the variations of the urine metabolome under basal conditions becomes critical in order to avoid confounding effects in cohort studies. Such physiological information is however very scarce in the literature and in metabolomics databases so far. Here we studied the influence of age, body mass index (BMI), and gender on metabolite concentrations in a large cohort of 183 adults by using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). We implemented a comprehensive statistical workflow for univariate hypothesis testing and modeling by orthogonal partial least-squares (OPLS). This repository contains the data set from the negative ionization mode: 2 batches, 234 files (24 blanks + 26 QCs + 184 samples) in the Thermo .RAW (6.8 Go) and .mzML (18 Go) formats. The comprehensive analysis of this data set is publicly available on the Workflow4metabolomics.org e-infrastructure with two reference histories: 'W4M00002_Sacurine-comprehensive' corresponds to the preprocessing of the .mzML files, followed by signal drift and batch effect correction, normalization, filtering, statistics, and annotation of the peak table; 'W4M00001_Sacurine- statistics' starts with the peak table restricted to the 113 identified metabolites (see Roux et al. [1] for a full description and information about the annotation), and contains the statistical analysis (as described in associated publication except that the publication also describes the positive ionization mode). The intensities of the table provided in the m_sacurine.txt ISA file correspond to the peak table restricted to the 113 identified metabolites (i.e. are identical to the input of the 'W4M00001_Sacurine-statistics' history). Note that in both histories, the HU_096 sample is filtered out during the Hotelling/Quantile/MissingValue quality control sample filter, leading to 183 samples for the subsequent statistical analyzes. Notes: The 'sampling' field indicates the 9 successive weeks during which samples were collected. The 'subset' field indicates a subset of 36 files (6 blanks + 10 QCs + 20 samples) which still contain significant physiological variations (and can be used as e.g. demo or teaching material). Acknowledgements: The authors are grateful to Philippe Rocca-Serra for his help in preparing the ISA files. References: [1] Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C. 2012. Annotation of the Human Adult Urinary Metabolome and Metabolite Identification Using Ultra High Performance Liquid Chromatography Coupled to a Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer. Anal Chem. Aug 7;84(15):6429-37. doi: 10.1021/ac300829f.
Question: Write a study description for the study titled 'Virus-induced codon-specific reprogramming to favor viral RNA translation'.
Answer: Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed translational changes that occur upon CHIKV infection at the ER and the cytosol. We show that CHIKV infection induces codon-specific reprogramming of the host translation machinery to favor the translation of viral RNA genomes over host mRNAs with an otherwise optimal codon usage. This reprogramming was mostly apparent at the ER, where CHIKV RNAs are efficiently translated. Mechanistically, it involves CHIKV-induced overexpression of KIAA1456, an enzyme that modifies the wobble U34 position in the anticodon of tRNAs, which we find is required for proper decoding of codons that are highly enriched in CHIKV RNAs. Our findings demonstrate an unprecedented interplay of viruses with the host tRNA epitranscriptome to adapt the host translation machinery to viral production.
Question: Write a study description for the study titled 'Dietary Supplementation with Fermented Chinese Herbal Compounds Enhance Lamb Growth Performance via Targeted Modulation of Gastrointestinal Microbiota'.
Answer: This study adopted the MRM wide-targeted metabolomics approach to detect metabolites in herbal plant samples. Using ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (QTrap 6500+), combined with specific extraction and separation methods, qualitative and quantitative analysis of multiple metabolites in plant samples was achieved, providing data support for the study of metabolic characteristics of herbal plants.
Question: Write a study description for the study titled 'Adipocyte-specific Zeb1 confers breast cancer progression by triggering the tumor-associated adipose microenvironment remodeling'.
Answer: Upon penetrating the basement membrane, breast cancer cells directly interact with their surrounding adipose tissue, which forms a unique tumor-associated adipose microenvironment (TAME). However, the underlying mechanism involved in the regulation of lipid metabolic remodeling in the TAME remains elusive. Herein, we identified a Zeb1-orchestrated bidirectional communication between breast cancer cells and their adjacent cancer-associated adipocytes (CAAs). At the molecular level, breast cancer cells, through the secretion of adrenomedullin (AM), induce downregulation of Zeb1 expression to activate the Atgl/Hsl/Scd-depedent lipolysis in CAAs, which subsequently results in the release of palmitoleic acid (POA) into the TAME. In turn, accumulated POA triggers the malignant growth and metastasis of breast cancer cells and their production of AM via an ARA-PDG2-mediated membrane phospholipid replacement mechanism. Importantly, disruption of Zeb1-dependent lipolytic activity and/or membrane phospholipid remodeling within the TAME, severely diminishes the aggressiveness of breast cancer in vitro and in vivo
Question: Write a study description for the study titled 'Holistic Characterization of a Salmonella Typhimurium Infection Model Using Integrated Molecular Imaging'.
Answer: A more complete and holistic view on host–microbe interactions is needed to understand the physiological and cellular barriers that affect the efficacy of drug treatments and allow the discovery and development of new therapeutics. Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Salmonella Typhimurium infection in the liver of a mouse model using the S. Typhimurium strains SL3261 and SL1344. This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. IMC revealed a marked increase in immune cell markers and localization in immune aggregates in infected tissues. A correlative computational method (network analysis) was deployed to find metabolic features associated with infection and revealed metabolic clusters of acetyl carnitines, as well as phosphatidylcholine and phosphatidylethanolamine plasmalogen species, which could be associated with pro-inflammatory immune cell types. By developing an IMC marker for the detection of Salmonella LPS, we were further able to identify and characterize those cell types which contained S. Typhimurium.
Question: Write a study description for the study titled 'Molecular structural diversity of mitochondrial cardiolipins'.
Answer: Current strategies used to quantitatively describe the biological diversity of lipids by mass spectrometry are often limited in assessing the exact structural variability of individual molecular species in detail. A major challenge is represented by the extensive isobaric overlap present among lipids, hampering their accurate identification. This is especially true for cardiolipins, a mitochondria-specific class of phospholipids, which are functionally involved in many cellular functions, including energy metabolism, cristae structure, and apoptosis. Substituted with four fatty acyl side chains, cardiolipins offer a particularly high potential to achieve complex mixtures of molecular species. Here, we demonstrate how systematically generated high-performance liquid chromatography-mass spectral data can be utilized in a mathematical structural modeling approach, to comprehensively analyze and characterize the molecular diversity of mitochondrial cardiolipin compositions in cell culture and disease models, cardiolipin modulation experiments, and a broad variety of frequently studied model organisms.
Question: Write a study description for the study titled 'Metabolomics Insights in Early Childhood Caries'.
Answer: Dental caries is characterized by a dysbiotic shift at the biofilm-tooth surface interface, yet comprehensive biochemical characterizations of the biofilm are scant. We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study's analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North Carolina and were enrolled in a community-based cross-sectional study of early childhood oral health. Clinical examinations were conducted by calibrated examiners in community locations using International Caries Detection and Classification System (ICDAS) criteria. Supragingival plaque collected from the facial/buccal surfaces of all primary teeth in the upper-left quadrant was analyzed using ultra-performance liquid chromatography-tandem mass spectrometry. Associations between individual metabolites and 18 clinical traits (based on different ECC definitions and sets of tooth surfaces) were quantified using Brownian distance correlations (dCor) and linear regression modeling of log2-transformed values, applying a false discovery rate multiple testing correction. A tree-based pipeline optimization tool (TPOT)-machine learning process was used to identify the best-fitting ECC classification metabolite model. There were 503 named metabolites identified, including microbial, host, and exogenous biochemicals. Most significant ECC-metabolite associations were positive (i.e., upregulations/enrichments). The localized ECC case definition (ICDAS ≥1 caries experience within the surfaces from which plaque was collected) had the strongest correlation with the metabolome (dCor P = 8 × 10-3). Sixteen metabolites were significantly associated with ECC after multiple testing correction, including fucose (P = 3.0 × 10-6) and N-acetylneuraminate (p = 6.8 × 10-6) with higher ECC prevalence, as well as catechin (P = 4.7 × 10-6) and epicatechin (P = 2.9 × 10-6) with lower. Catechin, epicatechin, imidazole propionate, fucose, 9,10-DiHOME, and N-acetylneuraminate were among the top 15 metabolites in terms of ECC classification importance in the automated TPOT model. These supragingival biofilm metabolite findings provide novel insights in ECC biology and can serve as the basis for the development of measures of disease activity or risk assessment.
Question: Write a study description for the study titled 'Effect of L-carnitine administration on lipid and metabolite content in sheep infraspinatus muscle after tendon release'.
Answer: Metabolites and lipid species were measured using ultrahigh performance lipid chromatography – tandem mass spectrometry in biopsies of infraspinatus muscle after 2 weeks of tendon release in the operated and contralateral muscle. A group of animals received oral treatment with L-carnitine.
Question: Write a study description for the study titled 'Development and validation of the PyMS Mass Spectrometry software'.
Answer: To provide useful data for development and validation of the PyMS Mass Spectrometry software, a test dataset was run at Metabolomics Australia. A biologically complex mix of a biological background material (foetal calf serum), spiked with 2-fold increasing amounts of a mix of metabolite standards. In addition, a single sample consisting of a simple mix of 45 metabolites representing a variety of chemical classes (sufars, organic acids, amino acids, sugar phosphates), was run through a standard Metabolomics Australia GC-MS analysis. The resulting data is a valuable tool in testing GC-MS data analysis software.
Question: Write a study description for the study titled 'Disease phenotype prediction in multiple sclerosis'.
Answer: Progressive multiple sclerosis (PMS) is currently diagnosed retrospectively. Here, we work towards a set of biomarkers that could assist in early diagnosis of PMS. A selection of cerebrospinal fluid metabolites (n=15) was shown to differentiate between PMS and its preceding phenotype in an independent cohort (AUC=0.93). Complementing the classifier with conformal prediction showed that highly confident predictions could be made, and that three out of eight patients developing PMS within three years of sample collection were predicted as PMS at that time point. Finally, this methodology was applied to PMS patients part of a clinical trial for intrathecal treatment with rituximab. The methodology showed that 68% of the patients decreased their similarity to the PMS phenotype one year after treatment. In conclusion, the inclusion of confidence predictors contributes with more information compared to traditional machine learning, and this information is relevant for disease monitoring.Cohort 1 assays are reported in the current study MTBLS1464.Cohort 2 assays are reported in MTBLS558.
Question: Write a study description for the study titled 'Proteolytic-Resistant Self-Assembling Peptide Nanofibers Combat Specific Bacterial Infections via Trap-and-Kill'.
Answer: The rise in global antibiotic resistance highlights the urgent need for effective antimicrobial agents. Antimicrobial peptides (AMPs) offer a potential solution to combat bacterial resistance. However, key challenges remain in addressing the limitations of current peptide drugs and biomaterials, such as narrow action modes, poor protease stability, and challenges in pathogen-specific targeting. This study introduces a series of multifunctional AMPs by integrating self-assembling systems. By regulating the length of cationic amino acid side chains, the optimized peptide Nhar was identified as a triple-functional candidate with the potential to solve these limitations. In aqueous solutions, Nhar self-assembles into nanofibers that trap pathogens, prevent their spread, and selectively kill Gram-positive bacteria. Nhar demonstrates remarkable protease resistance, retaining antimicrobial activity even under 10 mg/mL protease conditions. It induces bacterial death primarily through membrane disruption and multiple synergistic mechanisms. In a Staphylococcus aureus induced mouse bacteremia model, Nhar showed promising therapeutic potential. This work offer important insights for developing multifunctional antimicrobial therapies.
Question: Write a study description for the study titled 'Metabolomic profiles in short day, before bolting, single leaf analysis, Arabidopsis thaliana'.
Answer: Metabolomic profiles in short or long day, before and after bolting, single leaf analysis, Arabidopsis thaliana
Question: Write a study description for the study titled 'Unique metabolism of different glucosinolates in larvae and adults of a leaf beetle specialised on Brassicaceae'.
Answer: Brassicaceae plants contain glucosinolates, which are hydrolysed by myrosinases to toxic products such as isothiocyanates and nitriles, acting as defences. Herbivores have evolved various detoxification strategies, which are reviewed here. Larvae of Phaedon cochleariae (Coleoptera: Chrysomelidae) metabolise hydrolysis products of benzenic glucosinolates by conjugation with aspartic acid. In this study, we investigated whether P. cochleariae uses the same metabolic pathway for structurally different glucosinolates, whether the metabolism differs between adults and larvae and which hydrolysis products are formed as intermediates. Feeding experiments were performed with leaves of watercress (Nasturtium officinale, Brassicaceae) and pea (Pisum sativum, non-Brassicaceae), to which glucosinolates with structurally different side chains (benzenic, indole or aliphatic) or their hydrolysis products were applied. Samples were analysed by UHPLC-QTOF-MS/MS or TD-GC-MS. The same aspartic acid conjugates as previously identified in larvae were also detected as major metabolites of benzenic glucosinolates in adults. Indol-3-ylmethyl glucosinolate was mainly metabolised to N-(1H-indol-3-ylcarbonyl) glutamic acid in adults and larvae, while the metabolism of 2-propenyl glucosinolate remains unclear. The metabolism may thus proceed primarily via isothiocyanates rather than via nitriles, while the hydrolysis occurs independently of plant myrosinases. A detoxification by conjugation with these amino acids is not yet known from other Brassicaceae-feeders.
Question: Write a study description for the study titled 'Comparison analysis of metabolite profiling in seeds and bark of Ulmus parvifolia, a Chinese medicine species'.
Answer: Ulmus parvifolia (U. parvifolia) was traditionally used in the treatment of some diseases such as inflammation, diarrhea and fevers. With the wide application of molecular biotechnology in plant development and utilization, the pharmaceutical value and chemical composition of the bark and leaves of U. parvifolia had been studied. However, metabolic signatures of seeds have not been studied. Seeds and bark of U. parvifolia were collected at the seeds ripening stage and metabolite profiling was performed through the untargeted metabolomics approach. A total of 2,578 and 2,207 metabolites were identified in seeds and bark, respectively. In particular, 574 differential metabolites were identified from the two parts of U. parvifolia, including flavonoids, terpene glycosides, triterpenoids and sesquiterpenoids. There are some bioactive compounds with antioxidant, anti-inflammatory and anti-cancer activities in these metabolites. More metabolites belonged to flavonoids and sesquiterpenoids were up-regulated in seeds than that in bark. There were more varieties of terpene glycosides and triterpenoids in bark than seeds. The pathway enrichment was performed, while flavonoid biosynthesis and flavone and flavonol biosynthesis were worthy of attention. Metabolic signatures of U. parvifolia seeds and bark were analyzed by untargeted metabolomics approach. Metabolite profiling, characteristics of differential metabolites and pathway enrichment were performed to evaluate the pharmaceutical value of seeds and bark. This study provided a scientific basis for the complementary use of the two different parts of U. parvifolia as a Chinese medicinal material.
Question: Write a study description for the study titled 'An ancient residue metabolomics-based method to distinguish use of closely related plant species in ancient pipes'.
Answer: Residues from ancient artifacts can help identify which plant species were used for their psychoactive properties, providing important information regarding the deep-time co-evolutionary relationship between plants and humans. However, relying on the presence or absence of one or several biomarkers has limited the ability to confidently connect residues to particular plants. We describe a comprehensive metabolomics-based approach that can distinguish closely related species and provide greater confidence in species use determinations. An approximately 1430-year-old pipe from central Washington State not only contained nicotine, but also had strong evidence for the smoking of Nicotiana quadrivalvis and Rhus glabra, as opposed to several other species in this pre-contact pipe. Analysis of a post-contact pipe suggested use of different plants, including the introduced trade tobacco, Nicotiana rustica. Ancient residue metabolomics provides a new frontier in archaeo-chemistry, with greater precision to investigate the evolution of drug use and similar plant-human co-evolutionary dynamics.
Question: Write a study description for the study titled 'Elucidations on the structures of some putative flavonoids identified in postharvest withered grapes (Vitis vinifera L.) by quadrupole time-of-flight mass spectrometry'.
Answer: Grape dehydration is an oenological process used for production of high-quality reinforced and sweet wines. High-resolution mass spectrometry (ultrahigh-performance liquid chromatography/quadrupole time-of-flight [UHPLC/QTOF]) was used to deepen the characterization of some flavonoids previously proposed in Corvina and Raboso Piave withered grapes. By performing a targeted data analysis workflow and orthogonal identification approaches (tandem mass spectrometry [MS/MS]), in silico fragmentation, and calculation of putative retention time), elucidation on the structures of six compounds previously proposed was achieved (taxifolin-pentoside, two tetrahydroxyflavanone-hexoside derivatives, a tetrahydroxy-dimethoxyflavanone-hexoside derivative, a pentahydroxyflavone, and peonidin-O-pentoside); and the structures of four putative new grape flavonoids were characterized (dihydromyricetin-O-hexoside, taxifolin-di-O-hexoside, isorhamnetin, and a pinoquercetin isomer). Findings enlarge the panorama of flavonoids in grape and of their possible biosynthetic pathways.
Question: Write a study description for the study titled 'Multitrait engineering of Hassawi red rice for sustainable cultivation'.
Answer: Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals. However, Hassawi has a long growth cycle, high cultivation costs, low productivity, and susceptibility to lodging. Here, to improve these undesirable traits via genome editing, we established efficient regeneration and Agrobacterium-mediated transformation protocols for Hassawi. In addition, we generated the first high-quality reference genome and targeted the key flowering repressor gene, Hd4, thus shortening the plant's lifecycle and height. Using CRISPR/Cas9 multiplexing, we simultaneously disrupted negative regulators of flowering time (Hd2, Hd4, and Hd5), grain size (GS3), grain number (GN1a), and plant height (Sd1). The resulting homozygous mutant lines flowered extremely early (∼56 days) and had shorter stems (approximately 107 cm), longer grains (by 5.1%), and more grains per plant (by 50.2%), thereby enhancing overall productivity. Furthermore, the awns of grains were 86.4% shorter compared to unedited plants. Moreover, the modified rice grain displayed improved nutritional attributes. As a result, the modified Hassawi rice combines several desirable traits that can incentivize large-scale cultivation and reduce malnutrition.