LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'RBC Balanced Immuno-inflammatory Signatures Identify Advanced Breast Cancer Patients on CDK4/6 Inhibitors at Increased Risk of Progression and Death'.
Answer: Recent studies show red blood cell (RBC) plays an essential role in regulating immunity. Nevertheless, the association of immuno-inflammatory parameters, especially RBC balanced signatures, with survival outcomes and adverse events still require investigation for advanced breast cancer (ABC) patients receiving cyclin-dependent kinases 4/6 inhibitor (CDKI). Herein, the predictive and prognostic performance of novel RBC balanced immuno-inflammatory (RBC-IMM) parameters is evaluated relative to classical-IMM ones. A total of 100 CDKI-treated ABC patients are included. The RBC-IMM score prominently recognizes patients at high risk of progression-free survival (PFS) events (P < 0.001), death (P < 0.001), grade 3/4 leukopenia (P = 0.010) and increased aspartate aminotransferase (P = 0.049). Interestingly, RBC-IMM score predicts the PFS more accurately than classical-IMM score (AUC = 0.766 and 0.596, P = 0.005). Clinico+RBC_index exhibits superior performance to clinico_index in terms of PFS with the addition of RBC-IMM score to clinical features. Furthermore, metabolomics analysis identifies phosphatidylcholine (PtdCho) notably involved in the interplay between RBC-mediated immuno-inflammation and CDKI efficacy, based on which clinico+PtdCho_index is developed to optimize PFS prediction of clinico_index. All these findings indicate that novel RBC-IMM related parameters have the advantage of identifying benefit and safety in CDKI-treated ABC patients over classical indicators, offering clinical implications of underlying mechanisms for erythroid lineage specific differential metabolites.
Question: Write a study description for the study titled 'Transcriptome and metabolome changes in Chinese cedar during cold acclimation reveal the roles of flavonoids in needle discoloration and cold resistance'.
Answer: Cryptomeria fortunei growth and development are usually affected by low temperatures. Despite the evergreen nature of this species, most needles turn yellowish-brown in cold winters. The underlying discoloration mechanisms that cause this phenomenon in response to cold acclimation remain poorly understood. Here, we measured the pigment content and ultrastructure of normal wild-type (Wt) and evergreen mutant (GM) C. fortunei needles and performed integrated transcriptomic and metabolomic analyses to explore potential discoloration mechanisms. The results showed that the needle chlorophyll content of these two genotypes decreased in winter. Wt needles showed greater decrease in the chlorophyll content and local destruction of chloroplast ultrastructure, and contained larger amounts of flavonoids than GM needles, as shown by metabolomics analysis. We subsequently identified key differentially expressed genes in the flavonoid biosynthesis pathway and observed significantly upregulated flavonol synthase (FLS) expression in Wt needles compared to GM needles, that significantly increased the anthoxanthin (flavones and flavonols) content, which is likely a key factor underlying the difference in needle color between these two genotypes. Therefore, flavonoid metabolism may play important roles in the cold resistance and needle discoloration of C. fortunei, and our results provide an excellent foundation for the molecular mechanism of C. fortunei in response to cold stress.
Question: Write a study description for the study titled 'Fu brick tea polysaccharides modulate fecal metabolites in mice with colitis'.
Answer: To investigate the effects of Fu Brick Tea Polysaccharides on fecal metabolites in mice with DSS-induced colitis, and to evaluate the changes in these metabolites using untargeted metabolomics.
Question: Write a study description for the study titled 'Pharmacokinetic and urinary profiling reveals prednisolone/cortisol ratio as a valid biomarker for prednisolone administration'.
Answer: In Europe, synthetic corticosteroids are not allowed in animal breeding fro growth-promoting purposes. Nevertheless, a high prevalence of non-compliant urine samples was recently reported for prednisolone, however, without any indication of unauthorized use. Within this context, 20b-dihydroprednisolone and the prednisolone/cortisol ratio have been suggested as potential tools to discriminate between exogenous and endogenous urinary prednisolone. In this study, the validity of these strategies was verified by investigating the urinary excretion profiles of relevant glucocorticoids in bovines, subjected to either 1) exogenous prednisolone treatment per os (PO), 2) exogenous prednisolone treatment by intra-muscular injection (IM), 3) tetracosactide hexaacetate (ACTH) to induce endogenous prednisolone formation, and 4) animals at slaughter to simulate natural stress conditions. For treatments the exogenous treatments, both growth-promoting and therapeutic prednisolone doses were considered. Bovine urine samples were analysed by liquid chromatography and mass spectrometry.
Question: Write a study description for the study titled 'Red-Fleshed Apple Anthocyanin Extracts Attenuate Male Reproductive System Dysfunction Caused by Busulfan in Mice (Apple extract; UPLC-MS/MS assay)'.
Answer: In this research, we analyzed the effect of oral administration of red-fleshed apple anthocyanin extract (RAAE) on busulfan-treated mice. At first, we showed that the most abundant component in RAAE was cyanidin 3-O-galactoside. To determine the effect of RAAE, mice were divided into control and four different concentrations of RAAE feeding treatment groups (BA0, no RAAE; BA0.1, 0.1 mg/kg; BA1, 1 mg/kg; BA5, 5 mg/kg) following busulfan injection. We observed that RAAE treatments displayed ameliorative effects on male reproductive system dysfunction caused by busulfan, including recovering the irregular arrangements of seminiferous tubules, increasing the number of spermatogonia and spermatocytes, improving sperm concentration by three-fold in BA0.1 and improving sperm motility by two-fold in BA1. LC-MS/MS analysis showed significant up- or down-regulation of certain metabolites such as lysophosphatidylcholine (LysoPC), L-arginine, glycine, anandamide, and L-carnitine, which could contribute to the positive effects of RAAE, especially in PBA1 (plasma of BA1) and PBA5 (plasma of BA5). Taken together, our results indicate that 1 mg/kg of RAAE is a suitable concentration for rescuing spermatogenesis in mice. Our research suggests that RAAE could be a potential nutraceutical for protecting spermatogenesis after busulfan therapy in cancer.UPLC-MS/MS assay of Apple extract is reported in the current study MTBLS2863.UPLC-MS/MS assays of Mouse blood plasma are reported in MTBLS2782.
Question: Write a study description for the study titled 'MaHPIC Experiment 06: Quantitative Metabolomics from Macaca mulatta infected with Plasmodium knowlesi sporozoites to produce and integrate clinical, hematological, parasitological, omics, telemetric and histopathological measures of acute primary infection'.
Answer: Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in four malaria-naive male rhesus macaques (Macaca mulatta), approximately five years of age. After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected. Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes. After inoculation, the macaques were profiled longitudinally for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements. The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infections or at the peak of parasitemias. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomics analyses. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses. Physiological data noted above were continuously captured via the implanted telemetry devices.  Within the MaHPIC, this project is known as 'Experiment 06'. This dataset was produced by Dr. Regina Cordy and Manoj Khadka at Emory University. To access other publicly available results from E06 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO). Linked Studies: Malaria Host-Pathogen Interaction Center (MaHPIC)
Question: Write a study description for the study titled 'Long-term application of biogas slurry altered the microbial community structure and metabolites in rhizosphere soil of poplar plantations'.
Answer: We aim to investigate the changes in the structure and function of rhizosphere microorganisms when different concentrations of biogas slurry are applied to the rhizosphere of poplar trees. By measuring the variations and types of rhizosphere metabolites, we can determine the microbial changes and their impact on the rhizosphere microenvironment of poplar trees.
Question: Write a study description for the study titled 'Cyclooxygenase-2, Asymmetric Dimethylarginine, and the Cardiovascular Hazard From Nonsteroidal Anti-Inflammatory Drugs (Murine and human plasma quantitative L-arginine and methylarginines UPLC-MS/MS assay)'.
Answer: "BACKGROUND: Large-scale, placebo-controlled trials established that nonsteroidal anti-inflammatory drugs confer a cardiovascular hazard: this has been attributed to depression of cardioprotective products of cyclooxygenase (COX)-2, especially prostacyclin. An alternative mechanism by which nonsteroidal anti-inflammatory drugs might constrain cardioprotection is by enhancing the formation of methylarginines in the kidney that would limit the action of nitric oxide throughout the vasculature.METHODS: Targeted and untargeted metabolomics were used to investigate the effect of COX-2 deletion or inhibition in mice and in osteoarthritis patients exposed to nonsteroidal anti-inflammatory drugs on the l-arginine/nitric oxide pathway.RESULTS: Analysis of the plasma and renal metabolome was performed in postnatal tamoxifen-inducible Cox-2 knockout mice, which exhibit normal renal function and blood pressure. This revealed no changes in arginine and methylarginines compared with their wild-type controls. Moreover, the expression of genes in the l-arginine/nitric oxide pathway was not altered in the renal medulla or cortex of tamoxifen inducible Cox-2 knockout mice. Therapeutic concentrations of the selective COX-2 inhibitors, rofecoxib, celecoxib, and parecoxib, none of which altered basal blood pressure or renal function as reflected by plasma creatinine, failed to elevate plasma arginine and methylarginines in mice. Finally, plasma arginine or methylarginines were not altered in osteoarthritis patients with confirmed exposure to nonsteroidal anti-inflammatory drugs that inhibit COX-1 and COX-2. By contrast, plasma asymmetrical dimethylarginine was increased in mice infused with angiotensin II sufficient to elevate blood pressure and impair renal function. Four weeks later, blood pressure, plasma creatinine, and asymmetrical dimethylarginine were restored to normal levels. The increase in asymmetrical dimethylarginine in response to infusion with angiotensin II in celecoxib-treated mice was also related to transient impairment of renal function.CONCLUSIONS: Plasma methylarginines are not altered by COX-2 deletion or inhibition but rather are elevated coincident with renal compromise.Murine and human plasma quantitative L-arginine and methylarginines UPLC-MS/MS assay protocols and data are reported in the current study MTBLS685.Murine kidney and plasma UPLC-MS/MS assay protocols and data are reported in MTBLS680."
Question: Write a study description for the study titled 'A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella'.
Answer: Pathogenic bacteria proliferating inside mammalian host cells need to rapidly adapt to the intracellular environment. How they achieve this and scavenge essential nutrients from the host has been an open question due to the difficulties in distinguishing between bacterial and host metabolites in situ. Here we capitalized on the inability of mammalian cells to metabolize mannitol to develop a stable isotopic labeling approach to track Salmonella enterica metabolites during intracellular proliferation in host macrophage and epithelial cells. By measuring label incorporation into Salmonella metabolites with liquid chromatography-mass spectrometry, and combining it with metabolic modeling, we identify relevant carbon sources used by Salmonella, uncover routes of their metabolization, and quantify relative reaction rates in central carbon metabolism. Our results underline the importance of the Entner-Doudoroff pathway and the phosphoenolpyruvate carboxylase for intracellularly proliferating Salmonella. More broadly, our metabolic labeling strategy opens novel avenues for understanding the metabolism of pathogens inside host cells.
Question: Write a study description for the study titled 'Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (C)'.
Answer: Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons.We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, longterm, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated sampling. A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics.
Question: Write a study description for the study titled 'Determining predictive metabolomic biomarkers of meniscal injury in dogs with cranial cruciate ligament disease'.
Answer: OBJECTIVES: This study used hydrogen nuclear magnetic resonance spectroscopy (1H NMR) for the first-time to examine differences in the metabolomic profile of stifle joint synovial fluid from dogs with cranial cruciate ligament rupture with and without meniscal injuries, in order to identify biomarkers of meniscal injury.METHODS: Stifle joint synovial fluid was collected from dogs undergoing stifle joint surgery or arthrocentesis for lameness investigations at three veterinary hospitals in the North-West of England. Samples underwent 1H NMR spectroscopy and metabolite identification. We used multivariate and univariate statistical analysis to identify differences in the metabolomic profile between dogs with cranial cruciate ligament rupture and meniscal injury, cranial cruciate ligament rupture without meniscal injury, and neither cranial cruciate ligament rupture nor meniscal injury, taking into consideration clinical variables.RESULTS: 154 samples of canine synovial fluid were included in the study. 64 metabolites were annotated to the 1H NMR spectra. Six spectral regions were found to be significantly altered (false discovery rate adjusted p-value <0.05) between groups with cranial cruciate ligament rupture with and without meniscal injury, including three attributed to NMR mobile lipids (mobile lipid -CH3 [p=0.016], mobile lipid -n(CH3)3 [p=0.017], mobile unsaturated lipid [p=0.031]).CLINICAL SIGNIFICANCE: We identified an increase in NMR mobile lipids in the synovial fluid of dogs with meniscal injury which are of interest as potential biomarkers of meniscal injury, as well as understanding the metabolic processes that occur with meniscal injury.
Question: Write a study description for the study titled 'SAR11 Cells Rely on Enzyme Multifunctionality to Transport and Metabolize a Range of Polyamine Compounds'.
Answer: In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, Ca. Pelagibacter st. HTCC7211 and C. P. ubique st. HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggests that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize.
Question: Write a study description for the study titled 'We characterize the anti-phage function of a type IV TA system, ShosTA toxin-antitoxin system provides phage defense via DNA damage and repair'.
Answer: Widespread in bacteria and archaea, Toxin-antitoxin (TA) systems have been recently demonstrated to function in phage defense. Here we characterize the anti-phage function of a type IV TA system, ShosTA. Using structural and biochemical approaches, we show that ShosT couples phosphoribosyltransferase and pyrophosphatase activities to disrupt purine metabolism, resulting in DNA duplication, cell filamentation and ultimate cell death. ShosA binds DNA and likely recruits other proteins to facilitate DNA recombination to antagonize ShosT’s toxicity
Question: Write a study description for the study titled 'Prediction of complex phenotypes using the Drosophila melanogaster metabolome'.
Answer: Understanding the genotype-phenotype map and how variation at different levels of biological organization is associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at DNA level and on intermediate endophenotypes, such as RNA, proteins and metabolites. This can facilitate our understanding of the link between genotypes and molecular and functional organismal phenotypes. Here, we use the Drosophila melanogaster Genetic Reference Panel and nuclear magnetic resonance (NMR) metabolomics to investigate the ability of the metabolome to predict organismal phenotypes. We performed NMR metabolomics on four replicate pools of male flies from each of 170 different isogenic lines. Our results show that metabolite profiles are variable among the investigated lines and that this variation is highly heritable. Second, we identify genes associated with metabolome variation. Third, using the metabolome gave better prediction accuracies than genomic information for four of five quantitative traits analyzed. Our comprehensive characterization of population-scale diversity of metabolomes and its genetic basis illustrates that metabolites have large potential as predictors of organismal phenotypes. This finding is of great importance, e.g., in human medicine, evolutionary biology and animal and plant breeding.
Question: Write a study description for the study titled 'Fragmentation patterns of methyloxime-trimethylsilyl derivatives of constitutive mono- and disaccharide isomers analyzed by gas chromatography/field ionization mass spectrometry'.
Answer: In saccharide analysis by gas chromatography/mass spectrometry (GC/MS), electron ionization (EI) is used almost exclusively, whereas other gentler methods of ionization are rarely used. Field ionization (FI) is recognized as a GC/MS ionization method that causes fewer fragment ions, but only few studies are available on its use in saccharide analysis. To evaluate the usefulness of FI in profiling isomeric saccharides by GC/MS and to explore its potential application in metabolome analysis, we compared EI, chemical ionization (CI), and FI spectral patterns of consecutive mono- and disaccharides derivatized with methoxamine-HCl and N-methyl-N-(trimethylsilyl)trifluoroacetamide. FI produced molecular ions and fragment ions characteristic of constitutive isomeric disaccharides. All of the derivatized saccharides that originally had free anomeric OH showed methyloxime-moiety fragment ions, attributable to the cleavage between C2 and C3. Some fragment ions in FI were indicative of the position of dihexose linkages. Although EI with lowered voltage (18 V, 130 °C) produced fewer fragment ions than conventional EI (70 V, 250 °C) did, fragmentation patterns were different from those of FI. Our data show that FI is useful for distinguishing isomeric saccharides in qualitative analyses.