LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Pomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor (in vitro): A Promising Source of Novel Antiviral Drugs'.
Answer: Plant extracts are rich in bioactive compounds, such as polyphenols, sesquiterpenes, and triterpenes, which potentially have antiviral activities. As a consequence of the coronavirus disease 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, thousands of scientists have been working tirelessly trying to understand the biology of this new virus and the disease pathophysiology, with the main goal of discovering effective preventive treatments and therapeutic agents. Plant-derived secondary metabolites may play key roles in preventing and counteracting the rapid spread of SARS-CoV-2 infections by inhibiting the activity of several viral proteins, in particular those involved in the virus entry into the host cells and its replication. Using in vitro approaches, we investigated the role of a pomegranate peel extract (PPE) in attenuating the interaction between the SARS-CoV-2 Spike glycoprotein and the human angiotensin-converting enzyme 2 receptor, and on the activity of the virus 3CL protease. Although further studies will be determinant to assess the efficacy of this extract in vivo, our results opened new promising opportunities to employ natural extracts for the development of effective and innovative therapies in the fight against SARS-CoV-2.
Question: Write a study description for the study titled 'MaHPIC Experiment 03: Metabolomics from Macaca mulatta infected with Plasmodium coatneyi Hackeri strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute, recrudescent, and chronic infections'.
Answer: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks. The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 100 days. The different clinical phases of the infection were clinically determined for each subject. Blood-stage curative doses of artemether were administered to all subjects at the end of the study. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 03'. This dataset was produced by Dean Jones at Emory University. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://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).Linked Studies: Malaria Host-Pathogen Interaction Center (MaHPIC)
Question: Write a study description for the study titled 'Metabolomics study of different tissues of mume 'Longyan' plant grafted on mume rootstock and peach rootstock (Stem)'.
Answer: Background: Grafting with the dwarf rootstock is an efficient method to control the plant height in fruit production. However, the molecular mechanism is still unclear. Our previous study showed that the plants with Prunus mume rootstock exhibit a considerable reduction in plant height, internode length and number of nodes compared with Prunus persica rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by ‘P. mume’ rootstocks through transcriptome and metabolomic analysis with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’. Results: The findings of the study indicate a significant decrease in brassinolide levels in plants that were grafted onto ‘P. mume’ rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased in the research. The present work observed a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto ‘P. mume’ rootstocks. Auxin signaling cues promote PmARF3 transcription, which directly controls this upregulation. Through its binding to PmBAS1 and PmSAUR36 gene promoters, PmLBD3 promotes endogenous brassinolide inactivation and inhibits cell proliferation. Conclusions: Auxin signaling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and caused dwarf plants in stone fruits.Stem analysis is reported in the current study MTBLS10062.Leaf analysis is reported in MTBLS10083.Root analysis is reported in MTBLS10051.
Question: Write a study description for the study titled 'Desorption electrospray ionisation mass spectrometry imaging of esophageal lymph mode metastases'.
Answer: Lymph node metastases (LNM) and primary tumour samples were analysed using desorption electrospray ionisation mass spectrometry imaging (DESI MSI). Current assessment of LNM depends on subjective histopathological assessment, whereas analysis by DESI MSI permits an entirely objective assessment. The mass spectral data revealed specific lipidomic patterns across samples, which were shown to correspond to the immunohistochemical image. Statistical prediction of LNM samples was performed using the esophageal adenocarcinoma samples with sensitivity and specificity of 89.5% and 100%, respectively.
Question: Write a study description for the study titled 'Differential analysis of physicochemical properties and small molecule metabolites in glutinous and non-glutinous sorghum'.
Answer: In this study, using 2 glutinous sorghum and 2 non-glutinous sorghum as research objects, and their differences in grain appearance color, peel thickness, starch structure and small molecule metabolites were analyzed and compared. The results showed that the grain of 2 glutinous sorghum was red, and the grain of 2 non-glutinous sorghum was white. The thickness of pericarp (pericarp layer and seed layer) of glutinous sorghum (49.35-78.16 μm) was significantly higher than that of non-glutinous sorghum (33.39-49.03 μm) (P＜0.05). The starch grains of glutinous sorghum were mainly oval-shaped and loosely arranged, while those in non-glutinous sorghum were irregular and tightly arranged. There were significant differences in the small molecule metabolites composition among different sorghum varieties. The marker metabolite of glutinous sorghum was catechin, while the marker metabolite of non-glutinous sorghum was 5-hydroxyindole-3-acetic acid. This study revealed significant differences in pericarp thickness, starch morphology, and small molecule metabolites between glutinous and non-glutinous sorghum, which was helpful to distinguish different sorghum varieties and lay a foundation for analyzing the relationship between liquor and grain.
Question: Write a study description for the study titled 'Pu-erh tea and theabrownin ameliorate metabolic syndrome in mice via potential microbiota-gut-liver-brain interactions'.
Answer: Metabolic syndrome (MS) is a common metabolic disorder characterized by obesity, insulin resistance, cardiovascular disease and gut microbiota dysbiosis. Pu-erh tea and its ingredient theabrownin have known functions on the reduction of body weight gain and fat accumulation. However, few studies systematicly analyze the different contributions and mechanisms of their anti-metabolic syndrome functions through multi-omics combination analysis. Here, we used metagenomics, transcriptomics and metabolomics technology to investigate the anti-metabolic syndrome mechanism of Pu-erh tea and theabrownin in MS mice. Our results suggested that Pu-erh tea and theabrownin interventions could improve the physiological functions of liver, jejunum and adipose tissues in MS mice. Hepatic transcriptome revealed that both interventions could regulate the circadian rhythm pathway. Glycerophospholipid and linoleic acid metabolism were also modulated by both interventions through serum and brain metabolome analysis. Faecal metagenome demonstrated that both interventions could increase the relative abundance of Clostridiales bacterium 42_27, Blautia coccoides and Firmicutes bacterium ASF500, but decrease the relative abundance of Brevundimonas vesicularis. Otherwise, compared with Pu-erh tea, theabrownin markedly upregulated the levels of hepatic antioxidants (i.e., SOD, GSH), prominently downregulated hepatic inflammatory factors (i.e., IL-1, IL-6, TNF-α) and malondialdehyde oxidant, but modestly reduced obesity-associated short-chain fatty acids in faeces in MS mice. Taken together, our data provided insights into the homogeneous and heterogeneous natural biological functions of theabrownin and Pu-erh tea in the treatment of metabolic syndrome.
Question: Write a study description for the study titled 'MetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Standard mixture assay)'.
Answer: We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS/MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis. With its stringent identification algorithm requiring matches by both MS and MS/MS data, MetaboKit provides identification results with significantly greater specificity than the competing software packages without loss in sensitivity. The proposed MS/MS-based screening of ISFs also reduces the chance of unverifiable identification of ISFs considerably. MetaboKit's quantification module produced peak area values highly correlated with known concentrations in a DIA analysis of the metabolite standards at both MS1 and MS2 levels. Moreover, the analysis of Cdk1Liv-/- mouse livers showed that MetaboKit can identify a wide range of lipid species and their ISFs, and quantitatively reconstitute the well-characterized fatty liver phenotype in these mice. In DIA data, the MS1-level and MS2-level peak area data produced similar fold change estimates in the differential abundance analysis, and the MS2-level peak area data allowed for quantitative comparisons in compounds whose precursor ion chromatogram was too noisy for peak integration.Standard mixture assay is reported in the current study MTBLS1311.Mouse liver assays are reported in MTBLS1266.
Question: Write a study description for the study titled 'Lung Lipidomic Alterations in Beagle Dogs Infected with Toxocara canis'.
Answer: Toxocariasis, mainly caused by Toxocara canis, and to a lesser extent, Toxocara cati, is a neglected parasitic zoonosis. The mechanisms that underlie the changes in lipid metabolism of T. canis infection in Beagle dogs' lungs remain unclear. Lipidomics is a rapidly emerging approach that enables the global profiling of lipid composition by mass spectrometry. In this study, we performed a non-targeted lipidomic analysis of the lungs of Beagle dogs infected with the roundworm T. canis using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1197 lipid species were identified, of which 63, 88 and 157 lipid species were significantly altered at 24 h post-infection (hpi), 96 hpi and 36 days post-infection (dpi), respectively. This global lipidomic profiling identified infection-specific lipid signatures for lung toxocariasis, and represented a comprehensive comparison between the lipid composition of dogs' lungs in the presence and absence of T. canis infection. The potential roles of the identified lipid species in the pathogenesis of T. canis are discussed, which has important implications for better understanding the interaction mechanism between T. canis and the host lung.
Question: Write a study description for the study titled 'Classification of Parkinson’s Disease and Delineating Progression Markers from the Sebum Volatilome'.
Answer: Parkinson's Disease (PD) has been associated with a distinct odour, which emanates from the skin and is strongest in sebum-rich areas. In this study, sebum was sampled from participants using cotton gauze and the volatile components emanating from these swabs were analysed directly with thermal desorption gas chromatography-mass spectrometry (TD GC-MS). We analysed subjects with clinically established PD (n=46) along with healthy controls (n=28) sampled from two sites. The volatilome profiles obtained for PD and control cohorts were compared with the profile of participants (n=9) with idiopathic REM sleep behaviour disorder (iRBD) to investigate metabolite changes in probable prodromal PD. We also compared PD participants sampled at yearly intervals for a total of three years. Volatile compounds from TD GC-MS analysis were found in different quantities between PD, control and iRBD subjects. We found 55 significant features where abundance in samples from individuals with iRBD was intermediate between that found for PD and control samples. Significant features were found to be alkanes and fatty acid methyl esters (FAMEs), with other metabolites identified as an aldehyde, purine and tropinone. In olfactory analysis of the iRBD samples three out of nine were classified PD, and on clinical follow up two of these showed PD symptoms. Further, when analysing the volatilome from longitudinal PD sampling, almost two-thirds of the significant features showed differential regulation over the three visits. Our findings support the use of sebum as an accessible biofluid rich with measurable volatile compounds which alter in abundance in individuals with PD and iRBD, as the disease progresses.
Question: Write a study description for the study titled 'The Green Tea Modulates Large Intestinal Microbiome and Exo/Endogenous Metabolome altered through Chronic UVB-exposure (Endogenous assays)'.
Answer: The attenuating effects of green tea supplements (GTS) against the ultraviolet (UV) radiation induced skin damages are distinguished. However, the concomitant effects of GTS on the large intestinal microbiomes and associated metabolomes are largely unclear. Herein, we performed an integrated microbiome-metabolome analysis to uncover the esoteric links between gut microbiome and exo/endogenous metabolome maneuvered in the large intestine of UVB-exposed mice subjected to dietary GTS. In UVB-exposed mice groups (UVB), class Bacilli and order Bifidobacteriales were observed as discriminant taxa with decreased lysophospholipid levels compared to the unexposed mice groups subjected to normal diet (NOR). Conversely, in GTS fed UVB-exposed mice (U+GTS), the gut-microbiome diversity was greatly enhanced with enrichment in the classes, Clostridia and Erysipelotrichia, as well as genera, Allobaculum and Lachnoclostridium. Additionally, the gut endogenous metabolomes changed with an increase in amino acids, fatty acids, lipids, and bile acids contents coupled with a decrease in nucleobases and carbohydrate levels. The altered metabolomes exhibited high correlations with GTS enriched intestinal microflora. Intriguingly, the various conjugates of green tea catechins viz., sulfated, glucuronided, and methylated ones including their exogenous derivatives were detected from large intestinal contents and liver samples. Hence, we conjecture that the metabolic conversions for the molecular components in GTS strongly influenced the gut micro-environment in UVB-exposed mice groups, ergo modulate their gut-microbiome as well as exo/endogenous metabolomes.
Question: Write a study description for the study titled 'Metabolomics study for investigating chronic endoplasmic reticulum stress in Arabidopsis thaliana'.
Answer: The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This metabolomic dataset was produced from 14-day-old Arabidopsis thaliana seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT), bzip60 single mutant and the double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1A and INOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-overaccumulated metabolites which ones are dependent on IRE1s and/or bZIP60. Also, shoots and roots were harvested separately to determine organ-specific metabolic responses to Tm.
Question: Write a study description for the study titled 'Metabolomic/lipidomic profiling of COVID-19 and individual response to tocilizumab'.
Answer: The current pandemic emergence of novel coronavirus disease (COVID-19) poses a relevant threat to global health. SARS-CoV-2 infection is characterized by a wide range of clinical manifestations, ranging from absence of symptoms to severe forms that need intensive care treatment. Here, plasma-EDTA samples of 30 patients compared with age- and sex-matched controls were analyzed via untargeted nuclear magnetic resonance (NMR)-based metabolomics and lipidomics. With the same approach, the effect of tocilizumab administration was evaluated in a subset of patients. Despite the heterogeneity of the clinical symptoms, COVID-19 patients are characterized by common plasma metabolomic and lipidomic signatures (91.7% and 87.5% accuracy, respectively, when compared to controls). Tocilizumab treatment resulted in at least partial reversion of the metabolic alterations due to SARS-CoV-2 infection. In conclusion, NMR-based metabolomic and lipidomic profiling provides novel insights into the pathophysiological mechanism of human response to SARS-CoV-2 infection and to monitor treatment outcomes.
Question: Write a study description for the study titled 'Physiological extremes of the human blood metabolome: A metabolomics analysis of highly glycolytic, oxidative, and anabolic athletes'.
Answer: Human metabolism is highly variable. At one end of the spectrum, defects of enzymes, transporters, and metabolic regulation result in metabolic diseases such as diabetes mellitus or inborn errors of metabolism. At the other end of the spectrum, favorable genetics and years of training combine to result in physiologically extreme forms of metabolism in athletes. Here, we investigated how the highly glycolytic metabolism of sprinters, highly oxidative metabolism of endurance athletes, and highly anabolic metabolism of natural bodybuilders affect their serum metabolome at rest and after a bout of exercise to exhaustion. We used targeted mass spectrometry-based metabolomics to measure the serum concentrations of 151 metabolites and 43 metabolite ratios or sums in 15 competitive male athletes (6 endurance athletes, 5 sprinters, and 4 natural bodybuilders) and 4 untrained control subjects at fasted rest and 5 minutes after a maximum graded bicycle test to exhaustion. The analysis of all 194 metabolite concentrations, ratios and sums revealed that natural bodybuilders and endurance athletes had overall different metabolite profiles, whereas sprinters and untrained controls were more similar. Specifically, natural bodybuilders had 1.5 to 1.8-fold higher concentrations of specific phosphatidylcholines and lower levels of branched chain amino acids than all other subjects. Endurance athletes had 1.4-fold higher levels of a metabolite ratio showing the activity of carnitine-palmitoyl-transferase I and 1.4-fold lower levels of various alkyl-acyl-phosphatidylcholines. When we compared the effect of exercise between groups, endurance athletes showed 1.3-fold higher increases of hexose and of tetradecenoylcarnitine (C14:1). In summary, physiologically extreme metabolic capacities of endurance athletes and natural bodybuilders are associated with unique blood metabolite concentrations, ratios, and sums at rest and after exercise. Our results suggest that long-term specific training, along with genetics and other athlete-specific factors systematically change metabolite concentrations at rest and after exercise.
Question: Write a study description for the study titled 'Comprehensive systems biology analysis of a seven-month cigarette smoke inhalation study in C57BL/6 mice'.
Answer: Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of smoke derived from a prototype modified risk tobacco product (pMRTP) as compared to conventional cigarettes. We investigated physiological and histological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to a reference cigarette (3R4F) smoke or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure and cessation.  The dataset shared here describes the lipidomics analyses performed on lung, liver, and plasma of these mice at multiple time points. Lipids were characterized using, in addition to (untargeted) shotgun lipidomics, a set of targeted methods to specifically characterize sphingolipids, ceramides, triglycerides, eicosanoids, and gangliosides.