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1.
Background
Cerebral infarction caused by different reasons seems differ in fibrinogen levels, so the current work intends to explore the relationship between the fibrinogen level and subtypes of the TOAST criteria in the acute stage of ischemic stroke.Methods
A total of 577 case research objects were treated acute ischemic stroke patients in our hospital from December 2008 to December 2010, and blood samples within 72 hours of the onset were processed with the fibrinogen (PT-der) measurement. Classification of selected patients according to the TOAST Criteria was conducted to study the distribution of fibrinogen levels in the stroke subtypes.Results
The distribution of fibrinogen levels in the subtypes was observed to be statistically insignificant.Conclusions
In the acute stage of ischemic stroke, fibrinogen level was not related to the subtypes of the TOAST criteria.2.
Sonia Liggi Christine Hinz Zoe Hall Maria Laura Santoru Simone Poddighe John Fjeldsted Luigi Atzori Julian L. Griffin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):52
Introduction
Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow.Objectives
Merge in the same platform the steps required for metabolomics data processing.Methods
KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform.Results
The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation.Conclusion
KniMet provides the user with a local, modular and customizable workflow for the processing of both GC–MS and LC–MS open profiling data.3.
Bryan D. Emmett Daniel H. Buckley Margaret E. Smith Laurie E. Drinkwater 《Plant and Soil》2018,427(1-2):53-69
Background and aims
Phosphorus (P) availability is crucial for forest ecosystem productivity and soil organic matter (SOM) is an important source for P. This study was conducted to reveal carbon (C), nitrogen (N) and P distributions in functional SOM fractions. We hypothesised that (1) most of the organic P (Porg) is part of the particulate SOM, (2) particulate SOM stores increasing share of P with decreasing soil P content and (3) the C:Porg ratio of mineral-associated SOM is smaller than that of particulate SOM.Methods
We analysed soil samples from five temperate forest sites (Fagus sylvatica) under different geological parent material with a wide range of total P concentrations. Density fractionation was used to separate free light fraction (fLF), particulate SOM occluded within soil aggregates (occluded light fraction; oLF), and mineral associated SOM (heavy fraction; HF). We determined the mass balance of P in these fractions, in addition to the C and N concentrations. Additionally, the P speciation of the topsoil was analysed by X-ray absorption near edge structure (XANES) spectroscopy at the P K-edge.Results
The fLF contained 18–54% and the oLF 1–15% of total P (Ptot). High percentage of P in these light fractions was associated to soil minerals. Phosphorous in particulate SOM within aggregates tend to increase with decreasing soil P. The HF containing mineral-associated OM, comprised 38–71% of Ptot and their C:Porg ratios were consistently lower than those of the fLF irrespective of the P status of the soil.Conclusions
We show that all three functional SOM fractions contain variable amount of both organic and inorganic P species. The free light fraction shows no response to changing P stocks of soils.. Despite physically protected particulate SOM, oLF, becomes increasingly relevant as P cache in soils with declining P status.4.
Jamie V. de Seymour Stephanie Tu Xiaoling He Hua Zhang Ting-Li Han Philip N. Baker Karolina Sulek 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):79
Introduction
Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.Objective
Investigate the maternal hair metabolome for predictive biomarkers of ICP.Methods
The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.Results
Of 105 metabolites detected in hair, none were significantly associated with ICP.Conclusion
Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.5.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.6.
Background
The purpose of this study is to explore the potential of phase contrast imaging to detect fibrotic progress in its early stage; to investigate the feasibility of texture features for quantified diagnosis of liver fibrosis; and to evaluate the performance of back propagation (BP) neural net classifier for characterization and classification of liver fibrosis.Methods
Fibrous mouse liver samples were imaged by X-ray phase contrast imaging, nine texture measures based on gray-level co-occurrence matrix were calculated and the feasibility of texture features in the characterization and discrimination of liver fibrosis at early stages was investigated. Furthermore, 36 or 18 features were applied to the input of BP classifier; the classification performance was evaluated using receiver operating characteristic curve.Results
The phase contrast images displayed a vary degree of texture pattern from normal to severe fibrosis stages. The BP classifier could distinguish liver fibrosis among normal, mild, moderate and severe stages; the average accuracy was 95.1% for 36 features, and 91.1% for 18 features.Conclusion
The study shows that early stages of liver fibrosis can be discriminated by the morphological features on the phase contrast images. BP network model based on combination of texture features is demonstrated effective for staging liver fibrosis.7.
Hai-kun Ma Ana Pineda Andre W. G. van der Wurff T. Martijn Bezemer 《Plant and Soil》2018,431(1-2):257-272
Aim
To investigate the effects of biochar on biological and chemical phosphorus (P) processes and identify potential interactive effects between P fertilizer and biochar on P bioavailability in the rhizosphere of maize.Methods
We conducted a pot-experiment with maize in a sandy loam soil with two fertilizer levels (0 and 100 mg P kg ?1) and three biochars produced from soft wood (SW), rice husk (RH) and oil seed rape (OSR). Sequential P fractionation was performed on biochar, bulk soil, and rhizosphere soil samples. Acid and alkaline phosphatase activity and root exudates of citrate, glucose, fructose, and sucrose in the rhizosphere were determined.Results
RH and OSR increased readily available soil P, whereas SW had no effect. However, over time available P from the biochars moved to less available P pools (Al-P and Fe-P). There were no interactive effects between P fertilizer and biochar on P bioavailability. Exudates of glucose and fructose were strongly affected by especially RH, whereas sucrose was mostly affected by P fertilizer. Alkaline phosphatase activity was positively correlated with pH, and citrate was positively correlated with readily available P.Conclusion
Biochar effects on biological and chemical P processes in the rhizosphere are driven by biochar properties.8.
Gustavo Boitt Amanda Black Steve A. Wakelin Richard W. McDowell Leo M. Condron 《Plant and Soil》2018,427(1-2):163-174
Aims
We assessed and quantified the cumulative impact of 20 years of biomass management on the nature and bioavailability of soil phosphorus (P) accumulated from antecedent fertiliser inputs.Methods
Soil (0–2.5, 2.5–5, 5–10 cm) and plant samples were taken from replicate plots in a grassland field experiment maintained for 20 years under contrasting plant biomass regimen- biomass retained or removed after mowing. Analyses included dry matter production and P uptake, root biomass, total soil carbon (C), total nitrogen (N), total P, soil P fractionation, and 31P NMR spectroscopy.Results
Contemporary plant production and P uptake were over 2-fold higher for the biomass retained compared with the biomass removed regimes. Soil C, total P, soluble and labile forms of inorganic and organic soil P were significantly higher under biomass retention than removal.Conclusions
Reserves of soluble and labile inorganic P in soil were significantly depleted in response to continued long-term removal of P in plant biomass compared to retention. However, this was only sufficient to sustain plant production at half the level observed for the biomass retention after 20 years, which was partly attributed to limited mobilisation of organic P in response to P removal.9.
Background
In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.Methods
The physical basis of these intuitive maps is clarified by means of analytically solvable problems.Results
Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.Conclusion
Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.10.
Connor Black Olivier P. Chevallier Simon A. Haughey Julia Balog Sara Stead Steven D. Pringle Maria V. Riina Francesca Martucci Pier L. Acutis Mike Morris Dimitrios S. Nikolopoulos Zoltan Takats Christopher T. Elliott 《Metabolomics : Official journal of the Metabolomic Society》2017,13(12):153
Introduction
Fish fraud detection is mainly carried out using a genomic profiling approach requiring long and complex sample preparations and assay running times. Rapid evaporative ionisation mass spectrometry (REIMS) can circumvent these issues without sacrificing a loss in the quality of results.Objectives
To demonstrate that REIMS can be used as a fast profiling technique capable of achieving accurate species identification without the need for any sample preparation. Additionally, we wanted to demonstrate that other aspects of fish fraud other than speciation are detectable using REIMS.Methods
478 samples of five different white fish species were subjected to REIMS analysis using an electrosurgical knife. Each sample was cut 8–12 times with each one lasting 3–5 s and chemometric models were generated based on the mass range m/z 600–950 of each sample.Results
The identification of 99 validation samples provided a 98.99% correct classification in which species identification was obtained near-instantaneously (≈?2 s) unlike any other form of food fraud analysis. Significant time comparisons between REIMS and polymerase chain reaction (PCR) were observed when analysing 6 mislabelled samples demonstrating how REIMS can be used as a complimentary technique to detect fish fraud. Additionally, we have demonstrated that the catch method of fish products is capable of detection using REIMS, a concept never previously reported.Conclusions
REIMS has been proven to be an innovative technique to help aid the detection of fish fraud and has the potential to be utilised by fisheries to conduct their own quality control (QC) checks for fast accurate results.11.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.12.
Anita H. Lewin Peter Silinski James Hayes Amanda Gilbert S. Wayne Mascarella Herbert H. Seltzman 《Metabolomics : Official journal of the Metabolomic Society》2017,13(10):117
Introduction
Metabolomics analysis depends on the identification and validation of specific metabolites. This task is significantly hampered by the absence of well-characterized reference standards. The one-carbon carrier 10-formyltetrahydrofolate acts as a donor of formyl groups in anabolism, where it is a substrate in formyltransferase reactions in purine biosynthesis. It has been reported as an unstable substance and is currently unavailable as a reference standard for metabolomics analysis.Objectives
The current study was undertaken to provide the metabolomics community thoroughly characterized 10-formyltetrahydrofolate along with analytical methodology and guidelines for its storage and handling.Methods
Anaerobic base treatment of 5,10-methenyltetrahydrofolate chloride in the presence of antioxidant was utilized to prepare 10-formyltetrahydrofolate.Results
Pure 10-formyltetrahydrofolate has been prepared and physicochemically characterized. Conditions toward maintaining the stability of a solution of the dipotassium salt of 10-formyltetrahydrofolate have been determined.Conclusion
This study describes the facile preparation of pure (>90%) 10-formyltetrahydrofolate, its qualitative physicochemical characterization, as well as conditions to enable its use as a reference standard in physiologic samples.13.
Fertilization,soil and plant community characteristics determine soil microbial activity in managed temperate grasslands 总被引:1,自引:0,他引:1
Peter Dietrich Tina Buchmann Simone Cesarz Nico Eisenhauer Christiane Roscher 《Plant and Soil》2017,412(1-2):189-199
Background and aims
Contaminated soils can impede germination and growth of selected plant species, restricting effective phytoremediation strategies. The purpose of the present study was to enhance the germination and growth of saltgrass [Distichlis spicata (L.) Greene] by evaluating the efficacy of certain seed pretreatments and soil amendments.Methods
Ten seed pretreatment methods, two amendments, three soil depths and five saline levels were tested under greenhouse conditions.Results
Saltgrass germination and growth were negatively correlated with increasing salinity levels when NaCl > 85.6 mM. Among ten seed pretreatments (stratification + Proxy 24 h, hot water + Proxy 24 h, stratification, hot water + Proxy 48 h, Proxy 48 h, Proxy 24 h, hot water, scarification, gibberellins, and KMnO4), the two best methods were stratification + Proxy 24 h and hot water + Proxy 24 h for enhancing saltgrass germination, with the latter pretreatment being especially useful because of its shorter preparation time and high germination rates. Proxy is a commercial ethephon product. Potting soil (5.0 cm depth) was found to be the best amendment for saltgrass germination and growth in hydrocarbon-contaminated soils.Conclusion
We conclude that direct seeding of saline soils contaminated with petroleum hydrocarbons is a feasible phytoremediation strategy provided that appropriate seed pretreatments and amendments are utilized.14.
Yonghai Lu Jinling Fang Choon Nam Ong Shengsen Chen Ning Li Liang Cui Chong Huang Qinxia Ling Sin Eng Chia Mingquan Chen 《Metabolomics : Official journal of the Metabolomic Society》2017,13(1):6
Introduction
Arachidonic acid (AA)-derived prostaglandins recently have been implicated in pathogenesis of hepatocellular carcinoma (HCC). However, current understanding of omega-6-derived oxylipins that promote this disease remains limited, particularly on oxylipins derived from linoleic acid (LA).Objective
Hepatitis B virus (HBV) infection is a major risk factor for HCC in Asia, we thus quantified AA- and LA-derived oxylipins and the two parent polyunsaturated fatty acids in HBV-related HCC patients to assist in understanding of the molecular pathogenesis of HCC.Methods
Serum samples from 40 HBV-related HCC patients and 23 age-sex matched healthy controls were analyzed using liquid chromatography tandem mass spectrometry.Results
LA, LA-derived oxylipins such as 9-hydroxyoctadecadienoic acid (9-HODE), 13-HODE, 9,10-dihydroxyoctadecenoic acid (9,10-DiHOME), and 12,13-DiHOME, as well as AA-derived oxylipins such as 5,6-dihydroxyeicosatrienoic acid (5,6-DiHETrE), 11,12-DiHETrE, and 14,15-DiHETrE, were significantly elevated in HCC patients compared to healthy controls. Of these, LA, 13-HODE, and 9-HODE showed good potential in differentiating HCC patients from healthy controls (AUC >0.8).Conclusion
The study demonstrated LA- and AA-derived oxylipins via the lipoxygenase and cytochrome P450 pathways appeared to be most involved in the pathogenesis of HBV-related HCC.15.
Andrei Prodan Sultan Imangaliyev Henk S. Brand Martijn N. A. Rosema Evgeni Levin Wim Crielaard Bart J. F. Keijser Enno C. I. Veerman 《Metabolomics : Official journal of the Metabolomic Society》2016,12(9):147
Introduction
Understanding the changes occurring in the oral ecosystem during development of gingivitis could help improve prevention and treatment strategies for oral health. Erythritol is a non-caloric polyol proposed to have beneficial effects on oral health.Objectives
To examine the effect of experimental gingivitis and the effect of erythritol on the salivary metabolome and salivary functional biochemistry.Methods
In a two-week experimental gingivitis challenge intervention study, non-targeted, mass spectrometry-based metabolomic profiling was performed on saliva samples from 61 healthy adults, collected at five time-points. The effect of erythritol was studied in a randomized, controlled trial setting. Fourteen salivary biochemistry variables were measured with antibody- or enzymatic activity-based assays.Results
Bacterial amino acid catabolites (cadaverine, N-acetylcadaverine, and α-hydroxyisovalerate) and end-products of bacterial alkali-producing pathways (N-α-acetylornithine and γ-aminobutyrate) increased significantly during the experimental gingivitis. Significant changes were found in a set of 13 salivary metabolite ratios composed of host cell membrane lipids involved in cell signaling, host responses to bacteria, and defense against free radicals. An increase in mevalonate was also observed. There were no significant effects of erythritol. No significant changes were found in functional salivary biochemistry.Conclusions
The findings underline a dynamic interaction between the host and the oral microbial biofilm during an experimental induction of gingivitis.16.
Background and aims
We hypothesized that successful early ecosystem and soil development in these P-deficient soil materials will initially depend on effective re-establishment of P storage and cycling through organic matter. This hypothesis was tested in a 26-year chronosequence of seven lightly fertilized, oxidic soil materials restored to eucalypt forest communities after bauxite mining.Methods
Total P (Pt) status, Hedley P fractions and partial chemical speciation (NaOH-EDTA extraction and analysed using solution 31P NMR spectroscopy) were determined in the restored soils.Results
Concentrations of Pt and most Hedley fractions changed with restoration period, declined with depth and were strongly positively correlated with C and N concentrations. Biological P dominated the Labile and Intermediate P fractions while Long-term P was dominantly inorganic. Organic P concentrations in NaOH-EDTA extracts and their chemical natures were similar in restored and unburned native forest sites. Phosphomonoesters were the dominant class of organic P.Conclusions
Surprisingly rapid P accretion and fractional changes occurred over 26 years, largely in the surface soils and closely associated with organic matter status. Alkaline hydrolysis products of phosphodiesters and pyrophosphate indicated the importance of microbial P cycling. The important consequences for long-term ecosystem development and biological diversity require further study.17.
Antonio Murgia Christine Hinz Sonia Liggi Jùlìa Denes Zoe Hall James West Maria Laura Santoru Cristina Piras Cristina Manis Paolo Usai Luigi Atzori Julian L. Griffin Pierluigi Caboni 《Metabolomics : Official journal of the Metabolomic Society》2018,14(10):140
Background
Inflammatory bowel disease is a group of pathologies characterised by chronic inflammation of the intestine and an unclear aetiology. Its main manifestations are Crohn’s disease and ulcerative colitis. Currently, biopsies are the most used diagnostic tests for these diseases and metabolomics could represent a less invasive approach to identify biomarkers of disease presence and progression.Objectives
The lipid and the polar metabolite profile of plasma samples of patients affected by inflammatory bowel disease have been compared with healthy individuals with the aim to find their metabolomic differences. Also, a selected sub-set of samples was analysed following solid phase extraction to further characterise differences between pathological samples.Methods
A total of 200 plasma samples were analysed using drift tube ion mobility coupled with time of flight mass spectrometry and liquid chromatography for the lipid metabolite profile analysis, while liquid chromatography coupled with triple quadrupole mass spectrometry was used for the polar metabolite profile analysis.Results
Variations in the lipid profile between inflammatory bowel disease and healthy individuals were highlighted. Phosphatidylcholines, lyso-phosphatidylcholines and fatty acids were significantly changed among pathological samples suggesting changes in phospholipase A2 and arachidonic acid metabolic pathways. Variations in the levels of cholesteryl esters and glycerophospholipids were also found. Furthermore, a decrease in amino acids levels suggests mucosal damage in inflammatory bowel disease.Conclusions
Given good statistical results and predictive power of the model produced in our study, metabolomics can be considered as a valid tool to investigate inflammatory bowel disease.18.
Introduction
Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.Objectives
Assessment of the quality of raw data processing in untargeted metabolomics.Methods
Five published untargeted metabolomics studies, were reanalyzed.Results
Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.Conclusion
Incomplete raw data processing shows unexplored potential of current and legacy data.19.
Tie-juan Shao Zhi-xing He Zhi-jun Xie Hai-chang Li Mei-jiao Wang Cheng-ping Wen 《Metabolomics : Official journal of the Metabolomic Society》2016,12(4):70
Introduction
The differences in fecal metabolome between ankylosing spondylitis (AS)/rheumatoid arthritis (RA) patients and healthy individuals could be the reason for an autoimmune disorder.Objectives
The study explored the fecal metabolome difference between AS/RA patients and healthy controls to clarify human immune disturbance.Methods
Fecal samples from 109 individuals (healthy controls 34, AS 40, and RA 35) were analyzed by 1H NMR spectroscopy. Data were analyzed with principal component analysis (PCA) and orthogonal projection to latent structure discriminant (OPLS-DA) analysis.Results
Significant differences in the fecal metabolic profiles could distinguish AS/RA patients from healthy controls but could not distinguish between AS and RA patients. The significantly decreased metabolites in AS/RA patients were butyrate, propionate, methionine, and hypoxanthine. Significantly increased metabolites in AS/RA patients were taurine, methanol, fumarate, and tryptophan.Conclusion
The metabolome variations in feces indicated AS and RA were two homologous diseases that could not be distinguished by 1H NMR metabolomics.20.
Michael?Bonert Richard?L?Leask Jagdish?Butany C?Ross?Ethier Jerry?G?Myers K?Wayne?Johnston Matadial?Ojha