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Profiling Method (profiling + method)
Selected AbstractsAn Ultrasonic Profiling Method for the Inspection of Tubular StructuresCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 6 2007Francisco Gomez These graphs not only show the inner contour of the pipe but also integrate the intensity of the echoes employed to create the profile. The enhanced profile is generated by superimposing the peak intensity from the returning echoes at the calculated x, y, and z coordinates where it reflected from the pipe wall. The proposed method is capable of showing anomalous conditions, inside pipes filled with liquid, with dimensions smaller than the theoretical lateral and axial resolution of the transducer, in contrast to traditional methods where these kinds of defects are not disclosed. The proposed inspection method and its capabilities were validated through the realization of simulations and experiments. The presented approach was particularly developed with the aim of scanning internal sections of pipes filled with liquid using rotary ultrasonic sonars, but it is expected that this research could be expanded to the inspection of other submerged structures, such as water tanks, or pressurized vessels. [source] sgk1, a member of an RNA cluster associated with cell death in a model of Parkinson's diseaseEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2005Christine C. Stichel Abstract In an effort to gain deeper insight into the molecular processes underlying neurodegeneration in Parkinson's disease, we performed gene expression profiling at several early time points after MPTP-injection into old (1-year) mice. We used a PCR-based gene expression profiling method, digital expression pattern display (DEPD), a method of very high sensitivity and reproducibility, which displays almost all transcripts of a tissue. To identify cell death-associated genes, we defined clusters of differentially expressed transcripts with expression behaviour that correlated with the temporal profile of cell death progression and characterized one of these cell death clusters further. We selected one of the strongest regulated genes, the serum and glucocorticoid-regulated kinase 1 (sgk1), and validated its differential expression by Northern blot analysis, semiquantitative PCR and in situ hybridization. Up-regulation of sgk1 (i) coincides with the onset of dopaminergic cell death in both the 8-week acute and 1-year subacute MPTP models, (ii) spans the entire brain, (iii) is attenuated by the l -deprenyl-mediated inhibition of the MPTP conversion to its active metabolite MPP+ and (iv) is not induced by dehydration. This study demonstrated that the combination of the DEPD technology, clustering analysis and a detailed histopathology is a useful tool for elucidating molecular pathways in neurodegenerative diseases. [source] Functional profiling of uncommon VCAM1 promoter polymorphisms prevalent in African American populations,,HUMAN MUTATION, Issue 8 2007Gila Idelman Abstract Multiple variants of the vascular adhesion molecule-1 (VCAM1) promoter show increased nucleotide heterozygosity in the African American population. Using a novel transfection-based transcriptional pathway profiling method, we show that select uncommon variants are functionally hyperactive. Eight candidate VCAM1 promoter haplotypes comprising 13 previously identified SNPs were assessed for response to known mitogens. Activity was correlated with bioinformatic analysis of hyper- and hyporesponsive variants to identify the gain or loss of haplotype-specific transcription factor binding site (TFBS). Using this approach, a low frequency regulatory allele (c.,540A>G; dbSNP rs3783605:A>G), found in a hyperactive VCAM1 promoter haplotype, was shown to create a candidate binding site for ETS2 that was confirmed in vivo by chromatin immunoprecipitation. This report provides the first functional evaluation of VCAM1 promoter polymorphisms and establishes a hypothetical foundation for investigation of their role in the pathogenesis of VCAM1 -associated diseases that disproportionately afflict African Americans, including thromboembolic diseases, asthma, and multiple myeloma. Hum Mutat 28(8), 824,829, 2007. Published 2007, Wiley-Liss, Inc. [source] Impact behavior of hybrid composite platesJOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2010Metin Sayer Abstract This experimental study deals with the impact response of hybrid composite laminates. Two different hybrid composite laminates, aramid/glass and aramid/carbon, and two different stacking sequences, such as [0/0/90/90]A+ [90/90/0/0]G for AG1 and [0/90/±45]A+ [±45/90/0]G for AG2 and so on (see Table I), were chosen for impact testing. The impact energy was gradually increased until complete perforation took place, and an energy profiling method (EPM) was used to identify the perforation thresholds of composites. The damaged samples were visually inspected. The images of the several samples subjected to various impact energies were registered and used for comparison and identifying damage mechanisms. The perforation thresholds for [0/90/±45]s aramid/glass and aramid/carbon laminates were found to be approximately 5% higher than those for their counterparts with the [0/0/90/90]s stacking sequence. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010 [source] Highly sensitive and accurate profiling of carotenoids by supercritical fluid chromatography coupled with mass spectrometryJOURNAL OF SEPARATION SCIENCE, JSS, Issue 9 2009Atsuki Matsubara Abstract We attempted to establish a high-speed and high-resolution profiling method for a carotenoid mixture as a highly selective and highly sensitive detection method; the analysis was carried out by supercritical fluid chromatography (SFC) coupled with mass spectrometry (MS). When an octadecyl-bonded silica (ODS) particle-packed column was used for separation, seven carotenoids including structural isomers were successfully separated within 15 min. This result indicated not only improved separation but also improved throughput compared to the separation and throughput in RP-HPLC. The use of a monolithic ODS column resulted in additional improvement in both the resolution and the throughput; the analysis time was reduced to 4 min by increasing the flow rate. Furthermore, carotenoids in biological samples containing the complex matrices were separated effectively by using several monolithic columns whose back pressure was very low. The mass spectrometer allowed us to perform a more sensitive analysis than UV detection; the detection limit of each carotenoid was 50 pg or below. This is the first report of carotenoid analysis carried out by SFC-MS. The profiling method developed in this study will be a powerful tool for carrying out accurate profiling of biological samples. [source] Blanching and long-term freezing affect various bioactive compounds of vegetables in different waysJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 14 2003Riitta Puupponen-Pimiä Abstract An extensive study on the effects of blanching/freezing and long-term freezer storage on various bioactive compounds of more than 20 commonly used vegetables was performed. Effects were strongly plant species-dependent. Contents of dietary fibre components either were not affected or increased slightly. Minerals in general were also stable, but some losses of soluble minerals by leaching were observed. Phenolic antioxidants and vitamins were clearly more sensitive. Significant losses (20,30%) of antioxidant activity and total phenolics were detected in many vegetables. A qualitative HPLC profiling method for phenolic antioxidants was developed which proved to be very useful when evaluating the complex behaviour of phenolics during food processing. Up to one-third of vitamin C contents were lost during blanching, and further slight losses were detected during storage. Folic acid turned out to be very sensitive to blanching, with more than half of the vitamin being lost, but was stable during freezer storage. Carotenoids and sterols were not affected by blanching or freezer storage. The usefulness of the applied screening methods for evaluation of the effects of processing on vegetables is shown. Copyright © 2003 Society of Chemical Industry [source] Profiling MS proteomics data using smoothed non-linear energy operator and Bayesian additive regression treesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2009Shan He Abstract This paper proposes a novel profiling method for SELDI-TOF and MALDI-TOF MS data that integrates a novel peak detection method based on modified smoothed non-linear energy operator, correlation-based peak selection and Bayesian additive regression trees. The peak detection and classification performance of the proposed approach is validated on two publicly available MS data sets, namely MALDI-TOF simulation data and high-resolution SELDI-TOF ovarian cancer data. The results compared favorably with three state-of-the-art peak detection algorithms and four machine-learning algorithms. For the high-resolution ovarian cancer data set, seven biomarkers (m/z windows) were found by our method, which achieved 97.30 and 99.10% accuracy at 25th and 75th percentiles, respectively, from 50 independent cross-validation samples, which is significantly better than other profiling and dimensional reduction methods. The results show that the method is capable of finding parsimonious sets of biologically meaningful biomarkers with better accuracy than existing methods. Supporting Information material and MATLAB/R scripts to implement the methods described in the article are available at: http://www.cs.bham.ac.uk/szh/SourceCode-for-Proteomics.zip [source] Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomicsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 15 2009Albert Koulman The identification of quantitative trait loci (QTL) for plant metabolites requires the quantitation of these metabolites across a large range of progeny. We developed a rapid metabolic profiling method using both untargeted and targeted direct infusion tandem mass spectrometry (DIMSMS) with a linear ion trap mass spectrometer yielding sufficient precision and accuracy for the quantification of a large number of metabolites in a high-throughput environment. The untargeted DIMSMS method uses top-down data-dependent fragmentation yielding MS2 and MS3 spectra. We have developed software tools to assess the structural homogeneity of the MS2 and MS3 spectra hence their utility for phenotyping and genetical metabolomics. In addition we used a targeted DIMS(MS) method for rapid quantitation of specific compounds. This method was compared with targeted LC/MS/MS methods for these compounds. The DIMSMS methods showed sufficient precision and accuracy for QTL discovery. We phenotyped 200 individual Loliumperenne genotypes from a mapping population harvested in two consecutive years. Computational and statistical analyses identified 246 nominal m/z bins with sufficient precision and homogeneity for QTL discovery. Comparison of the data for specific metabolites obtained by DIMSMS with the results from targeted LC/MS/MS analysis showed that quantitation by this metabolic profiling method is reasonably accurate. Of the top 100 MS1 bins, 22 ions gave one or more reproducible QTL across the 2 years. Copyright © 2009 John Wiley & Sons, Ltd. 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