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Results 351 - 400 of 960
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Steele Paul T - - 2008
Actual or surrogate chemical, biological, radiological, nuclear, and explosive materials and illicit drug precursors can be rapidly detected and identified when in aerosol form by a Single-Particle Aerosol Mass Spectrometry (SPAMS) system. This entails not only the sampling of such particles but also the physical analysis and subsequent data analysis ...
Baú Domenico A - - 2008
In this work, we present a stochastic optimal control framework for assisting the management of the cleanup by pump-and-treat of polluted shallow aquifers. In the problem being investigated, hydraulic conductivity distribution and dissolved contaminant plume location are considered as the uncertain variables. The framework considers the subdivision of the cleanup ...
Ulintz, Peter J.
The proteomics field is driven by the need to develop increasingly high-throughput methods for the identification and characterization of proteins. The overall goal of this research is to improve the success rate of modern high-throughput proteomics studies. The focus is on developing computational strategies for increasing the number of identifications ...
Mathy Grégory - - 2008
In this review, we describe the various techniques available to carry out valid comparative proteomics, their advantages and their disadvantages according to the goal of the research. Two-dimensional electrophoresis and 2D-DIGE are compared to shotgun proteomics and SILE. We give our opinion on the best fields of application in the ...
Forshed Jenny - - 2008
Our goal in this paper is to show an analytical workflow for selecting protein biomarker candidates from SELDI-MS data. The clinical question at issue is to enable prediction of the complete remission (CR) duration for acute myeloid leukemia (AML) patients. This would facilitate disease prognosis and make individual therapy possible. ...
Imre Tímea - - 2008
N-glycan oligosaccharides of human serum alpha(1)-acid glycoprotein (AGP) samples isolated from 43 individuals (healthy individuals and patients with lymphoma and with ovarian tumor) were analyzed by MALDI-TOF mass spectrometry and a multivariate statistical method (linear discriminant analysis, LDA). 34 different glycan structures have been identified. From the glycosylation pattern determined ...
Sullivan Catherine A W - - 2008
Biomarker-driven cancer research is common in the current literature. Much of this research is a result of the increase in genomic and proteomic high-throughput technologies, which have increased our knowledge and also produced an abundance of data with unclear clinical significance. Immunohistochemistry-based assessment of protein expression is a natural validation ...
Feng Jian - - 2008
When performing bioinformatics analysis on tandem mass spectrometry data, there is a computational need to efficiently store and sort these semi-ordered datasets. To solve this problem, a new data structure based on dynamic arrays was designed and implemented in an algorithm that parses semi-ordered data made by Mascot, a separate ...
Falkner Jayson A - - 2008
A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to ...
Du Xiuxia - - 2008
Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still remain related to how best to extract ...
Dermísek Radovan - - 2008
We show that, in string models with the minimal supersymmetric standard model residing on D-branes, the bino mass can be generated in a geometrically separated hidden sector. Hypercharge mediation thus naturally teams up with anomaly mediation. The mixed scenario predicts a distinctive yet viable superpartner spectrum, provided that the ratio ...
Hamacher Michael - - 2008
The Human Proteome Organisation was launched in February 2001 as a result of the need of an international proteomic forum to improve the understanding of human diseases. The initiative dealing with the brain is the Human Proteome Organisation Brain Proteome Project chaired in Germany and Korea. In order to estimate ...
Rho Sangchul - - 2008
Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems ...
Hoffman Michael D - - 2008
More and more attention is being focused on the analysis of post-translational modifications (PTMs) on proteins as researchers are continually learning how essential they are for proper cellular function. As there are hundreds of different types of known PTMs, traditional methods of modification analysis are incapable of comprehensively monitoring for ...
Luo J - - 2008
A travel-time based approach is developed for estimating first-order reaction rate coefficients for transport with nonequilibrium linear mass transfer in heterogeneous media. Tracer transport in the mobile domain is characterized by a travel-time distribution, and mass transfer rates are described by a convolution product of concentrations in the mobile domain ...
Khan M S I - - 2008
In a quantitative single particle analysis, named the low-Z particle EPMA, number concentration data for chemical species encountered in aerosol sample are provided. However, it will be more useful if mass concentration data can be obtained from single particle analysis; i.e., the single particle analysis data for weight fractions of ...
Burton Richard F - - 2008
BACKGROUND: Body surface areas are usually estimated by means of a formula due in its general form to Du Bois and Du Bois (1916), i.e. area = C x mass(a) x height(b), where C, a and b are empirical constants. Its physical basis is unknown. AIM: The present study aimed ...
Stead David A - - 2008
Proteomics, the study of the protein complement of a biological system, is generating increasing quantities of data from rapidly developing technologies employed in a variety of different experimental workflows. Experimental processes, e.g. for comparative 2D gel studies or LC-MS/MS analyses of complex protein mixtures, involve a number of steps: from ...
Ceroni Alessio - - 2008
Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-throughput glycomics projects, ...
Barla Annalisa - - 2008
The search for predictive biomarkers of disease from high-throughput mass spectrometry (MS) data requires a complex analysis path. Preprocessing and machine-learning modules are pipelined, starting from raw spectra, to set up a predictive classifier based on a shortlist of candidate features. As a machine-learning problem, proteomic profiling on MS data ...
Hilario Melanie - - 2008
Mass-spectra based proteomic profiles have received widespread attention as potential tools for biomarker discovery and early disease diagnosis. A major data-analytical problem involved is the extremely high dimensionality (i.e. number of features or variables) of proteomic data, in particular when the sample size is small. This article reviews dimensionality reduction ...
Bellera Carine A - - 2008
It is common to define a change in health status or in a disease state on the basis of a sustained rise (or decline) in a biomarker over time. However, such observations are often subject to important variability unrelated to the underlying biologic process. The authors propose a method to ...
Daly D S - - 2008
Comparing a protein's concentrations across two or more treatments is the focus of many proteomics studies. A frequent source of measurements for these comparisons is a mass spectrometry (MS) analysis of a protein's peptide ions separated by liquid chromatography (LC) following its enzymatic digestion. Alas, LC-MS identification and quantification of ...
Fowler Bruce A - - 2008
There has been an increased appreciation over the last 20 years that chemical agents at very low dose levels can produce biological responses in protein expression patterns (proteomic responses) or alterations in sensitive metabolic pathways (metabolomic responses). Marked improvements in analytical methodologies, such as 2-D gel electrophoresis, matrix-assisted laser desorption-time ...
Deutsch Eric W - - 2008
Data processing is a central and critical component of a successful proteomics experiment, and is often the most time-consuming step. There have been considerable advances in the field of proteomics informatics in the past 5 years, spurred mainly by free and open-source software tools. Along with the gains afforded by ...
Schatschneider Christopher - - 2008
A core assumption of response to instruction or intervention (RTI) models is the importance of measuring growth in achievement over time in response to effective instruction or intervention. Many RTI models actively monitor growth for identifying individuals who need different levels of intervention. A large-scale (N=23,438), two-year longitudinal study of ...
Lê Cao Kim-Anh - - 2008
Recent biotechnology advances allow for multiple types of omics data, such as transcriptomic, proteomic or metabolomic data sets to be integrated. The problem of feature selection has been addressed several times in the context of classification, but needs to be handled in a specific manner when integrating data. In this ...
Enot David P - - 2008
Metabolome analysis by flow injection electrospray mass spectrometry (FIE-MS) fingerprinting generates measurements relating to large numbers of m/z signals. Such data sets often exhibit high variance with a paucity of replicates, thus providing a challenge for data mining. We describe data preprocessing and modeling methods that have proved reliable in ...
Hale John E - - 2008
Cerebrospinal fluid (CSF) provides an important source of potential biomarkers for brain disorders and therapeutic drug development. Applications of proteomic technology to the identification and quantification of proteins in CSF are increasing rapidly. Key to obtaining reproducible and reliable data about protein levels in CSF are standardization of methods for ...
Tong Joo Chuan - - 2008
Allergy is a prevalent health problem in developed countries. With advances in genomic and proteomic technologies, there is a rapid increase in allergy-related data, including allergen sequences, allergic cross-reactivity, molecular structures, clinical measurements, and atmospheric concentrations. The more and more complex allergy data is fueling the need for advanced ways ...
Ghosh Samiran - - 2008
BACKGROUND: The discovery of biomarkers is an important step towards the development of criteria for early diagnosis of disease status. Recently electrospray ionization (ESI) and matrix assisted laser desorption (MALDI) time-of-flight (TOF) mass spectrometry have been used to identify biomarkers both in proteomics and metabonomics studies. Data sets generated from ...
Carvalho Paulo C - - 2008
BACKGROUND: A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with ...
Andersson Malin - - 2008
As large genomic and proteomic datasets are generated from homogenates of various tissues, the need for information on the spatial localization of their encoded products has become more pressing. Matrix-assisted laser desorption-ionization (MALDI) imaging mass spectrometry (IMS) offers investigators the means with which to unambiguously study peptides and proteins with ...
Santamaria-Fernandez Rebeca - - 2008
A systematic comparison of delta34S measurements by multicollector inductively coupled plasma mass spectrometry (MCICPMS) using two different standardisation approaches and two different reference materials as working standards is reported for the first time. Full uncertainty budgets have been calculated using the Kragten approach. Internal standardisation by measuring Si ratios and ...
Lindon John C - - 2008
Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex ...
McGuire James N - - 2008
Biomarker discovery in clinical proteomics is being performed on relatively large patient cohorts by utilizing the high throughput of laser desorption/ionization mass spectrometry (MALDI- and SELDI-TOF-MS). Dealing directly with patient samples as opposed to working in cell or animal systems requires a host of considerations both before and after mass ...
Carpentier Sebastien Christian - - 2008
After separation through two-dimensional gel electrophoresis (2DE), several hundreds of individual protein abundances can be quantified in a cell population or sample tissue. Both a good experimental setup and a valid statistical approach are essential to get insight into the data and to draw correct conclusions. High-throughput 2DE proteomics yield ...
Hand David J - - 2008
The performance results of a wide range of different classifiers applied to proteomic mass spectra data, in a blind comparative assessment organised by Bart Mertens, are reviewed. The different approaches are summarised, issues of how to evaluate and compare the predictions are described, and the results of the different methods ...
Mertens Bart - - 2008
This paper gives a description of the structure of the classification competition on mass spectrometry proteomic data which is presented in this issue. All steps according to which the competition was run, leading up to the joint meeting, are explained. The paper gives further details on the data analyzed by ...
Böcker Sebastian - - 2008
Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating ...
Madhusudanan K P - - 2008
The ion abundances in the tandem mass spectra of oxocarbenium ions generated from aldohexoses and ketohexoses under electrospray ionization conditions depend on their stereochemistry. The ratios of the abundances of two of the major ions m/z 85 and 91 are different in the aldohexoses and the ketohexoses. Principal component analysis ...
Stanislaus Romesh - - 2008
In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the level of microarray genomics data or mass spectrometry approaches. The trend toward identifying encompassing data standards has been expanding from genomics to transcriptomics, ...
Befekadu Getachew K - - 2008
In this paper, a framework of probabilistic-based mixture regression models (PMRM) is presented for multi-class alignment of liquid chromatography-mass spectrometry (LC-MS) data. The proposed framework performs the alignment in both time and measurement spaces of the LC-MS spectra. The expectation maximization (EM) algorithm is used to estimate the joint parameters ...
Pérès Sabine - - 2008
In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which ...
Nikamanon Pornpat - - 2008
Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) mass-spectrometry-based HDX workflows are not publicly available. An integrated data pipeline (Solvent Explorer/TOF2H) has been ...
Lange Eva - - 2008
Liquid chromatography coupled to mass spectrometry (LC-MS) has become a prominent tool for the analysis of complex proteomics and metabolomics samples. In many applications multiple LC-MS measurements need to be compared, e. g. to improve reliability or to combine results from different samples in a statistical comparative analysis. As in ...
Soh Josephine L P - - 2008
The purpose of this research was to investigate the effects of particle size on the wet massing behavior of microcrystalline cellulose (MCC). In this study, a series of six fractionated MCC grades were customized and specially classified to yield different particle size varieties of the standard grade, Comprecel M101. All ...
Cairns David A - - 2008
Proteomic profiling using mass spectrometry (MS) is one of the most promising methods for the analysis of complex biological samples such as urine, serum and tissue for biomarker discovery. Such experiments are often conducted using MALDI-TOF (matrix-assisted laser desorption/ionisation time-of-flight) and SELDI-TOF (surface-enhanced laser desorption/ionisation time-of-flight) MS. Using such profiling ...
Sturm Marc - - 2008
Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the ...
Clarke Robert - - 2008
High-throughput genomic and proteomic technologies are widely used in cancer research to build better predictive models of diagnosis, prognosis and therapy, to identify and characterize key signalling networks and to find new targets for drug development. These technologies present investigators with the task of extracting meaningful statistical and biological information ...
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