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Results 351 - 400 of 974
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Sun Ying - - 2008
Vacancy ACE (VACE) is one of the ACE methods, and has been used to study binding interactions between different biomolecules. Thermodynamic binding constants can be estimated with nonlinear regression methods. With a highly efficient computer simulation program (SimDCCE), it is possible to demonstrate the detailed behaviors of each species during ...
Warwick G - - 2008
There have been significant recent advances in the understanding of the pathophysiology of pulmonary hypertension, and a growing number of therapeutic agents have become available to the treating physician. Traditional methods of diagnosing and monitoring this condition have comprised echocardiography and right heart catheterisation, in addition to functional measures, such ...
Kwon Deukwoo - - 2008
In recent years there has been an increased interest in using protein mass spectroscopy to discriminate diseased from healthy individuals with the aim of discovering molecular markers for disease. A crucial step before any statistical analysis is the pre-processing of the mass spectrometry data. Statistical results are typically strongly affected ...
Ramakrishnan Rajasekhar R Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA. - - 2008
Tracer enrichment data are fitted by multicompartmental models to estimate rate constants and fluxes or transport rates. In apolipoprotein turnover studies, mass measurements are also available, for example, apolipoprotein B levels in very low-density lipoprotein, intermediate-density lipoprotein, and low-density lipoprotein, and are often essential to calculate some of the rate ...
Choi Hyungwon - - 2008
Spectral counting has become a commonly used approach for measuring protein abundance in label-free shotgun proteomics. At the same time, the development of data analysis methods has lagged behind. Currently most studies utilizing spectral counts rely on simple data transforms and posthoc corrections of conventional signal-to-noise ratio statistics. However, these ...
Kessner Darren - - 2008
The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. ...
Carpentier Sebastien Christian - - 2008
Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. ...
McIlwain Sean - - 2008
MOTIVATION: In recent years stable isotopic labeling has become a standard approach for quantitative proteomic analyses. Among the many available isotopic labeling strategies, metabolic labeling is attractive for the excellent internal control it provides. However, analysis of data from metabolic labeling experiments can be complicated because the spacing between labeled ...
Mathivanan Suresh - - 2008
Clinical proteomics is an emerging field that deals with the use of proteomic technologies for medical applications. With a major objective of identifying proteins involved in pathological processes and as potential biomarkers, this field is already gaining momentum. Consequently, clinical proteomics data are being generated at a rapid pace, although ...
Oh Jung Hun - - 2008
MOTIVATION: Diseases normally progress through several stages. Therefore, biomarkers corresponding to each stage may exist. To deal with such a multi-category problem, including sample stage prediction and biomarker selection, we propose methods for classification and feature selection. The proposed classification method is based on two schemes: error-correcting output coding (ECOC) ...
Xu Hua H Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, - - 2008
Two new statistical models based on Monte Carlo Simulation (MCS) have been developed to score peptide matches in shotgun proteomic data and incorporated in a database search program, MassMatrix (www.massmatrix.net). The first model evaluates peptide matches based on the total abundance of matched peaks in the experimental spectra. The second ...
Romero Roberto - - 2008
Examination of the amniotic fluid proteome has been used to identify biomarkers for intra-amniotic inflammation as well as those that may be useful in predicting the outcome of preterm labor. The purpose of this study was to combine a novel computational method of pattern discovery with mass spectrometric proteomic profiling ...
Baggs E M EM School of Biological Sciences (Plant & Soil Science), University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK. - - 2008
Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes ...
Ramos-Fernández Antonio - - 2008
Tandem mass spectrometry-based proteomics is currently in great demand of computational methods that facilitate the elimination of likely false positives in peptide and protein identification. In the last few years, a number of new peptide identification programs have been described, but scores or other significance measures reported by these programs ...
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 X Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, - - 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 ...
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, ...
Burton Richard F RF Institute of Biomedical and Life Sciences, University of Glasgow, UK. - - 2008
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. The present study aimed to explain ...
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 ...
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