Search Results
Results 301 - 350 of 960
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Yun Dong - - 2009
Gel-based matrix-assisted laser desorption ionization-time of flight tandem mass spectrometer (MALDI TOF/TOF MS) is one of the dominant methods of current proteomics, utilizing both peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) for protein identification on a spot-to-spot basis. However, the unique impact of the quality of the corresponding ...
Forsell Caroline - - 2009
A new method is proposed for finding small sets of points on the body giving sufficient information for estimating the whole body center of mass (CoM), as well as the linear momenta (LM) and angular momenta (AM). In the underlying model each point (whose trajectory is tracked by a marker) ...
Dominguez F - - 2009
Relatively little is known about the proteome/secretome of the human preimplantation embryo, in particular the protein composition/secretion of the blastocyst just before implantation. Given the legal and ethical guidelines, new approaches are needed to study the human embryo proteome. At present, morphological assessment is the primary method used to determine ...
Liu Daren - - 2009
BACKGROUND: To develop a serum-specific protein fingerprint which is capable of differentiating samples from patients with pancreatic cancer and those with other pancreatic conditions. METHODS: We used SELDI-TOF-MS coupled with CM10 chips and bioinformatics tools to analyze a total of 118 serum samples in this study; 78 serum samples were ...
Kaiser Jan - - 2008
Gas isotope ratio mass spectrometers usually measure ion current ratios of molecules, not atoms. Often several isotopologues contribute to an ion current at a particular mass-to-charge ratio (m/z). Therefore, corrections have to be applied to derive the desired isotope ratios. These corrections are usually formulated in terms of isotope ratios ...
Wekerle H - - 2008
Experimental autoimmune encephalomyelitis (EAE) is often termed "the" model of human multiple sclerosis (MS). This is, however, an oversimplification. MS is a multifaceted disorder, with no single experimental model representing the entire complexity of the human disease. On the other hand, EAE comes in numerous, distinct variants, which may reflect ...
Grussenmeyer Thomas - - 2008
Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. ...
Young G C - - 2008
The introduction of 'compact' accelerator mass spectrometers into biomedical science, including use in drug metabolism and bioanalytical applications, is an exciting recent development. Comparisons are presented here between a more established and relatively large tandem accelerator which operates at up to 5 MV and a conventional laboratory-sized 250 kV single-stage ...
Cristiano E - - 2008
Hundreds of publications dealing with the prevalence of multiple sclerosis (MS) throughout the world exist, but little data have been published from South America. Epidemiological studies of MS vary according to environmental, racial and genetic factors; a better understanding of MS in South America would help us to elucidate the ...
Stangel Martin - - 2008
Current treatments for multiple sclerosis (MS) include immunomodulatory or immunosuppressive agents but no neuroprotective or regenerative therapy is available. From various animal models, we have learned that remyelination in the CNS is a potent neuroprotective mechanism. The knowledge about oligodendrocyte biology and the process of remyelination has greatly increased in ...
Ahmad Yasmeen Y Wellcome Trust Centre for Gene Regulation & Expression and School of Computing, University of Dundee, Dundee DD1 5EH, - - 2009
An experimental data handling system has been created as an update to the previous Nucleolar Proteome Database (NOPdb3.0: http://www.lamondlab.com/NOPdb3.0/). This updated system is able to manage large data sets identified by multiple mass spectrometry and has been used to analyse highly purified preparations of human nucleoli from different cell lines. ...
Benavente Fernando - - 2008
We applied a multiway approach to extract information from the analysis of protein isoforms by CE-ESI-MS. Metallothioneins (MT) are low-molecular-weight proteins (6-7 kDa) with a strong affinity for heavy-metal ions. Rabbit liver MT-I and MT-II fractions are purified from MT samples. At low pH, the bound metal ions were released ...
Gyulassy Attila - - 2008
The Morse-Smale (MS) complex has proven to be a useful tool in extracting and visualizing features from scalar-valued data. However, efficient computation of the MS complex for large scale data remains a challenging problem. We describe a new algorithm and easily extensible framework for computing MS complexes for large scale ...
Grussenmeyer Thomas - - 2008
Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. ...
Hundertmark C - - 2009
Mass spectrometry (MS) data are impaired by noise similar to many other analytical methods. Therefore, proteomics requires statistical approaches to determine the reliability of regulatory information if protein quantification is based on ion intensities observed in MS. We suggest a procedure to model instrument and workflow-specific noise behaviour of iTRAQ ...
Consoli A - - 2008
The initial polymerization reactions in particle forming Ar/He/C 2H 2 plasmas are studied using molecular beam mass spectrometry (MBMS). The measured mass spectra are disentangled and quantified with the help of Bayesian probability theory. This approach uses the measured mass spectra and the cracking patterns (CPs) of the species that ...
Caruso T - - 2009
Indirect measures of soil invertebrate body mass M based on equations relating the latter to body length (l) are becoming increasingly used due to the required painstaking laboratory work and the technical difficulties involved in obtaining some thousands of reliable weight estimates for animals that can be very small. The ...
Cruz-Monteagudo Maykel - - 2008
Numerical parameters of the molecular networks, also referred as Topological Indices or Connectivity Indices (CIs), have been used in Bioorganic and Medicinal Chemistry to find Quantitative Structure-Activity, Property or Toxicity Relationship (QSAR, QSPR and QSTR) models. QSPR models generally use CIs as inputs to predict the biological activity of compounds. ...
Gromov Pavel - - 2008
Cancer, being a major healthcare concern worldwide, is one of the main targets for the application of emerging proteomic technologies and these tools promise to revolutionize the way cancer will be diagnosed and treated in the near future. Today, as a result of the unprecedented advances that have taken place ...
Wilkins Marc R - - 2008
Proteomics is a data-rich discipline that makes extensive use of separation tools, mass spectrometry and bioinformatics to analyze and interpret the features and dynamics of the proteome. A major challenge for the field is how proteomics data can be stored and managed, such that data become permanent and can be ...
Schnöll-Bitai Irene - - 2008
The performances of several matrices were investigated for the accurate determination of the molecular mass distributions of pullulans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The ionic liquid matrix (ILM) 2,5-dihydroxybenzoic acid butylamine (DHBB) gave better and more reliable results than the crystalline matrices 2,5-dihydroxybenzoic acid (DHB) and 2,4,6-trihydroxyacetophenone ...
Paulovich Amanda G - - 2008
The application of "omics" technologies to biological samples generates hundreds to thousands of biomarker candidates; however, a discouragingly small number make it through the pipeline to clinical use. This is in large part due to the incredible mismatch between the large numbers of biomarker candidates and the paucity of reliable ...
Knappmiller Scott - - 2008
An electrostatic mass spectrometer for nanometer-sized charged aerosol particles in the mesosphere has been developed and tested. The analyzer is mounted on the forward end of a rocket and has a slit opening for admitting a continuous sample of air that is exhausted through ports at the sides. Within the ...
Ding Ying - - 2008
Robust statistical validation of peptide identifications obtained by tandem mass spectrometry and sequence database searching is an important task in shotgun proteomics. PeptideProphet is a commonly used computational tool that computes confidence measures for peptide identifications. In this paper, we investigate several limitations of the PeptideProphet modeling approach, including the ...
Cingöz A - - 2008
An in-line procedure for protein analysis using a trypsin-based immobilized enzymatic reactor (IMER) coupled to LC-MS/MS has been developed. Various IMERs were synthesized and characterized by estimating the digestion yield of a pattern peptide in UV detection. Laboratory-made IMERs were optimized by studying the effect of different parameters as the ...
Wright Steven - - 2009
The limitations of conventional machining and assembly techniques require that designs for quadrupole mass analyzers with rod diameters less than a millimeter are not merely scale versions of larger instruments. We show how silicon planar processing techniques and microelectromechanical systems (MEMS) design concepts can be used to incorporate complex features ...
Djouadi A - - 2008
We consider the fully constrained version of the next-to-minimal supersymmetric extension of the standard model (cNMSSM) in which a singlet Higgs superfield is added to the two doublets that are present in the minimal extension (MSSM). Assuming universal boundary conditions at a high scale for the soft supersymmetry-breaking mass parameters ...
Pham Tuan D - - 2008
Early prediction of the risk of cardiovascular events in patients with chest pain is critical in order to provide appropriate medical care for those with positive diagnosis. This paper introduces a computational methodology for predicting such events in the context of robust computerized classification using mass spectrometry data of blood ...
Poynard T - - 2008
This review summarizes the methodological aspects of the interpretation of non-invasive biomarkers in liver fibrosis. A scoring system has been updated to better compare the quality of fibrosis biomarkers. Several methodological issues are related to the classical methodology using biopsy, as this is considered the gold standard. However, from evidence-based ...
Tedford Nathan C - - 2008
Advances in protein phosphorylation analysis by mass spectrometry (MS) are enabling the generation of high quality, quantitative datasets of protein phosphorylation with a breadth of coverage and reproducibility not previously attainable. Comparisons of signaling responses in cells at a network level are now feasible and studies looking at cellular response ...
Bosch Gundula - - 2008
In order to validate a gel free quantitative proteomics assay for the model methylotrophic bacterium Methylobacterium extorquens AM1, we examined the M. extorquens AM1 proteome under single carbon (methanol) and multicarbon (succinate) growth, conditions that have been studied for decades and for which extensive corroborative data have been compiled. In ...
Huang Ying - - 2009
The classification accuracy of a continuous marker is typically evaluated with the receiver operating characteristic (ROC) curve. In this paper, we study an alternative conceptual framework, the "percentile value." In this framework, the controls only provide a reference distribution to standardize the marker. The analysis proceeds by analyzing the standardized ...
Sigdel Tara K - - 2008
The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. However, the task is daunting and requires collaborations among researchers working in the fields of ...
Vieira Ricardo Augusto Mendonça - - 2008
Models used to predict digestibility and fill of the dietary insoluble fibre (NDF) treat the ruminoreticular particulate mass as a single pool. The underlying assumption is that escape of particles follows first-order kinetics. In this paper, we proposed and evaluated a model of two ruminoreticular sequential NDF pools. The first ...
Bhattacharjee M - - 2008
We are studying variable selection in multiple regression models in which molecular markers and/or gene-expression measurements as well as intensity measurements from protein spectra serve as predictors for the outcome variable (i.e., trait or disease state). Finding genetic biomarkers and searching genetic-epidemiological factors can be formulated as a statistical problem ...
Strimas Rachel - - 2008
BACKGROUND: The high prevalence of obesity currently poses a global health crisis. Previous research has identified a novel link between obesity and Attention-Deficit/Hyperactivity Disorder (AD(H)D). Davis, Levitan, Smith, Tweed and Curtis [Davis, C., Levitan, R. D., Smith, M., Tweed, S., & Curtis, C. (2006). Associations among overeating, overweight, and attention ...
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 ...
Ramakrishnan Rajasekhar - - 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 ...
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 ...
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 - - 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 ...
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