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Results 301 - 350 of 974
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Li Haiquan - - 2009
Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods ...
Lustgarten Jonathan L - - 2009
The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In particular, we use the Empirical Proteomics ...
Locasale Jason W - - 2009
Advances in mass spectrometry among other technologies have allowed for quantitative, reproducible, proteome-wide measurements of levels of phosphorylation as signals propagate through complex networks in response to external stimuli under different conditions. However, computational approaches to infer elements of the signaling network strictly from the quantitative aspects of proteomics data ...
Tougas Terrence P - - 2009
This study of aerodynamic mass-weighted particle size distribution (APSD) data from orally inhaled products (OIPs) investigated whether a set of simpler (than currently used) metrics may be adequate to detect changes in APSD for quality control (QC) purposes. A range of OIPs was examined, and correlations between mass median aerodynamic ...
Huang Yuan-Jiao - - 2009
No satisfactory biomarkers are currently available to screen for nasopharyngeal carcinoma (NPC). We have developed and evaluated surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for detection and analysis of multiple proteins for distinguishing individuals with NPC from control individuals. A preliminary learning set and a classification tree of spectra ...
Thielen Bernhard - - 2009
Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other relevant data, e.g. ...
Phan John H - - 2009
Identifying and validating biomarkers from high-throughput gene expression data is important for understanding and treating cancer. Typically, we identify candidate biomarkers as features that are differentially expressed between two or more classes of samples. Many feature selection metrics rely on ranking by some measure of differential expression. However, interpreting these ...
Webb-Robertson Bobbie-Jo M BJ Pacific Northwest National Laboratory, Richland, WA 99352, - - 2009
High-throughput (HTP) technologies offer the capability to evaluate the genome, proteome, and metabolome of an organism at a global scale. This opens up new opportunities to define complex signatures of disease that involve signals from multiple types of biomolecules. However, integrating these data types is difficult due to the heterogeneity ...
Radivoyevitch Tomas T Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA. - - 2009
The Hill coefficient characterizes the extent to which an enzyme exhibits positive or negative cooperativity, but it provides no information regarding the mechanism of cooperativity. In contrast, models based on the equilibrium concept of mass action can suggest mechanisms of cooperativity, but there are often many such models and often ...
Qian Wei-Jun WJ Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, - - 2009
The quantitative comparison of protein abundances across a large number of biological or patient samples represents an important proteomics challenge that needs to be addressed for proteomics discovery applications. Herein, we describe a strategy that incorporates a stable isotope (18)O-labeled "universal" reference sample as a comprehensive set of internal standards ...
Befekadu Getachew K GK Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, - - 2009
A Bayesian multilevel functional mixed-effects model with group specific random-effects is presented for analysis of liquid chromatography-mass spectrometry (LC-MS) data. The proposed framework allows alignment of LC-MS spectra with respect to both retention time (RT) and mass-to-charge ratio (m/z). Affine transformations are incorporated within the model to account for any ...
Basu Nandita B - - 2009
Key attributes of the source zone and the expanding dissolved plume at a trichloroethene (TCE) site in Australia were evaluated using trends in groundwater monitoring data along with data from on-line volatile organic compound (VOC) samplers and passive flux meters (PFMs) deployed in selected wells. These data indicate that: (1) ...
Battle Andrew R - - 2009
The bacterial mechanosensitive (MS) channels of small (MscS) and large (MscL) conductance have functionally been reconstituted into giant unilamellar liposomes (GUVs) using an improved reconstitution method in the presence of sucrose. This method gives significant time savings (preparation times as little as 6h) compared to the classical method of protein ...
Song Haowei H Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United - - 2009
Lipidomics comprises large-scale studies of the structures, quantities, and functions of lipid molecular species. Recently developed mass spectrometric methods for lipid analyses, especially electrospray ionization (ESI) tandem mass spectrometry, permit identification and quantitation of an enormous variety of distinct lipid molecular species from small amounts of biological samples but generate ...
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 G Department of Chemical Engineering, University of Washington, Seattle, WA 98195, - - 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 TK Department of Pediatrics-Nephrology, Stanford University Medical School, Stanford University, Stanford, CA 94305, - - 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 ...
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