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Results 201 - 250 of 971
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Pridatchenko M L - - 2009
Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) ...
De Jager Philip L PL Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA. - - 2009
Prediction of susceptibility to multiple sclerosis (MS) might have important clinical applications, either as part of a diagnostic algorithm or as a means to identify high-risk individuals for prospective studies. We investigated the usefulness of an aggregate measure of risk of MS that is based on genetic susceptibility loci. We ...
Albaum Stefan P SP Computational Genomics, Center for Biotechnology (CeBiTec), Biodata Mining & Applied Neuroinformatics Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany. - - 2009
The goal of present -omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common ...
Aaltonen T - - 2009
We present an analysis of the mass of the X(3872) reconstructed via its decay to J/psi pi(+)pi(-) using 2.4 fb(-1) of integrated luminosity from pp collisions at square root(s)=1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. The possible existence of two nearby mass states is investigated. ...
Kathiravan Mathur Nadarajan - - 2010
This study presents the external mass transfer effects on the reduction of hexavalent chromium (Cr(VI)) using calcium alginate immobilized Bacillus sp. in a re-circulated packed bed batch reactor (RPBR). The effect of flow rate on the reduction Cr(VI) was studied. Theoretically calculated rate constants for various flow rates were analyzed ...
Redestig Henning - - 2009
Most mass spectrometry based metabolomics studies are semiquantitative and depend on efficient normalization techniques to suppress systematic error. A common approach is to include isotope-labeled internal standards (ISs) and then express the estimated metabolite abundances relative to the IS. Because of problems such as insufficient chromatographic resolution, however, the analytes ...
Apweiler Rolf - - 2009
Recent developments in proteomics technology offer new opportunities for clinical applications in hospital or specialized laboratories including the identification of novel biomarkers, monitoring of disease, detecting adverse effects of drugs, and environmental hazards. Advanced spectrometry technologies and the development of new protein array formats have brought these analyses to a ...
Riffle Michael M Department of Biochemistry, University of Washington, Seattle, WA 98195, - - 2009
The field of proteomics, particularly the application of MS analysis to protein samples, is well established and growing rapidly. Proteomic studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and ...
Mylonas Roman - - 2009
The diversity of experimental workflows involving LC-MS/MS and the extended range of mass spectrometers tend to produce extremely variable spectra. Variability reduces the accuracy of compound identification produced by commonly available software for a spectral library search. We introduce here a new algorithm that successfully matches MS/MS spectra generated by ...
Zam? Alberto - - 2010
Lymphoid and haematopoietic neoplasms comprise a broad spectrum of different tumours, classified by the World Health Organization (WHO) on the basis of a combination of morphology, immunophenotypic, genetic and clinical features. Up to date for many of these neoplasms no single feature is regarded as a diagnostic gold standard. The ...
Rusconi Filippo - - 2009
Since the middle of the 90s, mass spectrometry has evolved into an almost indispensable tool in structural studies on an ever-growing variety of (bio-)polymers, of which proteins, sugars and nucleic acids are the most prominent. Since the first public release of massXpert, the advances of mass spectrometry have motivated continuous ...
McConnachie Alan W - - 2009
In hierarchical cosmological models, galaxies grow in mass through the continual accretion of smaller ones. The tidal disruption of these systems is expected to result in loosely bound stars surrounding the galaxy, at distances that reach 10-100 times the radius of the central disk. The number, luminosity and morphology of ...
Burton Richard F - - 2010
It is almost a matter of dogma that human body mass in adults tends to vary roughly in proportion to the square of height (stature), as Quetelet stated in 1835. As he realised, perfect isometry or geometric similarity requires that body mass varies with height cubed, so there seems to ...
Vizcaíno Juan Antonio - - 2009
The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through ...
Giannopoulos G - - 2010
Terrorist attacks in New York have shocked the world community showing clearly the vulnerability of air transport in such events. However, the terrorist attacks in Madrid and London showed that land mass transport infrastructure is equally vulnerable in case of similar attacks. The fact that there has not been substantial ...
Khan Zia - - 2009
Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than ...
Lê Cao Kim-Anh - - 2009
With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical ...
Eisenacher Martin - - 2009
In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation ...
Ahmed Y - - 2009
Linesmen working on high voltage equipment occasionally report unpleasant discharges from equipment. The sensation is known as microshocks, which result from capacitive coupling of the linesmen to high voltage sources and subsequent discharging when in very close proximity to grounded objects. Often, this is just an annoyance, but the levels ...
Gogas H - - 2009
Biomarkers are tumour- or host-related factors that correlate with tumour biological behaviour and patient prognosis. High-throughput analytical techniques--DNA and RNA microarrays--have identified numerous possible biomarkers, but their relevance to melanoma progression, clinical outcome and the selection of optimal treatment strategies still needs to be established. The review discusses a possible ...
Ting Lily - - 2009
Comparative proteomics is a powerful analytical method for learning about the responses of biological systems to changes in growth parameters. To make confident inferences about biological responses, proteomics approaches must incorporate appropriate statistical measures of quantitative data. In the present work we applied microarray-based normalization and statistical analysis (significance testing) ...
Karpievitch Yuliya V - - 2009
LC-MS allows for the identification and quantification of proteins from biological samples. As with any high-throughput technology, systematic biases are often observed in LC-MS data, making normalization an important preprocessing step. Normalization models need to be flexible enough to capture biases of arbitrary complexity, while avoiding overfitting that would invalidate ...
Kultima Kim - - 2009
The performances of 10 different normalization methods on data of endogenous brain peptides produced with label-free nano-LC-MS were evaluated. Data sets originating from three different species (mouse, rat, and Japanese quail), each consisting of 35-45 individual LC-MS analyses, were used in the study. Each sample set contained both technical and ...
Chio Chia-Pin - - 2009
The main objective of this study was to develop parsimonious empirical models for predicting the mass and number concentrations of ultrafine particulate (UFP, aerodynamic diameter < 0.1 or 0.18 microm) in the atmospheric environment. We found strong correlations existed between the mass/number concentration of UFP and the mass concentration of ...
Zhang Yan J - - 2009
BACKGROUND: Many drugs for treatment of allergies, migraine headaches, inflammation, and other indications are administered into the nasal cavity providing access to the immune and central nervous systems. One of the concerns for using this route of administration is potential damage to the nasal epithelium and mucosal regions. We assembled ...
von Bloh W - - 2009
The unexpected diversity of exoplanets includes a growing number of super-Earth planets, i.e., exoplanets with masses of up to several Earth masses and a similar chemical and mineralogical composition as Earth. We present a thermal evolution model for a 10 Earth-mass planet orbiting a star like the Sun. Our model ...
Bradford Mark A - - 2009
Hartley et al. question whether reduction in R(mass), under experimental warming, arises because of the biomass method. We show the method they treat as independent yields the same result. We describe why the substrate-depletion hypothesis may not solely explain observed responses, and urge caution in interpretation of the seasonal data.
Sturm Marc - - 2009
Visualization of complex mass spectrometric data sets is becoming increasingly important in proteomics and metabolomics. We present TOPPView, an integrated data visualization and analysis tool for mass spectrometric data sets. TOPPView allows the visualization and comparison of individual mass spectra, two-dimensional LC-MS data sets and their accompanying metadata. By supporting ...
Ovelleiro David - - 2009
Current proteomic technology is capable of producing huge amounts of analytical information, which is often difficult to manage in a comprehensive form. Curation, further annotation and public communication of proteomic data require the development of standard data formats and efficient, multimedia database structures. We have implemented a workflow for the ...
Eisenacher Martin - - 2009
The Proteomics Data Collection (ProDaC) consortium, a "Coordination Action" funded by the 6th EU Framework Programme, started in October 2006. Its aim was to facilitate the collection and distribution of proteomics data and the public availability of data sets from proteomics experiments. Within the consortium standard formats are created and ...
Simon Gabriel M GM The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, - - 2009
Two proteomic methods were recently introduced to globally map proteolytic cleavage events in biological systems, one that characterized proteolyzed proteins by differential gel migration (PROTOMAP) and the other by enzymatic tagging and enrichment of the nascent N-terminal peptides generated by proteolysis (Subtiligase). Both technologies were applied to apoptosis, and each ...
Karpievitch Yuliya Y Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843, - - 2009
Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level. We present a statistical model that carefully accounts for informative missingness in ...
Goriely S - - 2009
We present the first Gogny-Hartree-Fock-Bogoliubov (HFB) model which reproduces nuclear masses with an accuracy comparable with the best mass formulas. In contrast with the Skyrme-HFB nuclear-mass models, an explicit and self-consistent account of all the quadrupole correlation energies are included within the 5D collective Hamiltonian approach. The final rms deviation ...
Hoffmann Nils - - 2009
We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used ...
Krambeck Frederick J - - 2009
Effective representation and characterization of biosynthetic pathways of glycosylation can be facilitated by mathematical modeling. This paper describes the expansion of a previously developed detailed model for N-linked glycosylation with the further application of the model to analyze MALDI-TOF mass spectra of human N-glycans in terms of underlying cellular enzyme ...
Aaltonen T - - 2009
We present a measurement of the tt[over ] differential cross section with respect to the tt[over ] invariant mass, dsigma/dM_{tt[over ]}, in pp[over ] collisions at sqrt[s]=1.96 TeV using an integrated luminosity of 2.7 fb;{-1} collected by the CDF II experiment. The tt[over ] invariant mass spectrum is sensitive to ...
Agoston Denes V - - 2009
Proteomics for blast traumatic brain injury (bTBI) research represents an exciting new approach that can greatly help to address the complex pathology of this condition. Antibody-based platforms, antibody microarrays (AbMA), and reverse capture protein microarrays (RCPM) can complement the classical methods based on 2D gel electrophoresis and mass spectrometry (2DGE/MS). ...
Cheng Ka-Wing - - 2009
Chemical model investigation showed that both epigallocatechin gallate (EGCG) and its peracetate, which has all the hydroxyl groups acetylated, effectively reduced the formation of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), the most abundant mutagenic heterocyclic amine found in foods. Mechanistic study was subsequently carried out to characterize the probable inhibitory mechanism involved. GC-MS analysis ...
Widory David - - 2009
Although explosives are easily identified with current instrumental techniques, it is generally impossible to distinguish between sources of the same substance. To alleviate this difficulty, we present a multi-stable isotope (delta13C, delta15N, delta18O, deltaD) approach for appraising the possibility of discriminating explosives. The results from 30 distinct PETN, TNT and ...
Cash Phillip - - 2009
The ability to discriminate bacterial isolates is important for a number of areas of research in Medical Microbiology, particularly in defining bacterial taxonomy and monitoring transmission in epidemiological investigations. Molecular techniques capable of typing bacteria at the level of the genome and proteome are now widely used for these investigations. ...
May Damon D Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, - - 2009
We describe and demonstrate the proteomics computational toolkit provided in the open-source msInspect software distribution. The toolkit includes modules written in Java and in the R statistical programming language to aid the rapid development of proteomics software applications. It contains tools for processing and manipulating standard MS data files, including ...
Bansard Carine - - 2009
This review briefly recapitulates the existing markers predictive of RA responsiveness to treatment, focusing on MTX alone or combined with a biologic. In addition to the demographic and clinical factors, an update is provided of the predictive biomarkers identified by large-scale gene and protein analyses that generated new insights into ...
Boyarsky Alexey - - 2009
Previous fits of sterile neutrino dark matter (DM) models to cosmological data ruled out masses smaller than approximately 8 keV, assuming a production mechanism that is not the best motivated from a particle physics point of view. Here we focus on a realistic extension of the standard model with three ...
Furchtgott Leon A - - 2009
The network of interactions underlying liver regeneration is robust and precise with liver resections resulting in controlled hyperplasia (cell proliferation) that terminates when the liver regains its lost mass. The interplay of cytokines and growth factors responsible for the inception and termination of this hyperplasia is not well understood. A ...
Torres-García Wandaliz - - 2009
MOTIVATION: Gene expression profiling technologies can generally produce mRNA abundance data for all genes in a genome. A dearth of proteomic data persists because identification range and sensitivity of proteomic measurements lag behind those of transcriptomic measurements. Using partial proteomic data, it is likely that integrative transcriptomic and proteomic analysis ...
Hussong Rene - - 2009
MOTIVATION: Mass spectrometry (MS) is one of the most important techniques for high-throughput analysis in proteomics research. Due to the large number of different proteins and their post-translationally modified variants, the amount of data generated by a single wet-lab MS experiment can easily exceed several gigabytes. Hence, the time necessary ...
Barger Vernon - - 2009
We study the minimal gauged U(1) B-L supersymmetric model and show that it provides an attractive theory for spontaneous R-parity violation. Both U(1) B-L and R parity are broken by the vacuum expectation value of the right-handed sneutrino (proportional to the soft supersymmetry masses), thereby linking the B-L and soft ...
Prentice Ross L - - 2009
Few strong and consistent associations have arisen from observational studies of dietary consumption in relation to chronic disease risk. Measurement error in self-reported dietary assessment may be obscuring many such associations. Attempts to correct for measurement error have mostly used a second self-report assessment in a subset of a study ...
Quandt Andreas - - 2009
The identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters ...
Oberg Ann L - - 2009
We review the fundamental principles of statistical experimental design, and their application to quantitative mass spectrometry-based proteomics. We focus on class comparison using Analysis of Variance (ANOVA), and discuss how randomization, replication and blocking help avoid systematic biases due to the experimental procedure, and help optimize our ability to detect ...
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