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Results 251 - 300 of 1000
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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 ...
Frank Ari M - - 2009
Accurate modeling of peptide fragmentation is necessary for the development of robust scoring functions for peptide-spectrum matches, which are the cornerstone of MS/MS-based identification algorithms. Unfortunately, peptide fragmentation is a complex process that can involve several competing chemical pathways, which makes it difficult to develop generative probabilistic models that describe ...
Lladó X - - 2009
During the last decade several algorithms have been proposed for automatic mass detection in mammographic images. However, almost all these methods suffer from a high number of false positives. In this paper we propose a new approach for tackling this false positive reduction problem. The key point of our proposal ...
Gambin Anna - - 2009
We have developed an integrated tool for statistical analysis of large-scale LC-MS profiles of complex protein mixtures comprising a set of procedures for data processing, selection of biomarkers used in early diagnostic and classification of patients based on their peptide mass fingerprints. Here, a novel boosting technique is proposed, which ...
Ling Xuefeng Bruce - - 2009
Rapid progress in technology, particularly in high-throughput biology, allows the analysis of thousands of genes or proteins simultaneously, where the multiple comparison problems occurs. Global false discovery rate (gFDR) analysis statistically controls this error, computing the ratio of the number of false positives over the total number of rejections. Local ...
Aaltonen T - - 2009
We report a measurement of the top-quark mass M_{t} in the dilepton decay channel tt[over ] --> bl;{'+} nu_{l};{'}b[over ]l;{-}nu[over ]_{l}. Events are selected with a neural network which has been directly optimized for statistical precision in top-quark mass using neuroevolution, a technique modeled on biological evolution. The top-quark mass ...
Goldsmith Paul - - 2010
BACKGROUND: In the past decade or so, a range of technologies have emerged that have shown promise in increasing our understanding of disease processes and progression. These advances are referred to as the "omics" technologies; genomics, transcriptomics, and proteomics. More recently, another "omics" approach has come to the fore: metabonomics, ...
Gullo Francesco - - 2009
Mass spectrometry (MS) approaches have been recently coupled with advanced data analysis techniques in order to enable clinicians to discover useful knowledge from MS data. However, effectively and efficiently handling and analyzing MS data requires to take into account a number of issues. In particular, the huge dimensionality and the ...
Ahmed Farid E - - 2009
This is the second article in a series, intended as a tutorial to provide the interested reader with an overview of the concepts not covered in part I, such as: the principles of ion-activation methods, the ability of mass-spectrometric methods to interface with various proteomic strategies, analysis techniques, bioinformatics and ...
Zhou Xiaobo - - 2009
Conventional biomarker discovery focuses mostly on the identification of single markers and thus often has limited success in disease diagnosis and prognosis. This study proposes a method to identify an optimized protein biomarker panel based on MS studies for predicting the risk of major adverse cardiac events (MACE) in patients. ...
Nebrich Grit - - 2009
In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large-scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract ...
Zheng Guangyong - - 2009
With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema ...
Eckel-Passow J E - - 2009
Mass spectrometry is a powerful tool with much promise in global proteomic studies. The discipline of statistics offers robust methodologies to extract and interpret high-dimensional mass-spectrometry data and will be a valuable contributor to the field. Here, we describe the process by which data are produced, characteristics of the data, ...
Dacheux Jean-Louis - - 2009
In all mammalian species, the final differentiation of the male germ cell occurs in the epididymal duct where the spermatozoa develop the ability to be motile and fertilize an ovum. Understanding of these biological processes is the key to understanding and controlling male fertility. Comparative studies between several mammals could ...
Gibbons Gary W - - 2009
We construct a natural measure on the space of Cabibbo-Kobayashi-Maskawa matrices in the standard model, assuming the fermion mass matrices are randomly selected from a distribution which incorporates the observed quark mass hierarchy. This measure allows us to assess the likelihood of Jarlskog's CP violation parameter J taking its observed ...
Aaltonen T - - 2009
We report on a search for inclusive production of squarks and gluinos in pp[over ] collisions at sqrt[s]=1.96 TeV, in events with large missing transverse energy and multiple jets of hadrons in the final state. The study uses a CDF Run II data sample corresponding to 2 fb(-1) of integrated ...
Kumar Chanchal - - 2009
Proteomics has made tremendous progress, attaining throughput and comprehensiveness so far only seen in genomics technologies. The consequent avalanche of proteome level data poses great analytical challenges for downstream interpretation. We review bioinformatic analysis of qualitative and quantitative proteomic data, focusing on current and emerging paradigms employed for functional analysis, ...
Aubert B - - 2009
We measure branching fractions and integrated rate asymmetries for the rare decays B-->K(*)l+l-, where l+l- is either e+e- or micro+micro-, using a sample of 384x10(6) BB events collected with the BABAR detector at the PEP-II e+e- collider. We find no evidence for direct CP or lepton-flavor asymmetries. However, for dilepton ...
West-Nørager Mikkel - - 2009
The emergence of new biological disease markers from mass spectrometric studies of serum proteomes has been quite limited. There are challenges regarding the analytical and statistical procedures, preanalytical variability, and study designs. In this serological study of ovarian cancer, we apply classification methods in a strictly designed study with standardized ...
Franz Ragna - - 2009
Allometric equations are often used to extrapolate traits in animals for which only body mass estimates are known, such as dinosaurs. One important decision can be whether these equations should be based on mammal, bird or reptile data. To address whether this choice will have a relevant influence on reconstructions, ...
Gertheiss Jan - - 2009
When feature selection in mass spectrometry is based on single m/z values, problems arise from the fact that variability is not only in vertical but also in horizontal direction, i.e. also slightly differing m/z values may correspond to the same feature. Hence, we propose to use the full spectra as ...
Pintilie Melania - - 2009
PURPOSE: Many recent studies have suggested the possibility that a variety of different biomarkers may be associated with treatment outcome. However, it is also apparent that some of these biomarkers are heterogeneously distributed within a tumor. Due to this heterogeneous distribution of the biomarker, the association sought may appear weak ...
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