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Results 251 - 300 of 980
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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 ...
Reeves Gabrielle A - - 2009
Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly ...
Kluge Bogusław - - 2009
Recent studies demonstrate that the peptides in the serum of cancer patients that are generated (ex vivo) as a result of tumor protease activity can be used for the detection and classification of cancer. In this paper, we propose the first formal approach to modeling exopeptidase activity from liquid chromatography-mass ...
Du Lihong - - 2009
A previously proposed partition equilibrium model for quantitative prediction of analyte response in electrospray ionization mass spectrometry is modified to yield an improved linear relationship. Analyte mass spectrometer response is modeled by a competition mechanism between analyte and background electrolytes that is based on partition equilibrium considerations. The correlation between ...
Clauset Aaron - - 2009
Within large taxonomic assemblages, the number of species with adult body mass M is characterized by a broad but asymmetric distribution, with the largest mass being orders of magnitude larger than the typical mass. This canonical shape can be explained by cladogenetic diffusion that is bounded below by a hard ...
Chen Shuo - - 2009
Mass spectrometry (MS) can generate high-throughput protein profiles for biomedical research to discover biologically related protein patterns/biomarkers. The noisy functional MS data collected by current technologies, however, require consistent, sensitive and robust data-processing techniques for successful biomedical application. Therefore, it is important to detect features precisely for each spectrum, quantify ...
Valente André X C N - - 2009
It is hoped that comprehensive mapping of protein physical interactions will facilitate insights regarding both fundamental cell biology processes and the pathology of diseases. To fulfill this hope, good solutions to 2 issues will be essential: (i) how to obtain reliable interaction data in a high-throughput setting and (ii) how ...
- - 2009
In this issue of Proteomics you will find the following highlighted articles:Spruce: things my father had taught and not taught meLesson No.1 "Never shake hands with a spruce" or more likely as a ten-year old, try to climb one. Spruce have more serious problems to deal with than little boys: ...
Jia Wei - - 2009
Core fucosylation (CF) patterns of some glycoproteins are more sensitive and specific than evaluation of their total respective protein levels for diagnosis of many diseases, such as cancers. Global profiling and quantitative characterization of CF glycoproteins may reveal potent biomarkers for clinical applications. However, current techniques are unable to reveal ...
Gehlenborg Nils - - 2009
We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein ...
De Laeter John R - - 2009
The 1914 Nobel Prize for Chemistry was awarded to Theodore Richards, whose work provided an insight into the history of the birth and evolution of matter as embedded in the atomic weights. However, the secret to unlocking the hieroglyphics contained in the atomic weights is revealed by a study of ...
Gujral Taranjit S - - 2009
Recording the state and dynamics of intracellular signaling networks in clinical specimens can help identify and validate biomarkers, but may also prove useful in developing and monitoring targeted therapies. Studying cell signaling on a system-wide level in solid tissue, however, is often not feasible using mass spectrometry, because this technique ...
Labrot Vincent - - 2009
The overall traffic of droplets in a network of microfluidic channels is strongly influenced by the liquid properties of the moving droplets. In particular, the effective hydrodynamic resistance of individual droplets plays a key role in their global behavior. Here we propose two simple and low-cost experimental methods for measuring ...
Oli Monika W - - 2009
In recent years, the term proteomics is often mentioned together with biomarker discovery, as proteomic studies have the capability of identifying unique and unobvious protein biomarkers from tissues or biofluids derived from animal models or human clinical samples inflicted with various diseases. Proteomics has yielded hundreds of potential biomarker candidates. ...
Fananapazir Nafeh - - 2009
Within clinical proteomics, mass spectrometry analysis of biological samples is emerging as an important high-throughput technology, capable of producing powerful diagnostic and prognostic models and identifying important disease biomarkers. As interest in this area grows, and the number of such proteomics datasets continues to increase, the need has developed for ...
Parikh Jignesh R - - 2009
BACKGROUND: Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet ...
Apweiler Rolf - - 2009
The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis, stratification of patients for specific treatment, or therapy monitoring. New protein array formats and improved spectrometry technologies have brought these analyses to ...
Margolin Adam A - - 2009
BACKGROUND: Advances in mass spectrometry-based proteomics have enabled the incorporation of proteomic data into systems approaches to biology. However, development of analytical methods has lagged behind. Here we describe an empirical Bayes framework for quantitative proteomics data analysis. The method provides a statistical description of each experiment, including the number ...
Ceccarelli Michele - - 2009
BACKGROUND: Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks) have to be analyzed as part of computational pipelines aimed at the realization of efficient predictive and ...
Law Wai S - - 2009
There is always a need to detect the presence of microorganisms, either as contaminants in food and pharmaceutical industries or bioindicators for disease diagnosis. Hence, it is important to develop efficient, rapid, and simple methods to detect microorganisms. Traditional culturing method is unsatisfactory due to its long incubation time. Molecular ...
Alonso Ariel - - 2009
In recent years the cost of drug development has increased the demands on efficiency in the selection of suitable drug candidates. Biomarkers for efficacy and safety could be a plausible strategy to improve this selection process. In the present work, we focus on the study and evaluation of different physiological ...
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