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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 ...
Alvarez Mar - - 2009
Microcantilevers based-biosensors are a new label-free technique that allows the direct detection of biomolecular interactions in a label-less way and with great accuracy by translating the biointeraction into a nanomechanical motion. Low cost and reliable standard silicon technologies are widely used for the fabrication of cantilevers with well-controlled mechanical properties. ...
Tan Niclas C - - 2009
BACKGROUND: Mass spectrometry-based biomarker discovery has long been hampered by the difficulty in reconciling lists of discriminatory peaks identified by different laboratories for the same diseases studied. We describe a multi-statistical analysis procedure that combines several independent computational methods. This approach capitalizes on the strengths of each to analyze the ...
Atiomo W - - 2009
BACKGROUND: The exact causes of polycystic ovary syndrome (PCOS) are uncertain, and treatment could be improved. Discovery-based approaches like 'proteomics' may result in faster insights into the causes of PCOS and improved treatment. OBJECTIVES: To identify the number and nature of proteomic biomarkers found in PCOS so far and to ...
Schmidt Frank - - 2009
BACKGROUND: Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments. RESULTS: In the present ...
Morrison Gavin - - 2009
Biomedical scientists are aggressively investigating biomarkers of disease and injury. The rationale for identifying biomarkers during pathological states, such as severe sepsis, is to improve clinical prognostication and stratify therapeutic interventions for optimal recovery. An added benefit of biomarker studies is knowledge genesis on pathophysiological mechanisms, critical information that provides ...
Bomphrey Richard J - - 2009
Despite a wealth of evidence demonstrating extraordinary maximal performance, little is known about the routine flight performance of insects. We present a set of techniques for benchmarking performance characteristics of insects in free flight, demonstrated using a model species, and comment on the significance of the performance observed. Free-flying blowflies ...
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 ...
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