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Sadygov Rovshan G - - 2010
We describe a method for ratio estimations in (18)O-water labeling experiments acquired from low resolution isotopically resolved data. The method is implemented in a software package specifically designed for use in experiments making use of zoom-scan mode data acquisition. Zoom-scan mode data allow commonly used ion trap mass spectrometers to ...
Lackner Susanne - - 2010
Nitrogen removal via nitrite has gained increasing attention in recent years due to its potential cost savings. Membrane-aerated biofilm reactors (MABRs) are one potential technology suitable to achieve nitritation. In this study we compared lab scale MABRs with conventional biofilm reactors to evaluate the influence of environmental conditions and operational ...
Allison Stuart A - - 2010
Modeling the electrophoretic mobility of peptides is examined in this study using a "coarse grained" bead model, or B model for short 8 and also a simpler "effective sphere" (ES) model. A comparison between the B and ES models is carried out for peptide models covering a broad range of ...
Wang Hao - - 2010
Non-model organisms represent the majority of life forms in our planet. However, the lack of genetic information hinders us to understand the unique biological phenomena in non-model organisms at the molecular level. In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula ...
Houston A I - - 2010
The extant auks show three strategies of chick rearing--precocial (chicks leave the nest site when a few days old), intermediate (young raised to a mass of around 20% of adult mass) and semi-precocial (young raised to a mass of around 65% of adult mass). It is not known which strategy ...
Konar Partha - - 2010
We propose a new model-independent technique for mass measurements in missing energy events at hadron colliders. We illustrate our method with the most challenging case of a single-step decay chain. We consider inclusive same-sign chargino pair production in supersymmetry, followed by leptonic decays to sneutrinos χ+ χ+ → ℓ+ ℓ'+ ...
Folco Luigi - - 2010
We report on the detection in southern Egypt of an impact crater 45 meters in diameter with a pristine rayed structure. Such pristine structures are typically observed on atmosphereless rocky or icy planetary bodies in the solar system. This feature and the association with an iron meteorite impactor and shock ...
Wood Jacqueline E - - 2010
The potential of analytical chemistry to predict sensory qualities of food materials is a major current theme. Standard practice is cross-validation (CV), where a set of chemical and associated sensory data is partitioned so chemometric models can be developed on training subsets, and validated on held-out subsets. CV demonstrates prediction, ...
Naegle Kristen M - - 2010
The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs ...
Wang Penghao - - 2010
MOTIVATION: Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identification of a protein is the critical first step in elucidating its biological function. Successful protein identification depends on various interrelated factors, including effective analysis ...
Shah Anuj R - - 2010
The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing ...
Vizcaíno Juan Antonio - - 2010
Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and ...
Rajalahti Tarja - - 2010
Mass spectral profiles from cerebrospinal fluid (CSF) are used as input to a novel multivariate approach to select features responsible for the separation of patients with multiple sclerosis (MS) from control groups. Our targeted statistical approach makes it possible to systematically remove features in the spectral fingerprints masking the components ...
Shariat Shahrokh F - - 2010
To critically review and illustrate current methodological and statistical considerations for bladder cancer biomarker discovery and evaluation. Original, review, and methodological articles, and editorials were reviewed and summarized. Biomarkers may be useful at multiple stages of bladder cancer management: early detection, diagnosis, staging, prognosis, and treatment; however, few novel biomarkers ...
Markuszewski Michal J - - 2010
In the postgenome-sequencing era, several large projects have been running recently. Proteomics and other analysis or structural biology are the most active today. Since the late 1990 s, metabolomics has been gaining importance in systems biology, as it provides real-world end points that complement and help in the interpretation of ...
Diamant Z - - 2010
A biological marker (biomarker) is a physical sign or laboratory measurement that can serve as an indicator of biological or pathophysiological processes or as a response to a therapeutic intervention. An applicable biomarker possesses the characteristics of clinical relevance (sensitivity and specificity for the disease) and is responsive to treatment ...
Aaltonen T - - 2010
We report a measurement of the ratio of the tt to Z/γ{*} production cross sections in sqrt[s]=1.96  TeV pp collisions using data corresponding to an integrated luminosity of up to 4.6  fb{-1}, collected by the CDF II detector. The tt cross section ratio is measured using two complementary methods, a b-jet tagging ...
Abels B - - 2010
PCT postprocessing commonly uses either the MS or a variant of the DC approach for modeling of voxel-based time-attenuation curves. There is an ongoing discussion about the respective merits and limitations of both methods, frequently on the basis of theoretic reasoning or simulated data. We performed a qualitative and quantitative ...
Gong R - - 2010
Flow-interruption tracer test is an effective approach to identify kinetic mass transfer processes for solute transport in subsurface media. By switching well pumping and resting, one may alter the dominant transport mechanism and generate special concentration patterns for identifying kinetic mass transfer processes. In the present research, we conducted three-phase ...
Roy Pascal - - 2011
The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. In recent years there has been a growing interest in using high throughput technologies for the detection of such biomarkers. In particular, mass spectrometry appears as an exciting tool with great potential. ...
Mueller Ryan S - - 2010
An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing ...
Zhou Min - - 2010
Recent progress in proteomics has identified vast arrays of interacting proteins together with knowledge of their post-translational modifications. A key challenge is to integrate this information with homology modelling and structural biology to provide a topological or even an atomic context for these modifications. Mass spectrometry (MS) is ideally placed ...
Morris John H JH Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, - - 2010
Linking proteomics and structural data is critical to our understanding of cellular processes, and interactive exploration of these complementary data sets can be extremely valuable for developing or confirming hypotheses in silico. However, few computational tools facilitate linking these types of data interactively. In addition, the tools that do exist ...
Grigsby Claude C - - 2010
The goal of this work was to design and implement a prototype software tool for the visualization and analysis of small molecule metabolite GC-MS and LC-MS data for biomarker discovery. The key features of the Metabolite Differentiation and Discovery Lab (MeDDL) software platform include support for the manipulation of large ...
Strohalm Martin - - 2010
While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the ...
Gruson D - - 2010
A single biomarker has an inherent specificity and sensitivity that cannot be improved, but multiple biomarkers can be combined to achieve improved clinical performances. This is the basis of multimarker strategies that integrate different biomarkers into a single score to support medical decisions. The simplest strategy determines ratios of different ...
Higdon Roger - - 2010
Large amounts of mass spectrometry (MS) proteomics data are now publicly available; however, little attention has been given to how to best combine these data and assess the error rates for protein identification. The objective of this article is to show how variation in the type and amount of data ...
Yu Kebing K Department of Chemistry, Brown University, Providence, RI 02903, - - 2010
Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated ...
Halevy Itay - - 2010
Sulfur isotopes in ancient sediments provide a record of past environmental conditions. The long-time-scale variability and apparent asymmetry in the magnitude of minor sulfur isotope fractionation in Archean sediments remain unexplained. Using an integrated biogeochemical model of the Archean sulfur cycle, we find that the preservation of mass-independent sulfur is ...
Niu Qian - - 2010
To identify novel serum protein biomarkers and establish diagnostic pattern for rheumatoid arthritis (RA) by using proteomic technology. Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with weak cationic exchange magnetic beads. A training set of spectra, derived from analyzing sera from 22 patients ...
Cazzola Mario - - 2010
Although there is increasing interest in using pulmonary biomarkers for a more complete and clinically relevant assessment of COPD and a plethora of biomarkers are becoming available, there is little information regarding their reproducibility and correlation with other outcome measurements in COPD. The lack of well-validated biomarkers that can be ...
Menschaert Gerben - - 2010
The term peptidomics for a new promising "omics" field was not introduced until the beginning of 2000. The approach has been proven successful in several domains such as neuroendocrine research and biomarker or drug discovery. This review reports on bioinformatics tools and methodologies within the peptidomics field and the application ...
Zhu Qi - - 2010
The enzymatic (18)O-labeling is a useful technique for reducing the influence of the between-spectrum variability on the results of mass-spectrometry experiments. A limitation of the technique is the possibility of an incomplete labeling, which may result in biased estimates of the relative peptide abundance. We propose a Markov-chain-based regression model ...
Cerqueira Fabio R - - 2010
The target-decoy search strategy has been successfully applied in shotgun proteomics for validating peptide and protein identifications. If, on one hand, this method has proven to be very efficient for error estimation, on the other hand, little attention has been paid to the resulting sensitivity. Only two scores are normally ...
Kirchner Marc - - 2010
Despite the efforts of the mass spectrometry (MS) community to migrate data representation toward modern file formats, legacy text formats still play an important role in MS data processing workflows. We provide a formal grammar and a portable, efficient C++ implementation for a Mascot Generic Format (MGF) parser. Software and ...
Courtiol Alexandre - - 2010
Many studies use representations of human body outlines to study how individual characteristics, such as height and body mass, affect perception of body shape. These typically involve reality-based stimuli (e.g., pictures) or manipulated stimuli (e.g., drawings). These two classes of stimuli have important drawbacks that limit result interpretations. Realistic stimuli ...
Gabbiani Chiara - - 2010
Since the discovery of cisplatin and its introduction in the clinics, metal compounds have been intensely investigated in view of their possible application in cancer therapy. In this frame, a deeper understanding of their mode of action, still rather obscure, might turn crucial for the design and the obtainment of ...
Wacey David - - 2010
The 3426-3350 Ma Strelley Pool Formation (SPF) is a silicified, dominantly sedimentary unit within the Pilbara Supergroup, Western Australia. It is found widely across the East Pilbara Terrane, and it forms a prominent marker horizon and separates the largely volcanic 3520-3427 Ma Warrawoona and 3350-3315 Ma Kelly groups. It has ...
Jarcuska Peter - - 2010
INTRODUCTION: Fibrogenesis is a typical reaction of the liver to injury. In the case of overstimulation of fibrogenesis clinically significant fibrosis and, eventually, cirrhosis occur. Treatment of liver cirrhosis is limited, therefore it is important to screen and monitor patients at risk of cirrhosis. Noninvasive parameters are ideal for this ...
Chao Tzu-Chiao - - 2010
The use of proteomics to profile biological fluids and identify therein biomarkers for cancer and other diseases was initially received with considerable excitement. However, results have fallen short of the expectations. Traditionally, protein biomarkers have been identified by measurement of relative expression changes between case and control samples from which ...
Souady Jamal - - 2010
Glycosphingolipids (GSLs) are major components of the outer leaflet of the cell membrane. These lipids are involved in many cell surface events and show disease-related expression changes. GSLs could thus serve as useful targets for biomarker discovery. The GSL structure is characterized by two entities: a hydrophilic glycan and a ...
Karp Natasha A - - 2010
iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates ...
Buyse Marc - - 2010
Biomarkers and surrogate end points have great potential for use in clinical oncology, but their statistical validation presents major challenges, and few biomarkers have been robustly confirmed. Provisional supportive data for prognostic biomarkers, which predict the likely outcome independently of treatment, is possible through small retrospective studies, but it has ...
Reemtsma Thorsten - - 2010
A two-dimensional diagram is proposed, in which the carbon number of each formula is plotted against its nominal mass, to visualize large sets of molecular formula data that can be derived from data generated by ultrahigh-resolution Fourier transform ion cyclotron resonance-MS. In such a carbon versus mass (CvM) diagram, each ...
Ray Patrick - - 2010
A biomarker may provide a diagnosis, assess disease severity or risk, or guide other clinical interventions such as the use of drugs. Although considerable progress has been made in standardizing the methodology and reporting of randomized trials, less has been accomplished concerning the assessment of biomarkers. Biomarker studies are often ...
Tseng George C - - 2010
High-throughput experiments have become more and more prevalent in biomedical research. The high-dimensional data have brought new challenges. Effective data reduction, summarization and visualization are important keys to initial exploration in the data mining. In this paper, we introduce a visualization tool, namely quantile map, to present information contained in ...
Huang Qizhi - - 2010
Biomarkers are needed to screen multiple stages in the clinical pathway of Barrett's oesophagus patients; from disease diagnosis to risk stratification and predicting response to therapy. Routes to the identification of biomarkers have been recognized by known molecular features of the disease and more recently through transcriptomic, methylation and proteomic ...
Christin Christin - - 2010
Time alignment of complex LC-MS data remains a challenge in proteomics and metabolomics studies. This work describes modifications of the Dynamic Time Warping (DTW) and the Parametric Time Warping (PTW) algorithms that improve the alignment quality for complex, highly variable LC-MS data sets. Regular DTW or PTW use one-dimensional profiles ...
Yunes Nicol?s - - 2010
We present the first models of extreme-mass-ratio inspirals within the effective-one-body (EOB) formalism, focusing on quasicircular orbits into nonrotating black holes. We show that the phase difference and (Newtonian-normalized) amplitude difference between analytical EOB and numerical Teukolsky-based gravitational waveforms can be reduced to less than or approximately 10{-1} rad and ...
Djidja Marie-Claude - - 2010
The development of tissue micro-array (TMA) technologies provides insights into high-throughput analysis of proteomics patterns from a large number of archived tumour samples. In the work reported here, matrix-assisted laser desorption/ionisation-ion mobility separation-mass spectrometry (MALDI-IMS-MS) profiling and imaging methodology has been used to visualise the distribution of several peptides and ...
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