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Balasubramanian Raji - - 2010
Sample handling and storage conditions in specimens frozen over long periods of time can severely impact marker levels. If laboratory technologies, practices and related protocols change over time, biomarker studies are potentially biased and report erroneous results. These issues and pitfalls are often overlooked in system biology studies using previously ...
Kuroda Junji - - 2010
The mass-spring chain allows accurate modeling of vibrating strings in all three spatial dimensions. [Rowland and Pask, Am. J. Phys. (1999).] However, such a model is for non-stiff strings. A stiff mass-spring string model is proposed, consisting of three or more cross-coupled parallel mass-spring chains.
Kuroda Junji - - 2010
The mass-spring chain allows accurate modeling of vibrating strings in all three spatial dimensions. [Rowland and Pask, Am. J. Phys. (1999)]. This presentation describes striking one or more adjacent masses of such a string model with a forcing function corresponding to the piano hammer [http://www.ioc.ee/stulov/PUB.htm]. An advantage of striking a ...
Perlova Tatiana Yu - - 2010
LC combined with MS/MS analysis of complex mixtures of protein digests is a reliable and sensitive method for characterization of protein phosphorylation. Peptide retention times (RTs) measured during an LC-MS/MS run depend on both the peptide sequence and the location of modified amino acids. These RTs can be predicted using ...
Moruz Luminita - - 2010
Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Most notably such predictions are used to weed out incorrect peptide-spectrum matches, and to design targeted proteomics experiments. In this study, we describe a RT predictor, ELUDE, which can be employed in both ...
Armirotti Andrea - - 2010
Over the last years, top-down (TD) MS has gained a remarkable space in proteomics, rapidly trespassing the limit between a promising approach and a solid, established technique. Several research groups worldwide have implemented TD analysis in their routine work on proteomics, deriving structural information on proteins with the level of ...
Durbin Kenneth R - - 2010
Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms ...
Lahesmaa-Korpinen Anna-Maria - - 2010
MS/MS is a widely used method for proteome-wide analysis of protein expression and PTMs. The thousands of MS/MS spectra produced from a single experiment pose a major challenge for downstream analysis. Standard programs, such as MASCOT, provide peptide assignments for many of the spectra, including identification of PTM sites, but ...
Wu Hui-Chung - - 2010
Two-dimensional electrophoresis (2-DE) has evolved into a robust separation technique in proteomic research. However, one of the major challenges in 2-DE experiments, the reproducibility of the first dimensional electrophoresis (IEF), has remained unsolved. It is well-known that the quality of IEF experiments is significantly affected by the salt interference. Nevertheless, ...
Ameredes Bill T - - 2011
Biomarkers ranging from simple to sophisticated have been used by man for many years of his existence. The main use for biomarkers over that time has been to assess relative states health and well-being, including the presence of functional limitations that presage debilitation and even death. In recent years, there ...
Wang Zimian - - 2010
Oxygen and carbon are the first and second abundant elements, respectively, in the human body by mass. Although many physiological and pathological processes are accompanied with alteration of total body oxygen (TBO) and carbon (TBC) masses, in vivo measurements of the two elements are limited. Up to now, almost all ...
Cotter Trish - - 2010
Effective mass media campaigns are hard to come by. A delicate blend of art and science is required to ensure content is technically accurate as well as being creatively engaging for the target audience. However, the most expensive component of a media campaign is not its development but its placement ...
Herrel Anthony - - 2011
Body size has a pervasive effect on animal functioning and life history with size dependent changes in performance and physiology throughout ontogeny being common in many ectothermic vertebrates. However, as selection on juvenile life history stages is strong, juveniles often offset the disadvantages of small body size by disproportionate levels ...
Pirko I I Mayo Clinic, Department of Neurology, College of Medicine, Rochester, MN 55905, USA. - - 2011
White matter (WM) lesions are the classic pathological hallmarks of multiple sclerosis (MS). However, MRI-based WM lesion load shows relatively poor correlation with functional outcome, resulting in the "clinico-radiological paradox" of MS. Unlike lesion based measures, volumetric MRI assessment of brain atrophy shows a strong correlation with functional outcome, and ...
Jovanovic Marko - - 2010
Efficient experimental strategies are needed to validate computationally predicted microRNA (miRNA) target genes. Here we present a large-scale targeted proteomics approach to validate predicted miRNA targets in Caenorhabditis elegans. Using selected reaction monitoring (SRM), we quantified 161 proteins of interest in extracts from wild-type and let-7 mutant worms. We demonstrate ...
Miernyk Ján A - - 2011
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved ...
Zamboni Anita - - 2010
The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification ...
Robbins Gwen - - 2010
Methods for estimating body mass from the human skeleton are often required for research in biological or forensic anthropology. There are currently only two methods for estimating body mass in subadults: the width of the distal femur metaphysis is useful for individuals 1-12 years of age and the femoral head ...
- - 2010
A Human Proteome Project has been proposed. To ensure that such a project will have a transformative impact on biology, its scope should be determined by wide and open discussion.
Schadt Eric E - - 2010
Today we can generate hundreds of gigabases of DNA and RNA sequencing data in a week for less than US$5,000. The astonishing rate of data generation by these low-cost, high-throughput technologies in genomics is being matched by that of other technologies, such as real-time imaging and mass spectrometry-based flow cytometry. ...
Ipsen Andreas - - 2010
It has long been recognized that estimates of isotopic abundance patterns may be instrumental in identifying the many unknown compounds encountered when conducting untargeted metabolic profiling using liquid chromatography/mass spectrometry. While numerous methods have been developed for assigning heuristic scores to rank the degree of fit of the observed abundance ...
Bonzon-Kulichenko Elena - - 2011
MS-based quantitative proteomics plays an increasingly important role in biological and medical research and the development of these techniques remains one of the most important challenges in mass spectrometry. Numerous stable isotope labeling approaches have been proposed. However, and particularly in the case of (18)O-labeling, a standard protocol of general ...
Gucek Marjan - - 2010
This review will summarize proteomic methods that are useful in studying the role of mitochondria in cardioprotection. The strengths and weaknesses of some of the different approaches are discussed. We focus on the cardiac mitochondrial proteome with emphasis on changes associated with cell death and protection, and we summarize how ...
Delgado Antonio - - 2010
We present a generalization of the next-to-minimal supersymmetric standard model, with an explicit μ term and a supersymmetric mass for the singlet superfield, as a route to alleviating the little hierarchy problem of the minimal supersymmetric standard model (MSSM). Though this model does not address the μ problem of the ...
Mischak Harald - - 2010
Clinical proteomics has yielded some early positive results-the identification of potential disease biomarkers-indicating the promise for this analytical approach to improve the current state of the art in clinical practice. However, the inability to verify some candidate molecules in subsequent studies has led to skepticism among many clinicians and regulatory ...
Szopinska Aleksandra - - 2010
The increasing popularity of proteomics has created a need for quantitative analysis methods. As a result, many different techniques are now available for performing gel-based or gel-free quantitative proteomic analysis of biological samples. These techniques provide an insight into global protein expression from identification to quantification, taking into account the ...
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 - - 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 ...
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