Search Results
Results 201 - 250 of 1001
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Aminian Minoo M Departments of Mathematical Science and Computer Science, Rensselaer Polytechnic Institute, Troy, New York, USA. - - 2010
We present a novel conformal Bayesian network (CBN) to classify strains of Mycobacterium tuberculosis Complex (MTBC) into six major genetic lineages based on two high-throuput biomarkers: mycobacterial interspersed repetitive units (MIRU) and spacer oligonucleotide typing (spoligotyping). MTBC is the causative agent of tuberculosis (TB), which remains one of the leading ...
ZieliƄski Andrzej - - 2010
Structured sanitary preparation to mass gatherings is based on the set of instructions and legal requirements which are different for different jurisdictions. In many countries special checklists are used for itemized scrutiny of the sanitary preparation to the event. Those checklists are present in two forms. One is relatively short ...
Coca Daniel - - 2010
High-throughput, MS-based proteomics studies are generating very large volumes of biologically relevant data. Given the central role of proteomics in emerging fields such as system/synthetic biology and biomarker discovery, the amount of proteomic data is expected to grow at unprecedented rates over the next decades. At the moment, there is ...
Tang Kai-Lin - - 2010
BACKGROUND: Recent advances in proteomics technologies such as SELDI-TOF mass spectrometry has shown promise in the detection of early stage cancers. However, dimensionality reduction and classification are considerable challenges in statistical machine learning. We therefore propose a novel approach for dimensionality reduction and tested it using published high-resolution SELDI-TOF data ...
Stephan Christian - - 2010
In Proteomics, fast enhancements with regard to technology are responsible for the creation of huge data sets. Consequently, in 2006 the European Commission funded a Coordination Action named ProDaC (Proteomics Data Collection) within the 6th EU Framework Programme to foster a community-wide data collection and data sharing. The aims of ...
Caffrey Rebecca E - - 2010
Surface Enhanced Laser/Desorption Ionization-time of flight (SELDI-TOF) mass spectrometry is a technique uniquely suited to the study of the urine proteome due to its salt tolerance, high-throughput, and small sample requirements. However, due to the extreme sensitivity of the technique, sample collection and storage conditions, as well as instrument protocols ...
Piruzian Eleonora - - 2010
Psoriasis is complex inflammatory skin pathology of autoimmune origin. Several cell types are perturbed in this pathology, and underlying signaling events are complex and still poorly understood. In order to gain insight into molecular machinery underlying the disease, we conducted a comprehensive meta-analysis of proteomics and transcriptomics of psoriatic lesions ...
Pluskal Tomás - - 2010
BACKGROUND: Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, ...
Sellers Kimberly F - - 2010
Numerous gel-based and nongel-based technologies are used to detect protein changes potentially associated with disease. The raw data, however, are abundant with technical and structural complexities, making statistical analysis a difficult task. Low-level analysis issues (including normalization, background correction, gel and/or spectral alignment, feature detection, and image registration) are substantial ...
Mischnick Petra - - 2010
Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch ...
Deutsch Eric W - - 2010
PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw ...
Cuomo Alessandro - - 2010
Stable isotope labeling with amino acids in cell culture (SILAC) has become increasingly popular as a quantitative proteomics (qProteomics) method. In combination with high-resolution mass spectrometry (MS) and new efficient algorithms for the analysis of quantitative MS data, SILAC has proven to be a potent tool for the in-depth characterization ...
Ling Xuefeng B XB Department of Pediatrics, Stanford University, Stanford, California, USA. - - 2010
Urine-based proteomic profiling is a novel approach that may result in the discovery of noninvasive biomarkers for diagnosing patients with different diseases, with the aim to ultimately improve clinical outcomes. Given new and emerging analytical technologies and data mining algorithms, the urine peptidome has become a rich resource to uncover ...
Emanuele Vincent A VA - - 2010
Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI) is a proteomics tool for biomarker discovery and other high throughput applications. Previous studies have identified various areas for improvement in preprocessing algorithms used for protein peak detection. Bottom-up approaches to preprocessing that emphasize modeling SELDI data acquisition are promising avenues of ...
Eriksson Jan - - 2010
The complexity of proteomes makes good experimental design essential for their successful investigation. Here, we describe how proteomics experiments can be modeled and how computer simulations of these models can be used to improve experimental designs.
Reinert Knut - - 2010
The automatic analysis of mass spectrometry data is becoming more and more important since increasingly larger datasets are readily available that cannot be evaluated manually. This has triggered the development of several open-source software libraries for the automatic analysis of such data. Among those is OpenMS together with TOPP (The ...
Ruiz-Romero C - - 2010
OBJECTIVE: Osteoarthritis (OA) is the most common rheumatic pathology. It is related to aging and is characterized primarily by cartilage degradation. Despite its high prevalence, the diagnostic methods currently available are limited and lack sensitivity. The focus of this review is the application of proteomic technologies in the search of ...
Xu Cheng-Jian - - 2010
Principal component analysis (PCA) is much used in exploring time-course biological data sets, but does not distinguish variation between time and subjects. This study proposes a new integrated approach by combining analysis of variance (ANOVA) and three component modeling methods. The former was used to separate the between- and within-subject ...
De Bock Muriel - - 2010
Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy ...
Abazov V M - - 2009
We present a direct measurement of the width of the W boson using the shape of the transverse mass distribution of W --> enu candidate events. Data from approximately 1 fb(-1) of integrated luminosity recorded at square root of s = 1.96 TeV by the D0 detector at the Fermilab ...
Tourlomousis Panagiotis - - 2010
Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a ...
Cohen Andrew L - - 2009
Several previous studies have examined the ability to judge the relative mass of objects in idealized collisions. With a newly developed technique of psychological Markov chain Monte Carlo sampling (A. N. Sanborn & T. L. Griffiths, 2008), this work explores participants' perceptions of different collision mass ratios. The results reveal ...
Yu Kebing K Department of Chemistry, Brown University, Providence, RI 02903, - - 2009
Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing ...
Ji Li - - 2010
Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results. The submission process is facilitated through ...
Miller Arnold I - - 2009
Environmental perturbations during mass extinctions were likely manifested differently in epicontinental seas than in open-ocean-facing habitats of comparable depth. Here, we present a dissection of origination and extinction in epicontinental seas versus open-ocean-facing coastal regions in the Permian through Cretaceous periods, an interval through which both settings are well represented ...
Gouw Joost W - - 2010
In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on ...
Vizcaíno Juan Antonio - - 2010
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 ...
Schwede Ronnie L - - 2010
The contaminant mass discharge crossing a control plane is an important metric in the assessment of natural attenuation at contaminated sites. For risk-assessment purposes, the mass discharge must be estimated together with a level of uncertainty. We present a conditional Monte Carlo approach that allows estimating the statistical distribution of ...
Pridatchenko M L - - 2009
Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) ...
Montecchi-Palazzi Luisa - - 2009
The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and ...
Ow Saw Yen - - 2009
The increasing popularity of iTRAQ for quantitative proteomics applications makes it necessary to evaluate its relevance, accuracy, and precision for biological interpretation. Here, we have assessed (a) the accuracy and precision of iTRAQ quantification in a controlled experimental setup, using low- and high-complexity protein mixtures; and (b) the potential pitfalls ...
De Jager Philip L PL Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA. - - 2009
Prediction of susceptibility to multiple sclerosis (MS) might have important clinical applications, either as part of a diagnostic algorithm or as a means to identify high-risk individuals for prospective studies. We investigated the usefulness of an aggregate measure of risk of MS that is based on genetic susceptibility loci. We ...
Albaum Stefan P SP Computational Genomics, Center for Biotechnology (CeBiTec), Biodata Mining & Applied Neuroinformatics Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany. - - 2009
The goal of present -omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common ...
Aaltonen T - - 2009
We present an analysis of the mass of the X(3872) reconstructed via its decay to J/psi pi(+)pi(-) using 2.4 fb(-1) of integrated luminosity from pp collisions at square root(s)=1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. The possible existence of two nearby mass states is investigated. ...
Redestig Henning - - 2009
Most mass spectrometry based metabolomics studies are semiquantitative and depend on efficient normalization techniques to suppress systematic error. A common approach is to include isotope-labeled internal standards (ISs) and then express the estimated metabolite abundances relative to the IS. Because of problems such as insufficient chromatographic resolution, however, the analytes ...
Riffle Michael M Department of Biochemistry, University of Washington, Seattle, WA 98195, - - 2009
The field of proteomics, particularly the application of MS analysis to protein samples, is well established and growing rapidly. Proteomic studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and ...
Apweiler Rolf - - 2009
Recent developments in proteomics technology offer new opportunities for clinical applications in hospital or specialized laboratories including the identification of novel biomarkers, monitoring of disease, detecting adverse effects of drugs, and environmental hazards. Advanced spectrometry technologies and the development of new protein array formats have brought these analyses to a ...
Kathiravan Mathur Nadarajan - - 2010
This study presents the external mass transfer effects on the reduction of hexavalent chromium (Cr(VI)) using calcium alginate immobilized Bacillus sp. in a re-circulated packed bed batch reactor (RPBR). The effect of flow rate on the reduction Cr(VI) was studied. Theoretically calculated rate constants for various flow rates were analyzed ...
Mylonas Roman - - 2009
The diversity of experimental workflows involving LC-MS/MS and the extended range of mass spectrometers tend to produce extremely variable spectra. Variability reduces the accuracy of compound identification produced by commonly available software for a spectral library search. We introduce here a new algorithm that successfully matches MS/MS spectra generated by ...
Zam? Alberto - - 2010
Lymphoid and haematopoietic neoplasms comprise a broad spectrum of different tumours, classified by the World Health Organization (WHO) on the basis of a combination of morphology, immunophenotypic, genetic and clinical features. Up to date for many of these neoplasms no single feature is regarded as a diagnostic gold standard. The ...
Rusconi Filippo - - 2009
Since the middle of the 90s, mass spectrometry has evolved into an almost indispensable tool in structural studies on an ever-growing variety of (bio-)polymers, of which proteins, sugars and nucleic acids are the most prominent. Since the first public release of massXpert, the advances of mass spectrometry have motivated continuous ...
McConnachie Alan W - - 2009
In hierarchical cosmological models, galaxies grow in mass through the continual accretion of smaller ones. The tidal disruption of these systems is expected to result in loosely bound stars surrounding the galaxy, at distances that reach 10-100 times the radius of the central disk. The number, luminosity and morphology of ...
Vizcaíno Juan Antonio - - 2009
The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through ...
Burton Richard F - - 2010
It is almost a matter of dogma that human body mass in adults tends to vary roughly in proportion to the square of height (stature), as Quetelet stated in 1835. As he realised, perfect isometry or geometric similarity requires that body mass varies with height cubed, so there seems to ...
Khan Zia - - 2009
Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than ...
Giannopoulos G - - 2010
Terrorist attacks in New York have shocked the world community showing clearly the vulnerability of air transport in such events. However, the terrorist attacks in Madrid and London showed that land mass transport infrastructure is equally vulnerable in case of similar attacks. The fact that there has not been substantial ...
Lê Cao Kim-Anh - - 2009
With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical ...
Gogas H - - 2009
Biomarkers are tumour- or host-related factors that correlate with tumour biological behaviour and patient prognosis. High-throughput analytical techniques--DNA and RNA microarrays--have identified numerous possible biomarkers, but their relevance to melanoma progression, clinical outcome and the selection of optimal treatment strategies still needs to be established. The review discusses a possible ...
Ahmed Y - - 2009
Linesmen working on high voltage equipment occasionally report unpleasant discharges from equipment. The sensation is known as microshocks, which result from capacitive coupling of the linesmen to high voltage sources and subsequent discharging when in very close proximity to grounded objects. Often, this is just an annoyance, but the levels ...
Eisenacher Martin - - 2009
In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation ...
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