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Eisenacher Martin - - 2011
To deal with the data flood of current mass spectrometry methods, standard data formats are needed. The Proteomics Standards Initiative (PSI) of the Human Proteome Organisation (HUPO) develops open storage and transfer standards for and with the community. The Proteomics Informatics work group of the PSI has recently released an ...
Eriksson Jan - - 2011
The success of mass spectrometry based proteomics depends on efficient methods for data analysis. These methods require a detailed understanding of the information value of the data. Here, we describe how the information value can be elucidated by performing simulations using synthetic data.
Jackman Katherine K Division of Neurobiology, Department of Neurology and Neuroscience, Weill Cornell Medical College, New York, NY, - - 2011
Ischemic stroke is among the leading causes of mortality and long-term disability in the western world. Despite enormous research activities in the last decades, current therapeutic options for acute stroke patients are still very limited. Reliable and realistic in vivo animal models represent sine qua non for -successful translation from ...
Gao Fan F Health Care Sciences Department, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9091, USA. - - 2011
The objective of this pilot study is twofold: 1) to extract key factors/features in sit-to-stand and stand-to-sit (STS) performed by an above knee (AK) amputee; 2) to propose a convenient way to quantify symmetry. One male unilateral transfemoral amputee participated in the pilot study. The subject was instructed to rise ...
Keall Michael D - - 2011
Home injury is thought to constitute a major health burden in most developed countries. However, efforts to address this burden have been hampered by reluctance from outside agencies to interfere with the home environment of individuals, even if it benefits the occupant's safety. This paper outlines cost-benefit evaluation methods established ...
Fukuda H - - 2011
Quantifying the additional costs of hospital-acquired infections (COHAI) is essential for developing cost-effective infection control measures. The methodological approaches to estimate these costs include case reviews, matched comparisons and regression analyses. The choice of cost estimation methodologies can affect the accuracy of the resulting estimates, however, with regression analyses generally ...
Ohashi T - - 2010
Evaluating surveillance results is important in estimating the risk of bovine spongiform encephalopathy (BSE) cases in a particular country, or in countries from which products are imported. Although various methods have been proposed for quantitative evaluation of surveillance results, no methods focusing on surveillance from a qualitative perspective have yet ...
Meijs Matthijs F L - - 2010
Left ventricular (LV) mass has a continuous relation with cardiovascular risk, and regression of LV mass induced by pharmacological treatment is associated with improved prognosis. Therefore, early identification of patients with a large LV mass is desired. We developed a model to predict LV mass in individual hypertensives at high ...
Bunk David M - - 2010
In order to improve the repeatability, comparability, and accuracy of MS-based proteomic measurements, there has been considerable international effort to develop appropriate reference materials. Although the majority of reference materials are developed to support measurement quality of routine assays, the development of reference materials for a diverse and changing research ...
Cao Liping - - 2010
A serum-specific protein 'fingerprint' model was established which is capable of evaluating the effect of chemotherapy (gemcitabine) of pancreatic adenocarcinoma. We used SELDI-TOF-MS coupled with CM10 chips and bioinformatics tools to analyze a total of 45 mouse serum samples from three groups: the healthy control group, the pancreatic cancer model ...
Cortes Diego F - - 2010
Recent developments in bioanalytical instrumentation, MS detection, and computational data analysis approaches have provided researchers with capabilities for interrogating the complex cellular glycoproteome, to help gain a better insight into the cellular and physiological processes that are associated with a disease and to facilitate the efforts centered on identifying disease-specific ...
Matheis Katja A - - 2011
The European InnoMed-PredTox project was a collaborative effort between 15 pharmaceutical companies, 2 small and mid-sized enterprises, and 3 universities with the goal of delivering deeper insights into the molecular mechanisms of kidney and liver toxicity and to identify mechanism-linked diagnostic or prognostic safety biomarker candidates by combining conventional toxicological ...
Alba David M - - 2010
The hominoid right partial humerus IPS4334, from the middle Miocene (MN 8) of Castell de Barberà (Vallès-Penedès Basin, Catalonia, Spain), is described. It preserves the mid-distal portion of the shaft until the proximal margins of the radial and coronoid fossae, as well as the proximal portion of the olecranon fossa; ...
Melamud Eugene - - 2010
Metabolomic analysis by liquid chromatography-high-resolution mass spectrometry results in data sets with thousands of features arising from metabolites, fragments, isotopes, and adducts. Here we describe a software package, Metabolomic Analysis and Visualization ENgine (MAVEN), designed for efficient interactive analysis of LC-MS data, including in the presence of isotope labeling. The ...
Howard Andrew W - - 2010
The questions of how planets form and how common Earth-like planets are can be addressed by measuring the distribution of exoplanet masses and orbital periods. We report the occurrence rate of close-in planets (with orbital periods less than 50 days), based on precise Doppler measurements of 166 Sun-like stars. We ...
Cao Da-Long - - 2011
Multiplex urine-based assay emerged outperforms single biomarker (e.g., prostate-specific antigen, PSA) for predicting prostate cancer (CaP), whereas its combined mode has to be fully optimized. Our aim is to determine whether a strategy of combining gene-based, protein-based, metabolite-based with positive, negative makers in urine could optimize a multiplex model for ...
Suter Laura L Hoffmann-La Roche AG, Basel, Switzerland. - - 2011
In this publication, we report the outcome of the integrated EU Framework 6 PROJECT: Predictive Toxicology (PredTox), including methodological aspects and overall conclusions. Specific details including data analysis and interpretation are reported in separate articles in this issue. The project, partly funded by the EU, was carried out by a ...
Wallace Jack - - 2010
Because sentences for drug possession depend on the mass of the seized drug, testing laboratories must often determine the summed mass of numerous items submitted under a single case. One common practice for this purpose is to continue analyzing and weighing samples until a legal threshold is passed, at which ...
Matthews Luke J - - 2011
Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of ...
Wu R Q - - 2011
Cancer is now viewed as a systems biology disease, and oral squamous cell carcinoma (OSCC) can be viewed in a similar fashion. In this paper, we highlight some of the novel molecular events in OSCC, revealed through an integrative strategy of systems biology based on high-throughput omics analysis such as ...
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 ...
Lahesmaa-Korpinen Anna-Maria AM Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, - - 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 ...
Durbin Kenneth R KR Department of Chemistry, The Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, - - 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 ...
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.
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 ...
Schadt Eric E EE Pacific Biosciences, Menlo Park, California 94025, USA. - - 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. ...
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 ...
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