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Lakoumentas John - - 2012
Prognosis of B-Chronic Lymphocytic Leukemia (B-CLL) remains a challenging problem in medical research and practice. While the parameters obtained by flow cytometry analysis form the basis of the diagnosis of the disease, the question whether these parameters offer additional prognostic information still remains open. In this work, we attempt to ...
Peluso Ilaria - - 2012
We propose a new data analysis approach for reactive oxygen species detection using Dihydrorhodamine123 in blood monocytes and neutrophils. This approach, based on data transformation using lymphocytes as internal standard, allows to appreciate free radical production by monocytes also without Phorbol 12-myristate 13-acetate (PMA) activation. In addition, this method is ...
Ramamoorthy Anand - - 2011
Instructions are an inextricable, yet poorly understood aspect of modern human life. In this paper we propose that instruction implementation and following can be understood as fast Hebbian learning in prefrontal cortex, which trains slower pathways (e.g., cortical-basal ganglia pathways). We present a computational model of instruction following that is ...
Perl Yonatan Sanz YS Department of Physics, FCEyN, University of Buenos Aires Ciudad Universitaria, Buenos Aires, - - 2011
We reconstruct the physiological parameters that control an avian vocal organ during birdsong production using recorded song. The procedure involves fitting the time dependent parameters of an avian vocal organ model. Computationally, the model is implemented as a dynamical system ruling the behavior of the oscillating labia that modulate the ...
Befekadu Getachew K GK Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, NW, Washington, DC 20057, USA. - - 2011
A novel framework of a probabilistic mixture regression model (PMRM) is presented for alignment of liquid chromatography-mass spectrometry (LC-MS) data with respect to retention time (RT) points. The expectation maximization algorithm is used to estimate the joint parameters of spline-based mixture regression models and prior transformation density models. The latter ...
Sibbald Matthew - - 2011
Clinicians are believed to use two predominant reasoning strategies: system 1 based pattern recognition, and system 2 based analytical reasoning. Balancing these cognitive reasoning strategies is widely believed to reduce diagnostic error. However, clinicians approach different problems with different reasoning strategies. This study explores whether clinicians have insight into their ...
Gjorgjieva Julijana - - 2011
Spontaneous activity is found in many regions of the developing nervous system; such activity is thought to be instructive for guiding developmental processes. In particular, the developing retina generates correlated patterns of activity known as retinal waves. We review the main theoretical models that have been developed to study the ...
Jho Eun Hea - - 2011
The combined toxic effects of Cd and Pb in the presence of different concentrations of Ca(2+) were predicted using the biotic ligand model (BLM), with the parameters derived from the Cd-only and Pb-only toxicity data. The BLM-based toxic unit (TU) approach and the proposed BLM-based f(mix) approach were used for ...
Gregori Dario - - 2011
OBJECTIVE: This article aims to describe the various approaches in multivariable modelling of healthcare costs data and to synthesize the respective criticisms as proposed in the literature. METHODS: /st> We present regression methods suitable for the analysis of healthcare costs and then apply them to an experimental setting in cardiovascular ...
Cai Zuansi - - 2011
Mass discharge is one metric rapidly gaining acceptance for assessing the performance of in situ groundwater remediation systems. Multilevel sampling transects provide the data necessary to make such estimates, often using the Thiessen Polygon method. This method, however, does not provide a direct estimate of uncertainty. We introduce a geostatistical ...
Feng Xue X China Military Institute of Chinese Materia Medica, Military Hospital of China, Beijing, People's Republic of China. - - 2011
Various Rhizoma coptidis are commonly used in clinical applications due to their strong antibacterial effect. The antibacterial effect of various R. coptidis were evaluated by microcalorimetry together with statistical analysis. The dried roots of Coptis chinensis Franch, Coptis deltoidea C.Y. Cheng et Hsiao, and Coptis teeta Wall (Ranunculaceae) were identified ...
Heller J - - 2011
Meticillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial and community-acquired pathogen with zoonotic potential. The relationship between MRSA in humans and companion animals is poorly understood. This study presents a quantitative exposure assessment, based on expert opinion and published data, in the form of a second order stochastic simulation model ...
McLachlan Helen L - - 2011
BACKGROUND AND AIMS: In Victoria, maternity services are under significant strain due to increased numbers of women giving birth and critical workforce shortages. Hospitals have experienced challenges in adequately staffing maternity units, particularly on postnatal wards. In 2008, a tertiary maternity hospital in Melbourne introduced a model where undergraduate midwifery ...
Hamacher Michael - - 2011
Several projects were initiated by the Human Proteome Organisation (HUPO) focusing on the proteome analysis of distinct human organs. The initiative dedicated to the brain, its development and correlated diseases is the HUPO Brain Proteome Project (HUPO BPP). An objective data submission, storage, and reprocessing strategy have been established with ...
Jefferys Stuart R - - 2011
This chapter describes using the Protein Inference Engine (PIE) to integrate various types of data--especially top down and bottom up mass spectrometer (MS) data--to describe a protein's posttranslational modifications (PTMs). PTMs include cleavage events such as the n-terminal loss of methionine and residue modifications like phosphorylation. Modifications are key elements ...
Jung Klaus - - 2011
High-throughput experiments in proteomics, such as 2-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS), yield usually high-dimensional data sets of expression values for hundreds or thousands of proteins which are, however, observed on only a relatively small number of biological samples. Statistical methods for the planning and analysis of experiments ...
Bauer Chris - - 2011
Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods ...
Turewicz Michael - - 2011
This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years ...
Barsnes Harald - - 2011
With the continuously growing amount of proteomics data being produced, it has become increasingly important to make these data publicly available so that they can be audited, reanalyzed, and reused. More and more journals are also starting to request the deposition of MS data in publicly available repositories for submitted ...
Bertsch Andreas - - 2011
Proteomics experiments based on state-of-the-art mass spectrometry produce vast amounts of data, which cannot be analyzed manually. Hence, software is needed which is able to analyze the data in an automated fashion. The need for robust and reusable software tools triggered the development of libraries implementing different algorithms for the ...
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 ...
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