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Parallel Analysis (parallel + analysis)
Selected AbstractsA Framework of Massively Parallel Analysis of Regional Earthquake ActivitiesACTA GEOLOGICA SINICA (ENGLISH EDITION), Issue 4 2009Huai ZHANG Abstract: Recent rapid progress in cyberinfrastructure in geosciences is providing seismologists an enormous boost for addressing multi-physical phenomena of regional seismic activities. The inherent nature of their multi-scale properties, from temporal to spatial spaces, makes it inevitably to be solved using large-scale computations and distributed parallel data processing schemes. Under such circumstance, using the advanced numerical algorithms and unstructured mesh generation technologies become the obstacles for modern seismologists. The main objective of this paper is to present a framework, which includes a parallel finite element simulation and distributed data infrastructure, to address the novel algorithms, state-of-the-art modeling and their implementation in regional seismicgenic systems. We also discuss and implement this framework to analyze the strong earthquake evolution processes in the Sichuan-Yunnan region. This study is the key to long-term seismic risk by estimates, providing a platform for predictive large-scale numerical simulation modeling of regional earthquake activities. [source] In situ assays demonstrate that interferon-gamma suppresses infection-stimulated hepatic fibrin deposition by promoting fibrinolysisJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 7 2006I. K. MULLARKY Summary.,Background:,Inflammatory cytokines potently impact hemostatic pathways during infection, but the tissue-specific regulation of coagulation and fibrinolysis complicates studies of the underlying mechanisms. Methods and Results:,Here, we describe assays that quantitatively measuring prothrombinase (PTase), protein C-ase (PCase) and plasminogen activator (PA) activities in situ, thereby facilitating studies of tissue-specific hemostasis. Using these assays, we investigate the mechanisms regulating hepatic fibrin deposition during murine toxoplasmosis and the means by which interferon-gamma (IFN- ,) suppresses infection-stimulated fibrin deposition. We demonstrate that Toxoplasma infection upregulates hepatic PTase, PCase, and PA activity. Wild type and gene-targeted IFN- , -deficient mice exhibit similar levels of infection-stimulated PTase activity. By contrast, IFN- , -deficiency is associated with increased PCase activity and reduced PA activity during infection. Parallel analyses of hepatic gene expression reveal that IFN- , -deficiency is associated with increased expression of thrombomodulin (TM), a key component of the PCase, increased expression of thrombin-activatable fibrinolysis inhibitor (TAFI), a PC substrate, and reduced expression of urokinase PA (u-PA). Conclusions:,These findings suggest that IFN- , suppresses infection-stimulated hepatic fibrin deposition by suppressing TM-mediated activation of TAFI, thereby destabilizing fibrin deposits, and concomitantly increasing hepatic u-PA activity, thereby promoting fibrinolysis. We anticipate that further application of these in situ assays will improve our understanding of tissue-specific hemostasis, its regulation by cytokines, and its dysregulation during coagulopathy. [source] Stage-specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis,GENES, CHROMOSOMES AND CANCER, Issue 1 2007Jens K. Habermann To identify sequential alterations of the genome, transcriptome, and proteome during colorectal cancer progression, we have analyzed tissue samples from 36 patients, including the complete mucosa-adenoma-carcinoma sequence from 8 patients. Comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis on 9K cDNA arrays identified 58 genes differentially expressed between normal mucosa and adenoma, 116 genes between adenoma and carcinoma, and 158 genes between primary carcinoma and liver metastasis (P < 0.001). Parallel analysis of our samples by CGH and expression profiling revealed a direct correlation of chromosomal copy number changes with chromosome-specific average gene expression levels. Protein expression was analyzed by two-dimensional gel electrophoresis and subsequent mass spectrometry. Although there was no direct match of differentially expressed proteins and genes, the majority of them belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal imbalances as well as specific gene and protein expression changes correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies directly affect average resident gene expression levels, thereby contributing to a massive deregulation of the cellular transcriptome. The identification of novel genes and proteins might deliver molecular targets for diagnostic and therapeutic interventions. © Wiley-Liss, Inc. [source] Morphological and biochemical analyses of otoliths of the ice-fish Chionodraco hamatus confirm a common origin with red-blooded speciesJOURNAL OF ANATOMY, Issue 1 2009Chiara Maria Motta Abstract The morphology and composition of the three otoliths of the Antarctic ice-fish Chionodraco hamatus were studied by scanning electron microscopy and X-ray diffraction. The composition of the sagitta, lapillus and asteriscus protein matrices was also analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, western blots and confocal laser scanning microscopy to reveal the presence of and to localize the calcium-binding proteins calmodulin, calbindin and S-100. Morphological results indicated that the otoliths in this ice-fish were similar to those of Trematomus bernacchii, a red-blooded Antarctic species [B. Avallone et al. (2003) J. Submicrosc. Cytol. Pathol. 35, 69,76], but rather different from those of other teleosts. These two Antarctic species possessed a completely vateritic asteriscus, whereas their sagitta and lapillus were made mostly of aragonite. Parallel analysis of protein patterns in C. hamatus and T. bernacchii revealed that the sagitta significantly differed from the lapillus and asteriscus in both species. The sagitta did not contain the S-100 protein and showed calmodulin and calbindin located in discontinuous or incremental zones, respectively. These results demonstrate that the otoliths of C. hamatus and T. bernacchii share more resemblances than differences and support the idea of a common origin of these species. [source] Parallel analysis of mutant human glucose 6-phosphate dehydrogenase in yeast using PCR colonies,BIOTECHNOLOGY & BIOENGINEERING, Issue 5 2005Joshua Merritt Abstract We demonstrate a highly parallel strategy to analyze the impact of single nucleotide mutations on protein function. Using our method, it is possible to screen a population and quickly identify a subset of functionally interesting mutants. Our method utilizes a combination of yeast functional complementation, growth competition of mutant pools, and polymerase colonies. A defined mutant human glucose-6-phosphate-dehydrogenase library was constructed which contains all possible single nucleotide missense mutations in the eight-residue glucose-6-phosphate binding peptide of the enzyme. Mutant human enzymes were expressed in a zwf1 (gene encoding yeast homologue) deletion strain of Saccharomyces cerevisiae. Growth rates of the 54 mutant strains arising from this library were measured in parallel in conditions selective for active hG6PD. Several residues were identified which tolerated no mutations (Asp200, His201 and Lys205) and two (Ile199 and Leu203) tolerated several substitutions. Arg198, Tyr202, and Gly204 tolerated only 1-2 specific substitutions. Generalizing from the positions of tolerated and non-tolerated amino acid substitutions, hypotheses were generated about the functional role of specific residues, which could, potentially, be tested using higher resolution/lower throughput methods. © 2005 Wiley Periodicals, Inc. [source] Struggling to Save Cash: Seasonal Migration and Vulnerability in West Bengal, IndiaDEVELOPMENT AND CHANGE, Issue 4 2003Ben Rogaly This article concerns an important but overlooked means by which able-bodied poor people get hold of lump sums of cash in rural West Bengal: seasonal migration for agricultural wage work. Drawing on a regional study of four migration streams, our main focus here is on the struggle to secure this cash by landless households in just one of those streams, originating in Murshidabad District. Case studies are used to illustrate the importance for women in nuclear families of maintaining supportive networks of kin for periods when men are absent. A parallel analysis is made of the negotiations between male migrant workers and their employers, at labour markets, during the period of work, and afterwards. The article then briefly discusses some of the contrasting ways in which remittances are used by landless households and owners of very small plots of land, in the context of rapid ecological change, demographic pressure and growing inequality. [source] Development of microreactor array chip-based measurement system for massively parallel analysis of enzymatic activityELECTRONICS & COMMUNICATIONS IN JAPAN, Issue 4 2009Yosuke Hosoi Abstract Microarray chip technology such as DNA chips, peptide chips, and protein chips is one of the promising approaches for achieving high-throughput screening (HTS) of biomolecule function since it has great advantages in feasibility of automated information processing due to one-to-one indexing between array position and molecular function as well as massively parallel sample analysis as a benefit of downsizing and large-scale integration. Mostly, however, the function that can be evaluated by such microarray chips is limited to affinity of target molecules. In this paper, we propose a new HTS system and enzymatic activity based on microreactor array chip technology. A prototype of the automated and massively parallel measurement system for fluorometric assay of enzymatic reactions was developed by the combination of microreactor array chips and a highly sensitive fluorescence microscope. Design strategy of microreactor array chips and an optical measurement platform for the high-throughput enzyme assay are discussed. © 2009 Wiley Periodicals, Inc. Electron Comm Jpn, 92(4): 35,41, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecj.10056 [source] Biomarker study of a municipal effluent dispersion plume in two species of freshwater musselsENVIRONMENTAL TOXICOLOGY, Issue 3 2002F. Gagné Abstract The toxicological effects of a primary-treated municipal effluent plume were investigated in two species of freshwater mussels, Elliptio complanata and Dreissena polymorpha, exposed for 62 days at sites upstream and downstream of an effluent outfall in the St. Lawrence River (Quebec, Canada). Levels of metallothioneins (MT), cytochrome P4501A1 activity, DNA damage, total lipids, relative levels of vitellins, and phagocytic activity (in E. complanata hemocytes) were determined after the exposure period. A parallel analysis measured heavy metals and coprostanol in mussel tissues. The results show that significant levels of coprostanol and some metals (specifically, Cu, Hg, Sb, Se, and Zn) had accumulated in mussels caged 5 km downstream of the effluent plume. Mixed-function oxidase activity, MT in gills, total lipids, DNA damage (in D. polymorpha only), and total hemolymph bacteria (in E. complanata only) had increased in these mussels, while levels of total cadmium (Cd), MT in digestive glands or whole soft tissues, phagocytic activity, and DNA damage in the digestive gland (in E. complanata only) were diminished. The exposure of mussels to surface waters contaminated by a municipal effluent led to many stress responses, depending on both the tissues and the species being examined. © 2002 Wiley Periodicals, Inc. Environ Toxicol 17: 149,159, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/tox.10046 [source] The five-factor personality inventory: cross-cultural generalizability across 13 countriesEUROPEAN JOURNAL OF PERSONALITY, Issue 5 2003A. A. Jolijn Hendriks In the present study, we investigated the structural invariance of the Five-Factor Personality Inventory (FFPI) across a variety of cultures. Self-report data sets from ten European and three non-European countries were available, representing the Germanic (Belgium, England, Germany, the Netherlands, USA), Romance (Italy, Spain), and Slavic branches (Croatia, Czech Republic, Slovakia) of the Indo-European languages, as well as the Semito-Hamitic (Israel) and Altaic (Hungary, Japan) language families. Each data set was subjected to principal component analysis, followed by varimax rotation and orthogonal Procrustes rotation to optimal agreement with (i) the Dutch normative structure and (ii) an American large-sample structure. Three criteria (scree test, internal consistency reliabilities of the varimax-rotated components, and parallel analysis) were used to establish the number of factors to be retained for rotation. Clear five-factor structures were found in all samples except in the smallest one (USA, N,=,97). Internal consistency reliabilities of the five components were generally good and high congruence was found between each sample structure and both reference structures. More than 80% of the items were equally stable within each country. Based on the results, an international FFPI reference structure is proposed. This reference structure can facilitate standardized communications about Big Five scores across research programmes. Copyright © 2003 John Wiley & Sons, Ltd. [source] Congestion control for multimedia applications in the wireless internetINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 7 2004Veselin Rakocevic Abstract This paper provides a parallel review of two important issues for the next-generation multimedia networking. Firstly, the emerging multimedia applications require a fresh approach to congestion control in the Internet. Currently, congestion control is performed by TCP; it is optimised for data traffic flows, which are inherently elastic. Audio and video traffic do not find the sudden rate fluctuations imposed by the TCP multiplicative-decrease control algorithm optimal. The second important issue is the mobility support for multimedia applications. Wireless networks are characterized by a substantial packet loss due to the imperfection of the radio medium. This increased packet loss disturbs the foundation of TCP's loss-based congestion control. This paper contributes to the ongoing discussion about the Internet congestion control by providing a parallel analysis of these two issues. The paper describes the main challenges, design guidelines, and existing proposals for the Internet congestion control, optimised for the multimedia traffic in the wireless network environment. Copyright © 2004 John Wiley & Sons, Ltd. [source] Advances in gene chip technique in Barrett's metaplasia and adenocarcinomaJOURNAL OF DIGESTIVE DISEASES, Issue 2 2008Xing Wei WANG Gene chip methods are applied to the study of gene expression. The differentially expressed genes in different specimens may be detected with parallel analysis by gene chip, which has greatly improved the traditional experiments in that only a single or several gene expressions need to be observed for each test, thereby speeding up the identification of differentially expressed genes and the construction of differential expression profiles. Many studies have applied this technology for Barrett's metaplasia and adenocarcinoma, and identified a number of candidate genes useful as biomarkers in cancer staging, prediction of recurrence, prognosis and treatment selection. This review described the gene expression profile and molecular changes related to Barrett's metaplasia and adenocarcinoma of the esophagus, with emphasis on its prognostic value and possibilities for targeted therapy in a clinical setting. [source] Microfluidic chips for mass spectrometry-based proteomicsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2009Jeonghoon Lee Abstract Microfluidic devices coupled to mass spectrometers have emerged as excellent tools for solving the complex analytical challenges associated with the field of proteomics. Current proteome identification procedures are accomplished through a series of steps that require many hours of labor-intensive work. Microfluidics can play an important role in proteomic sample preparation steps prior to mass spectral identification such as sample cleanup, digestion, and separations due to its ability to handle small sample quantities with the potential for high-throughput parallel analysis. To utilize microfluidic devices for proteomic analysis, an efficient interface between the microchip and the mass spectrometer is required. This tutorial provides an overview of the technologies and applications of microfluidic chips coupled to mass spectrometry for proteome analysis. Various approaches for combining microfluidic devices with electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are summarized and applications of chip-based separations and digestion technologies to proteomic analysis are presented. Copyright © 2009 John Wiley & Sons, Ltd. [source] A parallel analysis of individual and ecological data on residential radon and lung cancer in south-west EnglandJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2001Sarah Darby Parallel individual and ecological analyses of data on residential radon have been performed using information on cases of lung cancer and population controls from a recent study in south-west England. For the individual analysis the overall results indicated that the relative risk of lung cancer at 100 Bq m,3 compared with at 0 Bq m,3 was 1.12 (95% confidence interval (0.99, 1.27)) after adjusting for age, sex, smoking, county of residence and social class. In the ecological analysis substantial bias in the estimated effect of radon was present for one of the two counties involved unless an additional variable, urban,rural status, was included in the model, although this variable was not an important confounder in the individual level analysis. Most of the methods that have been recommended for overcoming the limitations of ecological studies would not in practice have proved useful in identifying this variable as an appreciable source of bias. [source] Modeling and Managing the Percentage of Satisfied Customers in Hidden and Revealed Waiting Line SystemsPRODUCTION AND OPERATIONS MANAGEMENT, Issue 1 2006Chester Chambers We perform an analysis of various queueing systems with an emphasis on estimating a single performance metric. This metric is defined to be the percentage of customers whose actual waiting time was less than their individual waiting time threshold. We label this metric the Percentage of Satisfied Customers (PSC.) This threshold is a reflection of the customers' expectation of a reasonable waiting time in the system given its current state. Cases in which no system state information is available to the customer are referred to as "hidden queues." For such systems, the waiting time threshold is independent of the length of the waiting line, and it is randomly drawn from a distribution of threshold values for the customer population. The literature generally assumes that such thresholds are exponentially distributed. For these cases, we derive closed form expressions for our performance metric for a variety of possible service time distributions. We also relax this assumption for cases where service times are exponential and derive closed form results for a large class of threshold distributions. We analyze such queues for both single and multi-server systems. We refer to cases in which customers may observe the length of the line as "revealed" queues." We perform a parallel analysis for both single and multi-server revealed queues. The chief distinction is that for these cases, customers may develop threshold values that are dependent upon the number of customers in the system upon their arrival. The new perspective this paper brings to the modeling of the performance of waiting line systems allows us to rethink and suggest ways to enhance the effectiveness of various managerial options for improving the service quality and customer satisfaction of waiting line systems. We conclude with many useful insights on ways to improve customer satisfaction in waiting line situations that follow directly from our analysis. [source] Liquid chromatography/electrospray ionization mass spectrometry for the characterization of twenty-three flavonoids in the extract of Dalbergia odoriferaRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 11 2005Rongxia Liu A method incorporating high-performance liquid chromatography (HPLC) with electrospray ionization and tandem mass spectrometry, with parallel analysis by HPLC with UV detection using a diode-array detector, was developed for the qualitative characterization of flavonoids in D. odorifera. Twenty-three flavonoids, including six isoflavones, six neoflavones, four isoflavanones, three flavanones, two chalcones, one isoflavanonol and one pterocarpan, were unambiguously identified by comparing their retention times, UV and MS spectra with those of authentic compounds. Furthermore, the collision-induced dissociations of the [MH], ions were studied to clarify the MS behavior of the different types of flavonoids. In negative ion ESI-MS all the flavonoids yielded prominent [MH], ions in the first order mass spectra. Fragments involving losses of CH, H2O, CO, C2H2O, and CO2 were observed in the MS/MS spectra. Each of the seven types of flavonoid showed characteristic MS/MS fragmentation patterns. The isoflavanones, flavanones and chalcones were observed to undergo retro-Diels-Alder fragmentations. The spectra of almost all the neoflavonoids unexpectedly exhibited only [MHCH3],. radical anions as base peaks without any further fragmentation. Substitution positions also remarkably influenced the fragmentation behavior, which could assist in distinction among the flavonoid isomers. The fragmentation rules deduced here could aid in the characterization of other flavonoids of these types. Copyright © 2005 John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||