WorldWideScience

Sample records for based enrichment method

  1. Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method

    Science.gov (United States)

    2015-03-01

    Technical Report ARWSB-TR-15002 Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method Michael F...4. TITLE AND SUBTITLE Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method 5a. CONTRACT NUMBER 5b...the RVE and how microdamage can be incorporated into the model . For many applications the material used in the multiscale model is some type of fiber

  2. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules contai...

  3. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio;

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules...... containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD...... enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved...

  4. Enriched goal-oriented error estimation for fracture problems solved by continuum-based shell extended finite element method

    Institute of Scientific and Technical Information of China (English)

    Zhi-jia LIN; Zhuo ZHUANG BU

    2014-01-01

    An enriched goal-oriented error estimation method with extended degrees of freedom is developed to estimate the error in the continuum-based shell extended finite element method. It leads to high quality local error bounds in three-dimensional fracture mechanics simulation which involves enrichments to solve the singularity in crack tip. This enriched goal-oriented error estimation gives a chance to evaluate this continuum-based shell extended finite element method simulation. With comparisons of reliability to the stress intensity factor calculation in stretching and bending, the accuracy of the continuum-based shell extended finite element method simulation is evaluated, and the reason of error is discussed.

  5. A combined enrichment/polymerase chain reaction based method for the routine screening of streptococcus agalactiae in pregnant women

    OpenAIRE

    MUNARI, F. M.; de-Paris,F.; Salton, G.D.; Lora,P.S; Giovanella, P.; Machado, A.B.M.P.; Laybauer, L.S.; Oliveira, K.R.P.; C. Ferri; Silveira, J.L.S.; Laurino,C.C.F.C; Xavier, R.M.; Barth,A.L.; S Echeverrigaray; Laurino, J.P.

    2012-01-01

    Group B Streptococcus (GBS) is the most common cause of life-threatening infection in neonates. Guidelines from CDC recommend universal screening of pregnant women for rectovaginal GBS colonization. The objective of this study was to compare the performance of a combined enrichment/PCR based method targeting the atr gene in relation to culture using enrichment with selective broth medium (standard method) to identify the presence of GBS in pregnant women. Rectovaginal GBS samples from women a...

  6. Validation of Flow Cytometry and Magnetic Bead-Based Methods to Enrich CNS Single Cell Suspensions for Quiescent Microglia.

    Science.gov (United States)

    Volden, T A; Reyelts, C D; Hoke, T A; Arikkath, J; Bonasera, S J

    2015-12-01

    Microglia are resident mononuclear phagocytes within the CNS parenchyma that intimately interact with neurons and astrocytes to remodel synapses and extracellular matrix. We briefly review studies elucidating the molecular pathways that underlie microglial surveillance, activation, chemotaxis, and phagocytosis; we additionally place these studies in a clinical context. We describe and validate an inexpensive and simple approach to obtain enriched single cell suspensions of quiescent parenchymal and perivascular microglia from the mouse cerebellum and hypothalamus. Following preparation of regional CNS single cell suspensions, we remove myelin debris, and then perform two serial enrichment steps for cells expressing surface CD11b. Myelin depletion and CD11b enrichment are both accomplished using antigen-specific magnetic beads in an automated cell separation system. Flow cytometry of the resultant suspensions shows a significant enrichment for CD11b(+)/CD45(+) cells (perivascular microglia) and CD11b(+)/CD45(-) cells (parenchymal microglia) compared to starting suspensions. Of note, cells from these enriched suspensions minimally express Aif1 (aka Iba1), suggesting that the enrichment process does not evoke significant microglial activation. However, these cells readily respond to a functional challenge (LPS) with significant changes in the expression of molecules specifically associated with microglia. We conclude that methods employing a combination of magnetic-bead based sorting and flow cytometry produce suspensions highly enriched for microglia that are appropriate for a variety of molecular and cellular assays.

  7. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

    Science.gov (United States)

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Adelson, David L.

    2017-01-01

    Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer’s disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology. PMID:28199395

  8. Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In proteome research, rapid and effective separation strategies are essential for successful protein identification due to the broad dynamic range of proteins in biological samples. Some important proteins are often expressed in ultra low abundance, thus making the pre-concentration procedure before mass spectrometric analysis prerequisite. The main purpose of enrichment is to isolate target molecules from complex mixtures to reduce sample complexity and facilitate the subsequent analyzing steps. The introduction of nanoparticles into this field has accelerated the development of enrichment methods. In this review, we mainly focus on recent developments of using different nanomaterials for pre-concentration of low-abundance peptides/ proteins, including those containing post-translational modifications, such as phosphorylation and glycosylation, prior to mass spectrometric analysis.

  9. A combined enrichment/polymerase chain reaction based method for the routine screening of Streptococcus agalactiae in pregnant women

    Directory of Open Access Journals (Sweden)

    F.M. Munari

    2012-03-01

    Full Text Available Group B Streptococcus (GBS is the most common cause of life-threatening infection in neonates. Guidelines from CDC recommend universal screening of pregnant women for rectovaginal GBS colonization. The objective of this study was to compare the performance of a combined enrichment/PCR based method targeting the atr gene in relation to culture using enrichment with selective broth medium (standard method to identify the presence of GBS in pregnant women. Rectovaginal GBS samples from women at ≥36 weeks of pregnancy were obtained with a swab and analyzed by the two methods. A total of 89 samples were evaluated. The prevalence of positive results for GBS detection was considerable higher when assessed by the combined enrichment/PCR method than with the standard method (35.9% versus 22.5%, respectively. The results demonstrated that the use of selective enrichment broth followed by PCR targeting the atr gene is a highly sensitive, specific and accurate test for GBS screening in pregnant women, allowing the detection of the bacteria even in lightly colonized patients. This PCR methodology may provide a useful diagnostic tool for GBS detection and contributes for a more accurate and effective intrapartum antibiotic and lower newborn mortality and morbidity.

  10. Network-based functional enrichment

    Directory of Open Access Journals (Sweden)

    Poirel Christopher L

    2011-11-01

    Full Text Available Abstract Background Many methods have been developed to infer and reason about molecular interaction networks. These approaches often yield networks with hundreds or thousands of nodes and up to an order of magnitude more edges. It is often desirable to summarize the biological information in such networks. A very common approach is to use gene function enrichment analysis for this task. A major drawback of this method is that it ignores information about the edges in the network being analyzed, i.e., it treats the network simply as a set of genes. In this paper, we introduce a novel method for functional enrichment that explicitly takes network interactions into account. Results Our approach naturally generalizes Fisher’s exact test, a gene set-based technique. Given a function of interest, we compute the subgraph of the network induced by genes annotated to this function. We use the sequence of sizes of the connected components of this sub-network to estimate its connectivity. We estimate the statistical significance of the connectivity empirically by a permutation test. We present three applications of our method: i determine which functions are enriched in a given network, ii given a network and an interesting sub-network of genes within that network, determine which functions are enriched in the sub-network, and iii given two networks, determine the functions for which the connectivity improves when we merge the second network into the first. Through these applications, we show that our approach is a natural alternative to network clustering algorithms. Conclusions We presented a novel approach to functional enrichment that takes into account the pairwise relationships among genes annotated by a particular function. Each of the three applications discovers highly relevant functions. We used our methods to study biological data from three different organisms. Our results demonstrate the wide applicability of our methods. Our algorithms are

  11. SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.

    Science.gov (United States)

    Yi, Ming; Stephens, Robert M

    2008-09-26

    Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data.

  12. Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.

    Directory of Open Access Journals (Sweden)

    Anna Kiialainen

    Full Text Available Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for massively parallel sequencing and single nucleotide polymorphism (SNP discovery, namely Nimblegen sequence capture arrays and the SureSelect liquid-based hybrid capture system. We prepared sequencing libraries from three HapMap samples using both methods, sequenced the libraries on the Illumina Genome Analyzer, mapped the sequencing reads back to the genome, and called variants in the sequences. 74-75% of the sequence reads originated from the targeted region in the SureSelect libraries and 41-67% in the Nimblegen libraries. We could sequence up to 99.9% and 99.5% of the regions targeted by capture probes from the SureSelect libraries and from the Nimblegen libraries, respectively. The Nimblegen probes covered 0.6 Mb more of the original 3.1 Mb target region than the SureSelect probes. In each sample, we called more SNPs and detected more novel SNPs from the libraries that were prepared using the Nimblegen method. Thus the Nimblegen method gave better results when judged by the number of SNPs called, but this came at the cost of more over-sampling.

  13. Development of a field sampling method based on magnetic nanoparticles for the enrichment of pesticides in aqueous samples.

    Science.gov (United States)

    Zhang, Lingyi; Sheng, Xiaoling; Zhang, Runsheng; Xiong, Zhichao; Wu, Zhongping; Yan, Songmao; Zhang, Yurong; Zhang, Weibing

    2014-12-07

    A field sampling method based on magnetic core-shell silica nanoparticles was developed for field sampling and the enrichment of low concentrations of pesticides in aqueous samples. The magnetic nanoparticles could be easily extracted from water samples by a custom-made magnetic nanoparticle collector. The recovery of 15 mg of magnetic particles from a 500 mL water sample was 90.8%. Mixtures of seven pesticides spiked into pure water and pond water were used as marker samples to evaluate the field sampling method. The average recoveries at three levels of spiking were in the range 60.0-104.7% with relative standard deviations method has good linearity with a correlation coefficient >0.9990 in the concentration range 0.5-15 μg L(-1). The results of the analysis of a sample of poisoned pond water indicate that this method is fast, convenient and efficient for the field sampling and enrichment of pesticides in aqueous samples.

  14. Assessment of phosphopeptide enrichment/precipitation method for LC-MS/MS based phosphoproteomic analysis of plant tissue

    DEFF Research Database (Denmark)

    Ye, Juanying; Rudashevskaya, Elena; Hansen, Thomas Aarup

      Introduction Mass spectrometry (MS) is a powerful technology for study of PTMs, including protein phosphorylation. Due to the low abundance of many phosphoproteins and the relatively poor ionization efficiency of phosphopeptides, specific enrichment of phosphopeptides prior to MS analysis is ne...... (MSA) method was used for phosphopeptide fragmentation. The resulting fragment ion spectra were processed with Proteome Discoverer software (Thermo Electron, Bremen, Germany). Results We first investigated the global phosphorylation profile of plant plasma membrane proteins by enriching...

  15. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

    DEFF Research Database (Denmark)

    Avila Arcos, Maria del Carmen; Cappellini, Enrico; Romero-Navarro, J Alberto

    2011-01-01

    The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples...

  16. Comparison of PCR-Based Diagnosis with Centrifuged-Based Enrichment Method for Detection of Borrelia persica in Animal Blood Samples

    Directory of Open Access Journals (Sweden)

    SR Naddaf

    2011-06-01

    Background: The mainstay of diagnosis of relapsing fever (RF is demonstration of the spirochetes in Giemsa-stained thick blood smears, but during non fever periods the bacteria are very scanty and rarely detected in blood smears by mi­cros­copy. This study is aimed to evaluate the sensitivity of different methods developed for detection of low-grade spi­ro­chetemia. Methods: Animal blood samples with low degrees of spirochetemia were tested with two PCRs and a nested PCR tar­get­ing flaB, GlpQ, and rrs genes. Also, a centrifuged-based enrichment method and Giemsa staining were per­formed on blood samples with various degrees of spirochetemia. Results: The flaB-PCR and nested rrs-PCR turned positive with various degrees of spirochetemia including the blood samples that turned negative with dark-field microscopy. The GlpQ-PCR was positive as far as at least one spi­ro­chete was seen in 5-10 microscopic fields. The sensitivity of GlpQ-PCR increased when DNA from Buffy Coat Layer (BCL was used as template. The centrifuged-based enrichment method turned positive with as low concentra­tion as 50 bacteria/ml blood, while Giemsa thick staining detected bacteria with concentrations ≥ 25000 bacteria/ml.  Conclusion: Centrifuged-based enrichment method appeared as much as 500-fold more sensitive than thick smears, which makes it even superior to some PCR assays. Due to simplicity and minimal laboratory requirements, this method can be considered a valuable tool for diagnosis of RF in rural health centers.  

  17. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

    Science.gov (United States)

    Ávila-Arcos, María C.; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno-Mayar, J. Víctor; Rasmussen, Morten; Fordyce, Sarah L.; Montiel, Rafael; Vielle-Calzada, Jean-Philippe; Willerslev, Eske; Gilbert, M. Thomas P.

    2011-01-01

    The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA. PMID:22355593

  18. GOMA: functional enrichment analysis tool based on GO modules

    Institute of Scientific and Technical Information of China (English)

    Qiang Huang; Ling-Yun Wu; Yong Wang; Xiang-Sun Zhang

    2013-01-01

    Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology.A variety of enrichment analysis tools have been developed in recent years,but most output a long list of significantly enriched terms that are often redundant,making it difficult to extract the most meaningful functions.In this paper,we present GOMA,a novel enrichment analysis method based on the new concept of enriched functional Gene Ontology (GO) modules.With this method,we systematically revealed functional GO modules,i.e.,groups of functionally similar GO terms,via an optimization model and then ranked them by enrichment scores.Our new method simplifies enrichment analysis results by reducing redundancy,thereby preventing inconsistent enrichment results among functionally similar terms and providing more biologically meaningful results.

  19. Effect of cooking method on the fatty acid content of reduced-fat and PUFA-enriched pork patties formulated with a konjac-based oil bulking system.

    Science.gov (United States)

    Salcedo-Sandoval, Lorena; Cofrades, Susana; Ruiz-Capillas, Claudia; Jiménez-Colmenero, Francisco

    2014-12-01

    The effect of cooking methods (electric grilling and pan-frying in olive oil) on the composition of reduced-fat and reduced-fat/PUFA enriched pork patties was studied. Fat reduction was performed by replacing pork backfat (38% and 100%) with konjac gel and PUFA-enrichment by replacing pork backfat (49%) with a konjac-based oil bulking system stabilizing a healthier oil combination (olive, linseed and fish oils). Cooking losses (13%-27%) were affected (pfat/improved sample containing the oil bulking system ranged between 1.4 and 1.6g/100g (0.47-0.51 from n-3 PUFAs), with EPA+DHA concentrations of around 75mg/100g. Konjac materials were successfully used to produce pork patties with a better lipid composition.

  20. Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations.

    Science.gov (United States)

    Kalyuzhnaya, Marina G; Zabinsky, Rebecca; Bowerman, Sarah; Baker, David R; Lidstrom, Mary E; Chistoserdova, Ludmila

    2006-06-01

    A fluorescence in situ hybridization-flow cytometry (FISH/FC)-based method was optimized using artificial mixtures of pure cultures of methanotrophic bacteria. Traditional oligonucleotide probes targeting 16S rRNAs of type I (MG84/705 probe) and type II (MA450 probe) methanotrophs were labeled with fluorescein or Alexa fluor and used for FISH, followed by fluorescence-activated FC analysis and cell sorting (FACS). The method resulted in efficient separation of target cells (type I or type II methanotrophs) from the artificial mixtures. The method was then applied for detection and enrichment of type I and type II methanotroph populations from a natural sample, Lake Washington sediment. Cells were extracted from the sediment, fixed, and subjected to FISH/FC/FACS. The resulting subpopulations were analyzed by reverse transcriptase PCR surveys of 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde-activating enzyme) genes. The functional gene analysis indicated specific separation of the type I and type II methanotroph populations. 16S rRNA gene analysis revealed that type I methanotrophs comprised 59% of the subpopulation separated using the type I-specific probe and that type II methanotrophs comprised 47.5% of the subpopulation separated using the type II-specific probe. Our data indicate that the FISH/FC/FACS protocol described can provide significant enrichment of microbial populations of interest from complex natural communities and that these can be used for genetic tests. We further tested the possibility of direct whole-genome amplification (WGA) from limited numbers of sorted cells, using artificial mixtures of microbes whose genome sequences are known. We demonstrated that efficient WGA can be achieved using 10(4) or more cells separated by 16S rRNA-specific FISH/FC/FACS, while fewer cells resulted in less specific WGA.

  1. Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

    KAUST Repository

    Abusamra, Heba

    2016-07-20

    The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

  2. Recommendations based on semantically enriched museum collections

    NARCIS (Netherlands)

    Wang, Y.; Stash, N.; Aroyo, L.; Gorgels, P.; Rutledge, L.; Schreiber, G.

    2008-01-01

    This article presents the CHIP demonstrator1 for providing personalized access to digital museum collections. It consists of three main components: Art Recommender, Tour Wizard, and Mobile Tour Guide. Based on the semantically enriched Rijksmuseum Amsterdam2 collection, we show how Semantic Web tech

  3. 77 FR 13367 - General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...

    Science.gov (United States)

    2012-03-06

    ... COMMISSION General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...- Hitachi Global Laser Enrichment, LLC (GLE) Uranium Enrichment Facility. On June 26, 2009, GLE submitted a... uranium enrichment facility (the ``proposed action''). The GLE proposes to locate the facility on...

  4. 77 FR 14838 - General Electric-Hitachi Global Laser Enrichment LLC, Commercial Laser-Based Uranium Enrichment...

    Science.gov (United States)

    2012-03-13

    ... COMMISSION General Electric-Hitachi Global Laser Enrichment LLC, Commercial Laser-Based Uranium Enrichment... applicant) to authorize construction of a laser-based uranium enrichment facility and possession and use of...-based uranium enrichment facility. Revisions to the application were submitted on March 23, 2010;...

  5. An improved cell recovery method for iron oxidizing bacterial (IOB) enrichments

    DEFF Research Database (Denmark)

    Yu, Ran; Graf, Joerg; Smets, Barth F.

    2008-01-01

    Two cell recovery methods for IOB enrichments were evaluated for DNA extraction and further PCR-based 16S rRNA gene clone library creation. One was a published method consisting of heating plus oxalic acid treatment and the other one was a new method based on enzymatic agarose digestion (using β-...

  6. A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology.

    Directory of Open Access Journals (Sweden)

    Liron Levkovitz

    Full Text Available BACKGROUND: Pancreatic adenocarcinoma (PAC is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs over-represented in the promoter regions of genes differentially expressed in PAC. Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection. METHODOLOGY: DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. We demonstrate DEMON's accuracy on simulated and real data sets. Applying DEMON to PAC-related data sets identifies the RUNX family as highly enriched in PAC-related genes. Using a novel experimental paradigm to distinguish between normal and PAC cells, we find that RUNX3 mRNA (but not RUNX1 or RUNX2 mRNAs exhibits time-dependent increases in normal but not in PAC cells. These increases are accompanied by changes in mRNA levels of putative RUNX gene targets. CONCLUSIONS: The integrated application of DEMON and a novel differentiation system led to the identification of a single family member, RUNX3, which together with four of its putative targets showed a robust response to a differentiation stimulus in healthy cells, whereas this regulatory mechanism was absent in PAC cells, emphasizing RUNX3 as a promising target for further studies.

  7. Glycoprotein enrichment method using a selective magnetic nano-probe platform (MNP) functionalized with lectins.

    Science.gov (United States)

    Cova, Marta; Oliveira-Silva, Rui; Ferreira, José Alexandre; Ferreira, Rita; Amado, Francisco; Daniel-da-Silva, Ana Luísa; Vitorino, Rui

    2015-01-01

    Protein post-translational modifications (PTMs) have increasingly become a research field of incredible importance to fully understand the regulation of biological processes in health and disease. Among PTMs, glycosylation is one of the most studied for which contributed the development and improvement of enrichment techniques. Nowadays, glycoprotein enrichment methods are based on lectin affinity, covalent interactions, and hydrophilic interaction liquid chromatography (HILIC). Nonetheless, the nanotechnology era has fetched new methods to enrich glycoproteins from complex samples as human biological fluids. For instance, magnetic nanoparticles (MNPs) are being used as an interesting enrichment approach allowing a better characterization of glycoproteins and glycopeptides.In this chapter, we describe an enrichment method based on MNPs functionalized with lectins (Concavalin A, wheat germ agglutinin, and Maackia amurensis lectin) to enrich specific sets of glycoproteins from biological fluids. Moreover, it is proposed a bioinformatic strategy to deal with data retrieved from mass spectrometry analysis of enriched samples aiming the identification of relevant biological processes modulated by a given stimuli and, ultimately, of new biomarkers for disease screening/management.

  8. Method for production of an isotopically enriched compound

    Science.gov (United States)

    Watrous, Matthew G.

    2012-12-11

    A method is presented for producing and isolating an isotopically enriched compound of a desired isotope from a parent radionuclide. The method includes forming, or placing, a precipitate containing a parent radionuclide of the desired daughter isotope in a first reaction zone and allowing sufficient time for the parent to decay into the desired gaseous daughter radioisotope. The method further contemplates collecting the desired daughter isotope as a solid in a second reaction zone through the application of temperatures below the freezing point of the desired isotope to a second reaction zone that is connected to the first reaction zone. Specifically, a method is presented for producing isotopically enriched compounds of xenon, including the radioactive isotope Xe-131m and the stable isotope Xe-131.

  9. On the role of enrichment and statical admissibility of recovered fields in a-posteriori error estimation for enriched finite element methods

    CERN Document Server

    González-Estrada, Octavio A; Bordas, Stéphane P A; Duflot, Marc; Kerfriden, Pierre; Giner, Eugenio

    2011-01-01

    Purpose: This paper aims at assessing the effect of (1) the statical admissibility of the recovered solution; (2) the ability of the recovered solution to represent the singular solution; on the accuracy, local and global effectivity of recovery-based error estimators for enriched finite element methods (e.g. the extended finite element method, XFEM). Design/methodology/approach: We study the performance of two recovery techniques. The first is a recently developed superconvergent patch recovery procedure with equilibration and enrichment (SPR-CX). The second is known as the extended moving least squares recovery (XMLS), which enriches the recovered solutions but does not enforce equilibrium constraints. Both are extended recovery techniques as the polynomial basis used in the recovery process is enriched with singular terms for a better description of the singular nature of the solution. Findings: Numerical results comparing the convergence and the effectivity index of both techniques with those obtained wit...

  10. Solution-based targeted genomic enrichment for precious DNA samples

    Directory of Open Access Journals (Sweden)

    Shearer Aiden

    2012-05-01

    Full Text Available Abstract Background Solution-based targeted genomic enrichment (TGE protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1 modifying or eliminating time consuming steps; 2 increasing yield to reduce input DNA and excessive PCR cycling; and 3 enhancing reproducible. Results We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. Conclusions This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.

  11. Improved methods for enrichment of organic ultra trace components for analysis by gas chromatography

    OpenAIRE

    Kloskowski, Adam

    2003-01-01

    This thesis describes some new methods for analysis oforganic trace components from air and water by gaschromatography. The work is particularly focused on thedevelopment of new technologies for analyte enrichment, usingsorbent-based concepts. Short lengths of open tubular columnswere examined for their potential use as denuders.Polydimethylsiloxane-based stationary phases as well as anadsorbent-based column were evaluated in an equilibrium mode oftrapping. For the analytes selected, detectio...

  12. Improved Methods for the Enrichment and Analysis of Glycated Peptides

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qibin; Schepmoes, Athena A; Brock, Jonathan W; Wu, Si; Moore, Ronald J; Purvine, Samuel O; Baynes, John; Smith, Richard D; Metz, Thomas O

    2008-12-15

    Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.

  13. Hybrid Enrichment Assay Methods for a UF6 Cylinder Verification Station: FY10 Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Leon E.; Jordan, David V.; Orton, Christopher R.; Misner, Alex C.; Mace, Emily K.

    2010-08-01

    Pacific Northwest National Laboratory (PNNL) is developing the concept of an automated UF6 cylinder verification station that would be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until the arrival of International Atomic Energy Agency (IAEA) inspectors. At the center of this unattended system is a hybrid enrichment assay technique that combines the traditional enrichment-meter method (based on the 186 keV peak from 235U) with non-traditional neutron-induced high-energy gamma-ray signatures (spawned primarily by 234U alpha emissions and 19F(alpha, neutron) reactions). Previous work by PNNL provided proof-of-principle for the non-traditional signatures to support accurate, full-volume interrogation of the cylinder enrichment, thereby reducing the systematic uncertainties in enrichment assay due to UF6 heterogeneity and providing greater sensitivity to material substitution scenarios. The work described here builds on that preliminary evaluation of the non-traditional signatures, but focuses on a prototype field system utilizing NaI(Tl) and LaBr3(Ce) spectrometers, and enrichment analysis algorithms that integrate the traditional and non-traditional signatures. Results for the assay of Type-30B cylinders ranging from 0.2 to 4.95 wt% 235U, at an AREVA fuel fabrication plant in Richland, WA, are described for the following enrichment analysis methods: 1) traditional enrichment meter signature (186 keV peak) as calculated using a square-wave convolute (SWC) algorithm; 2) non-traditional high-energy gamma-ray signature that provides neutron detection without neutron detectors and 3) hybrid algorithm that merges the traditional and non-traditional signatures. Uncertainties for each method, relative to the declared enrichment for each cylinder, are calculated and compared to the uncertainties from an attended

  14. Simple and efficient methods for enrichment and isolation of endonuclease modified cells.

    Directory of Open Access Journals (Sweden)

    Branden S Moriarity

    Full Text Available The advent of Transcription Activator-Like Effector Nucleases (TALENs, and similar technologies such as CRISPR, provide a straightforward and cost effective option for targeted gene knockout (KO. Yet, there is still a need for methods that allow for enrichment and isolation of modified cells for genetic studies and therapeutics based on gene modified human cells. We have developed and validated two methods for simple enrichment and isolation of single or multiplex gene KO's in transformed, immortalized, and human progenitor cells. These methods rely on selection of a phenotypic change such as resistance to a particular drug or ability to grow in a selective environment. The first method, termed co-transposition, utilizes integration of a piggyBac transposon vector encoding a drug resistance gene. The second method, termed co-targeting, utilizes TALENs to KO any gene that when lost induces a selectable phenotype. Using these methods we also show removal of entire genes and demonstrate that TALENs function in human CD34+ progenitor cells. Further, co-transposition can be used to generate conditional KO cell lines utilizing an inducible cDNA rescue transposon vector. These methods allow for robust enrichment and isolation of KO cells in a rapid and efficient manner.

  15. Adaptive enriched Galerkin methods for miscible displacement problems with entropy residual stabilization

    Science.gov (United States)

    Lee, Sanghyun; Wheeler, Mary F.

    2017-02-01

    We present a novel approach to the simulation of miscible displacement by employing adaptive enriched Galerkin finite element methods (EG) coupled with entropy residual stabilization for transport. In particular, numerical simulations of viscous fingering instabilities in heterogeneous porous media and Hele-Shaw cells are illustrated. EG is formulated by enriching the conforming continuous Galerkin finite element method (CG) with piecewise constant functions. The method provides locally and globally conservative fluxes, which are crucial for coupled flow and transport problems. Moreover, EG has fewer degrees of freedom in comparison with discontinuous Galerkin (DG) and an efficient flow solver has been derived which allows for higher order schemes. Dynamic adaptive mesh refinement is applied in order to reduce computational costs for large-scale three dimensional applications. In addition, entropy residual based stabilization for high order EG transport systems prevents spurious oscillations. Numerical tests are presented to show the capabilities of EG applied to flow and transport.

  16. Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

    Science.gov (United States)

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2015-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. "analogue bias", "artificial enrichment" and "false negative". In addition, we introduce our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylases (HDACs) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The leave-one-out cross-validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased as measured by property matching, ROC curves and AUCs.

  17. Enriching semantic knowledge bases for opinion mining in big data applications.

    Science.gov (United States)

    Weichselbraun, A; Gindl, S; Scharl, A

    2014-10-01

    This paper presents a novel method for contextualizing and enriching large semantic knowledge bases for opinion mining with a focus on Web intelligence platforms and other high-throughput big data applications. The method is not only applicable to traditional sentiment lexicons, but also to more comprehensive, multi-dimensional affective resources such as SenticNet. It comprises the following steps: (i) identify ambiguous sentiment terms, (ii) provide context information extracted from a domain-specific training corpus, and (iii) ground this contextual information to structured background knowledge sources such as ConceptNet and WordNet. A quantitative evaluation shows a significant improvement when using an enriched version of SenticNet for polarity classification. Crowdsourced gold standard data in conjunction with a qualitative evaluation sheds light on the strengths and weaknesses of the concept grounding, and on the quality of the enrichment process.

  18. Foraging-Based Enrichment Promotes More Varied Behaviour in Captive Australian Fur Seals (Arctocephalus pusillus doriferus.

    Directory of Open Access Journals (Sweden)

    David P Hocking

    Full Text Available During wild foraging, Australian fur seals (Arctocephalus pusillus doriferus encounter many different types of prey in a wide range of scenarios, yet in captive environments they are typically provided with a narrower range of opportunities to display their full repertoire of behaviours. This study aimed to quantitatively explore the effect of foraging-based enrichment on the behaviour and activity patterns displayed by two captive Australian fur seals at Melbourne Zoo, Australia. Food was presented as a scatter in open water, in a free-floating ball device, or in a static box device, with each treatment separated by control trials with no enrichment. Both subjects spent more time interacting with the ball and static box devices than the scatter feed. The total time spent pattern swimming was reduced in the enrichment treatments compared to the controls, while the time spent performing random swimming behaviours increased. There was also a significant increase in the total number of bouts of behaviour performed in all three enrichment treatments compared to controls. Each enrichment method also promoted a different suit of foraging behaviours. Hence, rather than choosing one method, the most effective way to increase the diversity of foraging behaviours, while also increasing variation in general activity patterns, is to provide seals with a wide range of foraging scenarios where food is encountered in different ways.

  19. A Novel Magnetic Separation Oxygen-enriched Method and the Influence of Temperature and Magnetic Field on Enrichment

    Institute of Scientific and Technical Information of China (English)

    Li WANG; Jun CAI; Ping WU; Lige TONG; Shufeng SUN

    2007-01-01

    A novel oxygen-enriched method is presented. Using two opposite magnetic poles of two magnets with certain distance forms a magnetic space having a field intensity gradient near its borders. When air injected into the magnetic space outflows from the magnetic space via its borders, oxygen molecules in air will experience the interception effect of the gradient magnetic field, but nitrogen molecules will outflow without hindrance. Thereby the continuous oxygen enrichment is realized. The results show that the maximum increment of oxygen concentration reaches 0.49% at 298 K when the maximum product of magnetic flux density and field intensity gradient is 563T2/m. The enrichment level is significantly influenced by the gas temperature and the magnetic field. The maximum increment of oxygen concentration drops to 0.16% when the gas temperature rises to 343 K, and drops to 0.09% when the maximum product of magnetic flux density and gradient is reduced to 101 T2/m from 563T2/m.

  20. Growth of 18O isotopically enriched ZnO nanorods by two novel VPT methods

    Science.gov (United States)

    Gray, Ciarán; Trefflich, Lukas; Röder, Robert; Ronning, Carsten; Henry, Martin O.; McGlynn, Enda

    2017-02-01

    We have developed two novel vapour phase transport methods to grow ZnO nanorod arrays isotopically enriched with 18O. Firstly, a three-step process used to grow natural and Zn-enriched ZnO nanorods has been further modified, by replacing the atmospheric O2 with enriched 18O2, in order to grow 18O-enriched ZnO nanorods using this vapour-solid method on chemical bath deposited buffer layers. In addition, 18O-enriched ZnO nanorods were successfully grown using 18O isotopically enriched ZnO source powders in a vapour-liquid-solid growth method. Scanning electron microscopy studies confirmed the success of both growth methods in terms of nanorod morphology, although in the case of the vapour-liquid-solid samples, the nanorods' c-axes were not vertically aligned due to the use of a non-epitaxial substrate. Raman and PL studies indicated clearly that O-enrichment was successful in both cases, although the results indicate that the enrichment is at a lower level in our samples compared to previous reports with the same nominal enrichment levels. The results of our studies also allow us to comment on both levels of enrichment achieved and on novel effects of the high temperature growth environment on the nanorod growth, as well as suggesting possible mechanisms for such effects. Very narrow photoluminescence line widths, far narrower than those reported previously in the literature for isotopically enriched bulk ZnO, are seen in both the vapour-solid and vapour-liquid-solid nanorod samples demonstrating their excellent optical quality and their potential for use in detailed optical studies of defects and impurities using low temperature photoluminescence.

  1. A new enrichment method for isolation of Bacillus thuringiensis from diverse sample types.

    Science.gov (United States)

    Patel, Ketan D; Bhanshali, Forum C; Chaudhary, Avani V; Ingle, Sanjay S

    2013-05-01

    New or more efficient methodologies having different principles are needed, as one method could not be suitable for isolation of organisms from samples of diverse types and from various environments. In present investigation, growth kinetics study revealed a higher germination rate, a higher growth rate, and maximum sporulation of Bacillus thuringiensis (Bt) compared to other Bacillus species. Considering these facts, a simple and efficient enrichment method was devised which allowed propagation of spores and vegetative cells of Bt and thereby increased Bt cell population proportionately. The new enrichment method yielded Bt from 44 out of 58 samples. Contrarily, Bt was isolated only from 16 and 18 samples by sodium acetate selection and dry heat pretreatment methods, respectively. Moreover, the percentages of Bt colonies isolated by the enrichment method were higher comparatively. Vegetative whole cell protein profile analysis indicated isolation of diverse population of Bt from various samples. Bt strains isolated by the enrichment method represented novel serovars and possibly new cry2 gene.

  2. 不同精制法松树木醋液中生物活性组分的富集%Enrichment of Bioactive Components in Pine Wood Vinegar Based on Different Refining Methods

    Institute of Scientific and Technical Information of China (English)

    许英梅; 高连连; 朴永哲; 刘巨涛; 张树彪

    2015-01-01

    Enrichment of main bioactive components in three different xiaoxing 'an mountains ’ pine vinegar made by standing only, distillation and membrane filtration was analyzed by GC-MS. Research results showed that among the three kinds of refining methods, the latter two could remove colored harmful macromolecules so that the color became lighter. Distillation pine vinegar was more conducive to enriching organic acid and membrane filtration pine vinegar pre-ferred to enrich phenol, guaiacol and even the total biological active component including acid and phenols.%采用GC-MS分析法研究了3种精制法所得木醋液对小兴安岭松树木醋液中主要生物活性组分羧酸和酚类的富集,包括物理静置法所得原松木醋液、蒸馏法所得松木醋液和膜过滤法所得松木醋液。结果表明,3种精制方法中,蒸馏法和膜过滤法都可以进一步去除原木醋液中的有色有害大分子,使颜色变浅。蒸馏法松木醋液有利于木醋液中乙酸等羧酸的富集;膜过滤法松木醋液有利于对苯酚和愈创木酚等酚类的富集,且对羧酸和酚类总的生物活性成分的富集较有优势。

  3. Does capillary racetrack-based enrichment reflect the diversity of uncultivated magnetotactic cocci in environmental samples?

    Science.gov (United States)

    Lin, Wei; Tian, Lanxiang; Li, Jinhua; Pan, Yongxin

    2008-02-01

    The racetrack-based PCR approach is widely used in phylogenetic analysis of magnetotactic bacteria (MTB), which are isolated from environmental samples using the capillary racetrack method. To evaluate whether the capillary racetrack-based enrichment can truly reflect the diversity of MTB in the targeted environmental sample, phylogenetic diversity studies of MTB enriched from the Miyun lake near Beijing were carried out, using both the capillary racetrack-based PCR and a modified metagenome-based PCR approach. Magnetotactic cocci were identified in the studied sample using both approaches. Comparative studies showed that three clusters of magnetotactic cocci were revealed by the modified metagenome-based PCR approach, while only one of them (e.g. MYG-22 sequence) was detected by the racetrack-based PCR approach from the studied sample. This suggests that the result of capillary racetrack-based enrichment might have been biased by the magnetotaxis of magnetotactic bacteria. It appears that the metagenome-based PCR approach better reflects the original diversity of MTB in the environmental sample.

  4. Isolation method (direct plating or enrichment) does not affect antimicrobial susceptibility of Campylobacter from chicken carcasses

    Science.gov (United States)

    To determine if Campylobacter isolation method influenced antimicrobial susceptibility results, the minimum inhibitory concentrations (MIC) of nine antimicrobials were compared for 291 pairs of Campylobacter isolates recovered from chicken carcass rinse samples using direct plating and an enrichment...

  5. Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method.

    Science.gov (United States)

    Dalmasso, Marion; Bolocan, Andrei Sorin; Hernandez, Marta; Kapetanakou, Anastasia E; Kuchta, Tomáš; Manios, Stavros G; Melero, Beatriz; Minarovičová, Jana; Muhterem, Meryem; Nicolau, Anca Ioana; Rovira, Jordi; Skandamis, Panagiotis N; Stessl, Beatrix; Wagner, Martin; Jordan, Kieran; Rodríguez-Lázaro, David

    2014-03-01

    Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is

  6. An Enrichment Method for Bio-samples Based on Circular Injection on a Microfluidic Chip%一种基于微流控芯片的生物样品循环给样富集方法

    Institute of Scientific and Technical Information of China (English)

    杜敏; 叶雄英; 冯金扬; 马增帅; 周兆英

    2012-01-01

    A microfluidic chip based circular injection method for bio-samples was presented. The microfluidic chip with an annular peristaltic micropump and electromagnetic microvalves was fabricated using PDMS (polydimethylsiloxane) soft lithography process. The chip was then integrated with an immune probe chip immobilized with rabbit IgG, and realized the circular injection of Goat-anti-rabbit IgG (FITC labeled) solution and sample enrichment. Higher fluorescence intensity was obtained using circular injection than that using static adsorption, under different sample concentrations and 3 min binding time. By increasing the pumping speed from 130 μL/min to 300 u.L/min, the immune binding speed with 50 mg/L sample concentration was accelerated evidently, which meant the detection limit at a given time could be lower, but for 200 mg/L sample concentration, the effect was weaker. Compared to the continuous injection mode with about 1. 8 mL of sample consumption, only 7 μL sample was needed to realize the coincident results with the circular injection mode.%提出了一种基于微流控芯片的生物样品循环给样方法,利用聚二甲基硅氧烷(PDMS)软光刻工艺制作了包括环形蠕动微泵和电磁微阀的微流控芯片,通过与免疫探针芯片的集成,实现了对探针芯片的循环给样及在其上的免疫样品富集.采用不同浓度的羊抗兔IgG(FITC标记)样品与兔IgG探针免疫结合3 min,得到循环流动比静态吸附的荧光光强值更高,可使检出限降低.对于50 mg/L羊抗兔IgG样品,流速从130 μL/min增至300 μL/min时,免疫结合的速度明显加快,可使同一时刻的检出限降低;而样品浓度提高到200 mg/L时,增大流速对免疫反应的促进效果弱于低浓度时的变化.在样品浓度50 mg/L和循环流速300 μL/min的条件下,循环给样方式仅需7μL样品溶液就得到了与持续进样约1.8 mL样品溶液基本一致的结果.

  7. Enrichment of the hydrogen-producing microbial community from marine intertidal sludge by different pretreatment methods

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hongyan [Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Shinan District, Qingdao 266071, Shandong (China); College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China); Graduate School, Chinese Academy of Sciences, Beijing 100039 (China); Wang, Guangce [Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Shinan District, Qingdao 266071, Shandong (China); College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China); Zhu, Daling; Pan, Guanghua [College of Marine Science and Engineering, University of Science and Technology, Tianjin 300457 (China)

    2009-12-15

    To determine the effects of pretreatment on hydrogen production and the hydrogen-producing microbial community, we treated the sludge from the intertidal zone of a bathing beach in Tianjin with four different pretreatment methods, including acid treatment, heat-shock, base treatment as well as freezing and thawing. The results showed that acid pretreatment significantly promoted the hydrogen production by sludge and provided the highest efficiency of hydrogen production among the four methods. The efficiency of the hydrogen production of the acid-pretreated sludge was 0.86 {+-} 0.07 mol H{sub 2}/mol glucose (mean {+-} S.E.), whereas that of the sludge treated with heat-shock, freezing and thawing, base method and control was 0.41 {+-} 0.03 mol H{sub 2}/mol glucose, 0.17 {+-} 0.01 mol H{sub 2}/mol glucose, 0.11 {+-} 0.01 mol H{sub 2}/mol glucose and 0.20 {+-} 0.04 mol H{sub 2}/mol glucose, respectively. The result of denaturing gradient gel electrophoresis (DGGE) showed that pretreatment methods altered the composition of the microbial community that accounts for hydrogen production. Acid and heat pretreatments were favorable to enrich the dominant hydrogen-producing bacterium, i.e. Clostridium sp., Enterococcus sp. and Bacillus sp. However, besides hydrogen-producing bacteria, much non-hydrogen-producing Lactobacillus sp. was also found in the sludge pretreated with base, freezing and thawing methods. Therefore, based on our results, we concluded that, among the four pretreatment methods using acid, heat-shock, base or freezing and thawing, acid pretreatment was the most effective method for promoting hydrogen production of microbial community. (author)

  8. WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.

    Directory of Open Access Journals (Sweden)

    Apratim Mitra

    Full Text Available BACKGROUND: Chromatin immunoprecipitation followed by next-generation sequencing is a genome-wide analysis technique that can be used to detect various epigenetic phenomena such as, transcription factor binding sites and histone modifications. Histone modification profiles can be either punctate or diffuse which makes it difficult to distinguish regions of enrichment from background noise. With the discovery of histone marks having a wide variety of enrichment patterns, there is an urgent need for analysis methods that are robust to various data characteristics and capable of detecting a broad range of enrichment patterns. RESULTS: To address these challenges we propose WaveSeq, a novel data-driven method of detecting regions of significant enrichment in ChIP-Seq data. Our approach utilizes the wavelet transform, is free of distributional assumptions and is robust to diverse data characteristics such as low signal-to-noise ratios and broad enrichment patterns. Using publicly available datasets we showed that WaveSeq compares favorably with other published methods, exhibiting high sensitivity and precision for both punctate and diffuse enrichment regions even in the absence of a control data set. The application of our algorithm to a complex histone modification data set helped make novel functional discoveries which further underlined its utility in such an experimental setup. CONCLUSIONS: WaveSeq is a highly sensitive method capable of accurate identification of enriched regions in a broad range of data sets. WaveSeq can detect both narrow and broad peaks with a high degree of accuracy even in low signal-to-noise ratio data sets. WaveSeq is also suited for application in complex experimental scenarios, helping make biologically relevant functional discoveries.

  9. Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited.

    Directory of Open Access Journals (Sweden)

    Karolina A Aberg

    Full Text Available Methyl-binding domain (MBD enrichment followed by deep sequencing (MBD-seq, is a robust and cost efficient approach for methylome-wide association studies (MWAS. MBD-seq has been demonstrated to be capable of identifying differentially methylated regions, detecting previously reported robust associations and producing findings that replicate with other technologies such as targeted pyrosequencing of bisulfite converted DNA. There are several kits commercially available that can be used for MBD enrichment. Our previous work has involved MethylMiner (Life Technologies, Foster City, CA, USA that we chose after careful investigation of its properties. However, in a recent evaluation of five commercially available MBD-enrichment kits the performance of the MethylMiner was deemed poor. Given our positive experience with MethylMiner, we were surprised by this report. In an attempt to reproduce these findings we here have performed a direct comparison of MethylMiner with MethylCap (Diagenode Inc, Denville, NJ, USA, the best performing kit in that study. We find that both MethylMiner and MethylCap are two well performing MBD-enrichment kits. However, MethylMiner shows somewhat better enrichment efficiency and lower levels of background "noise". In addition, for the purpose of MWAS where we want to investigate the majority of CpGs, we find MethylMiner to be superior as it allows tailoring the enrichment to the regions where most CpGs are located. Using targeted bisulfite sequencing we confirmed that sites where methylation was detected by either MethylMiner or by MethylCap indeed were methylated.

  10. A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science.

    Science.gov (United States)

    Godin, Elizabeth A; Wormington, Stephanie V; Perez, Tony; Barger, Michael M; Snyder, Kate E; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

    2015-01-01

    There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the "fuel" that will power a science and technology-driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers.

  11. Thermo-elastic extended meshfree method for fracture without crack tip enrichment

    Institute of Scientific and Technical Information of China (English)

    A. ASADPOUR

    2015-01-01

    This is the first manuscript presenting an extended meshfree method for thermo- elastic fracture which does not exploit a crack tip enrichment. The crack is modeled by partition of unity enrichment of the displacement and temperature field. Only a step function is employed that facilitates the implementation. To ensure that crack tip is at the correct position, a Lagrange multiplier field ahead of the crack tip is introduced along a line. The Lagrange multiplier nodal parameters are discretised with the available meshfree functions. Two benchmark examples illustrate the efficiency of the method.

  12. Assessment of the latest NGS enrichment capture methods in clinical context.

    Science.gov (United States)

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  13. A new method to track seed dispersal and recruitment using 15N isotope enrichment.

    Science.gov (United States)

    Carlo, Tomás A; Tewksbury, Joshua J; Martínez Del Río, Carlos

    2009-12-01

    Seed dispersal has a powerful influence on population dynamics, genetic structuring, evolutionary rates, and community ecology. Yet, patterns of seed dispersal are difficult to measure due to methodological shortcomings in tracking dispersed seeds from sources of interest. Here we introduce a new method to track seed dispersal: stable isotope enrichment. It consists of leaf-feeding plants with sprays of 15N-urea during the flowering stage such that seeds developed after applications are isotopically enriched. We conducted a greenhouse experiment with Solanum americanum and two field experiments with wild Capsicum annuum in southern Arizona, USA, to field-validate the method. First, we show that plants sprayed with 15N-urea reliably produce isotopically enriched progeny, and that delta 15N (i.e., the isotopic ratio) of seeds and seedlings is a linear function of the 15N-urea concentration sprayed on mothers. We demonstrate that three urea dosages can be used to distinctly enrich plants and unambiguously differentiate their offspring after seeds are dispersed by birds. We found that, with high urea dosages, the resulting delta 15N values in seedlings are 10(3) - 10(4) times higher than the delta 15N values of normal plants. This feature allows tracking not only where seeds arrive, but in locations where seeds germinate and recruit, because delta 15N enrichment is detectable in seedlings that have increased in mass by at least two orders of magnitude before fading to normal delta 15N values. Last, we tested a mixing model to analyze seed samples in bulk. We used the delta 15N values of batches (i.e., combined seedlings or seeds captured in seed traps) to estimate the number of enriched seeds coming from isotopically enriched plants in the field. We confirm that isotope enrichment, combined with batch-sampling, is a cheap, reliable, and user-friendly method for bulk-processing seeds and is thus excellent for the detection of rare dispersal events. This method could

  14. Enrichment, Amplification, and Sequence-Based Typing of Salmonella enterica and Other Foodborne Pathogens.

    Science.gov (United States)

    Edlind, Tom; Brewster, Jeffrey D; Paoli, George C

    2017-01-01

    Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing. Both methods typically require a pure culture, which adds to the cost and turnaround time. A more rapid and cost-effective method with sufficient discriminatory power would benefit food industries, regulatory agencies, and public health laboratories. To address this need, a novel enrichment, amplification, and sequence-based typing (EAST) approach was developed involving (i) overnight enrichment and total DNA preparation, (ii) amplification of polymorphic tandem repeat-containing loci with electrophoretic detection, and (iii) DNA sequencing and bioinformatic analysis to identify related strains. EAST requires 3 days or less and provides a strain resolution that exceeds serotyping and is comparable to pulsed-field gel electrophoresis. Evaluation with spiked ground turkey demonstrated its sensitivity (with a starting inoculum of ≤1 CFU/g) and specificity (with unique or nearly unique alleles relative to databases of >1,000 strains). In tests with unspiked retail chicken parts, 3 of 11 samples yielded S. enterica -specific PCR products. Sequence analysis of three distinct typing targets (SeMT1, SeCRISPR1, and SeCRISPR2) revealed consistent similarities to specific serotype Schwarzengrund, Montevideo, and Typhimurium strains. EAST provides a time-saving and cost-effective approach for detecting and typing foodborne S. enterica , and postenrichment steps can be commercially outsourced to facilitate its implementation. Initial studies with Listeria

  15. Methods applied in the large littoral mesocosms study of nutrient enrichment in rocky shore ecosystems - EULIT

    NARCIS (Netherlands)

    Bokn, T.L.; Hoell, E.E.; Kersting, K.; Moy, F.E.; Sorensen, K.

    2001-01-01

    Eight concrete land-based mesocosms have been set up for a study of the effect of nutrient enrichment on littoral hard bottom ecosystems. The construction of the mesocosms and the community establishment were initiated 2 yr ahead of the MAST-III project. The littoral communities were established by

  16. Electronic and optoelectronic devices based on chirality-enriched wafer-scale single-wall carbon nanotube thin films

    Science.gov (United States)

    Gao, Weilu; He, Xiaowei; Xie, Lijuan; Zhang, Qi; Haroz, Erik; Doorn, Stephen K.; Kono, Junichiro

    2015-03-01

    The unique and rich material properties of single-wall carbon nanotubes (SWCNTs) make them attractive for nano-electronic and optoelectronic applications. Slight changes in tube diameter and wrapping angle, defined by the chirality indices (n, m), can dramatically modify the bandstructure, which can be utilized for designing devices with tailored properties. However, it remains to be a challenge to fabricate macroscopic, single-chirality devices. Here, we introduce a simple way of producing chirality-enriched wafer-scale SWCNT films by combining recently developed solution-based polymer-modified sorting method and vacuum filtration. The produced thin films can be easily transferred onto any substrate to have a CMOS compatible wafer. We fabricated a transistor of (6,5)-enriched SWCNTs with an on/off ratio >103. Large-scale photothermoelectric-effect-based and photovoltaic-effect-based photodetectors made of (6,6)- and (6,5)-enriched films, respectively, will also be discussed.

  17. Rare earth element enrichment using membrane based solvent extraction

    Science.gov (United States)

    Makertiharta, I. G. B. N.; Dharmawijaya, P. T.; Zunita, M.; Wenten, I. G.

    2017-01-01

    The chemical, catalytic, electrical, magnetic, and optical properties of rare earth elements are required in broad applications. Rare earth elements have similar physical and chemical properties thus it is difficult to separate one from each other. Rare earth element is relatively abundant in earth's crust but rarely occur in high concentrated deposits. Traditionally, ion-exchange and solvent extraction techniques have been developed to separate and purify single rare earth solutions or compounds. Recently, membrane starts to gain attention for rare earth separation by combining membrane and proven technologies such as solvent extraction. Membrane-based process offers selective, reliable, energy efficient and easy to scale up separation. During membrane-based separation process, one phase passes through membrane pores while the other phase is rejected. There is no direct mixing of two phases thus the solvent loss is very low. Membrane can also lower solvent physical properties requirement (viscosity, density) and backmixing, eliminate flooding phenomenon and provide large interfacial area for mass transfer. This paper will summarize research efforts in developing membrane technology for rare earth element separation. Special attention will be given to solvent extraction related process as the commonly used method for rare earth element separation. Furthermore, membrane configuration and its potentials will also be discussed.

  18. A simple method for the absolute determination of uranium enrichment by high-resolution {gamma} spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Korob, R.O. [Unidad de Actividad Radioquimica y Quimica de las Radiaciones, Comision Nacional de Energia Atomica, Centro Atomico Ezeiza, Presbitero Juan Gonzalez y Aragon No. 15 Partido de Ezeiza, Provincia de Buenos Aires (Argentina)]. E-mail: korob@cae.cnea.gov.ar; Blasiyh Nuno, G.A. [Unidad de Actividad Gestion de Residuos Radiactivos, Comision Nacional de Energia Atomica, Centro Atomico Ezeiza, Presbitero Juan Gonzalez y Aragon No. 15 Partido de Ezeiza, Provincia de Buenos Aires (Argentina)

    2006-05-15

    A simple method for the determination of uranium enrichment using high-resolution {gamma} spectrometry is presented in this paper. The method relies solely on the {gamma}-ray emission probabilities of {sup 235}U and {sup 234m}Pa, and an iterative procedure for the least squares fit of a polynomial to a set of experimentally determined data. To ensure the reliability of the {sup 234m}Pa {gamma}-ray emission probabilities employed, a new determination of these probabilities was carried out using a combination of {gamma} spectrometry and Cerenkov counting of a purified {sup 234}Th solution. Using these new data, a maximum difference of {approx}5% has been found between the experimental and declared uranium enrichment in a set of solid and liquid samples containing uranium compounds.

  19. Method of oxygen-enriched two-stage underground coal gasification

    Institute of Scientific and Technical Information of China (English)

    Liu Hongtao; Chen Feng; Pan Xia; Yao Kai; Liu Shuqin

    2011-01-01

    Two-stage underground coal gasification was studied to improve the caloric value of the syngas and to extend gas production times. A model test using the oxygen-enriched two-stage coal gasification method was carried out. The composition of the gas produced, the time ratio of the two stages, and the role of the temperature field were analysed. The results show that oxygen-enriched two-stage gasification shortens the time of the first stage and prolongs the time of the second stage. Feed oxygen concentrations of 30%,35%, 40%, 45%, 60%, or 80% gave time ratios (first stage to second stage) of 1:0.12, 1:0.21, 1:0.51, 1:0.64,1:0.90, and 1:4.0 respectively. Cooling rates of the temperature field after steam injection decreased with time from about 19.1-27.4 ℃/min to 2.3-6.8 ℃/min. But this rate increased with increasing oxygen concentrations in the first stage. The caloric value of the syngas improves with increased oxygen concentration in the first stage. Injection of 80% oxygen-enriched air gave gas with the highest caloric value and also gave the longest production time. The caloric value of the gas obtained from the oxygenenriched two-stage gasification method lies in the range from 5.31 MJ/Nm3 to 10.54 MJ/Nm3.

  20. SNP-based pathway enrichment analysis for genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Potkin Steven G

    2011-04-01

    Full Text Available Abstract Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs, have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1 for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2 ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one

  1. Enriched Oxygen BAC Method in Advanced Treatment of Textile Dyeing-printing & Alkali-peeling Wastewater

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A novel Pressurized Enriched Oxygen Biological Activated Carbon (PRBAC) method in treating secondary effluent of textile dying-printing & alkali peeling wastewater was configured. The PRBAC reactor simply increased reactor pressure to create an enriched dissolved oxygen (DO) environment to stimulate the bioactivities of microbes on GAC surface for removing refractory organic matter. Rapid SmallScaled Column Test (RSSCT) was carried out to evaluate the adsorption characteristics of target stream constituents, and over 80% COD components were poorly adsorbable while about 82.5% color inducing matter and 85% UV254 surrogated matter were readily adsorbable. Compared with performances of normal BAC reactor under conventional DO condition, PRBAC achieved 20%, 10% and 50% more removal in COD, color and NH3-N abatement.

  2. Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership

    Directory of Open Access Journals (Sweden)

    Ernesto eIacucci

    2012-02-01

    Full Text Available High-throughput molecular biology studies, such as microarray assays of gene expression, two-hybrid experiments for detecting protein interactions, or ChIP-Seq experiments for transcription factor binding, often result in an interesting set of genes—say, genes that are co-expressed or bound by the same factor. One way of understanding the biological meaning of such a set is to consider what processes or functions, as defined in an ontology, are over-represented (enriched or under-represented (depleted among genes in the set. Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications. We consider the more general problem of computing p-values for arbitrary integer additive statistics, or weighted membership functions. Such membership functions can be used to represent, for example, prior knowledge on the role of certain genes or classifications, differential importance of different classifications or genes to the experimenter, hierarchical relationships between classifications, or different degrees of interestingness or evidence for specific genes. We describe a generic dynamic programming algorithm that can compute exact p-values for arbitrary integer additive statistics. We also describe several optimizations for important special cases, which can provide orders-of-magnitude speed up in the computations. We apply our methods to datasets describing oxidative phosphorylation and parturition and compare p-values based on computations of several different statistics for measuring enrichment. We find major differences between p-values resulting from these statistics, and that some statistics recover gold standard annotations of the data better than others. Our work establishes a theoretical and algorithmic basis for far richer notions of enrichment or depletion of gene sets with respect to gene ontologies than has previously been available.

  3. Porous membrane ultrafiltration-A novel method for enrichment of the active compounds from micro-plasma samples

    Science.gov (United States)

    Liu, Qingshan; Yin, Xiaoying; Sha, Biying; You, Jingjing

    2014-10-01

    To enrich the active compounds from plasma samples, a novel and simple method has been developed using a porous membrane envelope based on the ultrafiltration technique combining with high-performance liquid chromatography. The ultrafiltration device is a sealed porous membrane envelope prepared with a polypropylene sheet to effectively separate the active small molecules and large biomolecules, and a sample carrier is held inside the envelope to load plasma samples. The enrichment of hyperoside and isoquercitrin from rat plasma was used as an example. Significant factors of this method, such as membrane types, the desorption solvent, and the desorption time were optimized for the ultrafiltration method. Under the optimal conditions, correlation coefficients of 0.999 and 0.998 were obtained for hyperoside and isoquercitrin, respectively, with a linear range between 0.5 and 100 μg/mL. The absolute extraction recoveries from 83.2% to 86.8% were achieved. The detection limits of the method for hyperoside and isoquercitrin were 0.22 and 0.20 μg/mL, respectively. Compared with protein precipitation, solid-phase extraction and commercial ultrafiltration membrane methods, our proposed method demonstrates lower detection limits and lower cost for extraction. Also, it consumes less plasma samples and is found to be applicable to biological samples.

  4. Oxidative stability of fish oil-enriched mayonnaise-based salads

    DEFF Research Database (Denmark)

    Sørensen, Ann-Dorit Moltke; Nielsen, Nina Skall; Jacobsen, Charlotte

    2010-01-01

    The oxidative stability of fish oil-enriched mayonnaise-based salads and the influence of different vegetables in shrimp and tuna salads were evaluated. Moreover, the lipid oxidation in the presence of 1% oregano, rosemary, or thyme in fish oil-enriched tuna salad was assessed. The results obtained...... showed that the mayonnaise itself was more oxidatively stable without vegetables and tuna or shrimp, in spite of the higher oil content in mayonnaise (63 and 6.3% fish oil, respectively) compared to salads (∼24 and 2.4% fish oil, respectively). Surprisingly, the fish oil-enriched mayonnaise was only...... significantly different from the standard mayonnaise in the volatile concentration during the end of storage. In fish oil-enriched shrimp salad, asparagus had an anti-oxidative effect and shrimp a pro-oxidative effect, where the anti-oxidative effect of asparagus was strong enough to prevent the pro...

  5. Material classification and automatic content enrichment of images using supervised learning and knowledge bases

    Science.gov (United States)

    Mallepudi, Sri Abhishikth; Calix, Ricardo A.; Knapp, Gerald M.

    2011-02-01

    In recent years there has been a rapid increase in the size of video and image databases. Effective searching and retrieving of images from these databases is a significant current research area. In particular, there is a growing interest in query capabilities based on semantic image features such as objects, locations, and materials, known as content-based image retrieval. This study investigated mechanisms for identifying materials present in an image. These capabilities provide additional information impacting conditional probabilities about images (e.g. objects made of steel are more likely to be buildings). These capabilities are useful in Building Information Modeling (BIM) and in automatic enrichment of images. I2T methodologies are a way to enrich an image by generating text descriptions based on image analysis. In this work, a learning model is trained to detect certain materials in images. To train the model, an image dataset was constructed containing single material images of bricks, cloth, grass, sand, stones, and wood. For generalization purposes, an additional set of 50 images containing multiple materials (some not used in training) was constructed. Two different supervised learning classification models were investigated: a single multi-class SVM classifier, and multiple binary SVM classifiers (one per material). Image features included Gabor filter parameters for texture, and color histogram data for RGB components. All classification accuracy scores using the SVM-based method were above 85%. The second model helped in gathering more information from the images since it assigned multiple classes to the images. A framework for the I2T methodology is presented.

  6. Enriched Element-Free Galerkin Method for Fracture Analysis of Functionally Graded Piezoelectric Materials

    Directory of Open Access Journals (Sweden)

    Guang Wei Meng

    2015-01-01

    Full Text Available A new method using the enriched element-free Galerkin method (EEFGM to model functionally graded piezoelectric materials (FGPMs with cracks was presented. To improve the solution accuracy, extended terms were introduced into the approximation function of the conventional element-free Galerkin method (EFGM to describe the displacement and electric fields near the crack. Compared with the conventional EFGM, the new approach requires smaller domain to describe the crack-tip singular field. Additionally, the domain of the nodes was not affected by the crack. Therefore, the visibility method and the diffraction method were no longer needed. The mechanical response of FGPM was discussed, when its material parameters changed exponentially in a certain direction. The modified J-integrals for FGPM were deduced, whose results were compared with the results of the conventional EFGM and the analytical solution. Numerical example results illustrated that this method is feasible and precise.

  7. Protein expression and isotopic enrichment based on induction of the Entner-Doudoroff pathway in Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Refaeli, Bosmat [School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv (Israel); Goldbourt, Amir, E-mail: amirgo@post.tau.ac.il [School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv (Israel)

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer The Entner-Doudoroff pathway is induced during protein expression in E. coli. Black-Right-Pointing-Pointer 1-{sup 13}C-gluconate and {sup 15}NH{sub 4}Cl provide a carbonyl-amide protein backbone labeling scheme. Black-Right-Pointing-Pointer The enrichment pattern is determined by nuclear magnetic resonance. -- Abstract: The Entner-Doudoroff pathway is known to exist in many organisms including bacteria, archea and eukarya. Although the common route for carbon catabolism in Escherichia coli is the Embden-Meyerhof-Parnas pathway, it was shown that gluconate catabolism in E. coli occurs via the Entner-Doudoroff pathway. We demonstrate here that by supplying BL21(DE3) competent E.coli cells with gluconate in a minimal growth medium, protein expression can be induced. Nuclear magnetic resonance data of over-expressed ubiquitin show that by using [1-{sup 13}C]-gluconate as the only carbon source, and {sup 15}N-enriched ammonium chloride, sparse isotopic enrichment in the form of a spin-pair carbonyl-amide backbone enrichment is obtained. The specific amino acid labeling pattern is analyzed and is shown to be compatible with Entner-Doudoroff metabolism. Isotopic enrichment serves as a key factor in the biophysical characterization of proteins by various methods including nuclear magnetic resonance, mass spectrometry, infrared spectroscopy and more. Therefore, the method presented here can be applied to study proteins by obtaining sparse enrichment schemes that are not based on the regular glycolytic pathway, or to study the Entner-Doudoroff metabolism during protein expression.

  8. Enriching location-based games with navigational game activities

    DEFF Research Database (Denmark)

    Nadarajah, Stephanie Githa; Overgaard, Benjamin Nicholas; Pedersen, Peder Walz

    2017-01-01

    Mobile location-based games are experiences that entertain its players by requiring interactions mainly at points of interest (POIs). Navigation between POIs often involve the use of either a physical or digital map, not taking advantage of the opportunity available to engage users in activities...

  9. Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips.

    Science.gov (United States)

    Xu, Li-Ping; Chen, Yanxia; Yang, Gao; Shi, Wanxin; Dai, Bing; Li, Guannan; Cao, Yanhua; Wen, Yongqiang; Zhang, Xueji; Wang, Shutao

    2015-11-18

    A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing.

  10. NEAT: an efficient network enrichment analysis test

    OpenAIRE

    Signorelli, Mirko; Vinciotti, Veronica; Wit, Ernst C

    2016-01-01

    Background Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and are based on normality assumptions. Results We propose NEAT, a test for network enrichment analysis. The test is based on the hypergeometric distribution, which naturally arises ...

  11. Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data

    Directory of Open Access Journals (Sweden)

    Simpson David

    2006-03-01

    Full Text Available Abstract Background Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data. Results Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE, this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way cluster analysis was firstly performed. By clustering SAGE libraries, a hierarchical tree reflecting relationships between developmental stages was obtained. By clustering SAGE tags, a more comprehensive expression profile for photoreceptor cells was revealed. To demonstrate the usefulness of machine learning-based models in predicting functional associations from the SAGE data, three supervised classification models were compared. The results indicated that a relatively simple instance-based model (KStar model performed significantly better than relatively more complex algorithms, e.g. neural networks. To deal with the problem of functional class imbalance occurring in the dataset, two data re

  12. A semantically enriched web usage based recommendation model

    CERN Document Server

    Ramesh, C; Govardhan, A

    2011-01-01

    With the rapid growth of internet technologies, Web has become a huge repository of information and keeps growing exponentially under no editorial control. However the human capability to read, access and understand Web content remains constant. This motivated researchers to provide Web personalized online services such as Web recommendations to alleviate the information overload problem and provide tailored Web experiences to the Web users. Recent studies show that Web usage mining has emerged as a popular approach in providing Web personalization. However conventional Web usage based recommender systems are limited in their ability to use the domain knowledge of the Web application. The focus is only on Web usage data. As a consequence the quality of the discovered patterns is low. In this paper, we propose a novel framework integrating semantic information in the Web usage mining process. Sequential Pattern Mining technique is applied over the semantic space to discover the frequent sequential patterns. Th...

  13. THE INFLUENCE OF STORAGE CONDITIONS OF CANDIED FRUITS ENRICHED WITH VITAMIN C BY DIFFERENT METHODS ON ITS CONTENT

    Directory of Open Access Journals (Sweden)

    Agata Wypchoł

    2010-05-01

    Full Text Available The aim of this work was to study the effect of storage conditions of candied fruits enriched with vitamin C on its concentration in that product. The materials were candied fruits (black chokeberry and black currant enriched with vitamin C by two methods during their production. The final products were stored within 3 months at 8 and 20°C. On the basis of the results it was stated that enrichment method affected the concentration of the vitamin C in fruits measured during storage period at the above conditions. doi:10.5219/55

  14. A mathematical analysis of the selective enrichment of NECEEM-based non-SELEX.

    Science.gov (United States)

    Yu, Xinliang; Yu, Yixiong

    2014-08-01

    Non-Systematic Evolution of Ligands by EXponential enrichment (SELEX)selection of aptamers, a novel technology for aptamer selection from libraries of random DNA (or RNA) sequences, involves repetitive steps of partitioning without polymerase chain reaction (PCR) amplification between them. This selection is based on non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) and has exceptionally high efficiency. In this paper, a mathematical analysis was carried out to predict the levels of enrichment of non-SELEX selection under different conditions such as different protein concentrations and different efficiencies of partitioning. Investigated results suggest that the magnitude of the bulk affinity (k d) being 10(4) or 10(5) μM for the initial pool has no obvious effect on selective enrichment and that the first, second, and third rounds of non-SELEX selection have different optimum protein concentration values [T f] that give maximum enrichment levels when [T f] ranges from 0.0005 to 0.5 μM. The significance of analyzing selective enrichment of NECEEM-based non-SELEX with the efficiency of partitioning target-bound ligands from free ligands has been demonstrated.

  15. Wall modeling via function enrichment within a high-order DG method for RANS simulations of incompressible flow

    CERN Document Server

    Krank, Benjamin; Wall, Wolfgang A

    2016-01-01

    We present a novel approach to wall modeling for RANS within the discontinuous Galerkin method. Wall functions are not used to prescribe boundary conditions as usual but they are built into the function space of the numerical method as a local enrichment, in addition to the standard polynomial component. The Galerkin method then automatically finds the optimal solution among all shape functions available. This idea is fully consistent and gives the wall model vast flexibility in separated boundary layers or high adverse pressure gradients. The wall model is implemented in a high-order discontinuous Galerkin solver for incompressible flow complemented by the Spalart-Allmaras closure model. As benchmark examples we present turbulent channel flow starting from $Re_{\\tau}=180$ and up to $Re_{\\tau}=100{,}000$ as well as flow past periodic hills at Reynolds numbers based on the hill height of $Re_H=10{,}595$ and $Re_{H}=19{,}000$.

  16. Property Enrichment of Aged Nickel Base Superalloy Supercast 247A

    Directory of Open Access Journals (Sweden)

    Lavakumar Avala

    2013-12-01

    Full Text Available The commercial nickel-base superalloy Supercast 247A can be used for applications in which is required high mechanical strength and corrosion resistance at elevated temperatures, such as turbine blades and automotive turbocharger rotors. The mechanical properties are totally connected to the morphology, size and distribution of γ' phase and carbides. In order to improve the mechanical properties, the material is subjected to solution and aging heat treatment, to raise the volume fraction of γ' phase in the matrix and to form carbides at grain boundaries. In the present study the Supercast 247A superalloy was remelted and cast to obtain the desired polycrystalline test bars by controlling casting parameters, followed by the investigation of precipitation morphology and mechanical properties with respect to solution treatment and aging treatment. The experimental results show that by well controlled casting parameters the Supercast 247A owns excellent castability to form a superalloy with fine grain structure, resistance to indentation as well as superior strength.

  17. Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation.

    Science.gov (United States)

    Reis, Wieland G; Tomović, Željko; Weitz, R Thomas; Krupke, Ralph; Mikhael, Jules

    2017-03-20

    The potential of single-walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs.

  18. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    Science.gov (United States)

    Kim, Hanna

    2016-01-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at…

  19. Application of protein purification methods for the enrichment of a cytotoxin from Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Gatsos Xenia

    2012-12-01

    Full Text Available Abstract Background Campylobater jejuni, a major foodborne diarrhoeal pathogen is reported to produce a number of cytotoxins of which only a cytolethal distending toxin (CDT has been characterised so far. One or more additional cytotoxins other than CDT, including a Chinese hamster ovary (CHO cell active, Vero cell inactive cytotoxin, may mediate inflammatory diarrhoea. Our objective was to develop a method to enrich and thus partially characterise this cytotoxin, as a pathway to the eventual identification and characterisation of the toxin. Results A number of biochemical methods including cation- and anion-exchange chromatography were evaluated to enrich the cytotoxin from a cell lysate of a known cytotoxin-producing C. jejuni, C31. The cytotoxin in crude lysate was initially prepared by size-exclusion desalting and then subjected to high pressure liquid chromatography (HPLC ion-exchange fractionation. One pooled fraction (pool B was cytotoxic for CHO cells equivalent to crude toxin (tissue culture infectivity dose 50 [TCID50] of 1–2 μg/ml. The proteins of pool B were identified by mass spectrometry (MS after separation by SDS-PAGE and trypsin digestion. Also, pool B was directly digested with trypsin and then subjected to liquid chromatography tandem mass spectrometry (LCMS analysis for identification of lesser abundant proteins in the fraction. A total of 41 proteins were found in the fraction, which included enzymes involved in metabolic and transport functions. Eighteen non-cytoplasmic proteins including 2 major antigenic peptide proteins (PEB2 and PEB3 and 3 proteins of unknown function were also identified in the screen. Cytotoxicity in pool B was trypsin-sensitive indicating its protein nature. The cytotoxic activity was heat-stable to 50°C, and partially inactivated at 60-70°C. The pool B fraction also induced fluid accumulation in the adult rabbit ileal loop assay with cytotoxicity for mucosa confirming the presence of the

  20. Methods for reducing lipid oxidation in fish-oil-enriched energy bars

    DEFF Research Database (Denmark)

    Nielsen, Nina Skall; Jacobsen, Charlotte

    2009-01-01

    P>Fish oil (FO) enrichment of foods is relevant owing to the beneficial effects of omega-3 polyunsaturated fatty acids on human health. However, the susceptibility of FO to oxidation necessitates careful control to avoid this oxidation. In this study, energy bars were successfully supplemented...... with 5% FO. Heating of bars during baking did, apparently, not increase oxidation. Energy bars produced with neat FO were oxidatively unstable as measured by peroxide value, secondary volatile oxidation products and sensory analysis. Pre-emulsification of the FO with sodium caseinate in water offered...... similar protection towards oxidation as packaging the energy bars in modified atmosphere. These protection methods were although not as efficient as addition of FO as micro-encapsulated powder. Addition of the metal chelator ethylene diamine tetra-acetic acid (EDTA) (100-2000 ppm) to emulsified FO...

  1. Kernel-Based Semantic Relation Detection and Classification via Enriched Parse Tree Structure

    Institute of Scientific and Technical Information of China (English)

    Guo-Dong Zhou; Qiao-Ming Zhu

    2011-01-01

    This paper proposes a tree kernel method of semantic relation detection and classification (RDC) between named entities. It resolves two critical problems in previous tree kernel methods of RDC. First, a new tree kernel is presented to better capture the inherent structural information in a parse tree by enabling the standard convolution tree kernel with context-sensitiveness and approximate matching of sub-trees. Second, an enriched parse tree structure is proposed to well derive necessary structural information, e.g., proper latent annotations, from a parse tree. Evaluation on the ACE RDC corpora shows that both the new tree kernel and the enriched parse tree structure contribute significantly to RDC and our tree kernel method much outperforms the state-of-the-art ones.

  2. Enrichment of steroid hormones in water with porous and hydrophobic polymer-based SPE followed by HPLC-UV determination.

    Science.gov (United States)

    Hu, Yinfen; Zhang, Man; Tong, Changlun; Wu, Jianmin; Liu, Weiping

    2013-10-01

    There have been great concerns about the persistence of steroid hormones in surface water. Since the concentrations of these compounds in water samples are usually at a trace level, the efficient enrichment of steroid hormones is vital for further analysis. In this work, a porous and hydrophobic polymer was synthesized and characterized. The composition of solvent used as porogen in the synthetic process was shown to have an effect on the morphology of the polymer, which was successfully used as an SPE sorbent for simultaneously enriching steroid hormones in surface water samples. The recoveries of the steroid hormones on the custom-made polymer ranged from 93.4 to 106.2%, whereas those on commercialized ENVI-18, LC-18, and Oasis HLB ranged from 54.8 to 104.9, 66 to 93.6, and 77.2 to 106%, respectively. Five types of steroid hormones were simultaneously measured using HPLC-UV after they were enriched by the custom-made sorbent. Based on these findings, the SPE-HPLC method was developed. The LODs of this method for estriol, estradiol, estrone, androstenedione, progesterone were 0.07, 0.43, 0.61, 0.27, and 0.42 μg/L, respectively, while precision and reproducibility RSDs were <6.40 and 7.49%, respectively.

  3. Virus enrichment for single virus infection by using 3D insulator based dielectrophoresis.

    Science.gov (United States)

    Masuda, Taisuke; Maruyama, Hisataka; Honda, Ayae; Arai, Fumihito

    2014-01-01

    We developed an active virus filter (AVF) that enables virus enrichment for single virus infection, by using insulator-based dielectrophoresis (iDEP). A 3D-constricted flow channel design enabled the production of an iDEP force in the microfluidic chip. iDEP using a chip with multiple active virus filters (AVFs) was more accurate and faster than using a chip with a single AVF, and improved the efficiency of virus trapping. We utilized maskless photolithography to achieve the precise 3D gray-scale exposure required for fabrication of constricted flow channel. Influenza virus (A PR/8) was enriched by a negative DEP force when sinusoidal wave was applied to the electrodes within an amplitude range of 20 Vp-p and a frequency of 10 MHz. AVF-mediated virus enrichment can be repeated simply by turning the current ON or OFF. Furthermore, the negative AVF can inhibit virus adhesion onto the glass substrate. We then trapped and transported one of the enriched viruses by using optical tweezers. This microfluidic chip facilitated the effective transport of a single virus from AVFs towards the cell-containing chamber without crossing an electrode. We successfully transported the virus to the cell chamber (v = 10 µm/s) and brought it infected with a selected single H292 cell.

  4. Virus enrichment for single virus infection by using 3D insulator based dielectrophoresis.

    Directory of Open Access Journals (Sweden)

    Taisuke Masuda

    Full Text Available We developed an active virus filter (AVF that enables virus enrichment for single virus infection, by using insulator-based dielectrophoresis (iDEP. A 3D-constricted flow channel design enabled the production of an iDEP force in the microfluidic chip. iDEP using a chip with multiple active virus filters (AVFs was more accurate and faster than using a chip with a single AVF, and improved the efficiency of virus trapping. We utilized maskless photolithography to achieve the precise 3D gray-scale exposure required for fabrication of constricted flow channel. Influenza virus (A PR/8 was enriched by a negative DEP force when sinusoidal wave was applied to the electrodes within an amplitude range of 20 Vp-p and a frequency of 10 MHz. AVF-mediated virus enrichment can be repeated simply by turning the current ON or OFF. Furthermore, the negative AVF can inhibit virus adhesion onto the glass substrate. We then trapped and transported one of the enriched viruses by using optical tweezers. This microfluidic chip facilitated the effective transport of a single virus from AVFs towards the cell-containing chamber without crossing an electrode. We successfully transported the virus to the cell chamber (v = 10 µm/s and brought it infected with a selected single H292 cell.

  5. Rheology, fatty acid profile and quality characteristics of nutrient enriched pizza base.

    Science.gov (United States)

    Gupta, Chaitali Sen; Milind; Jeyarani, T; Rajiv, Jyotsna

    2015-05-01

    Enrichment of thick bread type pizza base (PZB) was done by substituting wheat flour (WF) with 5, 10 and 15 % soya protein isolate (SPI). The rheological characteristics of WF showed that water absorption increased, extensibility and peak viscosity decreased when level of SPI increased from 5 to 15 %. Baking studies showed that spread ratio decreased and hardness values of PZB increased with the increase in amount of SPI from 5 to15 %. Beyond 10 % SPI, the overall quality of PZB was adversely affected. To the optimal blend of 10 % SPI, 5 % psyllium husk (PH) was added and the hydrogenated fat was replaced by canola oil (CAN) in enriched PZB. The enriched PZB treated with combination of additives had 1.7 and 1.6 times more protein and dietary fiber than the control PZB. Fatty acid analysis showed that the enriched PZB had 58.65 % oleic, 6.58 % linolenic acid and 31.28 % polyunsaturated fatty acid and no Trans fat was present.

  6. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

    Directory of Open Access Journals (Sweden)

    Lingsheng Chen

    Full Text Available The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2 from 10 μL serum. Among them, 559 (n = 2 proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

  7. Nutrient enrichment reduces constraints on material flows in a detritus-based food web.

    Science.gov (United States)

    Cross, Wyatt F; Wallace, J Bruce; Rosemond, Amy D

    2007-10-01

    Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material storage and cycling in the ecosystem. Understanding mechanisms and predicting consequences of nutrient-induced changes in material flows requires a quantitative food web approach that combines information on consumer energetics and consumer-resource stoichiometry. We examined effects of a whole-system experimental nutrient enrichment on the trophic basis of production and the magnitude and pathways of carbon (C), nitrogen (N), and phosphorus (P) flows in a detritus-based stream food web. We compared the response of the treated stream to an adjacent reference stream throughout the study. Dietary composition and elemental flows varied considerably among invertebrate functional feeding groups. During nutrient enrichment, increased flows of leaf litter and amorphous detritus to shredders and gatherers accounted for most of the altered flows of C from basal resources to consumers. Nutrient enrichment had little effect on patterns of material flows but had large positive effects on the magnitude of C, N, and P flows to consumers (mean increase of 97% for all elements). Nutrient-specific food webs revealed similar flows of N and P to multiple functional groups despite an order of magnitude difference among groups in consumption of C. Secondary production was more strongly related to consumption of nutrients than C, and increased material flows were positively related to the degree of consumer-resource C:P and C:N imbalances. Nutrient enrichment resulted in an increased proportion of detrital C inputs consumed by primary consumers (from -15% to 35%) and a decreased proportion of invertebrate prey consumed by

  8. Stirred suspension bioreactors as a novel method to enrich germ cells from pre-pubertal pig testis.

    Science.gov (United States)

    Dores, C; Rancourt, D; Dobrinski, I

    2015-05-01

    To study spermatogonial stem cells the heterogeneous testicular cell population first needs to be enriched for undifferentiated spermatogonia, which contain the stem cell population. When working with non-rodent models, this step requires working with large numbers of cells. Available cell separation methods rely on differential properties of testicular cell types such as expression of specific cell surface proteins, size, density, or differential adhesion to substrates to separate germ cells from somatic cells. The objective of this study was to develop an approach that allowed germ cell enrichment while providing efficiency of handling large cell numbers. Here, we report the use of stirred suspension bioreactors (SSB) to exploit the adhesion properties of Sertoli cells to enrich cells obtained from pre-pubertal porcine testes for undifferentiated spermatogonia. We also compared the bioreactor approach with an established differential plating method and the combination of both: SSB followed by differential plating. After 66 h of culture, germ cell enrichment in SSBs provided 7.3 ± 1.0-fold (n = 9), differential plating 9.8 ± 2.4-fold (n = 6) and combination of both methods resulted in 9.1 ± 0.3-fold enrichment of germ cells from the initial germ cell population (n = 3). To document functionality of cells recovered from the bioreactor, we demonstrated that cells retained their functional ability to reassemble seminiferous tubules de novo after grafting to mouse hosts and to support spermatogenesis. These results demonstrate that the SSB allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability owing to handling.

  9. Numerical modeling of undersea acoustics using a partition of unity method with plane waves enrichment

    Science.gov (United States)

    Hospital-Bravo, Raúl; Sarrate, Josep; Díez, Pedro

    2016-05-01

    A new 2D numerical model to predict the underwater acoustic propagation is obtained by exploring the potential of the Partition of Unity Method (PUM) enriched with plane waves. The aim of the work is to obtain sound pressure level distributions when multiple operational noise sources are present, in order to assess the acoustic impact over the marine fauna. The model takes advantage of the suitability of the PUM for solving the Helmholtz equation, especially for the practical case of large domains and medium frequencies. The seawater acoustic absorption and the acoustic reflectance of the sea surface and sea bottom are explicitly considered, and perfectly matched layers (PML) are placed at the lateral artificial boundaries to avoid spurious reflexions. The model includes semi-analytical integration rules which are adapted to highly oscillatory integrands with the aim of reducing the computational cost of the integration step. In addition, we develop a novel strategy to mitigate the ill-conditioning of the elemental and global system matrices. Specifically, we compute a low-rank approximation of the local space of solutions, which in turn reduces the number of degrees of freedom, the CPU time and the memory footprint. Numerical examples are presented to illustrate the capabilities of the model and to assess its accuracy.

  10. A Convenient and Efficient Method to Enrich and Maintain Highly Proliferative Human Fetal Liver Stem Cells.

    Science.gov (United States)

    Guo, Xuan; Wang, Shu; Dou, Ya-ling; Guo, Xiang-fei; Chen, Zhao-li; Wang, Xin-wei; Shen, Zhi-qiang; Qiu, Zhi-gang; Jin, Min; Li, Jun-wen

    2015-06-01

    Pluripotent human hepatic stem cells have broad research and clinical applications, which are, however, restricted by both limited resources and technical difficulties with respect to isolation of stem cells from the adult or fetal liver. In this study, we developed a convenient and efficient method involving a two-step in situ collagenase perfusion, gravity sedimentation, and Percoll density gradient centrifugation to enrich and maintain highly proliferative human fetal liver stem cells (hFLSCs). Using this method, the isolated hFLSCs entered into the exponential growth phase within 10 days and maintained sufficient proliferative activity to permit subculture for at least 20 passages without differentiation. Immunocytochemistry, immunofluorescence, and flow cytometry results showed that these cells expressed stem cell markers, such as c-kit, CD44, epithelial cell adhesion molecule (EpCAM), oval cell marker-6 (OV-6), epithelial marker cytokeratin 18 (CK18), biliary ductal marker CK19, and alpha-fetoprotein (AFP). Gene expression analysis showed that these cells had stable mRNA expression of c-Kit, EpCAM, neural cell adhesion molecule (NCAM), CK19, CK18, AFP, and claudin 3 (CLDN-3) throughout each passage while maintaining low levels of ALB, but with complete absence of cytochrome P450 3A4 (C3A4), phosphoenolpyruvate carboxykinase (PEPCK), telomeric repeat binding factor (TRF), and connexin 26 (CX26) expression. When grown in appropriate medium, these isolated liver stem cells could differentiate into hepatocytes, cholangiocytes, osteoblasts, adipocytes, or endothelial cells. Thus, we have demonstrated a more economical and efficient method to isolate hFLSCs than magnetic-activated cell sorting (MACS). This novel approach may provide an excellent tool to isolate highly proliferative hFLSCs for tissue engineering and regenerative therapies.

  11. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.

    Directory of Open Access Journals (Sweden)

    Tim De Meyer

    Full Text Available DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existing implementations are numerous, and quality control and optimization require expensive external validation. Therefore, this study has two aims: 1 to identify a best performing kit for MBD-based enrichment using independent validation data, and 2 to evaluate whether quality evaluation can also be performed solely based on the characteristics of the generated sequences. Five commercially available kits for MBD enrichment were combined with Illumina GAIIx sequencing for three cell lines (HCT15, DU145, PC3. Reduced representation bisulfite sequencing data (all three cell lines and publicly available Illumina Infinium BeadChip data (DU145 and PC3 were used for benchmarking. Consistent large-scale differences in yield, sensitivity and specificity between the different kits could be identified, with Diagenode's MethylCap kit as overall best performing kit under the tested conditions. This kit could also be identified with the Fragment CpG-plot, which summarizes the CpG content of the captured fragments, implying that the latter can be used as a tool to monitor data quality. In conclusion, there are major quality differences between kits for MBD-based capturing of methylated DNA, with the MethylCap kit performing best under the used settings. The Fragment CpG-plot is able to monitor data quality based on inherent sequence data characteristics, and is therefore a cost-efficient tool for experimental optimization, but also to monitor quality throughout routine applications.

  12. Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Angelova, Angelina [University of Arizona; Park, Sang-Hycuk [University of Arizona; Kyndt, John [Bellevue University; Fitzsimmons, Kevin [University of Arizona; Brown, Judith K [University of Arizona

    2013-09-01

    With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

  13. A new method to measure iron absorption from the enrichment of 57Fe and 58Fe in young erythroid cells

    NARCIS (Netherlands)

    Heuvel, E.G.H.M. van den; Muys, T.; Pellegrom, H.; Bruyntjes, J.P.; Dokkum, W. van; Spanhaak, S.; Schaafsma, G.

    1998-01-01

    Iron absorption can be measured by the incorporation of stable iron isotopes into erythrocytes, 14 days after isotope administration. The disadvantage of this method is the high dose of isotopes needed to obtain a sufficient enrichment. Therefore, in this study cell fractions rich in young erythroid

  14. Innovative method for the enrichment of high-polarity bioactive molecules present at low concentrations in complex matrices.

    Science.gov (United States)

    Liu, Qing-Shan; He, Jie; Zhou, Wen-Bin; Gu, Yu-Long; Huang, Huoqiang; Li, Ke-Qin; Yin, Xiao-Ying

    2017-02-01

    Ginsenoside Rg1 is a valuable bioactive molecule but its high polarity and low concentration in complex mixtures makes it a challenge to separate Ginsenoside Rg1 from other saponins with similar structures, resulting in low extraction efficiency. The successful development of effective Rg1 molecularly imprinted polymers that exhibit high selectivity and adsorption may offer an improved method for the enrichment of active compounds. In this work, molecularly imprinted polymers were prepared with two different methods, precipitation polymerization or surface imprinted polymerization. Comparison of the adsorption abilities showed higher adsorption of the surface molecularly imprinted polymers prepared by surface imprinted polymerization, 46.80 mg/g, compared to the 27.74 mg/g observed for the molecularly imprinted polymers prepared by precipitation polymerization. Therefore, for higher adsorption of the highly polar Rg1, surface imprinted polymerization is a superior technique to make Rg1 molecularly imprinted polymers. The prepared surface molecularly imprinted polymers were tested as a solid-phase extraction column to directionally enrich Rg1 and its analogues from ginseng tea and total ginseng extracts. The column with surface molecularly imprinted polymers showed higher enrichment efficiency and better selectivity than a C18 solid-phase extraction column. Overall, a new, innovative method was developed to efficiently enrich high-polarity bioactive molecules present at low concentrations in complex matrices.

  15. Changes in the composition and structure of Mediterranean rocky-shore communities following a gradient of nutrient enrichment: descriptive study and test of proposed methods to assess water quality regarding macroalgae.

    Science.gov (United States)

    Arévalo, Raquel; Pinedo, Susana; Ballesteros, Enric

    2007-01-01

    Changes in the species composition and structure of Mediterranean macroalgal-dominated communities from the upper sublittoral zone are described along a gradient of nutrient enrichment coming from a urban sewage outfall. Ulva-dominated communities only appear close to the sewage outfall. Corallina-dominated communities replace ulvacean algae at intermediate levels of nutrient enrichment. Cystoseira-dominated communities thrive in the reference site but already appear at nutrient levels that are threefold higher than those reported from unpolluted sites. Assemblage variability of Cystoseira-dominated communities decreases along the gradient of nutrient enrichment. Methods based on the functional-form groups of macroalgae to assess the water quality provide equivocal results at intermediate levels of nutrient enrichment because species belonging to the same group can display a completely different response to pollution. Alternatively, methods based on indicator species showed correlated evidence among species abundances and pollution levels and seem to have better performances in water quality assessment.

  16. Depletion Gilding: An Ancient Method for Surface Enrichment of Gold Alloys

    CERN Document Server

    Sparavigna, Amelia Carolina

    2016-01-01

    Ancient objects made of noble metal alloys, that is, gold with copper and/or silver, can show the phenomenon of surface enrichment. This phenomenon is regarding the composition of the surface, which has a percentage of gold higher than that of the bulk. This enrichment is obtained by a depletion of the other elements of the alloy, which are, in some manner, removed. This depletion gilding process was used by pre-Columbian populations for their 'tumbaga', a gold-copper alloy, to give it the luster of gold.

  17. Enriched glucose and dextrin mannitol-based media modulates fibroblast behavior on bacterial cellulose membranes

    Energy Technology Data Exchange (ETDEWEB)

    Stumpf, Taisa R.; Pértile, Renata A.N. [Integrated Technologies Laboratory, Department of Chemical and Food Engineering (Brazil); Rambo, Carlos R., E-mail: rambo@intelab.ufsc.br [Department of Electrical Engineering, Federal University of Santa Catarina, Florianópolis 88040-900 (Brazil); Porto, Luismar M. [Integrated Technologies Laboratory, Department of Chemical and Food Engineering (Brazil)

    2013-12-01

    Bacterial cellulose (BC) produced by Gluconacetobacter hansenii is a suitable biopolymer for biomedical applications. In order to modulate the properties of BC and expand its use as substrate for tissue engineering mainly in the form of biomembranes, glucose or dextrin were added into a BC fermentation mannitol-based medium (BCGl and BCDe, respectively) under static culture conditions. SEM images showed effects on fiber density and porosity on both sides of the BC membranes. Both enriched media decreased the BET surface area, water holding capacity, and rehydration rate. Fourier transform infrared (attenuated total reflectance mode) spectroscopy (FTIR-ATR) analysis revealed no change in the chemical structure of BC. L929 fibroblast cells were seeded on all BC-based membranes and evaluated in aspects of cell adhesion, proliferation and morphology. BCG1 membranes showed the highest biological performance and hold promise for the use in tissue engineering applications. - Highlights: • Glucose and dextrin were used to modify culture media for BC production. • Microarchitecture of BC was different depending on the enriching agent. • Fibroblasts adhered on the surface of BC modified microarchitectures. • Fibroblasts adhered on glucose modified BC exhibited healthy cell morphology.

  18. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    Science.gov (United States)

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  19. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

    Directory of Open Access Journals (Sweden)

    Cox Juergen

    2012-11-01

    Full Text Available Abstract Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, the presence of protein domains or the membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software.

  20. Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders.

    LENUS (Irish Health Repository)

    Anney, Richard J L

    2012-02-01

    Recent genome-wide association studies (GWAS) have implicated a range of genes from discrete biological pathways in the aetiology of autism. However, despite the strong influence of genetic factors, association studies have yet to identify statistically robust, replicated major effect genes or SNPs. We apply the principle of the SNP ratio test methodology described by O\\'Dushlaine et al to over 2100 families from the Autism Genome Project (AGP). Using a two-stage design we examine association enrichment in 5955 unique gene-ontology classifications across four groupings based on two phenotypic and two ancestral classifications. Based on estimates from simulation we identify excess of association enrichment across all analyses. We observe enrichment in association for sets of genes involved in diverse biological processes, including pyruvate metabolism, transcription factor activation, cell-signalling and cell-cycle regulation. Both genes and processes that show enrichment have previously been examined in autistic disorders and offer biologically plausibility to these findings.

  1. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

    Directory of Open Access Journals (Sweden)

    Laura Acevedo-Pacheco

    2016-10-01

    Full Text Available Background: One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective: The aim was to determine and compare the essential amino acid (EAA scores, protein digestibility corrected amino acid scores (PDCAAS, and in vivo protein quality (protein digestibility, protein efficiency ratio (PER, biological values (BV, and net protein utilization (NPU values of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design: To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results: The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions: The proposed enrichment of cereal-based foods with soybean proteins greatly

  2. Towards an international standard for PCR-based detection of foodborne thermotolerant campylobacters: interaction of enrichment media and pre-PCR treatment on carcass rinse samples.

    Science.gov (United States)

    Josefsen, M H; Lübeck, P S; Hansen, F; Hoorfar, J

    2004-07-01

    As part of a large EU project for standardisation of polymerase chain reaction (PCR), a systematic evaluation of the interaction of enrichment media, type of DNA polymerase and pre-PCR sample treatment for a PCR detecting thermotolerant campylobacters was carried out. The growth-supporting capacity and PCR compatibility of enrichment in Preston, Mueller-Hinton and Bolton broth (blood-containing and blood-free) were evaluated. The effect of resin-based DNA extraction and DNA extraction by boiling on the final PCR assay was investigated. The time-course studies indicated that a 20-h sample enrichment in blood-containing Bolton broth, followed by a simple resin-based extraction of DNA and a PCR amplification using Tth polymerase, resulted in strong and clear PCR amplicons for target (287 bp) and internal amplification control (IAC, 124 bp). The enrichment PCR-based method, tested on 68 presumably naturally contaminated poultry-rinse samples, showed a diagnostic sensitivity of 97.5% (39 PCR-positive/40 total positive samples) and a diagnostic specificity of 100% (28 PCR-negative/28 total negative samples; P=0.32) when compared to a standard bacteriological method (ISO 10272).

  3. Efficient dielectrophoretic cell enrichment using a dielectrophoresis-well based system.

    Science.gov (United States)

    Abdul Razak, Mohd Azhar; Hoettges, Kai F; Fatoyinbo, Henry O; Labeed, Fatima H; Hughes, Michael P

    2013-01-01

    Whilst laboratory-on-chip cell separation systems using dielectrophoresis are increasingly reported in the literature, many systems are afflicted by factors which impede "real world" performance, chief among these being cell loss (in dead spaces, attached to glass and tubing surfaces, or sedimentation from flow), and designs with large channel height-to-width ratios (large channel widths, small channel heights) that make the systems difficult to interface with other microfluidic systems. In this paper, we present a scalable structure based on 3D wells with approximately unity height-to-width ratios (based on tubes with electrodes on the sides), which is capable of enriching yeast cell populations whilst ensuring that up to 94.3% of cells processed through the device can be collected in tubes beyond the output.

  4. Enriched glucose and dextrin mannitol-based media modulates fibroblast behavior on bacterial cellulose membranes.

    Science.gov (United States)

    Stumpf, Taisa R; Pértile, Renata A N; Rambo, Carlos R; Porto, Luismar M

    2013-12-01

    Bacterial cellulose (BC) produced by Gluconacetobacter hansenii is a suitable biopolymer for biomedical applications. In order to modulate the properties of BC and expand its use as substrate for tissue engineering mainly in the form of biomembranes, glucose or dextrin were added into a BC fermentation mannitol-based medium (BCGl and BCDe, respectively) under static culture conditions. SEM images showed effects on fiber density and porosity on both sides of the BC membranes. Both enriched media decreased the BET surface area, water holding capacity, and rehydration rate. Fourier transform infrared (attenuated total reflectance mode) spectroscopy (FTIR-ATR) analysis revealed no change in the chemical structure of BC. L929 fibroblast cells were seeded on all BC-based membranes and evaluated in aspects of cell adhesion, proliferation and morphology. BCG1 membranes showed the highest biological performance and hold promise for the use in tissue engineering applications.

  5. Comparison of subtypes of Listeria monocytogenes isolates from naturally contaminated watershed samples using a combination of non-selective and selective enrichment methods

    Science.gov (United States)

    Two enrichment methods for Listeria monocytogenes using Immuno Magnetic Separation were tested to determine if they selected the same subtypes of isolates. Both methods included a non-selective enrichment and one included subculture in Fraser Broth. Naturally contaminated watershed samples from the ...

  6. Ground-Based Network and Supersite Observations to Complement and Enrich EOS Research

    Science.gov (United States)

    Tsay, Si-Chee; Holben, Brent N.; Welton, Ellsworth J.

    2011-01-01

    Since 1997 NASA has been successfully launching a series of satellites - the Earth Observing System (EOS) - to intensively study, and gain a better understanding of, the Earth as an integrated system. Space-borne remote sensing observations, however, are often plagued by contamination of surface signatures. Thus, ground-based in-situ and remote-sensing measurements, where signals come directly from atmospheric constituents, the sun, and/or the Earth-atmosphere interactions, provide additional information content for comparisons that confirm quantitatively the usefulness of the integrated surface, aircraft, and satellite datasets. Through numerous participations, particularly but not limited to the EOS remote-sensing/retrieval and validation projects over the years, NASA/GSFC has developed and continuously refined ground-based networks and mobile observatories that proved to be vital in providing high temporal measurements, which complement and enrich the satellite observations. These are: the AERO NET (AErosol RObotic NETwork) a federation of ground-based globally distributed network of spectral sun-sky photometers; the MPLNET (Micro-Pulse Lidar NETwork, a similarly organized network of micro-pulse lidar systems measuring aerosol and cloud vertical structure continuously; and the SMART-COMMIT (Surface-sensing Measurements for Atmospheric Radiative Transfer - Chemical, Optical & Microphysical Measurements of In-situ Troposphere, mobile observatories, a suite of spectral radiometers and in-situ probes acquiring supersite measurements. Most MPLNET sites are collocated with those of AERONET, and both networks always support the deployment of SMART-COMMIT worldwide. These data products follow the data structure of EOS conventions: Level-0, instrument archived raw data; Level-1 (or 1.5), real-time data with no (or limited) quality assurance; Level-2, not real high temporal and spectral resolutions. In this talk, we will present NASA/GSFC groundbased facilities, serving

  7. Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

    Directory of Open Access Journals (Sweden)

    Cohen Nadine

    2009-03-01

    Full Text Available Abstract Background The monogenic disease osteogenesis imperfecta (OI is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI. Results We have improved methods for enriching regions of identity-by-descent (IBD shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis. Conclusion Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing.

  8. Vital pulp therapy using calcium-enriched mixture: An evidence-based review

    Directory of Open Access Journals (Sweden)

    Saeed Asgary

    2013-01-01

    Full Text Available Worldwide, casecontrol studies have revealed that the treatment outcomes of root canal therapy (RCT are generally favorable; however, the overall epidemiological success rate of RCT in the general population is relatively low. On the other hand, vitality of dental pulp is a key factor in the long-term prognosis of permanent teeth; in recent years, vital pulp therapy (VPT has received significant consideration as it has been revealed that the inflamed pulp has the potential to heal. In this review article, the current best evidence with regard to VPT using calcium-enriched mixture (CEM cement in human permanent/primary teeth is discussed. A strategy based on a search using keywords for CEM cement as well as VPT was applied.

  9. A design pattern for event-based processing of security-enriched SOAP messages

    DEFF Research Database (Denmark)

    Gruschka, Nils; Jensen, Meiko; Lo Iacono, Luigi

    2010-01-01

    For Web Services in Cloud Computing contexts, the efficient processing of XML documents is a major topic of interest. Especially for WS-Security-enriched messages, processing performance nowadays tends to become a major issue. Streaming XML processing approaches lead to valuable optimization due...... to lower resource consumption, but their adoption requires major conceptional changes in the processing application. In this paper, we present a pattern for architectural concepts that employ the SAX-based streaming processing approach. Its major benefit - apart from providing the performance advantage...... - consists in a convenient, modular architecture that can easily be extended with new modules and new types of events without modification of existing modules. © 2010 IEEE....

  10. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain.

    Science.gov (United States)

    Zhang, Chengqian; Ye, Zilu; Xue, Peng; Shu, Qingbo; Zhou, Yue; Ji, Yanlong; Fu, Ying; Wang, Jifeng; Yang, Fuquan

    2016-09-01

    N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins.

  11. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    Science.gov (United States)

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.

  12. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

    Science.gov (United States)

    McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  13. Methods of staining and visualization of sphingolipid enriched and non-enriched plasma membrane regions of Arabidopsis thaliana with fluorescent dyes and lipid analogues

    Directory of Open Access Journals (Sweden)

    Blachutzik Jörg O

    2012-08-01

    Full Text Available Abstract Background Sterols and Sphingolipids form lipid clusters in the plasma membranes of cell types throughout the animal and plant kingdoms. These lipid domains provide a medium for protein signaling complexes at the plasma membrane and are also observed to be principal regions of membrane contact at the inception of infection. We visualized different specific fluorescent lipophilic stains of the both sphingolipid enriched and non-sphingolipid enriched regions in the plasma membranes of live protoplasts of Arabidopsis thaliana. Results Lipid staining protocols for several fluorescent lipid analogues in plants are presented. The most emphasis was placed on successful protocols for the single and dual staining of sphingolipid enriched regions and exclusion of sphingolipid enriched regions on the plasma membrane of Arabidopsis thaliana protoplasts. A secondary focus was placed to ensure that these staining protocols presented still maintain cell viability. Furthermore, the protocols were successfully tested with the spectrally sensitive dye Laurdan. Conclusion Almost all existing staining procedures of the plasma membrane with fluorescent lipid analogues are specified for animal cells and tissues. In order to develop lipid staining protocols for plants, procedures were established with critical steps for the plasma membrane staining of Arabidopsis leaf tissue and protoplasts. The success of the plasma membrane staining protocols was additionally verified by measurements of lipid dynamics by the fluorescence recovery after photobleaching technique and by the observation of new phenomena such as time dependent lipid polarization events in living protoplasts, for which a putative physiological relevance is suggested.

  14. An automatic method for the enrichment of DICOM metadata using biomedical ontologies.

    Science.gov (United States)

    Perez, Wilson; Tello, Andres; Saquicela, Victor; Vidal, Maria-Esther; La Cruz, Alexandra

    2015-01-01

    This work is a novel contribution for enriching medical images using semantic annotations with a strategy for unifying different ontologies and instances of DICOM medical files. We present the L-MOM library (Library for Mapping of Ontological Metadata) as a tool for making an automatic mapping between instances of DICOM medical files and different medical ontologies (e.g., FMA, RadLex, MeSH). The main contributions are: i) the domain independent L-MOM library which is able to integrate DICOM metadata with ontologies from different domains; ii) a strategy to automatically annotate DICOM data with universally accepted medical ontologies, and provide values of similarity between ontologies and DICOM metadata; and iii) a framework to traverse ontological concepts that characterized clinical studies of patients registered in the framework catalog.

  15. BIM-based Modeling and Data Enrichment of Classical Architectural Buildings

    Directory of Open Access Journals (Sweden)

    Fabrizio Ivan Apollonio

    2012-12-01

    Full Text Available EnIn this paper we presented a BIM-based approach for the documentation of Architectural Heritage. Knowledge of classical architecture is first extracted from the treatises for parametric modeling in object level. Then we established a profile library based on semantic studies to sweep out different objects. Variants grow out from the parametric models by editing or regrouping parameters based on grammars. Multiple data including material, structure and real-life state are enriched with respect to different research motivations. The BIM models are expected to ease the modeling process and provide comprehensive data shared among different platforms for further simulations.ItIn questo articolo è presentata una procedura definita nell'ambito dei sistemi BIM con l'obiettivo di documentare il Patrimonio Architettonico. I dati conoscitivi relativi all'architettura classica sono, in una prima fase, ottenuti dai trattati al fine di modellare in maniera parametrica a livello di oggetti. Successivamente è stata definita una libreria di profili, basata su principi semantici, dalla quale è possibile ottenere oggetti differenti. Dati di natura differente, relativi ad esempio ai materiali, alle strutture, allo stato di fatto, sono implementati in funzione delle differenti esigenze. I modelli BIM hanno la potenzialità di facilitare le procedure di modellazione e di fornire informazioni e dati completi che possono essere condivisi tra piattaforme differenti per ulteriori simulazioni ed analisi.

  16. Gene-based analysis of regionally enriched cortical genes in GWAS data sets of cognitive traits and psychiatric disorders.

    Directory of Open Access Journals (Sweden)

    Kari M Ersland

    Full Text Available BACKGROUND: Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in three different cortical areas (frontomedial, temporal and occipital cortices of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the regionally enriched cortical genes to mine a genome-wide association study (GWAS of the Norwegian Cognitive NeuroGenetics (NCNG sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ (n = 3 samples and bipolar affective disorder (BP (n = 3 samples, to which cognitive impairment is linked. PRINCIPAL FINDINGS: At the single gene level, the temporal cortex enriched gene RAR-related orphan receptor B (RORB showed the strongest overall association, namely to a test of verbal intelligence (Vocabulary, P = 7.7E-04. We also applied gene set enrichment analysis (GSEA to test the candidate genes, as gene sets, for enrichment of association signal in the NCNG GWAS and in GWASs of BP and of SCZ. We found that genes differentially expressed in the temporal cortex showed a significant enrichment of association signal in a test measure of non-verbal intelligence (Reasoning in the NCNG sample. CONCLUSION: Our gene-based approach suggests that RORB could be involved in verbal intelligence differences, while the genes enriched in the temporal cortex might be important to intellectual functions as measured by a test of reasoning in the healthy population. These findings warrant further replication in independent samples on cognitive traits.

  17. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

    Directory of Open Access Journals (Sweden)

    Maher Christopher A

    2010-07-01

    Full Text Available Abstract Background Protein-DNA interaction constitutes a basic mechanism for the genetic regulation of target gene expression. Deciphering this mechanism has been a daunting task due to the difficulty in characterizing protein-bound DNA on a large scale. A powerful technique has recently emerged that couples chromatin immunoprecipitation (ChIP with next-generation sequencing, (ChIP-Seq. This technique provides a direct survey of the cistrom of transcription factors and other chromatin-associated proteins. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed to analyze the massive amount of data generated by this method. Results Here we introduce HPeak, a Hidden Markov model (HMM-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions. In contrast to the majority of available ChIP-Seq analysis software packages, HPeak is a model-based approach allowing for rigorous statistical inference. This approach enables HPeak to accurately infer genomic regions enriched with sequence reads by assuming realistic probability distributions, in conjunction with a novel weighting scheme on the sequencing read coverage. Conclusions Using biologically relevant data collections, we found that HPeak showed a higher prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative to the control sequences when compared to other currently available ChIP-Seq analysis approaches. Additionally, in comparison to the ChIP-chip assay, ChIP-Seq provides higher resolution along with improved sensitivity and specificity of binding site detection. Additional file and the HPeak program are freely available at http://www.sph.umich.edu/csg/qin/HPeak.

  18. Development of particle induced gamma-ray emission methods for nondestructive determination of isotopic composition of boron and its total concentration in natural and enriched samples.

    Science.gov (United States)

    Chhillar, Sumit; Acharya, Raghunath; Sodaye, Suparna; Pujari, Pradeep K

    2014-11-18

    We report simple particle induced gamma-ray emission (PIGE) methods using a 4 MeV proton beam for simultaneous and nondestructive determination of the isotopic composition of boron ((10)B/(11)B atom ratio) and total boron concentrations in various solid samples with natural isotopic composition and enriched with (10)B. It involves measurement of prompt gamma-rays at 429, 718, and 2125 keV from (10)B(p,αγ)(7)Be, (10)B(p, p'γ)(10)B, and (11)B(p, p'γ)(11)B reactions, respectively. The isotopic composition of boron in natural and enriched samples was determined by comparing peak area ratios corresponding to (10)B and (11)B of samples to natural boric acid standard. An in situ current normalized PIGE method, using F or Al, was standardized for total B concentration determination. The methods were validated by analyzing stoichiometric boron compounds and applied to samples such as boron carbide, boric acid, carborane, and borosilicate glass. Isotopic compositions of boron in the range of 0.247-2.0 corresponding to (10)B in the range of 19.8-67.0 atom % and total B concentrations in the range of 5-78 wt % were determined. It has been demonstrated that PIGE offers a simple and alternate method for total boron as well as isotopic composition determination in boron based solid samples, including neutron absorbers that are important in nuclear technology.

  19. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    Science.gov (United States)

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries.

  20. A method and software framework for enriching private biomedical sources with data from public online repositories.

    Science.gov (United States)

    Anguita, Alberto; García-Remesal, Miguel; Graf, Norbert; Maojo, Victor

    2016-04-01

    Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI).

  1. Feasibility study of an alkaline-based chemical treatment for the purification of polyhydroxybutyrate produced by a mixed enriched culture

    NARCIS (Netherlands)

    Jiang, Y.; Mikova, G.; Kleerebezem, R.; Van der Wielen, L.A.M.; Cuellar Soares, M.C.

    2015-01-01

    This study focused on investigating the feasibility of purifying polyhydroxybutyrate (PHB) from mixed culture biomass by alkaline-based chemical treatment. The PHB-containing biomass was enriched on acetate under non-sterile conditions. Alkaline treatment (0.2 M NaOH) together with surfactant SDS (0

  2. Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media.

    Science.gov (United States)

    Wang, Hua; Gill, Vikas S; Cheng, Chorng-Ming; Gonzalez-Escalona, Narjol; Irvin, Kari A; Zheng, Jie; Bell, Rebecca L; Jacobson, Andrew P; Hammack, Thomas S

    2015-04-01

    Foodborne outbreaks, involving pine nuts and peanut butter, illustrate the need to rapidly detect Salmonella in low moisture foods. However, the current Bacteriological Analytical Manual (BAM) culture method for Salmonella, using lactose broth (LB) as a pre enrichment medium, has not reliably supported real-time quantitative PCR (qPCR) assays for certain foods. We evaluated two qPCR assays in LB and four other pre enrichment media: buffered peptone water (BPW), modified BPW (mBPW), Universal Pre enrichment broth (UPB), and BAX(®) MP media to detect Salmonella in naturally-contaminated pine nuts (2011 outbreak). A four-way comparison among culture method, Pathatrix(®) Auto, VIDAS(®) Easy SLM, and qPCR was conducted. Automated DNA extraction techniques were compared with manual extraction methods (boiling or InstaGene™). There were no significant differences (P > 0.05) among the five pre enrichment media for pine nuts using the culture method. While both qPCR assays produced significantly (P ≤ 0.05) higher false negatives in 24 h pre enriched LB than in the other four media, they were as sensitive as the culture method in BPW, mBPW, UPB, and BAX media. The VIDAS Easy and qPCR were equivalent; Pathatrix was the least effective method. The Automatic PrepSEQ™ DNA extraction, using 1000 μL of pre enrichment, was as effective as manual extraction methods.

  3. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    Science.gov (United States)

    Kim, Hanna

    2016-04-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at increasing female students' interest in science and science-related careers. This study examined the effectiveness of InSTEP on 123 female students' pre-assessment and post-assessment changes in attitudes toward science and content knowledge of selected science concepts. An attitude survey, a science content test with multiple-choice questions, written assignments, and interviews to collect data were all used to measure students' attitudes and content knowledge. A within-group, repeated measure design was conducted, and the results indicated that at the post-intervention level, InSTEP increased the participants' positive attitudes toward science, science-related careers, and content knowledge of selected science concepts.

  4. Carcass enrichment detects Salmonella from broiler carcasses found to be negative by other sampling methods

    Science.gov (United States)

    The most frequently used methods to recover Salmonella from processed broiler chicken carcasses involve carcass rinsing or neck skin maceration. These methods are nondestructive and practical, but have limited sensitivity. The standard carcass rinse method uses only 7.5% of the residual rinsate an...

  5. Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE.

    Directory of Open Access Journals (Sweden)

    Sara C Novais

    Full Text Available Enchytraeus albidus (Oligochaeta is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1 development of suppressive subtractive hybridization (SSH libraries enriched for differentially expressed genes after metal and pesticide exposures; 2 sequencing and characterization of all generated cDNA inserts; 3 development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs. From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value ≤ 10(-5 and 37% had at least one Gene Ontology (GO term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/ was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies.

  6. Enrichment of putative human epidermal stem cells based on cell size and collagen type IV adhesiveness

    Institute of Scientific and Technical Information of China (English)

    Juxue Li; Enkui Duan; Chenglin Miao; Weixiang Guo; Liwei Jia; Jiaxi Zhou; Baohua Ma; Sha Peng; Shuang Liu; Yujing Cao

    2008-01-01

    The enrichment and identification of human epidermal stem cells (EpSCs) are of paramount importance for both basic research and clinical application. Although several approaches for the enrichment of EpSCs have been established, enriching a pure population of viable EpSCs is still a challenging task. An improved approach is worth developing to enhance the purity and viability of EpSCs. Here we report that cell size combined with collagen type IV adhesiveness can be used in an improved approach to enrich pure and viable human EpSCs. We separated the rapidly adherent keratinocytes into three populations that range in size from 5-7 μm (population A), to 7-9 μm (population B), to >9 μm (population C) in diameter, and found that human putative EpSCs could be further enriched in population A with the smallest size. Among the three populations, population A displayed the highest density of βl-integrin receptor, contained the highest percentage of cells in G0/G1 phase, showed the highest nucleus to cytoplasm ratio, and possessed the highest colony formation efficiency (CFE). When injected into murine blastocysts, these cells participated in multi-tissue formation. More significantly, compared with a previous approach that sorted putative EpSCs according to pl-integrin antibody staining, the viability of the EpSCs enriched by the improved approach was significantly enhanced. Our results provide a putative strategy for the enrichment of human EpSCs, and encourage further study into the role of cell size in stem cell biology.

  7. Material Base of in vivo Invigorating Qi and Enriching Blood of Bazhen Decoction by HPLC-ESI-MS

    Institute of Scientific and Technical Information of China (English)

    LI Wen-lan; BAI Jing; SUN Zhi; DU Juan; JI Yu-bin

    2012-01-01

    Objective To identify the in vivo metabolized chemical constituents in Bazhen Decoction(BZD)and to study the relationship between Siwu Decoction(SWD)and Sijunzi Decoction(SJZD)with BZD.Methods Analysis and comparison were carried out by HPLC-ESI-MS.Serum samples after ig administration of preparations such as SWD,SJZD,and BZD,with different ingredients were collected for analysis.Results Twenty-two components were detected after ig administration of BZD,and six of them were metabolites and others were original form of the components contained in BZD.The prototype constituents were atractylenolide Ⅰ,5-hydroxymethyl-furoic acid(5-HMFA),oxypaeoniflorin,atractylenolide Ⅲ,albiflorin,paeoniflorin,liquiritin,ferulic acid,ligustilide,and ginsenosides Rg1 and Rb1.The metabolized constituents were paeonimetabolin Ⅰ,glycyrrhetic acid monoglucuronide,glycyrrhetinic acid,and ginsenosides Rh1 and Rd.Conclusion The results also show that 5-HMFA,oxypaeoniflorin,albiflorin,paeoniflorin,ferulic acid,and ligustilide are common components absorbed into blood existing in both BZD and SWD,which are material base of enriching blood;Atractylenolide Ⅰ,atractylenolide Ⅲ,and liquiritin are common ingredients absorbed into blood existing in both BZD and SJZD,and they are material base of invigorating Qi.The results provide basic data for the further studies on the effective components,the effecting mechanism,and the quality control of BZD.

  8. A modified method by differential adhesion for enrichment of bladder cancer stem cells

    Directory of Open Access Journals (Sweden)

    Yong-tong Zhu

    Full Text Available ABSTRACT Purpose: In a previous study the vaccine was effective against bladder cancer in a mouse model. However, a small portion of tumors regrew because the vaccine could not eliminate bladder cancer stem cells (CSCs. In this study, we showed a modified method for the isolation of bladder CSCs using a combination of differential adhesion method and serum-free culture medium (SFM method. Materials and Methods: Trypsin-resistant cells and trypsin-sensitive cells were isolated from MB49, EJ and 5637 cells by a combination of differential adhesion method and SFM method. The CSCs characterizations of trypsin-resistant cells were verified by the flow cytometry, the western blotting, the quantitative polymerase chain reaction, the resistance to chemotherapy assay, the transwell assay, and the tumor xenograft formation assay. Results: Trypsin-resistant cells were isolated and identified in CSCs characters, with high expression of CSCs markers, higher resistance to chemotherapy, greater migration in vitro, and stronger tumorigenicity in vivo. Conclusion: Trypsin-resistant cells displayed specific CSCs properties. Our study showed trypsin-resistant cells were isolated successfully with a modified method using a combination of differential adhesion method and SFM method.

  9. Circulating tumour cells: the evolving concept and the inadequacy of their enrichment by EpCAM-based methodology for basic and clinical cancer research.

    Science.gov (United States)

    Grover, P K; Cummins, A G; Price, T J; Roberts-Thomson, I C; Hardingham, J E

    2014-08-01

    Increasing evidence suggests that circulating tumour cells (CTCs) are responsible for metastatic relapse and this has fuelled interest in their detection and quantification. Although numerous methods have been developed for the enrichment and detection of CTCs, none has yet reached the 'gold' standard. Since epithelial cell adhesion molecule (EpCAM)-based enrichment of CTCs offers several advantages, it is one of the most commonly used and has been adapted for high-throughput technology. However, emerging evidence suggests that CTCs are highly heterogeneous: they consist of epithelial tumour cells, epithelial-to-mesenchymal transition (EMT) cells, hybrid (epithelial/EMT(+)) tumour cells, irreversible EMT(+) tumour cells, and circulating tumour stem cells (CTSCs). The EpCAM-based approach does not detect CTCs expressing low levels of EpCAM and non-epithelial phenotypes such as CTSCs and those that have undergone EMT and no longer express EpCAM. Thus, the approach may lead to underestimation of the significance of CTCs, in general, and CTSCs and EMT(+) tumour cells, in particular, in cancer dissemination. Here, we provide a critical review of research literature on the evolving concept of CTCs and the inadequacy of their enrichment by EpCAM-based technology for basic and clinical cancer research. The review also outlines future perspectives in the field.

  10. Qualitative Methods Can Enrich Quantitative Research on Occupational Stress: An Example from One Occupational Group

    Science.gov (United States)

    Schonfeld, Irvin Sam; Farrell, Edwin

    2010-01-01

    The chapter examines the ways in which qualitative and quantitative methods support each other in research on occupational stress. Qualitative methods include eliciting from workers unconstrained descriptions of work experiences, careful first-hand observations of the workplace, and participant-observers describing "from the inside" a…

  11. Utilizing ion-pairing hydrophilic interaction chromatography solid phase extraction for efficient glycopeptide enrichment in glycoproteomics

    DEFF Research Database (Denmark)

    Mysling, Simon; Palmisano, Giuseppe; Højrup, Peter;

    2010-01-01

    Glycopeptide enrichment is a prerequisite to enable structural characterization of protein glycosylation in glycoproteomics. Here we present an improved method for glycopeptide enrichment based on zwitter-ionic hydrophilic interaction chromatography solid phase extraction (ZIC-HILIC SPE...

  12. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    Directory of Open Access Journals (Sweden)

    Orre Lotta

    2010-02-01

    Full Text Available Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS from six lung cancer cases (two adenocarcinomas, two squamous-cell carcinomas, two large-cell carcinomas and from two normal lung samples. The cell content of resulting ETS was evaluated with immunocytological stainings and compared with the histologic pattern of the original specimens. By means of a quantitative mass spectrometry-based method we evaluated the reproducibility of the sample preparation protocol and we assessed the proteome coverage by comparing lysates from ETS samples with the direct lysate of corresponding fresh-frozen samples. Results Cytological analyses on cytospin specimens showed that the percentage of tumoral cells in the ETS samples ranged from 20% to 70%. In the normal lung samples the percentage of epithelial cells was less then 10%. The reproducibility of the sample preparation protocol was very good, with coefficient of variation at the peptide level and at the protein level of 13% and 7%, respectively. Proteomics analysis led to the identification of a significantly higher number of proteins in the ETS samples than in the FF samples (244 vs 109, respectively. Albumin and hemoglobin were among the top 5 most abundant proteins identified in the FF samples, showing a high contamination with blood and plasma proteins, whereas ubiquitin and the mitochondrial ATP synthase 5A1 where among the top 5 most abundant proteins in the ETS samples. Conclusion The method is feasible and reproducible. We could obtain a fair enrichment of cells but the major benefit of the method

  13. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    OpenAIRE

    Orre Lotta; Bergman Per; Elmberger Göran; Pernemalm Maria; De Petris Luigi; Lewensohn Rolf; Lehtiö Janne

    2010-01-01

    Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS) from six lung cancer cases (two ade...

  14. Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis.

    Science.gov (United States)

    Zhang, Ying; Peng, Ye; Bin, Zhichao; Wang, Huijie; Lu, Haojie

    2016-08-31

    N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CVN-glycome in human serum, in which a total of 31 N-glycan masses were identified.

  15. Method Development to Increase Protein Enrichment During Dry Fractionation of Starch-Rich Legumes

    NARCIS (Netherlands)

    Pelgrom, P.J.M.; Boom, R.M.; Schutyser, M.A.I.

    2015-01-01

    A facile method was developed to establish milling settings that optimally separate starch granules from protein bodies and cell wall fibres for starch-rich legumes. Optimal separation was obtained for pea, bean, lentil and chickpea when the particle size distribution curve of flour and isolated sta

  16. Methods in Logic Based Control

    DEFF Research Database (Denmark)

    Christensen, Georg Kronborg

    1999-01-01

    Desing and theory of Logic Based Control systems.Boolean Algebra, Karnaugh Map, Quine McClusky's algorithm. Sequential control design. Logic Based Control Method, Cascade Control Method. Implementation techniques: relay, pneumatic, TTL/CMOS,PAL and PLC- and Soft_PLC implementation. PLC-design met......Desing and theory of Logic Based Control systems.Boolean Algebra, Karnaugh Map, Quine McClusky's algorithm. Sequential control design. Logic Based Control Method, Cascade Control Method. Implementation techniques: relay, pneumatic, TTL/CMOS,PAL and PLC- and Soft_PLC implementation. PLC...

  17. twzPEA: A Topology and Working Zone Based Pathway Enrichment Analysis Framework

    Science.gov (United States)

    Sensitive detection of involvement and adaptation of key signaling, regulatory, and metabolic pathways holds the key to deciphering molecular mechanisms such as those in the biomass-to-biofuel conversion process in yeast. Typical gene set enrichment analyses often do not use topology information in...

  18. Simple method for rapid determination of {sup 235}U in depleted or low enrichment uranium samples

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez-Becerril, J.; Fernandez-Valverde, S. [Instituto Nacional de Investigaciones Nucleares, Mexico City (Mexico)

    1995-05-01

    The aim of this study is to report the possibility of using {sup 104}Tc for the rapid quantification of {sup 235}U using both {gamma}-rays 43.53 and 74.67 keV, to choose these standards for a more accurate method. A further objective is to make a comparison with the results obtained from the relation {sup 131}Te/{sup 239}U. (author).

  19. Enrichment Method for the Isolation of Bioactive Actinomycetes From Mangrove Sediments of Andaman Islands, India

    Directory of Open Access Journals (Sweden)

    Baskaran, R.

    2011-01-01

    Full Text Available Various pre-treatment methods and three different media were employed for the isolation of bioactive actinomycetes from mangrove sediments of Andaman and Nicobar Islands, India. Sediments from four different sites of mangrove forest were collected and pre-treated by dry heat method, and the media were supplemented with cycloheximide 80 µg/mL and nalidixic acid 75 µg/mL. The mean actinomycetes population density in sediment samples were recorded as 22 CFU-10^-6/gm in KUA medium followed by 12 CFU-10^-6/gm in AIA medium and 8 CFU-10^-6/gm in SCA medium. A total of 42 actinomycetes were isolated, and all the isolates were evaluated for their antibacterial activity against pathogenic bacteria on two different media. Among 42 isolates tested, 22 species were found to be antibacterial metabolite producer against test bacteria namely, Staphylococcus aureus, Bacillus subtilis, Salmonella typhi and Klebsiella pneumoniae. Particularly, the actinomycete strains such as A101, A102, A107, A116, A121, A125, A130, F101, F102, F104, F106, De101 and De102 significantly inhibited the growth of all bacteria which were tested. Of these strains, A107 was identified as Streptomyces spp. This strain had the maximum activity against all used pathogens on both medium. Hence, the isolation, characterization and studies of secondary metabolites of actinomycetes from mangrove sediments in Andaman and Nicobar Island could be a pathway for discovery of antibiotics from marine actinomycetes.

  20. Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

    OpenAIRE

    Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

    2009-01-01

    In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) dat...

  1. A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.

    Science.gov (United States)

    Johansen, Eric; Schilling, Birgit; Lerch, Michael; Niles, Richard K; Liu, Haichuan; Li, Bensheng; Allen, Simon; Hall, Steven C; Witkowska, H Ewa; Regnier, Fred E; Gibson, Bradford W; Fisher, Susan J; Drake, Penelope M

    2009-10-01

    Glycans are an important class of post-translational modifications. Typically found on secreted and extracellular molecules, glycan structures signal the internal status of the cell. Glycans on tumor cells tend to have abundant sialic acid and fucose moieties. We propose that these cancer-associated glycan variants be exploited for biomarker development aimed at diagnosing early-stage disease. Accordingly, we developed a mass spectrometry-based workflow that incorporates chromatography on affinity matrices formed from lectins, proteins that bind specific glycan structures. The lectins Sambucus nigra (SNA) and Aleuria aurantia (AAL), which bind sialic acid and fucose, respectively, were covalently coupled to POROS beads (Applied Biosystems) and packed into PEEK columns for high pressure liquid chromatography (HPLC). Briefly, plasma was depleted of the fourteen most abundant proteins using a multiple affinity removal system (MARS-14; Agilent). Depleted plasma was trypsin-digested and separated into flow-through and bound fractions by SNA or AAL HPLC. The fractions were treated with PNGaseF to remove N-linked glycans, and analyzed by LC-MS/MS on a QStar Elite. Data were analyzed using Mascot software. The experimental design included positive controls-fucosylated and sialylated human lactoferrin glycopeptides-and negative controls-high mannose glycopeptides from Saccharomyces cerevisiae-that were used to monitor the specificity of lectin capture. Key features of this workflow include the reproducibility derived from the HPLC format, the positive identification of the captured and PNGaseF-treated glycopeptides from their deamidated Asn-Xxx-Ser/Thr motifs, and quality assessment using glycoprotein standards. Protocol optimization also included determining the appropriate ratio of starting material to column capacity, identifying the most efficient capture and elution buffers, and monitoring the PNGaseF-treatment to ensure full deglycosylation. Future directions include

  2. A method for enriching myeloid (CFU-GM) and erythroid (BFU-E) progenitor cells from human cord blood by accessory cell depletion.

    Science.gov (United States)

    Dowton, L A; Ma, D D

    1992-10-01

    Human cord blood provides a convenient alternative to bone marrow as a rich source of hemopoietic progenitor cells. This study reports a simple means for enriching a cord blood progenitor cell population by accessory cell depletion. Two methods of monocyte depletion were tested. A Cytodex 3 microcarrier system using collagen coated dextran beads was compared to the more commonly used method of plastic plate adhesion. The method of plastic plate adhesion gave a significantly higher cell recovery. T cell depletion using a recently characterized rat monoclonal antibody which fixes human complement was also investigated. A combined method of monocyte depletion by plate adhesion and T cell depletion resulted in the removal of > 96% of monocytes and > 98% of T cells. This led to a significant enrichment of myeloid (CFU-GM) and erythroid (BFU-E) colony growth. Such enriched progenitor cell populations provide a useful starting population for any study on hemopoiesis.

  3. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

    Science.gov (United States)

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-01

    The microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern. PMID:28071710

  4. Entropy-based benchmarking methods

    OpenAIRE

    2012-01-01

    We argue that benchmarking sign-volatile series should be based on the principle of movement and sign preservation, which states that a bench-marked series should reproduce the movement and signs in the original series. We show that the widely used variants of Denton (1971) method and the growth preservation method of Causey and Trager (1981) may violate this principle, while its requirements are explicitly taken into account in the pro-posed entropy-based benchmarking methods. Our illustrati...

  5. Activity based costing (ABC Method

    Directory of Open Access Journals (Sweden)

    Prof. Ph.D. Saveta Tudorache

    2008-05-01

    Full Text Available In the present paper the need and advantages are presented of using the Activity BasedCosting method, need arising from the need of solving the information pertinence issue. This issue has occurreddue to the limitation of classic methods in this field, limitation also reflected by the disadvantages ofsuch classic methods in establishing complete costs.

  6. Direct PCR - A rapid method for multiplexed detection of different serotypes of Salmonella in enriched pork meat samples.

    Science.gov (United States)

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Quyen, Than Linh; Engelsmann, Pia; Wolff, Anders; Bang, Dang Duong

    2017-04-01

    Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition. Four pairs of primers including a pair of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved by the method. Application of the multiplex Direct PCR to detect Salmonella in pork meat at slaughter reduces the time of detection from 5 to 6 days by conventional bacterial culture and serotyping methods to 14 h (including 12 h enrichment time). Furthermore, the method poses a possibility of miniaturization and integration into a point-of-need Lab-on-a-chip system for rapid online pathogen detection.

  7. Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

    DEFF Research Database (Denmark)

    Ersland, Kari M; Christoforou, Andrea; Stansberg, Christine;

    2012-01-01

    the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n......Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes...... in three different cortical areas (frontomedial, temporal and occipital cortices) of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used...

  8. Validation of a novel cognitive bias task based on difference in quantity of reinforcement for assessing environmental enrichment.

    Science.gov (United States)

    Keen, Heidi A; Nelson, O Lynne; Robbins, Charles T; Evans, Marc; Shepherdson, David J; Newberry, Ruth C

    2014-05-01

    Cognitive bias tasks purport to assess affective states via responses to ambiguous stimuli. We hypothesized that a novel cognitive bias task based on positive reinforcement using quantity differences would detect changes in affect in captive grizzly bears (Ursus arctos horribilis). We trained bears (n = 8) to respond differently (nose or paw touch) to two stimuli (light or dark gray cue cards), with responses counterbalanced across bears. The two cues signaled a small or large food reward, respectively. Responses to ambiguous probe stimuli (i.e., shades of gray) intermediate to the trained stimuli were classified as either 'optimistic,' appropriate for the larger reward, or 'pessimistic,' appropriate for the smaller reward. In Experiment 1, we explored the contrast in reward size necessary to detect a change in response across probe stimuli (large reward, 3 or 6 apple slices: small reward, 1 slice). We observed a change in response across probe stimuli, with no difference in response between reward-value groups, indicating that a contrast of 3:1 apple slices was sufficient to affect responses. In Experiment 2, we investigated cognitive bias after 2.1 h of exposure to enrichment items varying in attractiveness. Results were unaffected by enrichment type or time spent interacting with enrichments, indicating that the task failed to demonstrate criterion validity for comparing mood following exposure to different enrichment items. However, greater time spent pacing prior to testing was associated with 'optimistic' judgments. The data provide some support for use of cognitive bias tasks based on quantity differences in animal welfare assessments involving captive wildlife.

  9. L-Lactate-selective microbial sensor based on flavocytochrome b2-enriched yeast cells using recombinant and nanotechnology approaches.

    Science.gov (United States)

    Karkovska, Maria; Smutok, Oleh; Stasyuk, Nataliya; Gonchar, Mykhailo

    2015-11-01

    In the recent years, nanotechnology is the most developing branch due to a wide variety of potential applications in biomedical, biotechnological and agriculture fields. The binding nanoparticles with various biological molecules makes them attractive candidates for using in sensor technologies. The particularly actual is obtaining the bionanomembranes based on biocatalytic elements with improved sensing characteristics. The aim of this investigation is to study the properties of microbial L-lactate-selective sensor based on using the recombinant Hansenula polymorpha yeast cells overproducing flavocytochrome b2 (FC b2), as well as additionally enriched by the enzyme bound with gold nanoparticles (FC b2-nAu). Although, the high permeability of the living cells to nanoparticles is being intensively studied (mostly for delivery of drugs), the idea of using both recombinant technology and nanotechnology to increase the amount of the target enzyme in the biosensing layer is really novel. The FC b2-nAu-enriched living and permeabilized yeast cells were used for construction of a bioselective membrane of microbial L-lactate-selective amperometric biosensor. Phenazine methosulphate was served as a free defusing electron transfer mediator which provides effective electron transfer from the reduced enzyme to the electrode surface. It was shown that the output to L-lactate of FC b2-nAu-enriched permeabilized yeast cells is 2.5-fold higher when compared to the control cells. The obtained results confirm that additional enrichment of the recombinant yeast cell by the enzyme bound with nanoparticles improves the analytical parameters of microbial sensor.

  10. Pruned-enriched Rosenbluth method: Simulations of θ polymers of chain length up to 1 000 000

    Science.gov (United States)

    Grassberger, Peter

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional θ polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=106. For storage reasons, this is feasable only for polymers in a finite volume. For free θ polymers in infinite volume, we present very high statistics runs with N=10 000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. 102, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the θ point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire et al. [Macromolecules 19, 452 (1986) and later work].

  11. Efficient enrichment of hepatic cancer stem-like cells from a primary rat HCC model via a density gradient centrifugation-centered method.

    Directory of Open Access Journals (Sweden)

    Wei-hui Liu

    Full Text Available BACKGROUND: Because few definitive markers are available for hepatic cancer stem cells (HCSCs, based on physical rather than immunochemical properties, we applied a novel method to enrich HCSCs. METHODOLOGY: After hepatic tumor cells (HTCs were first isolated from diethylinitrosamine-induced F344 rat HCC model using percoll discontinuous gradient centrifugation (PDGC and purified via differential trypsinization and differential attachment (DTDA, they were separated into four fractions using percoll continuous gradient centrifugation (PCGC and sequentially designated as fractions I-IV (FI-IV. Morphological characteristics, mRNA and protein levels of stem cell markers, proliferative abilities, induced differentiation, in vitro migratory capacities, in vitro chemo-resistant capacities, and in vivo malignant capacities were determined for the cells of each fraction. FINDINGS: As the density of cells increased, 22.18%, 11.62%, 4.73% and 61.47% of primary cultured HTCs were segregated in FI-FIV, respectively. The cells from FIII (density between 1.041 and 1.062 g/ml displayed a higher nuclear-cytoplasmic ratio and fewer organelles and expressed higher levels of stem cell markers (AFP, EpCAM and CD133 than cells from other fractions (P<0.01. Additionally, in vitro, the cells from FIII showed a greater capacity to self-renew, differentiate into mature HTCs, transit across membranes, close scratches, and carry resistance to chemotherapy than did cells from any other fraction; in vivo, injection of only 1×10(4 cells from FIII could generate tumors not only in subcutaneous tissue but also in the livers of nude mice. CONCLUSIONS: Through our novel method, HCSC-like cells were successfully enriched in FIII. This study will greatly contribute to two important areas of biological interest: CSC isolation and HCC therapy.

  12. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Jia [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gaffrey, Matthew J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Su, Dian [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Genentech Inc., South San Francisco, CA (United States); Liu, Tao [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Camp, David G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qian, Weijun [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-12-12

    Reversible modifications on cysteine thiols play a significant role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation, and S-glutathionylation, have been recognized for their significance in various physiological and pathological processes. Here we describe in detail a resin-assisted thiol-affinity enrichment protocol for both biochemical and proteomics applications. This protocol serves as a general approach for specific isolation of thiol-containing proteins or peptides derived from reversible redox-modified proteins. This approach utilizes thiol-affinity resins to directly capture thiol-containing proteins or peptides through a disulfide exchange reaction followed by on-resin protein digestion and on-resin multiplexed isobaric labeling to facilitate LC-MS/MS based quantitative site-specific analysis of redox modifications. The overall approach requires a much simpler workflow with increased specificity compared to the commonly used biotin switch technique. By coupling different selective reduction strategies, the resin-assisted approach provides the researcher with a useful tool capable of enriching different types of reversible modifications on protein thiols. Procedures for selective enrichment and analyses of S-nitrosylation and total reversible cysteine oxidation are presented to demonstrate the utility of this general strategy.

  13. Rapid enrichment of leucocytes and genomic DNA from blood based on bifunctional core shell magnetic nanoparticles

    Science.gov (United States)

    Xie, Xin; Nie, Xiaorong; Yu, Bingbin; Zhang, Xu

    2007-04-01

    A series of protocols are proposed to extract genomic DNA from whole blood at different scales using carboxyl-functionalized magnetic nanoparticles as solid-phase absorbents. The enrichment of leucocytes and the adsorption of genomic DNA can be achieved with the same carboxyl-functionalized magnetic nanoparticles. The DNA bound to the bead surfaces can be used directly as PCR templates. By coupling cell separation and DNA purification, the whole operation can be accomplished in a few minutes. Our simplified protocols proved to be rapid, low cost, and biologically and chemically non-hazardous, and are therefore promising for microfabrication of a DNA-preparation chip and routine laboratory use.

  14. Potential seaweed-based food ingredients to inhibit lipid oxidation in fish-oil-enriched mayonnaise

    DEFF Research Database (Denmark)

    Honold, Philipp; Jacobsen, Charlotte; Jónsdóttir, Rósa

    2016-01-01

    and their partitioning between water and octanol. Additionally, the antioxidant activity of the extracts was evaluated in a fish-oil-enriched mayonnaise. Acetone and ethanol were found to extract the highest amount of phenolic compounds and carotenoids. Water used as extraction solvent, extracted some phenolic compounds...... but also higher amount of metals and chlorophyll derivates. It was proposed that extracts with high phenolic content and low iron content, such as the acetone and ethanol extract, would have the highest potential as antioxidants in foods. This was confirmed in the storage trial, where these extracts showed...

  15. Application of an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum.

    Science.gov (United States)

    Chen, Tao; Liu, Yongling; Zou, Denglang; Chen, Chen; You, Jinmao; Zhou, Guoying; Sun, Jing; Li, Yulin

    2014-01-01

    This study presents an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum. A new solvent system composed of petroleum ether/ethyl acetate/water (4:2:1, v/v/v) was developed for the liquid-liquid extraction of the crude extract from R. tanguticum. As a result, emodin, aloe-emodin, physcion, and chrysophanol were greatly enriched in the organic layer. In addition, an efficient method was successfully established to separate and purify the above anthraquinones by high-speed counter-current chromatography and preparative HPLC. This study supplies a new alternative method for the rapid enrichment, separation, and purification of emodin, aloe-emodin, physcione, and chrysophanol.

  16. Application of Condition-Based Monitoring Techniques for Remote Monitoring of a Simulated Gas Centrifuge Enrichment Plant

    Energy Technology Data Exchange (ETDEWEB)

    Hooper, David A [ORNL; Henkel, James J [ORNL; Whitaker, Michael [ORNL

    2012-01-01

    This paper presents research into the adaptation of monitoring techniques from maintainability and reliability (M&R) engineering for remote unattended monitoring of gas centrifuge enrichment plants (GCEPs) for international safeguards. Two categories of techniques are discussed: the sequential probability ratio test (SPRT) for diagnostic monitoring, and sequential Monte Carlo (SMC or, more commonly, particle filtering ) for prognostic monitoring. Development and testing of the application of condition-based monitoring (CBM) techniques was performed on the Oak Ridge Mock Feed and Withdrawal (F&W) facility as a proof of principle. CBM techniques have been extensively developed for M&R assessment of physical processes, such as manufacturing and power plants. These techniques are normally used to locate and diagnose the effects of mechanical degradation of equipment to aid in planning of maintenance and repair cycles. In a safeguards environment, however, the goal is not to identify mechanical deterioration, but to detect and diagnose (and potentially predict) attempts to circumvent normal, declared facility operations, such as through protracted diversion of enriched material. The CBM techniques are first explained from the traditional perspective of maintenance and reliability engineering. The adaptation of CBM techniques to inspector monitoring is then discussed, focusing on the unique challenges of decision-based effects rather than equipment degradation effects. These techniques are then applied to the Oak Ridge Mock F&W facility a water-based physical simulation of a material feed and withdrawal process used at enrichment plants that is used to develop and test online monitoring techniques for fully information-driven safeguards of GCEPs. Advantages and limitations of the CBM approach to online monitoring are discussed, as well as the potential challenges of adapting CBM concepts to safeguards applications.

  17. Full waveform inversion based on scattering angle enrichment with application to real dataset

    KAUST Repository

    Wu, Zedong

    2015-08-19

    Reflected waveform inversion (RWI) provides a method to reduce the nonlinearity of the standard full waveform inversion (FWI). However, the drawback of the existing RWI methods is inability to utilize diving waves and the extra sensitivity to the migrated image. We propose a combined FWI and RWI optimization problem through dividing the velocity into the background and perturbed components. We optimize both the background and perturbed components, as independent parameters. The new objective function is quadratic with respect to the perturbed component, which will reduce the nonlinearity of the optimization problem. Solving this optimization provides a true amplitude image and utilizes the diving waves to update the velocity of the shallow parts. To insure a proper wavenumber continuation, we use an efficient scattering angle filter to direct the inversion at the early stages to direct energy corresponding to large (smooth velocity) scattering angles to the background velocity update and the small (high wavenumber) scattering angles to the perturbed velocity update. This efficient implementation of the filter is fast and requires less memory than the conventional approach based on extended images. Thus, the new FWI procedure updates the background velocity mainly along the wavepath for both diving and reflected waves in the initial stages. At the same time, it updates the perturbation with mainly reflections (filtering out the diving waves). To demonstrate the capability of this method, we apply it to a real 2D marine dataset.

  18. AMD-associated genes encoding stress-activated MAPK pathway constituents are identified by interval-based enrichment analysis.

    Directory of Open Access Journals (Sweden)

    John Paul SanGiovanni

    Full Text Available PURPOSE: To determine whether common DNA sequence variants within groups of genes encoding elements of stress-activated mitogen-activated protein kinase (MAPK signaling pathways are, in aggregate, associated with advanced AMD (AAMD. METHODS: We used meta-regression and exact testing methods to identify AAMD-associated SNPs in 1177 people with AAMD and 1024 AMD-free elderly peers from 3 large-scale genotyping projects on the molecular genetics of AMD. SNPs spanning independent AAMD-associated genomic intervals were examined with a multi-locus-testing method (INRICH for enrichment within five sets of genes encoding constituents of stress-activated MAPK signaling cascades. RESULTS: Four-of-five pathway gene sets showed enrichment with AAMD-associated SNPs; findings persisted after adjustment for multiple testing in two. Strongest enrichment signals (P = 0.006 existed in a c-Jun N-terminal kinase (JNK/MAPK cascade (Science Signaling, STKE CMP_10827. In this pathway, seven independent AAMD-associated regions were resident in 6 of 25 genes examined. These included sequence variants in: 1 three MAP kinase kinase kinases (MAP3K4, MAP3K5, MAP3K9 that phosphorylate and activate the MAP kinase kinases MAP2K4 and MAP2K7 (molecules that phosphorylate threonine and tyrosine residues within the activation loop of JNK; 2 a target of MAP2K7 (JNK3A1 that activates complexes involved in transcriptional regulation of stress related genes influencing cell proliferation, apoptosis, motility, metabolism and DNA repair; and 3 NR2C2, a transcription factor activated by JNK1A1 (a drugable molecule influencing retinal cell viability in model systems. We also observed AAMD-related sequence variants resident in genes encoding PPP3CA (a drugable molecule that inactivates MAP3K5, and two genes (TGFB2, TGFBR2 encoding factors involved in MAPK sensing of growth factors/cytokines. CONCLUSIONS: Linkage disequilibrium (LD-independent genomic enrichment analysis yielded

  19. Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti{sup 4+}-SPE enrichment for mass spectrometric analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ying [Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032 (China); Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032 (China); Peng, Ye; Bin, Zhichao [Department of Chemistry, Fudan University, Shanghai 200032 (China); Wang, Huijie [Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032 (China); Lu, Haojie, E-mail: luhaojie@fudan.edu.cn [Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032 (China); Department of Chemistry, Fudan University, Shanghai 200032 (China); Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032 (China)

    2016-08-31

    N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti{sup 4+}-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti{sup 4+}-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CV<15%) as well as high sensitivity (LOD at fmol level). At last, the proposed method was successfully applied in the profiling of N-glycome in human serum, in which a total of 31 N-glycan masses were identified. - Graphical abstract: A selective enrichment method for the N-glycome is reported. N-glycans were chemically labeled with a phosphate derivatization reagent (AMS), then the phospho-containing glycans were enriched using Ti{sup 4+}-microspheres. - Highlights: • A highly specific N-glycans purification method based on phosphate derivatization combined with Ti{sup 4+}-SPE was developed

  20. Entropy-based benchmarking methods

    NARCIS (Netherlands)

    Temurshoev, Umed

    2012-01-01

    We argue that benchmarking sign-volatile series should be based on the principle of movement and sign preservation, which states that a bench-marked series should reproduce the movement and signs in the original series. We show that the widely used variants of Denton (1971) method and the growth pre

  1. BIOTECHNOLOGY AS A USEFUL TOOL FOR NUTRITIONAL IMPROVEMENT OF CEREAL-BASED MATERIALS ENRICHED WITH POLYUNSATURATED FATTY ACIDS AND PIGMENTS

    Directory of Open Access Journals (Sweden)

    M. Čertík

    2008-09-01

    Full Text Available Cereals represent a major food supply for humanity. Although these sources are rich in proteins and carbohydrates, many of them are deficient in several essential nutrients, such as polyunsaturated fatty acids (PUFAs and carotenoid pigments. One possible approach how to enhance the content of PUFAs or carotenoids in cereal diet is based on biotechnological transformation of cereal materials by solid state fermentations. This technique is powerful tool for effective valorisation of these resources to various types of value-added bioproducts with demanded properties and functions. Selected filamentous Mucorales fungi were applied for conversion of numerous agroindustrial substrates to bioproducts enriched with PUFAs, such as gamma-linolenic acid (GLA, dihomo-gamma-linolenic acid (DGLA, arachidonic acid (AA and eicosapentaenoic acid (EPA. On the other hand, a range of yeast species utilizing agroindustrial substrates were employed for formation of carotenoids, such as β-carotene, torulene, torularhodine and astaxanthin. Such naturally prepared cereal based bioproducts enriched with either PUFAs or carotenoid pigments may be used as an inexpensive food and feed supplement. The work was supported by grant VEGA No. 1/0747/08 from the Grant Agency of Ministry of Education, Slovak Republic.

  2. New Procedure to Obtain Polyphenol-Enriched Grapes Based on the Use of Chemical Elicitors.

    Science.gov (United States)

    Flores, Gema; Del Castillo, Maria Luisa Ruiz

    2016-09-01

    The effect of the postharvest treatment of methyl jasmonate enantiomers in conjunction with ethanol on bioformation of resveratrol and quercetin glycosides in grapes was evaluated. The antioxidant activity of treated grape extracts as compared with untreated extracts was also assayed. Exogenous (-)-methyl jasmonate in combination with ethanol induced a significant increase in the levels of resveratrol (from 27 to 39 μg g(-1)), quercetin-3-O-glucoside (from 59 to 136 μg g(-1)), quercetin-3-O-galactoside (from 398 to 807 μg g(-1)) and quercetin-3-O-rutinoside (from 23 to 43 μg g(-1)). (+)-Methyl jasmonate with ethanol also resulted in increase of quercetin-3-O-glucoside and quercetin-3-O-rutinoside. However, no (+)-methyl jasmonate effect was observed for resveratrol and quercetin-3-O-galactoside. Both (-)- and (+)-methyl jasmonate treatments provided with extracts with higher antioxidant activity. From the results found in the present work postharvest treatment with (-)-methyl jasmonate in conjunction with ethanol is proposed as a mean to obtain polyphenol-enriched grape extracts with improved antioxidant properties. The procedure here developed is proposed as a mean to obtain functional grapes. Extracts obtained from grapes treated with (-)-methyl jasmonate with ethanol can be particularly useful for industry due to their high antioxidant capacity.

  3. Development of functional milk desserts enriched with resistant starch based on consumers' perception.

    Science.gov (United States)

    Ares, Florencia; Arrarte, Eloísa; De León, Tania; Ares, Gastón; Gámbaro, Adriana

    2012-10-01

    Sensory characteristics play a key role in determining consumers' acceptance of functional foods. In this context, the aim of the present work was to apply a combination of sensory and consumer methodologies to the development of chocolate milk desserts enriched with resistant starch. Chocolate milk desserts containing modified waxy maize starch were formulated with six different concentrations of two types of resistant starch (which are part of insoluble dietary fiber). The desserts were evaluated by trained assessors using Quantitative Descriptive Analysis. Moreover, consumers scored their overall liking and willingness to purchase and answered an open-ended question. Resistant starch caused significant changes in the sensory characteristics of the desserts and a significant decrease in consumers' overall liking and willingness to purchase. Consumer data was analyzed applying survival analysis on overall liking scores, considering the risk on consumers liking and willing to purchase the functional products less than their regular counterparts. The proposed methodologies proved to be useful to develop functional foods taking into account consumers' perception, which could increase their success in the market.

  4. In vitro amphotericin B susceptibility of Malassezia pachydermatis determined by the CLSI broth microdilution method and Etest using lipid-enriched media.

    Science.gov (United States)

    Álvarez-Pérez, Sergio; Blanco, José L; Peláez, Teresa; Cutuli, Maite; García, Marta E

    2014-07-01

    We determined the in vitro amphotericin B susceptibility of 60 Malassezia pachydermatis isolates by the CLSI broth microdilution method and the Etest using lipid-enriched media. All isolates were susceptible at MICs of ≤ 1 μg/ml, confirming the high activity of amphotericin B against this yeast species. Overall, the essential agreement between the tested methods was high (80% and 96.7% after 48 h and 72 h, respectively), and all discrepancies were regarded as nonsubstantial.

  5. Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method

    NARCIS (Netherlands)

    Chang, Y.J.; Stephen, J.R.; Richter, A.P.; Venosa, A.D.; Bruggemann, J.; MacNaughton, S.J.; Kowalchuk, G.A.; Haines, J.R.; Kline, E.; White, D.C.

    2000-01-01

    Aerobically grown enrichment cultures derived from hydrocarbon- contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. Both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. The bacterial species composition

  6. Rapid enrichment of rare-earth metals by carboxymethyl cellulose-based open-cellular hydrogel adsorbent from HIPEs template.

    Science.gov (United States)

    Zhu, Yongfeng; Wang, Wenbo; Zheng, Yian; Wang, Feng; Wang, Aiqin

    2016-04-20

    A series of monolithic open-cellular hydrogel adsorbents based on carboxymethylcellulose (CMC) were prepared through high internal phase emulsions (HIPEs) and used to enrich the rare-earth metals La(3+) and Ce(3+). The changes of pore structure, and the effects of pH, contact time, initial concentration on the adsorption performance were systematically studied. The results show that the as-prepared monolithic hydrogel adsorbents possess good open-cellular framework structure and have fast adsorption kinetics and high adsorption capacity for La(3+) and Ce(3+). The involved adsorption system can reach equilibrium within 30min and the maximal adsorption capacity is determined to be 384.62mg/g for La(3+) and 333.33mg/g for Ce(3+). Moreover, these porous hydrogel adsorbents show an excellent adsorptive reusability for La(3+) and Ce(3+) through five adsorption-desorption cycles. Such a pore hierarchy structure makes this monolithic open-cellular hydrogel adsorbent be an effective adsorbent for effective enrichment of La(3+) and Ce(3+) from aqueous solution.

  7. SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R;

    2015-01-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse...

  8. A method to assess relative preference for training and environmental enrichment in captive wolves (Canis lupus and Canis lupus arctos).

    Science.gov (United States)

    Dorey, Nicole R; Mehrkam, Lindsay R; Tacey, Jay

    2015-11-01

    It is currently debated as to whether or not positive reinforcement training is enriching to captive animals. Although both husbandry training and environmental enrichment (EE) have been found to benefit animal welfare in captivity, to date, no systematic investigation has compared an animal's preference for performing a trained behavior to engaging freely with a stimuli provided as EE. In the current paper, we used four captive wolves to (1) test the efficacy of a paired-stimulus preference assessment to determine preference for engaging in a trained behavior as a choice; and to (2) use a paired-stimulus preference assessment to determine whether or not individuals prefer to engage in a previously trained behavior versus a previously encountered EE stimuli. Of the four subjects tested, visual inspection of the graphs revealed that two of the subjects preferred trained behavior stimuli and two of the subjects preferred EE stimuli; only one of the wolves had a statically higher preference for an EE stimulus over a trained behavior. We believe that letting the animals choose between these two events is the first step in answering the question of whether or not is training enriching, however more research needs to be done and suggestions for future research is discussed.

  9. Universal screening test based on analysis of circulating organ-enriched microRNAs: a novel approach to diagnostic screening.

    Science.gov (United States)

    Sheinerman, Kira S; Umansky, Samuil

    2015-03-01

    Early disease detection leads to more effective and cost-efficient treatment. It is especially important for cancer and neurodegenerative diseases, because progression of these pathologies leads to significant and frequently irreversible changes in underlying pathophysiological processes. At the same time, the development of specific screening tests for detection of each of the hundreds of human pathologies in asymptomatic stage may be impractical. Here, we discuss a recently proposed concept: the development of minimally invasive Universal Screening Test (UST) based on analysis of organ-enriched microRNAs in plasma and other bodily fluids. The UST is designed to detect the presence of a pathology in particular organ systems, organs, tissues or cell types without diagnosing a specific disease. Once the pathology is detected, more specific, and if necessary invasive and expensive, tests can be administered to precisely define the nature of the disease. Here, we discuss recent studies and analyze the data supporting the UST approach.

  10. An impact of an enriched visual - verbal information remittance, regarding crawl style swimming, learning and teaching effects basing on AWF students in Cracow

    Directory of Open Access Journals (Sweden)

    Kaca M.

    2012-02-01

    Full Text Available The main aim of this study was to define an enriched impact, visual -verbal information remittance in a swimming teaching process affecting free style progression. Research was done in academic year 2007/2008 and involved 158 students from AWF in Cracow. The main exploratory method was a natural pedagogic experiment. Experimental factor was a teaching method relied on an enriched visual - verbal information remittance. Acquired research scores reveal that the apply teaching method focused on the auto observation and self-assessment of one's own skills (with the use of parallel display, improve the effectiveness of teaching and learning crawl technique process.

  11. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    Energy Technology Data Exchange (ETDEWEB)

    Babauta, Jerome T. [Washington State Univ., Pullman, WA (United States); Atci, Erhan [Washington State Univ., Pullman, WA (United States); Ha, Phuc T. [Washington State Univ., Pullman, WA (United States); Lindemann, Stephen R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ewing, Timothy [Washington State Univ., Pullman, WA (United States); Call, Douglas R. [Washington State Univ., Pullman, WA (United States); Fredrickson, James K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Beyenal, Haluk [Washington State Univ., Pullman, WA (United States)

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

  12. DISPLACEMENT BASED SEISMIC DESIGN METHODS.

    Energy Technology Data Exchange (ETDEWEB)

    HOFMAYER,C.MILLER,C.WANG,Y.COSTELLO,J.

    2003-07-15

    A research effort was undertaken to determine the need for any changes to USNRC's seismic regulatory practice to reflect the move, in the earthquake engineering community, toward using expected displacement rather than force (or stress) as the basis for assessing design adequacy. The research explored the extent to which displacement based seismic design methods, such as given in FEMA 273, could be useful for reviewing nuclear power stations. Two structures common to nuclear power plants were chosen to compare the results of the analysis models used. The first structure is a four-story frame structure with shear walls providing the primary lateral load system, referred herein as the shear wall model. The second structure is the turbine building of the Diablo Canyon nuclear power plant. The models were analyzed using both displacement based (pushover) analysis and nonlinear dynamic analysis. In addition, for the shear wall model an elastic analysis with ductility factors applied was also performed. The objectives of the work were to compare the results between the analyses, and to develop insights regarding the work that would be needed before the displacement based analysis methodology could be considered applicable to facilities licensed by the NRC. A summary of the research results, which were published in NUREGICR-6719 in July 2001, is presented in this paper.

  13. A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

    Directory of Open Access Journals (Sweden)

    Jennifer R. Mandel

    2014-02-01

    Full Text Available Premise of the study: The Compositae (Asteraceae are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

  14. Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry

    DEFF Research Database (Denmark)

    Calvano, Cosima D; Zambonin, Carlo G; Jensen, Ole Nørregaard

    2008-01-01

    glycosylation profiles are associated with certain human ailments. Glycoprotein analysis by mass spectrometry of biological samples, such as blood serum, is hampered by sample complexity and the low concentration of the potentially informative glycopeptides and -proteins. We assessed the utility of lectin...... of 63 glycosylation sites in 38 proteins were identified by both methods, demonstrating distinct differences and complementarity. Serial application of custom-made microcolumns of mixed, immobilized lectins proved efficient for recovery and analysis of glycopeptides from serum samples of breast cancer...

  15. A Walk-based Semantically Enriched Tree Kernel Over Distributed Word Representations

    DEFF Research Database (Denmark)

    Srivastava, Shashank; Hovy, Dirk

    2013-01-01

    We propose a walk-based graph kernel that generalizes the notion of tree-kernels to continuous spaces. Our proposed approach subsumes a general framework for word-similarity, and in particular, provides a flexible way to incorporate distributed representations. Using vector representations......, such an approach captures both distributional semantic similarities among words as well as the structural relations between them (encoded as the structure of the parse tree). We show an efficient formulation to compute this kernel using simple matrix multiplication operations. We present our results on three...

  16. A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).

    Science.gov (United States)

    Fragoso-Martínez, Itzi; Salazar, Gerardo A; Martínez-Gordillo, Martha; Magallón, Susana; Sánchez-Reyes, Luna; Moriarty Lemmon, Emily; Lemmon, Alan R; Sazatornil, Federico; Granados Mendoza, Carolina

    2017-02-09

    We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia's s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing "phantom" spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches.

  17. Thermal breeder fuel enrichment zoning

    Science.gov (United States)

    Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

    1992-01-01

    A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

  18. Faith-Based Organizations and Veteran Reintegration: Enriching the Web of Support.

    Science.gov (United States)

    Werber, Laura; Derose, Kathryn Pitkin; Rudnick, Mollie; Harrell, Margaret C; Naranjo, Diana

    2015-11-30

    Faith-based organizations (FBOs) are an important community-based resource for veterans as they readjust to civilian life. Through interviews with both national-level and smaller, local FBOs, the authors sought to understand better the current and potential roles for FBOs in veteran reintegration. Interviewees suggested that veterans may look to FBOs for support because they offer privacy and confidentiality, two features that may be especially critical when a potential stigma is involved. Some FBOs have also developed a reputation as safe places for veterans, providing supportive, judgment-free environments. FBOs not only help veterans with spiritual matters but address diverse areas of veteran health and wellness, including vocation, education, financial and legal stability, shelter, access to goods and services, mental health, access to health care, physical health, family, and social networks. In some cases, the support is offered to veterans directly; in other instances, the support is indirect, via training individuals to help veterans or educating the public about them. In the process of providing support, FBOs interact with varied organizations, including government entities, private nonprofits, and one another, for training, outreach, referrals, information exchange, obtaining donations, and collaboration. Yet challenges exist, including insufficient connections with chaplains working in different settings and others in the web of support, resource and capacity constraints, lack of awareness of experience with veterans, issues related to religious philosophy or orientation, and characteristics of veterans themselves. To move forward, the authors offer recommendations for policymakers, organizations that interact with FBOs, and FBOs themselves to help FBOs engage fully in the web of reintegration support.

  19. Functional soy food based on flaxseed and quinoa and enriched with iron and Vitamin B12

    Directory of Open Access Journals (Sweden)

    Ana Carolina Braga

    2015-07-01

    Full Text Available A diet rich in food derived from vegetables reduces the risk of developing chronic and degenerative diseases and provides the essential nutrients for human consumption. Besides soybean, other foods of vegetal origin have been studied and incorporated in healthy formulations, such as quinoa and linseed. Current assay comprises a sensorial analysis of a product of vegetable origin, a soy product, based on quinoa and flaxseed, considered to be functional food, for its organoleptic characteristics acceptable by a sample group of 80 individuals. Several tests were conducted to reach an adequate formulation for the product, characterized by 11.1 g of protein content, 9.6 g of dietary fiber and low levels of lipids, since it had only 1.4 g. The resulting product revealed adequate microbiological conditions when subjected to microbiological analysis (coliforms at 45ºC; coliforms at 35ºC and Staphylococcus aureus. According to scores in the sensory analysis, it may be assumed that the product was accepted by the sample group. The favorable results indicate the possibility of consumers adhering to a processed diet rich in food derived from vegetables, with functional properties, to replace animal-derived food which is rich in saturated fats and low in fiber.

  20. Development of a real-time PCR method coupled with a selective pre-enrichment step for quantification of Morganella morganii and Morganella psychrotolerans in fish products.

    Science.gov (United States)

    Podeur, Gaëtan; Dalgaard, Paw; Leroi, Francoise; Prévost, Hervé; Emborg, Jette; Martinussen, Jan; Hansen, Lars Hestbjerg; Pilet, Marie-France

    2015-06-16

    Histamine fish poisoning is common and due to toxic concentrations of histamine often produced by Gram-negative bacteria in fin-fish products with a high content of the free amino acid histidine. The genus Morganella includes two species previously reported to cause incidents of histamine fish poisoning. Morganella morganii and Morganella psychrotolerans are both strong producer of histamine. However, little is known about the occurrence and critical stages for fish contamination with these bacteria. To elucidate contamination routes of Morganella, specific real-time quantitative PCR (RTi qPCR) methods for quantification of M. morganii and M. psychrotolerans have been developed. Selective primers amplified a 110 bp region of the vasD gene for M. psychrotolerans and a 171 bp region of the galactokinase gene for M. morganii. These primer-sets showed high specificity as demonstrated by using purified DNA from 23 other histamine producing bacteria and 26 isolates with no or limited histamine production. The efficiency of the qPCR reactions on artificially contaminated fish samples were 100.8% and 96.3% respectively. The limit of quantification (LOQ) without enrichment was 4 log CFU/g. A quantitative enrichment step with a selective medium was included and improved the sensitivity of the methods to a LOQ of below 50 CFU/g in seafood. RTi qPCR methods with or without enrichment were evaluated for enumeration of Morganella species in naturally contaminated fresh fish and lightly preserved seafood from Denmark. These new methods will contribute to a better understanding of the occurrence and histamine production by Morganella species in fish products, information that is essential to reduce the unacceptably high frequency of histamine fish poisoning.

  1. A Mimic of the Tumor Microenvironment: A Simple Method for Generating Enriched Cell Populations and Investigating Intercellular Communication.

    Science.gov (United States)

    Domogauer, Jason D; de Toledo, Sonia M; Azzam, Edouard I

    2016-09-20

    Understanding the early heterotypic interactions between cancer cells and the surrounding non-cancerous stroma is important in elucidating the events leading to stromal activation and establishment of the tumor microenvironment (TME). Several in vitro and in vivo models of the TME have been developed; however, in general these models do not readily permit isolation of individual cell populations, under non-perturbing conditions, for further study. To circumvent this difficulty, we have employed an in vitro TME model using a cell growth substrate consisting of a permeable microporous membrane insert that permits simple generation of highly enriched cell populations grown intimately, yet separately, on either side of the insert's membrane for extended co-culture times. Through use of this model, we are capable of generating greatly enriched cancer-associated fibroblast (CAF) populations from normal diploid human fibroblasts following co-culture (120 hr) with highly metastatic human breast carcinoma cells, without the use of fluorescent tagging and/or cell sorting. Additionally, by modulating the pore-size of the insert, we can control for the mode of intercellular communication (e.g., gap-junction communication, secreted factors) between the two heterotypic cell populations, which permits investigation of the mechanisms underlying the development of the TME, including the role of gap-junction permeability. This model serves as a valuable tool in enhancing our understanding of the initial events leading to cancer-stroma initiation, the early evolution of the TME, and the modulating effect of the stroma on the responses of cancer cells to therapeutic agents.

  2. History and Nature of Science enriched Problem-Based Learning on the origins of biodiversity and of continents and oceans

    Directory of Open Access Journals (Sweden)

    Cristina Sousa

    2014-09-01

    Full Text Available The episode of the History of Science (HOS on the theory of continental drift proposed by Alfred Wegener has been considered an excellent example for teaching students aspects of Nature of Science (NOS and the relation of Science with social and tecnological contexts. We implemented a NOS and HOS-enriched Problem-Based Learning environment at the middle (year 7 of the Portuguese National Curriculum and secondary level (year 10 for teaching the origins of biodiversity and of continents and oceans (mobilism.  The goal of providing detailed implementation practices is to adress the lack of how to in Problem-based learning (PBL implementation in classrooms for 12 to 16 year old students and is the first practical example of implementation using this episode of HOS for teaching geological mobilism integrated with evolution. Therefore, in this study, we provide specific suggestions for supporting teachers’ classroom efforts in implementing PBL, such as scaffolding. The ill-problem presented to students, without a single correct answer, was based on the phylogeny of extant and extinct ratite birds, described by Charles Darwin and the present geographical distribution. The evaluation of the students was focused on the chain of reasoning employed, and we performed a comparisation analysis of the problem’s solution presented by the students of both classes regarding the explanation of the phylogeny of ratites based on geological mobilism. We observed an overall improvement (25-77% of the percentages of students pre- and post-instruction adequate answers; therefore our PBL strategy was efficient.

  3. Determination of Trace Amounts of Gold in Soil Sample Using Plastic Foam Enrichment-ICP-MS Method%泡塑富集ICP-MS测定土壤中痕量金

    Institute of Scientific and Technical Information of China (English)

    余波

    2008-01-01

    The aim of this study is to determine the trace amount of gold in soil sample using plastic foam enrichment-ICP-MS method. The national standard reference materials including GAu-2,GAu-10,GAu-11 and GAu-13 were used for parallel determination by ICPMS. The results showed that the method performed well in detection limit, precision and accuracy, indicating that the plastic foam enrichment-ICP-MS method could be used to determine the trace amounts of gold in soil sample.

  4. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export Licensing Authority F Appendix F to Part 110 Energy NUCLEAR... pentafluoride (UF5) solid product collectors consisting of filter, impact, or cyclone-type collectors,...

  5. On-plate glycoproteins/glycopeptides selective enrichment and purification based on surface pattern for direct MALDI MS analysis.

    Science.gov (United States)

    Zeng, Zhoufang; Wang, Yandong; Guo, Xinhua; Wang, Ling; Lu, Nan

    2013-05-21

    In this paper, a novel method has been proposed to achieve selective enrichment and purification of glycoproteins/glycopeptides on a surface patterned sample support, which consists of a hydrophobic outer layer (F-SAM) and an internal boronic acid-modified gold microspot (900 μm). Upon deposition, the sample solution is firstly concentrated in a small area by repulsion of the hydrophobic outer layer, and then the glycoproteins/glycopeptides are selectively captured through boronic acid covalently binding in the inner layer. However, the non-glycosylated proteins/peptides or high concentration salts are removed after rinsing with alkaline solution. As a result, the detection sensitivity is improved by an order of magnitude greater than when using a stainless steel MALDI plate. With surface patterned sample support, the glycoproteins/glycopeptides can be detected even under interference from the excessive existing non-glycosylated proteins/peptides (10 times more than glycoproteins/glycopeptides). Simultaneously, high-quality mass spectra can be obtained even in the presence of urea (1 M), NaCl (1 M), or NH4HCO3 (200 mM). Therefore, this novel technique may be applied to high-throughput analysis of low-abundance glycoproteins/glycopeptides in complicated proteome research.

  6. Lutein-enriched emulsion-based delivery systems: Influence of pH and temperature on physical and chemical stability.

    Science.gov (United States)

    Davidov-Pardo, Gabriel; Gumus, Cansu Ekin; McClements, David Julian

    2016-04-01

    Lutein may be utilized in foods as a natural pigment or nutraceutical ingredient to improve eye health. Nevertheless, its use is limited by its poor water-solubility and chemical instability. We evaluated the effect of storage temperature and pH on the physical and chemical stability of lutein-enriched emulsions prepared using caseinate. The emulsions (initial droplet diameter=232 nm) remained physically stable at all incubation temperatures (5-70 °C); however the chemical degradation of lutein increased with increasing temperature (activation energy=38 kJ/mol). Solution pH had a major impact on the physical stability of the emulsions, causing droplet aggregation at pH 4 and 5. Conversely, the chemical stability of lutein was largely independent of the pH, with only a slight decrease in degradation at pH 8. This work provides important information for the rational design of emulsion-based delivery systems for a lipophilic natural dye and nutraceutical.

  7. GC/MS method for determining carbon isotope enrichment and concentration of underivatized short-chain fatty acids by direct aqueous solution injection of biogas digester samples.

    Science.gov (United States)

    Mulat, Daniel Girma; Feilberg, Anders

    2015-10-01

    In anaerobic digestion of organic matter, several metabolic pathways are involved during the simultaneous production and consumption of short-chain fatty acids (SCFA) in general and acetate in particular. Understanding the role of each pathway requires both the determination of the concentration and isotope enrichment of intermediates in conjunction with isotope labeled substrates. The objective of this study was to establish a rapid and simple GC/MS method for determining the isotope enrichment of acetate and concentration of underivatized short-chain fatty acids (SCFA) in biogas digester samples by direct liquid injection of acidified aqueous samples. Sample preparation involves only acidification, centrifugation and filtration of the aqueous solution followed by direct injection of the aqueous supernatant solution onto a polar column. With the sample preparation and GC/MS conditions employed, well-resolved and sharp peaks of underivatized SCFA were obtained in a reasonably short time. Good recovery (96.6-102.3%) as well as low detection (4-7 µmol/L) and quantification limits (14-22 µmol/L) were obtained for all the 6 SCFA studied. Good linearity was achieved for both concentration and isotope enrichment measurement with regression coefficients higher than 0.9978 and 0.9996, respectively. The method has a good intra- and inter-day precision with a relative standard deviation (RSD) below 6% for determining the tracer-to-tracee ratio (TTR) of both [2-(13)C]acetate and [U-(13)C]acetate. It has also a good intra- and inter-day precision with a RSD below 6% and 5% for determining the concentration of standard solution and biogas digester samples, respectively. Acidification of biogas digester samples with oxalic acid provided the low pH required for the protonation of SCFA and thus, allows the extraction of SCFA from the complex sample matrix. Moreover, oxalic acid was the source of formic acid which was produced in the injector set at high temperature. The produced

  8. Digestion and ruminal fermentation of cocoa pod silage based ration enriched by gliricidia and calliandra leaves on goats

    Directory of Open Access Journals (Sweden)

    Puastuti W

    2015-03-01

    Full Text Available In term of availability, cacao pod is potential for ruminant feed. According to its nutrients content, cacao pod can be used as feed fiber source. Protein sources materials must be added when cacao pod was ensilaged due to low protein content of this material. The aim of this study was to investigate digestibility value and end products of rumen fermentation of goat fed grass or cacao pod based ration. Randomized block design and 20 heads of lambs (16.95±2.36 kg to evaluated 5 type of rations: R (50% grass + 50% concentrate; S (50% cacao pod silage + 50% concentrate; SG (50% cacao pod-gliricidia silage + 50% concentrate; SK (50% cacao pod-calliandra silage + 50% concentrate dan SC (50% cacao pod-mixture of gliricidia-calliandra silage + 50% concentrate. Feeding trial was conducted for over 15 weeks. Measurements were taken on feed digestibility and rumen-fermentation end-products after 3 weeks of treatments. Results shows that nutrients digestibility was different significantly among the groups of treatments (P<0.05. Digestibillity of organic matter, NDF and energy of R ration was those of higher significantly (P<0.05 than those of other groups. N-ammonia of rumen from goat feed R ration was higher (P<0.05 than other groups. Total VFA and each component were different among the groups (P<0.05, however the value was similar among the groups of cacao pod silage rations. It is concluded that cacao pod silaged based rations enriched by Gliricidia and Calliandra leaves did not produce similar digestibility value and end products of rumen fermentation with grass based ration.

  9. Family, employment, and individual resource-based antecedents of maternal work-family enrichment from infancy through middle childhood.

    Science.gov (United States)

    Zhou, Nan; Buehler, Cheryl

    2016-07-01

    This study used data from the National Institute of Child Health and Human Development (NICHD) Study of Early Child Care and Youth Development (N = 1,019) to examine family, employment, and individual antecedents of maternal work-family enrichment from infancy through middle childhood. Work-family conflict and important confounding factors were controlled. From the family domain, higher income-to-needs ratio and social support were associated with higher work-family enrichment. From the employment domain, greater job rewards, benefits of employment for children, and work commitment were associated with higher work-family enrichment. From the individual domain, higher maternal education and extroversion were associated with higher work-family enrichment. No family, employment, and individual characteristics were associated with work-family conflict across time except for partner intimacy. In general, the results supported antecedents of work-family enrichment that supply needed resources. The present study contributed to the literature by identifying antecedents of maternal work-family enrichment across early child developmental stages, which goes beyond examinations of particular life stages and a work-family conflict perspective. Implications for theory and practice are discussed. (PsycINFO Database Record

  10. A novel thiol-affinity micropipette tip method using zinc(II)-cyclen-attached agarose beads for enrichment of cysteine-containing molecules.

    Science.gov (United States)

    Kusamoto, Hiroshi; Shiba, Akio; Koretake, Norinao; Fujioka, Haruto; Hieda, Yuhzo; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2016-09-15

    Cysteine-containing biomolecules are attractive targets in the study of thiol biology. Here we introduce a novel method for the selective enrichment of thiol-containing molecules using a thiol-capture zinc(II) complex of 1,4,7,10-tetraazacyclododecane (Zn(2+)-cyclen). Recognition of N-acetylcysteine amide by Zn(2+)-cyclen has been studied by potentiometric pH titration, revealing formation of a 1:1 thiolate-bound Zn(2+)-cyclen complex with a large thiolate-affinity constant of 10(6.2)M(-1) at 25°C and I=0.10M (NaCl). The Zn(2+)-bound thiolate anion is unexpectedly stable in aqueous solution at pH 7.8 under atmospheric conditions for a few days. These findings have contributed to the development of a convenient method for separation of thiol compounds by using a micropipette tip. A 200μL micropipette tip containing 10μL of hydrophilic cross-linked agarose beads attached to Zn(2+)-cyclen moieties was prepared. All steps for thiol-affinity separation (binding, washing, and eluting) are conducted using aqueous buffers at room temperature. The entire separation protocol requires less than 15min per sample. We demonstrate practical example separations of cysteine-containing molecules. This micropipette tip method would be used preferentially as an alternative to existing tools for reliable enrichment of thiol-containing molecules.

  11. 海洋细菌增菌培养方法的研究%Cultural methods of enrichment in ocean bacteria

    Institute of Scientific and Technical Information of China (English)

    马聪; 蒋学兵; 刘敏; 张在文; 王海东; 陈昌国; 郭建巍

    2008-01-01

    Objective To explore the effecitve cultural methods of enrichment in ocean bacteria. Methods Different kinds of cultural mediums were selectd to culture seawater bacteria. Results Both alkaline peptone water( APW) and halophilic bacteria liquid had good effects to Vibrio enrichment. NO. 2 nutrient broth was effective for ordinary bacteria. Eumycete could be isolated from seawater by cultural sabouraud liquid. Conclusions APW and halophilic bacteria liquid should be selected for Vibrio enrichment, NO. 2 nutrient broth for ordinary bacteria. Moreover, cultural sabouraud liquid can be effective for fungus.%目的 探讨理想的海洋细菌增菌培养方法.方法 选择不同种类的增菌培养液对海水中细菌进行增菌培养.结果 碱性蛋白胨水与嗜盐菌增菌液对海水弧菌具有良好的增菌效果,2号营养肉汤适合海水普通细菌的增菌培养,液体沙保氏增菌液能从海水中增菌培养出真菌.结论 海水中弧菌增菌应选用碱性蛋白胨水与嗜盐菌增菌液,增菌普通细菌应选用2号营养肉汤,真菌应选用液体沙保氏增菌液.

  12. Pressure-assisted electrokinetic injection for on-line enrichment in capillary electrophoresis-mass spectrometry: a sensitive method for measurement of ten haloacetic acids in drinking water.

    Science.gov (United States)

    Zhang, Huijuan; Zhu, Jiping; Aranda-Rodriguez, Rocio; Feng, Yong-Lai

    2011-11-07

    Haloacetic acids (HAAs) are by-products of the chlorination of drinking water containing natural organic matter and bromide. A simple and sensitive method has been developed for determination of ten HAAs in drinking water. The pressure-assisted electrokinetic injection (PAEKI), an on-line enrichment technique, was employed to introduce the sample into a capillary electrophoresis (CE)-electrospray ionization-tandem mass spectrometry system (ESI-MS/MS). HAAs were monitored in selected reaction monitoring mode. With 3 min of PAEKI time, the ten major HAAs (HAA10) in drinking water were enriched up to 20,000-fold into the capillary without compromising resolution. A simple solid phase clean-up method has been developed to eliminate the influence of ionic matrices from drinking water on PAEKI. Under conditions optimized for mass spectrometry, PAEKI and capillary electrophoresis, detection limits defined as three times ratio of signal to noise have been achieved in a range of 0.013-0.12 μg L(-1) for ten HAAs in water sample. The overall recoveries for all ten HAAs in drinking water samples were between 76 and 125%. Six HAAs including monochloro- (MCAA), dichloro- (DCAA), trichloro- (TCAA), monobromo- (MBAA), bromochloro- (BCAA), and bromodichloroacetic acids (BDCAA) were found in tap water samples collected.

  13. Analysis of isotope element by electrolytic enrichment method for ground water and surface water in Saurashtra region, Gujarat, India

    Directory of Open Access Journals (Sweden)

    Sajal Singh

    2016-12-01

    Full Text Available The present study has been aimed for the assessment of isotope element Tritium (3H. It is a great threat to human health and environment for lengthy duration. The tritium exists in earth in diverse forms such as (1 small amounts of natural tritium are produced by alpha decay of lithium-7, (2 natural atmospheric tritium is also generated by secondary neutron cosmic ray bombardment of nitrogen, (3 atmospheric nuclear bomb testing in the 1950s, although the contribution from nuclear power plants is small. Tritium or 3H is a radioactive isotope of hydrogen with a half-life of 12.32 ± 0.02 years. Water samples from ground water, surface water, and precipitation were collected from different locations in Gujarat area and were analyzed for the same. Distillation of samples was done to reduce the conductivity. Deuterium and Hydrogen were removed by the process of physico-chemical fractionation in the tritium enrichment unit. The basis of physico-chemical fractionation is the difference in the strength of bonds formed by the light vs. the heavier isotope of a given element. A total of 10 cycles (runs were executed using Quintals process. Tritium concentration files were created with help of WinQ and Quick start software in Quintals process (Liquid Scintillation Spectrometer. The concentration of tritium in terms of tritium units (TU of various samples has been determined. The TU values of the samples vary in the range of 0.90–6.62 TU.

  14. Enriching Education

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    "IPO" and "education" are two different animals, but they're beginning to cohabitate in China and hopefully will procreate smarts When the Beijing-based New Oriental School's parent company went public in New York on September 7, it essentially nullified the oxymoron "rich teacher."

  15. COMPANY VALUATION METHODS BASED ON PATRIMONY

    Directory of Open Access Journals (Sweden)

    SUCIU GHEORGHE

    2013-02-01

    Full Text Available The methods used for the company valuation can be divided into 3 main groups: methods based on patrimony,methods based on financial performance, methods based both on patrimony and on performance. The companyvaluation methods based on patrimony are implemented taking into account the balance sheet or the financialstatement. The financial statement refers to that type of balance in which the assets are arranged according to liquidity,and the liabilities according to their financial maturity date. The patrimonial methods are based on the principle thatthe value of the company equals that of the patrimony it owns. From a legal point of view, the patrimony refers to allthe rights and obligations of a company. The valuation of companies based on their financial performance can be donein 3 ways: the return value, the yield value, the present value of the cash flows. The mixed methods depend both onpatrimony and on financial performance or can make use of other methods.

  16. Development of a microprocessing-assisted cell-systematic evolution of ligands by exponential enrichment method for human umbilical vein endothelial cells

    Science.gov (United States)

    Terazono, Hideyuki; Kim, Hyonchol; Nomura, Fumimasa; Yasuda, Kenji

    2016-06-01

    We developed a microprocessing-assisted technique to select single-strand DNA aptamers that bind to unknown targets on the cell surface by modifying the conventional systematic evolution of ligands by exponential enrichment (cell-SELEX). Our technique involves 1) the specific selection of target-cell-surface-bound aptamers without leakage of intracellular components by trypsinization and 2) cloning of aptamers by microprocessing-assisted picking of single cells using magnetic beads. After cell-SELEX, the enriched aptamers were conjugated with magnetic beads. The aptamer-magnetic beads conjugates attached to target cells were collected individually by microassisted procedures using microneedles under a microscope. After that, the sequences of the collected magnetic-bead-bound aptamers were identified. As a result, a specific aptamer for the surface of target cells, e.g., human umbilical vein endothelial cells (HUVECs), was chosen and its specificity was examined using other cell types, e.g., HeLa cells. The results indicate that this microprocessing-assisted cell-SELEX method for identifying aptamers is applicable in biological research and clinical diagnostics.

  17. Quantitative analysis of low-abundance serological proteins with peptide affinity-based enrichment and pseudo-multiple reaction monitoring by hybrid quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Kim, Kwang Hoe; Ahn, Yeong Hee; Ji, Eun Sun; Lee, Ju Yeon; Kim, Jin Young; An, Hyun Joo; Yoo, Jong Shin

    2015-07-02

    Multiple reaction monitoring (MRM) is commonly used for the quantitative analysis of proteins during mass pectrometry (MS), and has excellent specificity and sensitivity for an analyte in a complex sample. In this study, a pseudo-MRM method for the quantitative analysis of low-abundance serological proteins was developed using hybrid quadrupole time-of-flight (hybrid Q-TOF) MS and peptide affinity-based enrichment. First, a pseudo-MRM-based analysis using hybrid Q-TOF MS was performed for synthetic peptides selected as targets and spiked into tryptic digests of human serum. By integrating multiple transition signals corresponding to fragment ions in the full scan MS/MS spectrum of a precursor ion of the target peptide, a pseudo-MRM MS analysis of the target peptide showed an increased signal-to-noise (S/N) ratio and sensitivity, as well as an improved reproducibility. The pseudo-MRM method was then used for the quantitative analysis of the tryptic peptides of two low-abundance serological proteins, tissue inhibitor of metalloproteinase 1 (TIMP1) and tissue-type protein tyrosine phosphatase kappa (PTPκ), which were prepared with peptide affinity-based enrichment from human serum. Finally, this method was used to detect femtomolar amounts of target peptides derived from TIMP1 and PTPκ, with good coefficients of variation (CV 2.7% and 9.8%, respectively), using a few microliters of human serum from colorectal cancer patients. The results suggest that pseudo-MRM using hybrid Q-TOF MS, combined with peptide affinity-based enrichment, could become a promising alternative for the quantitative analysis of low-abundance target proteins of interest in complex serum samples that avoids protein depletion.

  18. No Pain, No Gain? A Resource-Based Model of Work-to-Family Enrichment and Conflict

    Science.gov (United States)

    Chen, Zheng; Powell, Gary N.

    2012-01-01

    Work-family scholars tend to work in two largely disconnected research streams, focusing on either work-family enrichment--the positive side of the work-family interface--or work-family conflict--the negative side of this interface. The purpose of this study is to suggest a reconciliation of the two research streams by proposing and testing a…

  19. Oxidative Stability of Granola Bars Enriched with Multilayered Fish Oil Emulsion in the Presence of Novel Brown Seaweed Based Antioxidants

    DEFF Research Database (Denmark)

    Hermund, Ditte Baun; Karadaǧ, Ayşe; Andersen, Ulf

    2016-01-01

    Fucus vesiculosus extracts that have both radical scavenging activity and metal chelating ability in vitro were used as natural antioxidant in granola bars enriched with fish oil emulsion by using primary and secondary emulsion systems stabilized by sodium caseinate alone and sodium caseinate-chi...... were added to the granola bars especially in combination with acetone and ethanol extracts of Fucus vesiculosus....

  20. Injectable self-gelling composites for bone tissue engineering based on gellan gum hydrogel enriched with different bioglasses

    NARCIS (Netherlands)

    Douglas, T.E.; Piwowarczyk, W.; Pamula, E.; Liskova, J.; Schaubroeck, D.; Leeuwenburgh, S.C.; Brackman, G.; Balcaen, L.; Detsch, R.; Declercq, H.; Cholewa-Kowalska, K.; Dokupil, A.; Cuijpers, V.M.; Vanhaecke, F.; Cornelissen, R.; Coenye, T.; Boccaccini, A.R.; Dubruel, P.

    2014-01-01

    Hydrogels of biocompatible calcium-crosslinkable polysaccharide gellan gum (GG) were enriched with bioglass particles to enhance (i) mineralization with calcium phosphate (CaP); (ii) antibacterial properties and (iii) growth of bone-forming cells for future bone regeneration applications. Three biog

  1. An interactive segmentation method based on superpixel

    DEFF Research Database (Denmark)

    Yang, Shu; Zhu, Yaping; Wu, Xiaoyu

    2015-01-01

    This paper proposes an interactive image-segmentation method which is based on superpixel. To achieve fast segmentation, the method is used to establish a Graphcut model using superpixels as nodes, and a new energy function is proposed. Experimental results demonstrate that the authors' method has...... excellent performance in terms of segmentation accuracy and computation efficiency compared with other segmentation algorithm based on pixels....

  2. Digital Autofocusing Method Based on Contourlet Transform

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The autofocusing technique based on contourlet transform is discussed in this paper and an autofocusing method is proposed for images with much information in certain directions. The experimental results show that theproposed method can focus accurately and the sensitivity ratio is higher than that of the other autofocusing methods based on conventional image processing

  3. A novel tantalum-based sol-gel packed microextraction syringe for highly specific enrichment of phosphopeptides in MALDI-MS applications.

    Science.gov (United States)

    Çelikbıçak, Ömür; Atakay, Mehmet; Güler, Ülkü; Salih, Bekir

    2013-08-07

    A new tantalum-based sol-gel material was synthesized using a unique sol-gel synthesis pathway by PEG incorporation into the sol-gel structure without performing a calcination step. This improved its chemical and physical properties for the high capacity and selective enrichment of phosphopeptides from protein digests in complex biological media. The specificity of the tantalum-based sol-gel material for phosphopeptides was evaluated and compared with tantalum(V) oxide (Ta2O5) in different phosphopeptide enrichment applications. The tantalum-based sol-gel and tantalum(V) oxide were characterized in detail using FT-IR spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM), and also using a surface area and pore size analyzer. In the characterization studies, the surface morphology, pore volume, crystallinity of the materials and PEG incorporation into the sol-gel structure to produce a more hydrophilic material were successfully demonstrated. The X-ray diffractograms of the two different materials were compared and it was noted that the broad signals of the tantalum-based sol-gel clearly represented the amorphous structure of the sol-gel material, which was more likely to create enough surface area and to provide more accessible tantalum atoms for phosphopeptides to be easily adsorbed when compared with the neat and more crystalline structure of Ta2O5. Therefore, the phosphopeptide enrichment performance of the tantalum-based sol-gels was found to be remarkably higher than the more crystalline Ta2O5 in our studies. Phosphopeptides at femtomole levels could be selectively enriched using the tantalum-based sol-gel and detected with a higher signal-to-noise ratio by matrix-assisted laser desorption/ionization-mass spectrometer (MALDI-MS). Moreover, phosphopeptides in a tryptic digest of non-fat bovine milk as a complex real-world biological sample were retained with higher yield using a tantalum-based sol-gel. Additionally, the sol-gel material

  4. High-Affinity DNA Aptamer Generation Targeting von Willebrand Factor A1-Domain by Genetic Alphabet Expansion for Systematic Evolution of Ligands by Exponential Enrichment Using Two Types of Libraries Composed of Five Different Bases.

    Science.gov (United States)

    Matsunaga, Ken-Ichiro; Kimoto, Michiko; Hirao, Ichiro

    2017-01-11

    The novel evolutionary engineering method ExSELEX (genetic alphabet expansion for systematic evolution of ligands by exponential enrichment) provides high-affinity DNA aptamers that specifically bind to target molecules, by introducing an artificial hydrophobic base analogue as a fifth component into DNA aptamers. Here, we present a newer version of ExSELEX, using a library with completely randomized sequences consisting of five components: four natural bases and one unnatural hydrophobic base, 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). In contrast to the limited number of Ds-containing sequence combinations in our previous library, the increased complexity of the new randomized library could improve the success rates of high-affinity aptamer generation. To this end, we developed a sequencing method for each clone in the enriched library after several rounds of selection. Using the improved library, we generated a Ds-containing DNA aptamer targeting von Willebrand factor A1-domain (vWF) with significantly higher affinity (KD = 75 pM), relative to those generated by the initial version of ExSELEX, as well as that of the known DNA aptamer consisting of only the natural bases. In addition, the Ds-containing DNA aptamer was stabilized by introducing a mini-hairpin DNA resistant to nucleases, without any loss of affinity (KD = 61 pM). This new version is expected to consistently produce high-affinity DNA aptamers.

  5. Direct PCR - A rapid method for multiplexed detection of different serotypes of Salmonella in enriched pork meat samples

    DEFF Research Database (Denmark)

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas

    2017-01-01

    Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens...... of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using...... naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved...

  6. Development of Phage-Based Antibody Fragment Reagents for Affinity Enrichment of Bacterial Immunoglobulin G Binding Proteins.

    Science.gov (United States)

    Säll, Anna; Sjöholm, Kristoffer; Waldemarson, Sofia; Happonen, Lotta; Karlsson, Christofer; Persson, Helena; Malmström, Johan

    2015-11-06

    Disease and death caused by bacterial infections are global health problems. Effective bacterial strategies are required to promote survival and proliferation within a human host, and it is important to explore how this adaption occurs. However, the detection and quantification of bacterial virulence factors in complex biological samples are technically demanding challenges. These can be addressed by combining targeted affinity enrichment of antibodies with the sensitivity of liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS). However, many virulence factors have evolved properties that make specific detection by conventional antibodies difficult. We here present an antibody format that is particularly well suited for detection and analysis of immunoglobulin G (IgG)-binding virulence factors. As proof of concept, we have generated single chain fragment variable (scFv) antibodies that specifically target the IgG-binding surface proteins M1 and H of Streptococcus pyogenes. The binding ability of the developed scFv is demonstrated against both recombinant soluble protein M1 and H as well as the intact surface proteins on a wild-type S. pyogenes strain. Additionally, the capacity of the developed scFv antibodies to enrich their target proteins from both simple and complex backgrounds, thereby allowing for detection and quantification with LC-SRM MS, was demonstrated. We have established a workflow that allows for affinity enrichment of bacterial virulence factors.

  7. Augmenting Learning in an Out-of-school Context: The Cognitive and Affective Impact of Two Cryogenics-based Enrichment Programmes on Upper Primary Students

    Science.gov (United States)

    Caleon, Imelda S.; Subramaniam, R.

    2007-07-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it was found that both enrichment programmes were effective in promoting the learning of science concepts. Fair improvements, albeit only transient, in two attitude constructs, enjoyment of science and career preference, due to either CBEPs were detected. The CBEPs did not have any significant impact on the attitude construct relating to students’ views on the social implications of science. The impact of CBEPs showed signs of retention, specifically in the cognitive realm, and reasonable indications of influencing subsequent learning and activities of students.

  8. Simultaneous determination of silver and other heavy metals in aquatic environment receiving wastewater from industrial area, applying an enrichment method

    Directory of Open Access Journals (Sweden)

    Naeemullah

    2016-01-01

    Full Text Available In the present study, silver (Ag, cadmium (Cd, nickel (Ni, cobalt (Co and lead (Pb were simultaneously determined in water samples of fresh water canal receiving untreated effluents from an industrial area, of Sindh Pakistan. The analytes in the water sample were determined by CPE using ammonium pyrrolidinedithiocarbamate (APDC as a complexing agent and then entrapped in non-ionic surfactant, octylphenoxypolyethoxyethanol (Triton X-114. The surfactant rich phase was diluted with acidic ethanol prior to analysis by flame atomic absorption spectrometry. The variables affecting the complexation and extraction steps such as pH of sample solution, concentration of oxine and Triton X-114, equilibration temperature and time period for shaking were investigated in detail. The validation of the procedure was carried out by analysis of a certified reference sample of water (CRM1634e. Reliability of the proposed method was also checked by the standard addition method in a real sample at three concentration levels of all metals. Under the optimum conditions, the preconcentration of 10 mL sample solutions, allowed preconcentration factor of 20-fold. The lower limit of detection obtained for Ag, Cd, Ni, Co and Pb was 0.42, 0.48, 0.92, 0.62, and 1.42 μg L−1, respectively. The proposed procedure was successfully applied to waste and fresh water samples for simultaneous determination of different metals. The concentration of Ag, Cd, Ni, Co and Pb has shown a decreased trend from 46.5–6.96, 23.0–8.92, 30.2–12.8, 14.2–4.45 and 15.3–5.32 μg L−1, respectively from initial entrance of waste water along the downstream of canal.

  9. Circulating Tumor Cells: A Review of Non-EpCAM-Based Approaches for Cell Enrichment and Isolation

    OpenAIRE

    Gabriel, Marta,; Calleja, Lidia,; Chalopin, Antoine; Ory, Benjamin; Heymann, Dominique

    2016-01-01

    International audience; Background: Circulating tumor cells (CTCs) are biomarkers for non-invasively measuring the evolution of tumor genotypes during treatment and disease progression. Recent technical progress has made it possible to detect and characterize CTCs at the single-cell level in blood. Content: Most current methods are based on epithelial cell adhesion molecule (EpCAM) detection, but numerous studies have demonstrated that EpCAM is not a universal marker for CTC detection since i...

  10. Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications

    Directory of Open Access Journals (Sweden)

    Bekiranov Stefan

    2011-08-01

    Full Text Available Abstract Background The advent of ChIP-seq technology has made the investigation of epigenetic regulatory networks a computationally tractable problem. Several groups have applied statistical computing methods to ChIP-seq datasets to gain insight into the epigenetic regulation of transcription. However, methods for estimating enrichment levels in ChIP-seq data for these computational studies are understudied and variable. Since the conclusions drawn from these data mining and machine learning applications strongly depend on the enrichment level inputs, a comparison of estimation methods with respect to the performance of statistical models should be made. Results Various methods were used to estimate the gene-wise ChIP-seq enrichment levels for 20 histone methylations and the histone variant H2A.Z. The Multivariate Adaptive Regression Splines (MARS algorithm was applied for each estimation method using the estimation of enrichment levels as predictors and gene expression levels as responses. The methods used to estimate enrichment levels included tag counting and model-based methods that were applied to whole genes and specific gene regions. These methods were also applied to various sizes of estimation windows. The MARS model performance was assessed with the Generalized Cross-Validation Score (GCV. We determined that model-based methods of enrichment estimation that spatially weight enrichment based on average patterns provided an improvement over tag counting methods. Also, methods that included information across the entire gene body provided improvement over methods that focus on a specific sub-region of the gene (e.g., the 5' or 3' region. Conclusion The performance of data mining and machine learning methods when applied to histone modification ChIP-seq data can be improved by using data across the entire gene body, and incorporating the spatial distribution of enrichment. Refinement of enrichment estimation ultimately improved accuracy

  11. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active...... sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally...... valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects...

  12. Research on BOM based composable modeling method

    NARCIS (Netherlands)

    Zhang, M.; He, Q.; Gong, J.

    2013-01-01

    Composable modeling method has been a research hotpot in the area of Modeling and Simulation for a long time. In order to increase the reuse and interoperability of BOM based model, this paper put forward a composable modeling method based on BOM, studied on the basic theory of composable modeling m

  13. A reliable solid phase microextraction-gas chromatography-triple quadrupole mass spectrometry method for the assay of selenomethionine and selenomethylselenocysteine in aqueous extracts: difference between selenized and not-enriched selenium potatoes.

    Science.gov (United States)

    Gionfriddo, Emanuela; Naccarato, Attilio; Sindona, Giovanni; Tagarelli, Antonio

    2012-10-17

    A new analytical approach is exploited in the assay of selenium speciation in selenized and not selenium enriched potatoes based on the widely available solid-phase microextraction (SPME) coupled to-GC-triple quadrupole mass spectrometry (SPME-GC-QqQ MS) method. The assay of selenomethionine (SeMet) and selenomethylselenocysteine (SeMeSeCys) in potatoes here reported provides clues to the effectiveness of SPME technique combined with gas chromatography-tandem mass spectrometry, which could be of general use. For the exploitation of the GC method, the selected analytes were converted into their N(O,S)-alkoxycarbonyl alkyl esters derivatives by direct treatment with alkyl chloroformate in aqueous extracts. The performance of five SPME fibers and three chloroformates were tested in univariate mode and the best results were obtained using the divinylbenzene/carboxen/polydimethylsiloxane fiber and propylchloroformate. The variables affecting the efficiency of SPME analysis were optimized by the multivariate approach of design of experiment (DoE) and, in particular, a central composite design (CCD) was applied. Tandem mass spectrometry in selected reaction monitoring (SRM) has allowed the elimination of matrix interferences, providing reconstructed chromatograms with well-resolved peaks and the achievement of very satisfactory detection and quantification limits. Both precision and recovery of the proposed protocol tested at concentration of 8 and 40 μg kg(-1) (dry matter), offered values ranging from 82.3 to 116.3% and from 8.5 to 13.1% for recovery and precision, respectively. The application of the method to commercial samples of selenized and not selenium enriched potatoes proved that the Se fertilization increases significantly the concentration of these bioavailable selenoamino acids.

  14. Development of cryogenic low background detector based on enriched zinc molybdate crystal scintillators to search for neutrinoless double beta decay of $^{100}$Mo

    CERN Document Server

    Chernyak, Dmitry

    2015-01-01

    ZnMoO$_4$ scintillators with a mass of $\\sim$ 0.3 kg, as well as Zn$^{100}$MoO$_4$ crystals enriched in the isotope $^{100}$Mo were produced for the first time by using the low-thermal-gradient Czochralski technique. The optical and luminescent properties of the produced crystals were studied to estimate the progress in crystal growth quality. The low-temperature tests with a 313 g ZnMoO$_4$ and two enriched Zn$^{100}$MoO$_4$ crystals were performed aboveground in the Centre de Sciences Nucl\\'eaires et de Sciences de la Mati\\`ere. The low background measurements with a three ZnMoO$_4$ and two enriched detectors installed in the EDELWEISS set-up at the Laboratoire Souterrain de Modane were carried out. To optimize the light collection in ZnMoO$_4$ scintillating bolometers, we have simulated the collection of scintillation photons in a detector module for different geometries by Monte Carlo method using the GEANT4 package. Response to the 2$\

  15. Instance Based Methods --- A Brief Overview

    CERN Document Server

    Baumgartner, Peter; 10.1007/s13218-010-0002-x

    2012-01-01

    Instance-based methods are a specific class of methods for automated proof search in first-order logic. This article provides an overview of the major methods in the area and discusses their properties and relations to the more established resolution methods. It also discusses some recent trends on refinements and applications. This overview is rather brief and informal, but we provide a comprehensive literature list to follow-up on the details.

  16. Size-based enrichment of exfoliated tumor cells in urine increases the sensitivity for DNA-based detection of bladder cancer.

    Directory of Open Access Journals (Sweden)

    Elin Andersson

    Full Text Available Bladder cancer is diagnosed by cystoscopy, a costly and invasive procedure that is associated with patient discomfort. Analysis of tumor-specific markers in DNA from sediments of voided urine has the potential for non-invasive detection of bladder cancer; however, the sensitivity is limited by low fractions and small numbers of tumor cells exfoliated into the urine from low-grade tumors. The purpose of this study was to improve the sensitivity for non-invasive detection of bladder cancer by size-based capture and enrichment of tumor cells in urine. In a split-sample set-up, urine from a consecutive series of patients with primary or recurrent bladder tumors (N = 189 was processed by microfiltration using a membrane filter with a defined pore-size, and sedimentation by centrifugation, respectively. DNA from the samples was analyzed for seven bladder tumor-associated methylation markers using MethyLight and pyrosequencing assays. The fraction of tumor-derived DNA was higher in the filter samples than in the corresponding sediments for all markers (p<0.000001. Across all tumor stages, the number of cases positive for one or more markers was 87% in filter samples compared to 80% in the corresponding sediments. The largest increase in sensitivity was achieved in low-grade Ta tumors, with 82 out of 98 cases positive in the filter samples (84% versus 74 out of 98 in the sediments (75%. Our results show that pre-analytic processing of voided urine by size-based filtration can increase the sensitivity for DNA-based detection of bladder cancer.

  17. Reliability-based concurrent subspace optimization method

    Institute of Scientific and Technical Information of China (English)

    FAN Hui; LI Wei-ji

    2008-01-01

    To avoid the high computational cost and much modification in the process of applying traditional re-liability-based design optimization method, a new reliability-based concurrent subspace optimization approach is proposed based on the comparison and analysis of the existing muhidisciplinary optimization techniques and reli-ability assessment methods. It is shown through a canard configuration optimization for a three-surface transport that the proposed method is computationally efficient and practical with the least modification to the current de-terministic optimization process.

  18. Environmental enrichment for primates in laboratories

    Science.gov (United States)

    Buchanan-Smith, H. M.

    2010-06-01

    Environmental enrichment is a critical component of Refinement, one of the 3Rs underlying humane experimentation on animals. In this paper I discuss why primates housed in laboratories, which often have constraints of space and study protocols, are a special case for enrichment. I outline a framework for categorising the different types of enrichment, using the marmoset as a case study, and summarise the methods used to determine what animals want/prefer. I briefly review the arguments that enrichment does not negatively affect experimental outcomes. Finally I focus on complexity and novelty, choice and control, the underlying features of enrichment that makes it successful, and how combined with a thorough understanding of natural history we can put effective enrichment into practice in laboratories. Throughout the paper I emphasise the need to evaluate enrichment to ensure it is having the desired effect.

  19. Identification of enriched driver gene alterations in subgroups of non-small cell lung cancer patients based on histology and smoking status.

    Directory of Open Access Journals (Sweden)

    She-Juan An

    Full Text Available BACKGROUND: Appropriate patient selection is needed for targeted therapies that are efficacious only in patients with specific genetic alterations. We aimed to define subgroups of patients with candidate driver genes in patients with non-small cell lung cancer. METHODS: Patients with primary lung cancer who underwent clinical genetic tests at Guangdong General Hospital were enrolled. Driver genes were detected by sequencing, high-resolution melt analysis, qPCR, or multiple PCR and RACE methods. RESULTS: 524 patients were enrolled in this study, and the differences in driver gene alterations among subgroups were analyzed based on histology and smoking status. In a subgroup of non-smokers with adenocarcinoma, EGFR was the most frequently altered gene, with a mutation rate of 49.8%, followed by EML4-ALK (9.3%, PTEN (9.1%, PIK3CA (5.2%, c-Met (4.8%, KRAS (4.5%, STK11 (2.7%, and BRAF (1.9%. The three most frequently altered genes in a subgroup of smokers with adenocarcinoma were EGFR (22.0%, STK11 (19.0%, and KRAS (12.0%. We only found EGFR (8.0%, c-Met (2.8%, and PIK3CA (2.6% alterations in the non-smoker with squamous cell carcinoma (SCC subgroup. PTEN (16.1%, STK11 (8.3%, and PIK3CA (7.2% were the three most frequently enriched genes in smokers with SCC. DDR2 and FGFR2 only presented in smokers with SCC (4.4% and 2.2%, respectively. Among these four subgroups, the differences in EGFR, KRAS, and PTEN mutations were statistically significant. CONCLUSION: The distinct features of driver gene alterations in different subgroups based on histology and smoking status were helpful in defining patients for future clinical trials that target these genes. This study also suggests that we may consider patients with infrequent alterations of driver genes as having rare or orphan diseases that should be managed with special molecularly targeted therapies.

  20. MRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials.

    Science.gov (United States)

    Hua, Xue; Ching, Christopher R K; Mezher, Adam; Gutman, Boris A; Hibar, Derrek P; Bhatt, Priya; Leow, Alex D; Jack, Clifford R; Bernstein, Matt A; Weiner, Michael W; Thompson, Paul M

    2016-01-01

    The goal of this work was to assess statistical power to detect treatment effects in Alzheimer's disease (AD) clinical trials using magnetic resonance imaging (MRI)-derived brain biomarkers. We used unbiased tensor-based morphometry (TBM) to analyze n = 5,738 scans, from Alzheimer's Disease Neuroimaging Initiative 2 participants scanned with both accelerated and nonaccelerated T1-weighted MRI at 3T. The study cohort included 198 healthy controls, 111 participants with significant memory complaint, 182 with early mild cognitive impairment (EMCI) and 177 late mild cognitive impairment (LMCI), and 155 AD patients, scanned at screening and 3, 6, 12, and 24 months. The statistical power to track brain change in TBM-based imaging biomarkers depends on the interscan interval, disease stage, and methods used to extract numerical summaries. To achieve reasonable sample size estimates for potential clinical trials, the minimal scan interval was 6 months for LMCI and AD and 12 months for EMCI. TBM-based imaging biomarkers were not sensitive to MRI scan acceleration, which gave results comparable with nonaccelerated sequences. ApoE status and baseline amyloid-beta positron emission tomography data improved statistical power. Among healthy, EMCI, and LMCI participants, sample size requirements were significantly lower in the amyloid+/ApoE4+ group than for the amyloid-/ApoE4- group. ApoE4 strongly predicted atrophy rates across brain regions most affected by AD, but the remaining 9 of the top 10 AD risk genes offered no added predictive value in this cohort.

  1. A Simple Method for Measuring Carbon-13 Fatty Acid Enrichment in the Major Lipid Classes of Microalgae Using GC-MS

    Directory of Open Access Journals (Sweden)

    Sheik Nadeem Elahee Doomun

    2016-11-01

    Full Text Available A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS. NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS. The key is that isotope spectra can be measured without interference from co-eluting fatty acids or other molecules. Pre-fractionation of lipid extracts by SPE allows the measurement of 13C isotope incorporation into the three main lipid classes (phospholipids, glycolipids, neutral lipids in microalgae thus allowing the study of complex lipid biochemistry using relatively straightforward analytical technology. The high selectivity of GC is necessary as it allows the collection of mass spectra for individual fatty acids, including cis/trans isomers, of the PFB-derivatised fatty acids. The combination of solid-phase extraction and GC-MS enables the accurate determination of 13C incorporation into each lipid pool. Three solvent extraction protocols that are commonly used in lipidomics were also evaluated and are described here with regard to extraction efficiencies for lipid analysis in microalgae.

  2. Decision making based on data analysis methods

    OpenAIRE

    Sirola, Miki; Sulkava, Mika

    2016-01-01

    This technical report is based on four our recent articles:"Data fusion of pre-election gallups and polls for improved support estimates", "Analyzing parliamentary elections based on voting advice application data", "The Finnish car rejection reasons shown in an interactive SOM visualization tool", and "Network visualization of car inspection data using graph layout". Neural methods are applied in political and technical decision making. We introduce decision support schemes based on Self-Org...

  3. THE SUBSIDIARY NATURE OF THE UNJUST ENRICHMENT ACTION. CONTRACT-BASED ACTION VS. ACTIO DE IN REM VERSO. JURISPRUDENCE SEPARATION ONLY

    Directory of Open Access Journals (Sweden)

    Eugenia VOICHECI

    2014-05-01

    Full Text Available For the purpose of recovering a paid amount within the insured sum, however, in addition to the owed amount, the insurer sues his client for claims. Does the insurer have, to this end, a cleared way towards unjust enrichment? The provisions of the 1864 Civil Code do not contain definitions of ex contractu and actio de in rem verso. The doctrine has established the acceptability requirements of actio de in rem verso, however, it did not do the same for ex contractu, and there is no notable change to this matter after the Civil Code became effective. This situation is also maintained in the current Law No.287/2009 on the Civil Code. Hence, the separation of the configuration and enforcement area of the two types of actions continues to be done in terms of jurisprudence by strictly relating to the case at hand. The study starts from an actual case the settling of which highlights the issue of determining the subsidiary nature, hence the acceptability of the unjust enrichment. The purpose of this study is to re/focus on an old dichotomy, i.e. the contract-based action (ex contractu and the action based on an licit deed, that of unjust enrichment (actio de in rem verso. The primary goal of the study consists of highlighting the aspects that the provisions of the 1864 Civil Code and those of the new Civil Code have in common or not in terms of the two types of actions before the court, the doctrine-related solutions given as concerns the characteristics and legal status of the two actions and the fact that, in the nex Civil Code as well, the separation line between the two actions is determined on the basis of jurisprudence, being left at the judges' discretion and wisdom, with all related consequences thereof.

  4. Selective enrichment and determination of nicosulfuron in water and soil by a stir bar based on molecularly imprinted polymer coatings

    Energy Technology Data Exchange (ETDEWEB)

    Yang Lieqing; Zhao Xiaomin [College of Chemistry and Material Sciences, Shandong Agricultural University, Daizong Street No. 61, Taian, Shandong Province 271018 (China); Zhou Jie, E-mail: zhoujie@sdau.edu.cn [College of Chemistry and Material Sciences, Shandong Agricultural University, Daizong Street No. 61, Taian, Shandong Province 271018 (China)

    2010-06-18

    A new molecularly imprinted stir bar was prepared using nicosulfuron, a sulfonylurea herbicide, as a template. To achieve the selective and direct extraction of a target analyte from aqueous samples, several main parameters, including extraction time, pH value and contents of inorganic salt in the sample matrix, were investigated. Competitive sorption experiments showed that using six sulfonylureas as substrates the imprinted stir bar gave high selectivity and imprinted effect on the template nicosulfuron in comparison with the non-imprinted stir bar. Evidence was also presented by the scanning electronic microscopic images of the imprinted and non-imprinted stir bars. This resulted in a combined imprinted stir bar-HPLC-UV method allowing the determination of trace nicosulfuron from the sample matrix. Based on a signal to noise ratio of 3, the detection limits were 0.75 nM for the tap water and 12.0 nmol kg{sup -1} for the soil. The method showed good recoveries and precision, 93.4% (RSD 1.5%, n = 3) for 100 mL of tap water spiked with 2.0 nmol and 81.3% (RSD 2.6%, n = 3) for 10 g of soil spiked with 0.80 nmol, suggesting that the imprinted stir bar can be successfully applied to the preconcentration of nicosulfuron in real samples.

  5. Software Testing Method Based on Model Comparison

    Institute of Scientific and Technical Information of China (English)

    XIE Xiao-dong; LU Yan-sheng; MAO Cheng-yin

    2008-01-01

    A model comparison based software testing method (MCST) is proposed. In this method, the requirements and programs of software under test are transformed into the ones in the same form, and described by the same model describe language (MDL).Then, the requirements are transformed into a specification model and the programs into an implementation model. Thus, the elements and structures of the two models are compared, and the differences between them are obtained. Based on the diffrences, a test suite is generated. Different MDLs can be chosen for the software under test. The usages of two classical MDLs in MCST, the equivalence classes model and the extended finite state machine (EFSM) model, are described with example applications. The results show that the test suites generated by MCST are more efficient and smaller than some other testing methods, such as the path-coverage testing method, the object state diagram testing method, etc.

  6. Preparation of stir cake sorptive extraction based on polymeric ionic liquid for the enrichment of benzimidazole anthelmintics in water, honey and milk samples

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yulei [State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Siming Road, P.O. Box 1009, Xiamen 361005 (China); Zhang, Jie [Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences (China); Huang, Xiaojia, E-mail: hxj@xmu.edu.cn [State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Siming Road, P.O. Box 1009, Xiamen 361005 (China); Yuan, Dongxing [State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Siming Road, P.O. Box 1009, Xiamen 361005 (China)

    2014-08-20

    Highlights: • A new polymeric ionic liquid-based monolith was prepared. • The monolith was used as the extractive medium of stir cake sorptive extraction. • The SCSE–AMIIDB can extract benzimidazole anthelmintics (BAs) effectively. • A combination of SCSE–AMIIDB–LD–HPLC/DAD was developed. • The combination was applied to monitor trace BAs in water, milk and honey samples. - Abstract: In this work, a new stir cake sorptive extraction (SCSE) using polymeric ionic liquid monolith as sorbent was prepared. The sorbent was obtained by in situ copolymerization of an ionic liquid, 1-allyl-3-methylimidazolium bis[(trifluoro methyl)sulfonyl]imide (AMII) and divinylbenzene (DB) in the presence of N,N-dimethylformamide. The influence of the content of ionic liquid and the porogen in the polymerization mixture on extraction performance was studied thoroughly. The physicochemical properties of the polymeric ionic liquid were characterized by infrared spectroscopy, elemental analysis, scanning electron microscopy and mercury intrusion porosimetry. The usefulness of SCSE–AMIIDB was demonstrated by the enrichment of trace benzimidazole anthelmintics. Several parameters affecting the extraction efficiency were investigated, and under the optimized conditions, a simple and effective method for the determination of trace benzimidazoles residues in water, milk and honey samples was established by coupling SCSE–AMIIDB with high performance liquid chromatography/diode array detection (SCSE–AMIIDB–HPLC/DAD). Results indicated that the limits of detection (S/N = 3) for target compounds were 0.020–0.072 μg L{sup −1}, 0.035–0.10 μg L{sup −1} and 0.026–0.076 μg L{sup −1} in water, milk and honey samples, respectively. In addition, an acceptable reproducibility was achieved by evaluating the repeatability and intermediate precision with relative standard deviations (RSD) of less than 9% and 11%, respectively. Finally, the established AMII

  7. OPTIMASI PEMADATAM CEPAT PADA PENGAYAAN MINYAK IKAN HASIL SAMPING PENGALENGAN LEMURU DENGAN ASAM LEMAK w-3 MENGGUNAKAN METODE PERMUKAAN RESPON [Optimization of Rapid Solidification to Enrich Fish Oil from by-Product of Lemuru Canning Processing with w-3 batty Acids by Response Surface Method

    Directory of Open Access Journals (Sweden)

    Teti Estiasih1

    2005-12-01

    Full Text Available Oil from by-product of lemuru canning processing was a source of w-3 fatty acid but its characteristics had out been known. The content of w-3 fatty acids of this oil had to be increased. Various methods are available to enhance w-3 fatty acids concentration Rapid solidification was one of limited methods to enrich fish oil by w-3 fatty acids containing triglycerides.This research was conducted to optimize rapid solidification condition to enrich fish oil from by product of lemuru canning processing with w-3 fatty acids and characterize the enriched oil compared by International Association of Fish Meal and Oil Manufacturers standard. In optimization process, the content of EPA+OHA and yield .was maximized. A two-factors central composite design in Response Surface Method was used to study the effect of solvent-to-oil ratio (X1 and extraction time (X2. The response (Y is the multiplication of EPA+DHA content by yield.The results showed that under optimum conditions the maximum response were obtained at a solvent-to-oil ratio of 3,95:1(vw and extraction time of 24,93 hours. The w-3 fatty acids enriched fish oil had EPA+DHA content of 33,33% and yield of 9.40% (w/w.The produced w-3 fatty acids enriched fish oil had good quality based on food grade fish oil standard, unless Fe and Cu content. Chelation could reduce these oxidizing metals.

  8. Selective enrichment of metal-binding proteins based on magnetic core/shell microspheres functionalized with metal cations.

    Science.gov (United States)

    Fang, Caiyun; Zhang, Lei; Zhang, Xiaoqin; Lu, Haojie

    2015-06-21

    Metal binding proteins play many important roles in a broad range of biological processes. Characterization of metal binding proteins is important for understanding their structure and biological functions, thus leading to a clear understanding of metal associated diseases. The present study is the first to investigate the effectiveness of magnetic microspheres functionalized with metal cations (Ca(2+), Cu(2+), Zn(2+) and Fe(3+)) as the absorbent matrix in IMAC technology to enrich metal containing/binding proteins. The putative metal binding proteins in rat liver were then globally characterized by using this strategy which is very easy to handle and can capture a number of metal binding proteins effectively. In total, 185 putative metal binding proteins were identified from rat liver including some known less abundant and membrane-bound metal binding proteins such as Plcg1, Acsl5, etc. The identified proteins are involved in many important processes including binding, catalytic activity, translation elongation factor activity, electron carrier activity, and so on.

  9. Wavelet-based Multiresolution Particle Methods

    Science.gov (United States)

    Bergdorf, Michael; Koumoutsakos, Petros

    2006-03-01

    Particle methods offer a robust numerical tool for solving transport problems across disciplines, such as fluid dynamics, quantitative biology or computer graphics. Their strength lies in their stability, as they do not discretize the convection operator, and appealing numerical properties, such as small dissipation and dispersion errors. Many problems of interest are inherently multiscale, and their efficient solution requires either multiscale modeling approaches or spatially adaptive numerical schemes. We present a hybrid particle method that employs a multiresolution analysis to identify and adapt to small scales in the solution. The method combines the versatility and efficiency of grid-based Wavelet collocation methods while retaining the numerical properties and stability of particle methods. The accuracy and efficiency of this method is then assessed for transport and interface capturing problems in two and three dimensions, illustrating the capabilities and limitations of our approach.

  10. Factoring-based method for the design of a nuclear fuel

    Energy Technology Data Exchange (ETDEWEB)

    Guzman-Arriaga, Rafael; Espinosa-Paredes, Gilberto [Division de Ciencias Basicas e Ingenieria, Universidad Autonoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186 Col. Vicentina, Mexico 09340, D. F. (Mexico)

    2010-05-15

    In this work a simple method for a fuel lattice design is presented. The method is focused on finding the radial distribution of the fuel rods having different fissile contents to obtain a prescribed neutron multiplication factor k{sub {infinity}} to a certain discharge burnup and to minimize the rod power peaking. This method is based on the factorization of the fissile content of each fuel bar and the performance of this novel method was demonstrated with a fuel design composed of enriched uranium for a typical boiling water reactor (BWR). The results show that the factoring-based method for the design of a nuclear fuel converges to a minimum rod power peaking and a prescribed k{sub {infinity}} in few iterations. A comparative analysis shows that the proposed method is more efficient than existing methods. (author)

  11. Cloud Based Development Issues: A Methodical Analysis

    Directory of Open Access Journals (Sweden)

    Sukhpal Singh

    2012-11-01

    Full Text Available Cloud based development is a challenging task for various software engineering projects, especifically for those which demand extraordinary quality, reusability and security along with general architecture. In this paper we present a report on a methodical analysis of cloud based development problems published in major computer science and software engineering journals and conferences organized by various researchers. Research papers were collected from different scholarly databases using search engines within a particular period of time. A total of 89 research papers were analyzed in this methodical study and we categorized into four classes according to the problems addressed by them. The majority of the research papers focused on quality (24 papers associated with cloud based development and 16 papers focused on analysis and design. By considering the areas focused by existing authors and their gaps, untouched areas of cloud based development can be discovered for future research works.

  12. An analytical method for hydrogeochemical surveys: Inductively coupled plasma-atomic emission spectrometry after using enrichment coprecipitation with cobalt and ammonium pyrrolidine dithiocarbamate

    Science.gov (United States)

    Hopkins, D.M.

    1991-01-01

    Trace metals that are commonly associated with mineralization were concentrated and separated from natural water by coprecipitation with ammonium pyrollidine dithiocarbamate (APDC) and cobalt and determined by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). The method is useful in hydrogeochemical surveys because it permits preconcentration near the sample sites, and selected metals are preserved shortly after the samples are collected. The procedure is relatively simple: (1) a liter of water is filtered; (2) the pH is adjusted; (3) Co chloride and APDC are added to coprecipitate the trace metals; and (4) later, the precipitate is filtered, dissolved, and diluted to 10 ml for a 100-fold concentration enrichment of the separated metals. Sb(III), As(III), Cd, Cr, Cu, Fe, Pb, Mo, Ni, Ag, V, and Zn can then be determined simultaneously by ICP-AES. In an experiment designed to measure the coprecipitation efficiency, Sb(III), Cd and Ag were recovered at 70 to 75% of their original concentration. The remaining metals were recovered at 85 to 100% of their original concentrations, however. The range for the lower limits of determination for the metals after preconcentration is 0.1 to 3.0 ??g/l. The precision of the method was evaluated by replicate analyses of a Colorado creek water and two simulated water samples. The accuracy of the method was estimated using a water reference standard (SRM 1643a) certified by the U.S. National Bureau of Standards. In addition, the method was evaluated by analyzing groundwater samples collected near a porphyry copper deposit in Arizona and by analyzing meltwater from glacier-covered areas favorable for mineralization in south-central Alaska. The results for the ICP-AES analyses compared favorably with those obtained using the sequential technique of GFAAS on the acidified but unconcentrated water samples. ICP-AES analysis of trace-metal preconcentrates for hydrogeochemical surveys is more efficient than GFAAS because a

  13. Optimization of fuel rod enrichment distribution for BWR fuel assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Yasushi; Hida, Kazuki; Sakurada, Koichi; Yamamoto, Munenari [Toshiba Corp., Kawasaki, Kanagawa (Japan). Nuclear Engineering Lab.

    1996-09-01

    A practical method was developed for determining the optimum fuel enrichment distribution within a boiling water reactor fuel assembly. The method deals with two different optimization problems, i.e. the combinatorial optimization problem of grouping fuel rods into a given number of rod groups with the same enrichment, and the problem of determining an optimal enrichment for each fuel rod under the resultant rod-grouping pattern. In solving these problems, the primary goal is to minimize a predefined objective function over a given exposure period. The objective function used here is defined by the linear combination C{sub 1}X + C{sub 2}X{sub G}, where X and X{sub G} stand, respectively, for control variables giving constraint to the local power peaking factor and the gadolinium rod power. C{sub 1} and C{sub 2} are user-definable weighting factors to accommodate design preferences. The algorithm for solving this combinatorial optimization problem starts by finding the optimal enrichment vector without any rod-grouping, and promising candidates of rod-grouping patterns are found by exhaustive enumeration based on the resulting fuel enrichment ordering. This latter problem is solved using the method of approximation programming. A practical application is shown for a contemporary 8 x 8 Pu mixed-oxide fuel assembly with 10 gadolinium-poisoned rods. (author)

  14. Recommendation advertising method based on behavior retargeting

    Science.gov (United States)

    Zhao, Yao; YIN, Xin-Chun; CHEN, Zhi-Min

    2011-10-01

    Online advertising has become an important business in e-commerce. Ad recommended algorithms are the most critical part in recommendation systems. We propose a recommendation advertising method based on behavior retargeting which can avoid leakage click of advertising due to objective reasons and can observe the changes of the user's interest in time. Experiments show that our new method can have a significant effect and can be further to apply to online system.

  15. KNOWLEDGE BASED METHODS FOR VIDEO DATA RETRIEVAL

    OpenAIRE

    S.Thanga Ramya; P. Rangarajan

    2011-01-01

    Large collections of publicly available video data grow day by day, the need to query this dataefficiently becomes significant. Consequently, content-based retrieval of video data turns out to be achallenging and important problem. This paper addresses the specific aspect of inferring semanticsautomatically from raw video data using different knowledge-based methods. In particular, this paperfocuses on three techniques namely, rules, Hidden Markov Models (HMMs), and Dynamic BayesianNetworks (...

  16. Oil monitoring methods based on information theory

    Institute of Scientific and Technical Information of China (English)

    XIA Yan-chun; HUO Hua

    2009-01-01

    To evaluate the Wear condition of machines accurately,oil spectrographic entropy,mutual information and ICA analysis methods based on information theory are presented.A full-scale diagnosis utilizing all channels of spectrographic analysis can be obtained.By measuring the complexity and correlativity,the characteristics of wear condition of machines can be shown clearly.The diagnostic quality is improved.The analysis processes of these monitoring methods are given through the explanation of examples.The availability of these methods is validated and further research fields are demonstrated.

  17. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    John E McCormack

    Full Text Available Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture and high-throughput sequencing of ultraconserved elements (UCEs in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae and the sunbittern (Eurypygidae as well as between bustards (Otididae and turacos (Musophagidae. This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

  18. Enrichment, development, and assessment of Indian basil oil based antiseptic cream formulation utilizing hydrophilic-lipophilic balance approach.

    Science.gov (United States)

    Yadav, Narayan Prasad; Meher, Jaya Gopal; Pandey, Neelam; Luqman, Suaib; Yadav, Kuldeep Singh; Chanda, Debabrata

    2013-01-01

    The present work was aimed to develop an antiseptic cream formulation of Indian basil oil utilizing hydrophilic-lipophilic balance approach. In order to determine the required-hydrophilic lipophilic balance (rHLB) of basil oil, emulsions of basil oil were prepared by phase inversion temperature technique using water, Tween 80, and Span 80. Formulated emulsions were assessed for creaming (BE9; 9.8, BE10; 10.2), droplet size (BE18; 3.22 ± 0.09 μ m), and turbidity (BE18; 86.12 ± 2.1%). To ensure correctness of the applied methodology, rHLB of light liquid paraffin was also determined. After rHLB determination, basil oil creams were prepared with two different combinations of surfactants, namely, GMS : Tween 80 (1 : 3.45) and SLS : GMS (1 : 3.68), and evaluated for in vitro antimicrobial activity, skin irritation test, viscosity and consistency. The rHLB of basil oil and light liquid paraffin were found to be 13.36 ± 0.36 and 11.5 ± 0.35, respectively. Viscosity, and consistency parameters of cream was found to be consistent over 90 days. Cream formulations showed net zone of growth inhibition in the range of 5.0-11.3 mm against bacteria and 4.3-7.6 mm against fungi. Primary irritation index was found to be between 0.38 and1.05. Conclusively stable, consistent, non-irritant, enriched antiseptic basil oil cream formulations were developed utilizing HLB approach.

  19. Enrichment, Development, and Assessment of Indian Basil Oil Based Antiseptic Cream Formulation Utilizing Hydrophilic-Lipophilic Balance Approach

    Directory of Open Access Journals (Sweden)

    Narayan Prasad Yadav

    2013-01-01

    Full Text Available The present work was aimed to develop an antiseptic cream formulation of Indian basil oil utilizing hydrophilic-lipophilic balance approach. In order to determine the required-hydrophilic lipophilic balance (rHLB of basil oil, emulsions of basil oil were prepared by phase inversion temperature technique using water, Tween 80, and Span 80. Formulated emulsions were assessed for creaming (BE9; 9.8, BE10; 10.2, droplet size (BE18; 3.22 ± 0.09 μm, and turbidity (BE18; 86.12 ± 2.1%. To ensure correctness of the applied methodology, rHLB of light liquid paraffin was also determined. After rHLB determination, basil oil creams were prepared with two different combinations of surfactants, namely, GMS : Tween 80 (1 : 3.45 and SLS : GMS (1 : 3.68, and evaluated for in vitro antimicrobial activity, skin irritation test, viscosity and consistency. The rHLB of basil oil and light liquid paraffin were found to be 13.36 ± 0.36 and 11.5 ± 0.35, respectively. Viscosity, and consistency parameters of cream was found to be consistent over 90 days. Cream formulations showed net zone of growth inhibition in the range of 5.0–11.3 mm against bacteria and 4.3–7.6 mm against fungi. Primary irritation index was found to be between 0.38 and1.05. Conclusively stable, consistent, non-irritant, enriched antiseptic basil oil cream formulations were developed utilizing HLB approach.

  20. Enrichment, Development, and Assessment of Indian Basil Oil Based Antiseptic Cream Formulation Utilizing Hydrophilic-Lipophilic Balance Approach

    Science.gov (United States)

    Yadav, Narayan Prasad; Meher, Jaya Gopal; Pandey, Neelam; Luqman, Suaib; Yadav, Kuldeep Singh; Chanda, Debabrata

    2013-01-01

    The present work was aimed to develop an antiseptic cream formulation of Indian basil oil utilizing hydrophilic-lipophilic balance approach. In order to determine the required-hydrophilic lipophilic balance (rHLB) of basil oil, emulsions of basil oil were prepared by phase inversion temperature technique using water, Tween 80, and Span 80. Formulated emulsions were assessed for creaming (BE9; 9.8, BE10; 10.2), droplet size (BE18; 3.22 ± 0.09 μm), and turbidity (BE18; 86.12 ± 2.1%). To ensure correctness of the applied methodology, rHLB of light liquid paraffin was also determined. After rHLB determination, basil oil creams were prepared with two different combinations of surfactants, namely, GMS : Tween 80 (1 : 3.45) and SLS : GMS (1 : 3.68), and evaluated for in vitro antimicrobial activity, skin irritation test, viscosity and consistency. The rHLB of basil oil and light liquid paraffin were found to be 13.36 ± 0.36 and 11.5 ± 0.35, respectively. Viscosity, and consistency parameters of cream was found to be consistent over 90 days. Cream formulations showed net zone of growth inhibition in the range of 5.0–11.3 mm against bacteria and 4.3–7.6 mm against fungi. Primary irritation index was found to be between 0.38 and1.05. Conclusively stable, consistent, non-irritant, enriched antiseptic basil oil cream formulations were developed utilizing HLB approach. PMID:23984361

  1. Gender-enriched transcripts in Haemonchus contortus--predicted functions and genetic interactions based on comparative analyses with Caenorhabditis elegans.

    Science.gov (United States)

    Campbell, Bronwyn E; Nagaraj, Shivashankar H; Hu, Min; Zhong, Weiwei; Sternberg, Paul W; Ong, Eng K; Loukas, Alex; Ranganathan, Shoba; Beveridge, Ian; McInnes, Russell L; Hutchinson, Gareth W; Gasser, Robin B

    2008-01-01

    In the present study, a bioinformatic-microarray approach was employed for the analysis of selected expressed sequence tags (ESTs) from Haemonchus contortus, a key parasitic nematode of small ruminants. Following a bioinformatic analysis of EST data using a semiautomated pipeline, 1885 representative ESTs (rESTs) were selected, to which oligonucleotides (three per EST) were designed and spotted on to a microarray. This microarray was hybridized with cyanine-dye labelled cRNA probes synthesized from RNA from female or male adults of H. contortus. Differential hybridisation was displayed for 301 of the 1885 rESTs ( approximately 16%). Of these, 165 (55%) had significantly greater signal intensities for female cRNA and 136 (45%) for male cRNA. Of these, 113 with increased signals in female or male H. contortus had homologues in Caenorhabditis elegans, predicted to function in metabolism, information storage and processing, cellular processes and signalling, and embryonic and/or larval development. Of the rESTs with no known homologues in C. elegans, 24 ( approximately 40%) had homologues in other nematodes, four had homologues in various other organisms and 30 (52%) had no homology to any sequence in current gene databases. A genetic interaction network was predicted for the C. elegans orthologues of the gender-enriched H. contortus genes, and a focused analysis of a subset revealed a tight network of molecules involved in amino acid, carbohydrate or lipid transport and metabolism, energy production and conversion, translation, ribosomal structure and biogenesis and, importantly, those associated with meiosis and/or mitosis in the germline during oogenesis or spermatogenesis. This study provides a foundation for the molecular, biochemical and functional exploration of selected molecules with differential transcription profiles in H. contortus, for further microarray analyses of transcription in different developmental stages of H. contortus, and for an extended

  2. Effects of Gelatin-Based Edible Films Enriched with Laurel Essential Oil on the Quality of Rainbow Trout (Oncorhynchus mykiss Fillets During Refrigerated Storage

    Directory of Open Access Journals (Sweden)

    Tuba Baygar

    2014-01-01

    Full Text Available The effects of gelatin films enriched with laurel leaf essential oil on the quality of rainbow trout (Oncorhynchus mykiss during refrigerated storage at (4±1 °C were examined over a period of 26 days. Fish fillets were wrapped with 8 % gelatin films containing 0, 0.1 and 1 % (by volume per mass of laurel essential oil and vacuum packaged. Sensory (raw and cooked fish, microbiological (total viable counts, psychrotrophic bacteria counts, Enterobacteriaceae and lactic acid bacteria and chemical (proximate composition, pH, total volatile base nitrogen (TVB-N, thiobarbituric acid (TBA, free fatty acid (FFA and peroxide value (PV analysis, and colour measurement were carried out during the storage period and shelf-life was determined periodically. The obtained results showed that the gelatin film enriched with laurel essential oil was suitable for the preservation of rainbow trout fillet and the ability of laurel essential oil to preserve the film depended on its ratio. Combined effects of gelatin film and laurel essential oil (1 % by volume per mass was efficient in maintaining the quality characteristics at an acceptable level up to 22 days of storage, while the control and gelatin film without the essential oil reached an unacceptable level at 15 and 20 days, respectively.

  3. 基于大体积循环进样的低丰度蛋白质富集%Protein enrichment based on large volume recycling injection

    Institute of Scientific and Technical Information of China (English)

    张权青; 张磊; 高小迪; 张维冰; 张庆合

    2014-01-01

    发展了一种大体积循环进样方法,用于富集低丰度蛋白质。在优化的色谱分离条件下,通过增加蛋白质样品的上样体积提高低丰度蛋白质的绝对含量;进一步采用增加样品进样循环次数的方法提高蛋白质的富集效率。以猪肝提取蛋白质为样品,每次上样量500μL 的大体积11次循环进样。根据色谱峰的信号强弱,选择了在原始谱图中看不到色谱峰、有较少小峰和有较多小峰出现的时间段等有代表性的馏分进行研究。在中等极性的组分中,保留时间为11.38 min 和12.58 min 组分的富集效率分别提高了52倍和61倍,实验结果与理论富集效率相近。所发展的方法为生物蛋白质样品研究提供了一种新的富集制备及检测方法。%Biological proteins have great differences in size,hydrophobicity,pH and relative abundance. Especially,the relative contents of high-abundance proteins and low abundance proteins can reach 11 orders of magnitude or more in blood. However,the contents of proteins which have an important impact on the biological function and have related to major diseases are usually very low in body fluids or tissues. So,it is very meaningful to detect the low abun-dance proteins in biological samples. A method of large volume recycling injection was devel-oped as a new sample enrichment technology in this study. The low absolute contents of pro-teins in a sample were improved by increasing the volume of sample,and the enrichment effi-ciency was also increased with the addition of injection times. With the pork liver protein as an example,under the optimized conditions,the representative contents which were no peaks or little peaks and more peaks with low signals were studied. The contents of peaks at the reten-tion times of 11. 38 min and 12. 58 min were enriched by 11 time injections of 500 μL each time. The enrichment factors respectively reached 52 and 61 which were closed to

  4. The Effect of Different Mixing Methods on the pH and Solubility of Mineral Trioxide Aggregate and Calcium-Enriched Mixture

    Science.gov (United States)

    Shahi, Shahriar; Ghasemi, Negin; Rahimi, Saeed; Yavari, Hamid Reza; Samiei, Mohammad; Janani, Maryam; Bahari, Mahmood

    2015-01-01

    Introduction: The aim of this study was to evaluate the effect of different mixing techniques on the pH and solubility of mineral trioxide aggregate (MTA) and calcium-enriched mixture (CEM). Methods and Materials: Five samples were prepared from each biomaterial with different mixing techniques including hand-, amalgamator- or ultrasonic-mixing and were then placed in pre-weighted plastic tubes to determine their pH values. Each tube was then incubated in 10 mL deionized distilled water for 1 h at 37ºC. An electrode was placed in the fluid in each flask at 24ºC and the pH was recorded. In the next stage, six samples from each mixing technique/material were separately placed in glass bottles containing 50 mL of distilled water at 37ºC for 1 h and were let dry for 1 h at 37ºC. The samples’ weights were measured and recorded twice. The procedure was repeated at 1-, 7- and 21-day intervals. Data were analyzed with the repeated measures ANOVA (for solubility) and two-way ANOVA (for pH) and then the post-hoc Tukey’s test was done. Results: The pH of the materials was not significantly affected by mixing methods. (P=0.8 for CEM and P=0.1 for MTA). The solubility of all test groups was within the acceptable range (=3%). However, the solubility of CEM at 1- and 21-day intervals was significantly different (P=0.03 for 1 day and P=0.001 for 21 days). Different mixing techniques had significant effects on the solubility of MTA at the three time points (P=0.004, 0.003 and 0.002 for 1-, 7- and 21-day intervals, respectively). Conclusion: The pH of biomaterials was not influenced by the mixing technique and their solubility was within the acceptable range. PMID:25834601

  5. Autologous antibody capture to enrich immunogenic viruses for viral discovery.

    Science.gov (United States)

    Oude Munnink, Bas B; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T P; Ieven, Margareta; Goossens, Herman; de Jong, Menno D; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia

    2013-01-01

    Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.

  6. Facial Beautification Method Based on Age Evolution

    Institute of Scientific and Technical Information of China (English)

    CHEN Yan; DING Shou-hong; HU Gan-le; MA Li-zhuang

    2013-01-01

    This paper proposes a new facial beautification method using facial rejuvenation based on the age evolution. Traditional facial beautification methods only focus on the color of skin and deformation and do the transformation based on an experimental standard of beauty. Our method achieves the beauty effect by making facial image looks younger, which is different from traditional methods and is more reasonable than them. Firstly, we decompose the image into different layers and get a detail layer. Secondly, we get an age-related parameter:the standard deviation of the Gaussian distribution that the detail layer follows, and the support vector machine (SVM) regression is used to fit a function about the age and the standard deviation. Thirdly, we use this function to estimate the age of input image and generate a new detail layer with a new standard deviation which is calculated by decreasing the age. Lastly, we combine the original layers and the new detail layer to get a new face image. Experimental results show that this algo-rithm can make facial image become more beautiful by facial rejuvenation. The proposed method opens up a new way about facial beautification, and there are great potentials for applications.

  7. The effects of inquiry-based summer enrichment activities on rising eighth graders' knowledge of science processes, attitude toward science, and perceptions of scientists

    Science.gov (United States)

    Moore, Juanita Martin

    The purpose of this research was to examine the effects of summer science enrichment on eighth-graders' science process skills knowledge, attitude toward science and perceptions of scientists. A single group pre- and post-test design was used to test participants in a summer science enrichment camp, which took place over a three-week period in the summer of 2000. Participants, all of whom were residents of the Mississippi area known as the Delta, lived on the campus of Mississippi Valley State University for the entire course of the camp. Activities included several guided inquiry-based projects such as water rocket design and solar or battery-powered car design. Participants also took trips to an environmental camp in north Mississippi and to the Stennis Space Center on the Mississippi Gulf Coast. Participants worked on their projects in groups, supervised by an undergraduate student "mentor". Participants were encouraged to keep journals of their experiences throughout the camp, and the researcher developed a rubric to evaluate student journals for process knowledge, evidence of planning, reflective thought, and disposition toward science. Tests were used to evaluate student knowledge of process skills, attitude toward science, and perceptions of scientists. On the Test of Integrated Process Skills (Dillashaw & Okey, 1983), the students showed significant improvement overall, but when evaluated separately, males showed significant improvement while females did not. On the Attitude toward Science in School Assessment (Germane, 1988), data indicated that attitude toward science improved significantly for the group as a whole, but upon closer inspection, indicated a significant improvement for the female students only. On Chamber's Draw-a-Scientist Test (1983), analysis of student drawings indicated no significant change in stereotypical images of scientists for the group overall. However, boys' scores indicated a significant improvement when analyzed separately

  8. AN SVAD ALGORITHM BASED ON FNNKD METHOD

    Institute of Scientific and Technical Information of China (English)

    Chen Dong; Zhang Yan; Kuang Jingming

    2002-01-01

    The capacity of mobile communication system is improved by using Voice Activity Detection (VAD) technology. In this letter, a novel VAD algorithm, SVAD algorithm based on Fuzzy Neural Network Knowledge Discovery (FNNKD) method is proposed. The performance of SVAD algorithm is discussed and compared with traditional algorithm recommended by ITU G.729B in different situations. The simulation results show that the SVAD algorithm performs better.

  9. A Novel Reverse-Transcriptase Real-Time PCR Method for Quantification of Viable Vibrio Parahemolyticus in Raw Shrimp Based on a Rapid Construction of Standard Curve Method

    OpenAIRE

    Mengtong Jin; Haiquan Liu; Wenshuo Sun; Qin Li; Zhaohuan Zhang; Jibing Li; Yingjie Pan; Yong Zhao

    2015-01-01

    Vibrio parahemolyticus is an important pathogen that leads to food illness associated seafood. Therefore, rapid and reliable methods to detect and quantify the total viable V. parahaemolyticus in seafood are needed. In this assay, a RNA-based real-time reverse-transcriptase PCR (RT-qPCR) without an enrichment step has been developed for detection and quantification of the total viable V. parahaemolyticus in shrimp. RNA standards with the target segments were synthesized in vitro with T7 RNA p...

  10. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    Science.gov (United States)

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.

  11. CLEAN: CLustering Enrichment ANalysis

    Directory of Open Access Journals (Sweden)

    Medvedovic Mario

    2009-07-01

    Full Text Available Abstract Background Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation. Results We developed a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score. The score is derived by correlating the clustering structure as a whole with functional categories of interest. We directly demonstrate that integrating biological knowledge in this way improves the reproducibility of conclusions derived from cluster analysis. The CLEAN score differentiates between the levels of functional coherence for genes within the same cluster based on their membership in enriched functional categories. We show that this aspect results in higher reproducibility across independent datasets and produces more informative genes for distinguishing different sample types than the scores based on the traditional cluster-wide analysis. We also demonstrate the utility of the CLEAN framework in comparing clusterings produced by different algorithms. CLEAN was implemented as an add-on R package and can be downloaded at http://Clusteranalysis.org. The package integrates routines for calculating gene specific functional coherence scores and the open source interactive Java-based viewer Functional TreeView (FTreeView. Conclusion Our results indicate that using the gene-specific functional coherence score improves the reproducibility of the

  12. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach.

    Science.gov (United States)

    He, Zhe; Chen, Zhiwei; Oh, Sanghee; Hou, Jinghui; Bian, Jiang

    2017-03-27

    The widely known vocabulary gap between health consumers and healthcare professionals hinders information seeking and health dialogue of consumers on end-user health applications. The Open Access and Collaborative Consumer Health Vocabulary (OAC CHV), which contains health-related terms used by lay consumers, has been created to bridge such a gap. Specifically, the OAC CHV facilitates consumers' health information retrieval by enabling consumer-facing health applications to translate between professional language and consumer friendly language. To keep up with the constantly evolving medical knowledge and language use, new terms need to be identified and added to the OAC CHV. User-generated content on social media, including social question and answer (social Q&A) sites, afford us an enormous opportunity in mining consumer health terms. Existing methods of identifying new consumer terms from text typically use ad-hoc lexical syntactic patterns and human review. Our study extends an existing method by extracting n-grams from a social Q&A textual corpus and representing them with a rich set of contextual and syntactic features. Using K-means clustering, our method, simiTerm, was able to identify terms that are both contextually and syntactically similar to the existing OAC CHV terms. We tested our method on social Q&A corpora on two disease domains: diabetes and cancer. Our method outperformed three baseline ranking methods. A post-hoc qualitative evaluation by human experts further validated that our method can effectively identify meaningful new consumer terms on social Q&A.

  13. Background and Objective: Listeria monocytogenes is a bacterium transferred by foods and is the agent of many sporadic and epidemic diseases in humans. This study aimed to investigate the prevalence of L. monocytogenes and to determinine their antibiotic resistance profile in red meats. Material and Methods: this cross-sectional study was performed on 400 red meat samples obtained from industrial slaughterhouses placed in Kerman, Iran. First, the samples were enriched with Simultaneous Enrichment Broth (SEB, and then plated onto Palcam agar and Tryptic Soy Broth Yeast Extract Broth (TSAYE. After identification of the isolates based on biochemical tests and PCR, the isolates were checked for their antibiotic resistance profile using disk Diffusion Results: of 400 samples, 12 samples (3% were contaminated with different species of Listeria. Using PCR, hly gene was recognized in eight samples (2% of L. monocytogenes. Furthermore, there was a significant difference in isolation rate of lamb samples compared to cow ones. While all of the isolates were resistant to clindamycin, amikacin and chloramphenicol, they were sensitive to penicillin. Conclusion: in spite of low rate of infection in red meat samples in Kerman city, due to high risk of Listeria contamination in red meats, we recommend applying a routine screening to identify this bacterium in our county.

    Directory of Open Access Journals (Sweden)

    Kargar, M. (PhD

    2014-11-01

    Full Text Available Background and Objective: Listeria monocytogenes is a bacterium transferred by foods and is the agent of many sporadic and epidemic diseases in humans. This study aimed to investigate the prevalence of L. monocytogenes and to determinine their antibiotic resistance profile in red meats. Material and Methods: this cross-sectional study was performed on 400 red meat samples obtained from industrial slaughterhouses placed in Kerman, Iran. First, the samples were enriched with Simultaneous Enrichment Broth (SEB, and then plated onto Palcam agar and Tryptic Soy Broth Yeast Extract Broth (TSAYE. After identification of the isolates based on biochemical tests and PCR, the isolates were checked for their antibiotic resistance profile using disk Diffusion Results: of 400 samples, 12 samples (3% were contaminated with different species of Listeria. Using PCR, hly gene was recognized in eight samples (2% of L. monocytogenes. Furthermore, there was a significant difference in isolation rate of lamb samples compared to cow ones. While all of the isolates were resistant to clindamycin, amikacin and chloramphenicol, they were sensitive to penicillin. Conclusion: in spite of low rate of infection in red meat samples in Kerman city, due to high risk of Listeria contamination in red meats, we recommend applying a routine screening to identify this bacterium in our county

  14. A general modular framework for gene set enrichment analysis

    Directory of Open Access Journals (Sweden)

    Strimmer Korbinian

    2009-02-01

    Full Text Available Abstract Background Analysis of microarray and other high-throughput data on the basis of gene sets, rather than individual genes, is becoming more important in genomic studies. Correspondingly, a large number of statistical approaches for detecting gene set enrichment have been proposed, but both the interrelations and the relative performance of the various methods are still very much unclear. Results We conduct an extensive survey of statistical approaches for gene set analysis and identify a common modular structure underlying most published methods. Based on this finding we propose a general framework for detecting gene set enrichment. This framework provides a meta-theory of gene set analysis that not only helps to gain a better understanding of the relative merits of each embedded approach but also facilitates a principled comparison and offers insights into the relative interplay of the methods. Conclusion We use this framework to conduct a computer simulation comparing 261 different variants of gene set enrichment procedures and to analyze two experimental data sets. Based on the results we offer recommendations for best practices regarding the choice of effective procedures for gene set enrichment analysis.

  15. Lagrangian based methods for coherent structure detection

    Energy Technology Data Exchange (ETDEWEB)

    Allshouse, Michael R., E-mail: mallshouse@chaos.utexas.edu [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: tomp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2015-09-15

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  16. An attribute-based image segmentation method

    Directory of Open Access Journals (Sweden)

    M.C. de Andrade

    1999-07-01

    Full Text Available This work addresses a new image segmentation method founded on Digital Topology and Mathematical Morphology grounds. The ABA (attribute based absorptions transform can be viewed as a region-growing method by flooding simulation working at the scale of the main structures of the image. In this method, the gray level image is treated as a relief flooded from all its local minima, which are progressively detected and merged as the flooding takes place. Each local minimum is exclusively associated to one catchment basin (CB. The CBs merging process is guided by their geometric parameters as depth, area and/or volume. This solution enables the direct segmentation of the original image without the need of a preprocessing step or the explicit marker extraction step, often required by other flooding simulation methods. Some examples of image segmentation, employing the ABA transform, are illustrated for uranium oxide samples. It is shown that the ABA transform presents very good segmentation results even in presence of noisy images. Moreover, it's use is often easier and faster when compared to similar image segmentation methods.

  17. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.

    Science.gov (United States)

    Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

    2013-01-07

    Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms' taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.

  18. Chapter 11. Community analysis-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.

    2010-05-01

    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  19. The development of the MACE work-family enrichment instrument

    Directory of Open Access Journals (Sweden)

    Marissa de Klerk

    2013-03-01

    Full Text Available Orientation: An instrument based on a theoretical model is necessary to measure the positive side of the work-family interface.Research purpose: To develop items for measurement of work-family enrichment based on the elements contained within a theoretical model and to evaluate the latent trait functioning of these items.Motivation for the study: Major limitations exist regarding the conceptualisation and scale development of the positive side of the work-family interface.Research design, approach, and method: A quantitative research approach using scale development procedures was employed to develop the 95-item instrument. A cross-sectional survey design was used to collect data randomly from selected employees; data were processed using Rasch analysis.Main findings: The five-category scale works well for the most part, although a four-category scale could be considered. Thirty-five items either over-fitted or under-fitted the work-family enrichment model. Person ability was measured in the low to middle ranges of work-family enrichment. Participants’ experience of work-family enrichment could be represented accurately. Sub-scale items displayed misfit, bias or both.Practical/managerial implications: The developed instrument can be investigated further to identify work-family enrichment factors that can measure workers’ experience of enrichment in their work and family domains.Contribution/value-add: This study furthers theory building and empirical research in industrial psychology, by developing a new theory-based measuring instrument for the positive side of the work-family interface in the South African context. This study expanded on the model proposed by Greenhaus and Powell, by including all five categories of resources gains. Furthermore, the total of the resources was diversified, since some of the content of these resources encompasses multiple meanings.

  20. A cage-based training, cognitive testing and enrichment system optimized for rhesus macaques in neuroscience research.

    Science.gov (United States)

    Calapai, A; Berger, M; Niessing, M; Heisig, K; Brockhausen, R; Treue, S; Gail, A

    2017-02-01

    In neurophysiological studies with awake non-human primates (NHP), it is typically necessary to train the animals over a prolonged period of time on a behavioral paradigm before the actual data collection takes place. Rhesus monkeys (Macaca mulatta) are the most widely used primate animal models in system neuroscience. Inspired by existing joystick- or touch-screen-based systems designed for a variety of monkey species, we built and successfully employed a stand-alone cage-based training and testing system for rhesus monkeys (eXperimental Behavioral Intrument, XBI). The XBI is mobile and easy to handle by both experts and non-experts; animals can work with only minimal physical restraints, yet the ergonomic design successfully encourages stereotypical postures with a consistent positioning of the head relative to the screen. The XBI allows computer-controlled training of the monkeys with a large variety of behavioral tasks and reward protocols typically used in systems and cognitive neuroscience research.

  1. Formulation and characterization of a nutritional pumpkin-based whey beverages, enriched with oatmeal and passion fruit

    Directory of Open Access Journals (Sweden)

    Alex Valencia

    2015-12-01

    Full Text Available In this work, the effect on the addition of oatmeal (Avena sativa and passion fruit (Passiflora edulis in the content of fiber, calcium, iron, phosphorus and A vitamin in beverage formulation based on pumpkin (Cucurbita maxima, milk and whey, was determined. The beverages undergone significant changes during the storage time, the pH decreased as the acidity showed a slight increase. The coordinates of CIELAB (L *, a * and b * were located in quadrant 1 indicating a clear tendency to yellow caused by the presence of carotenoids from the pumpkin and passion fruit. Based on the sensory analysis it was selected best treatment who was higher in 3 of the 4 parameters evaluated. This sample also presented a pseudoplastic behavior with a consistency index of 3.57 Pa.s0.24 and a shelf life of 9 days

  2. Custom Fusion Methode Based on Borda

    Directory of Open Access Journals (Sweden)

    Issam Abdelbaki

    2016-10-01

    Full Text Available Searching for information on the Internet is not only an activity newly rediscovered, but also a strategic tool to achieve a wide variety of information. Indeed, it’s extremely important to know how to find the information quickly and efficiently. Unfortunately, the Web is so huge and so little structured, that gathering precise, fair and useful information becomes an expensive task. In order to define an information retrieval tool (meta search engine that brings together multiple sources of information search, interest must be credited to the merger phase of search engines results. On the other hand, information search systems tend primarily to model the user with a profile and then to integrate it into the information access chain, to better meet its specific needs. This paper presents a custom fusion method based on Borda method and values retrieved from the user profile. We evaluated our approach on multiple domains and we present some experimental results.

  3. Kernel method-based fuzzy clustering algorithm

    Institute of Scientific and Technical Information of China (English)

    Wu Zhongdong; Gao Xinbo; Xie Weixin; Yu Jianping

    2005-01-01

    The fuzzy C-means clustering algorithm(FCM) to the fuzzy kernel C-means clustering algorithm(FKCM) to effectively perform cluster analysis on the diversiform structures are extended, such as non-hyperspherical data, data with noise, data with mixture of heterogeneous cluster prototypes, asymmetric data, etc. Based on the Mercer kernel, FKCM clustering algorithm is derived from FCM algorithm united with kernel method. The results of experiments with the synthetic and real data show that the FKCM clustering algorithm is universality and can effectively unsupervised analyze datasets with variform structures in contrast to FCM algorithm. It is can be imagined that kernel-based clustering algorithm is one of important research direction of fuzzy clustering analysis.

  4. Trinocular Calibration Method Based on Binocular Calibration

    Directory of Open Access Journals (Sweden)

    CAO Dan-Dan

    2012-10-01

    Full Text Available In order to solve the self-occlusion problem in plane-based multi-camera calibration system and expand the measurement range, a tri-camera vision system based on binocular calibration is proposed. The three cameras are grouped into two pairs, while the public camera is taken as the reference to build the global coordinate. By calibration of the measured absolute distance and the true absolute distance, global calibration is realized. The MRE (mean relative error of the global calibration of the two camera pairs in the experiments can be as low as 0.277% and 0.328% respectively. Experiment results show that this method is feasible, simple and effective, and has high precision.

  5. On Task-based English Learning Method

    Institute of Scientific and Technical Information of China (English)

    朱蕾

    2010-01-01

    @@ Task-Based learning(TBL)is becoming a catchword in English circles.The new national English Curricular Syllabus also recommends the use of the TBL approach in classroom teaching.The purpose of learning a foreign language is the most direct communicative in the target language,and speaking is the most direct communicative method.In recent years,with the publication of the New Curriculum Standard by the State Education Department,the teaching reform in middle and primary schools has been being implemented step by step.

  6. Improving data management and dissemination in web based information systems by semantic enrichment of descriptive data aspects

    Science.gov (United States)

    Gebhardt, Steffen; Wehrmann, Thilo; Klinger, Verena; Schettler, Ingo; Huth, Juliane; Künzer, Claudia; Dech, Stefan

    2010-10-01

    The German-Vietnamese water-related information system for the Mekong Delta (WISDOM) project supports business processes in Integrated Water Resources Management in Vietnam. Multiple disciplines bring together earth and ground based observation themes, such as environmental monitoring, water management, demographics, economy, information technology, and infrastructural systems. This paper introduces the components of the web-based WISDOM system including data, logic and presentation tier. It focuses on the data models upon which the database management system is built, including techniques for tagging or linking metadata with the stored information. The model also uses ordered groupings of spatial, thematic and temporal reference objects to semantically tag datasets to enable fast data retrieval, such as finding all data in a specific administrative unit belonging to a specific theme. A spatial database extension is employed by the PostgreSQL database. This object-oriented database was chosen over a relational database to tag spatial objects to tabular data, improving the retrieval of census and observational data at regional, provincial, and local areas. While the spatial database hinders processing raster data, a "work-around" was built into WISDOM to permit efficient management of both raster and vector data. The data model also incorporates styling aspects of the spatial datasets through styled layer descriptions (SLD) and web mapping service (WMS) layer specifications, allowing retrieval of rendered maps. Metadata elements of the spatial data are based on the ISO19115 standard. XML structured information of the SLD and metadata are stored in an XML database. The data models and the data management system are robust for managing the large quantity of spatial objects, sensor observations, census and document data. The operational WISDOM information system prototype contains modules for data management, automatic data integration, and web services for data

  7. Digestion and ruminal fermentation of cocoa pod silage based ration enriched by gliricidia and calliandra leaves on goats

    OpenAIRE

    Puastuti W; Widiawati Y; Wina E

    2015-01-01

    In term of availability, cacao pod is potential for ruminant feed. According to its nutrients content, cacao pod can be used as feed fiber source. Protein sources materials must be added when cacao pod was ensilaged due to low protein content of this material. The aim of this study was to investigate digestibility value and end products of rumen fermentation of goat fed grass or cacao pod based ration. Randomized block design and 20 heads of lambs (16.95±2.36 kg) to evaluated 5 type of ration...

  8. The limitations of simple gene set enrichment analysis assuming gene independence.

    Science.gov (United States)

    Tamayo, Pablo; Steinhardt, George; Liberzon, Arthur; Mesirov, Jill P

    2016-02-01

    Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods.

  9. A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies

    Directory of Open Access Journals (Sweden)

    Simon Uribe-Convers

    2014-01-01

    Full Text Available Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing. Our approach can be used to generate templates from any DNA source for next-generation sequencing. Here we test our approach by amplifying complete chloroplast genomes, and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear and mitochondrial regions. Methods and Results: Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. Conclusions: Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies.

  10. Bus Based Synchronization Method for CHIPPER Based NoC

    Directory of Open Access Journals (Sweden)

    D. Muralidharan

    2016-01-01

    Full Text Available Network on Chip (NoC reduces the communication delay of System on Chip (SoC. The main limitation of NoC is power consumption and area overhead. Bufferless NoC reduces the area complexity and power consumption by eliminating buffers in the traditional routers. The bufferless NoC design should include live lock freeness since they use hot potato routing. This increases the complexity of bufferless NoC design. Among the available propositions to reduce this complexity, CHIPPER based bufferless NoC is considered as one of the best options. Live lock freeness is provided in CHIPPER through golden epoch and golden packet. All routers follow some synchronization method to identify a golden packet. Clock based method is intuitively followed for synchronization in CHIPPER based NoCs. It is shown in this work that the worst-case latency of packets is unbearably high when the above synchronization is followed. To alleviate this problem, broadcast bus NoC (BBus NoC approach is proposed in this work. The proposed method decreases the worst-case latency of packets by increasing the golden epoch rate of CHIPPER.

  11. Screening Key Genes Associated with the Development and Progression of Non-small Cell Lung Cancer Based on Gene-enrichment Analysis and Meta-analysis

    Directory of Open Access Journals (Sweden)

    Wenwu HE

    2012-07-01

    Full Text Available Background and objective Non-small cell lung cancer (NSCLC is one of the most common malignant tumors; however, its causes are still not completely understood. This study was designed to screen the key genes and pathways related to NSCLC occurrence and development and to establish the scientific foundation for the genetic mechanisms and targeted therapy of NSCLC. Methods Both gene set-enrichment analysis (GSEA and meta-analysis (meta were used to screen the critical pathways and genes that might be corretacted with the development and progression of lung cancer at the transcription level. Results Using the GSEA and meta methods, focal adhesion and regulation of actin cytoskeleton were determined to be the more prominent overlapping significant pathways. In the focal adhesion pathway, 31 genes were statistically significant (P<0.05, whereas in the regulation of actin cytoskeleton pathway, 32 genes were statistically significant (P<0.05. Conclusion The focal adhesion and the regulation of actin cytoskeleton pathways might play important roles in the occurrence and development of NSCLC. Further studies are needed to determine the biological function for the positiue genes.

  12. Development and characterization of a nanodendritic silver-based solid-phase extraction sorbent for selective enrichment of endocrine-disrupting chemicals in water and milk samples.

    Science.gov (United States)

    Gao, Yuanji; Xia, Bing; Liu, Jie; Ji, Baocheng; Ma, Fengwei; Ding, Lisheng; Li, Bangjing; Zhou, Yan

    2015-11-01

    In this study, 4-[4-phenylazo-phenoxy] butyl-1-thiol (AzSH) functionalized nanodendritic silver (AzS@AgNDs) materials were prepared as a solid-phase extraction (SPE) sorbent for the selective extraction of estrogens. AzS@AgNDs possess an extremely large surface-to-volume ratio and a small average particle size. The performance of the material was evaluated by selective enrichment of hexestrol, diethylstilbestrol, dienestrol and bisphenol A in water and milk samples followed by rapid ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC-ESI-MS) analyses. The results exhibited that AzS@AgNDs had excellent adsorption capability for the targeted estrogens. The limits of detection of the four estrogens ranged from 0.1 to 5.0 pg/mL. The recoveries of the estrogens spiked into tap water were over the range of 83.6-105.3% with relative standard deviations of 2.8-6.0%. The results indicated the capability of this method for the rapid determination of estrogens in milk and other environmental water samples. In addition, this method would be useful for the determination of human exposure and health risk assessments trace level of endocrine-disrupting compounds (EDCs) in drinking water.

  13. ProbCD: enrichment analysis accounting for categorization uncertainty

    Directory of Open Access Journals (Sweden)

    Shmulevich Ilya

    2007-10-01

    Full Text Available Abstract Background As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. Results We developed an open-source R-based software to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. Conclusion We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i the stochastic nature of the high-throughput experimental techniques and (ii probabilistic gene annotation.

  14. Membrane-based gas separation of ethylene/ethylene oxide mixtures for product enrichment in microreactor technology.

    Science.gov (United States)

    Schiewe, B; Staudt-Bickel, C; Vuin, A; Wegner, G

    2001-04-17

    For the off-gas product separation in an ethylene oxide microreactor, new concepts need to be developed. Instead of using the technical process of low-temperature distillation, the performance of gas separation through a dense polymeric membrane was investigated. Different noncrosslinked and crosslinked 6FDA-based polyimides and copolyimides (6FDA=4,4'-hexafluoroisopropylidene diphthalic anhydride) were screened as potential membrane materials. The polymer structure of the membrane material was found to influence the solubility of ethylene oxide and ethylene. The introduction of polar substituents in the polymer backbone increases the solubility selectivity drastically. For permeation experiments in the same pressure range, a novel setup was developed using microstructured membrane supports. With this device, different polymer membranes were tested with respect to the pure gas permeability of ethylene oxide and ethylene as a function of the feed pressure, so that plasticisation effects could be discussed. For different polyimides and copolyimides, ideal ethylene oxide/ethylene selectivities between 3 and 4.5 were found combined with permeabilities between 1.8 and 80.8 barrer.

  15. Recovery of Listeria monocytogenes from vacuum-sealed packages of frankfurters: comparison of the U.S. Department of Agriculture (USDA) food safety and inspection service product composite enrichment method, the USDA Agricultural Research Service (ARS) product composite rinse method, and the USDA-ARS package rinse method.

    Science.gov (United States)

    Luchansky, John B; Porto, Anna C S; Wallace, F Morgan; Call, Jeffrey E

    2002-03-01

    This study compared three methods for the recovery of Listeria monocytogenes from commercially prepared and vacuum-packaged frankfurters that were inoculated with a five-strain mixture of this pathogen at averages of 22 and 20,133 CFU per package over three trials. The presence and levels of the pathogen were determined by (i) the U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) product composite enrichment method, involving the selective enrichment of a 25-g composite of product and the subsequent plating of this product onto selective agar plates; (ii) the USDA Agricultural Research Service (ARS) product composite rinse method, involving the rinsing of a 25-g composite of product with 0.1% peptone water and the subsequent plating of a portion of the rinse fluid directly onto selective agar plates; and (iii) the USDA-ARS package rinse method, involving the use of 25 ml of 0.1% peptone water to rinse the entire contents of a package and the subsequent plating of a portion of the rinse fluid directly onto selective agar plates. For packages inoculated with 20,133 CFU. L. monocytogenes was recovered at a frequency (percentage of packages positive) of 100% by each of the three methods. The pathogen was recovered at efficiencies (percentages of recovery of L. monocytogenes) of 43 and 94% with the USDA-ARS product rinse method and the USDA-ARS package rinse method, respectively. For packages inoculated with 22 CFU, L. monocytogenes was recovered at frequencies of 17, 10, and 100% by the USDA-FSIS product composite enrichment method, the USDA-ARS product composite rinse method, and the USDA-ARS package rinse method, respectively. The pathogen was recovered at efficiencies of 20 and 95% with the USDA-ARS product composite rinse method and the USDA-ARS package rinse method, respectively. In a related study, the USDA-ARS package rinse method was the only method that detected the pathogen in 60 packages from each of five brands of frankfurters

  16. Multicenter validation of PCR-based method for detection of Salmonella in chicken and pig samples

    DEFF Research Database (Denmark)

    Malorny, B.; Cook, N.; D'Agostino, M.;

    2004-01-01

    As part of a standardization project, an interlaboratory trial including 15 laboratories from 13 European countries was conducted to evaluate the performance of a noproprietary polymerase chain reaction (PCR)-based method for the detection of Salmonella on artificially contaminated chicken rinse...... and pig swab samples. The 3 levels were 1-10, 10-100, and 100-1000 colony-forming units (CFU)/100 mL. Sample preparations, including inoculation and pre-enrichment in buffered peptone water (BPW), were performed centrally in a German laboratory; the pre-PCR sample preparation (by a resin-based method...... specificity was 80.1% (with 85.7% accordance and 67.5% concordance) for chicken rinse, and 91.7% (with 100% accordance and 83.3% concordance) for pig swab. Thus, the interlaboratory variation due to personnel, reagents, thermal cyclers, etc., did not affect the performance of the method, which...

  17. Deuterium enrichment of interstellar dusts

    Science.gov (United States)

    Das, Ankan; Chakrabarti, Sandip Kumar; Majumdar, Liton; Sahu, Dipen

    2016-07-01

    High abundance of some abundant and simple interstellar species could be explained by considering the chemistry that occurs on interstellar dusts. Because of its simplicity, the rate equation method is widely used to study the surface chemistry. However, because the recombination efficiency for the formation of any surface species is highly dependent on various physical and chemical parameters, the Monte Carlo method is best suited for addressing the randomness of the processes. We carry out Monte-Carlo simulation to study deuterium enrichment of interstellar grain mantle under various physical conditions. Based on the physical properties, various types of clouds are considered. We find that in diffuse cloud regions, very strong radiation fields persists and hardly a few layers of surface species are formed. In translucent cloud regions with a moderate radiation field, significant number of layers would be produced and surface coverage is mainly dominated by photo-dissociation products such as, C, CH_3, CH_2D, OH and OD. In the intermediate dense cloud regions (having number density of total hydrogen nuclei in all forms ˜2 × 10^4 cm^{-3}), water and methanol along with their deuterated derivatives are efficiently formed. For much higher density regions (˜10^6 cm^{-3}), water and methanol productions are suppressed but surface coverage of CO, CO_2, O_2, O_3 are dramatically increased. We find a very high degree of fractionation of water and methanol. Observational results support a high fractionation of methanol but surprisingly water fractionation is found to be low. This is in contradiction with our model results indicating alternative routes for de-fractionation of water.

  18. Community-aware user profile enrichment in folksonomy.

    Science.gov (United States)

    Xie, Haoran; Li, Qing; Mao, Xudong; Li, Xiaodong; Cai, Yi; Rao, Yanghui

    2014-10-01

    In the era of big data, collaborative tagging (a.k.a. folksonomy) systems have proliferated as a consequence of the growth of Web 2.0 communities. Constructing user profiles from folksonomy systems is useful for many applications such as personalized search and recommender systems. The identification of latent user communities is one way to better understand and meet user needs. The behavior of users is highly influenced by the behavior of their neighbors or community members, and this can be utilized in constructing user profiles. However, conventional user profiling techniques often encounter data sparsity problems as data from a single user is insufficient to build a powerful profile. Hence, in this paper we propose a method of enriching user profiles based on latent user communities in folksonomy data. Specifically, the proposed approach contains four sub-processes: (i) tag-based user profiles are extracted from a folksonomy tripartite graph; (ii) a multi-faceted folksonomy graph is constructed by integrating tag and image affinity subgraphs with the folksonomy tripartite graph; (iii) random walk distance is used to unify various relationships and measure user similarities; (iv) a novel prototype-based clustering method based on user similarities is used to identify user communities, which are further used to enrich the extracted user profiles. To evaluate the proposed method, we conducted experiments using a public dataset, the results of which show that our approach outperforms previous ones in user profile enrichment.

  19. Graph-based Methods for Orbit Classification

    Energy Technology Data Exchange (ETDEWEB)

    Bagherjeiran, A; Kamath, C

    2005-09-29

    An important step in the quest for low-cost fusion power is the ability to perform and analyze experiments in prototype fusion reactors. One of the tasks in the analysis of experimental data is the classification of orbits in Poincare plots. These plots are generated by the particles in a fusion reactor as they move within the toroidal device. In this paper, we describe the use of graph-based methods to extract features from orbits. These features are then used to classify the orbits into several categories. Our results show that existing machine learning algorithms are successful in classifying orbits with few points, a situation which can arise in data from experiments.

  20. Microsatellite DNA capture from enriched libraries.

    Science.gov (United States)

    Gonzalez, Elena G; Zardoya, Rafael

    2013-01-01

    Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

  1. Pose measurement method based on geometrical constraints

    Institute of Scientific and Technical Information of China (English)

    Zimiao Zhang; Changku Sun; Pengfei Sun; Peng Wang

    2011-01-01

    @@ The pose estimation method based on geometric constraints is studied.The coordinates of the five feature points in the camera coordinate system are calculated to obtain the pose of an object on the basis of the geometric constraints formed by the connective lines of the feature points and the coordinates of the feature points on the CCD image plane; during the solution process,the scaling and orthography projection model is used to approximate the perspective projection model.%The pose estimation method based on geometric constraints is studied. The coordinates of the five feature points in the camera coordinate system are calculated to obtain the pose of an object on the basis of the geometric constraints formed by the connective lines of the feature points and the coordinates of the feature points on the CCD image plane; during the solution process, the scaling and orthography projection model is used to approximate the perspective projection model. The initial values of the coordinates of the five feature points in the camera coordinate system are obtained to ensure the accuracy and convergence rate of the non-linear algorithm. In accordance with the perspective projection characteristics of the circular feature landmarks, we propose an approach that enables the iterative acquisition of accurate target poses through the correction of the perspective projection coordinates of the circular feature landmark centers. Experimental results show that the translation positioning accuracy reaches ±0.05 mm in the measurement range of 0-40 mm, and the rotation positioning accuracy reaches ±0.06° in the measurement range of 4°-60°.

  2. Mixed hemimicelles solid-phase extraction based on sodium dodecyl sulfate-coated nano-magnets for selective adsorption and enrichment of illegal cationic dyes in food matrices prior to high-performance liquid chromatography-diode array detection detection.

    Science.gov (United States)

    Qi, Ping; Liang, Zhi-an; Wang, Yu; Xiao, Jian; Liu, Jia; Zhou, Qing-qiong; Zheng, Chun-hao; Luo, Li-Ni; Lin, Zi-hao; Zhu, Fang; Zhang, Xue-wu

    2016-03-11

    In this study, mixed hemimicelles solid-phase extraction (MHSPE) based on sodium dodecyl sulfate (SDS) coated nano-magnets Fe3O4 was investigated as a novel method for the extraction and separation of four banned cationic dyes, Auramine O, Rhodamine B, Basic orange 21 and Basic orange 22, in condiments prior to HPLC detection. The main factors affecting the extraction of analysts, such as pH, surfactant and adsorbent concentrations and zeta potential were studied and optimized. Under optimized conditions, the proposed method was successful applied for the analysis of banned cationic dyes in food samples such as chili sauce, soybean paste and tomato sauce. Validation data showed the good recoveries in the range of 70.1-104.5%, with relative standard deviations less than 15%. The method limits of determination/quantification were in the range of 0.2-0.9 and 0.7-3μgkg(-1), respectively. The selective adsorption and enrichment of cationic dyes were achieved by the synergistic effects of hydrophobic interactions and electrostatic attraction between mixed hemimicelles and the cationic dyes, which also resulted in the removal of natural pigments interferences from sample extracts. When applied to real samples, RB was detected in several positive samples (chili powders) within the range from 0.042 to 0.177mgkg(-1). These results indicate that magnetic MHSPE is an efficient and selective sample preparation technique for the extraction of banned cationic dyes in a complex matrix.

  3. Satellite Formation based on SDDF Method

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2014-04-01

    Full Text Available The technology of satellite formation flying has being a research focus in flight application. The relative position and velocity between satellites are basic parameters to achieve the control of formation flight during the satellite formation flying mission. In order to improve the navigation accuracy, a new filter different from Extended Kalman Filter (EKF should be adopted to estimate the errors of relative position and velocity, which is based on the nonlinearity of the kinetic model for the satellite formation flying. A nonlinear Divided Difference Filter (DDF based on Stirling interpolation formula was proposed in this paper. According to the linearity of the measurement equation for the filter, a simplified differential filter was designed by means of expanding the polynomial of the nonlinear system equation and linear approximating of the finite differential interpolation. Digital simulation experiment for the relative positioning of satellite formation flying was carried out. The result demonstrates that the filter proposed in this paper has a higher filtering accuracy, faster convergence speed and better stability. Compared with the EKF, the estimation accuracy of the relative position and velocity has improved by 77.1%and 47% respectively in the method of simplified DDF, which indicates the significance for practical applications. 

  4. Improving stability and activity of cross-linked enzyme aggregates based on polyethylenimine in hydrolysis of fish oil for enrichment of polyunsaturated fatty acids.

    Science.gov (United States)

    Yan, Jinyong; Gui, Xiaohua; Wang, Guilong; Yan, Yunjun

    2012-02-01

    Cross-linking of enzyme aggregates from recombinant Geotrichum sp. lipase based on polyethylenimine (PEI) was applied to hydrolyze fish oil for enrichment of polyunsaturated fatty acids successfully. Through acetone precipitation and cross-linking of physical aggregates using glutaraldehyde in the presence of PEI, firmly cross-linked enzyme aggregates (PEI-CLEAs) were prepared. They could maintain more than 65% of relative hydrolysis degree after incubation in the range of 50-55 °C for 4 h and maintain more than 85% of relative hydrolysis degree after being treated by acetone, tert-butyl alcohol and octane for 4 h. PEI-CLEAs increased hydrolysis degree to 42% from 12% by free lipase. After five batch reactions, PEI-CLEAs still maintained 72% of relative hydrolysis degree. Hydrolysis of fish oil by PEI-CLEAs produced glycerides containing concentrated EPA and DHA in good yield. PEI-CLEAs had advantages over general CLEAs and free lipase in initial reaction rate, hydrolysis degree, thermostability, organic solvent tolerance and reusability.

  5. Uranium Conversion & Enrichment

    Energy Technology Data Exchange (ETDEWEB)

    Karpius, Peter Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-06

    The isotopes of uranium that are found in nature, and hence in ‘fresh’ Yellowcake’, are not in relative proportions that are suitable for power or weapons applications. The goal of conversion then is to transform the U3O8 yellowcake into UF6. Conversion and enrichment of uranium is usually required to obtain material with enough 235U to be usable as fuel in a reactor or weapon. The cost, size, and complexity of practical conversion and enrichment facilities aid in nonproliferation by design.

  6. Selective enrichment and desalting of hydrophilic peptides using graphene oxide.

    Science.gov (United States)

    Jiang, Miao; Qi, Linyu; Liu, Peiru; Wang, Zijun; Duan, Zhigui; Wang, Ying; Liu, Zhonghua; Chen, Ping

    2016-08-01

    The wide variety and low abundance of peptides in tissue brought great difficulties to the separation and identification of peptides, which is not in favor of the development of peptidomics. RP-HPLC, which could purify small molecules based on their hydrophobicity, has been widely used in the separation and enrichment of peptide due to its fast, good reproducibility and high resolution. However, RP-HPLC requires the instrument and expensive C18 column and its sample capacity is also limited. Recently, graphene oxide has been applied to the adsorption of amino acids. However, the enrichment efficiency and selectivity of graphene oxide for peptides remain unclear. In this study, the adsorption efficiency and selectivity of graphene oxide and RP-C18 matrix were compared on trypsinized α-actin and also on tissue extracts from pituitary gland and hippocampus. For α-actin, there exhibit similar elution peaks for total trypsinized products and those adsorpted by GO and C18 matrix. But peptides adsorbed by GO showed the higher hydrophilic peaks than which adsorbed by C18 matrix. The resulted RP-HPLC profile showed that most of peptides enriched by graphene oxide were eluted at low concentration of organic solvent, while peptides adsorbed by RP-C18 matrix were mostly eluted at relatively high concentration. Moreover, mass spectrometry analysis suggested that, in pituitary sample, there were 495 peptides enriched by graphene oxide, 447 peptides enriched by RP-C18 matrix while in hippocampus sample 333 and 243 peptides respectively. The GRAVY value analysis suggested that the graphene oxide has a stronger adsorption for highly hydrophilic peptides compared to the RP-C18 matrix. Furthermore, the combination of these two methods could notably increase the number of identification peptides but also the number of predicted protein precursors. Our study provided a new thought to the role of graphene oxide during the enrichment of peptides from tissue which should be useful for

  7. Preparation of stir cake sorptive extraction based on polymeric ionic liquid for the enrichment of benzimidazole anthelmintics in water, honey and milk samples.

    Science.gov (United States)

    Wang, Yulei; Zhang, Jie; Huang, Xiaojia; Yuan, Dongxing

    2014-08-20

    In this work, a new stir cake sorptive extraction (SCSE) using polymeric ionic liquid monolith as sorbent was prepared. The sorbent was obtained by in situ copolymerization of an ionic liquid, 1-allyl-3-methylimidazolium bis[(trifluoro methyl)sulfonyl]imide (AMII) and divinylbenzene (DB) in the presence of N,N-dimethylformamide. The influence of the content of ionic liquid and the porogen in the polymerization mixture on extraction performance was studied thoroughly. The physicochemical properties of the polymeric ionic liquid were characterized by infrared spectroscopy, elemental analysis, scanning electron microscopy and mercury intrusion porosimetry. The usefulness of SCSE-AMIIDB was demonstrated by the enrichment of trace benzimidazole anthelmintics. Several parameters affecting the extraction efficiency were investigated, and under the optimized conditions, a simple and effective method for the determination of trace benzimidazoles residues in water, milk and honey samples was established by coupling SCSE-AMIIDB with high performance liquid chromatography/diode array detection (SCSE-AMIIDB-HPLC/DAD). Results indicated that the limits of detection (S/N=3) for target compounds were 0.020-0.072 μg L(-1), 0.035-0.10 μg L(-1) and 0.026-0.076 μg L(-1) in water, milk and honey samples, respectively. In addition, an acceptable reproducibility was achieved by evaluating the repeatability and intermediate precision with relative standard deviations (RSD) of less than 9% and 11%, respectively. Finally, the established AMII-SCSE-HPLC/DAD method was successfully applied for the determination of benzimidazoles residues in milk, honey and environmental water samples. Recoveries obtained for the determination of benzimidazole anthelmintics in spiking samples ranged from 70.2% to 117.6%, with RSD below 12% in all cases.

  8. Profile of World Uranium Enrichment Programs-2009

    Energy Technology Data Exchange (ETDEWEB)

    Laughter, Mark D [ORNL

    2009-04-01

    It is generally agreed that the most difficult step in building a nuclear weapon is acquiring fissile material, either plutonium or highly enriched uranium (HEU). Plutonium is produced in a nuclear reactor, whereas HEU is produced using a uranium enrichment process. Enrichment is also an important step in the civil nuclear fuel cycle, in producing low enriched uranium (LEU) for use as fuel for nuclear reactors to generate electricity. However, the same equipment used to produce LEU for nuclear reactor fuel can also be used to produce HEU for weapons. Safeguards at an enrichment plant are the array of assurances and verification techniques that ensure uranium is not diverted or enriched to HEU. There are several techniques for enriching uranium. The two most prevalent are gaseous diffusion, which uses older technology and requires a lot of energy, and gas centrifuge separation, which uses more advanced technology and is more energy efficient. Gaseous diffusion plants (GDPs) provide about 40% of current world enrichment capacity but are being phased out as newer gas centrifuge enrichment plants (GCEPs) are constructed. Estimates of current and future enrichment capacity are always approximate, due to the constant upgrades, expansions, and shutdowns occurring at enrichment plants, largely determined by economic interests. Currently, the world enrichment capacity is approximately 56 million kilogram separative work units (SWU) per year, with 22.5 million in gaseous diffusion and more than 33 million in gas centrifuge plants. Another 34 million SWU/year of capacity is under construction or planned for the near future, almost entirely using gas centrifuge separation. Other less-efficient techniques have also been used in the past, including electromagnetic and aerodynamic separations, but these are considered obsolete, at least from a commercial perspective. Laser isotope separation shows promise as a possible enrichment technique of the future but has yet to be

  9. The Low Chamber Pancreatic Cancer Cells Had Stem-Like Characteristics in Modified Transwell System: Is It a Novel Method to Identify and Enrich Cancer Stem-Like Cells?

    Directory of Open Access Journals (Sweden)

    Dongqing Wang

    2014-01-01

    Full Text Available Cancer stem cells (CSCs or cancer-initiating cells (CICs play an important role in tumor initiation, progression, metastasis, chemoresistance, and recurrence. It is important to construct an effective method to identify and isolate CSCs for biotherapy of cancer. During the past years, many researchers had paid more attention to it; however, this method was still on seeking. Therefore, compared to the former methods that were used to isolate the cancer stem cell, in the present study, we tried to use modified transwell system to isolate and enrich CSCs from human pancreatic cancer cell lines (Panc-1. Our results clearly showed that the lower chamber cells in modified transwell system were easily forming spheres; furthermore, these spheres expressed high levels of stem cell markers (CD133/CD44/CD24/Oct-4/ESA and exhibited chemoresistance, underwent epithelial-to-mesenchymal transition (EMT, and possessed the properties of self-renewal in vitro and tumorigenicity in vivo. Therefore, we speculated that modified transwell assay system, as a rapid and effective method, can be used to isolate and enrich CSCs.

  10. Enriching the Catalog

    Science.gov (United States)

    Tennant, Roy

    2004-01-01

    After decades of costly and time-consuming effort, nearly all libraries have completed the retrospective conversion of their card catalogs to electronic form. However, bibliographic systems still are really not much more than card catalogs on wheels. Enriched content that Amazon.com takes for granted--such as digitized tables of contents, cover…

  11. Region-based multisensor image fusion method

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Image fusion should consider the priori knowledge of the source images to be fused, such as the characteristics of the images and the goal of image fusion, that is to say, the knowledge about the input data and the application plays a crucial role. This paper is concerned on multiresolution (MR) image fusion. Considering the characteristics of the multisensor (SAR and FLIR etc) and the goal of fusion, which is to achieve one image in possession of the contours feature and the target region feature. It seems more meaningful to combine features rather than pixels. A multisensor image fusion scheme based on K-means cluster and steerable pyramid is presented. K-means cluster is used to segment out objects in FLIR images. The steerable pyramid is a multiresolution analysis method, which has a good property to extract contours information at different scales. Comparisons are made with the relevant existing techniques in the literature. The paper concludes with some examples to illustrate the efficiency of the proposed scheme.

  12. Subjective evidence based ethnography: method and applications.

    Science.gov (United States)

    Lahlou, Saadi; Le Bellu, Sophie; Boesen-Mariani, Sabine

    2015-06-01

    Subjective Evidence Based Ethnography (SEBE) is a method designed to access subjective experience. It uses First Person Perspective (FPP) digital recordings as a basis for analytic Replay Interviews (RIW) with the participants. This triggers their memory and enables a detailed step by step understanding of activity: goals, subgoals, determinants of actions, decision-making processes, etc. This paper describes the technique and two applications. First, the analysis of professional practices for know-how transferring purposes in industry is illustrated with the analysis of nuclear power-plant operators' gestures. This shows how SEBE enables modelling activity, describing good and bad practices, risky situations, and expert tacit knowledge. Second, the analysis of full days lived by Polish mothers taking care of their children is described, with a specific focus on how they manage their eating and drinking. This research has been done on a sub-sample of a large scale intervention designed to increase plain water drinking vs sweet beverages. It illustrates the interest of SEBE as an exploratory technique in complement to other more classic approaches such as questionnaires and behavioural diaries. It provides the detailed "how" of the effects that are measured at aggregate level by other techniques.

  13. The Standardization Method of Address Information for POIs from Internet Based on Positional Relation

    Directory of Open Access Journals (Sweden)

    WANG Yong

    2016-05-01

    Full Text Available As points of interest (POIon the internet, exists widely incomplete addresses and inconsistent literal expressions, a fast standardization processing method of network POIs address information based on spatial constraints was proposed. Based on the model of the extensible address expression, first of all, address information of POI was segmented and extracted. Address elements are updated by means of matching with the address tree layer by layer. Then, by defining four types of positional relations, corresponding set are selected from standard POI library as candidate for enrichment and amendment of non-standard address. At last, the fast standardized processing of POI address information was achieved with the help of backtracking address elements with minimum granularity. Experiments in this paper proved that the standardization processing of an address can be realized by means of this method with higher accuracy in order to build the address database.

  14. The Numerical Simulation of the Crack Elastoplastic Extension Based on the Extended Finite Element Method

    Directory of Open Access Journals (Sweden)

    Xia Xiaozhou

    2013-01-01

    Full Text Available In the frame of the extended finite element method, the exponent disconnected function is introduced to reflect the discontinuous characteristic of crack and the crack tip enrichment function which is made of triangular basis function, and the linear polar radius function is adopted to describe the displacement field distribution of elastoplastic crack tip. Where, the linear polar radius function form is chosen to decrease the singularity characteristic induced by the plastic yield zone of crack tip, and the triangle basis function form is adopted to describe the displacement distribution character with the polar angle of crack tip. Based on the displacement model containing the above enrichment displacement function, the increment iterative form of elastoplastic extended finite element method is deduced by virtual work principle. For nonuniform hardening material such as concrete, in order to avoid the nonsymmetry characteristic of stiffness matrix induced by the non-associate flowing of plastic strain, the plastic flowing rule containing cross item based on the least energy dissipation principle is adopted. Finally, some numerical examples show that the elastoplastic X-FEM constructed in this paper is of validity.

  15. Principle of Advance Detection of Water-enriched Body with Mine Transient Electromagnetic Method and Its Application%矿井瞬变电磁法富水体超前探测原理及应用研究

    Institute of Scientific and Technical Information of China (English)

    李云波; 李好

    2013-01-01

      由于对煤矿工作面顶底板和掘进工作面前方富水构造情况不清,导致近年来煤矿井下水害频发。介绍了矿井瞬变电磁法超前探测原理、井下探测工艺、数据采集和资料处理流程,总结出富水异常体解释和划分方法。应用YCS40矿用本安型瞬变电磁观测系统对霍州煤电集团文明煤矿掘进工作面进行了超前探测研究,结果表明矿井瞬变电磁法能够比较准确地预报掘进工作面前方100 m内的富水异常体。%The unclear water-enriched structure in the roof and floor strata of the coal face and in front of the heading face led to the frequent occurrence of mine water disasters in recent years. This paper described the advance detection principle, underground detection technology,data acquisition and data processing of the mine transient electromagnetic method and summarized the explanation and classification methods of the abnormal water-enriched body. The advance detection research was carried out with YCS40 transient electromagnetic observation system in Wenming Mine of Huozhou Coal Electricity Group Co. , Ltd. ,and research results showed that the use of the mine transient electromagnetic method can more accurately predict the water-enriched anomaly in 10m range in front of the heading face.

  16. Triptycene-based ladder monomers and polymers, methods of making each, and methods of use

    KAUST Repository

    Pinnau, Ingo

    2015-02-05

    Embodiments of the present disclosure provide for a triptycene-based A-B monomer, a method of making a triptycene-based A-B monomer, a triptycene-based ladder polymer, a method of making a triptycene-based ladder polymers, a method of using triptycene-based ladder polymers, a structure incorporating triptycene-based ladder polymers, a method of gas separation, and the like.

  17. DNA-based methods of geochemical prospecting

    Science.gov (United States)

    Ashby, Matthew

    2011-12-06

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  18. Reactor Physics Methods and Preconceptual Core Design Analyses for Conversion of the Advanced Test Reactor to Low-Enriched Uranium Fuel Annual Report for Fiscal Year 2012

    Energy Technology Data Exchange (ETDEWEB)

    David W. Nigg; Sean R. Morrell

    2012-09-01

    Under the current long-term DOE policy and planning scenario, both the ATR and the ATRC will be reconfigured at an appropriate time within the next several years to operate with low-enriched uranium (LEU) fuel. This will be accomplished under the auspices of the Reduced Enrichment Research and Test Reactor (RERTR) Program, administered by the DOE National Nuclear Security Administration (NNSA). At a minimum, the internal design and composition of the fuel element plates and support structure will change, to accommodate the need for low enrichment in a manner that maintains total core excess reactivity at a suitable level for anticipated operational needs throughout each cycle while respecting all control and shutdown margin requirements and power distribution limits. The complete engineering design and optimization of LEU cores for the ATR and the ATRC will require significant multi-year efforts in the areas of fuel design, development and testing, as well as a complete re-analysis of the relevant reactor physics parameters for a core composed of LEU fuel, with possible control system modifications. Ultimately, revalidation of the computational physics parameters per applicable national and international standards against data from experimental measurements for prototypes of the new ATR and ATRC core designs will also be required for Safety Analysis Report (SAR) changes to support routine operations with LEU. This report is focused on reactor physics analyses conducted during Fiscal Year (FY) 2012 to support the initial development of several potential preconceptual fuel element designs that are suitable candidates for further study and refinement during FY-2013 and beyond. In a separate, but related, effort in the general area of computational support for ATR operations, the Idaho National Laboratory (INL) is conducting a focused multiyear effort to introduce modern high-fidelity computational reactor physics software and associated validation protocols to replace

  19. Selective trace enrichment of acidic pharmaceuticals in real water and sediment samples based on solid-phase extraction using multi-templates molecularly imprinted polymers.

    Science.gov (United States)

    Duan, Yan-Ping; Dai, Chao-Meng; Zhang, Ya-Lei; Ling-Chen

    2013-01-03

    A novel multi-templates molecularly imprinted polymer (MIP), using acidic pharmaceuticals mixture (ibuprofen (IBP), naproxen (NPX), ketoprofen (KEP), diclofenac (DFC), and clofibric acid (CA)) as the template, was prepared as solid-phase extraction (SPE) material for the quantitative enrichment of acidic pharmaceuticals in environmental samples and off-line coupled with liquid chromatography-mass spectrometry (LC/MS/MS). Washing solvent was optimized in terms of kind and volume for removing the matrix constituents nonspecifically adsorbed on the MIP. When 1L of water sample spiked at 1μg/L was loaded onto the cartridge, the binding capacity of the MIP cartridge were 48.7μg/g for KEP, 60.7μg/g for NPX, 52μg/g for CA, 61.3μg/g for DFC and 60.7μg/g for IBP, respectively, which are higher than those of the commercial single template MIP in organic medium (e.g. toluene) reported in the literature. Recoveries of the five acidic pharmaceuticals extracted from 1L of real water samples such as lake water and wastewater spiked at 1μg/L were more than 95%. The recoveries of acidic pharmaceuticals extracted from 10-g sediment sample spiked at the 10ng/g level were in the range of 77.4-90.6%. To demonstrate the potential of the MIP obtained, a comparison with commercial C18 SPE cartridge was performed. Molecularly imprinted solid-phase extraction (MISPE) cartridge showed higher recoveries than commercial C18 SPE cartridge for acidic pharmaceuticals. These results showed the suitability of the MISPE method for the selective extraction of a group of structurally related compounds such as acidic pharmaceuticals.

  20. Detection of water enrichment in complex faults by mine transient electromagnetic Method%复杂断层带富水性矿井瞬变电磁法探测研究

    Institute of Scientific and Technical Information of China (English)

    杜库实; 程久龙; 王和固; 闫国才; 王作路

    2013-01-01

    复杂断层带富水性的探测关系到矿井的采掘安全。探讨了矿井瞬变电磁法超前探测的基本原理与技术方法,分析了断层带富水性的地球物理响应特征,结合某矿巷道掘进前方断层带出水位置的矿井瞬变电磁法探测,提出了立体探测方案,对探测结果进行了分析解释,得到钻探验证。研究表明,利用矿井瞬变电磁探测技术可以有效地获得掘进巷道前方复杂断层带的富水程度、位置和范围,可以为掘进巷道防治水工作提供可靠的技术保障。%The detection of water enrichment in complex fault zones matters in mining and drilling safety .This paper studied the basic principles and techniques of advanced detection by mine transient electromagnetic method (MTEM) ,analyzed the geophysics responding characteristics of water enrichment in complex faults .Combined with a case study on detection of the water-inrush location between complex faults ahead of drilling roadway using MTEM in a coal mine ,this paper provided the projects of 3D detection , interpreted the detecting results of apparent resistivity ,and finally the results were proved by borehole drilling .The research results indicated that it is very effective and convenient to obtain the water enrichment extent ,location and scope between complex faults ahead of drilling roadway by MTEM .The method can provide reliable technical support for preventing water-inrush in roadway drilling .

  1. Multifractal Framework Based on Blanket Method

    Science.gov (United States)

    Paskaš, Milorad P.; Reljin, Irini S.; Reljin, Branimir D.

    2014-01-01

    This paper proposes two local multifractal measures motivated by blanket method for calculation of fractal dimension. They cover both fractal approaches familiar in image processing. The first two measures (proposed Methods 1 and 3) support model of image with embedded dimension three, while the other supports model of image embedded in space of dimension three (proposed Method 2). While the classical blanket method provides only one value for an image (fractal dimension) multifractal spectrum obtained by any of the proposed measures gives a whole range of dimensional values. This means that proposed multifractal blanket model generalizes classical (monofractal) blanket method and other versions of this monofractal approach implemented locally. Proposed measures are validated on Brodatz image database through texture classification. All proposed methods give similar classification results, while average computation time of Method 3 is substantially longer. PMID:24578664

  2. New deghosting method based on generalized triangulation

    Institute of Scientific and Technical Information of China (English)

    Bai Jing; Wang Guohong; Xiu Jianjuan; Wang Xiaobo

    2009-01-01

    A new deghosting method baaed on the generalized triangulation is presented. First, two intersection points corresponding to the emitter position are obtained by utilizing two azimuth angles and two elevation angles from two jammed 3-D radars (or 2-D passive sensors). Then, hypothesis testing baaed deghosting method in the multiple target scenarios is proposed using the two intersection points. In order to analyze the performance of the proposed method, the correct association probability of the true targets and the incorrect association probability of the ghost targets are defined. Finally, the Monte Carlo simulations are given for the proposed method compared with the hinge angle method in the cases of both two and three radars. The simulation results show that the proposed method has better performance than the hinge angle method in three radars case.

  3. Shelf-life study of Indian traditional food based nutraceutical (oryzanol) enriched instant mixes Bhath-OZ and Upma-OZ.

    Science.gov (United States)

    Baby Latha, R; Debnath, Sukumar; Sarmandal, C V; Hemavathy, J; Khatoon, Sakina; Gopala Krishna, A G; Lokesh, B R

    2014-01-01

    To provide nutraceutical such as oryzanol through food, two instant mixes based on the Indian traditional food cuisine Bisibele bhath and Upma(Bhath-OZ and Upma-OZ) were developed and evaluated for shelf-life. The formulations contained cereals, pulses, and spices along with oryzanol enriched oil and were packed in 200gauge/50 gauge metallized polyester packaging material and stored under ambient (27 °C 65%RH) and accelerated conditions (37 °C/92%RH). Samples were withdrawn periodically and peroxide value (PV), free fatty acid value (FFA), fatty acid composition, oryzanol, and total tocopherols content were estimated. Sensory evaluation of reconstituted products was also carried out. Oryzanol content (610 and 550 mg%) did not change appreciably in Bhath-OZ and Upma-OZ respectively. The peroxide value under ambient condition increased from 1.1 to 9.3 meq.O2/kg and 2.24 to 9.02 meq.O2/kg during the 6 month storage study at 27 °C and 65% RH, while under accelerated conditions at 37 °C and 92%RH, it increased from 1.12 to 8.54 meq. O2/kg and 2.24 to 6.96 meq. O2/kg during 2 month storage period. Bhath-OZ and Upma-OZ packed in metallized polyester pouches stored at 27 °C and 65% RH had a shelf-life of 4 months without affecting the oryzanol content and quality of instant mixes during the storage period.

  4. Tailor-Made Stable Zr(IV)-Based Metal-Organic Frameworks for Laser Desorption/Ionization Mass Spectrometry Analysis of Small Molecules and Simultaneous Enrichment of Phosphopeptides.

    Science.gov (United States)

    Chen, Lianfang; Ou, Junjie; Wang, Hongwei; Liu, Zhongshan; Ye, Mingliang; Zou, Hanfa

    2016-08-10

    Although thousands of metal-organic frameworks (MOFs) have been fabricated and widely applied in gas storage/separations, adsorption, catalysis, and so on, few kinds of MOFs have been used as adsorption materials while simultaneously serving as matrixes to analyze small molecules for laser desorption/ionization mass spectrometry (LDI-MS). Herein, a new concept is introduced to design and synthesize MOFs as both adsorption materials and matrixes according to the structure of ligands and common matrixes. The proof of concept design was demonstrated by selection of 2,5-pyridinedicarboxylic acid (PDC) and 2,5-dihydroxyterephthalic acid (DHT) as ligands for synthesis of MOFs. Two Zr(IV)-based MOFs of UiO-66-PDC and UiO-66-(OH)2 were synthesized and applied for the first time as new matrixes for analysis of small molecules by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Both of them showed low matrix interferences, high ionization efficiency, and good reproducibility when used as matrixes. A variety of small molecules, including saccharides, amino acids, nucleosides, peptides, alkaline drugs, and natural products, were analyzed. In addition, UiO-66-(OH)2 exhibited potential for application in the quantitative determination of glucose and pyridoxal 5'-phosphate. Furthermore, thanks to its intrinsically large surface area and highly ordered pores, UiO-66-(OH)2 also showed sensitive and specific enrichment of phosphopeptides prior to MS analysis. These results demonstrated that this strategy can be used to efficiently screen tailor-made MOFs as matrixes to analyze small molecules by MALDI-TOF-MS.

  5. A microfluidic based optical particle detection method

    Science.gov (United States)

    Dou, James; Chen, Lu; Nayyar, Rakesh; Aitchison, Stewart

    2012-03-01

    An optical particle detection and analysis method is presented. This method combines the capillary microfluidics, integrated optics and novel image acquisition and analysis algorithms to form the basis of a portable or handheld cytometer instrument. Experimental results provided shows the testing results are closely matched with conventional flow cytometer data.

  6. Profile of World Uranium Enrichment Programs - 2007

    Energy Technology Data Exchange (ETDEWEB)

    Laughter, Mark D [ORNL

    2007-11-01

    of the future, but has yet to be demonstrated commercially. In the early 1980s, six countries developing gas centrifuge technology (United States, United Kingdom, Germany, the Netherlands, Japan, and Australia) along with the International Atomic Energy Agency (IAEA) and the European Atomic Energy Community (EURATOM) began developing effective safeguards techniques for GCEPs. This effort was known as the Hexapartite Safeguards Project (HSP). The HSP had the goal of maximizing safeguards effectiveness while minimizing the cost to the operator and inspectorate, and adopted several recommendations, such as the acceptance of limited-frequency unannounced access (LFUA) inspections in cascade halls, and the use of nondestructive assay (NDA) measurements and tamper-indicating seals. While only the HSP participants initially committed to implementing all the measures of the approach, it has been used as a model for the safeguards applied to GCEPs in additional states. This report provides a snapshot overview of world enrichment capacity in 2007, including profiles of the uranium enrichment programs of individual states. It is based on open-source information, which is dependent on unclassified sources and may therefore not reflect the most recent developments. In addition, it briefly describes some of the safeguards techniques being used at various enrichment plants, including implementation of HSP recommendations.

  7. Rapid Column-Free Enrichment of Mononuclear Cells from Solid Tissues.

    Science.gov (United States)

    Scoville, Steven D; Keller, Karen A; Cheng, Stephanie; Zhang, Michael; Zhang, Xiaoli; Caligiuri, Michael A; Freud, Aharon G

    2015-07-30

    We have developed a rapid negative selection method to enrich rare mononuclear cells from human tissues. Unwanted and antibody-tethered cells are selectively depleted during a Ficoll separation step, and there is no need for magnetic-based reagents and equipment. The new method is fast, customizable, inexpensive, remarkably efficient, and easy to perform, and per sample the overall cost is less than one-tenth the cost associated with a magnetic column-based method.

  8. Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Ronald C.; Sanfilippo, Antonio P.; McDermott, Jason E.; Baddeley, Robert L.; Riensche, Roderick M.; Jensen, Russell S.; Verhagen, Marc; Pustejovsky, James

    2011-02-18

    Transcriptional regulatory networks are being determined using “reverse engineering” methods that infer connections based on correlations in gene state. Corroboration of such networks through independent means such as evidence from the biomedical literature is desirable. Here, we explore a novel approach, a bootstrapping version of our previous Cross-Ontological Analytic method (XOA) that can be used for semi-automated annotation and verification of inferred regulatory connections, as well as for discovery of additional functional relationships between the genes. First, we use our annotation and network expansion method on a biological network learned entirely from the literature. We show how new relevant links between genes can be iteratively derived using a gene similarity measure based on the Gene Ontology that is optimized on the input network at each iteration. Second, we apply our method to annotation, verification, and expansion of a set of regulatory connections found by the Context Likelihood of Relatedness algorithm.

  9. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    present in the hypothalamus, miR-7a, was the only miRNA found to be enriched in the hypothalamus, with low or no expression in other parts of the central nervous system (CNS). Within the hypothalamus, strong miR-7a expression was distinct and restricted to some hypothalamic nuclei and adjacent areas. mi...

  10. Definition of new trace-metal proxies for the controls on organic matter enrichment in marine sediments based on Mn, Co, Mo and Cd concentrations

    NARCIS (Netherlands)

    Sweere, T.; Van den Boorn, S.; Dickson, A.J.; Reichart, G.-J.

    2016-01-01

    Trace metal enrichments in sedimentary deposits are of prime interest because they are governed by processes that also control the production and preservation of organic matter. Consequently, trace metals have been used in reconstructions of the (palaeo)depositional environment of organic-rich depos

  11. Towards an international standard for PCR-based detection of foodborne thermotolerant campylobacters: interaction of enrichment media and pre-PCR treatment on carcass rinse samples

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Lübeck, Peter Stephensen; Hansen, F.

    2004-01-01

    As part of a large EU project for standardisation of polymerase chain reaction (PCR), a systematic evaluation of the interaction of enrichment media, type of DNA polymerase and pre-PCR sample treatment for a PCR detecting thermotolerant campylobacters was carried out. The growth-supporting capaci...

  12. LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

    Science.gov (United States)

    Dong, Xinran; Hao, Yun; Wang, Xiao; Tian, Weidong

    2016-01-11

    Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher's exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO's usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher.

  13. Appraisal of {sup 15}N enrichment and {sup 15}N natural abundance methods for estimating N{sub 2} fixation by understorey Acacia leiocalyx and A. disparimma in a native forest of subtropical Australia

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Shahla Hosseini; Xu, Zhihong; Blumfield, Timothy J. [Griffith Univ., Nathan, Brisbane, QLD (Australia). School of Biomolecular and Physical Sciences, Environmental Futures Centre; Sun, Fangfang [Guangdong Academy of Agricultural Sciences, Guangzhou (China). Research Centre for Quality, Safety and Standard of Agricultural Products; Chen, Chengrong [Griffith Univ., Nathan, Brisbane, QLD (Australia). School of Environment, Environmental Futures Centre; Wild, Clyde [Griffith Univ., Gold Coast, QLD (Australia). School of Environment, Environmental Futures Centre

    2012-05-15

    Purpose: It is anticipated that global climate change will increase the frequency of wildfires in native forests of eastern Australia. Understorey legumes such as Acacia species play an important role in maintaining ecosystem nitrogen (N) balance through biological N fixation (BNF). This is particularly important in Australian native forests with soils of low nutrient status and frequent disturbance of the nutrient cycles by fires. This study aimed to examine {sup 15}N enrichment and {sup 15}N natural abundance techniques in terms of their utilisation for evaluation of N{sub 2} fixation of understorey acacias and determine the relationship between species ecophysiological traits and N{sub 2} fixation. Materials and methods: A trial was established at sites 1 and 2 located at Toohey Forest, Queensland, Australia, a eucalypt-dominated native forest, to examine the determination of BNF using {sup 15}N enrichment and {sup 15}N natural abundance methods. Toohey Forest is an urban forest and subjected to frequent fuel reduction burns to protect the adjacent properties. Plant physiological status was measured to determine the relationship between physiological and N{sub 2} fixation activities. Results and discussion: Both {sup 15}N enrichment and {sup 15}N natural abundance techniques may be used to estimate N{sub 2} fixation of acacia tree species. The estimation of BNF using {sup 15}N enrichment was higher than those of the {sup 15}N natural abundance method. A grass reference plant, Themeda triandra, as well as tree reference plants provided an appropriate {delta}{sup 15}N signal. Potential B values for Acacia spp. between -0.3 permille and 1.0 permille provided an acceptable BNF estimation. This suburban forest is located nearby a busy highway leading to N deposition over time with consequent negative {delta}{sup 15}N signal. This N deposition may explain the separation between the {delta}{sup 15}N signal of the acacias and that of the reference plants which led to

  14. Enrichment-ELISA for Detection of Salmonella typhi From Food and Water Samples

    Institute of Scientific and Technical Information of China (English)

    S.KUMAR; K.BALAKRISHNA; HV.BATRA

    2008-01-01

    Objective Development of monoclonal antibody based sandwich enzyme linked immunosorbant assay(sELISA)for rapid detection of Salmonella enterica serovar typhi(S.typhi) from food and water samples and optimization of enrichment procedures for use with the developed sELISA to increase the detection Sensitivity of the assay. Methods Spleen cells from BALB/c mice immunized with flagellin(H=d)antigen of S.typhi were fused with Sp2/0 myeloma cells.The hybridoma cell line specific to H=d antigen was established.characterized and ascites raised against one of these clones.The hypefimmune serum to flagellin antigen was raised in New Zealand White rabbits.An sELISA was developed using polyclonalantibody as capture and monoelonal antibody as detection antibody.To design the efficient culture sUrategies for use with the sELISA.different pre-enrichment and enrichment brothswere evaluated.The mediaincluded buffered peptonewater(BPW)and brain heart infusion broth for pre-enrichment and selenite F broth and Rappaport-Vassiliadis broth as enrichment broths.The developed sELISA with preceding enrichment step in BPW(Enrichment-ELISA)was evaluated in various food samples artificially inoculated with S. typhi bacteria.Various food(30)and water(35)samples collected from field were also tested by Enrichment-ELISA and culture method. Results Out of four specific clones to H=d antigen,one clone(#2/56.IgG2a isotype)was usedin sELISA.The sELISA had the detectionlimit of 104-105 cfu of S.typhi.Of the various broths used with sELISA,BPW was found to yield maximum ELISA values.Enrichment-ELISA,when tested in artificially inoculated food samples,generally,could detect 102S.typhi cfu/mL within 10 h from variousfood rinses(meat,vegetable)and milk samples.After overnight enrichment in BPW,as less as 2 bacteria per 10 mL of milk,meat rinse.and chicken rinse could be detected.Only one of the field samples(water)gave false positive result by Enrichment-ELISA.Conclusion In comparison to culture

  15. New ITF measure method based on fringes

    Science.gov (United States)

    Fang, Qiaoran; Liu, Shijie; Gao, Wanrong; Zhou, You; Liu, HuanHuan

    2016-01-01

    With the unprecedented developments of the intense laser and aerospace projects', the interferometer is widely used in detecting middle frequency indicators of the optical elements, which put forward very high request towards the interferometer system transfer function (ITF). Conventionally, the ITF is measured by comparing the power spectra of known phase objects such as high-quality phase step. However, the fabrication of phase step is complex and high-cost, especially in the measurement of large-aperture interferometer. In this paper, a new fringe method is proposed to measure the ITF without additional objects. The frequency was changed by adjusting the number of fringes, and the normalized transfer function value was measured at different frequencies. The ITF value measured by fringe method was consistent with the traditional phase step method, which confirms the feasibility of proposed method. Moreover, the measurement error caused by defocus was analyzed. The proposed method does not require the preparation of a step artifact, which greatly reduces the test cost, and is of great significance to the ITF measurement of large aperture interferometer.

  16. Model-based methods for linkage analysis.

    Science.gov (United States)

    Rice, John P; Saccone, Nancy L; Corbett, Jonathan

    2008-01-01

    The logarithm of an odds ratio (LOD) score method originated in a seminal article by Newton Morton in 1955. The method is broadly concerned with issues of power and the posterior probability of linkage, ensuring that a reported linkage has a high probability of being a true linkage. In addition, the method is sequential so that pedigrees or LOD curves may be combined from published reports to pool data for analysis. This approach has been remarkably successful for 50 years in identifying disease genes for Mendelian disorders. After discussing these issues, we consider the situation for complex disorders where the maximum LOD score statistic shares some of the advantages of the traditional LOD score approach, but is limited by unknown power and the lack of sharing of the primary data needed to optimally combine analytic results. We may still learn from the LOD score method as we explore new methods in molecular biology and genetic analysis to utilize the complete human DNA sequence and the cataloging of all human genes.

  17. LEVEL SET METHODS BASED ON DISTANCE FUNCTION

    Institute of Scientific and Technical Information of China (English)

    王德军; 唐云; 于洪川; 唐泽圣

    2003-01-01

    Some basic problems on the level set methods were discussed, such as the method used to preserve the distance function, the existence and uniqueness of solution for the level set equations. The main contribution is to prove that in a neighborhood of the initial zero level set, the level set equations with the restriction of the distance function have a unique solution, which must be the signed distance function with respect to the evolving surface. Some skillful approaches were used: Noticing that any solution for the original equation was a distance function, the original level set equations were transformed into a simpler alternative form. Moreover, since the new system was not a classical one, the system was transforned into an ordinary one, for which the implicit function method was adopted.

  18. AN EVEN COMPONENT BASED FACE RECOGNITION METHOD

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This paper presents a novel face recognition algorithm. To provide additional variations to training data set, even-odd decomposition is adopted, and only the even components (half-even face images) are used for further processing. To tackle with shift-variant problem,Fourier transform is applied to half-even face images. To reduce the dimension of an image,PCA (Principle Component Analysis) features are extracted from the amplitude spectrum of half-even face images. Finally, nearest neighbor classifier is employed for the task of classification. Experimental results on ORL database show that the proposed method outperforms in terms of accuracy the conventional eigenface method which applies PCA on original images and the eigenface method which uses both the original images and their mirror images as training set.

  19. A novel method for fast enrichment and monitoring of hexavalent and trivalent chromium at the ppt level with modified silica MCM-41 and its determination by inductively coupled plasma optical emission spectrometry

    Directory of Open Access Journals (Sweden)

    Ganjali Mohammad Reza

    2006-01-01

    Full Text Available Chromium(III at the ng L-1 level was extracted using partially silylated MCM-41 modified by a tetraazamacrocyclic compound (TAMC and determined by inductively coupled plasma optical emision spectrometry (ICP OES. The extraction time and efficiency, pH and flow rate, type and minimum amount of stripping acid, and break- through volume were investigated. The method's enrichment factor and detection limit are 300 and 45.5 pg mL-1, respectively. The maximum capacity of the 10 mg of modified silylated MCM-41 was found to be 400.5?4.7 µg for Cr(III. The method was applied to the determination of Cr(III and Cr(VI in the wastewater of the chromium electroplating industry and in environmental and biological samples (black tea, hot and black pepper.

  20. A numerical method based on probability theory

    Institute of Scientific and Technical Information of China (English)

    唐立; 邹捷中; 杨文胜

    2003-01-01

    By using the connections between Brownian family with drift and elliptic differential equations, an efficient probabilistic computing method is given. This method is applied to a wide-range Diriehlet problem. Detail analysis and deduction of solving the problem are offered. The stochastic representation of the solution to the problem makes a 3-dimensional problem turned into a 2-dimensional problem. And an auxiliary ball is constructed. The strong Markov property and the joint distributions of the time and place of hitting spheres for Brownian family with drift are employed. Finally, good convergence of the numerical solution to the problem over domain with arbitrary boundary is obtained.

  1. HMM-Based Gene Annotation Methods

    Energy Technology Data Exchange (ETDEWEB)

    Haussler, David; Hughey, Richard; Karplus, Keven

    1999-09-20

    Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

  2. A novel method for simultaneous measurement of concentration and enrichment of NO synthesis-specific amino acids in human plasma using stable isotopes and LC/MS ion trap analysis.

    Science.gov (United States)

    Oosterink, J Efraim; Buijs, Nikki; van Goudoever, Johannes B; Schierbeek, Henk

    2014-05-01

    Stable isotope studies offer the opportunity to study the in-depth metabolic pathway of glutamine, citrulline, and arginine amino acids involved in NO synthesis. The use of multiple stable isotopes can be used to elucidate the exact transformation of glutamine to citrulline and arginine de novo synthesis. This novel method provides a purification step using cation exchange resin in combination with a rapid and easy derivatization procedure for a precise and robust measurement of the concentration and isotopic enrichments of NO synthesis-specific amino acids using a liquid chromatography mass spectrometry (LC/MS) ion trap system with high sensitivity and selectivity. The ethyl chloroformate derivatization procedure is beneficial in terms of robustness, velocity, simplicity, and derivative stability. In addition, the ethyl chloroformate derivatization can be performed at room temperature in an aqueous environment without incubation and the isolation of the derivatives from the reaction mixture also serves as a purification step. The concentration and enrichment of NO synthesis-specific amino acids as well as phenylalanine and tyrosine to determine protein turnover, were measured with good inter-day precision for the concentration (glutamine-citrulline-arginine pathway by using stable isotope studies.

  3. 尿素包合法富集鱼油乙酯中的EPA和DHA%Enrichment of EPA and DHA from Fish Oil Ethyl Ester by Urea Inclusion Method

    Institute of Scientific and Technical Information of China (English)

    单幸福; 李江; 郑晓林; 许媛; 刘发义

    2016-01-01

    采用尿素包合法富集鱼油乙酯中的二十碳五烯酸(EPA)和二十二碳六烯酸(DHA),通过单因素实验和正交实验确定最优富集工艺为:m(尿素)∶m(鱼油乙酯)为1.5∶1、V (乙醇)∶m(鱼油乙酯)为3∶1、包合时间1 h、包合温度75℃、结晶温度25℃,一次包合的 EPA+DHA含量可达85%以上,收率60%。%Eicosapentaenoic acid(EPA)and decosahexaenoic acid(DHA)from fish oil ethyl ester were en-riched by an urea inclusion method.The optimum enrichment process obtained by a single factor experiment and an orthogonal experiment were as follows:m(urea)∶m(fish oil ethyl ester)of 1 .5∶1 ,V(ethanol)∶m(fish oil ethyl ester)of 3∶1,inclusion time of 1 h,inclusion temperature of 75 ℃,crystallization temperature of 25 ℃. Under above conditions,the total content of EPA and DHA from fish oil ethyl ester reached 85%,and the yield was 6 0%.

  4. Hybrid Enrichment Verification Array: Module Characterization Studies

    Energy Technology Data Exchange (ETDEWEB)

    Zalavadia, Mital A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Leon E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McDonald, Benjamin S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kulisek, Jonathan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mace, Emily K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Deshmukh, Nikhil S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-01

    The work presented in this report is focused on the characterization and refinement of the Hybrid Enrichment Verification Array (HEVA) approach, which combines the traditional 186-keV 235U signature with high-energy prompt gamma rays from neutron capture in the detector and surrounding collimator material, to determine the relative enrichment and 235U mass of the cylinder. The design of the HEVA modules (hardware and software) deployed in the current field trial builds on over seven years of study and evolution by PNNL, and consists of a ø3''×3'' NaI(Tl) scintillator coupled to an Osprey digital multi-channel analyzer tube base from Canberra. The core of the HEVA methodology, the high-energy prompt gamma-ray signature, serves as an indirect method for the measurement of total neutron emission from the cylinder. A method for measuring the intrinsic efficiency of this “non-traditional” neutron signature and the results from a benchmark experiment are presented. Also discussed are potential perturbing effects on the non-traditional signature, including short-lived activation of materials in the HEVA module. Modeling and empirical results are presented to demonstrate that such effects are expected to be negligible for the envisioned implementation scenario. In comparison to previous versions, the new design boosts the high-energy prompt gamma-ray signature, provides more flexible and effective collimation, and improves count-rate management via commercially available pulse-processing electronics with a special modification prompted by PNNL.

  5. Scope-Based Method Cache Analysis

    DEFF Research Database (Denmark)

    Huber, Benedikt; Hepp, Stefan; Schoeberl, Martin

    2014-01-01

    , as it requests memory transfers at well-defined instructions only. In this article, we present a new cache analysis framework that generalizes and improves work on cache persistence analysis. The analysis demonstrates that a global view on the cache behavior permits the precise analyses of caches which are hard......The quest for time-predictable systems has led to the exploration of new hardware architectures that simplify analysis and reasoning in the temporal domain, while still providing competitive performance. For the instruction memory, the method cache is a conceptually attractive solution...

  6. Enrichment of fetal cells from maternal blood by high gradient magnetic cell sorting (double MACS) for PCR-based genetic analysis.

    Science.gov (United States)

    Büsch, J; Huber, P; Pflüger, E; Miltenyi, S; Holtz, J; Radbruch, A

    1994-12-01

    For simple and effective isolation of fetal cells from peripheral maternal blood, we combined depletion of maternal cells and enrichment of fetal cells by high-gradient magnetic cell separation (MACS). First CD45+ and CD14+ cells were depleted from maternal peripheral blood mononuclear cells by MACS. From the depleted fraction, CD71+ erythroid cells were enriched up to 80 per cent by MACS. This double-MACS' procedure yielded an average depletion rate of 780-fold and an average enrichment rate of 500-fold, with approximate recovery rates of 40-55 per cent. For paternity testing, cells from unseparated blood and the various fractions were analysed for polymorphism of the HLA-DQ-A1 locus and D1S80 locus by the polymerase chain reaction (PCR). In CD45-/CD71+ sorted cells from maternal blood, but not in unfractionated cells from maternal blood or CD45-/CD14- cells, paternal alleles could be detected. In the CD45-/CD71+ fraction, the relative frequency of paternal alleles compared with maternal alleles ranged from 1 in 20 to 1 in 200 (determined by titration and depending on the quality of separation and biological variation). In 7 out of 11 cases, between weeks 12 and 25 of gestation, we could identify paternal alleles by PCR, either HLA-DQ-A1 or D1S80. This double-MACS procedure is simple, fast, efficient, and reliable for non-invasive prenatal diagnosis.

  7. Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.

    LENUS (Irish Health Repository)

    Kenny, Elaine M

    2011-02-01

    Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.

  8. Triptycene-based dianhydrides, polyimides, methods of making each, and methods of use

    KAUST Repository

    Ghanem, Bader

    2015-12-30

    A triptycene-based monomer, a method of making a triptycene-based monomer, a triptycene-based aromatic polyimide, a method of making a triptycene- based aromatic polyimide, methods of using triptycene-based aromatic polyimides, structures incorporating triptycene-based aromatic polyimides, and methods of gas separation are provided. Embodiments of the triptycene-based monomers and triptycene-based aromatic polyimides have high permeabilities and excellent selectivities. Embodiments of the triptycene-based aromatic polyimides have one or more of the following characteristics: intrinsic microporosity, good thermal stability, and enhanced solubility. In an exemplary embodiment, the triptycene-based aromatic polyimides are microporous and have a high BET surface area. In an exemplary embodiment, the triptycene-based aromatic polyimides can be used to form a gas separation membrane.

  9. Proposal for Scrambled Method based on NTRU

    Directory of Open Access Journals (Sweden)

    Ahmed Tariq Sadiq

    2015-08-01

    Full Text Available Scrambling is widely used to protect the security of data files such as text, image, video or audio files; however, it is not the most efficient method to protect the security of the data files. This article uses NTRU public key cryptosystem to increase the robustness of scrambling of sound files. In this work, we convert the sound file into text, and then scramble it in the following way: first, we encrypt the header of the sound file then, scramble the data of the file after the header in three stages. In each stage we scramble the data of the sound file and keep the original order of data in an array then, the three arrays are encrypted by the sender and sent with the encrypted header to the receiver in one file, while the scrambled data of the sound file is sent to the receiver in another file. We have tested the proposed method on several sound files; the results show that the time of encryption and decryption is reduced to approximately one-third, or less, compared to encrypting the file using NTRU.

  10. [Culture based diagnostic methods for tuberculosis].

    Science.gov (United States)

    Baylan, Orhan

    2005-01-01

    Culture methods providing isolates for identification and drug susceptibility testing, still represent the gold standard for the definitive diagnosis of tuberculosis, although the delay in obtaining results still remains a problem. Traditional solid media are recommended for use along with liquid media in primary isolation of mycobacteria. At present, a number of elaborate culture systems are available commercially. They range from simple bottles and tubes such as MGIT (BD Diagnostic Systems, USA), Septi-Chek AFB (BD, USA) and MB Redox (Biotest Diagnostics, USA) to semiautomated system (BACTEC 460TB, BD, USA) and fully automated systems (BACTEC 9000 MB [BD, USA], BACTEC MGIT 960 [BD, USA], ESP Culture System II [Trek Diagnostics, USA], MB/BacT ALERT 3D System [BioMérieux, NC], TK Culture System [Salubris Inc, Turkey]). Culture methods available today are sufficient to permit laboratories to develop an algoritm that is optimal for patients and administrative needs. In this review article, the culture systems used for the diagnosis of tuberculosis, their mechanisms, advantages and disadvantages have been discussed under the light of recent literature.

  11. The Enriched Effect Calculus: Syntax and Semantics

    DEFF Research Database (Denmark)

    Møgelberg, Rasmus Ejlers; Simpson, Alex; Egger, Jeff

    2014-01-01

    . The second half of the article investigates models for the enriched effect calculus, based on enriched category theory. We give several examples of such models, relating them to models of standard effect calculi (such as those based on monads), and to models of intuitionistic linear logic. We also prove...

  12. GALERKIN MESHLESS METHODS BASED ON PARTITION OF UNITY QUADRATURE

    Institute of Scientific and Technical Information of China (English)

    ZENG Qing-hong; LU De-tang

    2005-01-01

    Numerical quadrature is an important ingredient of Galerkin meshless methods. A new numerical quadrature technique, partition of unity quadrature (PUQ),for Galerkin meshless methods was presented. The technique is based on finite covering and partition of unity. There is no need to decompose the physical domain into small cell. It possesses remarkable integration accuracy. Using Element-free Galerkin methods as example, Galerkin meshless methods based on PUQ were studied in detail. Meshing is always not required in the procedure of constitution of approximate function or numerical quadrature, so Galerkin meshless methods based on PUQ are "truly"meshless methods.

  13. Algebraic Verification Method for SEREs Properties via Groebner Bases Approaches

    Directory of Open Access Journals (Sweden)

    Ning Zhou

    2013-01-01

    Full Text Available This work presents an efficient solution using computer algebra system to perform linear temporal properties verification for synchronous digital systems. The method is essentially based on both Groebner bases approaches and symbolic simulation. A mechanism for constructing canonical polynomial set based symbolic representations for both circuit descriptions and assertions is studied. We then present a complete checking algorithm framework based on these algebraic representations by using Groebner bases. The computational experience result in this work shows that the algebraic approach is a quite competitive checking method and will be a useful supplement to the existent verification methods based on simulation.

  14. Beam Parameters Measurement Based On Tv Methods

    CERN Document Server

    Klimenkov, E; Milichenko, Yu; Voevodin, V

    2004-01-01

    The paper describes hardware and software used to control TV-cameras and to process TV-images of luminescent screens placed along the beam transfer lines. Industrial devices manually control the movements and focusing of the cameras. All devices are linked to PC via PCI interfaces with homemade drivers for Linux OS and provide both selection of camera and digitizing of video signal synchronized with beam. One part of software provides means to set initial parameters using PC consol. Thus an operator can choose contrast, brightness, some number of significant points on TV-image to calculate beam position and its size. Second part supports remote TV controls and data processing from Control Rooms of U-70 complex using set initial parameters. First experience and results of the method realization are discussed.

  15. Adaptive Mixture Methods Based on Bregman Divergences

    CERN Document Server

    Donmez, Mehmet A; Kozat, Suleyman S

    2012-01-01

    We investigate adaptive mixture methods that linearly combine outputs of $m$ constituent filters running in parallel to model a desired signal. We use "Bregman divergences" and obtain certain multiplicative updates to train the linear combination weights under an affine constraint or without any constraints. We use unnormalized relative entropy and relative entropy to define two different Bregman divergences that produce an unnormalized exponentiated gradient update and a normalized exponentiated gradient update on the mixture weights, respectively. We then carry out the mean and the mean-square transient analysis of these adaptive algorithms when they are used to combine outputs of $m$ constituent filters. We illustrate the accuracy of our results and demonstrate the effectiveness of these updates for sparse mixture systems.

  16. GoBean: a Java GUI application for visual exploration of GO term enrichments.

    Science.gov (United States)

    Lee, Sanghyuk; Cha, Ji-Young; Kim, Hyeonjin; Yu, Ungsik

    2012-02-01

    We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

  17. Determination of trace anions in liquefied petroleum gas using liquid absorption and electrokinetic migration for enrichment followed by ion chromatography.

    Science.gov (United States)

    Li, Meilan; Yang, Jianmin; Li, Hai-Fang; Lin, Jin-Ming

    2012-06-01

    A simple sample enrichment technique, electrokinetic migration enrichment in single phase using a designed device, coupled with ion chromatography is presented for the determination of four anions (H(2)PO(4)(-), Cl(-), NO(3)(-), and SO(4)(2-)) in liquefied petroleum gas by liquid adsorption. The electrokinetic migration enrichment is based on the phenomenon of ion electrokinetic migration to the opposite electrode. When the anions migrated to the anode in a smaller volume chamber under the electric field, the concentration was realized. The main parameters affecting enrichment efficiency of applied voltage and enrichment time were investigated. The ion chromatography condition for anions separation was also studied. Under the optimal electrokinetic migration enrichment and ion chromatography conditions, the four anions were detected simultaneously with good linear relationship (r(2) = 0.9908-0.9968) and high precisions (less than 5% of the relative standard deviations of peak areas). The limits of detection of anions (S/N of 3) were in the range of 8-600 μg L(-1). The enrichment factors of the four anions ranged from 3.1 to 5.8. The established method was successfully applied to the analysis of the trace anions in liquefied petroleum gas by liquid adsorption with satisfactory results. The advantages of this method are simple operation and low cost.

  18. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    Thingholm, Tine E.; Larsen, Martin R.

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively...... charged metal ions such as Fe3+, Ga3+, Al3+, Zr4+, and Ti4+ has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from...

  19. Online trapping and enrichment ultra performance liquid chromatography-tandem mass spectrometry method for sensitive measurement of 'arginine-asymmetric dimethylarginine cycle' biomarkers in human exhaled breath condensate

    Energy Technology Data Exchange (ETDEWEB)

    Di Gangi, Iole Maria, E-mail: giordano@pediatria.unipd.it [Chromatography and Mass Spectrometry Laboratory, Department of Women' s and Children' s Health, University of Padova (Italy); Pirillo, Paola [Chromatography and Mass Spectrometry Laboratory, Department of Women' s and Children' s Health, University of Padova (Italy); Carraro, Silvia [Unit of Allergy and Respiratory Diseases, Department of Women' s and Children' s Health, University of Padova (Italy); Gucciardi, Antonina; Naturale, Mauro [Chromatography and Mass Spectrometry Laboratory, Department of Women' s and Children' s Health, University of Padova (Italy); Baraldi, Eugenio [Unit of Allergy and Respiratory Diseases, Department of Women' s and Children' s Health, University of Padova (Italy); Giordano, Giuseppe [Chromatography and Mass Spectrometry Laboratory, Department of Women' s and Children' s Health, University of Padova (Italy)

    2012-11-19

    Highlights: Black-Right-Pointing-Pointer Simultaneous quantification of 'arginine-ADMA cycle' metabolites developed in EBC. Black-Right-Pointing-Pointer EBC is a non-invasive matrix highly useful in patients with respiratory diseases. Black-Right-Pointing-Pointer Method, fast, precise and accurate, is suitable in the pediatric clinical studies. Black-Right-Pointing-Pointer Sensitivity is increased using on-line trapping and enrichment-UPLC-MS/MS method. Black-Right-Pointing-Pointer EBC measurements in asthmatic adolescents confirm that ADMA is increased in asthma. - Abstract: Background: Exhaled breath condensate (EBC) is a biofluid collected non invasively that, enabling the measurement of several biomarkers, has proven useful in the study of airway inflammatory diseases, including asthma, COPD and cystic fibrosis. To the best of our knowledge, there is no previous report of any analytical method to detect ADMA in EBC. Objectives: Aim of this work was to develop an online sample trapping and enrichment system, coupled with an UPLC-MS/MS method, for simultaneous quantification of seven metabolites related to 'Arginine-ADMA cycle', using the isotopic dilution. Methods: Butylated EBC samples were trapped in an online cartridge, washed before and after each injection with cleanup solution to remove matrix components and switched inline into the high pressure analytical column. Multiple reaction monitoring in positive mode was used for analyte quantification by tandem mass spectrometry. Results: Validation studies were performed in EBC to examine accuracy, precision and robustness of the method. For each compound, the calibration curves showed a coefficient of correlation (r{sup 2}) greater than 0.992. Accuracy (%Bias) was <3% except for NMMA and H-Arg (<20%), intra- and inter-assay precision (expressed as CV%) were within {+-}20% and recovery ranged from 97.1 to 102.8% for all analytes. Inter-day variability analysis on 20 EBC of adult subjects did

  20. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    Thingholm, Tine E.; Larsen, Martin R.

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively...

  1. Enrichment of Acinetobacter spp. from food samples.

    Science.gov (United States)

    Carvalheira, Ana; Ferreira, Vânia; Silva, Joana; Teixeira, Paula

    2016-05-01

    Relatively little is known about the role of foods in the chain of transmission of acinetobacters and the occurrence of different Acinetobacter spp. in foods. Currently, there is no standard procedure to recover acinetobacters from food in order to gain insight into the food-related ecology and epidemiology of acinetobacters. This study aimed to assess whether enrichment in Dijkshoorn enrichment medium followed by plating in CHROMagar™ Acinetobacter medium is a useful method for the isolation of Acinetobacter spp. from foods. Recovery of six Acinetobacter species from food spiked with these organisms was compared for two selective enrichment media (Baumann's enrichment and Dijkshoorn's enrichment). Significantly (p Acinetobacter was applied to detect Acinetobacter spp. in different foods. Fourteen different presumptive acinetobacters were recovered and assumed to represent nine different strains on the basis of REP-PCR typing. Eight of these strains were identified by rpoB gene analysis as belonging to the species Acinetobacter johnsonii, Acinetobacter calcoaceticus, Acinetobacter guillouiae and Acinetobacter gandensis. It was not possible to identify the species level of one strain which may suggests that it represents a distinct species.

  2. Uranium enrichment management review: summary of analysis

    Energy Technology Data Exchange (ETDEWEB)

    1981-01-01

    In May 1980, the Assistant Secretary for Resource Applications within the Department of Energy requested that a group of experienced business executives be assembled to review the operation, financing, and management of the uranium enrichment enterprise as a basis for advising the Secretary of Energy. After extensive investigation, analysis, and discussion, the review group presented its findings and recommendations in a report on December 2, 1980. The following pages contain background material on which that final report was based. This report is arranged in chapters that parallel those of the uranium enrichment management review final report - chapters that contain summaries of the review group's discussion and analyses in six areas: management of operations and construction; long-range planning; marketing of enrichment services; financial management; research and development; and general management. Further information, in-depth analysis, and discussion of suggested alternative management practices are provided in five appendices.

  3. The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications

    Directory of Open Access Journals (Sweden)

    A. Saskia Venne

    2014-09-01

    Full Text Available More than 450 post-translational modifications (PTMs are known, however, currently only some of those can be enriched and analyzed from complex samples such as cell lysates. Therefore, we need additional methods and concepts to improve our understanding about the dynamic crosstalk of PTMs and the highly context-dependent regulation of protein function by so-called ‘PTM codes’. The mere focus on affinity-based enrichment techniques may not be sufficient to achieve this ambitious goal. However, the complementary use of two-dimensional chromatography-based strategies such as COFRADIC and ChaFRADIC might open new avenues for enriching a variety of so far inaccessible PTMs for large-scale proteome studies.

  4. [The use of total enteral formula with enriched nutrient in home Low Calorie Diet(LCD)therapy based on regular meal].

    Science.gov (United States)

    Hata, Akiko; Ibata, Takeshi; Shinoki, Keiji; Ando, Yukiko; Hirata, Takahiro; Kojima, Atsuko; Nishijima, Ritsuko; Doi, Seiko; Komuro, Ryutaro; Iijima, Shohei

    2010-12-01

    We made a low calorie diet(LCD)menu which added two commercial supporting nutritional supplements to a meal. Because a conventional formula food is very expensive, the patient was not able to afford it at home. Those supplements are a total enteral formula with enriched nutrient(ACURE EN800)and vitamin-mineral rich drink(V CRESC). The contents of vitamin and mineral in this menu satisfied the dietary reference intakes, though protein was a little low. However, we could keep the price low compared to the formula food. The patient was able to switch over to home LCD therapy with the menu.

  5. Auditory-model-based Feature Extraction Method for Mechanical Faults Diagnosis

    Institute of Scientific and Technical Information of China (English)

    LI Yungong; ZHANG Jinping; DAI Li; ZHANG Zhanyi; LIU Jie

    2010-01-01

    It is well known that the human auditory system possesses remarkable capabilities to analyze and identify signals. Therefore, it would be significant to build an auditory model based on the mechanism of human auditory systems, which may improve the effects of mechanical signal analysis and enrich the methods of mechanical faults features extraction. However the existing methods are all based on explicit senses of mathematics or physics, and have some shortages on distinguishing different faults, stability, and suppressing the disturbance noise, etc. For the purpose of improving the performances of the work of feature extraction, an auditory model, early auditory(EA) model, is introduced for the first time. This auditory model transforms time domain signal into auditory spectrum via bandpass filtering, nonlinear compressing, and lateral inhibiting by simulating the principle of the human auditory system. The EA model is developed with the Gammatone filterbank as the basilar membrane. According to the characteristics of vibration signals, a method is proposed for determining the parameter of inner hair cells model of EA model. The performance of EA model is evaluated through experiments on four rotor faults, including misalignment, rotor-to-stator rubbing, oil film whirl, and pedestal looseness. The results show that the auditory spectrum, output of EA model, can effectively distinguish different faults with satisfactory stability and has the ability to suppress the disturbance noise. Then, it is feasible to apply auditory model, as a new method, to the feature extraction for mechanical faults diagnosis with effect.

  6. AN IMAGE RETRIEVAL METHOD BASED ON SPATIAL DISTRIBUTION OF COLOR

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Color histogram is now widely used in image retrieval. Color histogram-based image retrieval methods are simple and efficient but without considering the spatial distribution information of the color. To overcome the shortcoming of conventional color histogram-based image retrieval methods, an image retrieval method based on Radon Transform (RT) is proposed. In order to reduce the computational complexity,wavelet decomposition is used to compress image data. Firstly, images are decomposed by Mallat algorithm.The low-frequency components are then projected by RT to generate the spatial color feature. Finally the moment feature matrices which are saved along with original images are obtained. Experimental results show that the RT based retrieval is more accurate and efficient than traditional color histogram-based method in case that there are obvious objects in images. Further more, RT based retrieval runs significantly faster than the traditional color histogram methods.

  7. Gravimetric enrichment of high lipid and starch accumulating microalgae.

    Science.gov (United States)

    Hassanpour, Morteza; Abbasabadi, Mahsa; Ebrahimi, Sirous; Hosseini, Maryam; Sheikhbaglou, Ahmad

    2015-11-01

    This study presents gravimetric enrichment of mixed culture to screen starch and lipid producing species separately in a sequencing batch reactor. In the enriched starch-producing mixed culture photobioreactor, the starch content at the end of steady state batch became 3.42 times the beginning of depletion. Whereas in the enriched lipid-producing photobioreactor, the lipid content at the end of steady state batch became 3 times the beginning of famine phase. The obtained results revealed that the gravimetric enrichment is a suitable screening method for specific production of storage compounds in none-sterile large-scaled condition.

  8. 2H2O incorporation into hepatic acetyl-CoA and de novo lipogenesis as measured by Krebs cycle-mediated 2H-enrichment of glutamate and glutamine.

    Science.gov (United States)

    Silva, Ana Maria; Martins, Fatima; Jones, John G; Carvalho, Rui

    2011-12-01

    Deuterated water is widely used for measuring de novo lipogenesis on the basis of quantifying lipid (2)H-enrichment relative to that of body water. However, incorporation of (2)H-enrichment from body water into newly synthesized lipid molecules is incomplete therefore the true lipid precursor enrichment differs from that of body water. We describe a novel measurement of de novo lipogenesis that is based on a true precursor-product analysis of hepatic acetyl-CoA and triglyceride methyl enrichments from deuterated water. After deuterated water administration to seven in situ and seven perfused livers, acetyl-CoA methyl enrichment was inferred from (2)H nuclear magnetic resonance analysis of hepatic glutamate/glutamine (Glx) enrichment and triglyceride methyl enrichment was directly determined by (2)H nuclear magnetic resonance of triglycerides. Acetyl-CoA (2) H-enrichment was 71% ± 1% that of body water for in situ livers and 53% ± 2% of perfusate water for perfused livers. From the ratio of triglyceride-methyl/acetyl-CoA enrichments, fractional de novo lipogenesis rates of 0.97% ± 0.09%/2 hr and 7.92% ± 1.47%/48 hr were obtained for perfused and in situ liver triglycerides, respectively. Our method reveals that acetyl-CoA enrichment is significantly less than body water both for in situ and perfused livers. Furthermore, the difference between acetyl-CoA and body water enrichments is sensitive to the experimental setting.

  9. Semantically Enriched Web Usage Mining for Predicting User Future Movements

    Directory of Open Access Journals (Sweden)

    Suresh Shirgave

    2013-10-01

    Full Text Available Explosive and quick growth of the World Wide Web has resulted in intricate Web sites, demanding enhanced user skills and sophisticated tools to help the Web user to find the desired information. Finding desired information on the Web has become a critical ingredient of everyday personal, educational, and business life. Thus, there is a demand for more sophisticated tools to help the user to navigate a Web site and find the desired information. The users must be provided with information and services specific to their needs, rather than an undifferentiated mass of information. For discovering interesting and frequent navigation patterns from Web server logs many Web usage mining techniques have been applied. The recommendation accuracy of solely usage based techniques can be improved by integrating Web site content and site structure in the personalization process.Herein, we propose Semantically enriched Web Usage Mining method (SWUM, which combines the fields of Web Usage Mining and Semantic Web. In the proposed method, the undirected graph derived from usage data is enriched with rich semantic information extracted from the Web pages and the Web site structure. The experimental results show that the SWUM generates accurate recommendations with integration of usage, semantic data and Web site structure. The results shows that proposed method is able to achieve 10-20% better accuracy than the solely usage based model, and 5-8% better than an ontology based model.

  10. Experimental research on biomass particle combustion characteristics based on oxygen-enriched conditions%基于富氧条件的生物质颗粒燃烧特性实验研究

    Institute of Scientific and Technical Information of China (English)

    朱艳艳; 张林华; 崔永章; 李凯; 吕文超

    2013-01-01

    Oxygen-enriched combustion is an important method to solve the low temperature problem of biomass pellet fuel direct combustion. In order to study the combustion characteristics of biomass pellet fuel in the oxygen-enrich conditions, the paper utilizes thermal gravimetric analysis method to carry out combustion characteristics test about com stalks, cotton stalks and sawdust. Through the analysis of TG-DTG curves of three straws in different oxygen concentrations, we study the effect of oxygen-enriched conditions on combustion characteristics index of the three typical biomass pellet fuels. The results show that the burnout temperature interval of three biomass pellet fuels in the oxygen-enriched conditions reduced nearly 100 ℃ than that in the air, and fixed carbon combustion maximum rate is 2 -2. 75 times that in the air. In addition, fuel combustion characteristic index rises rapidly in the oxygen-enriched conditions, and the increase margin of corn stalk is the largest, so the promoting role of corn stalk is the strongest.%富氧燃烧是解决生物质能源直接燃烧温度低问题的重要方法.文章采用热重分析法分别对玉米、棉秆以及木屑进行燃烧特性试验,通过分析不同氧气浓度下三种秸秆的TG-DTG曲线,研究富氧条件对三种典型生物质颗粒燃料燃烧特性指数的影响.结果表明:富氧条件下三种生物质颗粒燃料燃尽温度区间比空气中减少近100℃,挥发分最大析出速率是空气中的2 ~2.75倍;富氧条件下,燃料的燃烧特性指数迅速上升,且玉米杆的上升幅度最大,表明富氧对玉米杆促进作用最强.

  11. Systems and methods for interpolation-based dynamic programming

    KAUST Repository

    Rockwood, Alyn

    2013-01-03

    Embodiments of systems and methods for interpolation-based dynamic programming. In one embodiment, the method includes receiving an object function and a set of constraints associated with the objective function. The method may also include identifying a solution on the objective function corresponding to intersections of the constraints. Additionally, the method may include generating an interpolated surface that is in constant contact with the solution. The method may also include generating a vector field in response to the interpolated surface.

  12. A Summary of Actinide Enrichment Technologies and Capability Gaps

    Energy Technology Data Exchange (ETDEWEB)

    Patton, Bradley D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Robinson, Sharon M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-01-01

    The evaluation performed in this study indicates that a new program is needed to efficiently provide a national actinide radioisotope enrichment capability to produce milligram-to-gram quantities of unique materials for user communities as summarized in Table 1. This program xiv should leverage past actinide enrichment, the recent advances in stable isotope enrichment, and assessments of the future requirements to cost effectively develop this capability while establishing an experience base for a new generation of researchers in this vital area. Preliminary evaluations indicate that an EMIS device would have the capability to meet the future needs of the user community for enriched actinides. The EMIS technology could be potentially coupled with other enrichment technologies, such as irradiation, as pre-enrichment and/or post-enrichment systems to increase the throughput, reduce losses of material, and/or reduce operational costs of the base EMIS system. Past actinide enrichment experience and advances in the EMIS technology applied in stable isotope separations should be leveraged with this new evaluation information to assist in the establishment of a domestic actinide radioisotope enrichment capability.

  13. Subpixel edge detection method based on low-frequency filtering

    Science.gov (United States)

    Bylinsky, Yosip Y.; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

    2016-09-01

    A method of edge detection in images is proposed basing that based on low-frequency filtering. The method uses polynomial interpolation to determine the coordinates of the edge point with subpixel accuracy. Some experiments have been results also have been provided.

  14. An improved bit shuffling pixels-based image scrambling method

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hong; WANG Hong-xia; WANG Jin

    2011-01-01

    @@ Compared with the Arnold transform, the image scrambling method based on bit shuffling pixels is much more secure, and has higher efficiency and speed.However, the key space of this bit shuffling pixels based method is too small to resist exhaustive search attack.Therefore, an improved method based on chaos is proposed in this paper.The security of the improved scheme is enhanced by increasing the number of the keys.Theoretical analysis and experimental results show that the proposed method is effective and has higher security.

  15. Online Fault Diagnosis Method Based on Nonlinear Spectral Analysis

    Institute of Scientific and Technical Information of China (English)

    WEI Rui-xuan; WU Li-xun; WANG Yong-chang; HAN Chong-zhao

    2005-01-01

    The fault diagnosis based on nonlinear spectral analysis is a new technique for the nonlinear fault diagnosis, but its online application could be limited because of the enormous compution requirements for the estimation of general frequency response functions. Based on the fully decoupled Volterra identification algorithm, a new online fault diagnosis method based on nonlinear spectral analysis is presented, which can availably reduce the online compution requirements of general frequency response functions. The composition and working principle of the method are described, the test experiments have been done for damping spring of a vehicle suspension system by utilizing the new method, and the results indicate that the method is efficient.

  16. A Meta-Path-Based Prediction Method for Human miRNA-Target Association

    Directory of Open Access Journals (Sweden)

    Jiawei Luo

    2016-01-01

    Full Text Available MicroRNAs (miRNAs are short noncoding RNAs that play important roles in regulating gene expressing, and the perturbed miRNAs are often associated with development and tumorigenesis as they have effects on their target mRNA. Predicting potential miRNA-target associations from multiple types of genomic data is a considerable problem in the bioinformatics research. However, most of the existing methods did not fully use the experimentally validated miRNA-mRNA interactions. Here, we developed RMLM and RMLMSe to predict the relationship between miRNAs and their targets. RMLM and RMLMSe are global approaches as they can reconstruct the missing associations for all the miRNA-target simultaneously and RMLMSe demonstrates that the integration of sequence information can improve the performance of RMLM. In RMLM, we use RM measure to evaluate different relatedness between miRNA and its target based on different meta-paths; logistic regression and MLE method are employed to estimate the weight of different meta-paths. In RMLMSe, sequence information is utilized to improve the performance of RMLM. Here, we carry on fivefold cross validation and pathway enrichment analysis to prove the performance of our methods. The fivefold experiments show that our methods have higher AUC scores compared with other methods and the integration of sequence information can improve the performance of miRNA-target association prediction.

  17. Neuron enriched nuclear proteome isolated from human brain.

    Science.gov (United States)

    Dammer, Eric B; Duong, Duc M; Diner, Ian; Gearing, Marla; Feng, Yue; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

    2013-07-05

    The brain consists of diverse cell types including neurons, astrocytes, oligodendrocytes, and microglia. The isolation of nuclei from these distinct cell populations provides an opportunity to identify cell-type-specific nuclear proteins, histone modifications, and regulation networks that are altered with normal brain aging or neurodegenerative disease. In this study, we used a method by which intact neuronal and non-neuronal nuclei were purified from human post-mortem brain employing a modification of fluorescence activated cell sorting (FACS) termed fluorescence activated nuclei sorting (FANS). An antibody against NeuN, a neuron specific splicing factor, was used to isolate neuronal nuclei. Utilizing mass spectrometry (MS) based label-free quantitative proteomics, we identified 1755 proteins from sorted NeuN-positive and negative nuclear extracts. Approximately 20% of these proteins were significantly enriched or depleted in neuronal versus non-neuronal populations. Immunoblots of primary cultured rat neuron, astrocyte, and oligodendrocyte extracts confirmed that distinct members of the major nucleocytoplasmic structural linkage complex (LINC), nesprin-1 and nesprin-3, were differentially enriched in neurons and astrocytes, respectively. These comparative proteomic data sets also reveal a number of transcription and splicing factors that are selectively enriched in a cell-type-specific manner in human brain.

  18. Expansion of U. S. uranium enrichment capacity. Final environmental statement

    Energy Technology Data Exchange (ETDEWEB)

    1976-04-01

    Reasonably foreseeable environmental, social, economic, and technological costs and benefits of postulated expansion of U. S. enrichment capacity through the year 2000 and reasonably available alternatives to such expansion are described. Both the gas centrifuge and gaseous diffusion methods for the enrichment of uranium are considered in this impact assessment. (JGB)

  19. Targeted enrichment of genomic DNA regions for next generation sequencing

    NARCIS (Netherlands)

    Mertens, F.; El-Sharawy, A.; Sauer, S.; Van Helvoort, J.; Van der Zaag, P.J.; Franke, A.; Nilsson, M.; Lehrach. H.; Brookes, A.

    2011-01-01

    In this review we discuss the latest targeted enrichment methods, and aspects of their utilization along with second generation sequencing for complex genome analysis. In doing so we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a pow

  20. Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

    Directory of Open Access Journals (Sweden)

    Alexander Kaever

    Full Text Available A major challenge in current systems biology is the combination and integrative analysis of large data sets obtained from different high-throughput omics platforms, such as mass spectrometry based Metabolomics and Proteomics or DNA microarray or RNA-seq-based Transcriptomics. Especially in the case of non-targeted Metabolomics experiments, where it is often impossible to unambiguously map ion features from mass spectrometry analysis to metabolites, the integration of more reliable omics technologies is highly desirable. A popular method for the knowledge-based interpretation of single data sets is the (Gene Set Enrichment Analysis. In order to combine the results from different analyses, we introduce a methodical framework for the meta-analysis of p-values obtained from Pathway Enrichment Analysis (Set Enrichment Analysis based on pathways of multiple dependent or independent data sets from different omics platforms. For dependent data sets, e.g. obtained from the same biological samples, the framework utilizes a covariance estimation procedure based on the nonsignificant pathways in single data set enrichment analysis. The framework is evaluated and applied in the joint analysis of Metabolomics mass spectrometry and Transcriptomics DNA microarray data in the context of plant wounding. In extensive studies of simulated data set dependence, the introduced correlation could be fully reconstructed by means of the covariance estimation based on pathway enrichment. By restricting the range of p-values of pathways considered in the estimation, the overestimation of correlation, which is introduced by the significant pathways, could be reduced. When applying the proposed methods to the real data sets, the meta-analysis was shown not only to be a powerful tool to investigate the correlation between different data sets and summarize the results of multiple analyses but also to distinguish experiment-specific key pathways.

  1. Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

    Science.gov (United States)

    Kaever, Alexander; Landesfeind, Manuel; Feussner, Kirstin; Morgenstern, Burkhard; Feussner, Ivo; Meinicke, Peter

    2014-01-01

    A major challenge in current systems biology is the combination and integrative analysis of large data sets obtained from different high-throughput omics platforms, such as mass spectrometry based Metabolomics and Proteomics or DNA microarray or RNA-seq-based Transcriptomics. Especially in the case of non-targeted Metabolomics experiments, where it is often impossible to unambiguously map ion features from mass spectrometry analysis to metabolites, the integration of more reliable omics technologies is highly desirable. A popular method for the knowledge-based interpretation of single data sets is the (Gene) Set Enrichment Analysis. In order to combine the results from different analyses, we introduce a methodical framework for the meta-analysis of p-values obtained from Pathway Enrichment Analysis (Set Enrichment Analysis based on pathways) of multiple dependent or independent data sets from different omics platforms. For dependent data sets, e.g. obtained from the same biological samples, the framework utilizes a covariance estimation procedure based on the nonsignificant pathways in single data set enrichment analysis. The framework is evaluated and applied in the joint analysis of Metabolomics mass spectrometry and Transcriptomics DNA microarray data in the context of plant wounding. In extensive studies of simulated data set dependence, the introduced correlation could be fully reconstructed by means of the covariance estimation based on pathway enrichment. By restricting the range of p-values of pathways considered in the estimation, the overestimation of correlation, which is introduced by the significant pathways, could be reduced. When applying the proposed methods to the real data sets, the meta-analysis was shown not only to be a powerful tool to investigate the correlation between different data sets and summarize the results of multiple analyses but also to distinguish experiment-specific key pathways.

  2. Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

    Science.gov (United States)

    Daquigan, Ninalynn; Grim, Christopher J.; White, James R.; Hanes, Darcy E.; Jarvis, Karen G.

    2016-01-01

    Culture based methods are commonly employed to detect pathogens in food and environmental samples. These methods are time consuming and complex, requiring multiple non-selective and selective enrichment broths, and usually take at least 1 week to recover and identify pathogens. Improving pathogen detection in foods is a primary goal for regulatory agencies and industry. Salmonella detection in food relies on a series of culture steps in broth formulations optimized to resuscitate Salmonella and reduce the abundance of competitive bacteria. Examples of non-selective pre-enrichment broths used to isolate Salmonella from food include Lactose, Universal Pre-enrichment, BPW, and Trypticase Soy broths. Tetrathionate (TT) and Rappaport–Vassiliadis (RV) broths are employed after a 24-h non-selective enrichment to select for Salmonella and hamper the growth of competitive bacteria. In this study, we tested a new formulation of TT broth that lacks brilliant green dye and has lower levels of TT . We employed this TT broth formulation in conjunction with a 6-h non-selective pre-enrichment period and determined that Salmonella recovery was possible one day earlier than standard food culture methods. We tested the shortened culture method in different non-selective enrichment broths, enumerated Salmonella in the non-selective enrichments, and used 16S rRNA gene sequencing to determine the proportional abundances of Salmonella in the TT and RV selective enrichments. Together these data revealed that a 6-h non-selective pre-enrichment reduces the levels of competitive bacteria inoculated into the selective TT and RV broths, enabling the recovery of Salmonella 1 day earlier than standard culture enrichment methods. PMID:28082968

  3. A New Robust Image Matching Method Based on Distance Reciprocal

    Institute of Scientific and Technical Information of China (English)

    赵春江; 施文康; 邓勇

    2004-01-01

    Object matching between two-dimensional images is an important problem in computer vision. The purpose of object matching is to decide the similarity between two objects. A new robust image matching method based on distance reciprocal was presented. The distance reciprocal is based on human visual perception. This method is simple and effective. Moreover, it is robust against noise. The experiments show that this method outperforms the Hausdorff distance, when the images with noise interfered need to be recognized.

  4. Method for detecting software anomalies based on recurrence plot analysis

    OpenAIRE

    Michał Mosdorf

    2012-01-01

    Presented paper evaluates method for detecting software anomalies based on recurrence plot analysis of trace log generated by software execution. Described method for detecting software anomalies is based on windowed recurrence quantification analysis for selected measures (e.g. Recurrence rate - RR or Determinism - DET). Initial results show that proposed method is useful in detecting silent software anomalies that do not result in typical crashes (e.g. exceptions).

  5. Method for detecting software anomalies based on recurrence plot analysis

    Directory of Open Access Journals (Sweden)

    Michał Mosdorf

    2012-03-01

    Full Text Available Presented paper evaluates method for detecting software anomalies based on recurrence plot analysis of trace log generated by software execution. Described method for detecting software anomalies is based on windowed recurrence quantification analysis for selected measures (e.g. Recurrence rate - RR or Determinism - DET. Initial results show that proposed method is useful in detecting silent software anomalies that do not result in typical crashes (e.g. exceptions.

  6. Power quality events recognition using a SVM-based method

    Energy Technology Data Exchange (ETDEWEB)

    Cerqueira, Augusto Santiago; Ferreira, Danton Diego; Ribeiro, Moises Vidal; Duque, Carlos Augusto [Department of Electrical Circuits, Federal University of Juiz de Fora, Campus Universitario, 36036 900, Juiz de Fora MG (Brazil)

    2008-09-15

    In this paper, a novel SVM-based method for power quality event classification is proposed. A simple approach for feature extraction is introduced, based on the subtraction of the fundamental component from the acquired voltage signal. The resulting signal is presented to a support vector machine for event classification. Results from simulation are presented and compared with two other methods, the OTFR and the LCEC. The proposed method shown an improved performance followed by a reasonable computational cost. (author)

  7. Wind Turbine Gearbox Fault Diagnosis Method Based on Riemannian Manifold

    OpenAIRE

    Shoubin Wang; Xiaogang Sun; Chengwei Li

    2014-01-01

    As multivariate time series problems widely exist in social production and life, fault diagnosis method has provided people with a lot of valuable information in the finance, hydrology, meteorology, earthquake, video surveillance, medical science, and other fields. In order to find faults in time sequence quickly and efficiently, this paper presents a multivariate time series processing method based on Riemannian manifold. This method is based on the sliding window and uses the covariance mat...

  8. Efficient Option Pricing Methods Based on Fourier Series Expansions

    Institute of Scientific and Technical Information of China (English)

    Deng DING; Sio Chong U

    2011-01-01

    A novel option pricing method based on Fourier-cosine series expansion was proposed by Fang and Oosterlee. Developing their idea, three new option pricing methods based on Fourier, Fourier-cosine and Fourier-sine series expansions are presented in this paper, which are more efficient when the option prices are calculated with many strike prices. A series of numerical experiments under different exp-Lévy models are also given to compare these new methods with the Fang and Oosterlee's method and other methods.

  9. Correlation theory-based signal processing method for CMF signals

    Science.gov (United States)

    Shen, Yan-lin; Tu, Ya-qing

    2016-06-01

    Signal processing precision of Coriolis mass flowmeter (CMF) signals affects measurement accuracy of Coriolis mass flowmeters directly. To improve the measurement accuracy of CMFs, a correlation theory-based signal processing method for CMF signals is proposed, which is comprised of the correlation theory-based frequency estimation method and phase difference estimation method. Theoretical analysis shows that the proposed method eliminates the effect of non-integral period sampling signals on frequency and phase difference estimation. The results of simulations and field experiments demonstrate that the proposed method improves the anti-interference performance of frequency and phase difference estimation and has better estimation performance than the adaptive notch filter, discrete Fourier transform and autocorrelation methods in terms of frequency estimation and the data extension-based correlation, Hilbert transform, quadrature delay estimator and discrete Fourier transform methods in terms of phase difference estimation, which contributes to improving the measurement accuracy of Coriolis mass flowmeters.

  10. Profile of World Uranium Enrichment Programs-2009

    Energy Technology Data Exchange (ETDEWEB)

    Laughter, Mark D [ORNL

    2009-04-01

    . It is based entirely on open-source information, which is dependent on published sources and may therefore not be completely accurate or reflect the most recent developments. Consequently, readers should not assume that information cited here has the endorsement of either ORNL or the U.S. Department of Energy. We are merely reporting what's been reported. In addition, this report briefly describes some of the safeguards techniques being used at various enrichment plants, including implementation of HSP recommendations.

  11. Development Issues on Linked Data Weblog Enrichment

    Science.gov (United States)

    Ruiz-Rube, Iván; Cornejo, Carlos M.; Dodero, Juan Manuel; García, Vicente M.

    In this paper, we describe the issues found during the development of LinkedBlog, a Linked Data extension for WordPress blogs. This extension enables to enrich text-based and video information contained in blog entries with RDF triples that are suitable to be stored, managed and exploited by other web-based applications. The issues have to do with the generality, usability, tracking, depth, security, trustiness and performance of the linked data enrichment process. The presented annotation approach aims at maintaining web-based contents independent from the underlying ontological model, by providing a loosely coupled RDFa-based approach in the linked data application. Finally, we detail how the performance of annotations can be improved through a semantic reasoner.

  12. Deployable nuclear fleet based on available quantities of uranium and reactor types – the case of fast reactors started up with enriched uranium

    Directory of Open Access Journals (Sweden)

    Baschwitz Anne

    2016-01-01

    Full Text Available International organizations regularly produce global energy demand scenarios. To account for the increasing population and GDP trends, as well as to encompass evolving energy uses while satisfying constraints on greenhouse gas emissions, long-term installed nuclear power capacity scenarios tend to be more ambitious, even after the Fukushima accident. Thus, the amounts of uranium or plutonium needed to deploy such capacities could be limiting factors. This study first considers light-water reactors (LWR, GEN III using enriched uranium, like most of the current reactor technologies. It then examines the contribution of future fast reactors (FR, GEN IV operating with an initial fissile load and then using depleted uranium and recycling their own plutonium. However, as plutonium is only available in limited quantity since it is only produced in nuclear reactors, the possibility of starting up these Generation IV reactors with a fissile load of enriched uranium is also explored. In one of our previous studies, the uranium consumption of a third-generation reactor like an EPR™ was compared with that of a fast reactor started up with enriched uranium (U5-FR. For a reactor lifespan of 60 years, the U5-FR consumes three times less uranium than the EPR and represents a 60% reduction in terms of separative work units (SWU, though its requirements are concentrated over the first few years of operation. The purpose of this study is to investigate the relevance of U5-FRs in a nuclear fleet deployment configuration. Considering several power demand scenarios and assuming different finite quantities of available natural uranium, this paper examines what types of reactors must be deployed to meet the demand. The deployment of light-water reactors only is not sustainable in the long run. Generation IV reactors are therefore essential. Yet when started up with plutonium, the number of reactors that can be deployed is also limited. In a fleet deployment

  13. Enrichment and identification of glycoproteins in human saliva using lectin magnetic bead arrays.

    Science.gov (United States)

    Caragata, Michael; Shah, Alok K; Schulz, Benjamin L; Hill, Michelle M; Punyadeera, Chamindie

    2016-03-15

    Aberrant glycosylation of proteins is a hallmark of tumorigenesis and could provide diagnostic value in cancer detection. Human saliva is an ideal source of glycoproteins due to the relatively high proportion of glycosylated proteins in the salivary proteome. Moreover, saliva collection is noninvasive and technically straightforward, and the sample collection and storage is relatively easy. Although differential glycosylation of proteins can be indicative of disease states, identification of differential glycosylation from clinical samples is not trivial. To facilitate salivary glycoprotein biomarker discovery, we optimized a method for differential glycoprotein enrichment from human saliva based on lectin magnetic bead arrays (saLeMBA). Selected lectins from distinct reactivity groups were used in the saLeMBA platform to enrich salivary glycoproteins from healthy volunteer saliva. The technical reproducibility of saLeMBA was analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the glycosylated proteins enriched by each lectin. Our saLeMBA platform enabled robust glycoprotein enrichment in a glycoprotein- and lectin-specific manner consistent with known protein-specific glycan profiles. We demonstrated that saLeMBA is a reliable method to enrich and detect glycoproteins present in human saliva.

  14. Assembly and Irradiation Modeling of Residual Stresses in Low-Enriched Uranium Foil-Based Annular Targets for Molybdenum-99 Production

    Directory of Open Access Journals (Sweden)

    Srisharan G. Govindarajan

    2013-01-01

    Full Text Available This paper considers a composite cylindrical structure, with low-enriched uranium (LEU foil enclosed between two aluminum 6061-T6 cylinders. A recess is cut all around the outer circumference of the inner tube to accommodate the LEU foil of open-cross section. To obtain perfect contact at the interfaces of the foil and the tubes, an internal pressure is applied to the inner tube, thereby plastically and elastically deforming it. The residual stresses resulting from the assembly process are used along with a thermal stress model to predict the stress margins in the cladding during irradiation. The whole process was simulated as a steady-state two-dimensional problem using the commercial finite element code Abaqus FEA. The irradiation behavior of the annular target has been presented, and the effect of the assembly residual stresses has been discussed.

  15. Module-based functional pathway enrichment analysis of a protein-protein interaction network to study the effects of intestinal microbiota depletion in mice.

    Science.gov (United States)

    Jia, Zhen-Yi; Xia, Yang; Tong, Danian; Yao, Jing; Chen, Hong-Qi; Yang, Jun

    2014-06-01

    Complex communities of microorganisms play important roles in human health, and alterations in the intestinal microbiota may induce intestinal inflammation and numerous diseases. The purpose of this study was to identify the key genes and processes affected by depletion of the intestinal microbiota in a murine model. The Affymetrix microarray dataset GSE22648 was downloaded from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified using the limma package in R. A protein-protein interaction (PPI) network was constructed for the DEGs using the Cytoscape software, and the network was divided into several modules using the MCODE plugin. Furthermore, the modules were functionally annotated using the PiNGO plugin, and DEG-related pathways were retrieved and analyzed using the GenMAPP software. A total of 53 DEGs were identified, of which 26 were upregulated and 27 were downregulated. The PPI network of these DEGs comprised 3 modules. The most significant module-related DEGs were the cytochrome P450 (CYP) 4B1 isozyme gene (CYP4B1) in module 1, CYP4F14 in module 2 and the tachykinin precursor 1 gene (TAC1) in module 3. The majority of enriched pathways of module 1 and 2 were oxidation reduction pathways (metabolism of xenobiotics by CYPs) and lipid metabolism-related pathways, including linoleic acid and arachidonic acid metabolism. The neuropeptide signaling pathway was the most significantly enriched functional pathway of module 3. In conclusion, our findings strongly suggest that intestinal microbiota depletion affects cellular metabolism and oxidation reduction pathways. In addition, this is the first time, to the best of our knowledge, that the neuropeptide signaling pathway is reported to be affected by intestinal microbiota depletion in mice. The present study provides a list of candidate genes and processes related to the interaction of microbiota with the intestinal tract.

  16. 植物油中挥发性风味物质的富集方法研究进展%RESEARCH PROGRESS ON ENRICHMENT METHODS OF VOLATILE FLAVOR COMPONENTS IN VEGETABLE OIL

    Institute of Scientific and Technical Information of China (English)

    从珊; 张国治; 黄纪念; 张丽霞; 葛凤全

    2012-01-01

    This paper mainly introduced the common enrichment methods of volatile flavor components in vegetable oil, including distillation (steam distillation, vacuum distillation and simultaneous distillation extraction) , headspace extraction (dynamic headspace extraction and static headspace extraction) , solid phase mi-croextraction , and supercritical CO2 fluid extraction. The paper also described the advantages and disadvantages of each method to provide some reference to the researchers who study the flavor of oils.%介绍了植物油中挥发性风味物质的常见富集方法,包括蒸馏法(水蒸气蒸馏法、真空减压蒸馏法、同时蒸馏萃取法)、顶空萃取法(动态顶空萃取法、静态顶空萃取法)、固相微萃取法和超临界CO2流体萃取法.描述了每种方法的优缺点,给油脂风味的研究者提供一定的参考.

  17. Highly sensitive methods for electroanalytical chemistry based on nanotubule membranes.

    Science.gov (United States)

    Kobayashi, Y; Martin, C R

    1999-09-01

    Two new methods of electroanalysis are described. These methods are based on membranes containing monodisperse Au nanotubules with inside diameters approaching molecular dimensions. In one method, the analyte species is detected by measuring the change in trans-membrane current when the analyte is added to the nanotubule-based cell. The second method entails the use of a concentration cell based on the nanotubule membrane. In this case, the change in membrane potential is used to detect the analyte. Detection limits as low as 10(-11) M have been achieved. Hence, these methods compete with even the most sensitive of modern analytical methodologies. In addition, excellent molecular-sized-based selectivity is observed.

  18. Kernel based eigenvalue-decomposition methods for analysing ham

    DEFF Research Database (Denmark)

    Christiansen, Asger Nyman; Nielsen, Allan Aasbjerg; Møller, Flemming

    2010-01-01

    conditions and finding useful additives to hinder the color to change rapidly. To be able to prove which methods of storing and additives work, Danisco wants to monitor the development of the color of meat in a slice of ham as a function of time, environment and ingredients. We have chosen to use multi...... methods, such as PCA, MAF or MNF. We therefore investigated the applicability of kernel based versions of these transformation. This meant implementing the kernel based methods and developing new theory, since kernel based MAF and MNF is not described in the literature yet. The traditional methods only...... have two factors that are useful for segmentation and none of them can be used to segment the two types of meat. The kernel based methods have a lot of useful factors and they are able to capture the subtle differences in the images. This is illustrated in Figure 1. You can see a comparison of the most...

  19. Map-based control method for vehicle stability enhancement

    Institute of Scientific and Technical Information of China (English)

    Moon-Young Yoon; Seung-Hwan Baek; Kwang-Suk Boo; Heung-Seob Kim

    2015-01-01

    This work proposes a map-based control method to improve a vehicle’s lateral stability, and the performance of the proposed method is compared with that of the conventional model-referenced control method. Model-referenced control uses the sliding mode method to determine the compensated yaw moment;in contrast, the proposed map-based control uses the compensated yaw moment map acquired by vehicle stability analysis. The vehicle stability region is calculated by a topological method based on the trajectory reversal method. A 2-DOF vehicle model and Pacejka’s tire model are used to evaluate the proposed map-based control method. The properties of model-referenced control and map-based control are compared under various road conditions and driving inputs. Model-referenced control uses a control input to satisfy the linear reference model, and it generates unnecessary tire lateral forces that may lead to worse performance than an uncontrolled vehicle with step steering input on a road with a low friction coefficient. However, map-based control determines a compensated yaw moment to maintain the vehicle within the stability region, so the typical responses of vehicle enable to converge rapidly. The simulation results with sine and step steering show that map-based control provides better the tracking responsibility and control performance than model-referenced control.

  20. Hydrogen-enriched fuels

    Energy Technology Data Exchange (ETDEWEB)

    Roser, R. [NRG Technologies, Inc., Reno, NV (United States)

    1998-08-01

    NRG Technologies, Inc. is attempting to develop hardware and infrastructure that will allow mixtures of hydrogen and conventional fuels to become viable alternatives to conventional fuels alone. This commercialization can be successful if the authors are able to achieve exhaust emission levels of less than 0.03 g/kw-hr NOx and CO; and 0.15 g/kw-hr NMHC at full engine power without the use of exhaust catalysts. The major barriers to achieving these goals are that the lean burn regimes required to meet exhaust emissions goals reduce engine output substantially and tend to exhibit higher-than-normal total hydrocarbon emissions. Also, hydrogen addition to conventional fuels increases fuel cost, and reduces both vehicle range and engine output power. Maintaining low emissions during transient driving cycles has not been demonstrated. A three year test plan has been developed to perform the investigations into the issues described above. During this initial year of funding research has progressed in the following areas: (a) a cost effective single-cylinder research platform was constructed; (b) exhaust gas speciation was performed to characterize the nature of hydrocarbon emissions from hydrogen-enriched natural gas fuels; (c) three H{sub 2}/CH{sub 4} fuel compositions were analyzed using spark timing and equivalence ratio sweeping procedures and finally; (d) a full size pick-up truck platform was converted to run on HCNG fuels. The testing performed in year one of the three year plan represents a baseline from which to assess options for overcoming the stated barriers to success.

  1. A Spatialization-based Method for Checking and Updating Metadata

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    In this paper the application of spatialization technology on metadata quality check and updating was discussed. A new method based on spatialization was proposed for checking and updating metadata to overcome the deficiency of text based methods with the powerful functions of spatial query and analysis provided by GIS software. This method employs the technology of spatialization to transform metadata into a coordinate space and the functions of spatial analysis in GIS to check and update spatial metadata in a visual environment. The basic principle and technical flow of this method were explained in detail, and an example of implementation using ArcMap of GIS software was illustrated with a metadata set of digital raster maps. The result shows the new method with the support of interaction of graph and text is much more intuitive and convenient than the ordinary text based method, and can fully utilize the functions of GIS spatial query and analysis with more accuracy and efficiency.

  2. Multi-pattern Matching Methods Based on Numerical Computation

    Directory of Open Access Journals (Sweden)

    Lu Jun

    2013-01-01

    Full Text Available Multi-pattern matching methods based on numerical computation are advanced in this paper. Firstly it advanced the multiple patterns matching algorithm based on added information. In the process of accumulating of information, the select method of byte-accumulate operation will affect the collision odds , which means that the methods or bytes involved in the different matching steps should have greater differences as much as possible. In addition, it can use balanced binary tree to manage index to reduce the average searching times, and use the characteristics of a given pattern set by setting the collision field to eliminate collision further. In order to reduce the collision odds in the initial step, the information splicing method is advanced, which has greater value space than added information method, thus greatly reducing the initial collision odds. Multiple patterns matching methods based on numerical computation fits for large multi-pattern matching.

  3. Conceptual bases of the brand valuation by cost method

    Directory of Open Access Journals (Sweden)

    G.Y. Studinska

    2015-03-01

    Full Text Available The necessity of valuing intangible assets in accordance with international trends is substantiated. The brand is seen as more important component of intangible assets, as an effective management tool company. The benefits and uses of brand evaluation results are investigated. System monocriterion cost brand evaluation methods is analyzed. In particular, methods that require evaluation by the time factor (current and forecast methods and methods for factor comparison base (relative and absolute. The cost method of brand valuation through market transactions in accordance J.Common’s classification is considered in detail. The explanation of the difference between method a summation of all costs and method of brand valuation through market transactions is provided. The advantages and disadvantages considered cost method of brand valuation are investigated. The cost method as the relative-predicted of the brand valuation, «The method of determining the proportion of the brand from the discounted total costs» is grounded

  4. A New Method for Riccati Differential Equations Based on Reproducing Kernel and Quasilinearization Methods

    Directory of Open Access Journals (Sweden)

    F. Z. Geng

    2012-01-01

    Full Text Available We introduce a new method for solving Riccati differential equations, which is based on reproducing kernel method and quasilinearization technique. The quasilinearization technique is used to reduce the Riccati differential equation to a sequence of linear problems. The resulting sets of differential equations are treated by using reproducing kernel method. The solutions of Riccati differential equations obtained using many existing methods give good approximations only in the neighborhood of the initial position. However, the solutions obtained using the present method give good approximations in a larger interval, rather than a local vicinity of the initial position. Numerical results compared with other methods show that the method is simple and effective.

  5. Fuzzy Clustering Method for Web User Based on Pages Classification

    Institute of Scientific and Technical Information of China (English)

    ZHAN Li-qiang; LIU Da-xin

    2004-01-01

    A new method for Web users fuzzy clustering based on analysis of user interest characteristic is proposed in this article.The method first defines page fuzzy categories according to the links on the index page of the site, then computes fuzzy degree of cross page through aggregating on data of Web log.After that, by using fuzzy comprehensive evaluation method, the method constructs user interest vectors according to page viewing times and frequency of hits, and derives the fuzzy similarity matrix from the interest vectors for the Web users.Finally, it gets the clustering result through the fuzzy clustering method.The experimental results show the effectiveness of the method.

  6. Theory-Based Lexicographical Methods in a Functional Perspective

    DEFF Research Database (Denmark)

    Tarp, Sven

    2014-01-01

    This contribution provides an overview of some of the methods used in relation to the function theory. It starts with a definition of the concept of method and the relation existing between theory and method. It establishes an initial distinction between artisanal and theory-based methods...... of various methods used in the different sub-phases of the overall dictionary compilation process, from the making of the concept to the preparation for publication on the chosen media, with focus on the Internet. Finally, it briefly discusses some of the methods used to create and test the function theory...

  7. A Fast Leak Locating Method Based on Wavelet Transform

    Institute of Scientific and Technical Information of China (English)

    GE Chuanhu; YANG Hongying; YE Hao; WANG Guizeng

    2009-01-01

    The problem of leak location is actually a time delay estimation (TDE) problem. Since most exist-ing TDE methods may encounter the problem of high computational complexity when used for online leak location. This paper presents a fast leak locating method based on wavelet transform (WT). The method first gets a rough estimate of the time delay from the WT coefficients of the pressure signals at the largest scale, then keeps refining the estimate using WT coefficients on smaller and smaller scales. Quantitative analyses and test results based on real data show that the method reduces the computational complexity while main-taining the time delay estimation accuracy.

  8. Data Mining and Knowledge Discovery via Logic-Based Methods

    CERN Document Server

    Triantaphyllou, Evangelos

    2010-01-01

    There are many approaches to data mining and knowledge discovery (DM&KD), including neural networks, closest neighbor methods, and various statistical methods. This monograph, however, focuses on the development and use of a novel approach, based on mathematical logic, that the author and his research associates have worked on over the last 20 years. The methods presented in the book deal with key DM&KD issues in an intuitive manner and in a natural sequence. Compared to other DM&KD methods, those based on mathematical logic offer a direct and often intuitive approach for extracting easily int

  9. Image mosaic method based on SIFT features of line segment.

    Science.gov (United States)

    Zhu, Jun; Ren, Mingwu

    2014-01-01

    This paper proposes a novel image mosaic method based on SIFT (Scale Invariant Feature Transform) feature of line segment, aiming to resolve incident scaling, rotation, changes in lighting condition, and so on between two images in the panoramic image mosaic process. This method firstly uses Harris corner detection operator to detect key points. Secondly, it constructs directed line segments, describes them with SIFT feature, and matches those directed segments to acquire rough point matching. Finally, Ransac method is used to eliminate wrong pairs in order to accomplish image mosaic. The results from experiment based on four pairs of images show that our method has strong robustness for resolution, lighting, rotation, and scaling.

  10. Network Traffic Anomalies Identification Based on Classification Methods

    Directory of Open Access Journals (Sweden)

    Donatas Račys

    2015-07-01

    Full Text Available A problem of network traffic anomalies detection in the computer networks is analyzed. Overview of anomalies detection methods is given then advantages and disadvantages of the different methods are analyzed. Model for the traffic anomalies detection was developed based on IBM SPSS Modeler and is used to analyze SNMP data of the router. Investigation of the traffic anomalies was done using three classification methods and different sets of the learning data. Based on the results of investigation it was determined that C5.1 decision tree method has the largest accuracy and performance and can be successfully used for identification of the network traffic anomalies.

  11. Enrichment of stable iostopes by electromagnetic isotope separation and plasma separation

    Energy Technology Data Exchange (ETDEWEB)

    Aaron, W.S.; Bigelow, T.S.; Collins, E.D.; Tracy, J.G. [Oak Ridge National Lab., TN (United States)

    1996-10-01

    Enriched stable isotopes for use in research, medicine, and industrial applications have been provided by the Oak Ridge National Laboratory for almost fifty years. The enrichment method employed is the Electromagnetic Isotope Separation (EMIS) process. Recent reviews of alternative separation processes have indicated that the Plasma Separation Process (PSP) is best suited to complement the current EMIS process. The PSP is based on the ion cyclotron resonance of a charged particle in a uniform magnetic field. This process, along with an overview of the EMIS process and their complementary use will be described. Use of the Proof of Principle, M2B, and the Production Prototype Module (PPM) devices will augment the current process to provide better enriched products for the user.

  12. Ellipse-based shape description and retrieval method

    Institute of Scientific and Technical Information of China (English)

    李向阳; 潘云鹤

    2002-01-01

    Using a group of ellipses to approach the shape contour, a new shape retrieval method is presented in this paper. In order to keep shape-based retrieval invariant to its position, orientation and size, the shape normalization method is presented. From our research, any closed shape contour can be uniquely decomposed into a group of ellipses, and the original shape contour can be re-constructed using the decomposed ellipses. The ellipse-based shape description and similar retrieval method is introduced in this paper. Based on ellipse's contribution to shape contour, the decomposed ellipses are parted into low-order ellipses and high-order ellipses. The low-order ellipses measure the macroscopic feature of a shape contour, and the high-order ellipses measure the microscopic feature. The two-phase shape matching method is given. Through the experiment test, our method has better shape retrieval effect.

  13. Searching chromosomal landmarks in Indian lentils through EMA-based Giemsa staining method.

    Science.gov (United States)

    Jha, Timir Baran; Halder, Mihir

    2016-09-01

    Lentil is one of the oldest protein-rich food crop with only one cultivated and six wild species. India is one important cultivator, producer and consumer of lentils and possesses a large number of germplasms. All species of lentil show 2n = 14 chromosomes. The primary objective of the present paper is to search chromosomal landmarks through enzymatic maceration and air drying (EMA)-based Giemsa staining method in five Indian lentil species not reported elsewhere at a time. Additionally, gametic chromosome analysis, tendril formation and seed morphology have been studied to ascertain interspecific relationships in lentils. Chromosome analysis in Lens culinaris, Lens orientalis and Lens odemensis revealed that they contain intercalary sat chromosome and similar karyotypic formula, while Lens nigricans and Lens lamottei showed presence of terminal sat chromosomes not reported earlier. This distinct morphological feature in L. nigricans and L. lamottei may be considered as chromosomal landmark. Meiotic analysis showed n = 7 bivalents in L. culinaris, L. nigricans and L. lamottei. No tendril formation was observed in L. culinaris, L. orientalis and L. odemensis while L. nigricans and L. lamottei developed very prominent tendrils. Based on chromosomal analysis, tendril formation and seed morphology, the five lentil species can be separated into two distinct groups. The outcome of this research may enrich conventional and biotechnological breeding programmes in lentil and may facilitate an easy and alternative method for identification of interspecific hybrids.

  14. Convergence of a residual based artificial viscosity finite element method

    KAUST Repository

    Nazarov, Murtazo

    2013-02-01

    We present a residual based artificial viscosity finite element method to solve conservation laws. The Galerkin approximation is stabilized by only residual based artificial viscosity, without any least-squares, SUPG, or streamline diffusion terms. We prove convergence of the method, applied to a scalar conservation law in two space dimensions, toward an unique entropy solution for implicit time stepping schemes. © 2012 Elsevier B.V. All rights reserved.

  15. Memristor Crossbar-based Hardware Implementation of IDS Method

    OpenAIRE

    Merrikh-Bayat, Farnood; Bagheri-Shouraki, Saeed; Rohani, Ali

    2010-01-01

    Ink Drop Spread (IDS) is the engine of Active Learning Method (ALM), which is the methodology of soft computing. IDS, as a pattern-based processing unit, extracts useful information from a system subjected to modeling. In spite of its excellent potential in solving problems such as classification and modeling compared to other soft computing tools, finding its simple and fast hardware implementation is still a challenge. This paper describes a new hardware implementation of IDS method based o...

  16. A New Nonlinear Compound Forecasting Method Based on ANN

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper the compound-forecasting method is discussed. The compound-forecasting method is one of the hotspots in the current predication. Firstly, the compound-forecasting method is introduced and various existing compound-forecasting methods arediscussed. Secondly, the Artificial Neural Network (ANN) is brought in compound-prediction research and a nonlinear compound-prediction model based on ANN is presented. Finally, inorder to avoid irregular weight, a new method is presented which uses principal component analyses to increase the availability of compound-forecasting information. Higherforecasting precision is achieved in practice.

  17. An Adaptive Background Subtraction Method Based on Kernel Density Estimation

    Directory of Open Access Journals (Sweden)

    Mignon Park

    2012-09-01

    Full Text Available In this paper, a pixel-based background modeling method, which uses nonparametric kernel density estimation, is proposed. To reduce the burden of image storage, we modify the original KDE method by using the first frame to initialize it and update it subsequently at every frame by controlling the learning rate according to the situations. We apply an adaptive threshold method based on image changes to effectively subtract the dynamic backgrounds. The devised scheme allows the proposed method to automatically adapt to various environments and effectively extract the foreground. The method presented here exhibits good performance and is suitable for dynamic background environments. The algorithm is tested on various video sequences and compared with other state-of-the-art background subtraction methods so as to verify its performance.

  18. A Channelization-Based DOA Estimation Method for Wideband Signals

    Directory of Open Access Journals (Sweden)

    Rui Guo

    2016-07-01

    Full Text Available In this paper, we propose a novel direction of arrival (DOA estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR using direct wideband radio frequency (RF digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method.

  19. A Channelization-Based DOA Estimation Method for Wideband Signals.

    Science.gov (United States)

    Guo, Rui; Zhang, Yue; Lin, Qianqiang; Chen, Zengping

    2016-07-04

    In this paper, we propose a novel direction of arrival (DOA) estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM) and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS) are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR) using direct wideband radio frequency (RF) digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method.

  20. A CT Image Segmentation Algorithm Based on Level Set Method

    Institute of Scientific and Technical Information of China (English)

    QU Jing-yi; SHI Hao-shan

    2006-01-01

    Level Set methods are robust and efficient numerical tools for resolving curve evolution in image segmentation. This paper proposes a new image segmentation algorithm based on Mumford-Shah module. The method is used to CT images and the experiment results demonstrate its efficiency and veracity.

  1. Noise reduction method based on weighted manifold decomposition

    Institute of Scientific and Technical Information of China (English)

    Gan Jian-Chao; Xiao Xian-Ci

    2004-01-01

    A noise reduction method based on weighted manifold decomposition is proposed in this paper, which does not need knowledge of the chaotic dynamics and choosing number of eigenvalues. The simulation indicates that the performance of this method can increase the signal-to-noise ratio of noisy chaotic time series.

  2. Competition assignment problem algorithm based on Hungarian method

    Institute of Scientific and Technical Information of China (English)

    KONG Chao; REN Yongtai; GE Huiling; DENG Hualing

    2007-01-01

    Traditional Hungarian method can only solve standard assignment problems, while can not solve competition assignment problems. This article emphatically discussed the difference between standard assignment problems and competition assignment problems. The kinds of competition assignment problem algorithms based on Hungarian method and the solutions of them were studied.

  3. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    Science.gov (United States)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-09-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  4. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    Science.gov (United States)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  5. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    Science.gov (United States)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-09-14

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  6. Effects of Almond- and Olive Oil-Based Docosahexaenoic- and Vitamin E-Enriched Beverage Dietary Supplementation on Inflammation Associated to Exercise and Age

    Science.gov (United States)

    Capó, Xavier; Martorell, Miquel; Sureda, Antoni; Riera, Joan; Drobnic, Franchek; Tur, Josep Antoni; Pons, Antoni

    2016-01-01

    n-3-polyunsaturated fatty acids and polyphenols are potential key factors for the treatment and prevention of chronic inflammation associated to ageing and non-communicable diseases. The aim was to analyse effects of an almond and olive oil beverage enriched with α-tocopherol and docosahexaenoic, exercise and age on inflammatory plasma markers, and immune gene expression in peripheral blood mononuclear cells (PBMCs). Five young and five senior athletes who were supplemented for five weeks with a functional beverage performed a stress test under controlled conditions before and after beverage supplementation. Blood samples were taken immediately before and 1 h after each test. Plasma, erythrocytes and PBMCs were isolated. Beverage supplementation increased plasmatic Tumour Necrosis Factor α (TNFα) levels depending on age and exercise. Exercise increased plasma non esterified fatty acids (NEFAs), soluble Intercellular adhesion molecule 3 (sICAM3) and soluble L-selectin (sL-Selectin), and this increase was attenuated by the supplementation. Exercise increased PGE2 plasma levels in supplemented young and in senior placebo athletes. Exercise increased NFkβ-activated levels in PBMCs, which are primed to a pro-inflammatory response increasing pro-inflammatory genes expression after the exercise mainly in the young group after the supplementation. The functional beverage supplementation to young athletes enhances a pro-inflammatory circulating environment in response to the exercise that was less evident in the senior group. PMID:27735833

  7. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

    Directory of Open Access Journals (Sweden)

    Zachary W Bent

    Full Text Available Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.

  8. Identification of Distinct Breast Cancer Stem Cell Populations Based on Single-Cell Analyses of Functionally Enriched Stem and Progenitor Pools

    Directory of Open Access Journals (Sweden)

    Nina Akrap

    2016-01-01

    Full Text Available The identification of breast cancer cell subpopulations featuring truly malignant stem cell qualities is a challenge due to the complexity of the disease and lack of general markers. By combining extensive single-cell gene expression profiling with three functional strategies for cancer stem cell enrichment including anchorage-independent culture, hypoxia, and analyses of low-proliferative, label-retaining cells derived from mammospheres, we identified distinct stem cell clusters in breast cancer. Estrogen receptor (ERα+ tumors featured a clear hierarchical organization with switch-like and gradual transitions between different clusters, illustrating how breast cancer cells transfer between discrete differentiation states in a sequential manner. ERα− breast cancer showed less prominent clustering but shared a quiescent cancer stem cell pool with ERα+ cancer. The cellular organization model was supported by single-cell data from primary tumors. The findings allow us to understand the organization of breast cancers at the single-cell level, thereby permitting better identification and targeting of cancer stem cells.

  9. Effects of Almond- and Olive Oil-Based Docosahexaenoic- and Vitamin E-Enriched Beverage Dietary Supplementation on Inflammation Associated to Exercise and Age

    Directory of Open Access Journals (Sweden)

    Xavier Capó

    2016-10-01

    Full Text Available n-3-polyunsaturated fatty acids and polyphenols are potential key factors for the treatment and prevention of chronic inflammation associated to ageing and non-communicable diseases. The aim was to analyse effects of an almond and olive oil beverage enriched with α-tocopherol and docosahexaenoic, exercise and age on inflammatory plasma markers, and immune gene expression in peripheral blood mononuclear cells (PBMCs. Five young and five senior athletes who were supplemented for five weeks with a functional beverage performed a stress test under controlled conditions before and after beverage supplementation. Blood samples were taken immediately before and 1 h after each test. Plasma, erythrocytes and PBMCs were isolated. Beverage supplementation increased plasmatic Tumour Necrosis Factor α (TNFα levels depending on age and exercise. Exercise increased plasma non esterified fatty acids (NEFAs, soluble Intercellular adhesion molecule 3 (sICAM3 and soluble L-selectin (sL-Selectin, and this increase was attenuated by the supplementation. Exercise increased PGE2 plasma levels in supplemented young and in senior placebo athletes. Exercise increased NFkβ-activated levels in PBMCs, which are primed to a pro-inflammatory response increasing pro-inflammatory genes expression after the exercise mainly in the young group after the supplementation. The functional beverage supplementation to young athletes enhances a pro-inflammatory circulating environment in response to the exercise that was less evident in the senior group.

  10. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

    Science.gov (United States)

    Bent, Zachary W; Brazel, David M; Tran-Gyamfi, Mary B; Hamblin, Rachelle Y; VanderNoot, Victoria A; Branda, Steven S

    2013-01-01

    Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq) to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.

  11. Nanoliter-volume protein enrichment, tryptic digestion, and partial separation based on isoelectric points by CE for MALDI mass spectral analysis.

    Science.gov (United States)

    Nesbitt, Chandra A; Jurcic, Kristina; Yeung, Ken K-C

    2008-01-01

    Sequence-specific proteolysis is an important part of protein identification by MS. Digestion of protein is commonly performed in-solution, in sample vials with volumes ranging from milli- to microliters. When digestion is performed with a sample volume below 1 microL, handling of solution and potential sample loss via adsorption become significant issues. In this report, a proof of concept for the digestion of a small volume protein solution inside a capillary was demonstrated using a discontinuous buffer system previously studied (Nesbitt, C. A., et al. J. Chromatogr. A 2005, 1073, 175-180). Upon voltage application, a pH junction was created by the discontinuous buffer. Using myoglobin as an example, the protein molecules were enriched at the junction with an estimated volume of a few nanoliters. A protease, trypsin, was then introduced to myoglobin at the junction by coenrichment to induce in-capillary digestion. The voltage application was then suspended to provide the necessary time (2 h) for the proteolysis to proceed. When completed, voltage application was resumed, and the discontinuous buffer reconcentrated the peptides formed from digestion. Importantly, the refocused peptides appeared to roughly elute according to their pIs, resulting in a partial separation. Direct sample deposition from capillary was performed to facilitate mass spectral analysis by MALDI. The partial separation, according to pI, offered the potential benefits of MALDI MS signal enhancement and provided supplementary pI information for peptide identity assignment.

  12. A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

    Directory of Open Access Journals (Sweden)

    Gregory W. Stull

    2013-02-01

    Full Text Available Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms. Methods and Results: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization-based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 eudicots, two monocots, which were subsequently sequenced on a single lane of the Illumina GAIIx with single-end, 100-bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717×, even for the two monocots. Conclusions: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvements to this methodology are feasible. With this general approach and probe set, it should be possible to sequence more than 300 essentially complete plastid genomes in a single Illumina GAIIx lane (achieving 50× mean coverage. However, given the complications of pooling numerous samples for multiplex sequencing and the limited number of barcodes (e.g., 96 available in commercial kits, we recommend 96 samples as a current practical maximum for multiplex plastome sequencing. This high-throughput approach should facilitate large-scale plastid genome sequencing at any level of phylogenetic diversity in angiosperms.

  13. Enriched environment induces higher CNPase positive cells in aged rat hippocampus.

    Science.gov (United States)

    Zhao, Yuan-Yu; Shi, Xiao-Yan; Zhang, Lei; Wu, Hong; Chao, Feng-Lei; Huang, Chun-Xia; Gao, Yuan; Qiu, Xuan; Chen, Lin; Lu, Wei; Tang, Yong

    2013-10-25

    It had been reported that enriched environment was beneficial for the brain cognition and for the neurons and synapses in hippocampus. Previous study reported that the oligodendrocyte density in hippocampus was increased when the rats were reared in the enriched environment from weaning to adulthood. However, biological conclusions based on density were difficult to interpret because the changes in density could be due to an alteration of total quantity and/or an alteration in the reference volume. In the present study, we used unbiased stereological methods to investigate the effect of enriched environment on the total number of 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) positive cells in CA1 and dentate gyrus (DG) of the hippocampus in aged rats. Our results indicated that there was significant difference in the total numbers of CNPase positive cells in both CA1 and DG between enriched environment group and standard environment group. The present study provided the first evidence for the protective effects of enriched environment on the CNPase positive cells in aged hippocampus.

  14. A Semantic Retrieval Method Based on the Fuzzy Reasoning

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper gives a semantic fuzzy retrieval method of multimedia object,discusses the principle of fuzzy semantic retrieval technique,presents a fuzzy reasoning mechanism based on the knowledge base,and designs the relevant reasoning algorithms.Researchful results have innovative significance.

  15. Role-based Integration Method of Enterprise Information System

    Institute of Scientific and Technical Information of China (English)

    YU Ming-hui; FEI Qi; CHEN Xue-guang

    2002-01-01

    This paper analyzes the current situation of enterprise information system and methods of system integration at first. Then a role-based analyzing method is proposed. It can help confirm the keystone of the construction of information system and the direction of system integration. At last, a case study on theintegration of material dispatching information system in a large-scale project is presented briefly. It shows that this new method is more effective than the others are.

  16. A New Video Coding Method Based on Improving Detail Regions

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The Moving Pictures Expert Group (MPEG) and H.263 standard coding method is widely used in video compression. However, the visual quality of detail regions such as eyes and mouth is not content in people at the decoder, as far as the conference telephone or videophone is concerned. A new coding method based on improving detail regions is presented in this paper. Experimental results show that this method can improve the visual quality at the decoder.

  17. Method of designing developable surface based on engineering requirement

    Institute of Scientific and Technical Information of China (English)

    YANG Ji-xin; LIU Zhe; LIU Jian

    2006-01-01

    The paper deals with the principle of envelope of a one-parameter plane family to design developable surfaces. Three methods of designing developable surfaces are presented. They are designing a developable surface based on one curve on it and its normal line, designing a developable surface based on two curves on it and designing a developable surface based on one curve and one surface. They meet the requirements of engineering fields.

  18. A method for selecting training samples based on camera response

    Science.gov (United States)

    Zhang, Leihong; Li, Bei; Pan, Zilan; Liang, Dong; Kang, Yi; Zhang, Dawei; Ma, Xiuhua

    2016-09-01

    In the process of spectral reflectance reconstruction, sample selection plays an important role in the accuracy of the constructed model and in reconstruction effects. In this paper, a method for training sample selection based on camera response is proposed. It has been proved that the camera response value has a close correlation with the spectral reflectance. Consequently, in this paper we adopt the technique of drawing a sphere in camera response value space to select the training samples which have a higher correlation with the test samples. In addition, the Wiener estimation method is used to reconstruct the spectral reflectance. Finally, we find that the method of sample selection based on camera response value has the smallest color difference and root mean square error after reconstruction compared to the method using the full set of Munsell color charts, the Mohammadi training sample selection method, and the stratified sampling method. Moreover, the goodness of fit coefficient of this method is also the highest among the four sample selection methods. Taking all the factors mentioned above into consideration, the method of training sample selection based on camera response value enhances the reconstruction accuracy from both the colorimetric and spectral perspectives.

  19. An Efficient Method for Reliability-based Multidisciplinary Design Optimization

    Institute of Scientific and Technical Information of China (English)

    Fan Hui; Li Weiji

    2008-01-01

    Design for modem engineering system is becoming multidisciplinary and incorporates practical uncertainties; therefore, it is necessary to synthesize reliability analysis and the multidiscipLinary design optimization (MDO) techniques for the design of complex engineering system. An advanced first order second moment method-based concurrent subspace optimization approach is proposed based on the comparison and analysis of the existing multidisciplinary optimization techniques and the reliability analysis methods. It is seen through a canard configuration optimization for a three-surface transport that the proposed method is computationally efficient and practical with the least modification to the current deterministic optimization process.

  20. The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

    KAUST Repository

    Theofilatos, Konstantinos A.

    2013-07-12

    Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://biotools.ceid.upatras.gr/hint-kb/), a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, cal-culatesasetoffeaturesofinterest and computesaconfidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.

  1. γ-Determination of 235U Enrichment in Inspection Techniques

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The uranium enrichment analysis method was studied and established for the thick shielding uranium samples. The analysis errors are less than 5% at the conditions of 1-3 cm iron shielding for 235U

  2. A HMM-Based Method for Vocal Fold Pathology Diagnosis

    Directory of Open Access Journals (Sweden)

    Vahid Majidnezhad

    2012-11-01

    Full Text Available Acoustic analysis is a proper method in vocal fold pathology diagnosis so that it can complement and in some cases replace the other invasive, based on direct vocal fold observations methods. There are different approaches for vocal fold pathology diagnosis. This paper presents a method based on hidden markov model which classifies speeches into two classes: the normal and the pathological. Two hidden markov models are trained based on these two classes of speech and then the trained models are used to classify the dataset. The proposed method is able to classify the speeches with an accuracy of 93.75%. The results of this algorithm provide insights that can help biologists and computer scientists design high-performance system for detection of vocal fold pathology diagnosis.

  3. WLAN indoor location method based on artificial neural network

    Institute of Scientific and Technical Information of China (English)

    Zhou Mu; Sun Ying; Xu Yubin; Deng Zhian; Meng Weixiao

    2010-01-01

    WLAN indoor location method based on artificial neural network (ANN) is analyzed.A three layer feed-forward ANN model offers the benefits of reducing time cost of the layout of an indoor location system, saving storage cost of the radio map establishment and enhancing real-time capacity in the on-line phase.According to the analysis of SNR distributions of recorded beacon signal samples and discussion about the multi-mode phenomenon, the one map method is proposed for the purpose of simplifying ANN input values and increasing location performances.Based on the simulations and comparison analysis with other two typical indoor location methods, K-nearest neighbor (KNN) and probability, the feasibility and effectiveness of ANN-based indoor location method are verified with average location error of 2.37m and location accuracy of 78.6% in 3m.

  4. A new earthquake location method based on the waveform inversion

    CERN Document Server

    Wu, Hao; Huang, Xueyuan; Yang, Dinghui

    2016-01-01

    In this paper, a new earthquake location method based on the waveform inversion is proposed. As is known to all, the waveform misfit function is very sensitive to the phase shift between the synthetic waveform signal and the real waveform signal. Thus, the convergence domain of the conventional waveform based earthquake location methods is very small. In present study, by introducing and solving a simple sub-optimization problem, we greatly expand the convergence domain of the waveform based earthquake location method. According to a large number of numerical experiments, the new method expands the range of convergence by several tens of times. This allows us to locate the earthquake accurately even from some relatively bad initial values.

  5. Patch nearfield acoustic holography based on the equivalent source method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    On the basis of nearfield acoustic holography (NAH) based on the equivalent source method (ESM), patch NAH based on the ESM is proposed. The method overcomes the shortcoming in the conventional NAH that the hologram surface should be larger than the source surface. It need not to discretize the whole source and its measurement need not to cover the whole source. The measurement may be performed over the region of interest, and the reconstruction can be done in the region directly. The method is flexible in applications, stable in computation, and very easy to implement. It has good potential applications in engineering. The nu- merical simulations show the invalidity of the conventional NAH based on the ESM and prove the validities of the proposed method for reconstructing a partial source and the regularization for reducing the error effect of the pressure measured on the hologram surface.

  6. Patch nearfield acoustic holography based on the equivalent source method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    On the basis of nearfield acoustic holography (NAH) based on the equivalent source method (ESM), patch NAH based on the ESM is proposed. The method overcomes the shortcoming in the conventional NAH that the hologram surface should be larger than the source surface. It need not to discretize the whole source and its measurement need not to cover the whole source. The measurement may be performed over the region of interest, and the reconstruction can be done in the region directly. The method is flexible in applications, stable in computation, and very easy to implement. It has good potential applications in engineering. The numerical simulations show the invalidity of the conventional NAH based on the ESM and prove the validities of the proposed method for reconstructing a partial source and the regularization for reducing the error effect of the pressure measured on the hologram surface.

  7. Key Updating Methods for Combinatorial Design Based Key Management Schemes

    Directory of Open Access Journals (Sweden)

    Chonghuan Xu

    2014-01-01

    Full Text Available Wireless sensor network (WSN has become one of the most promising network technologies for many useful applications. However, for the lack of resources, it is different but important to ensure the security of the WSNs. Key management is a corner stone on which to build secure WSNs for it has a fundamental role in confidentiality, authentication, and so on. Combinatorial design theory has been used to generate good-designed key rings for each sensor node in WSNs. A large number of combinatorial design based key management schemes have been proposed but none of them have taken key updating into consideration. In this paper, we point out the essence of key updating for the unital design based key management scheme and propose two key updating methods; then, we conduct performance analysis on the two methods from three aspects; at last, we generalize the two methods to other combinatorial design based key management schemes and enhance the second method.

  8. Integrated navigation method based on inertial navigation system and Lidar

    Science.gov (United States)

    Zhang, Xiaoyue; Shi, Haitao; Pan, Jianye; Zhang, Chunxi

    2016-04-01

    An integrated navigation method based on the inertial navigational system (INS) and Lidar was proposed for land navigation. Compared with the traditional integrated navigational method and dead reckoning (DR) method, the influence of the inertial measurement unit (IMU) scale factor and misalignment was considered in the new method. First, the influence of the IMU scale factor and misalignment on navigation accuracy was analyzed. Based on the analysis, the integrated system error model of INS and Lidar was established, in which the IMU scale factor and misalignment error states were included. Then the observability of IMU error states was analyzed. According to the results of the observability analysis, the integrated system was optimized. Finally, numerical simulation and a vehicle test were carried out to validate the availability and utility of the proposed INS/Lidar integrated navigational method. Compared with the test result of a traditional integrated navigation method and DR method, the proposed integrated navigational method could result in a higher navigation precision. Consequently, the IMU scale factor and misalignment error were effectively compensated by the proposed method and the new integrated navigational method is valid.

  9. 柑橘全爪螨微卫星位点鉴定与信息分析%Analysis of Microsatellite Loci fromPanonychus citri Based on Enriched Microsatellite Library and Transcriptome Dataset

    Institute of Scientific and Technical Information of China (English)

    魏丹丹; 刘燕; 杜洋; 李刚; 李婷; 袁明龙; 王进军

    2016-01-01

    重复类型,占总数的53.86%;其次为两碱基核心重复类型,占总数的43.36%;而四、五、六碱基重复类型以及复合型的SSR数量均较少,且数量差异不大,共占EST-SSR总数的2.78%。柑橘全爪螨EST-SSR核心重复次数主要集中在5—10次。【结论】采用磁珠富集法,并将酶切、接头连接一步化,可提高个体微小的螨类及微小昆虫SSR的富集效率。柑橘全爪螨gSSR核心重复次数要远多于从转录组数据库获得的EST-SSR。总体而言,gSSR和EST-SSR中的三碱基重复SSR具有更好的优化率。此外,柑橘全爪螨gSSR具有微卫星家族现象。%Objective] The objective of this study is to construct the microsatellite-enriched libraries, and identify genomic- microsatellite (gSSR) from the genome of the citrus red mite,Panonychus citri. Meanwhile, a large number of gene-microsatellite (EST-SSR) markers were also indentified from the transcriptome database ofP. citri. Based on these SSR sequences, the selected SSR primer pairs were validated.[Method]On the basis of isolating high quality genomic DNA ofP. citri, enriched microsatellite libraries were constructed by streptavidin-coated magnetic beads utilizing methodologies that exploit the strong affinity between biotin and the protein streptavidin. A fast and easy protocol was proposed through a combination of two different published methods. Briefly, genomic DNA was digested by the restriction enzyme and then ligated to designed adaptors. Microsatellite-containing DNA fragments were captured by streptavidin-coated magnetic beads. The beads affinity capture of microsatellite repeats using biotinylated oligonucleotide probes. Subsequently, PCR was used to amplify the captured molecules for transferring single strand DNA to double strand DNA. The PCR products were then ligated to pGEM-T Easy vector and transformed into Trans5α competent cells. Then, clones from these libraries were screened for microsatellite content. Meanwhile

  10. Comparison of three targeted enrichment strategies on the SOLiD sequencing platform.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    Full Text Available Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing (NGS, whole genome sequencing of humans is still not a viable option for the majority of genetics laboratories. This is particularly true in the case of complex disease studies, where large sample sets are often required to achieve adequate statistical power. To fully leverage the potential of NGS technology on large sample sets, several methods have been developed to selectively enrich for regions of interest. Enrichment reduces both monetary and computational costs compared to whole genome sequencing, while allowing researchers to take advantage of NGS throughput. Several targeted enrichment approaches are currently available, including molecular inversion probe ligation sequencing (MIPS, oligonucleotide hybridization based approaches, and PCR-based strategies. To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCR-based approach. Target regions were selected from exons and evolutionarily conserved areas throughout the human genome. Probe and primer pair design was carried out for all three methods using their respective informatics pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 methods. SOLiD sequencing results were analyzed for several metrics, including consistency of coverage depth across samples, on-target versus off-target efficiency, allelic bias, and genotype concordance with array-based genotyping data. Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples. Nimblegen performance was similar at read depths at 20× and below. Both Raindance and Nimblegen SeqCap exhibited tighter distributions of read depth

  11. NONLINEAR DATA RECONCILIATION METHOD BASED ON KERNEL PRINCIPAL COMPONENT ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In the industrial process situation, principal component analysis (PCA) is a general method in data reconciliation.However, PCA sometime is unfeasible to nonlinear feature analysis and limited in application to nonlinear industrial process.Kernel PCA (KPCA) is extension of PCA and can be used for nonlinear feature analysis.A nonlinear data reconciliation method based on KPCA is proposed.The basic idea of this method is that firstly original data are mapped to high dimensional feature space by nonlinear function, and PCA is implemented in the feature space.Then nonlinear feature analysis is implemented and data are reconstructed by using the kernel.The data reconciliation method based on KPCA is applied to ternary distillation column.Simulation results show that this method can filter the noise in measurements of nonlinear process and reconciliated data can represent the true information of nonlinear process.

  12. Wind Turbine Gearbox Fault Diagnosis Method Based on Riemannian Manifold

    Directory of Open Access Journals (Sweden)

    Shoubin Wang

    2014-01-01

    Full Text Available As multivariate time series problems widely exist in social production and life, fault diagnosis method has provided people with a lot of valuable information in the finance, hydrology, meteorology, earthquake, video surveillance, medical science, and other fields. In order to find faults in time sequence quickly and efficiently, this paper presents a multivariate time series processing method based on Riemannian manifold. This method is based on the sliding window and uses the covariance matrix as a descriptor of the time sequence. Riemannian distance is used as the similarity measure and the statistical process control diagram is applied to detect the abnormity of multivariate time series. And the visualization of the covariance matrix distribution is used to detect the abnormity of mechanical equipment, leading to realize the fault diagnosis. With wind turbine gearbox faults as the experiment object, the fault diagnosis method is verified and the results show that the method is reasonable and effective.

  13. NETWORK INTRUSION DETECTION METHOD BASED ON RS-MSVM

    Institute of Scientific and Technical Information of China (English)

    Xiao Yun; Han Chongzhao; Zheng Qinghua; Zhang Junjie

    2006-01-01

    A new method called RS-MSVM (Rough Set and Multi-class Support Vector Machine) is proposed for network intrusion detection. This method is based on rough set followed by MSVM for attribute reduction and classification respectively. The number of attributes of the network data used in this paper is reduced from 41 to 30 using rough set theory. The kernel function of HVDM-RBF (Heterogeneous Value Difference Metric Radial Basis Function), based on the heterogeneous value difference metric of heterogeneous datasets, is constructed for the heterogeneous network data. HVDM-RBF and one-against-one method are applied to build MSVM. DARPA (Defense Advanced Research Projects Agency) intrusion detection evaluating data were used in the experiment. The testing results show that our method outperforms other methods mentioned in this paper on six aspects: detection accuracy, number of support vectors, false positive rate, false negative rate, training time and testing time.

  14. Color Restoration Method Based on Spectral Information Using Normalized Cut

    Institute of Scientific and Technical Information of China (English)

    Tetsuro Morimoto; Tohru Mihashi; Katsushi Ikeuchi

    2008-01-01

    This paper proposes a novel method for color restoration that can effectively apply accurate color based on spectral information to a segmented image using the normalized cut technique. Using the proposed method, we can obtain a digital still camera image and spectral information in different environments. Also, it is not necessary to estimate reflectance spectra using a spectral database such as other methods. The synthesized images are accurate and high resolution. The proposed method effectively works in making digital archive contents. Some experimental results are demonstrated in this paper.

  15. A perceptual hashing method based on luminance features

    Science.gov (United States)

    Luo, Siqing

    2011-02-01

    With the rapid development of multimedia technology, content based searching and image authentication has become strong requirements. Image hashing technique has been proposed to meet them. In this paper, an RST (Rotation, Scaling, and Translation) resistant image hash algorithm is presented. In this method, the geometric distortions are extracted and adjusted by normalization. The features of the image are generated from the high-rank moments of luminance distribution. With the help of the efficient image representation capability of high-rank moments, the robustness and discrimination of proposed method are improved. The experimental results show that the proposed method is better than some existing methods in robustness under rotation attack.

  16. FUZZY IDENTIFICATION METHOD BASED ON A NEW OBJECTIVE FUNCTION

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A method of fuzzy identification based on a new objective function is proposed. The method could deal with the issue that input variables of a system have an effect on the input space while output variables of the system do not exert an influence on the input space in the proposed objective functions of fuzzy clustering. The method could simultaneously solve the problems about structure identification and parameter estimation; thus it makes the fuzzy model become optimal. Simulation example demonstrates that the method could identify non-linear systems and obviously improve modeling accuracy.

  17. A Novel Method for Solving KdV Equation Based on Reproducing Kernel Hilbert Space Method

    Directory of Open Access Journals (Sweden)

    Mustafa Inc

    2013-01-01

    Full Text Available We propose a reproducing kernel method for solving the KdV equation with initial condition based on the reproducing kernel theory. The exact solution is represented in the form of series in the reproducing kernel Hilbert space. Some numerical examples have also been studied to demonstrate the accuracy of the present method. Results of numerical examples show that the presented method is effective.

  18. A reservoir skeleton-based multiple point geostatistics method

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Traditional stochastic reservoir modeling,including object-based and pixel-based methods,cannot solve the problem of reproducing continuous and curvilinear reservoir objects. The paper first dives into the various stochastic modeling methods and extracts their merits,then proposes the skeleton-based multiple point geostatistics(SMPS) for the fluvial reservoir. The core idea is using the skeletons of reservoir objects to restrict the selection of data patterns. The skeleton-based multiple point geostatistics consists of two steps. First,predicting the channel skeleton(namely,channel centerline) by using the method in object-based modeling. The paper proposes a new method of search window to predict the skeleton. Then forecasting the distributions of reservoir objects using multiple point geostatistics with the restriction of channel skeleton. By the restriction of channel centerline,the selection of data events will be more reasonable and the realization will be achieved more really. The checks by the conceptual model and the real reservoir show that SMPS is much better than Sisim(sequential indicator simulation) ,Snesim(Single Normal Equation Simulation) and Simpat(simulation with patterns) in building the fluvial reservoir model. This new method will contribute to both the theoretical research of stochastic modeling and the oilfield developments of constructing highly precise reservoir geological models.

  19. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae.

    Directory of Open Access Journals (Sweden)

    Simon Uribe-Convers

    Full Text Available Advances in high-throughput sequencing (HTS have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array. The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities for every locus in every sample or--more importantly--recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300 bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500 bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500 bp for 349 samples.

  20. NOVEL RADAR SIGNAL SORTING METHOD BASED ON GEOMETRIC COVERING

    Institute of Scientific and Technical Information of China (English)

    万建; 国强; 宋文明

    2013-01-01

    With the increase of complexity of electromagnetic environment and continuous appearance of advanced system radars ,signals received by radar reconnaissance receivers become even more intensive and complex .There-fore ,traditional radar sorting methods based on neural network algorithms and support vector machine (SVM ) cannot process them effectively .Aiming at solving this problem ,a novel radar signal sorting method based on the cloud model theory and the geometric covering algorithm is proposed .By applying the geometric covering algo-rithm to divide input signals into different covering domains based on their distribution characteristics ,the method can overcome a typical problem that it is easy for traditional sorting algorithms to fall into the local extrema due to the use of complex nonlinear equation to describe input signals .The method uses the cloud model to describe the membership degree between signals to be sorted and their covering domains ,thus it avoids the disadvantage that traditional sorting methods based on hard clustering cannot deinterleave the signal samples with overlapped param-eters .Experimental results show that the presented method can effectively sort advanced system radar signals with overlapped parameters in complex electromagnetic environment .

  1. A flower image retrieval method based on ROI feature

    Institute of Scientific and Technical Information of China (English)

    洪安祥; 陈刚; 李均利; 池哲儒; 张亶

    2004-01-01

    Flower image retrieval is a very important step for computer-aided plant species recognition. In this paper, we propose an efficient segmentation method based on color clustering and domain knowledge to extract flower regions from flower images. For flower retrieval, we use the color histogram of a flower region to characterize the color features of flower and two shape-based features sets, Centroid-Contour Distance (CCD) and Angle Code Histogram (ACH), to characterize the shape features of a flower contour. Experimental results showed that our flower region extraction method based on color clustering and domain knowledge can produce accurate flower regions. Flower retrieval results on a database of 885 flower images collected from 14 plant species showed that our Region-of-Interest (ROI) based retrieval approach using both color and shape features can perform better than a method based on the global color histogram proposed by Swain and Ballard (1991) and a method based on domain knowledge-driven segmentation and color names proposed by Das et al.(1999).

  2. A flower image retrieval method based on ROI feature

    Institute of Scientific and Technical Information of China (English)

    洪安祥; 陈刚; 李均利; 池哲儒; 张亶

    2004-01-01

    Flower image retrieval is a very important step for computer-aided plant species recognition.In this paper,we propose an efficient segmentation method based on color clustering and domain knowledge to extract flower regions from flower images.For flower retrieval,we use the color histogram of a flower region to characterize the color features of flower and two shape-based features sets,Centroid-Contour Distance(CCD)and Angle Code Histogram(ACH),to characterize the shape features of a flower contour.Experimental results showed that our flower region extraction method based on color clustering and domain knowledge can produce accurate flower regions.Flower retrieval results on a database of 885 flower images collected from 14 plant species showed that our Region-of-Interest(ROD based retrieval approach using both color and shape features can perform better than a method based on the global color histogram proposed by Swain and Ballard(1991)and a method based on domain knowledge-driven segmentation and color names proposed by Das et al.(1999).

  3. Combining target enrichment with barcode multiplexing for high throughput SNP discovery

    Directory of Open Access Journals (Sweden)

    Lunke Sebastian

    2010-11-01

    Full Text Available Abstract Background The primary goal of genetic linkage analysis is to identify genes affecting a phenotypic trait. After localisation of the linkage region, efficient genetic dissection of the disease linked loci requires that functional variants are identified across the loci. These functional variations are difficult to detect due to extent of genetic diversity and, to date, incomplete cataloguing of the large number of variants present both within and between populations. Massively parallel sequencing platforms offer unprecedented capacity for variant discovery, however the number of samples analysed are still limited by cost per sample. Some progress has been made in reducing the cost of resequencing using either multiplexing methodologies or through the utilisation of targeted enrichment technologies which provide the ability to resequence genomic areas of interest rather that full genome sequencing. Results We developed a method that combines current multiplexing methodologies with a solution-based target enrichment method to further reduce the cost of resequencing where region-specific sequencing is required. Our multiplex/enrichment strategy produced high quality data with nominal reduction of sequencing depth. We undertook a genotyping study and were successful in the discovery of novel SNP alleles in all samples at uniplex, duplex and pentaplex levels. Conclusion Our work describes the successful combination of a targeted enrichment method and index barcode multiplexing to reduce costs, time and labour associated with processing large sample sets. Furthermore, we have shown that the sequencing depth obtained is adequate for credible SNP genotyping analysis at uniplex, duplex and pentaplex levels.

  4. Facial Feature Extraction Method Based on Coefficients of Variances

    Institute of Scientific and Technical Information of China (English)

    Feng-Xi Song; David Zhang; Cai-Kou Chen; Jing-Yu Yang

    2007-01-01

    Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) are two popular feature ex- traction techniques in statistical pattern recognition field. Due to small sample size problem LDA cannot be directly applied to appearance-based face recognition tasks. As a consequence, a lot of LDA-based facial feature extraction techniques are proposed to deal with the problem one after the other. Nullspace Method is one of the most effective methods among them. The Nullspace Method tries to find a set of discriminant vectors which maximize the between-class scatter in the null space of the within-class scatter matrix. The calculation of its discriminant vectors will involve performing singular value decomposition on a high-dimensional matrix. It is generally memory- and time-consuming. Borrowing the key idea in Nullspace method and the concept of coefficient of variance in statistical analysis we present a novel facial feature extraction method, i.e., Discriminant based on Coefficient of Variance (DCV) in this paper. Experimental results performed on the FERET and AR face image databases demonstrate that DCV is a promising technique in comparison with Eigenfaces, Nullspace Method, and other state-of-the-art facial feature extraction methods.

  5. Optimization of fuel rod enrichment distribution to minimize rod power peaking throughout life within BWR fuel assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Yasushi; Hida, Kazuki; Sakurada, Koichi; Yamamoto, Munenari [Toshiba Corp., Kawasaki, Kanagawa (Japan). Nuclear Engineering Lab.

    1997-01-01

    A practical method was developed for determining the optimum fuel enrichment distribution within a boiling water reactor fuel assembly. The method deals with two different optimization problems, i.e. a combinatorial optimization problem grouping fuel rods into a given number of rod groups with the same enrichment, and a problem determining an optimal enrichment for each fuel rod under the resultant rod-grouping pattern. In solving these problems, the primary goal is to minimize a predefined objective function over a given exposure period. The objective function used here is defined by a linear combination: C{sub 1}X+C{sub 2}X{sub G}, where X and X{sub G} stand for a control variable to give the constraint respectively for a local power peaking factor and a gadolinium rod power, and C{sub 1} and C{sub 2} are user-definable weighting factor to accommodate the design preference. The algorithm of solving the combinatorial optimization problem starts with finding the optimal enrichment vector without any rod-grouping, and promising candidates of rod-grouping patterns are found by exhaustive enumeration based on the resulting fuel enrichment ordering, and then the latter problem is solved by using the method of approximation programming. The practical application of the present method is shown for a contemporary 8x8 Pu mixed-oxide fuel assembly with 10 gadolinium-poisoned rods. (author)

  6. A hybrid method for pancreas extraction from CT image based on level set methods.

    Science.gov (United States)

    Jiang, Huiyan; Tan, Hanqing; Fujita, Hiroshi

    2013-01-01

    This paper proposes a novel semiautomatic method to extract the pancreas from abdominal CT images. Traditional level set and region growing methods that request locating initial contour near the final boundary of object have problem of leakage to nearby tissues of pancreas region. The proposed method consists of a customized fast-marching level set method which generates an optimal initial pancreas region to solve the problem that the level set method is sensitive to the initial contour location and a modified distance regularized level set method which extracts accurate pancreas. The novelty in our method is the proper selection and combination of level set methods, furthermore an energy-decrement algorithm and an energy-tune algorithm are proposed to reduce the negative impact of bonding force caused by connected tissue whose intensity is similar with pancreas. As a result, our method overcomes the shortages of oversegmentation at weak boundary and can accurately extract pancreas from CT images. The proposed method is compared to other five state-of-the-art medical image segmentation methods based on a CT image dataset which contains abdominal images from 10 patients. The evaluated results demonstrate that our method outperforms other methods by achieving higher accuracy and making less false segmentation in pancreas extraction.

  7. Investigating the distribution of some (but not all implicatures using corpora and web-based methods

    Directory of Open Access Journals (Sweden)

    Judith Degen

    2015-05-01

    Full Text Available A prevalent, but to date untested, assumption about lexicalized scalar implicatures such as those from some to not all, is that they fall into the class of GCIs and as such, constitute a homogeneous class of highly regularized and context-independent implicatures. This paper reports a test of this assumption in which linguistically untrained participants’ implicature strength judgments were collected for naturally occurring utterances containing the word some in a large-scale corpus-based web study. The results indicate that implicature strength is highly variable and systematically dependent on features of the linguistic context such as the partitive, determiner strength, and discourse accessibility. These results call into question the GCI status of scalar implicatures from some to not all and demonstrate the usefulness of corpora and web-based methods for challenging received wisdom, enriching the empirical landscape, and informing theory in pragmatics. http://dx.doi.org/10.3765/sp.8.11 BibTeX info

  8. Testability integrated evaluation method based on testability virtual test data

    Institute of Scientific and Technical Information of China (English)

    Liu Guanjun; Zhao Chenxu; Qiu Jing; Zhang Yong

    2014-01-01

    Testability virtual test is a new test method for testability verification, which has the advantages such as low cost, few restrictions and large sample of test data. It can be used to make up the deficiency of testability physical test. In order to take the advantage of testability virtual test data effectively and to improve the accuracy of testability evaluation, a testability integrated eval-uation method is proposed in this paper based on testability virtual test data. Considering the char-acteristic of testability virtual test data, the credibility analysis method for testability virtual test data is studied firstly. Then the integrated calculation method is proposed fusing the testability vir-tual and physical test data. Finally, certain helicopter heading and attitude system is presented to demonstrate the proposed method. The results show that the testability integrated evaluation method is feasible and effective.

  9. A Method of Image Symmetry Detection Based on Phase Information

    Institute of Scientific and Technical Information of China (English)

    WU Jun; YANG Zhaoxuan; FENG Dengchao

    2005-01-01

    Traditional methods for detecting symmetry in image suffer greatly from the contrast of image and noise, and they all require some preprocessing. This paper presents a new method of image symmetry detection. This method detects symmetry with phase information utilizing logGabor wavelets, because phase information is stable and significant, while symmetric points produce patterns easy to be recognised and confirmable in local phase. Phase method does not require any preprocessing, and its result is accurate or invariant to contrast, rotation and illumination conditions. This method can detect mirror symmetry, rotating symmetry and curve symmetry at one time. Results of experiment show that, compared with pivotal element algorithm based on intensity information, phase method is more accurate and robust.

  10. International Conference on Robust Rank-Based and Nonparametric Methods

    CERN Document Server

    McKean, Joseph

    2016-01-01

    The contributors to this volume include many of the distinguished researchers in this area. Many of these scholars have collaborated with Joseph McKean to develop underlying theory for these methods, obtain small sample corrections, and develop efficient algorithms for their computation. The papers cover the scope of the area, including robust nonparametric rank-based procedures through Bayesian and big data rank-based analyses. Areas of application include biostatistics and spatial areas. Over the last 30 years, robust rank-based and nonparametric methods have developed considerably. These procedures generalize traditional Wilcoxon-type methods for one- and two-sample location problems. Research into these procedures has culminated in complete analyses for many of the models used in practice including linear, generalized linear, mixed, and nonlinear models. Settings are both multivariate and univariate. With the development of R packages in these areas, computation of these procedures is easily shared with r...

  11. PPA BASED PREDICTION-CORRECTION METHODS FOR MONOTONE VARIATIONAL INEQUALITIES

    Institute of Scientific and Technical Information of China (English)

    He Bingsheng; Jiang Jianlin; Qian Maijian; Xu Ya

    2005-01-01

    In this paper we study the proximal point algorithm (PPA) based predictioncorrection (PC) methods for monotone variational inequalities. Each iteration of these methods consists of a prediction and a correction. The predictors are produced by inexact PPA steps. The new iterates are then updated by a correction using the PPA formula. We present two profit functions which serve two purposes: First we show that the profit functions are tight lower bounds of the improvements obtained in each iteration. Based on this conclusion we obtain the convergence inexactness restrictions for the prediction step. Second we show that the profit functions are quadratically dependent upon the step lengths, thus the optimal step lengths are obtained in the correction step. In the last part of the paper we compare the strengths of different methods based on their inexactness restrictions.

  12. Three Methods for Occupation Coding Based on Statistical Learning

    Directory of Open Access Journals (Sweden)

    Gweon Hyukjun

    2017-03-01

    Full Text Available Occupation coding, an important task in official statistics, refers to coding a respondent’s text answer into one of many hundreds of occupation codes. To date, occupation coding is still at least partially conducted manually, at great expense. We propose three methods for automatic coding: combining separate models for the detailed occupation codes and for aggregate occupation codes, a hybrid method that combines a duplicate-based approach with a statistical learning algorithm, and a modified nearest neighbor approach. Using data from the German General Social Survey (ALLBUS, we show that the proposed methods improve on both the coding accuracy of the underlying statistical learning algorithm and the coding accuracy of duplicates where duplicates exist. Further, we find defining duplicates based on ngram variables (a concept from text mining is preferable to one based on exact string matches.

  13. Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

    DEFF Research Database (Denmark)

    Bohlin, Jon; Snipen, Lars; Cloeckaert, Axel

    2010-01-01

    , genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses). RESULTS: We found that the oligonucleotide based methods gave different results compared to that of the proteome based methods. Differences were also found...... than proteome comparisons between species in genus Brucella and genus Ochrobactrum. Pan-genomic analyses indicated that uptake of DNA from outside genus Brucella appears to be limited. CONCLUSIONS: While both the proteome based methods and the Markov chain based genomic signatures were able to reflect...

  14. Robust Speech Recognition Method Based on Discriminative Environment Feature Extraction

    Institute of Scientific and Technical Information of China (English)

    HAN Jiqing; GAO Wen

    2001-01-01

    It is an effective approach to learn the influence of environmental parameters,such as additive noise and channel distortions, from training data for robust speech recognition.Most of the previous methods are based on maximum likelihood estimation criterion. However,these methods do not lead to a minimum error rate result. In this paper, a novel discrimina-tive learning method of environmental parameters, which is based on Minimum ClassificationError (MCE) criterion, is proposed. In the method, a simple classifier and the Generalized Probabilistic Descent (GPD) algorithm are adopted to iteratively learn the environmental parameters. Consequently, the clean speech features are estimated from the noisy speech features with the estimated environmental parameters, and then the estimations of clean speech features are utilized in the back-end HMM classifier. Experiments show that the best error rate reduction of 32.1% is obtained, tested on a task of 18 isolated confusion Korean words, relative to a conventional HMM system.

  15. Analysis of Dynamic Modeling Method Based on Boundary Element

    Directory of Open Access Journals (Sweden)

    Xu-Sheng Gan

    2013-07-01

    Full Text Available The aim of this study was to study an improved dynamic modeling method based on a Boundary Element Method (BEM. The dynamic model was composed of the elements such as the beam element, plate element, joint element, lumped mass and spring element by the BEM. An improved dynamic model of a machine structure was established based on plate-beam element system mainly. As a result, the dynamic characteristics of a machine structure were analyzed and the comparison of computational results and experimental’s showed the modeling method was effective. The analyses indicate that the introduced method inaugurates a good way for analyzing dynamic characteristics of a machine structure efficiently.

  16. Image Mosaic Method Based on SIFT Features of Line Segment

    Directory of Open Access Journals (Sweden)

    Jun Zhu

    2014-01-01

    Full Text Available This paper proposes a novel image mosaic method based on SIFT (Scale Invariant Feature Transform feature of line segment, aiming to resolve incident scaling, rotation, changes in lighting condition, and so on between two images in the panoramic image mosaic process. This method firstly uses Harris corner detection operator to detect key points. Secondly, it constructs directed line segments, describes them with SIFT feature, and matches those directed segments to acquire rough point matching. Finally, Ransac method is used to eliminate wrong pairs in order to accomplish image mosaic. The results from experiment based on four pairs of images show that our method has strong robustness for resolution, lighting, rotation, and scaling.

  17. Local coding based matching kernel method for image classification.

    Directory of Open Access Journals (Sweden)

    Yan Song

    Full Text Available This paper mainly focuses on how to effectively and efficiently measure visual similarity for local feature based representation. Among existing methods, metrics based on Bag of Visual Word (BoV techniques are efficient and conceptually simple, at the expense of effectiveness. By contrast, kernel based metrics are more effective, but at the cost of greater computational complexity and increased storage requirements. We show that a unified visual matching framework can be developed to encompass both BoV and kernel based metrics, in which local kernel plays an important role between feature pairs or between features and their reconstruction. Generally, local kernels are defined using Euclidean distance or its derivatives, based either explicitly or implicitly on an assumption of Gaussian noise. However, local features such as SIFT and HoG often follow a heavy-tailed distribution which tends to undermine the motivation behind Euclidean metrics. Motivated by recent advances in feature coding techniques, a novel efficient local coding based matching kernel (LCMK method is proposed. This exploits the manifold structures in Hilbert space derived from local kernels. The proposed method combines advantages of both BoV and kernel based metrics, and achieves a linear computational complexity. This enables efficient and scalable visual matching to be performed on large scale image sets. To evaluate the effectiveness of the proposed LCMK method, we conduct extensive experiments with widely used benchmark datasets, including 15-Scenes, Caltech101/256, PASCAL VOC 2007 and 2011 datasets. Experimental results confirm the effectiveness of the relatively efficient LCMK method.

  18. Simple noise-reduction method based on nonlinear forecasting

    Science.gov (United States)

    Tan, James P. L.

    2017-03-01

    Nonparametric detrending or noise reduction methods are often employed to separate trends from noisy time series when no satisfactory models exist to fit the data. However, conventional noise reduction methods depend on subjective choices of smoothing parameters. Here we present a simple multivariate noise reduction method based on available nonlinear forecasting techniques. These are in turn based on state-space reconstruction for which a strong theoretical justification exists for their use in nonparametric forecasting. The noise reduction method presented here is conceptually similar to Schreiber's noise reduction method using state-space reconstruction. However, we show that Schreiber's method has a minor flaw that can be overcome with forecasting. Furthermore, our method contains a simple but nontrivial extension to multivariate time series. We apply the method to multivariate time series generated from the Van der Pol oscillator, the Lorenz equations, the Hindmarsh-Rose model of neuronal spiking activity, and to two other univariate real-world data sets. It is demonstrated that noise reduction heuristics can be objectively optimized with in-sample forecasting errors that correlate well with actual noise reduction errors.

  19. XML-based product information processing method for product design

    Science.gov (United States)

    Zhang, Zhen Yu

    2012-01-01

    Design knowledge of modern mechatronics product is based on information processing as the center of the knowledge-intensive engineering, thus product design innovation is essentially the knowledge and information processing innovation. Analysis of the role of mechatronics product design knowledge and information management features, a unified model of XML-based product information processing method is proposed. Information processing model of product design includes functional knowledge, structural knowledge and their relationships. For the expression of product function element, product structure element, product mapping relationship between function and structure based on the XML model are proposed. The information processing of a parallel friction roller is given as an example, which demonstrates that this method is obviously helpful for knowledge-based design system and product innovation.

  20. Method of infrared image enhancement based on histogram

    Institute of Scientific and Technical Information of China (English)

    WANG Liang; YAN Jie

    2011-01-01

    Aiming at the problem in infrared image enhancement, a new method is given based on histogram. Using the gray character- istics of target, the upper-bouod threshold is selected adaptively and the histogram is processed by the threshold. After choosing the gray transform function based on the gray level distribution of image, the gray transformation is done during histogram equalization. Finally, the enhanced image is obtained. Compared with histogram equalization (HE), histogram double equalization (HDE) and plateau histogram equalization (PE), the simulation results demonstrate that the image enhancement effect of this method has obvious superiority. At the same time, its operation speed is fast and real-time ability is excellent.

  1. Designing fuzzy inference system based on improved gradient descent method

    Institute of Scientific and Technical Information of China (English)

    Zhang Liquan; Shao Cheng

    2006-01-01

    The distribution of sampling data influences completeness of rule base so that extrapolating missing rules is very difficult. Based on data mining, a self-learning method is developed for identifying fuzzy model and extrapolating missing rules, by means of confidence measure and the improved gradient descent method. The proposed approach can not only identify fuzzy model, update its parameters and determine optimal output fuzzy sets simultaneously, but also resolve the uncontrollable problem led by the regions that data do not cover. The simulation results show the effectiveness and accuracy of the proposed approach with the classical truck backer-upper control problem verifying.

  2. Research of Stamp Forming Simulation Based on Finite Element Method

    Institute of Scientific and Technical Information of China (English)

    SU Xaio-ping; XU Lian

    2008-01-01

    We point out that the finite element method offers a greta functional improvement for analyzing the stamp forming process of an automobile panel. Using the finite element theory and the simulation method of sheet stamping forming, the element model of sheet forming is built based on software HyperMesh,and the simulation of the product's sheet forming process is analyzed based on software Dynaform. A series of simulation results are obtained. It is clear that the simulation results from the theoretical basis for the product's die design and are useful for selecting process parameters.

  3. A Robust Digital Watermark Extracting Method Based on Neural Network

    Institute of Scientific and Technical Information of China (English)

    GUOLihua; YANGShutang; LIJianhua

    2003-01-01

    Since watermark removal software, such as StirMark, has succeeded in washing watermarks away for most of the known watermarking systems, it is necessary to improve the robustness of watermarking systems. A watermark extracting method based on the error Back propagation (BP) neural network is presented in this paper, which can efficiently improve the robustness of watermarking systems. Experiments show that even if the watermarking systems are attacked by the StirMark software, the extracting method based on neural network can still efficiently extract the whole watermark information.

  4. Potential Energy Surfaces Using Algebraic Methods Based on Unitary Groups

    Directory of Open Access Journals (Sweden)

    Renato Lemus

    2011-01-01

    Full Text Available This contribution reviews the recent advances to estimate the potential energy surfaces through algebraic methods based on the unitary groups used to describe the molecular vibrational degrees of freedom. The basic idea is to introduce the unitary group approach in the context of the traditional approach, where the Hamiltonian is expanded in terms of coordinates and momenta. In the presentation of this paper, several representative molecular systems that permit to illustrate both the different algebraic approaches as well as the usual problems encountered in the vibrational description in terms of internal coordinates are presented. Methods based on coherent states are also discussed.

  5. CONSTRUCTION METHOD OF KNOWLEDGE MAP BASED ON DESIGN PROCESS

    Institute of Scientific and Technical Information of China (English)

    SU Hai; JIANG Zuhua

    2007-01-01

    Due to the increasing amount and complexity of knowledge in product design, the knowledge map based on design process is presented as a tool to reuse product design process, promote the product design knowledge sharing. The relationship between design task flow and knowledge flow is discussed; A knowledge organizing method based on design task decomposition and a visualization method to support the knowledge retrieving and sharing in product design are proposed. And a knowledge map system to manage the knowledge in product design process is built with Visual C++ and SVG. Finally, a brief case study is provided to illustrate the construction and application of knowledge map in fuel pump design.

  6. IDEF method-based simulation model design and development framework

    Directory of Open Access Journals (Sweden)

    Ki-Young Jeong

    2009-09-01

    Full Text Available The purpose of this study is to provide an IDEF method-based integrated framework for a business process simulation model to reduce the model development time by increasing the communication and knowledge reusability during a simulation project. In this framework, simulation requirements are collected by a function modeling method (IDEF0 and a process modeling method (IDEF3. Based on these requirements, a common data model is constructed using the IDEF1X method. From this reusable data model, multiple simulation models are automatically generated using a database-driven simulation model development approach. The framework is claimed to help both requirement collection and experimentation phases during a simulation project by improving system knowledge, model reusability, and maintainability through the systematic use of three descriptive IDEF methods and the features of the relational database technologies. A complex semiconductor fabrication case study was used as a testbed to evaluate and illustrate the concepts and the framework. Two different simulation software products were used to develop and control the semiconductor model from the same knowledge base. The case study empirically showed that this framework could help improve the simulation project processes by using IDEF-based descriptive models and the relational database technology. Authors also concluded that this framework could be easily applied to other analytical model generation by separating the logic from the data.

  7. Hybrid Fundamental Solution Based Finite Element Method: Theory and Applications

    OpenAIRE

    Changyong Cao; Qing-Hua Qin

    2015-01-01

    An overview on the development of hybrid fundamental solution based finite element method (HFS-FEM) and its application in engineering problems is presented in this paper. The framework and formulations of HFS-FEM for potential problem, plane elasticity, three-dimensional elasticity, thermoelasticity, anisotropic elasticity, and plane piezoelectricity are presented. In this method, two independent assumed fields (intraelement filed and auxiliary frame field) are employed. The formulations for...

  8. A robust tolerance design method based on process capability

    Institute of Scientific and Technical Information of China (English)

    曹衍龙; 杨将新; 吴昭同; 吴立群

    2004-01-01

    This paper presents a method for robust tolerance design in terms of Process Capability Indices (PCI) . The component tolerance and the suitable manufacturing processes can be selected based on the real manufacturing context. The robustness of design feasibility under the effect of uncertainties is also discussed. A comparison between the results obtained by the proposed model and other methods indicates that robust and reliable tolerance can be obtained.

  9. A robust tolerance design method based on process capability

    Institute of Scientific and Technical Information of China (English)

    CAO Yan-long(曹衍龙); YANG Jiang-xin(杨将新); WU Zhao-tong(吴昭同); WU Li-qun(吴立群)

    2004-01-01

    This paper presents a method for robust tolerance design in terms of Process Capability Indices (PCI). The component tolerance and the suitable manufacturing processes can be selected based on the real manufacturing context. The robustness of design feasibility under the effect of uncertainties is also discussed. A comparison between the results obtained by the proposed model and other methods indicates that robust and reliable tolerance can be obtained.

  10. Propagator-based methods for recursive subspace model identification

    OpenAIRE

    Mercère, Guillaume; Bako, Laurent; Lecoeuche, Stéphane

    2008-01-01

    International audience; The problem of the online identification of multi-input multi-output (MIMO) state-space models in the framework of discrete-time subspace methods is considered in this paper. Several algorithms, based on a recursive formulation of the MIMO output error state-space (MOESP) identification class, are developed. The main goals of the proposed methods are to circumvent the huge complexity of eigenvalues or singular values decomposition techniques used by the offline algorit...

  11. New de-interlacing method based on adaptive weight

    Institute of Scientific and Technical Information of China (English)

    赵建伟; 古雪丰; 王朋; 刘重庆

    2004-01-01

    De-interlacing is very important when converting interlaced pictures to progressive pictures in format conversion.Multi-formats digital broadcast and progressive display requires the de-interlacing technique. An adaptive weight deinterlacing method is proposed. It combines motion compensation technique with directional-based spatio-temporal filter efficiently. Experiment results indicate that the method can keep edge continuity and sharpness effectively, reduce the artifacts in motion areas, and shows better visual performance when the estimated motion vectors are inaccurate.

  12. Progress of DNA-based Methods for Species Identification

    Institute of Scientific and Technical Information of China (English)

    HU Zhen; ZHANG Su-hua; WANG Zheng; BIAN Ying-nan; LI Cheng-tao

    2015-01-01

    Species identification of biological samples is widely used in such fields as forensic science and food industry. A variety of accurate and reliable methods have been developed in recent years. The cur-rent reviewshows common target genes and screening criteria suitable for species identification, and de-scribed various DNA-based molecular biology methods about species identification. Additionally, it dis-cusses the future development of species identification combined with real-time PCR and sequencing technologies.

  13. Challenges when developing omega-3 enriched foods

    DEFF Research Database (Denmark)

    Jacobsen, Charlotte

    2010-01-01

    the influence of important factors such as oil quality, delivery systems for omega-3 fatty acids, processing conditions, composition of the food matrix on lipid oxidation in different omega-3 enriched foods (milk, yoghurt, mayonnaise and mayonnaise-based salads, dressing, energy bar and fish paté). Moreover......Due to the polyunsaturated nature of omega-3 fatty acids, lipid oxidation is a major challenge when developing omega-3 enriched foods. In multiphase food systems, several factors can affect lipid oxidation and efficacy of antioxidants, added to prevent lipid oxidation. This review discusses......, the effect of different antioxidants (tocopherol, EDTA, lactoferrin, caffeic acid, ascorbic acid, ascorbyl palmitate, propyl gallate, gallic acid, as well as lipophilized antioxidants) is compared in different food systems....

  14. Uranium enrichment activities: the SILVA program

    Energy Technology Data Exchange (ETDEWEB)

    Guyot, J.; Cazalet, J.; Camarcat, N.; Figuet, J.

    1994-12-31

    Through its commitment to a nuclear electricity generation policy, France holds today a specific position in the uranium enrichment market thanks to the modern multinational EURODIF gaseous diffusion plant. France has, altogether, a long-term goal in developing SILVA, a laser uranium enrichment process, based on the selective photo-ionization of U-235. After reviewing the fundamentals of SILVA (the laser system with copper vapor lasers and dye lasers and the separator system), a description of the general organization of the R and D program is provided going through basic research, subsystems assessment, production demonstrations and simulations (with the LACAN code), plant design and economics. The general schedule of SILVA is outlined, leading to the possible construction of a commercial plant. 7 figs., 11 refs.

  15. How to Reach Evidence-Based Usability Evaluation Methods.

    Science.gov (United States)

    Marcilly, Romaric; Peute, Linda

    2017-01-01

    This paper discusses how and why to build evidence-based knowledge on usability evaluation methods. At each step of building evidence, requisites and difficulties to achieve it are highlighted. Specifically, the paper presents how usability evaluation studies should be designed to allow capitalizing evidence. Reciprocally, it presents how evidence-based usability knowledge will help improve usability practice. Finally, it underlines that evaluation and evidence participate in a virtuous circle that will help improve scientific knowledge and evaluation practice.

  16. An Improved Minimum Distance Method Based on Artificial Neural Networks

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    MDM (minimum distance method) is a very popular algorithm in state recognition. But it has a presupposition, that is, the distance within one class must be shorter enough than the distance between classes. When this presupposition is not satisfied, the method is no longer valid. In order to overcome the shortcomings of MDM, an improved mi nimum distance method (IMDM) based on ANN (artificial neural networks) is presented. The simulation results demonstrate that IMDM has two advantages, that is, the rate of recognition is faster and the accuracy of recognition is higher compared with MDM.

  17. A Design Method of Business Application Framework Based on

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper discusses design and implementation method of BusinessAppl ication Framework based on software patterns, and then presents MVC pattern of a rchitecture and the method of dynamical update promulgation for Business Applica tion Framework. We discuss adaptation of Abstract Factory for the kern el functionality of Business Application Framework, such as data creation, manip ulation, composition, etc. It also presents class model and its class st ructure of Abstract Factory pattern. Finally, we briefly discuss the update, mod ification, and reconstruction method of Business Application Framework.

  18. A Method of Attribute Reduction Based on Rough Set

    Institute of Scientific and Technical Information of China (English)

    LI Chang-biao; SONG Jian-ping

    2005-01-01

    The logging attribute optimization is an important task in the well-logging interpretation.A method of attribute reduction is presented based on rough set. Firstly, the core information of the sample by a general reductive method is determined. Then, the significance of dispensable attribute in the reduction-table is calculated. Finally, the minimum relative reduction set is achieved. The typical calculation and quantitative computation of reservoir parameter in oil logging show that the method of attribute reduction is greatly effective and feasible in logging interpretation.

  19. Improved method for pulse sorting based on PRI transform

    Science.gov (United States)

    Ren, Chunhui; Cao, Junqing; Fu, Yusheng; Barner, Kenneth E.

    2014-06-01

    To solve the problem of pulse sorting in complex electromagnetic environment, we propose an improved method for pulse sorting through in-depth analysis of the PRI transform algorithm principle and the advantages and disadvantages in this paper. The method is based on the traditional PRI transform algorithm, using spectral analysis of PRI transform spectrum to estimate the PRI centre value of jitter signal. Simulation results indicate that, the improved sorting method overcome the shortcomings of the traditional PRI jitter separation algorithm which cannot effectively sort jitter pulse sequence, in addition to the advantages of simple and accurate.

  20. Optimal Route Selection Method Based on Vague Sets

    Institute of Scientific and Technical Information of China (English)

    GUO Rui; DU Li min; WANG Chun

    2015-01-01

    Optimal route selection is an important function of vehicle trac flow guidance system. Its core is to determine the index weight for measuring the route merits and to determine the evaluation method for selecting route. In this paper, subjective weighting method which relies on driver preference is used to determine the weight and the paper proposes the multi-criteria weighted decision method based on vague sets for selecting the optimal route. Examples show that, the usage of vague sets to describe route index value can provide more decision-making information for route selection.

  1. A online credit evaluation method based on AHP and SPA

    Science.gov (United States)

    Xu, Yingtao; Zhang, Ying

    2009-07-01

    Online credit evaluation is the foundation for the establishment of trust and for the management of risk between buyers and sellers in e-commerce. In this paper, a new credit evaluation method based on the analytic hierarchy process (AHP) and the set pair analysis (SPA) is presented to determine the credibility of the electronic commerce participants. It solves some of the drawbacks found in classical credit evaluation methods and broadens the scope of current approaches. Both qualitative and quantitative indicators are considered in the proposed method, then a overall credit score is achieved from the optimal perspective. In the end, a case analysis of China Garment Network is provided for illustrative purposes.

  2. Chemical Equilibrium, Unit 4: Equilibria in Acid-Base Systems. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    Science.gov (United States)

    Settle, Frank A., Jr.

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this acid-base equilibria unit includes objectives, prerequisites, pretest, a discussion of equilibrium constants, and 20 problem sets.…

  3. A Clustering Method Based on the Maximum Entropy Principle

    Directory of Open Access Journals (Sweden)

    Edwin Aldana-Bobadilla

    2015-01-01

    Full Text Available Clustering is an unsupervised process to determine which unlabeled objects in a set share interesting properties. The objects are grouped into k subsets (clusters whose elements optimize a proximity measure. Methods based on information theory have proven to be feasible alternatives. They are based on the assumption that a cluster is one subset with the minimal possible degree of “disorder”. They attempt to minimize the entropy of each cluster. We propose a clustering method based on the maximum entropy principle. Such a method explores the space of all possible probability distributions of the data to find one that maximizes the entropy subject to extra conditions based on prior information about the clusters. The prior information is based on the assumption that the elements of a cluster are “similar” to each other in accordance with some statistical measure. As a consequence of such a principle, those distributions of high entropy that satisfy the conditions are favored over others. Searching the space to find the optimal distribution of object in the clusters represents a hard combinatorial problem, which disallows the use of traditional optimization techniques. Genetic algorithms are a good alternative to solve this problem. We benchmark our method relative to the best theoretical performance, which is given by the Bayes classifier when data are normally distributed, and a multilayer perceptron network, which offers the best practical performance when data are not normal. In general, a supervised classification method will outperform a non-supervised one, since, in the first case, the elements of the classes are known a priori. In what follows, we show that our method’s effectiveness is comparable to a supervised one. This clearly exhibits the superiority of our method.

  4. Production and use of mycotoxins uniformly enriched with stable isotopes for their dosage in biological samples: (3) Tools for pharmacokinetics and as internal standards

    Energy Technology Data Exchange (ETDEWEB)

    Bravin, F.; Delaforge, M.; Duca, R.C. [CNRS, URA 2096, F-91191 Gif Sur Yvette (France); Bravin, F.; Delaforge, M.; Duca, R.C. [CEA Saclay, DSV, DBJC, SBFM, F-91191 Gif Sur Yvette (France); Pean, M. [CEA Cadarache, DEVM, GRAP, St Paul Les Durance (France); Puel, O. [INRA, Lab Pharmacol Toxicol, UR 66, Toulouse (France)

    2007-07-01

    Pharmacological studies of exogenous compounds often encounter problems: these compounds are in such infinitesimal amount in their biological matrices, that they require particular detection method. We have implemented an alternative method to the usual radioactivity, based on incorporation of stable isotopes, through the example of biosynthesis of uniformly {sup 13}C enriched mycotoxins. The isotopic cluster obtained from a 10% {sup 13}C enrichment of several mycotoxins (and their metabolites) can be easily recovered from biological tissue samples by mass spectrometry allowing an easy discrimination from natural non-enriched compounds. We illustrate such pharmacological approaches by in vitro zearalenone metabolism. Such enriched compound can also be used as internal standard with high reliability in order to quantify mycotoxins in contaminated food samples. (authors)

  5. gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

    Science.gov (United States)

    Chevrier, Sandy; Boidot, Romain

    2014-01-01

    The widespread use of Next Generation Sequencing has opened up new avenues for cancer research and diagnosis. NGS will bring huge amounts of new data on cancer, and especially cancer genetics. Current knowledge and future discoveries will make it necessary to study a huge number of genes that could be involved in a genetic predisposition to cancer. In this regard, we developed a Nextera design to study 11 complete genes involved in DNA damage repair. This protocol was developed to safely study 11 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD50, RAD51C, RAD80, and TP53) from promoter to 3'-UTR in 24 patients simultaneously. This protocol, based on transposase technology and gDNA enrichment, gives a great advantage in terms of time for the genetic diagnosis thanks to sample multiplexing. This protocol can be safely used with blood gDNA. PMID:25350069

  6. Chaotic Encryption Method Based on Life-Like Cellular Automata

    CERN Document Server

    Machicao, Marina Jeaneth; Bruno, Odemir M

    2011-01-01

    We propose a chaotic encryption method based on Cellular Automata(CA), specifically on the family called the "Life-Like" type. Thus, the encryption process lying on the pseudo-random numbers generated (PRNG) by each CA's evolution, which transforms the password as the initial conditions to encrypt messages. Moreover, is explored the dynamical behavior of CA to reach a "good" quality as PRNG based on measures to quantify "how chaotic a dynamical system is", through the combination of the entropy, Lyapunov exponent, and Hamming distance. Finally, we present the detailed security analysis based on experimental tests: DIEHARD and ENT suites, as well as Fouriers Power Spectrum, used as a security criteria.

  7. Method of coating an iron-based article

    Science.gov (United States)

    Magdefrau, Neal; Beals, James T.; Sun, Ellen Y.; Yamanis, Jean

    2016-11-29

    A method of coating an iron-based article includes a first heating step of heating a substrate that includes an iron-based material in the presence of an aluminum source material and halide diffusion activator. The heating is conducted in a substantially non-oxidizing environment, to cause the formation of an aluminum-rich layer in the iron-based material. In a second heating step, the substrate that has the aluminum-rich layer is heated in an oxidizing environment to oxidize the aluminum in the aluminum-rich layer.

  8. A Localization Method for Multistatic SAR Based on Convex Optimization.

    Directory of Open Access Journals (Sweden)

    Xuqi Zhong

    Full Text Available In traditional localization methods for Synthetic Aperture Radar (SAR, the bistatic range sum (BRS estimation and Doppler centroid estimation (DCE are needed for the calculation of target localization. However, the DCE error greatly influences the localization accuracy. In this paper, a localization method for multistatic SAR based on convex optimization without DCE is investigated and the influence of BRS estimation error on localization accuracy is analysed. Firstly, by using the information of each transmitter and receiver (T/R pair and the target in SAR image, the model functions of T/R pairs are constructed. Each model function's maximum is on the circumference of the ellipse which is the iso-range for its model function's T/R pair. Secondly, the target function whose maximum is located at the position of the target is obtained by adding all model functions. Thirdly, the target function is optimized based on gradient descent method to obtain the position of the target. During the iteration process, principal component analysis is implemented to guarantee the accuracy of the method and improve the computational efficiency. The proposed method only utilizes BRSs of a target in several focused images from multistatic SAR. Therefore, compared with traditional localization methods for SAR, the proposed method greatly improves the localization accuracy. The effectivity of the localization approach is validated by simulation experiment.

  9. A Localization Method for Multistatic SAR Based on Convex Optimization.

    Science.gov (United States)

    Zhong, Xuqi; Wu, Junjie; Yang, Jianyu; Sun, Zhichao; Huang, Yuling; Li, Zhongyu

    2015-01-01

    In traditional localization methods for Synthetic Aperture Radar (SAR), the bistatic range sum (BRS) estimation and Doppler centroid estimation (DCE) are needed for the calculation of target localization. However, the DCE error greatly influences the localization accuracy. In this paper, a localization method for multistatic SAR based on convex optimization without DCE is investigated and the influence of BRS estimation error on localization accuracy is analysed. Firstly, by using the information of each transmitter and receiver (T/R) pair and the target in SAR image, the model functions of T/R pairs are constructed. Each model function's maximum is on the circumference of the ellipse which is the iso-range for its model function's T/R pair. Secondly, the target function whose maximum is located at the position of the target is obtained by adding all model functions. Thirdly, the target function is optimized based on gradient descent method to obtain the position of the target. During the iteration process, principal component analysis is implemented to guarantee the accuracy of the method and improve the computational efficiency. The proposed method only utilizes BRSs of a target in several focused images from multistatic SAR. Therefore, compared with traditional localization methods for SAR, the proposed method greatly improves the localization accuracy. The effectivity of the localization approach is validated by simulation experiment.

  10. Comparative study, based on metamodels, of methods for controlling performance

    Directory of Open Access Journals (Sweden)

    Aitouche Samia

    2012-05-01

    Full Text Available The continuing evolution of technology and human behavior puts the company in an uncertain and evolving environment. The company must be responsive and even proactive; therefore, control performance becomes increasingly difficult. Choosing the best method of ensuring control by the management policy of the company and its strategy is also a decision problem. The aim of this paper is the comparative study of three methods: the Balanced Scorecard, GIMSI and SKANDIAs NAVIGATOR for choosing the best method for ensuring the orderly following the policy of the company while maintaining its durability. Our work is divided into three parts. We firstly proposed original structural and kinetic metamodels for the three methods that allow an overall view of a method. Secondly, based on the three metamodels, we have drawn a generic comparison to analyze completeness of the method. Thirdly, we performed a restrictive comparison based on a restrictive set of criteria related to the same aspect example organizational learning, which is one of the bricks of knowledge management for a reconciliation to a proactive organization in an environment disturbed and uncertain, and the urgent needs. We note that we applied the three methods are applied in our precedent works. [1][23

  11. A Matrix Pencil Algorithm Based Multiband Iterative Fusion Imaging Method

    Science.gov (United States)

    Zou, Yong Qiang; Gao, Xun Zhang; Li, Xiang; Liu, Yong Xiang

    2016-01-01

    Multiband signal fusion technique is a practicable and efficient way to improve the range resolution of ISAR image. The classical fusion method estimates the poles of each subband signal by the root-MUSIC method, and some good results were get in several experiments. However, this method is fragile in noise for the proper poles could not easy to get in low signal to noise ratio (SNR). In order to eliminate the influence of noise, this paper propose a matrix pencil algorithm based method to estimate the multiband signal poles. And to deal with mutual incoherent between subband signals, the incoherent parameters (ICP) are predicted through the relation of corresponding poles of each subband. Then, an iterative algorithm which aimed to minimize the 2-norm of signal difference is introduced to reduce signal fusion error. Applications to simulate dada verify that the proposed method get better fusion results at low SNR.

  12. SET OPERATOR-BASED METHOD OF DENOISING MEDICAL VOLUME DATA

    Institute of Scientific and Technical Information of China (English)

    程兵; 郑南宁; 袁泽剑

    2002-01-01

    Objective To investigate impulsive noise suppression of medical volume data. Methods The volume data is represented as level sets and a special set operator is defined and applied to filtering it. The small connected components, which are likely to be produced by impulsive noise, are eliminated after the filtering process. A fast algorithm that uses a heap data structure is also designed. Results Compared with traditional linear filters such as a Gaussian filter, this method preserves the fine structure features of the medical volume data while removing noise, and the fast algorithm developed by us reduces memory consumption and improves computing efficiency. The experimental results given illustrate the efficiency of the method and the fast algorithm. Conclusion The set operator-based method shows outstanding denoising properties in our experiment, especially for impulsive noise. The method has a wide variety of applications in the areas of volume visualization and high dimensional data processing.

  13. Total-variation-based methods for gravitational wave denoising

    CERN Document Server

    Torres, Alejandro; Font, José A; Ibáñez, José M

    2014-01-01

    We describe new methods for denoising and detection of gravitational waves embedded in additive Gaussian noise. The methods are based on Total Variation denoising algorithms. These algorithms, which do not need any a priori information about the signals, have been originally developed and fully tested in the context of image processing. To illustrate the capabilities of our methods we apply them to two different types of numerically-simulated gravitational wave signals, namely bursts produced from the core collapse of rotating stars and waveforms from binary black hole mergers. We explore the parameter space of the methods to find the set of values best suited for denoising gravitational wave signals under different conditions such as waveform type and signal-to-noise ratio. Our results show that noise from gravitational wave signals can be successfully removed with our techniques, irrespective of the signal morphology or astrophysical origin. We also combine our methods with spectrograms and show how those c...

  14. Study on UPF Harmonic Current Detection Method Based on DSP

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, H J [Northwestern Polytechnical University, Xi' an 710072 (China); Pang, Y F [Xi' an University of Technology, Xi' an 710048 (China); Qiu, Z M [Xi' an University of Technology, Xi' an 710048 (China); Chen, M [Northwestern Polytechnical University, Xi' an 710072 (China)

    2006-10-15

    Unity power factor (UPF) harmonic current detection method applied to active power filter (APF) is presented in this paper. The intention of this method is to make nonlinear loads and active power filter in parallel to be an equivalent resistance. So after compensation, source current is sinusoidal, and has the same shape of source voltage. Meanwhile, there is no harmonic in source current, and the power factor becomes one. The mathematic model of proposed method and the optimum project for equivalent low pass filter in measurement are presented. Finally, the proposed detection method applied to a shunt active power filter experimental prototype based on DSP TMS320F2812 is developed. Simulation and experiment results indicate the method is simple and easy to implement, and can obtain the real-time calculation of harmonic current exactly.

  15. Nonlinear fault diagnosis method based on kernel principal component analysis

    Institute of Scientific and Technical Information of China (English)

    Yan Weiwu; Zhang Chunkai; Shao Huihe

    2005-01-01

    To ensure the system run under working order, detection and diagnosis of faults play an important role in industrial process. This paper proposed a nonlinear fault diagnosis method based on kernel principal component analysis (KPCA). In proposed method, using essential information of nonlinear system extracted by KPCA, we constructed KPCA model of nonlinear system under normal working condition. Then new data were projected onto the KPCA model. When new data are incompatible with the KPCA model, it can be concluded that the nonlinear system isout of normal working condition. Proposed method was applied to fault diagnosison rolling bearings. Simulation results show proposed method provides an effective method for fault detection and diagnosis of nonlinear system.

  16. [Segmentation Method for Liver Organ Based on Image Sequence Context].

    Science.gov (United States)

    Zhang, Meiyun; Fang, Bin; Wang, Yi; Zhong, Nanchang

    2015-10-01

    In view of the problems of more artificial interventions and segmentation defects in existing two-dimensional segmentation methods and abnormal liver segmentation errors in three-dimensional segmentation methods, this paper presents a semi-automatic liver organ segmentation method based on the image sequence context. The method takes advantage of the existing similarity between the image sequence contexts of the prior knowledge of liver organs, and combines region growing and level set method to carry out semi-automatic segmentation of livers, along with the aid of a small amount of manual intervention to deal with liver mutation situations. The experiment results showed that the liver segmentation algorithm presented in this paper had a high precision, and a good segmentation effect on livers which have greater variability, and can meet clinical application demands quite well.

  17. Enrichment of light hydrocarbon mixture

    Science.gov (United States)

    Yang; Dali; Devlin, David; Barbero, Robert S.; Carrera, Martin E.; Colling, Craig W.

    2010-08-10

    Light hydrocarbon enrichment is accomplished using a vertically oriented distillation column having a plurality of vertically oriented, nonselective micro/mesoporous hollow fibers. Vapor having, for example, both propylene and propane is sent upward through the distillation column in between the hollow fibers. Vapor exits neat the top of the column and is condensed to form a liquid phase that is directed back downward through the lumen of the hollow fibers. As vapor continues to ascend and liquid continues to countercurrently descend, the liquid at the bottom of the column becomes enriched in a higher boiling point, light hydrocarbon (propane, for example) and the vapor at the top becomes enriched in a lower boiling point light hydrocarbon (propylene, for example). The hollow fiber becomes wetted with liquid during the process.

  18. A method to manage the model base in DSS

    Institute of Scientific and Technical Information of China (English)

    孙成双; 李桂君

    2004-01-01

    How to manage and use models in DSS is a most important subject. Generally, it costs a lot of money and time to develop the model base management system in the development of DSS and most are simple in function or cannot be used efficiently in practice. It is a very effective, applicable, and economical choice to make use of the interfaces of professional computer software to develop a model base management system. This paper presents the method of using MATLAB, a well-known statistics software, as the development platform of a model base management system. The main functional framework of a MATLAB-based model base managementsystem is discussed. Finally, in this paper, its feasible application is illustrated in the field of construction projects.

  19. End of Enrichment Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Ding Yuan

    2010-06-09

    The age and composition of special nuclear material (SNM) offers a great deal of forensic information; e.g., likely producer or country of origin. Nuclear materials (nuclides) decay at different rates, often in a chain fashion; therefore, the composition of the nuclides changes over time. Trace nuclides in special nuclear material often carry more information regarding age and original composition, but trace nuclides can be easily lost in 'approximations.' Current decay calculation technology is based on a matrix Taylor approximation that is imprecise in nature and time-consuming to compute. Better computational technology for decay calculation and age estimation is needed. This project offers better Nuclear Forensics technology solutions for these needs.

  20. Preparing Students for Flipped or Team-Based Learning Methods

    Science.gov (United States)

    Balan, Peter; Clark, Michele; Restall, Gregory

    2015-01-01

    Purpose: Teaching methods such as Flipped Learning and Team-Based Learning require students to pre-learn course materials before a teaching session, because classroom exercises rely on students using self-gained knowledge. This is the reverse to "traditional" teaching when course materials are presented during a lecture, and students are…