WorldWideScience

Sample records for list enrichment analysis

  1. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.

    Science.gov (United States)

    Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, Avi

    2013-04-15

    System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

  2. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

    National Research Council Canada - National Science Library

    Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, Avi

    2013-01-01

    .... Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive...

  3. 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

  4. 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

  5. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

    Directory of Open Access Journals (Sweden)

    Steinfeld Israel

    2009-02-01

    Full Text Available Abstract Background Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database. In particular, a variety of tools that perform GO enrichment analysis are currently available. Most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set. A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results. Results GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression. GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list. Building on a complete theoretical characterization of the underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations. This enables rigorous statistical analysis of thousand of genes and thousands of GO terms in order of seconds. The output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched GO terms. Conclusion GOrilla is an efficient GO analysis tool with unique features that make a useful addition to the existing repertoire of GO enrichment tools. GOrilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation. GOrilla is publicly available at: http://cbl-gorilla.cs.technion.ac.il

  6. Lists2Networks: Integrated analysis of gene/protein lists

    Directory of Open Access Journals (Sweden)

    Ma'ayan Avi

    2010-02-01

    Full Text Available Abstract Background Systems biologists are faced with the difficultly of analyzing results from large-scale studies that profile the activity of many genes, RNAs and proteins, applied in different experiments, under different conditions, and reported in different publications. To address this challenge it is desirable to compare the results from different related studies such as mRNA expression microarrays, genome-wide ChIP-X, RNAi screens, proteomics and phosphoproteomics experiments in a coherent global framework. In addition, linking high-content multilayered experimental results with prior biological knowledge can be useful for identifying functional themes and form novel hypotheses. Results We present Lists2Networks, a web-based system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. Conclusions Lists2Networks is a user friendly web-based software system expected to significantly ease the computational analysis process for experimental systems biologists employing high-throughput experiments at multiple layers of regulation. The system is freely available at http://www.lists2networks.org.

  7. 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.

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

    Science.gov (United States)

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

    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. PMID:23237213

  9. 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 ...

  10. Pathway enrichment and co-expression cluster analysis - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Pathway enrichment and co-expression cluster analysis Data detail Data name Pathway enrich...a.nbdc01389-003.V002 No Update V1 10.18908/lsdba.nbdc01389-003.V001 - Description of data contents Pathway enrich.../ File size: 86 MB Simple search URL - Data acquisition method - Data analysis method Co-expression cluster analysis Gostat enrich...ment analysis Pathway enrichment analysis Number of data en...ite Policy | Contact Us Pathway enrichment and co-expression cluster analysis - FANTOM5 | LSDB Archive ...

  11. 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.

  12. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  13. An application of MeSH enrichment analysis in livestock.

    Science.gov (United States)

    Morota, G; Peñagaricano, F; Petersen, J L; Ciobanu, D C; Tsuyuzaki, K; Nikaido, I

    2015-08-01

    An integral part of functional genomics studies is to assess the enrichment of specific biological terms in lists of genes found to be playing an important role in biological phenomena. Contrasting the observed frequency of annotated terms with those of the background is at the core of overrepresentation analysis (ORA). Gene Ontology (GO) is a means to consistently classify and annotate gene products and has become a mainstay in ORA. Alternatively, Medical Subject Headings (MeSH) offers a comprehensive life science vocabulary including additional categories that are not covered by GO. Although MeSH is applied predominantly in human and model organism research, its full potential in livestock genetics is yet to be explored. In this study, MeSH ORA was evaluated to discern biological properties of identified genes and contrast them with the results obtained from GO enrichment analysis. Three published datasets were employed for this purpose, representing a gene expression study in dairy cattle, the use of SNPs for genome-wide prediction in swine and the identification of genomic regions targeted by selection in horses. We found that several overrepresented MeSH annotations linked to these gene sets share similar concepts with those of GO terms. Moreover, MeSH yielded unique annotations, which are not directly provided by GO terms, suggesting that MeSH has the potential to refine and enrich the representation of biological knowledge. We demonstrated that MeSH can be regarded as another choice of annotation to draw biological inferences from genes identified via experimental analyses. When used in combination with GO terms, our results indicate that MeSH can enhance our functional interpretations for specific biological conditions or the genetic basis of complex traits in livestock species.

  14. 10 CFR Appendix H to Part 110 - Illustrative List of Electromagnetic Enrichment Plant Equipment and Components Under NRC Export...

    Science.gov (United States)

    2010-01-01

    ... Equipment and Components Under NRC Export Licensing Authority H Appendix H to Part 110 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Pt. 110, App. H Appendix H to Part 110—Illustrative List of Electromagnetic Enrichment Plant Equipment and Components...

  15. 10 CFR Appendix G to Part 110 - Illustrative List of Plasma Separation Enrichment Plant Equipment and Components Under NRC Export...

    Science.gov (United States)

    2010-01-01

    ... Equipment and Components Under NRC Export Licensing Authority G Appendix G to Part 110 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Pt. 110, App. G Appendix G to Part 110—Illustrative List of Plasma Separation Enrichment Plant Equipment and...

  16. A Component Analysis of Marriage Enrichment.

    Science.gov (United States)

    Buston, Beverley G.; And Others

    Although marriage enrichment programs have been shown to be effective for many couples, a multidimensional approach to assessment is needed in investigating these groups. The components of information and social support in successful marriage enrichment programs were compared in a completely crossed 2 x 2 factorial design with repeated measures.…

  17. Uranium Enrichment Analysis With Electromechanical Cooled HPGe Detector

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The Micro_trans_SPEC-100 portable high-resolution gamma-ray radioisotope identifier was used for the uranium enrichment analysis demonstration. Micro_trans_SPEC utilize stirling-cycle cooler and integrated detector, signal electronics and analysis

  18. AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast

    Directory of Open Access Journals (Sweden)

    Danny A Bitton

    2015-11-01

    Full Text Available Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists can provide valuable insights and testable hypotheses. To systematically detect these enrichments can be challenging and time-consuming, because relevant data to compare against query gene lists are spread over many different sources. We have developed AnGeLi (Analysis of Gene Lists, an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast, Schizosaccharomyces pombe. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. AnGeLi uses robust statistics which can be tailored to specific needs. It also provides the option to upload user-defined gene sets to compare against the query list. Through an integrated data submission form, AnGeLi encourages the community to contribute additional curated gene lists to further increase the usefulness of this resource and to get the most from the ever increasing large-scale experiments. AnGeLi offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool through which S. pombe researchers can uncover fresh perspectives and unexpected connections from genomic data. AnGeLi is freely available at: www.bahlerlab.info/AnGeLi

  19. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available f you use data from this database, please be sure attribute this database as follows: ... PGDBj Registered plan... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  20. miEAA: microRNA enrichment analysis and annotation.

    Science.gov (United States)

    Backes, Christina; Khaleeq, Qurratulain T; Meese, Eckart; Keller, Andreas

    2016-07-08

    Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance. Building on our experience with the gene set analysis toolkit GeneTrail, we implemented the miRNA Enrichment Analysis and Annotation tool (miEAA). MiEAA is a web-based application that offers a variety of commonly applied statistical tests such as over-representation analysis and miRNA set enrichment analysis, which is similar to Gene Set Enrichment Analysis. Besides the different statistical tests, miEAA also provides rich functionality in terms of miRNA categories. Altogether, over 14 000 miRNA sets have been added, including pathways, diseases, organs and target genes. Importantly, our tool can be applied for miRNA precursors as well as mature miRNAs. To make the tool as useful as possible we additionally implemented supporting tools such as converters between different miRBase versions and converters from miRNA names to precursor names. We evaluated the performance of miEAA on two sets of miRNAs that are affected in lung adenocarcinomas and have been detected by array analysis. The web-based application is freely accessible at: http://www.ccb.uni-saarland.de/mieaa_tool/.

  1. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...d 1 README README_e.html - 2 Registered plant list pgdbj_dna_marker_linkage_map_plant_species_list_en.zip (2...Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  2. 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.

  3. Separate enrichment analysis of pathways for up- and downregulated genes.

    Science.gov (United States)

    Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

    2014-03-06

    Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

  4. 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.

  5. Increasing the performance of tritium analysis by electrolytic enrichment.

    Science.gov (United States)

    Groning, M; Auer, R; Brummer, D; Jaklitsch, M; Sambandam, C; Tanweer, A; Tatzber, H

    2009-06-01

    Several improvements are described for the existing tritium enrichment system at the Isotope Hydrology Laboratory of the International Atomic Energy Agency for processing natural water samples. The improvements include a simple method for pretreatment of electrolytic cells to ensure a high tritium separation factor, an improved design of the exhaust system for explosive gases, and a vacuum distillation line for faster initial preparation of water samples for electrolytic enrichment and for tritium analysis. Achievements included the reduction of variation of individual enrichment parameters of all cells to less than 1% and an improvement of 50% of the stability of the background mean. It resulted in an improved detection limit of less than 0.4 TU (at 2s), important for application of tritium measurements in the future at low concentration levels, and resulted in measurement precisions of+/-0.2 TU and+/-0.15 TU for liquid scintillation counting and for gas proportional counting, respectively.

  6. Genome analysis methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...ear Year of genome analysis Sequencing method Sequencing method Read counts Read counts Covered genome region Covered...otation method Number of predicted genes Number of predicted genes Genome database Genome database informati... License Update History of This Database Site Policy | Contact Us Genome analysis... methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  7. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

    Science.gov (United States)

    Thomson, John P.; Hunter, Jennifer M.; Nestor, Colm E.; Dunican, Donncha S.; Terranova, Rémi; Moggs, Jonathan G.; Meehan, Richard R.

    2013-01-01

    The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC. PMID:24214958

  8. LISSAT Analysis of a Generic Centrifuge Enrichment Plant

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, H; Elayat, H A; O?Connell, W J; Szytel, L; Dreicer, M

    2007-05-31

    The U.S. Department of Energy (DOE) is interested in developing tools and methods for use in designing and evaluating safeguards systems for current and future plants in the nuclear power fuel cycle. The DOE is engaging several DOE National Laboratories in efforts applied to safeguards for chemical conversion plants and gaseous centrifuge enrichment plants. As part of the development, Lawrence Livermore National Laboratory has developed an integrated safeguards system analysis tool (LISSAT). This tool provides modeling and analysis of facility and safeguards operations, generation of diversion paths, and evaluation of safeguards system effectiveness. The constituent elements of diversion scenarios, including material extraction and concealment measures, are structured using directed graphs (digraphs) and fault trees. Statistical analysis evaluates the effectiveness of measurement verification plans and randomly timed inspections. Time domain simulations analyze significant scenarios, especially those involving alternate time ordering of events or issues of timeliness. Such simulations can provide additional information to the fault tree analysis and can help identify the range of normal operations and, by extension, identify additional plant operational signatures of diversions. LISSAT analyses can be used to compare the diversion-detection probabilities for individual safeguards technologies and to inform overall strategy implementations for present and future plants. Additionally, LISSAT can be the basis for a rigorous cost-effectiveness analysis of safeguards and design options. This paper will describe the results of a LISSAT analysis of a generic centrifuge enrichment plant. The paper will describe the diversion scenarios analyzed and the effectiveness of various safeguards systems alternatives.

  9. Further Enrichment and Analysis of Rat CFU-s

    Science.gov (United States)

    1990-01-01

    argon laser was tuned to the UV and was used to excite the DAPI-DNA complex. By gating on the APC- Ox720 and PhyB-x22- cells, a new FITC-W3/13...Thy-I and light scatter properties of CFU-s from cortisone pre-treated rats. The cortisone treatment diminished marrow lymphocytes and separated them...from cortisone - resistant CFU-s. Starting with marrow from normal rats, Goldschneider et al. Further Enrichment and Analysis of Rat CFU-s 190 A

  10. An Item Factor Analysis of the Mooney Problem Check List

    Science.gov (United States)

    Stewart, David W.; Deiker, Thomas

    1976-01-01

    Explores the factor structure of the Mooney Problem Check List (MPCL) at the junior and senior high school level by undertaking a large obverse factor analysis of item responses in three adolescent criterion groups. (Author/DEP)

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

    Science.gov (United States)

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

    2009-01-01

    Nonenzymatic 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 online wash of column-bound glycated peptides using 50 mM ammonium acetate, followed by elution with 100 mM acetic acid. 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. 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 of glycated peptides and corresponding glycated proteins identified by LC–MS/MS. PMID:18989935

  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. The tensor product in Wadler's analysis of lists

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis

    1992-01-01

    We consider abstract interpretation (in particular strictness analysis) for pairs and lists. We begin by reviewing the well-known fact that the best known description of a pair of elements is obtained using the tensor product rather than the cartesian product. We next present a generalisation...... of Wadler's strictness analysis for lists using the notion of open set. Finally, we illustrate the intimate connection between the case analysis implicit in Wadler's strictness analysis and the precision that the tensor product allows for modelling the inverse cons operation....

  14. The tensor product in Wadler's analysis of lists

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis

    1992-01-01

    We consider abstract interpretation (in particular strictness analysis) for pairs and lists. We begin by reviewing the well-known fact that the best known description of a pair of elements is obtained using the tensor product rather than the cartesian product. We next present a generalisation...... of Wadler's strictness analysis for lists using the notion of open set. Finally, we illustrate the intimate connection between the case analysis implicit in Wadler's strictness analysis and the precision that the tensor product allows for modelling the inverse cons operation....

  15. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...f This Database Date Update contents 2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant DB... link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj Registered... Policy | Contact Us Update History of This Database - PGDBj Registered plant lis

  16. The tensor product in Wadler's analysis of lists

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis

    1994-01-01

    We consider abstract interpretation (in particular strictness analysis) for pairs and lists. We begin by reviewing the well-known fact that the best known description of a pair of elements is obtained using the tensor product rather than the cartesian product. We next present a generalisation of ...

  17. Parameterized Analysis of Paging and List Update Algorithms

    DEFF Research Database (Denmark)

    Dorrigiv, Reza; Ehmsen, Martin R.; López-Ortiz, Alejandro

    2015-01-01

    It is well-established that input sequences for paging and list update have locality of reference. In this paper we analyze the performance of algorithms for these problems in terms of the amount of locality in the input sequence. We define a measure for locality that is based on Denning’s working...... that a larger cache leads to a better performance. We also apply the parameterized analysis framework to list update and show that certain randomized algorithms which are superior to MTF in the classical model are not so in the parameterized case, which matches experimental results....

  18. Bed capacity and surgical waiting lists: a simulation analysis

    Directory of Open Access Journals (Sweden)

    Manel Antelo

    2015-12-01

    Full Text Available Waiting time for elective surgery is a key problem in the current medical world. This paper aims to reproduce, by a Monte Carlo simulation model, the relationship between hospital capacity, inpatient activity, and surgery waiting list size in teaching hospitals. Inpatient activity is simulated by fitting a Normal distribution to real inpatient activity data, and the effect of the number of beds on inpatient activity is modelled with a linear regression model. Analysis is performed with data of the University Multi-Hospital Complex of Santiago de Compostela (Santiago de Compostela, Spain, by considering two scenarios regarding the elastiticity of demand with bed increase. If demand does not grow with an increase on bed capacity, small changes lead to drastic reductions in the waiting lists. However, if demand grows as bed capacity does, adding additional capacity merely makes waiting lists worse.

  19. Analysis of the Spanish-speaking mailing list RADIOLOGIA.

    Science.gov (United States)

    Rodriguez-Recio, Francisco Javier; Sendra-Portero, Francisco

    2007-07-01

    The objective of this study was to analyse the mailing list RADIOLOGIA during its first 5 years of operation (from 1998 to 2003). A survey questionnaire was sent to evaluate the characteristics of subscribers and to score (from 0 to 9) the functionality, usefulness and quality of the mailing list. All messages sent to the list during the evaluated period were classified and quantified. A social network analysis was performed from all messages replied to during 2001 and 2002 with the option "reply to" included in the subject. One hundred and forty (36.8%) responses were collected from 380 subscribers, mainly radiologists (90.0%). 80% of responders were located in Spain, 16% in Latin America, and 4% in other places. The obtained scores (mean+/-standard deviation) were: functionality 7.4+/-1.3; usefulness 7.0+/-1.4; and quality of e-mail contents 6.0+/-1.4. During the evaluated period 2700 e-mail messages were sent to the list, with a monthly distribution of 44.3+/-26.0. The list functioning has been based on an active minority of subscribers that provided information and responses to the rest of the subscribers, a ring of active members that participated in discussions, and about 50% of passive members.

  20. Pan-European backcasting exercise, enriched with regional perspective, and including a list of short-term policy options

    OpenAIRE

    KOK, K.; Vliet, Van; Bärlund, I.; Sendzimir, J.; Dubel, A.

    2011-01-01

    This deliverable reports on the results of the third and final pan-European stakeholder meeting and secondly, on the enrichment with a Pilot Area and regional perspective. The main emphasis is on backcasting as a means to arrive at long-term strategies and short-term (policy) actions.

  1. 10 CFR Appendix E to Part 110 - Illustrative List of Chemical Exchange or Ion Exchange Enrichment Plant Equipment and Components...

    Science.gov (United States)

    2010-01-01

    ... purification and electrolytic cells for reducing the uranium U+6 or U+4 to U+3. These systems produce uranium... designed or prepared electrochemical reduction cells to reduce uranium from one valence state to another for uranium enrichment using the chemical exchange process. The cell materials in contact with...

  2. Uranium Enrichment: Analysis of Decontamination and Decommissioning Scenarios

    Science.gov (United States)

    1991-11-01

    from a September 1991 report entitled Preliminary Cost Estimate Decontamination & Decommissioning of the Gaseous Diffusion Plants , prepared for DOE by...DOE) three aging uranium enrichment plants . These plants are located in Oak Ridge, Tennessee; Paducah , Kentucky; and Portsmouth, Ohio. On October 16... Diffusion Plants Assessment of Costs for Remedial Actions. This report was prepared for DOE by Martin Marietta Energy Systems, DOE’s management and

  3. Web Document Analysis for Companies Listed in Bursa Malaysia

    CERN Document Server

    Othman, Mohd Shahizan; Salim, Juhana

    2009-01-01

    This paper discusses a research on web document analysis for companies listed on Bursa Malaysia which is the forerunner of financial and investment center in Malaysia. Data set used in this research are from the company web documents listed in the Main Board and Second Board on Bursa Malaysia. This research has used the Web Resources Extraction System which was developed by the research group mainly to extract information for the web documents involved. Our research findings have shown that the level of website usage among the companies on Bursa Malaysia is still minimal. Furthermore, research has also found that 60.02 percent of the image files are utilized making it the most used type of file in creating websites.

  4. Enrichment/isolation of phosphorylated peptides on hafnium oxide prior to mass spectrometric analysis.

    Science.gov (United States)

    Rivera, José G; Choi, Yong Seok; Vujcic, Stefan; Wood, Troy D; Colón, Luis A

    2009-01-01

    Hafnium oxide (hafnia) exhibits unique enrichment properties towards phosphorylated peptides that are complementary to those of titanium oxide (titania) and zirconium oxide (zirconia) for use with mass spectrometric analysis in the field of proteomics.

  5. Transmutation Analysis of Enriched Uranium and Deep Burn High Temperature Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Michael A. Pope

    2012-07-01

    High temperature reactors (HTRs) have been under consideration for production of electricity, process heat, and for destruction of transuranics for decades. As part of the transmutation analysis efforts within the Fuel Cycle Research and Development (FCR&D) campaign, a need was identified for detailed discharge isotopics from HTRs for use in the VISION code. A conventional HTR using enriched uranium in UCO fuel was modeled having discharge burnup of 120 GWd/MTiHM. Also, a deep burn HTR (DB-HTR) was modeled burning transuranic (TRU)-only TRU-O2 fuel to a discharge burnup of 648 GWd/MTiHM. For each of these cases, unit cell depletion calculations were performed with SCALE/TRITON. Unit cells were used to perform this analysis using SCALE 6.1. Because of the long mean free paths (and migration lengths) of neutrons in HTRs, using a unit cell to represent a whole core can be non-trivial. The sizes of these cells were first set by using Serpent calculations to match a spectral index between unit cell and whole core domains. In the case of the DB-HTR, the unit cell which was arrived at in this way conserved the ratio of fuel to moderator found in a single block of fuel. In the conventional HTR case, a larger moderator-to-fuel ratio than that of a single block was needed to simulate the whole core spectrum. Discharge isotopics (for 500 nuclides) and one-group cross-sections (for 1022 nuclides) were delivered to the transmutation analysis team. This report provides documentation for these calculations. In addition to the discharge isotopics, one-group cross-sections were provided for the full list of 1022 nuclides tracked in the transmutation library.

  6. Solid-phase enrichment and analysis of electrophilic natural products

    Directory of Open Access Journals (Sweden)

    Frank Wesche

    2017-03-01

    Full Text Available In search for new natural products, which may lead to the development of new drugs for all kind of applications, novel methods are needed. Here we describe the identification of electrophilic natural products in crude extracts via their reactivity against azide as a nucleophile followed by their subsequent enrichment using a cleavable azide-reactive resin (CARR. Using this approach, natural products carrying epoxides and α,β-unsaturated enones as well as several unknown compounds were identified in crude extracts from entomopathogenic Photorhabdus bacteria.

  7. Phytotoxicity and Plant Productivity Analysis of Tar-Enriched Biochars

    Science.gov (United States)

    Keller, M. L.; Masiello, C. A.; Dugan, B.; Rudgers, J. A.; Capareda, S. C.

    2008-12-01

    Biochar is one of the three by-products obtained by the pyrolysis of organic material, the other two being syngas and bio-oil. The pyrolysis of biomass has generated a great amount of interest in recent years as all three by-products can be put toward beneficial uses. As part of a larger project designed to evaluate the hydrologic impact of biochar soil amendment, we generated a biochar through fast pyrolysis (less than 2 minutes) of sorghum stock at 600°C. In the initial biochar production run, the char bin was not purged with nitrogen. This inadvertent change in pyrolysis conditions produced a fast-pyrolysis biochar enriched with tars. We chose not to discard this batch, however, and instead used it to test the impact of tar-enriched biochars on plants. A suite of phytotoxicity tests were run to assess the effects of tar-rich biochar on plant germination and plant productivity. We designed the experiment to test for negative effects, using an organic carbon and nutrient-rich, greenhouse- optimized potting medium instead of soil. We used Black Seeded Simpson lettuce (Lactuca sativa) as the test organism. We found that even when tars are present within biochar, biochar amendment up to 10% by weight caused increased lettuce germination rates and increased biomass productivity. In this presentation, we will report the statistical significance of our germination and biomass data, as well as present preliminary data on how biochar amendment affects soil hydrologic properties.

  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 meta-analysis of the effects of nutrient enrichment on litter decomposition in streams

    OpenAIRE

    Ferreira, Verónica; Castagneyrol, Bastien; Koricheva, Julia; Gulis, Vladislav; Chauvet, Eric; Manuel A. S Graça

    2015-01-01

    International audience; The trophic state of many streams is likely to deteriorate in the future due to the continuing increase in human-induced nutrient availability. Therefore, it is of fundamental importance to understand how nutrient enrichment affects plant litter decomposition, a key ecosystem-level process in forest streams. Here, we present a meta-analysis of 99 studies published between 1970 and 2012 that reported the effects of nutrient enrichment on litter decomposition in running ...

  10. Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome

    Directory of Open Access Journals (Sweden)

    Gaora Peadar Ó

    2010-10-01

    Full Text Available Abstract Background Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of

  11. An Economical Method for Static Headspace Enrichment for Arson Analysis

    Science.gov (United States)

    Olesen, Bjorn

    2010-01-01

    Static headspace analysis of accelerants from suspected arsons is accomplished by placing an arson sample in a sealed container with a carbon strip suspended above the sample. The sample is heated, cooled to room temperature, and then the organic components are extracted from the carbon strip with carbon disulfide followed by gas chromatography…

  12. Glycopeptide enrichment and separation for protein glycosylation analysis

    NARCIS (Netherlands)

    Ongay, Sara; Boychenko, Oleksandr; Govorukhina, Natalia; Bischoff, Rainer

    2012-01-01

    Protein glycosylation plays key roles in many biological processes. In addition, alterations in protein glycosylation have been related to different diseases, as well as may affect the properties of recombinant proteins used as human therapeutics. For this reason, protein glycosylation analysis is o

  13. 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.

  14. 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.

  15. A meta-analysis of the effects of nutrient enrichment on litter decomposition in streams.

    Science.gov (United States)

    Ferreira, Verónica; Castagneyrol, Bastien; Koricheva, Julia; Gulis, Vladislav; Chauvet, Eric; Graça, Manuel A S

    2015-08-01

    The trophic state of many streams is likely to deteriorate in the future due to the continuing increase in human-induced nutrient availability. Therefore, it is of fundamental importance to understand how nutrient enrichment affects plant litter decomposition, a key ecosystem-level process in forest streams. Here, we present a meta-analysis of 99 studies published between 1970 and 2012 that reported the effects of nutrient enrichment on litter decomposition in running waters. When considering the entire database, which consisted of 840 case studies, nutrient enrichment stimulated litter decomposition rate by approximately 50%. The stimulation was higher when the background nutrient concentrations were low and the magnitude of the nutrient enrichment was high, suggesting that oligotrophic streams are most vulnerable to nutrient enrichment. The magnitude of the nutrient-enrichment effect on litter decomposition was higher in the laboratory than in the field experiments, suggesting that laboratory experiments overestimate the effect and their results should be interpreted with caution. Among field experiments, effects of nutrient enrichment were smaller in the correlative than in the manipulative experiments since in the former the effects of nutrient enrichment on litter decomposition were likely confounded by other environmental factors, e.g. pollutants other than nutrients commonly found in streams impacted by human activity. However, primary studies addressing the effect of multiple stressors on litter decomposition are still few and thus it was not possible to consider the interaction between factors in this review. In field manipulative experiments, the effect of nutrient enrichment on litter decomposition depended on the scale at which the nutrients were added: stream reach > streamside channel > litter bag. This may have resulted from a more uniform and continuous exposure of microbes and detritivores to nutrient enrichment at the stream-reach scale. By

  16. BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

    OpenAIRE

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-01-01

    Background Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology,...

  17. Comparative Analysis of the Development of Agricultural Listed Companies

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    On the basis of industrial division of China’s Securities Regulatory Commission,listed companies in the processing industry of agro-products and food production industry have also been incorporated into agricultural listed companies.Developmental discrepancy of agricultural listed companies is analyzed.The main manifestations are small population quantity,slow development,weak growing capacity,relatively poor rationality and unbalanced regional distribution.The internal causes of this kind of situation lie in the weak quality and inadequate developmental driving force of agricultural listed companies,while the external causes are the capital chasing and unbalanced political support of the country.Therefore,the key of quickening the development of agricultural listed companies is inner power and external competition.Thus,the political thoughts of the development of agricultural listed companies are proposed.

  18. Analysis list - ChIP-Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us ChIP-Atla...3 Description of data contents A list of metadata to generate file paths of analysis provided on ChIP-Atlas,...e class. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Analysis list - ChIP-Atlas | LSDB Archive ...

  19. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

    Directory of Open Access Journals (Sweden)

    Jesús Lascorz

    2011-01-01

    Full Text Available Background: A large number of gene expression profiling (GEP studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-regulated in colorectal carcinogenesis. Materials and Methods: We started the analysis with 242 unique annotated genes that had been reported by any of three recent meta-analyses covering GEP studies on genes differentially expressed in carcinoma vs normal mucosa. Most of these genes (218, 91.9% had been reported in at least three GEP studies. These 242 genes were submitted to bioinformatic analysis using a total of nine tools to detect enrichment of Gene Ontology (GO categories or Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. As a final consistency criterion the pathway categories had to be enriched by several tools to be taken into consideration. Results: Our pathway-based enrichment analysis identified the categories of ribosomal protein constituents, extracellular matrix receptor interaction, carbonic anhydrase isozymes, and a general category related to inflammation and cellular response as significantly and consistently overrepresented entities. Conclusions: We triaged the genes covered by the published GEP literature on colorectal carcinogenesis and subjected them to multiple enrichment tools in order to identify the consistently enriched gene categories. These turned out to have known functional relationships to cancer development and thus deserve further investigation.

  20. A new ANEW: Evaluation of a word list for sentiment analysis in microblogs

    CERN Document Server

    Nielsen, Finn Årup

    2011-01-01

    Sentiment analysis of microblogs such as Twitter has recently gained a fair amount of attention. One of the simplest sentiment analysis approaches compares the words of a posting against a labeled word list, where each word has been scored for valence, -- a 'sentiment lexicon' or 'affective word lists'. There exist several affective word lists, e.g., ANEW (Affective Norms for English Words) developed before the advent of microblogging and sentiment analysis. I wanted to examine how well ANEW and other word lists performs for the detection of sentiment strength in microblog posts in comparison with a new word list specifically constructed for microblogs. I used manually labeled postings from Twitter scored for sentiment. Using a simple word matching I show that the new word list may perform better than ANEW, though not as good as the more elaborate approach found in SentiStrength.

  1. 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.

  2. [Meta-analysis of stable carbon and nitrogen isotopic enrichment factors for aquatic animals].

    Science.gov (United States)

    Guo, Liang; Sun, Cui-ping; Ren, Wei-zheng; Zhang, Jian; Tang, Jian-iun; Hu, Liana-liang; Chen, Xin

    2016-02-01

    Isotopic enrichment factor (Δ, the difference between the δ value of food and a consumer tissue) is an important parameter in using stable isotope analysis (SIA) to reconstruct diets, characterize trophic relationships, elucidate patterns of resource allocation, and construct food webs. Isotopic enrichment factor has been considered as a constancy value across a broad range of animals. However, recent studies showed that the isotopic enrichment factor differed among various types of animals although the magnitude of variation was not clear. Here, we conducted a meta-analysis to synthesize and compare Δ13C and Δ15N among four types of aquatic animals (teleosts, crustaceans, reptiles and molluscs). We searched for papers published before 2014 on Web of Science and CNKI using the key words "stable isotope or isotopic fractionation or fractionation factor or isotopic enrichment or trophic enrichment". Forty-two publications that contain 140 studies on Δ13C and 159 studies on Δ15N were obtained. We conducted three parallel meta-analyses by using three types of weights (the reciprocal of variance as weights, the sample size as weights, and equal weights). The results showed that no significant difference in Δ13C among different animal types (teleosts 1.0 per thousand, crustaceans 1.3 per thousand, reptiles 0.5 per thousand, and molluscs 1.5 per thousand), while Δ15N values were significantly different (teleosts 2.4 per thousand, crustaceans 3.6 per thousand, reptiles 1.0 per thousand and molluscs 2.5 per thousand). Our results suggested that the overall mean of Δ13C could be used as a general enrichment factor, but Δ15N should be chosen according to the type of aquatic animals in using SIA to analyze trophic relationships, patterns of resource allocation and food webs.

  3. Gene set enrichment analysis for non-monotone association and multiple experimental categories

    OpenAIRE

    Heinloth Alexandra N; Irwin Richard D; Dai Shuangshuang; Lin Rongheng; Boorman Gary A; Li Leping

    2008-01-01

    Abstract Background Recently, microarray data analyses using functional pathway information, e.g., gene set enrichment analysis (GSEA) and significance analysis of function and expression (SAFE), have gained recognition as a way to identify biological pathways/processes associated with a phenotypic endpoint. In these analyses, a local statistic is used to assess the association between the expression level of a gene and the value of a phenotypic endpoint. Then these gene-specific local statis...

  4. Measurement system analysis (MSA) of the isotopic ratio for uranium isotope enrichment process control

    Energy Technology Data Exchange (ETDEWEB)

    Medeiros, Josue C. de; Barbosa, Rodrigo A.; Carnaval, Joao Paulo R., E-mail: josue@inb.gov.br, E-mail: rodrigobarbosa@inb.gov.br, E-mail: joaocarnaval@inb.gov.br [Industrias Nucleares do Brasil (INB), Rezende, RJ (Brazil)

    2013-07-01

    Currently, one of the stages in nuclear fuel cycle development is the process of uranium isotope enrichment, which will provide the amount of low enriched uranium for the nuclear fuel production to supply 100% Angra 1 and 20% Angra 2 demands. Determination of isotopic ration n({sup 235}U)/n({sup 238}U) in uranium hexafluoride (UF{sub 6} - used as process gas) is essential in order to control of enrichment process of isotopic separation by gaseous centrifugation cascades. The uranium hexafluoride process is performed by gas continuous feeding in separation unit which uses the centrifuge force principle, establishing a density gradient in a gas containing components of different molecular weights. The elemental separation effect occurs in a single ultracentrifuge that results in a partial separation of the feed in two fractions: an enriched on (product) and another depleted (waste) in the desired isotope ({sup 235}UF{sub 6}). Industrias Nucleares do Brasil (INB) has used quadrupole mass spectrometry (QMS) by electron impact (EI) to perform isotopic ratio n({sup 235}U)/n({sup 238}U) analysis in the process. The decision of adjustments and change te input variables are based on the results presented in these analysis. A study of stability, bias and linearity determination has been performed in order to evaluate the applied method, variations and systematic errors in the measurement system. The software used to analyze the techniques above was the Minitab 15. (author)

  5. reMelting curve analysis as a tool for enrichment monitoring in the SELEX process.

    Science.gov (United States)

    Vanbrabant, Jeroen; Leirs, Karen; Vanschoenbeek, Katrijn; Lammertyn, Jeroen; Michiels, Luc

    2014-02-07

    Current aptamer selection procedures enable limited control and transparency on how the DNA selection pool is evolving. Affinity tests and binding analyses are not always informative. Here we show that real-time PCR provides a valuable tool for the follow-up of aptamer selection. Limited time, work and amount of amplified ssDNA make this an interesting instrument to set-up a SELEX design and monitor the enrichment of oligonucleotides. reMelting Curve Analysis (rMCA) after reannealing under stringent conditions provides information about enrichment, compared to a random library. Monitoring the SELEX process and optimising conditions by means of the proposed methods can increase the selection efficiency in a controlled way. rMCA is applied in enrichment simulations and three different selection procedures. Our results imply that rMCA can be used for different SELEX designs and different targets. SELEX pool diversity analysis by rMCA has been proven to be a useful, reproducible tool to detect and evaluate enrichment of specific binding aptamers while the selection procedure is being performed.

  6. Efficiency Analysis of Listed Power Companies Based on Malmquist Index

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This paper improved the known study for technical progress in Malmquist productivity index calculating. In the method, all the possible movements for decision making units (DMUs) are listed, and the condition that several DMUs lie on the productivity frontier is analyzed. The dynamic efficiencies of Chinese listed power companies from 1997 to 2006 were evaluated. The empirical results indicate that the improved method is effective.

  7. Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

    Directory of Open Access Journals (Sweden)

    Che Anney

    2009-06-01

    Full Text Available Abstract Background One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. Results We now introduce a new Pathway Pattern Extraction Pipeline (PPEP, which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public

  8. MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken.

    Science.gov (United States)

    Morota, Gota; Beissinger, Timothy M; Peñagaricano, Francisco

    2016-01-01

    Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO), and more recently by Medical Subject Headings (MeSH). Here, we report a suite of MeSH packages for chicken in Bioconductor, and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published datasets that were employed represent (i) differentially expressed genes, and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports the findings obtained from GO analysis, but also that MeSH is able to further enrich the representation of biological knowledge and often provide more interpretable results. Based on the hierarchical structures of MeSH and GO, we computed semantic similarities among vocabularies, as well as semantic similarities among selected genes. These yielded the similarity levels between significant functional terms, and the annotation of each gene yielded the measures of gene similarity. Our findings show the benefits of using MeSH as an alternative choice of annotation in order to draw biological inferences from a list of genes of interest. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the understanding of the genetic basis of complex traits.

  9. Children's Homes in the Croatian Press in 2012: an Analysis of Jutarnji list and Večernji list

    Directory of Open Access Journals (Sweden)

    Danijel Labaš

    2014-12-01

    Full Text Available Children in the media is a popular topic in the literature on media literacy, but results indicate that much of the media content is not written in accordance with the existing legislation. This paper presents research on children's homes in the Croatian newspapers Jutarnji list and Večernji list in the period from 1 January to 31 December 2012. We conduct a content analysis that includes 60 newspaper articles about children's homes. The total number directly indicates that the coverage of children's homes as a relevant social issue is lacking. Both media and its audience must be more responsible in the context of reporting about children's homes. Therefore, this paper aims to point out the need for a special sensibility when reporting on children's homes, but also the greater need for the equal treatment of children connected to all social groups in the media.

  10. Constraints on the Parental Melts of Enriched Shergottites from Image Analysis and High Pressure Experiments

    Science.gov (United States)

    Collinet, M.; Medard, E.; Devouard, B.; Peslier, A.

    2012-01-01

    Martian basalts can be classified in at least two geochemically different families: enriched and depleted shergottites. Enriched shergottites are characterized by higher incompatible element concentrations and initial Sr-87/Sr-86 and lower initial Nd-143/Nd-144 and Hf-176/Hf-177 than depleted shergottites [e.g. 1, 2]. It is now generally admitted that shergottites result from the melting of at least two distinct mantle reservoirs [e.g. 2, 3]. Some of the olivine-phyric shergottites (either depleted or enriched), the most magnesian Martian basalts, could represent primitive melts, which are of considerable interest to constrain mantle sources. Two depleted olivine-phyric shergottites, Yamato (Y) 980459 and Northwest Africa (NWA) 5789, are in equilibrium with their most magnesian olivine (Fig. 1) and their bulk rock compositions are inferred to represent primitive melts [4, 5]. Larkman Nunatak (LAR) 06319 [3, 6, 7] and NWA 1068 [8], the most magnesian enriched basalts, have bulk Mg# that are too high to be in equilibrium with their olivine megacryst cores. Parental melt compositions have been estimated by subtracting the most magnesian olivine from the bulk rock composition, assuming that olivine megacrysts have partially accumulated [3, 9]. However, because this technique does not account for the actual petrography of these meteorites, we used image analysis to study these rocks history, reconstruct their parent magma and understand the nature of olivine megacrysts.

  11. A new ANEW: Evaluation of a word list for sentiment analysis in microblogs

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup

    2011-01-01

    Sentiment analysis of microblogs such as Twitter has recently gained a fair amount of attention. One of the simplest sentiment analysis approaches compares the words of a posting against a labeled word list, where each word has been scored for valence, — a “sentiment lexicon” or “affective word...... lists”. There exist several affective word lists, e.g., ANEW (Affective Norms for English Words) developed before the advent of microblogging and sentiment analysis. I wanted to examine how well ANEW and other word lists performs for the detection of sentiment strength in microblog posts in comparison...... with a new word list specifically constructed for microblogs. I used manually labeled postings from Twitter scored for sentiment. Using a simple word matching I show that the new word list may perform better than ANEW, though not as good as the more elaborate approach found in SentiStrength....

  12. 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.

  13. 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...

  14. Specific On-Plate Enrichment of Phosphorylated Peptides for Direct MALDI-TOF MS Analysis

    OpenAIRE

    Qiao, L.; Roussel, C.; Wan, J.; P. Yang; Girault, H H; Liu, B.

    2007-01-01

    An on-plate specific enrichment method is presented for the direct analysis of peptides phosphorylation. An array of sintered TiO2 nanoparticle spots was prepared on a stainless steel plate to provide porous substrate with a very large specific surface and durable functions. These spots were used to selectively capture phosphorylated peptides from peptide mixtures, and the immobilized phosphopeptides could then be analyzed directly by MALDI MS after washing away the nonphos- phorylated pepti...

  15. An integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection

    Science.gov (United States)

    Liu, Hai-Tao; Wen, Zhi-Yu; Xu, Yi; Shang, Zheng-Guo; Peng, Jin-Lan; Tian, Peng

    2017-09-01

    In this paper, an integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection was purposed based on microfluidic chips dielectrophoresis technique and electrochemical impedance detection principle. The microsystems include microfluidic chip, main control module, and drive and control module, and signal detection and processing modulet and result display unit. The main control module produce the work sequence of impedance detection system parts and achieve data communication functions, the drive and control circuit generate AC signal which amplitude and frequency adjustable, and it was applied on the foodborne pathogens impedance analysis microsystems to realize the capture enrichment and impedance detection. The signal detection and processing circuit translate the current signal into impendence of bacteria, and transfer to computer, the last detection result is displayed on the computer. The experiment sample was prepared by adding Escherichia coli standard sample into chicken sample solution, and the samples were tested on the dielectrophoresis chip capture enrichment and in-situ impedance detection microsystems with micro-array electrode microfluidic chips. The experiments show that the Escherichia coli detection limit of microsystems is 5 × 104 CFU/mL and the detection time is within 6 min in the optimization of voltage detection 10 V and detection frequency 500 KHz operating conditions. The integrated microfluidic analysis microsystems laid the solid foundation for rapid real-time in-situ detection of bacteria.

  16. A novel titanium dioxide-polydimethylsiloxane plate for phosphopeptide enrichment and mass spectrometry analysis.

    Science.gov (United States)

    Chen, Chao-Jung; Lai, Chien-Chen; Tseng, Mei-Chun; Liu, Yu-Ching; Liu, Yu-Huei; Chiou, Liang-Wei; Tsai, Fuu-Jen

    2014-02-17

    The phosphorylation of proteins is a major post-translational modification that is required for the regulation of many cellular processes and activities. Mass spectrometry signals of low-abundance phosphorylated peptides are commonly suppressed by the presence of abundant non-phosphorylated peptides. Therefore, one of the major challenges in the detection of low-abundance phosphopeptides is their enrichment from complex peptide mixtures. Titanium dioxide (TiO2) has been proven to be a highly efficient approach for phosphopeptide enrichment and is widely applied. In this study, a novel TiO2 plate was developed by coating TiO2 particles onto polydimethylsiloxane (PDMS)-coated MALDI plates, glass, or plastic substrates. The TiO2-PDMS plate (TP plate) could be used for on-target MALDI-TOF analysis, or as a purification plate on which phosphopeptides were eluted out and subjected to MALDI-TOF or nanoLC-MS/MS analysis. The detection limit of the TP plate was ∼10-folds lower than that of a TiO2-packed tip approach. The capacity of the ∼2.5 mm diameter TiO2 spots was estimated to be ∼10 μg of β-casein. Following TiO2 plate enrichment of SCC4 cell lysate digests and nanoLC-MS/MS analysis, ∼82% of the detected proteins were phosphorylated, illustrating the sensitivity and effectiveness of the TP plate for phosphoproteomic study.

  17. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.

    Science.gov (United States)

    Tabas-Madrid, Daniel; Nogales-Cadenas, Ruben; Pascual-Montano, Alberto

    2012-07-01

    Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs-genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely available at http://genecodis.cnb.csic.es.

  18. Parameterized analysis of paging and list update algorithms

    DEFF Research Database (Denmark)

    Dorrigiv, Reza; Ehmsen, Martin R.; López-Ortiz, Alejandro

    2009-01-01

    It is well-established that input sequences for paging and list update have locality of reference. In this paper we analyze the performance of algorithms for these problems in terms of the amount of locality in the input sequence. We define a measure for locality that is based on Denning's working...... to a better performance. We obtain similar separation for list update algorithms. Lastly, we show that, surprisingly, certain randomized algorithms which are superior to MTF in the classical model are not so in the parameterized case, which matches experimental results. © 2010 Springer-Verlag Berlin...

  19. The evolution analysis of listed companies co-holding non-listed financial companies based on two-mode heterogeneous networks

    Science.gov (United States)

    An, Pengli; Li, Huajiao; Zhou, Jinsheng; Chen, Fan

    2017-10-01

    Complex network theory is a widely used tool in the empirical research of financial markets. Two-mode and multi-mode networks are new trends and represent new directions in that they can more accurately simulate relationships between entities. In this paper, we use data for Chinese listed companies holding non-listed financial companies over a ten-year period to construct two networks: a two-mode primitive network in which listed companies and non-listed financial companies are considered actors and events, respectively, and a one-mode network that is constructed based on the decreasing-mode method in which listed companies are considered nodes. We analyze the evolution of the listed company co-holding network from several perspectives, including that of the whole network, of information control ability, of implicit relationships, of community division and of small-world characteristics. The results of the analysis indicate that (1) China's developing stock market affects the share-holding condition of listed companies holding non-listed financial companies; (2) the information control ability of co-holding networks is focused on a few listed companies and the implicit relationship of investment preference between listed companies is determined by the co-holding behavior; (3) the community division of the co-holding network is increasingly obvious, as determined by the investment preferences among listed companies; and (4) the small-world characteristics of the co-holding network are increasingly obvious, resulting in reduced communication costs. In this paper, we conduct an evolution analysis and develop an understanding of the factors that influence the listed companies co-holding network. This study will help illuminate research on evolution analysis.

  20. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    Science.gov (United States)

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  1. ANALYSIS OF RESIN AND FATTY ACIDS ENRICHED IN PAPERMAKING PROCESS WATERS

    Directory of Open Access Journals (Sweden)

    Piia Valto

    2010-02-01

    Full Text Available The applicability of a special pilot-scale installation (Short Circulation Device was studied for demonstrating the enrichment of selected resin and fatty acids in process waters when increasing water reuse during the manufacture of paper. The traditional gas chromatography with flame ionization detection (GC-FID, turbidity, and online sample enrichment (solid phase extraction, SPE for atmospheric pressure chemical ionization-mass spectrometry (APCI-MS measurements were used for the analysis of the resin and fatty acids. The data from all the measurements with unbleached thermomechanical pulp (TMP process waters were in a good agreement, and correlation coefficients (R2 > 0.9 were obtained in each case. Rapid information about the levels of wood extractives in papermaking process waters is of great importance, and it offers a suitable way to predict oncoming pitch problems. It was concluded that the routine control of the extractives level in papermaking process waters is possible by all these methods.

  2. Instrumental neutron activation analysis of an enriched 28Si single-crystal

    CERN Document Server

    DAgostino, G; Giordani, L; Mana, G; Oddone, M

    2013-01-01

    The determination of the Avogadro constant plays a key role in the redefinition of the kilogram in terms of a fundamental constant. The present experiment makes use of a silicon single-crystal highly enriched in 28Si that must have a total impurity mass fraction smaller than a few parts in 109. To verify this requirement, we previously developed a relative analytical method based on neutron activation for the elemental characterization of a sample of the precursor natural silicon crystal WASO 04. The method is now extended to fifty-nine elements and applied to a monoisotopic 28Si single-crystal that was grown to test the achievable enrichment. Since this crystal was likely contaminated, this measurement tested also the detection capabilities of the analysis. The results quantified contaminations by Ge, Ga, As, Tm, Lu, Ta, W and Ir and, for a number of the detectable elements, demonstrated that we can already reach the targeted 1 ng/g detection limit.

  3. Multilayer interparticle linking hybrid MOF-199 for noninvasive enrichment and analysis of plant hormone ethylene.

    Science.gov (United States)

    Zhang, Zhuomin; Huang, Yichun; Ding, Weiwei; Li, Gongke

    2014-04-01

    Ethylene, an important plant hormone, is of utmost importance during many developmental processes of plants. However, the efficient enrichment and analysis of trace ethylene still remains a challenge. A simple and mild multilayer interparticle linking strategy was proposed to fabricate a novel hybrid MOF-199 enrichment coating. Strong chemical interparticle linkages throughout the coating improved the durability and reproducibility of hybrid MOF-199 coating dramatically. This coating performed a significant extraction superiority of ethylene over commonly used commercial coatings, attributed to the multiple interactions including "molecular sieving effect", hydrogen bonding, open metal site interaction, and π-π affinity. The hybridization of multiwalled carbon nanotubes (MWCNTs) with MOF-199 further improved the enrichment capability and also acted as a hydrophobic "shield" to prevent the open metal sites of MOF-199 from being occupied by water molecules, which effectively improved the moisture-resistant property of MOF-199/CNTs coating. Finally, this novel enrichment method was successfully applied for the noninvasive analysis of trace ethylene, methanol, and ethanol from fruit samples with relatively high humidity. The low detection limit was 0.016 μg/L for ethylene. It was satisfactory that trace ethylene could be actually detected from fruit samples by this noninvasive method. Good recoveries of spiked grape, wampee, blueberry, and durian husk samples were obtained in the range of 90.0-114%, 79.4-88.6%, 78.5-86.8%, and 85.2-105% with the corresponding relative standard deviations of 4.8-9.8%, 6.9-8.9%, 3.8-8.1%, and 9.3-10.5% (n = 3), respectively.

  4. Analysis of Pecking Order Theory on Chinese Listed Companies

    Institute of Scientific and Technical Information of China (English)

    初保驹; 林舒嫄

    2013-01-01

    This study tests the order of firms’ financing choices based on a sample consists of 150 Chinese listed companies. And it indicates that China’s listed companies did not follow the theoretical ‘Pecking Order’ (Myers,1984), but a ‘new order’- internal fund, equity, and debt - to make their financial choices. This is because firm’s gearing ratio and solvency did not show a high degree of correlation in China’s capital market, which leads to the preference of using equity. Besides, there are some other reasons: low cost of issuing equity, ineffective financial management, immaturity of capital market, not well developed bond market, and lack of an effective credit rating system.

  5. Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available uence of marker and related papers. Data file File name: pgdbj_dna_marker_linkage...isition method The information of markers was collected from other databases and/or papers. Data analysis me

  6. Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

    Science.gov (United States)

    Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

    2016-06-27

    Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

  7. Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.

    Science.gov (United States)

    Kofler, Robert; Schlötterer, Christian

    2012-08-01

    An analysis of gene set [e.g. Gene Ontology (GO)] enrichment assumes that all genes are sampled independently from each other with the same probability. These assumptions are violated in genome-wide association (GWA) studies since (i) longer genes typically have more single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Herein, we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that GO tests on GWA data could result in a substantial number of false-positive GO terms. Permutation tests implemented in Gowinda eliminate these biases, but maintain sufficient power to detect enrichment of GO terms. Since sufficient resolution for large datasets requires millions of permutations, we use multi-threading to keep computation times reasonable. Gowinda is implemented in Java (v1.6) and freely available on http://code.google.com/p/gowinda/ christian.schloetterer@vetmeduni.ac.at Manual: http://code.google.com/p/gowinda/wiki/Manual. Test data and tutorial: http://code.google.com/p/gowinda/wiki/Tutorial. http://code.google.com/p/gowinda/wiki/VALIDATION.

  8. Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis.

    Science.gov (United States)

    Naba, Alexandra; Clauser, Karl R; Hynes, Richard O

    2015-07-23

    The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins that provides biophysical and biochemical cues that are major regulators of cell proliferation, survival, migration, etc. The ECM plays important roles in development and in diverse pathologies including cardio-vascular and musculo-skeletal diseases, fibrosis, and cancer. Thus, characterizing the composition of ECMs of normal and diseased tissues could lead to the identification of novel prognostic and diagnostic biomarkers and potential novel therapeutic targets. However, the very nature of ECM proteins (large in size, cross-linked and covalently bound, heavily glycosylated) has rendered biochemical analyses of ECMs challenging. To overcome this challenge, we developed a method to enrich ECMs from fresh or frozen tissues and tumors that takes advantage of the insolubility of ECM proteins. We describe here in detail the decellularization procedure that consists of sequential incubations in buffers of different pH and salt and detergent concentrations and that results in 1) the extraction of intracellular (cytosolic, nuclear, membrane and cytoskeletal) proteins and 2) the enrichment of ECM proteins. We then describe how to deglycosylate and digest ECM-enriched protein preparations into peptides for subsequent analysis by mass spectrometry.

  9. BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

    Science.gov (United States)

    Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

    2015-02-21

    Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

  10. Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions

    Directory of Open Access Journals (Sweden)

    Lin Yong

    2009-11-01

    Full Text Available Abstract Background Dorsal root ganglion (DRG neurons are primary sensory neurons that conduct neuronal impulses related to pain, touch and temperature senses. Plasma membrane (PM of DRG cells plays important roles in their functions. PM proteins are main performers of the functions. However, mainly due to the very low amount of DRG that leads to the difficulties in PM sample collection, few proteomic analyses on the PM have been reported and it is a subject that demands further investigation. Results By using aqueous polymer two-phase partition in combination with high salt and high pH washing, PMs were efficiently enriched, demonstrated by western blot analysis. A total of 954 non-redundant proteins were identified from the plasma membrane-enriched preparation with CapLC-MS/MS analysis subsequent to protein separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE or shotgun digestion. 205 (21.5% of the identified proteins were unambiguously assigned as PM proteins, including a large number of signal proteins, receptors, ion channel and transporters. Conclusion The aqueous polymer two-phase partition is a simple, rapid and relatively inexpensive method. It is well suitable for the purification of PMs from small amount of tissues. Therefore, it is reasonable for the DRG PM to be enriched by using aqueous two-phase partition as a preferred method. Proteomic analysis showed that DRG PM was rich in proteins involved in the fundamental biological processes including material exchange, energy transformation and information transmission, etc. These data would help to our further understanding of the fundamental DRG functions.

  11. A novel community driven software for functional enrichment analysis of extracellular vesicles data

    DEFF Research Database (Denmark)

    Pathan, Mohashin; Keerthikumar, Shivakumar; Chisanga, David

    2017-01-01

    fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably......, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe...

  12. Specific on-plate enrichment of phosphorylated peptides for direct MALDI-TOF MS analysis.

    Science.gov (United States)

    Qiao, Liang; Roussel, Christophe; Wan, Jingjing; Yang, Pengyuan; Girault, Hubert H; Liu, Baohong

    2007-12-01

    An on-plate specific enrichment method is presented for the direct analysis of peptides phosphorylation. An array of sintered TiO 2 nanoparticle spots was prepared on a stainless steel plate to provide porous substrate with a very large specific surface and durable functions. These spots were used to selectively capture phosphorylated peptides from peptide mixtures, and the immobilized phosphopeptides could then be analyzed directly by MALDI MS after washing away the nonphosphorylated peptides. beta-Casein and protein mixtures were employed as model samples to investigate the selection efficiency. In this strategy, the steps of phosphopeptide capture, purification, and subsequent mass spectrometry analysis are all successfully accomplished on a single target plate, which greatly reduces sample loss and simplifies analytical procedures. The low detection limit, small sample size, and rapid selective entrapment show that this on-plate strategy is promising for online enrichment of phosphopeptides, which is essential for the analysis of minute amount of samples in high-throughput proteome research.

  13. Environmental Efficiency Analysis of Listed Cement Enterprises in China

    Directory of Open Access Journals (Sweden)

    Fang Zhang

    2016-05-01

    Full Text Available China’s cement production has been the highest worldwide for decades and contributes significant environmental pollution. Using a non-radical DEA model with slacks-based measure (SBM, this paper analyzes the environmental efficiency of China’s listed cement companies. The results suggest that the average mean of the environmental efficiency for the listed cement enterprises shows a decreasing trend in 2012 and 2013. There is a significant imbalance in environmental efficiency in these firms ranging from very low to very high. Further investigation finds that enterprise size and property structure are key factors. Increasing production concentration and decreasing the share of government investment could improve the environmental efficiency. The findings also suggest that effectively monitoring pollution products can improve environmental efficiency quickly, whereas pursuit for excessive profitability without keeping the same pace in energy saving would cause a sharp drop in environmental efficiency. Based on these findings, we proposed that companies in the Chinese cement sector might consider restructuring to improve environmental efficiency. They also need to make a trade-off between profitability and environmental protection. Finally, the Chinese government should reduce ownership control and management interventions in cement companies.

  14. Uranium enrichment using gas centrifugation. An analysis focusing export control; Urananrikning med gascentrifugering. En analys med fokus paa exportkontroll

    Energy Technology Data Exchange (ETDEWEB)

    Oliver, Lena; Peterson, Jenny; Wilhelmsen, Katarina [Swedish Defense Research Inst., Stockholm (Sweden)

    2005-08-01

    The Swedish Defence Research Agency, FOI, has performed a study on uranium enrichment by gas centrifugation. The theory and principles of gas centrifugation is described in this report and relevant equipment used in the process has been identified. Different aspects of operating a gas centrifuge facility - and its indicators - are also presented. The separation efficiency and the flow of material through a centrifuge are very small, and therefore, a large number of centrifuges in cascades is needed to produce a larger amount of enriched uranium within a reasonable time. Countries with nuclear weapons ambitions often show an interest in gas centrifuges to produce weapons grade uranium - if they have managed to acquire the technology - because of the efficiency of the process and since it is relatively easy to conceal. Most equipment used in gas centrifuge facilities is under export control to prevent clandestine uranium enrichment. The Nuclear Suppliers' Group has compiled lists of nuclear related equipment and components that are of importance to export control. The control lists have also been included in the EU legislation.

  15. Associations between DNA methylation and schizophrenia-related intermediate phenotypes - a gene set enrichment analysis.

    Science.gov (United States)

    Hass, Johanna; Walton, Esther; Wright, Carrie; Beyer, Andreas; Scholz, Markus; Turner, Jessica; Liu, Jingyu; Smolka, Michael N; Roessner, Veit; Sponheim, Scott R; Gollub, Randy L; Calhoun, Vince D; Ehrlich, Stefan

    2015-06-03

    Multiple genetic approaches have identified microRNAs as key effectors in psychiatric disorders as they post-transcriptionally regulate expression of thousands of target genes. However, their role in specific psychiatric diseases remains poorly understood. In addition, epigenetic mechanisms such as DNA methylation, which affect the expression of both microRNAs and coding genes, are critical for our understanding of molecular mechanisms in schizophrenia. Using clinical, imaging, genetic, and epigenetic data of 103 patients with schizophrenia and 111 healthy controls of the Mind Clinical Imaging Consortium (MCIC) study of schizophrenia, we conducted gene set enrichment analysis to identify markers for schizophrenia-associated intermediate phenotypes. Genes were ranked based on the correlation between DNA methylation patterns and each phenotype, and then searched for enrichment in 221 predicted microRNA target gene sets. We found the predicted hsa-miR-219a-5p target gene set to be significantly enriched for genes (EPHA4, PKNOX1, ESR1, among others) whose methylation status is correlated with hippocampal volume independent of disease status. Our results were strengthened by significant associations between hsa-miR-219a-5p target gene methylation patterns and hippocampus-related neuropsychological variables. IPA pathway analysis of the respective predicted hsa-miR-219a-5p target genes revealed associated network functions in behavior and developmental disorders. Altered methylation patterns of predicted hsa-miR-219a-5p target genes are associated with a structural aberration of the brain that has been proposed as a possible biomarker for schizophrenia. The (dys)regulation of microRNA target genes by epigenetic mechanisms may confer additional risk for developing psychiatric symptoms. Further study is needed to understand possible interactions between microRNAs and epigenetic changes and their impact on risk for brain-based disorders such as schizophrenia.

  16. Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC.

    Science.gov (United States)

    Totten, Sarah M; Feasley, Christa L; Bermudez, Abel; Pitteri, Sharon J

    2017-03-03

    Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.

  17. Partial Safety Analysis for a Reduced Uranium Enrichment Core for the High Flux Isotope Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Primm, Trent [ORNL; Gehin, Jess C [ORNL

    2009-04-01

    A computational model of the reactor core of the High Flux Isotope Rector (HFIR) was developed in order to analyze non-destructive accidents caused by transients during reactor operation. The reactor model was built for the latest version of the nuclear analysis software package called Program for the Analysis of Reactor Transients (PARET). Analyses performed with the model constructed were compared with previous data obtained with other tools in order to benchmark the code. Finally, the model was used to analyze the behavior of the reactor under transients using a different nuclear fuel with lower enrichment of uranium (LEU) than the fuel currently used, which has a high enrichment of uranium (HEU). The study shows that the presence of fertile isotopes in LEU fuel, which increases the neutron resonance absorption, reduces the impact of transients on the fuel and enhances the negative reactivity feedback, thus, within the limitations of this study, making LEU fuel appear to be a safe alternative fuel for the reactor core.

  18. Transcriptomic analysis of the effects of a fish oil enriched diet on murine brains.

    Directory of Open Access Journals (Sweden)

    Rasha Hammamieh

    Full Text Available The health benefits of fish oil enriched with high omega-3 polyunsaturated fatty acids (n-3 PUFA are widely documented. Fish oil as dietary supplements, however, show moderate clinical efficacy, highlighting an immediate scope of systematic in vitro feedback. Our transcriptomic study was designed to investigate the genomic shift of murine brains fed on fish oil enriched diets. A customized fish oil enriched diet (FD and standard lab diet (SD were separately administered to two randomly chosen populations of C57BL/6J mice from their weaning age until late adolescence. Statistical analysis mined 1,142 genes of interest (GOI differentially altered in the hemibrains collected from the FD- and SD-fed mice at the age of five months. The majority of identified GOI (∼ 40% encodes proteins located in the plasma membrane, suggesting that fish oil primarily facilitated the membrane-oriented biofunctions. FD potentially augmented the nervous system's development and functions by selectively stimulating the Src-mediated calcium-induced growth cascade and the downstream PI3K-AKT-PKC pathways. FD reduced the amyloidal burden, attenuated oxidative stress, and assisted in somatostatin activation-the signatures of attenuation of Alzheimer's disease, Parkinson's disease, and affective disorder. FD induced elevation of FKBP5 and suppression of BDNF, which are often linked with the improvement of anxiety disorder, depression, and post-traumatic stress disorder. Hence we anticipate efficacy of FD in treating illnesses such as depression that are typically triggered by the hypoactivities of dopaminergic, adrenergic, cholinergic, and GABAergic networks. Contrastingly, FD's efficacy could be compromised in treating illnesses such as bipolar disorder and schizophrenia, which are triggered by hyperactivities of the same set of neuromodulators. A more comprehensive investigation is recommended to elucidate the implications of fish oil on disease pathomechanisms, and the

  19. 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...

  20. The Dual Listing of Austrian Companies in Vienna and Frankfurt: Dependence Analysis

    Directory of Open Access Journals (Sweden)

    Lukasz Gurgul

    2015-03-01

    Full Text Available International capital flows can be hampered by a variety of barriers such as transaction costs, information costs, and legal restrictions. The solution in this situation can be dual listing. The framework of the research presented here assumes that domestic securities are dually listed on a foreign capital market, while none of the foreign securities is dually listed on the domestic capital market. This paper is concerned with a dependence analysis of the log-levels and returns of Austrian stocks listed in Frankfurt and Vienna. The important issue is dynamic linear and non-linear causality between log-levels (returns of prices and the indices ATX and DAX. In this context the important directions of causality are found along with the level of relations of the selected types of causality.

  1. MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken

    Directory of Open Access Journals (Sweden)

    Gota Morota

    2016-08-01

    Full Text Available Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO, and more recently by Medical Subject Headings (MeSH. Here, we report a suite of MeSH packages for chicken in Bioconductor, and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published datasets that were employed represent (i differentially expressed genes, and (ii candidate genes under selective sweep or epistatic selection. The comparison of MeSH with GO overrepresentation analyses suggested not only that MeSH supports the findings obtained from GO analysis, but also that MeSH is able to further enrich the representation of biological knowledge and often provide more interpretable results. Based on the hierarchical structures of MeSH and GO, we computed semantic similarities among vocabularies, as well as semantic similarities among selected genes. These yielded the similarity levels between significant functional terms, and the annotation of each gene yielded the measures of gene similarity. Our findings show the benefits of using MeSH as an alternative choice of annotation in order to draw biological inferences from a list of genes of interest. We argue that the use of MeSH in conjunction with GO will be instrumental in facilitating the understanding of the genetic basis of complex traits.

  2. Relationship Analysis between Profitability and Capital Structure of the Food Industry Listed Companies

    Directory of Open Access Journals (Sweden)

    Yazhou Xiong

    2015-08-01

    Full Text Available This study aims to analyze the relation between profitability and capital structure of the food industry listed company and improve their capital structure. According to income rank of the food industry listed companies in China on August 1, 2014, provided by Chinese commerce intelligence network, this study makes a study on the growth level and operating status of the food industry listed companies from their panel data of third quarter report in 2014 and the profitability of enterprises is one of the important content of corporate financial analysis; corporate capital structure directly affects the business performance and long-term development. This study selects 4 indicators which mainly affect the profitability of enterprise, uses the method of factor analysis to make the comprehensive evaluation score on the 21 representative food industry listed companies in China, and carries on the correlation analysis and regression analysis to the assets and liabilities rate of the enterprise which is a main index to reflect the capital the structure, obtains the relationship between profitability and capital structure of the food industry listed companies.

  3. Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core

    Science.gov (United States)

    Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.

    2003-01-01

    The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.

  4. Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset.

    Directory of Open Access Journals (Sweden)

    Maja T Lindenmeyer

    Full Text Available Glomerular diseases account for the majority of cases with chronic renal failure. Several genes have been identified with key relevance for glomerular function. Quite a few of these genes show a specific or preferential mRNA expression in the renal glomerulus. To identify additional candidate genes involved in glomerular function in humans we generated a human renal glomerulus-enriched gene expression dataset (REGGED by comparing gene expression profiles from human glomeruli and tubulointerstitium obtained from six transplant living donors using Affymetrix HG-U133A arrays. This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus. Genes with 'a priori' known prominent glomerular expression served for validation and were all found in the novel dataset (e.g. CDKN1, DAG1, DDN, EHD3, MYH9, NES, NPHS1, NPHS2, PDPN, PLA2R1, PLCE1, PODXL, PTPRO, SYNPO, TCF21, TJP1, WT1. The mRNA expression of several novel glomerulus-enriched genes in REGGED was validated by qRT-PCR. Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance. This finding was further validated by assessing the expression of the axon guidance molecules neuritin (NRN1 and roundabout receptor ROBO1 and -2. In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons. A systematic analysis of this glomerulus-specific gene expression dataset allows the detection of target molecules and biological processes involved in glomerular biology and renal disease.

  5. Ames S-32 O-16 O-18 Line List for High-Resolution Experimental IR Analysis

    Science.gov (United States)

    Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

    2016-01-01

    By comparing to the most recent experimental data and spectra of the SO2 628 ?1/?3 bands (see Ulenikov et al., JQSRT 168 (2016) 29-39), this study illustrates the reliability and accuracy of the Ames-296K SO2 line list, which is accurate enough to facilitate such high-resolution spectroscopic analysis. The SO2 628 IR line list is computed on a recently improved potential energy surface (PES) refinement, denoted Ames-Pre2, and the published purely ab initio CCSD(T)/aug-cc-pVQZ dipole moment surface. Progress has been made in both energy level convergence and rovibrational quantum number assignments agreeing with laboratory analysis models. The accuracy of the computed 628 energy levels and line list is similar to what has been achieved and reported for SO2 626 and 646, i.e. 0.01-0.03 cm(exp -1) for bands up to 5500 cm(exp -1). During the comparison, we found some discrepancies in addition to overall good agreements. The three-IR-list based feature-by-feature analysis in a 0.25 cm(exp -1) spectral window clearly demonstrates the power of the current Ames line lists with new assignments, correction of some errors, and intensity contributions from varied sources including other isotopologues. We are inclined to attribute part of detected discrepancies to an incomplete experimental analysis and missing intensity in the model. With complete line position, intensity, and rovibrational quantum numbers determined at 296 K, spectroscopic analysis is significantly facilitated especially for a spectral range exhibiting such an unusually high density of lines. The computed 628 rovibrational levels and line list are accurate enough to provide alternatives for the missing bands or suspicious assignments, as well as helpful to identify these isotopologues in various celestial environments. The next step will be to revisit the SO2 828 and 646 spectral analyses.

  6. Ames 32S16O18O line list for high-resolution experimental IR analysis

    Science.gov (United States)

    Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

    2016-12-01

    By comparing to the most recent experimental data and spectra of the SO2 628 ν1/ν3 bands (see Ulenikov et al., JQSRT 168 (2016) 29-39), this study illustrates the reliability and accuracy of the Ames-296K SO2 line list, which is accurate enough to facilitate such high-resolution spectroscopic analysis. The SO2 628 IR line list is computed on a recently improved potential energy surface (PES) refinement, denoted Ames-Pre2, and the published purely ab initio CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface. Progress has been made in both energy level convergence and rovibrational quantum number assignments agreeing with laboratory analysis models. The accuracy of the computed 628 energy levels and line list is similar to what has been achieved and reported for SO2 626 and 646, i.e. 0.01-0.03 cm-1 for bands up to 5500 cm-1. During the comparison, we found some discrepancies in addition to overall good agreements. The three-IR-list based feature-by-feature analysis in a 0.25 cm-1 spectral window clearly demonstrates the power of the current Ames line lists with new assignments, correction of some errors, and intensity contributions from varied sources including other isotopologues. We are inclined to attribute part of detected discrepancies to an incomplete experimental analysis and missing intensity in the model. With complete line position, intensity, and rovibrational quantum numbers determined at 296 K, spectroscopic analysis is significantly facilitated especially for a spectral range exhibiting such an unusually high density of lines. The computed 628 rovibrational levels and line list are accurate enough to provide alternatives for the missing bands or suspicious assignments, as well as helpful to identify these isotopologues in various celestial environments. The next step will be to revisit the SO2 828 and 646 spectral analyses.

  7. Enrichments for phototrophic bacteria and characterization by morphology and pigment analysis

    Science.gov (United States)

    Brune, D.

    1985-01-01

    The purpose of this investigation was to examine several sulfide containing environments for the presence of phototrophic bacteria and to obtain enriched cultures of some of the bacteria present. The field sites were Alum Rock State Park, the Palo Alto salt marsh, the bay area salt ponds, and Big Soda Lake (near Fallon, Nevada). Bacteria from these sites were characterized by microscopic examination, measurement of in vitro absorption spectra, and analysis of carotenoid pigments. Field observations at one of the bay area salt ponds, in which the salt concentration was saturating (about 30 percent NaCl) and the sediments along the shore of the pond covered with a gypsum crust, revealed a layer of purple photosynthetic bacteria under a green layer in the gypsum crust. Samples of this gypsum crust were taken to the laboratory to measure light transmission through the crust and to try to identify the purple photosynthetic bacteria present in this extremely saline environment.

  8. A comparative analysis of the Libyan national essential medicines list and the WHO model list of essential medicines

    Directory of Open Access Journals (Sweden)

    Asma Abubakr Mustafa

    2010-12-01

    Full Text Available Aim and Objectives: To examine the concordance of the Libyan Pharmaceutical List of Essential Medicines (LPLEM with the World Health Organization Model List of Essential Medicines 2009 (WMLEM 2009. Methods: The concordance between generic medicines listed in the WMLEM 2009 (standard reference list and the LPLEM 2006 (comparator list was evaluated. Results: The total number of Basic Essential Medicines (BEMs listed on the WMLEM 2009 was 347. The total number of generic medicines listed on the LPLEM was 584. Although the LPLEM has more listed medicines, only 270 (77.6% of BEMs from the WMLEM were listed as available. However, 25 of the 77 missing medicines were deemed to have appropriate alternatives. A total of 52 medicines from the WMLEM 2009 were therefore missing from the LPLEM. Discrepancies compared to the WMLEM 2009 were identified in 15 out of 29 therapeutic sections. The highest discrepancy rate from the WMLEM 2009 was in the anti-infective section (35 missing medicines. Missing BEMs were noted in many subclassifications of the anti-infective medicines section, but omissions were particularly prevalent in the antibacterial medicines subsection (11 missing medicines. Antituberculosis medications had the highest discrepancy rate for antibacterial BEMs with one-third of the single medicines recommended by the WHO in the WMLEM 2009 not listed on the LPLEM. Of the 314 additional medicines on the LPLEM, 18 were deemed to be irrational non-essential medicines. Conclusion: The LPLEM does not include several essential medicines recommended by the WHO in the WMLEM 2009. These discrepancies may have serious public health implications for management of some infectious diseases, particularly, tuberculosis and HIV.

  9. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

    Science.gov (United States)

    Tan, Boonfei; Jane Fowler, S; Laban, Nidal Abu; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

    2015-01-01

    Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities. PMID:25734684

  10. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples.

    Science.gov (United States)

    Tan, Boonfei; Fowler, S Jane; Abu Laban, Nidal; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

    2015-09-01

    Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.

  11. Comparison of immunoaffinity chromatography enrichment and nuclease P1 procedures for 32P-postlabelling analysis of PAH- DNA adducts

    NARCIS (Netherlands)

    Randerath, K.; Sriram, P.; Moorthy, B.; Aston, J.P.; Baan, R.A.; Berg, P.T.M. van den; Booth, E.D.; Watson, W.P.

    1998-01-01

    32P-postlabelling analysis for detecting DNA adducts formed by polycyclic aromatic compounds is one of the most widely used techniques for assessing genotoxicity associated with these compounds. In cases where the formation of adducts is extremely low, a crucial step in the analysis is an enrichment

  12. 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

  13. Reactivity insertion transient analysis for KUR low-enriched uranium silicide fuel core

    OpenAIRE

    Shen, Xiuzhong; Nakajima, Ken; Unesaki, Hironobu; Mishima, Kaichiro

    2013-01-01

    The purpose of this study is to realize the full core conversion from the use of High Enriched Uranium (HEU) fuels to the use of Low Enriched Uranium (LEU) fuels in Kyoto University Research Reactor (KUR). Although the conversion of nuclear energy sources is required to keep the safety margins and reactor reliability based on KUR HEU core, the uranium density (3.2 gU/cm3) and enrichment (20%) of LEU fuel (U3Si2–AL) are quite different from the uranium density (0.58 gU/cm3) and enrichment (93%...

  14. Integrative Analysis of Gene Expression Data Including an Assessment of Pathway Enrichment for Predicting Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Pingzhao Hu

    2006-01-01

    Full Text Available Background: Microarray technology has been previously used to identify genes that are differentially expressed between tumour and normal samples in a single study, as well as in syntheses involving multiple studies. When integrating results from several Affymetrix microarray datasets, previous studies summarized probeset-level data, which may potentially lead to a loss of information available at the probe-level. In this paper, we present an approach for integrating results across studies while taking probe-level data into account. Additionally, we follow a new direction in the analysis of microarray expression data, namely to focus on the variation of expression phenotypes in predefined gene sets, such as pathways. This targeted approach can be helpful for revealing information that is not easily visible from the changes in the individual genes. Results: We used a recently developed method to integrate Affymetrix expression data across studies. The idea is based on a probe-level based test statistic developed for testing for differentially expressed genes in individual studies. We incorporated this test statistic into a classic random-effects model for integrating data across studies. Subsequently, we used a gene set enrichment test to evaluate the significance of enriched biological pathways in the differentially expressed genes identified from the integrative analysis. We compared statistical and biological significance of the prognostic gene expression signatures and pathways identified in the probe-level model (PLM with those in the probeset-level model (PSLM. Our integrative analysis of Affymetrix microarray data from 110 prostate cancer samples obtained from three studies reveals thousands of genes significantly correlated with tumour cell differentiation. The bioinformatics analysis, mapping these genes to the publicly available KEGG database, reveals evidence that tumour cell differentiation is significantly associated with many

  15. 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.

  16. An evolution analysis of executive-based listed company relationships using complex networks

    Science.gov (United States)

    An, Feng; Gao, Xiangyun; Guan, Jianhe; Li, Huajiao; Liu, Qian

    2016-04-01

    This paper addresses the problem of relationship analysis of listed companies. It mainly focuses on the analysis of affiliation relationship network among listed companies based on the co-attendance behavior of senior executives. In order to solve this problem we propose a two-stage method. In stage 1, we propose a method of network construction which can change the two-mode affiliation network to one-mode network using model-descending process, and in stage 2, we analyze the networks from stage 1 in four aspects includes analysis of topological characteristic, influence distribution, information control ability distribution and small world phenomenon. We then took a case of Chinese listed companies' executive-based network as an example of the method and the results of the case study showed that the co-attendance behaviors of executives became more widespread (the number and percentage of related listed companies increased 624% and 322%) and that more companies preferred to relate to others on this level, improving the stability of the massive company structures.

  17. Gene set enrichment analysis and ingenuity pathway analysis of metastatic clear cell renal cell carcinoma cell line.

    Science.gov (United States)

    Khan, Mohammed I; Dębski, Konrad J; Dabrowski, Michał; Czarnecka, Anna M; Szczylik, Cezary

    2016-08-01

    In recent years, genome-wide RNA expression analysis has become a routine tool that offers a great opportunity to study and understand the key role of genes that contribute to carcinogenesis. Various microarray platforms and statistical approaches can be used to identify genes that might serve as prognostic biomarkers and be developed as antitumor therapies in the future. Metastatic renal cell carcinoma (mRCC) is a serious, life-threatening disease, and there are few treatment options for patients. In this study, we performed one-color microarray gene expression (4×44K) analysis of the mRCC cell line Caki-1 and the healthy kidney cell line ASE-5063. A total of 1,921 genes were differentially expressed in the Caki-1 cell line (1,023 upregulated and 898 downregulated). Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) approaches were used to analyze the differential-expression data. The objective of this research was to identify complex biological changes that occur during metastatic development using Caki-1 as a model mRCC cell line. Our data suggest that there are multiple deregulated pathways associated with metastatic clear cell renal cell carcinoma (mccRCC), including integrin-linked kinase (ILK) signaling, leukocyte extravasation signaling, IGF-I signaling, CXCR4 signaling, and phosphoinositol 3-kinase/AKT/mammalian target of rapamycin signaling. The IPA upstream analysis predicted top transcriptional regulators that are either activated or inhibited, such as estrogen receptors, TP53, KDM5B, SPDEF, and CDKN1A. The GSEA approach was used to further confirm enriched pathway data following IPA.

  18. Fuel handling accident analysis for the University of Missouri Research Reactor's High Enriched Uranium to Low Enriched Uranium fuel conversion initiative

    Science.gov (United States)

    Rickman, Benjamin

    In accordance with the 1986 amendment concerning licenses for research and test reactors, the MU Research Reactor (MURR) is planning to convert from using High-Enriched Uranium (HEU) fuel to the use of Low-Enriched Uranium (LEU) fuel. Since the approval of a new LEU fuel that could meet the MURR's performance demands, the next phase of action for the fuel conversion process is to create a new Safety Analysis Report (SAR) with respect to the LEU fuel. A component of the SAR includes the Maximum Hypothetical Accident (MHA) and accidents that qualify under the class of Fuel Handling Accidents (FHA). In this work, the dose to occupational staff at the MURR is calculated for the FHAs. The radionuclide inventory for the proposed LEU fuel was calculated using the ORIGEN2 point-depletion code linked to the MURR neutron spectrum. The MURR spectrum was generated from a Monte Carlo Neutron transPort (MCNP) simulation. The coupling of these codes create MONTEBURNS, a time-dependent burnup code. The release fraction from each FHA within this analysis was established by the methodology of the 2006 HEU SAR, which was accepted by the NRC. The actual dose methodology was not recorded in the HEU SAR, so a conservative path was chosen. In compliance to NUREG 1537, when new methodology is used in a HEU to LEU analysis, it is necessary to re-evaluate the HEU accident. The Total Effective Dose Equivalent (TEDE) values were calculated in addition to the whole body dose and thyroid dose to operation personnel. The LEU FHA occupational TEDE dose was 349 mrem which is under the NRC regulatory occupational dose limit of 5 rem TEDE, and under the LEU MHA limit of 403 mrem. The re-evaluated HEU FHA occupational TEDE dose was 235 mrem, which is above the HEU MHA TEDE dose of 132 mrem. Since the new methodology produces a dose that is larger than the HEU MHA, we can safely assume that it is more conservative than the previous, unspecified dose.

  19. Neighbor overlap is enriched in the yeast interaction network: analysis and implications.

    Directory of Open Access Journals (Sweden)

    Ariel Feiglin

    Full Text Available The yeast protein-protein interaction network has been shown to have distinct topological features such as a scale free degree distribution and a high level of clustering. Here we analyze an additional feature which is called Neighbor Overlap. This feature reflects the number of shared neighbors between a pair of proteins. We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient. Our analysis also reveals that pairs of proteins with high Neighbor Overlap have higher sequence similarity, more similar GO annotations and stronger genetic interactions than pairs with low ones. Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap. We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation.

  20. An enriched 1D finite element for the buckling analysis of sandwich beam-columns

    Science.gov (United States)

    Sad Saoud, Kahina; Le Grognec, Philippe

    2016-06-01

    Sandwich constructions have been widely used during the last few decades in various practical applications, especially thanks to the attractive compromise between a lightweight and high mechanical properties. Nevertheless, despite the advances achieved to date, buckling still remains a major failure mode for sandwich materials which often fatally leads to collapse. Recently, one of the authors derived closed-form analytical solutions for the buckling analysis of sandwich beam-columns under compression or pure bending. These solutions are based on a specific hybrid formulation where the faces are represented by Euler-Bernoulli beams and the core layer is described as a 2D continuous medium. When considering more complex loadings or non-trivial boundary conditions, closed-form solutions are no more available and one must resort to numerical models. Instead of using a 2D computationally expensive model, the present paper aims at developing an original enriched beam finite element. It is based on the previous analytical formulation, insofar as the skin layers are modeled by Timoshenko beams whereas the displacement fields in the core layer are described by means of hyperbolic functions, in accordance with the modal displacement fields obtained analytically. By using this 1D finite element, linearized buckling analyses are performed for various loading cases, whose results are confronted to either analytical or numerical reference solutions, for validation purposes.

  1. Measurements and analysis of critical assemblies for research reactors with mixed enrichments

    Energy Technology Data Exchange (ETDEWEB)

    Deen, J.R.; Snelgrove, J.L.; Hobbs, R.W.

    1982-01-01

    As part of the RERTR Program whole-core demonstration in the Ford Nuclear Reactor (FNR) at the University of Michigan, data have been obtained which will allow more extensive validation of neutronics methods for whole-core calculations of an equilibrium high-enriched-uranium (HEU) core and a fresh low-enriched-uranium (LEU) core. A series of experiments designed to provide the data needed for these validations has been performed in the Pool Critical Assembly (PCA) at the Oak Ridge National laboratory (ORNL). This paper reports the results of the measurements and of the subsequent validation calculations performed at ANL. Measurements were made on approximately 20 different critical configurations in the PCA during the period June 15 to 26, 1981. The normal PCA fuel elements contained high-enriched uranium (HEU, 93 wt% /sup 235/U) while the reduced-enrichment fuel elements, obtained for irradiation testing in the Oak Ridge Research Reactor (ORR) under the fuel demonstration activity of the RERTR Program, contained either medium-enriched uranium (MEU, 45 wt% /sup 235/U) or low-enriched uranium (LEU, 19.8 wt% /sup 235/U).

  2. A study on friability, hardness and fiber content analysis of fiber enriched milk tablet

    Science.gov (United States)

    Suzihaque, M. U. H.; Irfan, M. H.; Ibrahim, U. K.

    2017-06-01

    This study was performed to analyze the friability, hardness and fiber content of fiber enriched milk tablet derived from five different local fiber sources such as carrot, spinach, dragon fruit, mango and watermelon. Cow milk was mixed to complement with the tablet as a protein source. The powder were spray dried at 100°C, 120°C and 140°C and freeze dried at -60°C. The mixture of fruits and milk were made into equal ratio with the addition of 15 maltodextrin as a carrier. Tablets formed were used for friability and hardness test while dried powder were used for fiber content analysis. Dragon fruit tablet dried at 140°C have the highest friability with 11. 42 of weight loss. The second highest friability was spinach tablet dried at 100°C and 120°C drying temp erature with 9.30 and 9.28 respectively. The lowest friability was exhibited by carrot, mango and watermelon tablet at 100°C and dragon fruit at 120°C while carrot and spinach at 140°C. In contras t, none of the freeze dried tablets showed any weight loss hence they are not friable. For hardness test, all of the freeze dried showed to have higher tensile strength than spray dried, where carrot showed to be the highest at 2.27 Newton and the lowest were spray dried mango at 0.16 Newton. In fiber content analysis, freeze dried mango have the highest fiber content followed by freeze dried carrot and 140°C s pray dried carrot. It can be concluded that the higher the spray dry temperature, the more friable is the tablet. While, high friability leads to lower hardness of tablets. In terms of fiber content, the higher the spray dry temperature, the lower the fiber content found.

  3. Geographic analysis of Red List Rhododendron (Ericaceae) taxa by country of origin identifies priorities for ex situ conservation

    NARCIS (Netherlands)

    MacKay, M.B.; Gardiner, S.E.

    2017-01-01

    A Red List assessment is insufficient to determine priorities for ex situ conservation in large genera such as Rhododendron, where there may be hundreds of taxa in any one Red List category. We have utilised an analysis of the geographic origins of 1?215 taxa of Rhododendron (Ericaceae) as a method

  4. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2011-07-01

    Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

  5. Glycemic index and microstructure analysis of a newly developed fiber enriched cookie.

    Science.gov (United States)

    Schuchardt, Jan Philipp; Wonik, Jasmin; Bindrich, Ute; Heinemann, Michaela; Kohrs, Heike; Schneider, Inga; Möller, Katharina; Hahn, Andreas

    2016-01-01

    A diet with a high glycemic index (GI) is associated with an elevated risk for obesity or type 2 diabetes. We investigated the GI of a newly-developed fiber enriched cookie and characterized the microstructure of ingredients used. In a study with 26 non-diabetic healthy volunteers it was shown that the fiber enriched cookie has a GI of 58.9 in relation to white bread as reference. Using a conversion factor of 1.4, the GI of the fiber enriched cookie in relation to a glucose-solution is 42.0 and can be classified as a low-GI food. Postprandial insulin concentration was significantly lower after consumption of fiber enriched cookies compared to white bread. Glucose release after in vitro digestion was significantly lower from fiber enriched cookies compared to other cookies tested. In addition to its high percentage of fiber, the cookies' low GI can be attributed to the limited gelatinization potential of the starch granules found in the ingredients used. Using confocal laser scanning microscopy it is shown that starch granule surface area of whole grain barley flour, spelt flour and oat flakes bears cluster-shaped protein-NSPS complexes that preferentially absorb water in conditions of water shortage and thereby prevent starch gelatinization.

  6. Work-family enrichment, work-family conflict, and marital satisfaction: a dyadic analysis.

    Science.gov (United States)

    van Steenbergen, Elianne F; Kluwer, Esther S; Karney, Benjamin R

    2014-04-01

    This study was designed to examine whether spouses' work-to-family (WF) enrichment experiences account for their own and their partner's marital satisfaction, beyond the effects of WF conflict. Data were collected from both partners of 215 dual-earner couples with children. As hypothesized, structural equation modeling revealed that WF enrichment experiences accounted for variance in individuals' marital satisfaction, over and above WF conflict. In line with our predictions, this positive link between individuals' WF enrichment and their marital satisfaction was mediated by more positive marital behavior, and more positive perceptions of the partner's behavior. Furthermore, evidence for crossover was found. Husbands who experienced more WF enrichment were found to show more marital positivity (according to their wives), which related to increased marital satisfaction in their wives. No evidence of such a crossover effect from wives to husbands was found. The current findings not only highlight the added value of studying positive spillover and crossover effects of work into the marriage, but also suggest that positive spillover and crossover effects on marital satisfaction might be stronger than negative spillover and crossover are. These results imply that organizational initiatives of increasing job enrichment may make employees' marital life happier and can contribute to a happy, healthy, and high-performing workforce.

  7. Bacterial community analysis in chlorpyrifos enrichment cultures via DGGE and use of bacterial consortium for CP biodegradation.

    Science.gov (United States)

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2014-10-01

    The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6-7.4 mg L(-1) day(-1) of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L(-1) day(-1) of CP (100 mg L(-1)). Addition of glucose as an additional C source increased the degradation capacity by 8-14 %. After inoculation of contaminated soil with CP (200 mg kg(-1)) disappearance rates were 3.83-4.30 mg kg(-1) day(-1) for individual strains and 4.76 mg kg(-1) day(-1) for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  8. Designed synthesis of MOF-derived magnetic nanoporous carbon materials for selective enrichment of glycans for glycomics analysis.

    Science.gov (United States)

    Sun, Nianrong; Zhang, Xiangmin; Deng, Chunhui

    2015-04-21

    In this work, magnetic nanoporous carbon (NPC) materials were synthesized by choosing a MOF as a sacrificial template and a carbon precursor. The obtained Co-ZIF-67 materials showed strong magnetic response, high surface area, a uniform size of mesopores and high carbon content. The Co-ZIF-67 materials were successfully applied to glycomics analysis by enriching N-linked glycans in bio-samples with high selectivity and efficiency.

  9. Work-family enrichment, work-family conflict, and marital satisfaction: A dyadic analysis

    NARCIS (Netherlands)

    Steenbergen, E.F. van; Kluwer, E.S.; Karney, B.R.

    2014-01-01

    This study was designed to examine whether spouses' work-to-family (WF) enrichment experiences account for their own and their partner's marital satisfaction, beyond the effects of WF conflict. Data were collected from both partners of 215 dual-earner couples with children. As hypothesized, structur

  10. 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...

  11. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

    Science.gov (United States)

    2017-01-01

    We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL) mapping into genome-wide genetic association analysis of complex traits, with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic variants and the colocalizations of the two types of association signals. We introduce a natural Bayesian hierarchical model that treats the latent association status of molecular QTLs as SNP-level annotations for candidate SNPs of complex traits. We detail a computational procedure to seamlessly perform enrichment, fine-mapping and colocalization analyses, which is a distinct feature compared to the existing colocalization analysis procedures in the literature. The proposed approach is computationally efficient and requires only summary-level statistics. We evaluate and demonstrate the proposed computational approach through extensive simulation studies and analyses of blood lipid data and the whole blood eQTL data from the GTEx project. In addition, a useful utility from our proposed method enables the computation of expected colocalization signals using simple characteristics of the association data. Using this utility, we further illustrate the importance of enrichment analysis on the ability to discover colocalized signals and the potential limitations of currently available molecular QTL data. The software pipeline that implements the proposed computation procedures, enloc, is freely available at https://github.com/xqwen/integrative. PMID:28278150

  12. Behavioral analysis of Wistar rats fed with a flaxseed based diet added to an environmental enrichment.

    Science.gov (United States)

    Azevedo de Meneses, J; Junqueira Lopes, C A; Coca Velarde, L G; Teles Boaventura, G

    2011-01-01

    Flaxseed has a high content of n-3 fatty acids and its intake associated with an environmental enrichment may promote distinct behavioral results upon habituation and animal behavior. This work aimed to evaluating animal behavior under the use of these two tools in the Open Field Test. Thirty-six male Wistar rats were divided into 6 groups (n = 6): FEEG, receiving chow made up of flaxseed and kept in enriched environment; FSEG, receiving flaxseed based diet and kept in a standard environment; CEEG, receiving casein based diet and kept in enriched environment; CSEG, receiving casein based chow and kept in standard environment; MCEEG, receiving chow made up of casein but modified so as to provide the same content of fibers and lipids found in flaxseed diet and kept in enriched environment; MCSEG, receiving modified casein based diet and kept in standard environment. All animals were kept under controlled temperature, collective cages and dark/light cycle, receiving chow and water ad libitum, except for MCEEG and MCSEG, which were pair fed with FEEG and FSEG, respectively. Chow intake and animal body weight were evaluated twice in a week. Animals were maintained in these groups from the first until the second month of life, by the time when 3 day tests in Open Field Test began. Finishing the tests, animals were sacrificed and their brains were obtained in order to calculate the relative brain weight. Our results show an interplay between flaxseed and environmental enrichment in habituation to a new environment, making the animals more manageable and less stressed.

  13. Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping.

    Science.gov (United States)

    Smelter, Andrey; Rouchka, Eric C; Moseley, Hunter N B

    2017-08-16

    Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values. However, peak grouping is further complicated by multiple sources of variance in peak position limiting the effectiveness of grouping methods that utilize uniform match tolerances. In addition, no method currently exists for deriving peak positional variances from single peak lists for grouping peaks into spin systems, i.e. spin system grouping within a single peak list. Therefore, we developed a complementary pair of peak list registration analysis and spin system grouping algorithms designed to overcome these limitations. We have implemented these algorithms into an approach that can identify multiple dimension-specific positional variances that exist in a single peak list and group peaks from a single peak list into spin systems. The resulting software tools generate a variety of useful statistics on both a single peak list and pairwise peak list alignment, especially for quality assessment of peak list datasets. We used a range of low and high quality experimental solution NMR and solid-state NMR peak lists to assess performance of our registration analysis and grouping algorithms. Analyses show that an algorithm using a single iteration and uniform match tolerances approach is only able to recover from 50 to 80% of the spin systems due to the presence of multiple sources of variance. Our algorithm recovers additional spin systems by reevaluating match tolerances in multiple iterations. To facilitate evaluation of the

  14. Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; SukHa Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7%of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2%were involved in cellular components, 24.2%were involved molecular functions, and 64.6%were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in

  15. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-02-01

    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  16. Analysis of GEANT4 Physics List Properties in the 12 GeV MOLLER Simulation Framework

    Science.gov (United States)

    Haufe, Christopher; Moller Collaboration

    2013-10-01

    To determine the validity of new physics beyond the scope of the electroweak theory, nuclear physicists across the globe have been collaborating on future endeavors that will provide the precision needed to confirm these speculations. One of these is the MOLLER experiment - a low-energy particle experiment that will utilize the 12 GeV upgrade of Jefferson Lab's CEBAF accelerator. The motivation of this experiment is to measure the parity-violating asymmetry of scattered polarized electrons off unpolarized electrons in a liquid hydrogen target. This measurement would allow for a more precise determination of the electron's weak charge and weak mixing angle. While still in its planning stages, the MOLLER experiment requires a detailed simulation framework in order to determine how the project should be run in the future. The simulation framework for MOLLER, called ``remoll'', is written in GEANT4 code. As a result, the simulation can utilize a number of GEANT4 coded physics lists that provide the simulation with a number of particle interaction constraints based off of different particle physics models. By comparing these lists with one another using the data-analysis application ROOT, the most optimal physics list for the MOLLER simulation can be determined and implemented. This material is based upon work supported by the National Science Foundation under Grant No. 714001.

  17. 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...

  18. (30)Si mole fraction of a silicon material highly enriched in (28)Si determined by instrumental neutron activation analysis.

    Science.gov (United States)

    D'Agostino, Giancarlo; Di Luzio, Marco; Mana, Giovanni; Oddone, Massimo; Pramann, Axel; Prata, Michele

    2015-06-01

    The latest determination of the Avogadro constant, carried out by counting the atoms in a pure silicon crystal highly enriched in (28)Si, reached the target 2 × 10(-8) relative uncertainty required for the redefinition of the kilogram based on the Planck constant. The knowledge of the isotopic composition of the enriched silicon material is central; it is measured by isotope dilution mass spectrometry. In this work, an independent estimate of the (30)Si mole fraction was obtained by applying a relative measurement protocol based on Instrumental Neutron Activation Analysis. The amount of (30)Si isotope was determined by counting the 1266.1 keV γ-photons emitted during the radioactive decay of the radioisotope (31)Si produced via the neutron capture reaction (30)Si(n,γ)(31)Si. The x((30)Si) = 1.043(19) × 10(-6) mol mol(-1) is consistent with the value currently adopted by the International Avogadro Coordination.

  19. 30Si Mole Fraction of a Silicon Material Highly Enriched in 28Si Determined by Instrumental Neutron Activation Analysis

    CERN Document Server

    D'Agostino, Giancarlo; Mana, Giovanni; Oddone, Massimo; Pramann, Axel; Prata, Michele

    2016-01-01

    The latest determination of the Avogadro constant, carried out by counting the atoms in a pure silicon crystal highly enriched in 28Si, reached the target 2x10-8 relative uncertainty required for the redefinition of the kilogram based on the Planck constant. The knowledge of the isotopic composition of the enriched silicon material is central; it is measured by isotope dilution mass spectrometry. In this work, an independent estimate of the 30Si mole fraction was obtained by applying a relative measurement protocol based on Instrumental Neutron Activation Analysis. The amount of 30Si isotope was determined by counting the 1266.1 keV gamma-photons emitted during the radioactive decay of the radioisotope 31Si produced via the neutron capture reaction 30Si(n,gamma)31Si. The x(30Si) = 1.043(19)x10-6 mol mol-1 is consistent with the value currently adopted by the International Avogadro Coordination.

  20. Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants.

    Science.gov (United States)

    Duan, Jubao; Sanders, Alan R; Moy, Winton; Drigalenko, Eugene I; Brown, Eric C; Freda, Jessica; Leites, Catherine; Göring, Harald H H; Gejman, Pablo V

    2015-08-15

    We searched a gene expression dataset comprised of 634 schizophrenia (SZ) cases and 713 controls for expression outliers (i.e., extreme tails of the distribution of transcript expression values) with SZ cases overrepresented compared with controls. These outlier genes were enriched for brain expression and for genes known to be associated with neurodevelopmental disorders. SZ cases showed higher outlier burden (i.e., total outlier events per subject) than controls for genes within copy number variants (CNVs) associated with SZ or neurodevelopmental disorders. Outlier genes were enriched for CNVs and for rare putative regulatory variants, but this only explained a small proportion of the outlier subjects, highlighting the underlying presence of additional genetic and potentially, epigenetic mechanisms.

  1. Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis

    DEFF Research Database (Denmark)

    Liu, Shanlin; Wang, Xin; Xie, Lin

    2016-01-01

    . The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (>99%). Furthermore, the massive volume of sequence...... data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www.1kite.org). A mock sample containing 49 species was used...... to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by approximately 100-fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias...

  2. Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis.

    Directory of Open Access Journals (Sweden)

    Harriet T Parsons

    Full Text Available Our understanding of the contribution of Golgi proteins to cell wall and wood formation in any woody plant species is limited. Currently, little Golgi proteomics data exists for wood-forming tissues. In this study, we attempted to address this issue by generating and analyzing Golgi-enriched membrane preparations from developing xylem of compression wood from the conifer Pinus radiata. Developing xylem samples from 3-year-old pine trees were harvested for this purpose at a time of active growth and subjected to a combination of density centrifugation followed by free flow electrophoresis, a surface charge separation technique used in the enrichment of Golgi membranes. This combination of techniques was successful in achieving an approximately 200-fold increase in the activity of the Golgi marker galactan synthase and represents a significant improvement for proteomic analyses of the Golgi from conifers. A total of thirty known Golgi proteins were identified by mass spectrometry including glycosyltransferases from gene families involved in glucomannan and glucuronoxylan biosynthesis. The free flow electrophoresis fractions of enriched Golgi were highly abundant in structural proteins (actin and tubulin indicating a role for the cytoskeleton during compression wood formation. The mass spectrometry proteomics data associated with this study have been deposited to the ProteomeXchange with identifier PXD000557.

  3. Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

    Science.gov (United States)

    Tozaki, T; Inoue, S; Mashima, S; Ohta, M; Miura, N; Tomita, M

    2000-04-01

    Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

  4. Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome.

    Science.gov (United States)

    Tan, Haiyan; Wu, Zhiping; Wang, Hong; Bai, Bing; Li, Yuxin; Wang, Xusheng; Zhai, Bo; Beach, Thomas G; Peng, Junmin

    2015-01-01

    Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive loss of cognitive function. One of the pathological hallmarks of AD is the formation of neurofibrillary tangles composed of abnormally hyperphosphorylated tau protein, but global deregulation of protein phosphorylation in AD is not well analyzed. Here, we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution LC-MS/MS. During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a nonphosphopeptide competitor to reduce background. The procedure was further tuned with respect to peptide-to-bead ratio, phosphopeptide recovery, and purity. Using this refined method and 9 h LC-MS/MS, we analyzed phosphoproteome in one milligram of digested AD brain lysate, identifying 5243 phosphopeptides containing 3715 nonredundant phosphosites on 1455 proteins, including 31 phosphosites on the tau protein. This modified enrichment method is simple and highly efficient. The AD case study demonstrates its feasibility of dissecting phosphoproteome in a limited amount of postmortem human brain. All MS data have been deposited in the ProteomeXchange with identifier PXD001180 (http://proteomecentral.proteomexchange.org/dataset/PXD001180).

  5. Ethical Disputes and Credibility of Daily Newspapers-Content Analysis of Front Page Newspaper Articles in Jutarnji list and Večernji list

    Directory of Open Access Journals (Sweden)

    Dunja Majstorović

    2010-12-01

    Full Text Available Among the more common assertions regarding the media is the existence of a large number of ethical disputes in front page news articles in daily newspapers. Therefore, the main goal of this studyis to establish the number of ethical disputes in articles placed on the front pages of Croatia’s two main dailies, Jutarnji list and Večernji list (sample of one month. In the course of the research three hypotheses were made with the purpose of verifying their accuracy. Using content analysis as the primary method for analysis, the ethically disputable articles were divided into the following categories: anonymous sources, biased display of events, violations of human rights, inappropriate reporting, and headlines that fail to match the text. The same articles were then classifi ed into categories according to their topics. The results of this study confi rm all three hypotheses, the fi rst of which is that there are a large number of ethical disputes in the analyzed articles. In Jutarnji list 26 articles (of 95 analyzed articles contained 30 ethical disputes and in Večernji list 23 articles (of 108 analyzed contained 29 ethical disputes. Further, this study concludes that there is a distinct similarity in the number of ethical disputes in the articles in both newspapers. The results verify the third hypothesis; the largest number of ethically disputable articles centered on topics related to domestic politics. The results of the research indicate a violation of journalism ethics which can be explained by increasing sensationalism in daily newspapers. The result of inappropriate reporting has a significant impact on the decline of credibility of newspapers as a medium.

  6. CoPub: a literature-based keyword enrichment tool for microarray data analysis

    Science.gov (United States)

    Frijters, Raoul; Heupers, Bart; van Beek, Pieter; Bouwhuis, Maurice; van Schaik, René; de Vlieg, Jacob; Polman, Jan; Alkema, Wynand

    2008-01-01

    Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl. PMID:18442992

  7. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

    Directory of Open Access Journals (Sweden)

    Bendahmane Abdelhafid

    2011-05-01

    Full Text Available Abstract Background Melon (Cucumis melo, an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. Result We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs and 3,073 single nucleotide polymorphisms (SNPs in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but

  8. Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis

    Science.gov (United States)

    Markiewicz, P. J.; Thielemans, K.; Schott, J. M.; Atkinson, D.; Arridge, S. R.; Hutton, B. F.; Ourselin, S.

    2016-07-01

    In this technical note we propose a rapid and scalable software solution for the processing of PET list-mode data, which allows the efficient integration of list mode data processing into the workflow of image reconstruction and analysis. All processing is performed on the graphics processing unit (GPU), making use of streamed and concurrent kernel execution together with data transfers between disk and CPU memory as well as CPU and GPU memory. This approach leads to fast generation of multiple bootstrap realisations, and when combined with fast image reconstruction and analysis, it enables assessment of uncertainties of any image statistic and of any component of the image generation process (e.g. random correction, image processing) within reasonable time frames (e.g. within five minutes per realisation). This is of particular value when handling complex chains of image generation and processing. The software outputs the following: (1) estimate of expected random event data for noise reduction; (2) dynamic prompt and random sinograms of span-1 and span-11 and (3) variance estimates based on multiple bootstrap realisations of (1) and (2) assuming reasonable count levels for acceptable accuracy. In addition, the software produces statistics and visualisations for immediate quality control and crude motion detection, such as: (1) count rate curves; (2) centre of mass plots of the radiodistribution for motion detection; (3) video of dynamic projection views for fast visual list-mode skimming and inspection; (4) full normalisation factor sinograms. To demonstrate the software, we present an example of the above processing for fast uncertainty estimation of regional SUVR (standard uptake value ratio) calculation for a single PET scan of 18F-florbetapir using the Siemens Biograph mMR scanner.

  9. Enrichment and Analysis of Non-enzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron Transfer Dissociation Mass Spectrometry

    Science.gov (United States)

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W. C.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus. PMID:17488106

  10. Facile synthesis of titania nanoparticles coated carbon nanotubes for selective enrichment of phosphopeptides for mass spectrometry analysis.

    Science.gov (United States)

    Yan, Yinghua; Lu, Jin; Deng, Chunhui; Zhang, Xiangmin

    2013-03-30

    In this work, titania nanoparticles coated carbon nanotubes (denoted as CNTs/TiO2 composites) were synthesized through a facile but effective solvothermal reaction using titanium isopropoxide as the titania source, isopropyl alcohol as the solvent and as the basic catalyst in the presence of hydrophilic carbon nanotubes. Characterizations using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) indicate that the CNTs/TiO2 composites consist of CNT core and a rough outer layer formed by titania nanoparticles (5-10nm). Measurements using wide angle X-ray diffraction (WAXRD), zeta potential and N2 sorption reveal that the titania shell is formed by anatase titania nanoparticles, and the composites have a high specific surface area of about 104 m(2)/g. By using their high surface area and affinity to phosphopeptides, the CNTs/TiO2 composites were applied to selectively enrich phosphopeptides for mass spectrometry analysis. The high selectivity and capacity of the CNTs/TiO2 composites have been demonstrated by effective enrichment of phosphopeptides from digests of phosphoprotein, protein mixtures of β-casein and bovine serum albumin, human serum and rat brain samples. These results foresee a promising application of the novel CNTs/TiO2 composites in the selective enrichment of phosphopeptides.

  11. HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

    Science.gov (United States)

    Deng, Yue; Gao, Lin; Wang, Bingbo; Guo, Xingli

    2015-01-01

    Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO. HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).

  12. Photocatalytically patterned TiO2 arrays for on-plate selective enrichment of phosphopeptides and direct MALDI MS analysis.

    Science.gov (United States)

    Wang, Hui; Duan, Jicheng; Cheng, Quan

    2011-03-01

    We report the development of photocatalytically patterned TiO(2) arrays for selective on-plate enrichment and direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of phosphopeptides. A thin TiO(2) nanofilm with controlled porosity is prepared on gold-covered glass slides by a layer-by-layer (LbL) deposition/calcination process. The highly porous and rough nanostructure offers high surface area for selective binding of phosphorylated species. The patterned arrays are generated using an octadecyltrichlorosilane (OTS) coating in combination of UV irradiation with a photomask, followed by NaOH etching. The resulting hydrophilic TiO(2) spots are thus surrounded by a hydrophobic OTS layer, which can facilitate the enrichment of low-abundance components by confining a large volume sample into a small area. The TiO(2) arrays exhibit high specificity toward phosphopeptides in complex samples including phosphoprotein digests and human serum, and the detection can be made in the fmole range. Additional advantages of the arrays include excellent stability, reusability/reproducibility, and low cost. This method has been successfully applied to the analysis of phosphopeptides in nonfat milk. The patterned TiO(2) arrays provide an attractive interface for performing on-plate reactions, including selective capture of target species for MALDI-MS analysis, and can serve as a versatile lab-on-a-chip platform for high throughput analysis in phosphoproteome research.

  13. The list of strains and growth conditions - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ge list Name list of images Large image The zip file of the images (Large image) Small image The zip file of the...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us The... Rice Growth Monitoring for The Phenotypic Functional Analysis The list of strains and gr...owth conditions Data detail Data name The list of strains and growth conditions DOI 10.18908/lsdba.nbdc00945...-001 Description of data contents The list of strains and growth conditions for respective samples. Data fil

  14. Effect of Glutamine Enriched Nutrition Support on Surgical Patients with Gastrointestinal Tumor: A Meta-Analysis of Randomized Controlled Trials

    Institute of Scientific and Technical Information of China (English)

    Kai Kang; Xiao-Liang Shu; Yong-Sheng Zhang; Xian-Li Liu; Jian Zhao

    2015-01-01

    Background:Associations between glutamine (Gln) enriched nutrition support and surgical patients with gastrointestinal (GI) tumor remain controversy.The purpose of this meta-analysis was to assess the effect of Gln enriched nutrition support on surgical patients with GI tumor in term of relevant biochemical indices,immune indices,and clinical outcomes.Methods:Six databases were systematically searched to find eligible randomized controlled trials (RCTs) from 1966 to May 2014.When estimated the analysis indexes,the relative risk (RR) was used as the effect size of the categorical variable,while the weighted mean difference (MD) was used as the effect size of a continuous variable.Meta-analysis was conducted with Rev Man 5.2.Results:Thirteen RCTs,involving 1034 patients,were included in the meta-analysis.The analysis showed that Gln enriched nutrition support was more effective in increasing serum albumin (MD:0.10; 95% confidence interval [CI]:0.02-0.18; P < 0.05),serum prealbumin (MD:1.98; 95% CI:1.40-2.55; P < 0.05) and serum transferring (MD:0.35; 95% CI:0.12-0.57; P < 0.05),concentration of IgG (MD:1.26; 95% CI:0.90-1.63; P < 0.05),IgM (MD:0.18; 95% CI:0.11-0.25; P < 0.05),IgA (MD:0.22; 95% CI:0.10-0.33; P < 0.05),CD3+ (MD:3.71; 95% CI:2.57-4.85; P < 0.05) and CD4/CD8 ratio (MD:0.27; 95% CI:0.12-0.42; P < 0.05).Meanwhile,it was more significant in decreasing the incidence of infectious complications (RR:0.67; 95% CI:0.50-0.90; P < 0.05) and shortening the length of hospital stay (MD:-1.72; 95% CI:-3.31--0.13; P < 0.05).Conclusions:Glutamine enriched nutrition support was superior in improving immune function,reducing the incidence of infectious complications and shortening the length of hospital stay,playing an important role in the rehabilitation of surgical GI cancer patients.

  15. Information Spillover, Profit Opportunities, and Return Deviations Analysis: The Case of Cross-Listed BHP Billiton

    National Research Council Canada - National Science Library

    Roger Su; Ronghua Yi; Keith Hooper; Amitabh Dutta

    2013-01-01

      This paper examines (1) whether a cross-listed company spillover effect starts from an earlier time zone market to a later time zone market, whether investors can find profit opportunities from cross-listed share trading, and (2...

  16. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    Science.gov (United States)

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-05-18

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy.

  17. Gogadget: An R Package for Interpretation and Visualization of GO Enrichment Results.

    Science.gov (United States)

    Nota, Benjamin

    2017-05-01

    Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO terms might be desirable. The R package gogadget provides functions to modify GO analysis results, with a simple filter strategy. Furthermore, it groups redundant GO terms with hierarchical clustering and presents the results in a colorful heatmap. The filtered GO term enrichment results can also be exported by the package for subsequent analysis in Cytoscape Enrichment Map. The R package is freely available under the terms of the GNU GPLv3 at https://sourceforge.net/projects/gogadget/. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Uranium enrichment using laser and plasma separation - an analysis focussing on export control; Urananrikning med laser och plasmaseparation - en analys med fokus paa exportkontroll

    Energy Technology Data Exchange (ETDEWEB)

    Oliver, Lena; Wilhelmsen, Katarina; Wirstam, Jens (Swedish Defence Research Agency, FOI, Stockholm (SE))

    2007-07-01

    The Swedish Defence Research Agency, FOI, has under contract work financed by the Swedish Nuclear Power Inspectorate, SKI, performed a study on uranium enrichment by laser-based processes and plasma separation. None of these processes are at present used on an industrial scale for uranium enrichment. However, these are processes of high efficiency which implicates that plants employing any of these processes for production of fissile material for nuclear weapons can be small in size and easily hidden. This has also been the case for laser enrichment. Special emphasis has been put on the understanding of the governing physical principles of the different processes. In the report the AVLIS and MLIS processes are described in some detail while CRISLA and SILEX are treated in less detail. The plasma separation process is described in a separate section. Limiting physical parameters for the different processes are discussed and equipment relevant to the different technologies is described. Further, some indicators of the different processes are identified and listed. In the final chapter known research programs where these processes have been used are listed. Since none of the described technologies has been used on an industrial scale, information on plant design and running is scarce

  19. Learning by listing: A content analysis of students' perceptions of older adults and grandparents.

    Science.gov (United States)

    Hoogland, Aasha I; Hoogland, Charles E

    2016-02-23

    Views of specific older adults may differ substantially from views of older adults in general, and such views may influence preconceived notions of aging that students bring into the classroom. Using an in-class activity, the authors tested the hypothesis that grandparents, about whom we know more individuated information, would be characterized by different, and more positive, descriptors than older adults. Following verbal prompts, undergraduates (N = 98) listed terms describing older adults and grandparents. Conventional and directed content analysis with a multistage coding scheme was employed. Results revealed that descriptors were primarily negative (e.g., sick) and emphasized physical characteristics (e.g., wrinkly) for older adults but were more positive (e.g., sweet) and highlighted personality characteristics (e.g., kind) for grandparents. Although mentioned less often for grandparents, health-related and physical characteristics were predominantly negative for both groups. This word-listing exercise highlighted heterogeneity in views of older adults and underscored the value of studying gerontology.

  20. Starch and protein analysis of wheat bread enriched with phenolics-rich sprouted wheat flour.

    Science.gov (United States)

    Świeca, Michał; Dziki, Dariusz; Gawlik-Dziki, Urszula

    2017-08-01

    Wheat flour in the bread formula was replaced with sprouted wheat flour (SF) characterized by enhanced nutraceutical properties, at 5%, 10%, 15% and 20% levels. The addition of SF slightly increased the total protein content; however, it decreased their digestibility. Some qualitative and quantitative changes in the electrophoretic pattern of proteins were also observed; especially, in the bands corresponding with 27kDa and 15-17kDa proteins. These results were also confirmed by SE-HPLC technique, where a significant increase in the content of proteins and peptides (molecular masses breads with 20% of SF. Bread enriched with sprouted wheat flour had more resistant starch, but less total starch, compared to control bread. The highest in vitro starch digestibility was determined for the control bread. The studied bread with lowered nutritional value but increased nutritional quality can be used for special groups of consumers (obese, diabetic). Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. 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.

  2. An analysis of strategic performance measures of companies listed on the JSE securities exchange South Africa

    Directory of Open Access Journals (Sweden)

    JHvH de Wet

    2014-07-01

    Full Text Available This study highlights the importance of economic profits (EVA and their long-term effects on shareholder value (MVA. South African companies listed on the JSE were analysed and it is evident that the relative measure of internal performance (spreads can be used to rank companies in terms of value creation. Individual companies and sectors were also placed on a financial strategy matrix, which evaluated companies according to spreads and cash management. The sales growth less the SGR percentage, was used to indicate cash management. Statistical tests (regression analysis were done on the data to test the validity of the financial strategy matrix model. The results showed that there is a positive relationship between spreads and shareholder value, but sales growth less the sustainable growth rate does not contribute significantly to shareholder value.

  3. Serum cytokine profiling and enrichment analysis reveal the involvement of immunological and inflammatory pathways in stable patients with chronic obstructive pulmonary disease

    Directory of Open Access Journals (Sweden)

    Bade G

    2014-08-01

    Full Text Available Geetanjali Bade,1 Meraj Alam Khan,2 Akhilesh Kumar Srivastava,1 Parul Khare,1 Krishna Kumar Solaiappan,1 Randeep Guleria,3 Nades Palaniyar,2 Anjana Talwar1 1Department of Physiology, All India Institute of Medical Sciences, New Delhi, India; 2Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Department of Laboratory Medicine and Pathobiology, and Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; 3Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India Abstract: Chronic obstructive pulmonary disease (COPD is a major global health problem. It results from chronic inflammation and causes irreversible airway damage. Levels of different serum cytokines could be surrogate biomarkers for inflammation and lung function in COPD. We aimed to determine the serum levels of different biomarkers in COPD patients, the association between cytokine levels and various prognostic parameters, and the key pathways/networks involved in stable COPD. In this study, serum levels of 48 cytokines were examined by multiplex assays in 30 subjects (control, n=9; COPD, n=21. Relationships between serum biomarkers and forced expiratory volume in 1 second, peak oxygen uptake, body mass index, dyspnea score, and smoking were assessed. Enrichment pathways and networks analyses were implemented, using a list of cytokines showing differential expression between healthy controls and patients with COPD by Cytoscape and GeneGo Metacore™ softwares (Thomson-Reuters Corporation, New York, NY, USA. Concentrations of cutaneous T-cell attracting chemokine, eotaxin, hepatocyte growth factor, interleukin 6 (IL-6, IL-16, and stem cell factor are significantly higher in COPD patients compared with in control patients. Notably, this study identifies stem cell factor as a biomarker for COPD. Multiple regression analysis predicts that cutaneous T

  4. Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi.

    Directory of Open Access Journals (Sweden)

    Khajamohiddin Syed

    Full Text Available Genome sequencing of basidiomycetes, a group of fungi capable of degrading/mineralizing plant material, revealed the presence of numerous cytochrome P450 monooxygenases (P450s in their genomes, with some exceptions. Considering the large repertoire of P450s found in fungi, it is difficult to identify P450s that play an important role in fungal metabolism and the adaptation of fungi to diverse ecological niches. In this study, we followed Sir Charles Darwin's theory of natural selection to identify such P450s in model basidiomycete fungi showing a preference for different types of plant components degradation. Any P450 family comprising a large number of member P450s compared to other P450 families indicates its natural selection over other P450 families by its important role in fungal physiology. Genome-wide comparative P450 analysis in the basidiomycete species, Phanerochaete chrysosporium, Phanerochaete carnosa, Agaricus bisporus, Postia placenta, Ganoderma sp. and Serpula lacrymans, revealed enrichment of 11 P450 families (out of 68 P450 families, CYP63, CYP512, CYP5035, CYP5037, CYP5136, CYP5141, CYP5144, CYP5146, CYP5150, CYP5348 and CYP5359. Phylogenetic analysis of the P450 family showed species-specific alignment of P450s across the P450 families with the exception of P450s of Phanerochaete chrysosporium and Phanerochaete carnosa, suggesting paralogous evolution of P450s in model basidiomycetes. P450 gene-structure analysis revealed high conservation in the size of exons and the location of introns. P450s with the same gene structure were found tandemly arranged in the genomes of selected fungi. This clearly suggests that extensive gene duplications, particularly tandem gene duplications, led to the enrichment of selective P450 families in basidiomycetes. Functional analysis and gene expression profiling data suggest that members of the P450 families are catalytically versatile and possibly involved in fungal colonization of plant

  5. Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue.

    Science.gov (United States)

    Fragnoud, Romain; Flamand, Marie; Reynier, Frederic; Buchy, Philippe; Duong, Vasna; Pachot, Alexandre; Paranhos-Baccala, Glaucia; Bedin, Frederic

    2015-11-14

    Dengue is the most widespread mosquito-borne viral disease of public health concern. In some patients, endothelial cell and platelet dysfunction lead to life-threatening hemorrhagic dengue fever or dengue shock syndrome. Prognostication of disease severity is urgently required to improve patient management. The pathogenesis of severe dengue has not been fully elucidated, and the role of host proteins associated with viral particles has received little exploration. The proteomes of virion-enriched fractions purified from plasma pools of patients with dengue fever or severe dengue were compared. Virions were purified by ultracentrifugation combined with a water-insoluble polyelectrolyte-based technique. Following in-gel hydrolysis, peptides were analyzed by nano-liquid chromatography coupled to ion trap mass spectrometry and identified using data libraries. Both dengue fever and severe dengue viral-enriched fractions contained identifiable viral envelope proteins and host cellular proteins. Canonical pathway analysis revealed the identified host proteins are mainly involved in the coagulation cascade, complement pathway or acute phase response signaling pathway. Some host proteins were over- or under-represented in plasma from patients with severe dengue compared to patients with dengue fever. ELISAs were used to validate differential expression of a selection of identified host proteins in individual plasma samples of patients with dengue fever compared to patients with severe dengue. Among 22 host proteins tested, two could differentiate between dengue fever and severe dengue in two independent cohorts (olfactomedin-4: area under the curve (AUC), 0.958; and platelet factor-4: AUC, 0.836). A novel technique of virion-enrichment from plasma has allowed to identify two host proteins that have prognostic value for classifying patients with acute dengue who are more likely to develop a severe dengue. The impact of these host proteins on pathogenicity and disease outcome

  6. 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...

  7. Enrichment of PrPSc in formalin-fixed, paraffin-embedded tissues prior to analysis by Western blot.

    Science.gov (United States)

    Nicholson, Eric M

    2011-07-01

    Diagnosis of prion disease is primarily through immunodetection of the infectious agent. Typically, 2 distinct procedures are recommended for a definitive diagnosis, with immunohistochemistry and Western blot providing the most information as to the specific isolate in question. In the past, these approaches required formalin-fixed, paraffin-embedded tissue and fresh or frozen tissue, respectively; however, methods have been developed that allow for use of fixed tissue for Western blot. The present study describes a method of enriching PrP(Sc) in formalin-fixed, paraffin-embedded tissues prior to Western blot analysis for the detection of PrP(Sc). With this modified procedure, 5 times the previously reported sample size may be used for analysis, greatly enhancing the sensitivity of this procedure.

  8. Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells.

    Science.gov (United States)

    Man, Petr; Novák, Petr; Cebecauer, Marek; Horváth, Ondrej; Fiserová, Anna; Havlícek, Vladimír; Bezouska, Karel

    2005-01-01

    Glycosphingolipid-enriched microdomains (GEM) are membrane entities that concentrate glycosylphosphatiolylinositol(GPI)-anchored, acylated and membrane proteins important for immune receptor signaling. Using rat leukemic cell line RNK-16 we have initiated proteomic studies of microdomains in natural killer (NK) cells. Isolated plasma membranes were treated with Brij 58, or Nonidet-P40, or sodium carbonate. Extracts were separated by sucrose density gradient centrifugation into very light membrane, medium light membrane and heavy fractions, and a complete protein profile was analyzed by tandem mass spectrometry. Up to 250 proteins were unambiguously identified in each analyzed fraction. The first study of the proteome of NK cell GEM revealed several new aspects including identification of molecules not expected to be expressed in rat NK cells (e.g., NAP-22) or associated with GEM (e.g., NKR-P1, CD45, CD2). Moreover, it provided clear data consolidating controversial views concerning the occurrence of major histcompatibility complex glycoproteins and RT6.1/CD73/CD38 complex in NK cells. Our results also identified a large number of receptors as candidates for future functional studies.

  9. Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis.

    Science.gov (United States)

    De, Arpita; Sparreboom, Wouter; van den Berg, Albert; Carlen, Edwin T

    2014-09-01

    Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (μSPE) system for the capture and elution of low concentrations of hm-DNA (≤1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 μl elution volume and 92% efficiency using a 100 μl elution volume.

  10. 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

  11. LA-ICP-MS analysis of isolated phosphatic grains indicates selective rare earth element enrichment during reworking and transport processes

    Science.gov (United States)

    Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

    2016-04-01

    water chemistry under certain well constrained circumstances of primary authigenesis. Are these conditions not met, REE patterns are more likely to reflect complex enrichment processes that likely already started to occur during reworking over geologically relatively short time frames. Similarities in the REE patterns of clearly detrital and biogenic phosphate further suggest that the often observed 'hat-shaped' pattern in biogenic phosphates can easily result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Finally, cluster analysis coupled with sedimentological considerations proved a valuable tool for the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

  12. Dopamine Transporter Neuroimaging as an Enrichment Biomarker in Early Parkinson's Disease Clinical Trials: A Disease Progression Modeling Analysis.

    Science.gov (United States)

    Conrado, Daniela J; Nicholas, Timothy; Tsai, Kuenhi; Macha, Sreeraj; Sinha, Vikram; Stone, Julie; Corrigan, Brian; Bani, Massimo; Muglia, Pierandrea; Watson, Ian A; Kern, Volker D; Sheveleva, Elena; Marek, Kenneth; Stephenson, Diane T; Romero, Klaus

    2017-07-27

    Given the recognition that disease-modifying therapies should focus on earlier Parkinson's disease stages, trial enrollment based purely on clinical criteria poses significant challenges. The goal herein was to determine the utility of dopamine transporter neuroimaging as an enrichment biomarker in early motor Parkinson's disease clinical trials. Patient-level longitudinal data of 672 subjects with early-stage Parkinson's disease in the Parkinson's Progression Markers Initiative (PPMI) observational study and the Parkinson Research Examination of CEP-1347 Trial (PRECEPT) clinical trial were utilized in a linear mixed-effects model analysis. The rate of worsening in the motor scores between subjects with or without a scan without evidence of dopamine transporter deficit was different both statistically and clinically. The average difference in the change from baseline of motor scores at 24 months between biomarker statuses was -3.16 (90% confidence interval [CI] = -0.96 to -5.42) points. Dopamine transporter imaging could identify subjects with a steeper worsening of the motor scores, allowing trial enrichment and 24% reduction of sample size. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Clinical and Translational Science published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  13. The Protection of Children’s Privacy in Večernji List and Jutarnji List 2010-2013: A Comparative Analysis

    Directory of Open Access Journals (Sweden)

    Lana Ciboci

    2014-06-01

    Full Text Available According to research conducted in 2010 and 2011 (Ciboci et. al., 2011; Vlainić, 2012 children's rights are often violated in Croatian daily newspapers. Since then, the public worked hard on the promotion and protection of children's rights, particularly in the media. The legal protection of children's privacy in the media was increased, as well. The aim of this study is to determine whether the policy of reporting on children in the two most read Croatian daily newspapers - Večernji list and Jutarnji list - has changed, in relation to the first survey conducted in 2010. This paper uses quantitative content analysis in order to determine whether daily newspapers violate children's rights less often and protect their identity in those cases where it is necessary to protect the child's well-being, We analyze all of the articles about children that were published in each edition of the two newspapers, from January 1, 2013 to June 30, 2013, 636 newspaper articles in total. The study found that the newspapers violated the rights of children in the text of the articles more often in 2010 than in 2013. The identity of children in the photographs was revealed equally in 2013 as in 2010. However, in comparison to 2010 in 2013 was recorded more frequent disclosure of the identity of children's parents in the photographs.

  14. Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer.

    Science.gov (United States)

    Fang, Xiaocong; Netzer, Michael; Baumgartner, Christian; Bai, Chunxue; Wang, Xiangdong

    2013-02-01

    Cigarette smoking is the most demonstrated risk factor for the development of lung cancer, while the related genetic mechanisms are still unclear. The preprocessed microarray expression dataset was downloaded from Gene Expression Omnibus database. Samples were classified according to the disease state, stage and smoking state. A new computational strategy was applied for the identification and biological interpretation of new candidate genes in lung cancer and smoking by coupling a network-based approach with gene set enrichment analysis. Network analysis was performed by pair-wise comparison according to the disease states (tumor or normal), smoking states (current smokers or nonsmokers or former smokers), or the disease stage (stages I-IV). The most activated metabolic pathways were identified by gene set enrichment analysis. Panels of top ranked gene candidates in smoking or cancer development were identified, including genes involved in cell proliferation and drug metabolism like cytochrome P450 and WW domain containing transcription regulator 1. Semaphorin 5A and protein phosphatase 1F are the common genes represented as major hubs in both the smoking and cancer related network. Six pathways, e.g. cell cycle, DNA replication, RNA transport, protein processing in endoplasmic reticulum, vascular smooth muscle contraction and endocytosis were commonly involved in smoking and lung cancer when comparing the top ten selected pathways. New approach of bioinformatics for biomarker identification and validation can probe into deep genetic relationships between cigarette smoking and lung cancer. Our studies indicate that disease-specific network biomarkers, interaction between genes/proteins, or cross-talking of pathways provide more specific values for the development of precision therapies for lung. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.

    Science.gov (United States)

    Chen, Lei; Zhang, Yu-Hang; Wang, ShaoPeng; Zhang, YunHua; Huang, Tao; Cai, Yu-Dong

    2017-01-01

    Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.

  16. 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

  17. Heating Two Types of Enriched Margarine: Complementary Analysis of Phytosteryl/Phytostanyl Fatty Acid Esters and Phytosterol/Phytostanol Oxidation Products.

    Science.gov (United States)

    Scholz, Birgit; Menzel, Nicole; Lander, Vera; Engel, Karl-Heinz

    2016-04-06

    Two phytosteryl and/or phytostanyl fatty acid ester-enriched margarines were subjected to common heating procedures. UHPLC-APCI-MS analysis resulted for the first time in comprehensive quantitative data on the decreases of individual phytosteryl/-stanyl fatty acid esters upon heating of enriched foods. These data were complemented by determining the concurrently formed phytosterol/-stanol oxidation products (POPs) via online LC-GC. Microwave-heating led to the least decreases of esters of approximately 5% in both margarines. Oven-heating of the margarine in a casserole caused the greatest decreases, with 68 and 86% esters remaining, respectively; the impact on individual esters was more pronounced with increasing degree of unsaturation of the esterified fatty acids. In the phytosteryl/-stanyl ester-enriched margarine, approximately 20% of the ester losses could be explained by the formation of POPs; in the phytostanyl ester-enriched margarine, the POPs accounted for <1% of the observed ester decreases.

  18. 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.

  19. On-plate selective enrichment and self-desalting of peptides/proteins for direct MALDI MS analysis.

    Science.gov (United States)

    Zeng, Zhoufang; Wang, Yandong; Shi, Shoulei; Wang, Lifeng; Guo, Xinhua; Lu, Nan

    2012-03-06

    In this paper, a new technique has been proposed to achieve simultaneous peptides/proteins enrichment and wash-free self-desalting on a novel sample support with a circle hydrophobic-hydrophilic-hydrophobic pattern. Upon deposition, the sample solution is first concentrated in a small area by repulsion of the hydrophobic outer layer, and then, the peptides/proteins and coexisting salt contaminants are selectively captured in different regions of the pattern through strong hydrophobic and hydrophilic attractions, respectively. As a result, the detection sensitivity is improved by 2 orders of magnitude better than the use of the traditional MALDI plate, and high-quality mass spectra are obtained even in the presence of NaCl (1 M), NH(4)HCO(3) (100 mM), or urea (1 M). The practical application of this method is further demonstrated by the successful analysis of myoglobin digests with high sequence coverage, demonstrating the great potential in proteomic research.

  20. MPS analysis of the mtDNA hypervariable regions on the MiSeq with improved enrichment.

    Science.gov (United States)

    Holland, Mitchell M; Wilson, Laura A; Copeland, Sarah; Dimick, Gloria; Holland, Charity A; Bever, Robert; McElhoe, Jennifer A

    2017-07-01

    The non-coding displacement (D) loop of the human mitochondrial (mt) genome contains two hypervariable regions known as HVR1 and HVR2 that are most often analyzed by forensic DNA laboratories. The massively parallel sequencing (MPS) protocol from Illumina (Human mtDNA D-Loop Hypervariable Region protocol) utilizes four sets of established PCR primer pairs for the initial amplification (enrichment) step that span the hypervariable regions. Transposase adapted (TA) sequences are attached to the 5'-end of each primer, allowing for effective library preparation prior to analysis on the MiSeq, and AmpliTaq Gold DNA polymerase is the enzyme recommended for amplification. The amplification conditions were modified by replacing AmpliTaq Gold with TaKaRa Ex Taq® HS, along with an enhanced PCR buffer system. The resulting method was compared to the recommended protocol and to a conventional non-MPS approach used in an operating forensic DNA laboratory. The modified amplification conditions gave equivalent or improved results, including when amplifying low amounts of DNA template from hair shafts which are a routine evidence type in forensic mtDNA cases. Amplification products were successfully sequenced using an MPS approach, addressing sensitivity of library preparation, evaluation of precision and accuracy through repeatability and reproducibility, and mixture studies. These findings provide forensic laboratories with a robust and improved enrichment method as they begin to implement the D-loop protocol from Illumina. Given that Ex Taq® HS is a proofreading enzyme, using this approach should allow for improved analysis of low-level mtDNA heteroplasmy.

  1. Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets

    OpenAIRE

    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 techn...

  2. High information throughput analysis of nucleotides and their isotopically enriched isotopologues by direct-infusion FTICR-MS.

    Science.gov (United States)

    Lorkiewicz, Pawel; Higashi, Richard M; Lane, Andrew N; Fan, Teresa W-M

    2012-01-01

    Fourier transform-ion cyclotron resonance-mass spectrometry (FTICR-MS) is capable of acquiring unmatched quality of isotopologue data for stable isotope resolved metabolomics (SIRM). This capability drives the need for a continuous ion introduction for obtaining optimal isotope ratios. Here we report the simultaneous analysis of mono and dinucleotides from crude polar extracts by FTICR-MS by adapting an ion-pairing sample preparation method for LC-MS analysis. This involves a rapid cleanup of extracted nucleotides on pipet tips containing a C(18) stationary phase, which enabled global analysis of nucleotides and their (13)C isotopologues at nanomolar concentrations by direct infusion nanoelectrospray FTICR-MS with 5 minutes of data acquisition. The resolution and mass accuracy enabled computer-assisted unambiguous assignment of most nucleotide species, including all phosphorylated forms of the adenine, guanine, uracil and cytosine nucleotides, NAD(+), NADH, NADP(+), NADPH, cyclic nucleotides, several UDP-hexoses, and all their (13)C isotopologues. The method was applied to a SIRM study on human lung adenocarcinoma A549 cells grown in [U-(13)C] glucose with or without the anti-cancer agent methylseleninic acid. At m/z resolving power of 400,000, (13)C-isotopologues of nucleotides were fully resolved from all other elemental isotopologues, thus allowing their (13)C fractional enrichment to be accurately determined. The method achieves both high sample and high information throughput analysis of nucleotides for metabolic pathway reconstruction in SIRM investigations.

  3. rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs.

    Science.gov (United States)

    Hundt, Christian; Hildebrandt, Andreas; Schmidt, Bertil

    2016-09-23

    Gene Set Enrichment Analysis (GSEA) is a popular method to reveal significant dependencies between predefined sets of gene symbols and observed phenotypes by evaluating the deviation of gene expression values between cases and controls. An established measure of inter-class deviation, the enrichment score, is usually computed using a weighted running sum statistic over the whole set of gene symbols. Due to the lack of analytic expressions the significance of enrichment scores is determined using a non-parametric estimation of their null distribution by permuting the phenotype labels of the probed patients. Accordingly, GSEA is a time-consuming task due to the large number of required permutations to accurately estimate the nominal p-value - a circumstance that is even more pronounced during multiple hypothesis testing since its estimate is lower-bounded by the inverse number of samples in permutation space. We present rapidGSEA - a software suite consisting of two tools for facilitating permutation-based GSEA: cudaGSEA and ompGSEA. cudaGSEA is a CUDA-accelerated tool using fine-grained parallelization schemes on massively parallel architectures while ompGSEA is a coarse-grained multi-threaded tool for multi-core CPUs. Nominal p-value estimation of 4,725 gene sets on a data set consisting of 20,639 unique gene symbols and 200 patients (183 cases + 17 controls) each probing one million permutations takes 19 hours on a Xeon CPU and less than one hour on a GeForce Titan X GPU while the established GSEA tool from the Broad Institute (broadGSEA) takes roughly 13 days. cudaGSEA outperforms broadGSEA by around two orders-of-magnitude on a single Tesla K40c or GeForce Titan X GPU. ompGSEA provides around one order-of-magnitude speedup to broadGSEA on a standard Xeon CPU. The rapidGSEA suite is open-source software and can be downloaded at https://github.com/gravitino/cudaGSEA as standalone application or package for the R framework.

  4. The list of growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us The... Rice Growth Monitoring for The Phenotypic Functional Analysis The list of growth image f...iles Data detail Data name The list of growth image files DOI 10.18908/lsdba.nbdc00945-002 Description of data contents The...ies 7 entries - About This Database Database Description Download License Update History of This Database Si...te Policy | Contact Us The list of growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  5. Conceptual design and economic analysis of a light water reactor fuel enricher/regenerator. FY 1978 year-end report

    Energy Technology Data Exchange (ETDEWEB)

    Grand, P; Kouts, H J; Powell, J R; Steinberg, M; Takahashi, H

    1979-05-01

    A study has been performed to evaluate the use of high-energy particle accelerators as nuclear fuel enrichers and nuclear fuel regenerators. This builds on ideas that have been current for many years. The new study has, however, explored some novel approaches that have not been examined before. A specific conceptual system chosen for more detailed study would stretch the energy available from natural uranium by a factor of about 3, reduce the separative work requirements by a factor of about 4, and reduce the volume of spent fuel to be stored by a factor of 2, compared to the current once-through light water reactor (LWR) fuel cycle. The concept avoids the need for chemical reprocessing of spent fuel, and would permit continued use of LWR's beyond the time when limitations on fuel resources might otherwise lead to their being phased out. This concept, which is called the Linear Accelerator Fuel Enricher/Regenerator, is therefore viewed as offering a practical means of stretching the use of the nuclear fuel resource in the framework of the existing light water reactor fuel cycle. This report describes and analyzes the concept referred to. An explanation of the principles underlying the concept is given. Particular attention is devoted to engineering feasibility, proliferation resistance, and economics. It is seen that the concept draws on only proven technology as regards bothaccelerator design and the fuel irradiation process, and is adapted to existing LWR designs with no change except in fuel-handling practices. A preliminary evaluation of radiation damage, coolant options, and power conversion systems is provided. Neutronic, thermal-hydraulic, and burnup calculations are presented. An analysis is made of fuel economy. Approximate costs of electric power produced using this concept are evaluated and discussed. Estimated development costs of commercialization are provided.

  6. A preliminary analysis of library holdings as compared to the basic resources for pharmacy education list.

    Science.gov (United States)

    Vaughan, K T L V; Lerner, Rachel C

    2013-01-01

    The catalogs of 11 university libraries were analyzed against the Basic Resources for Pharmaceutical Education (BRPE) to measure the percent coverage of the core total list as well as the core sublist. There is no clear trend in this data to link school age, size, or rank with percentage of coverage of the total list or the "First Purchase" core list when treated as independent variables. Approximately half of the schools have significantly higher percentages of core titles than statistically expected. Based on this data, it is difficult to predict what percentage of titles on the BRPE a library will contain.

  7. Investigation of the fire at the Uranium Enrichment Laboratory. Analysis of samples and pressurization experiment/analysis of container

    Energy Technology Data Exchange (ETDEWEB)

    Akabori, Mitsuo; Minato, Kazuo; Watanabe, Kazuo [eds.] [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-05-01

    To investigate the cause of the fire at the Uranium Enrichment Laboratory of the Tokai Research Establishment on November 20, 1997, samples of uranium metal waste and scattered residues were analyzed. At the same time the container lid that had been blown off was closely inspected, and the pressurization effects of the container were tested and analyzed. It was found that 1) the uranium metal waste mainly consisted of uranium metal, carbides and oxides, whose relative amounts were dependent on the particle size, 2) the uranium metal waste hydrolyzed to produce combustible gases such as methane and hydrogen, and 3) the lid of the outer container could be blown off by an explosive rise of the inner pressure caused by combustion of inflammable gas mixture. (author)

  8. Value added analysis and its distribution: a study on BOVESPA-listed banks using ANOVA

    National Research Council Canada - National Science Library

    Leonardo José Seixas Pinto; Fátima de Souza Freire

    2013-01-01

      The value added generated by the financial institutions listed on BOVESPA and its distribution in the years between 2007 to 2011 are the subject of this research which shows how banks divided his...

  9. Microarray analysis reveals the actual specificity of enrichment media used for food safety assessment.

    Science.gov (United States)

    Kostić, Tanja; Stessl, Beatrix; Wagner, Martin; Sessitsch, Angela

    2011-06-01

    Microbial diagnostic microarrays are tools for simultaneous detection and identification of microorganisms in food, clinical, and environmental samples. In comparison to classic methods, microarray-based systems have the potential for high throughput, parallelism, and miniaturization. High specificity and high sensitivity of detection have been demonstrated. A microbial diagnostic microarray for the detection of the most relevant bacterial food- and waterborne pathogens and indicator organisms was developed and thoroughly validated. The microarray platform based on sequence-specific end labeling of oligonucleotides and the phylogenetically robust gyrB marker gene allowed a highly specific (resolution on genus and/or species level) and sensitive (0.1% relative and 10(4) CFU absolute sensitivity) detection of the target pathogens. In initial challenge studies of the applicability of microarray-based food analysis, we obtained results demonstrating the questionable specificity of standardized culture-dependent microbiological detection methods. Taking into consideration the importance of reliable food safety assessment methods, comprehensive performance assessment is essential. Results demonstrate the potential of this new pathogen diagnostic microarray to evaluate culture-based standard methods in microbiological food analysis.

  10. Pathways enrichment analysis for differentially expressed genes in squamous lung cancer.

    Science.gov (United States)

    Qian, Liqiang; Luo, Qingquan; Zhao, Xiaojing; Huang, Jia

    2014-01-01

    Squamous lung cancer (SQLC) is a common type of lung cancer, but its oncogenesis mechanism is not so clear. The aim of this study was to screen the potential pathways changed in SQLC and elucidate the mechanism of it. Published microarray data of GSE3268 series was downloaded from Gene Expression Omnibus (GEO). Significance analysis of microarrays was performed using software R, and differentially expressed genes (DEGs) were harvested. The functions and pathways of DEGs were mapped in Gene Otology and KEGG pathway database, respectively. A total of 2961 genes were filtered as DEGs between normal and SQLC cells. Cell cycle and metabolism were the mainly changed functions of SQLC cells. Meanwhile genes such as MCM, RFC, FEN1, and POLD may induce SQLC through DNA replication pathway, and genes such as PTTG1, CCNB1, CDC6, and PCNA may be involved in SQLC through cell cycle pathway. It is demonstrated that pathway analysis is useful in the identification of target genes in SQLC.

  11. Compiling an OPEC Word List: A Corpus-Informed Lexical Analysis

    Directory of Open Access Journals (Sweden)

    Ebtisam Saleh Aluthman

    2017-01-01

    Full Text Available The present study is conducted within the borders of lexicographic research, where corpora have increasingly become all-pervasive. The overall goal of this study is to compile an open-source OPEC[1] Word List (OWL that is available for lexicographic research and vocabulary learning related to English language learning for the purpose of oil marketing and oil industries. To achieve this goal, an OPEC Monthly Reports Corpus (OMRC comprising of 1,004,542 words was compiled. The OMRC consists of 40 OPEC monthly reports released between 2003 and 2015. Consideration was given to both range and frequency criteria when compiling the OWL which consists of 255 word types. Along with this basic goal, this study aims to investigate the coverage of the most well-recognised word lists, the General Service List of English Words (GSL (West ,1953  and  the Academic Word List (AWL (Coxhead, 2000 in the OMRC corpus. The 255 word types included in the OWL are not overlapping with either the AWL or the GSL. Results suggest the necessity of making this discipline-specific word list for ESL students of oil marketing industries. The availability of the OWL has significant pedagogical contributions to curriculum design, learning activities and the overall process of vocabulary learning in the context of teaching English for specific purposes (ESP. Keywords: Vocabulary Profiling- Vocabulary Learning- Word List- OPEC- ESP OPEC stands for Organisation of Petroleum Exporting Countries.

  12. Stable-isotope analysis of a deep-sea benthic-fish assemblage: evidence of an enriched benthic food web.

    Science.gov (United States)

    Boyle, M D; Ebert, D A; Cailliet, G M

    2012-04-01

    In this study, fishes and invertebrates collected from the continental slope (1000 m) of the eastern North Pacific Ocean were analysed using stable-isotope analysis (SIA). Resulting trophic positions (T(P) ) were compared to known diets and habitats from the literature. Dual isotope plots indicated that most species groups (invertebrates and fishes) sorted as expected along the carbon and nitrogen axes, with less intraspecific variability than interspecific variability. Results also indicated an isotopically distinct benthic and pelagic food web, as the benthic food web was more enriched in both nitrogen and carbon isotopes. Trophic positions from SIA supported this finding, resulting in the assignment of fishes to different trophic positions from those expected based on published dietary information. These differences can be explained largely by the habitat of the prey and the percentage of the diet that was scavenged. A mixing model estimated dietary contributions of prey similar to those of the known diet of Bathyraja trachura from stomach-content analysis (SCA). Linear regressions indicated that trophic positions calculated from SIA and SCA, when plotted against B. trachura total length for 32 individuals, exhibited similar variation and patterns. Only the T(P) from SCA yielded significant results (stomach content: P 0·05). © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  13. Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions.

    Science.gov (United States)

    Zhang, Yingjie; Thas, Olivier

    2016-01-01

    Constrained ordination methods aims at finding an environmental gradient along which the species abundances are maximally separated. The species response functions, which describe the expected abundance as a function of the environmental score, are according to the ecological fundamental niche theory only meaningful if they are bell-shaped. Many classical model-based ordination methods, however, use quadratic regression models without imposing the bell-shape and thus allowing for meaningless U-shaped response functions. The analysis output (e.g. a biplot) may therefore be potentially misleading and the conclusions are prone to errors. In this paper we present a log-likelihood ratio criterion with a penalisation term to enforce more bell-shaped response shapes. We report the results of a simulation study and apply our method to metagenomics data from microbial ecology.

  14. Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.

    Science.gov (United States)

    Gu, Zhuoya; Jin, Ke; Crabbe, M James C; Zhang, Yang; Liu, Xiaolin; Huang, Yanyan; Hua, Mengyi; Nan, Peng; Zhang, Zhaolei; Zhong, Yang

    2016-04-01

    Transposable elements (TEs) have no longer been totally considered as "junk DNA" for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10(-4); IMR90: r = 0.934, P = 2 × 10(-2); Promoter: hESC: r = 0.995, P = 3.8 × 10(-4); IMR90: r = 0.996, P = 3.2 × 10(-4)). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.

  15. Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

    Directory of Open Access Journals (Sweden)

    Zhuoya Gu

    2016-02-01

    Full Text Available ABSTRACT Transposable elements (TEs have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016 and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10−4; IMR90: r = 0.934, P = 2 × 10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4. Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue

  16. Genomic-bioinformatic analysis of transcripts enriched in the third-stage larva of the parasitic nematode Ascaris suum.

    Directory of Open Access Journals (Sweden)

    Cui-Qin Huang

    Full Text Available Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3 of A. suum was constructed by suppressive-subtractive hybridization (SSH, and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498 shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer. Using gene ontology (GO, 235 of these molecules were assigned to 'biological process' (n = 68, 'cellular component' (n = 50, or 'molecular function' (n = 117. Of the 91 clusters assembled, 56 molecules (61.5% had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5% had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors, and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein-protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50 to be involved in apoptosis and insulin signaling (2%, ATP synthesis (2%, carbon metabolism (6%, fatty acid biosynthesis (2%, gap junction (2%, glucose metabolism (6%, or porphyrin metabolism (2%, although 34 (68% of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%, anchored (2%, and/or transmembrane (12% proteins. Functionally, 17 (34% of them were predicted to be associated with (non-wild-type RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb (13 types; 58.8%, larval arrest

  17. Performance evaluation and bacteria analysis of AFB-MFC enriched with high-strength synthetic wastewater.

    Science.gov (United States)

    Huang, Jian-sheng; Guo, Yong; Yang, Ping; Li, Chong-ming; Gao, Hui; Feng, Li; Zhang, Yun

    2014-01-01

    In order to study the performance and bacterial communities of an anaerobic fluidized bed microbial fuel cell (AFB-MFC) system, the 16S rDNA gene sequencing was applied, and high-strength synthetic wastewater was treated by the AFB-MFC system. The high-strength synthetic wastewater, in which the concentrations of chemical oxygen demand (COD), nitrite nitrogen, and nitrate nitrogen were above 19,000, 2,516-3,871 and 927-1,427 mg/L, was treated by the AFB-MFC system. The removal efficiency of COD, nitrite nitrogen, and nitrate nitrogen reached 70-89, 98 and 98%, while the maximum voltage was 394 mV. The bacteria analysis revealed the presence of Alistipes putredinis, Carnobacterium sp., Victivallis vadensis, Klebsiella pneumoniae, Thauera sp., Parabacteroides merdae, Parvimonas micra, Parabacteroides sp., and Desulfomicrobium baculatum in the anode chamber. In addition, the Klebsiella pneumoniae was observed to have the capability of organic degradation and electricity generation, while the Thauera sp. has the capability of denitrification.

  18. A meta-analysis of the combined effect of housing and environmental enrichment characteristics on the behaviour and performance of pigs

    NARCIS (Netherlands)

    Averos, X.; Brossard, L.; Dourmad, J.Y.; Greef, de K.H.; Edge, H.L.; Edwards, S.A.; Meunier-Salaün, M.C.

    2010-01-01

    To quantify the combined effect of housing conditions and environmental enrichment on the behaviour and performance of pigs, a meta-analysis was performed using information from 45 experiments in 42 published manuscripts. Multiple regression models were applied to evaluate the effects of space allow

  19. RNA-Seq for enrichment and analysis of IRF5 transcript expression in SLE.

    Directory of Open Access Journals (Sweden)

    Rivka C Stone

    Full Text Available Polymorphisms in the interferon regulatory factor 5 (IRF5 gene have been consistently replicated and shown to confer risk for or protection from the development of systemic lupus erythematosus (SLE. IRF5 expression is significantly upregulated in SLE patients and upregulation associates with IRF5-SLE risk haplotypes. IRF5 alternative splicing has also been shown to be elevated in SLE patients. Given that human IRF5 exists as multiple alternatively spliced transcripts with distinct function(s, it is important to determine whether the IRF5 transcript profile expressed in healthy donor immune cells is different from that expressed in SLE patients. Moreover, it is not currently known whether an IRF5-SLE risk haplotype defines the profile of IRF5 transcripts expressed. Using standard molecular cloning techniques, we identified and isolated 14 new differentially spliced IRF5 transcript variants from purified monocytes of healthy donors and SLE patients to generate an IRF5 variant transcriptome. Next-generation sequencing was then used to perform in-depth and quantitative analysis of full-length IRF5 transcript expression in primary immune cells of SLE patients and healthy donors by next-generation sequencing. Evidence for additional alternatively spliced transcripts was obtained from de novo junction discovery. Data from these studies support the overall complexity of IRF5 alternative splicing in SLE. Results from next-generation sequencing correlated with cloning and gave similar abundance rankings in SLE patients thus supporting the use of this new technology for in-depth single gene transcript profiling. Results from this study provide the first proof that 1 SLE patients express an IRF5 transcript signature that is distinct from healthy donors, 2 an IRF5-SLE risk haplotype defines the top four most abundant IRF5 transcripts expressed in SLE patients, and 3 an IRF5 transcript signature enables clustering of SLE patients with the H2 risk haplotype.

  20. Competitive Market Analysis of Transplant Centers and Discrepancy of Wait-Listing of Recipients for Kidney Transplantation.

    Science.gov (United States)

    Cho, P S; Saidi, R F; Cutie, C J; Ko, D S C

    2015-01-01

    There are over 250 kidney transplant programs in the USA. To determine if highly competitive regions, defined as regions with a higher number of transplant centers, will approve and wait-list more end-stage renal disease (ESRD) candidates for transplant despite consistent incidence and prevalence of ESRD nationwide. ESRD Network and OPTN data completed in 2011 were obtained from all transplant centers including listing data, market saturation, market share, organs transplanted, and ESRD prevalence. Herfindahl-Hirschman Index (HHI) was used to measure the size of firms in relation to the industry to determine the amount of competition. States were separated into 3 groups (HHI1800 considered highly concentrated). The percentage of ESRD patients listed in competitive, moderate, and highly concentrated regions were 19.73%, 17.02%, and 13.75%, respectively. The ESRD listing difference between competitive versus highly concentrated was significant (pmarket share. Our analysis of the available national data suggests a discrepancy in access for ESRD patient to transplantation due to transplant center competition.

  1. A Computer-Aided Bibliometrics System for Journal Citation Analysis and Departmental Core Journal Ranking List Generation

    Directory of Open Access Journals (Sweden)

    Yih-Chearng Shiue

    2004-12-01

    Full Text Available Due to the tremendous increase and variation in serial publications, faculties in department of university are finding it difficult to generate and update their departmental core journal list regularly and accurately, and libraries are finding it difficult to maintain their current serial collection for different departments. Therefore, the evaluation of a departmental core journal list is an important task for departmental faculties and librarians. A departmental core journal list not only helps departments understand research performances of faculties and students, but also helps librarians make decisions about which journals to retain and which to cancel. In this study, a Computer-Aided Bibliometrics System was implemented and two methodologies (JCDF and LibJF were proposed in order to generate a departmental core journal ranking list and make the journal citation analysis. Six departments were taken as examples, with MIS as the major one. One journal citation pattern was found and the ratio of Turning point-to-No. journal was always around 0.07 among the 10 journals and 6 departments. After comparing with four methodologies via overlapping rate and standard deviation distances, the two proposed methodologies were shown to be better than questionnaire and library subscription method.

  2. A Multidimensional System for Phosphopeptide Analysis Using TiO{sub 2} Enrichment and Ion-exchange Chromatography with Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Kun; Yoo, Jisun; Kim, Eunmin; Kim, Jin Young; Kim, Young Hwan; Yoo, Jong Shin [Korea Basic Science Institute, Ochang (Korea, Republic of); Oh, Han Bin [Sogang Univ., Seoul (Korea, Republic of)

    2012-10-15

    Although offline enrichment of phosphorylated peptides is widely used, enrichment for phosphopeptides using TiO{sub 2} is often performed manually, which is labor-intensive and can lead to irreproducible results. To address the problems associated with offline enrichment and to improve the effectiveness of phosphopeptide detection, we developed an automated online enrichment system for phosphopeptide analysis. A standard protein mixture comprising BSA, fetuin, crystalline, α-casein and β-casein, and ovalbumin was assessed using our new system. Our multidimensional system has four main parts: a sample pump, a 20-mm TiO{sub 2}-based column, a weak anion-exchange, and a strong cation-exchange (2:1 WAX:SCX) separation column with LC/MS. Phosphorylated peptides were successfully detected using the TiO{sub 2}-based online system with little interference from nonphosphorylated peptides. Our results confirmed that our online enrichment system is a simple and efficient method for detecting phosphorylated peptides.

  3. Neutron activation analysis of the 30Si content of highly enriched 28Si: proof of concept and estimation of the achievable uncertainty

    CERN Document Server

    D'Agostino, Giancarlo; Oddone, Massimo; Prata, Michele; Bergamaschi, Luigi; Giordani, Laura

    2014-01-01

    We investigated the use of neutron activation to estimate the 30Si mole fraction of the ultra-pure silicon material highly enriched in 28Si for the measurement of the Avogadro constant. Specifically, we developed a relative method based on Instrumental Neutron Activation Analysis and using a natural-Si sample as a standard. To evaluate the achievable uncertainty, we irradiated a 6 g sample of a natural-Si material and modeled experimentally the signal that would be produced by a sample of the 28Si-enriched material of similar mass and subjected to the same measurement conditions. The extrapolation of the expected uncertainty from the experimental data indicates that a measurement of the 30Si mole fraction of the 28Si-enriched material might reach a 4% relative combined standard uncertainty.

  4. MBROLE 2.0-functional enrichment of chemical compounds.

    Science.gov (United States)

    López-Ibáñez, Javier; Pazos, Florencio; Chagoyen, Mónica

    2016-07-01

    Metabolites Biological Role (MBROLE) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms. Since its release in 2011, MBROLE has been used by different groups worldwide to analyse metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE2, accessible at http://csbg.cnb.csic.es/mbrole2 MBROLE2 has been supplemented with 10 databases not available in the previous version, which allow analysis over a larger, richer set of vocabularies including metabolite-protein and drug-protein interactions. This new version performs automatic conversion of compound identifiers from different databases, thus simplifying usage. In addition, the user interface has been redesigned to generate an interactive, more intuitive representation of the results.

  5. Comparison and analysis of biological agent category lists based on biosafety and biodefense.

    Directory of Open Access Journals (Sweden)

    Deqiao Tian

    Full Text Available Biological agents pose a serious threat to human health, economic development, social stability and even national security. The classification of biological agents is a basic requirement for both biosafety and biodefense. We compared and analyzed the Biological Agent Laboratory Biosafety Category list and the defining criteria according to the World Health Organization (WHO, the National Institutes of Health (NIH, the European Union (EU and China. We also compared and analyzed the Biological Agent Biodefense Category list and the defining criteria according to the Centers for Disease Control and Prevention (CDC of the United States, the EU and Russia. The results show some inconsistencies among or between the two types of category lists and criteria. We suggest that the classification of biological agents based on laboratory biosafety should reduce the number of inconsistencies and contradictions. Developing countries should also produce lists of biological agents to direct their development of biodefense capabilities.To develop a suitable biological agent list should also strengthen international collaboration and cooperation.

  6. Analysis of airborne radiometric data. Volume 2. Description, listing, and operating instructions for the code DELPHI/MAZAS. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Sperling, M.; Shreve, D.C.

    1978-12-01

    The computer code DELPHI is an interactive English language command system for the analysis of airborne radiometric data. The code includes modules for data reduction, data simulation, time filtering, data adjustment and graphical presentation of the results. DELPHI is implemented in FORTRAN on a DEC-10 computer. This volume gives a brief set of operations instructions, samples of the output obtained from hard copies of the display on a Tektronix terminal and finally a listing of the code.

  7. The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology.

    Science.gov (United States)

    Ruskova, Lenka; Raclavsky, Vladislav

    2011-09-01

    Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

  8. Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer.

    Science.gov (United States)

    Mazza, Tommaso; Mazzoccoli, Gianluigi; Fusilli, Caterina; Capocefalo, Daniele; Panza, Anna; Biagini, Tommaso; Castellana, Stefano; Gentile, Annamaria; De Cata, Angelo; Palumbo, Orazio; Stallone, Raffaella; Rubino, Rosa; Carella, Massimo; Piepoli, Ada

    2016-05-19

    Alterations in the balance of mRNA and microRNA (miRNA) expression profiles contribute to the onset and development of colorectal cancer. The regulatory functions of individual miRNA-gene pairs are widely acknowledged, but group effects are largely unexplored. We performed an integrative analysis of mRNA-miRNA and miRNA-miRNA interactions using high-throughput mRNA and miRNA expression profiles obtained from matched specimens of human colorectal cancer tissue and adjacent non-tumorous mucosa. This investigation resulted in a hypernetwork-based model, whose functional backbone was fulfilled by tight micro-societies of miRNAs. These proved to modulate several genes that are known to control a set of significantly enriched cancer-enhancer and cancer-protection biological processes, and that an array of upstream regulatory analyses demonstrated to be dependent on miR-145, a cell cycle and MAPK signaling cascade master regulator. In conclusion, we reveal miRNA-gene clusters and gene families with close functional relationships and highlight the role of miR-145 as potent upstream regulator of a complex RNA-RNA crosstalk, which mechanistically modulates several signaling pathways and regulatory circuits that when deranged are relevant to the changes occurring in colorectal carcinogenesis. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. 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.

  10. Development of magnetic graphene @hydrophilic polydopamine for the enrichment and analysis of phthalates in environmental water samples.

    Science.gov (United States)

    Wang, Xianying; Song, Guoxin; Deng, Chunhui

    2015-01-01

    Magnetic graphene @hydrophilic polydopamine composites were successfully fabricated via a simple solvothermal reaction and self-polymerization of dopamine. Benefit from the excellent characteristics of strong magnetic responsivity, super-hydrophilicity and abundant π-electron system, the prepared material showed great potential as a magnetic solid phase extraction (MSPE) sorbent. In this work, six kinds of phthalates (PAEs) were selected as the target analytes to evaluate the extraction ability of the adsorbents combined with MSPE-GC-MS. And various extraction parameters were optimized by selecting the pH value of samples, the amount of sorbents, adsorption and desorption time, the type and volume of eluting solution. Meanwhile, the whole extraction process could be finished in 30 min. Under the optimized conditions, validations of the method were evaluated as well. And the results presented excellent linearity with a wide range of 50-20,000 μg/L (R(2)>0.9991). The detection of limits were in the range from 0.05-5 μg/L (S/N=3). Therefore, the novel magnetic graphene@polydopamine composites were successfully used as the sorbents for the enrichment and analysis of PAEs in real water samples. This proposed method provided a simple, efficient and sensitive approach for the determination of aromatic compounds in real environmental samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. 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/.

  12. Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers

    Directory of Open Access Journals (Sweden)

    Sun Xiao

    2007-04-01

    Full Text Available Abstract Background Although prognostic biomarkers specific for particular cancers have been discovered, microarray analysis of gene expression profiles, supported by integrative analysis algorithms, helps to identify common factors in molecular oncology. Similarities of Ordered Gene Lists (SOGL is a recently proposed approach to meta-analysis suitable for identifying features shared by two data sets. Here we extend the idea of SOGL to the detection of significant prognostic marker genes from microarrays of multiple data sets. Three data sets for leukemia and the other six for different solid tumors are used to demonstrate our method, using established statistical techniques. Results We describe a set of significantly similar ordered gene lists, representing outcome comparisons for distinct types of cancer. This kind of similarity could improve the diagnostic accuracies of individual studies when SOGL is incorporated into the support vector machine algorithm. In particular, we investigate the similarities among three ordered gene lists pertaining to mesothelioma survival, prostate recurrence and glioma survival. The similarity-driving genes are related to the outcomes of patients with lung cancer with a hazard ratio of 4.47 (p = 0.035. Many of these genes are involved in breakdown of EMC proteins regulating angiogenesis, and may be used for further research on prognostic markers and molecular targets of gene therapy for cancers. Conclusion The proposed method and its application show the potential of such meta-analyses in clinical studies of gene expression profiles.

  13. Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis

    DEFF Research Database (Denmark)

    Thingholm, Tine E; Jensen, Ole N; Larsen, Martin R

    2009-01-01

    Phospho-proteomics relies on methods for efficient purification and sequencing of phosphopeptides from highly complex biological systems using low amounts of starting material. Current methods for phosphopeptide enrichment, e.g., immobilized metal affinity chromatography and titanium dioxide...

  14. 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.

  15. The analysis of capital structure of Chinese real estate listed companies

    Institute of Scientific and Technical Information of China (English)

    LI Peng-yan; LUO Qing-sheng; AO Li-feng

    2005-01-01

    Capital structure is the basis for assessing the efficiency of enterprise financing activity. The rational capital structure could reduce the cost of capital and plays an important role in managing a company. Thus this paper, based on the real estate listed companies on Shenzhen and Shanghai stock markets, analyzes the factors which influence capital structure, such as profitability, size, collateral value of assets, growth, stockholder's equity, concentration degree of control power, ownership attribute, and applied statistics tools used to help the real estate listed companies optimize the structure of capital.

  16. Basic Library List.

    Science.gov (United States)

    Duren, William L., Jr.

    Reported is an initial attempt to define a minimal college mathematics library. Included is a list of some 300 books, from which approximately 170 are to be chosen to form a basic library in undergraduate mathematics. The areas provided for in this list include Algebra, Analysis, Applied Mathematics, Geometry, Topology, Logic, Foundations and Set…

  17. State ownership and corporate performance: A quantile regression analysis of Chinese listed companies

    NARCIS (Netherlands)

    Li, T.; Sun, L.; Zou, L.

    2009-01-01

    This study assesses the impact of government shareholding on corporate performance using a sample of 643 non-financial companies listed on the Chinese stock exchanges. In view of the controversial empirical findings in the literature and the limitations of the least squares regressions, we adopt the

  18. Word Recognition Error Analysis: Comparing Isolated Word List and Oral Passage Reading

    Science.gov (United States)

    Flynn, Lindsay J.; Hosp, John L.; Hosp, Michelle K.; Robbins, Kelly P.

    2011-01-01

    The purpose of this study was to determine the relation between word recognition errors made at a letter-sound pattern level on a word list and on a curriculum-based measurement oral reading fluency measure (CBM-ORF) for typical and struggling elementary readers. The participants were second, third, and fourth grade typical and struggling readers…

  19. ANALYSIS OF THE INDICATORS SPECIFIC TO ENTITIES LISTED ON THE CAPITAL MARKET AND THEIR ROLE IN QUANTIFYING COMPANY PERFORMANCE

    Directory of Open Access Journals (Sweden)

    Maria Daniela BONDOC

    2014-06-01

    Full Text Available The paper aims at presenting certain indicators specific to entities listed on the capital market and their analysis based on the financial statements of C.N.T.E.E. Transelectrica S.A., listed on the Bucharest Stock Exchange: growth stock exchange indices (market capitalization, earnings per share, price to book ratio, price to sales ratio, price earnings ratio, cash EPS and dividend stock exchange ratios (dividend per share, dividend yield, and dividend payout ratio. The research methodology involved studying the financial statements of the entity for the 2009-2013 period. The case study method was used to study the evolution of the stock exchange indices and opinions were formulated concerning the performance reflected by the analysed indices.

  20. An Emperical Analysis of the Corperate Ownership Concentration on the Operation Performance after IPOs of Chinese listed SMEs

    Science.gov (United States)

    Jiming, Li; Xing, Sun

    The purpose of this paper is to investigates whether the large shareholders of small and medium firms (SMEs) take advantage of the inside information and decrease their shares before their operation performance begins to decline after the Initial Public Offerings (IPOs). By using the data from annual reports of SMEs listed on Shenzhen Stock Exchange in China from 2004 to 2006, this study explores both the relationship and the interaction effects between the change of operation performance and the ownership concentration of SMEs around their IPOs. The statistic analysis indicates that there is a significantly positive relationship between the ownership concentration and their operation performance after IPOs during the sample period. Moreover, the companies with higher ownership decreasing encounter more severe operation performance decline, which sugests that the listed companies intend to package their book profits before IPOs for the sake of increasing their issuing prices and enlarge their financing scales.

  1. 15N enrichment of ammonium, glutamine-amide and urea, measured via mass isotopomer analysis of hexamethylenetetramine.

    Science.gov (United States)

    Yang, D; Puchowicz, M A; David, F; Powers, L; Halperin, M L; Brunengraber, H

    1999-11-01

    Ammonium is an important intermediate of protein metabolism and is a key component of acid-base balance. Investigations of the metabolism of NH(4)(+) in vivo using isotopic techniques are difficult because of the low concentration of NH(4)(+) in biological fluids and because of frequent artifactual isotopic dilution of the enrichment of NH(4)(+) during the assay. A new gas chromatographic mass spectrometric method was designed to monitor the (15)N enrichment and concentration of NH(4)(+) in vivo. These are both calculated from the mass isotopomer distribution of hexamethylenetetramine (HMT) formed by reacting NH(4)(+) with formaldehyde. The enrichment of NH(4)(+) is amplified four times since the HMT molecule contains four atoms of nitrogen derived from NH(4)(+). This allows the measurement of low (15)N enrichment of NH(4)(+), down to 0.1%. (15)N enrichment of urea and of the amide N of L-glutamine are measured by enzymatic release of NH(4)(+) and conversion of the latter to HMT. These new techniques facilitate in vivo investigations of the metabolism of NH(4)(+) and related compounds.

  2. Phospholipase C isozymes are deregulated in colorectal cancer--insights gained from gene set enrichment analysis of the transcriptome.

    Directory of Open Access Journals (Sweden)

    Stine A Danielsen

    Full Text Available Colorectal cancer (CRC is one of the most common cancer types in developed countries. To identify molecular networks and biological processes that are deregulated in CRC compared to normal colonic mucosa, we applied Gene Set Enrichment Analysis to two independent transcriptome datasets, including a total of 137 CRC and ten normal colonic mucosa samples. Eighty-two gene sets as described by the Kyoto Encyclopedia of Genes and Genomes database had significantly altered gene expression in both datasets. These included networks associated with cell division, DNA maintenance, and metabolism. Among signaling pathways with known changes in key genes, the "Phosphatidylinositol signaling network", comprising part of the PI3K pathway, was found deregulated. The downregulated genes in this pathway included several members of the Phospholipase C protein family, and the reduced expression of two of these, PLCD1 and PLCE1, were successfully validated in CRC biopsies (n = 70 and cell lines (n = 19 by quantitative analyses. The repression of both genes was found associated with KRAS mutations (P = 0.005 and 0.006, respectively, and we observed that microsatellite stable carcinomas with reduced PLCD1 expression more frequently had TP53 mutations (P = 0.002. Promoter methylation analyses of PLCD1 and PLCE1 performed in cell lines and tumor biopsies revealed that methylation of PLCD1 can contribute to reduced expression in 40% of the microsatellite instable carcinomas. In conclusion, we have identified significantly deregulated pathways in CRC, and validated repression of PLCD1 and PLCE1 expression. This illustrates that the GSEA approach may guide discovery of novel biomarkers in cancer.

  3. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto

    2013-04-01

    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series Cross-Section Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  4. A near infrared line list for \\NH: Analysis of a Kitt Peak spectrum after 35 years

    CERN Document Server

    Barton, Emma J; Tennyson, Jonathan; Béguier, S; Campargue, A

    2016-01-01

    A Fourier Transform (FT) absorption spectrum of room temperature NH3 in the region 7400 - 8600 cm-1 is analysed using a variational line list and ground state energies determined using the MARVEL procedure. The spectrum was measured by Dr Catherine de Bergh in 1980 and is available from the Kitt Peak data center. The centers and intensities of 8468 ammonia lines were retrieved using a multiline fitting procedure. 2474 lines are assigned to 21 bands providing 1692 experimental energies in the range 7000 - 9000 cm-1. The spectrum was assigned by the joint use of the BYTe variational line list and combination differences. The assignments and experimental energies presented in this work are the first for ammonia in the region 7400 - 8600 cm-1, considerably extending the range of known vibrational-excited states

  5. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto

    2013-04-01

    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series CrossSection Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  6. Enriching Discovery Layers: A Product Comparison of Content Enrichment Services Syndetic Solutions and Content Café 2

    Directory of Open Access Journals (Sweden)

    Allison DaSilva

    2014-10-01

    Full Text Available A comparative analysis of content enrichment services, Syndetic Solutions and Content Café 2, was undertaken to explore which service would provide public library users with a superior online search and discovery experience through the enriched data elements offered, specifically looking at the cover image data element and exploring what factors impact the display of said element. A data-set of 250 items in five different formats, including books, CDs, DVDs, e-books, and video games, was searched in four North American public libraries’ discovery layers to compare the integration, extent, and quality of the cover image data element supplied by Syndetic Solutions and Content Café 2. Based on an analysis of the URLs, ISBNs, and UPCs for each of the 250 items, it was determined that the integration, and therefore the display, of the cover image data element was impacted by: (1 whether or not an ISBN or UPC was listed in the MARC bibliographic record; (2 which ISBN or UPC was listed, as items could potentially have more than one; (3 the inclusion of both ISBNs and UPCs in the record and the settings of the discovery tool; (4 the order in which the ISBNs or UPCs were listed in the record; and (5 whether or not Syndetic Solutions or Content Café 2 had the image data in its database at the time of the search. The quality of the cover image displayed was found to be impacted by the size requested by the library and the size of the image provided by the publisher. These findings may also have implications for the integration of other enriched data elements.

  7. Effects of plant stanol or sterol-enriched diets on lipid profiles in patients treated with statins: systematic review and meta-analysis

    Science.gov (United States)

    Han, Shufen; Jiao, Jun; Xu, Jiaying; Zimmermann, Diane; Actis-Goretta, Lucas; Guan, Lei; Zhao, Youyou; Qin, Liqiang

    2016-01-01

    Efficacy and safety data from trials with suitable endpoints have shown that non-statin medication in combination with a statin is a potential strategy to further reduce cardiovascular events. We aimed to evaluate the overall effect of stanol- or sterol-enriched diets on serum lipid profiles in patients treated with statins by conducting a meta-analysis of randomized controlled trials (RCTs). We used the PubMed, Cochrane library and ClinicalTrials.gov databases to search for literature published up to December 2015. Trials were included in the analysis if they were RCTs evaluating the effect of plant stanols or sterols in patients under statin therapy that reported corresponding data on serum lipid profiles. We included 15 RCTs involving a total of 500 participants. Stanol- or sterol-enriched diets in combination with statins, compared with statins alone, produced significant reductions in total cholesterol of 0.30 mmol/L (95% CI −0.36 to −0.25) and low-density lipoprotein (LDL) cholesterol of 0.30 mmol/L (95% CI −0.35 to −0.25), but not in high-density lipoprotein cholesterol or triglycerides. These results persisted in the subgroup analysis. Our meta-analysis provides further evidence that stanol- or sterol-enriched diets additionally lower total cholesterol and LDL-cholesterol levels in patients treated with statins beyond that achieved by statins alone. PMID:27539156

  8. Visual search of neuropil-enriched RNAs from brain in situ hybridization data through the image analysis pipeline hippo-ATESC.

    Directory of Open Access Journals (Sweden)

    Roberto Ugolotti

    Full Text Available MOTIVATION: RNA molecules specifically enriched in the neuropil of neuronal cells and in particular in dendritic spines are of great interest for neurobiology in virtue of their involvement in synaptic structure and plasticity. The systematic recognition of such molecules is therefore a very important task. High resolution images of RNA in situ hybridization experiments contained in the Allen Brain Atlas (ABA represent a very rich resource to identify them and have been so far exploited for this task through human-expert analysis. However, software tools that may automatically address the same objective are not very well developed. RESULTS: In this study we describe an automatic method for exploring in situ hybridization data and discover neuropil-enriched RNAs in the mouse hippocampus. We called it Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing. Bioinformatic validation showed that the Hippo-ATESC is very efficient in the recognition of RNAs which are manually identified by expert curators as neuropil-enriched on the same image series. Moreover, we show that our method can also highlight genes revealed by microdissection-based methods but missed by human visual inspection. We experimentally validated our approach by identifying a non-coding transcript enriched in mouse synaptosomes. The code is freely available on the web at http://ibislab.ce.unipr.it/software/hippo/.

  9. Determinant Agents Analysis of Dividend Policies Practiced by Companies Listed in Great Britain and France

    OpenAIRE

    Raluca-Georgiana MOSCU

    2012-01-01

    Dividend policy is one of the most intriguing topics in financial research. Even now, economists provide considerable attention and thought to solving the dividend puzzle, resulting a large number of conflicting hypotheses, theories and explanations. This paper aims to determine the dividend policies for 209 listed on London Stock Exchange and Paris Stock Exchange in 2010 and to explain their dividend payment behavior. So this paper investigates why companies in different countries have estab...

  10. Natural personal care products—analysis of ingredient lists and legal situation

    OpenAIRE

    Klaschka, Ursula

    2016-01-01

    Background Many natural substances are classified as dangerous substances according to the European regulation on classification and labelling. Are they used in natural personal care products today? One hundred ingredient lists were analyzed to find this out. Results All products with natural substances contained dangerous natural substances or they contained natural substances, for which the information about their classification as dangerous substances is not available. 54 natural substance...

  11. Evaluation of phosphopeptide enrichment strategies for quantitative TMT analysis of complex network dynamics in cancer-associated cell signalling

    Directory of Open Access Journals (Sweden)

    Benedetta Lombardi

    2015-03-01

    Full Text Available Defining alterations in signalling pathways in normal and malignant cells is becoming a major field in proteomics. A number of different approaches have been established to isolate, identify and quantify phosphorylated proteins and peptides. In the current report, a comparison between SCX prefractionation versus an antibody based approach, both coupled to TiO2 enrichment and applied to TMT labelled cellular lysates, is described. The antibody strategy was more complete for enriching phosphopeptides and allowed the identification of a large set of proteins known to be phosphorylated (715 protein groups with a minimum number of not previously known phosphorylated proteins (2.

  12. 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

  13. Antioxidant activity and sensory analysis of a rosmarinic acid-enriched extract of garden sage (Salvia officinalis)

    Science.gov (United States)

    A novel extract of S. officinalis (garden sage) was prepared using supercritical carbon dioxide (SC-CO2) extraction, followed by a Soxhlet hot water extraction. The resulting extract was enriched in polyphenols, including rosmarinic acid (RA), which has shown promising health benefits in animals. Th...

  14. Selective enrichment of sialic acid-containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry

    DEFF Research Database (Denmark)

    Palmisano, Giuseppe; Lendal, Sara Eun; Engholm-Keller, Kasper

    2010-01-01

    of glycosylation sites and the characterization of glycan structures. In this paper, we describe a protocol for the selective enrichment of SA-containing glycopeptides using a combination of titanium dioxide (TiO(2)) and hydrophilic interaction liquid chromatography (HILIC). The selectivity of TiO(2) toward SA...

  15. Redox properties of catechins and enriched green tea extracts effectively preserve L-5-methyltetrahydrofolate: assessment using cyclic voltammetry analysis.

    Science.gov (United States)

    Rozoy, Elodie; Araya-Farias, Monica; Simard, Stéphan; Kitts, David; Lessard, Jean; Bazinet, Laurent

    2013-06-01

    A cyclic voltammetry (CV) study was performed in pH 5.5 Britton-Robinson buffer at room temperature to study the stability of 1mM l-5-methyltetrahydrofolate (l-5-MTHF) in combination with epigallocatechin-gallate-enriched extract (EGCGe) and epigallocatechin-enriched extract (EGCe). The combination of l-5-MTHF with enriched catechin extracts provided enhanced stability of l-5-MTHF over a period of 12h under ambient air conditions at pH 5.5. CV experiments showed that increasing the concentrations of EGCGe or EGCe extracts from 80 to 400mg/L produced a decrease in the second oxidation peak of l-5-MTHF. Thus, we calculated that l-5-MTHF remained at nearly 90% when in the presence of enriched tea extracts, compared to 74% without the tea antioxidants. The catechins responsible for this preservation were EGCG and C, confirmed by LC-MS. Compared to covalent link only low interaction (hydrogen bonds) between the different catechins present in the tea extract would stabilise l-5-MTHF. Rather, it was hypothesised that EGCGe and EGCe were effective agents to preserve l-5-MTHF, through a mechanism that also involved the redox potential of catechins to maintain l-5-MTHF in its reduced form.

  16. List manipulation in Turbo Prolog

    Directory of Open Access Journals (Sweden)

    V.Cotelea

    1995-06-01

    Full Text Available The present paper is concerned with list processing in Turbo Prolog language. It doesn't claim to be an exhaustive description of operations which can be performed upon lists. Nevertheless adduced programs are most representative, more or less known to specialists in logic programming domain. By means of examples are explained the list manipulation techniques, use of recursion, declarative comparison of predicates, analysis and fixation of acceptable prototypes and some problems of predicates' inconsistency. Index terms. Prolog, list, recursion.

  17. National reimbursement listing determinants of new cancer drugs: a retrospective analysis of 58 cancer treatment appraisals in 2007-2016 in South Korea.

    Science.gov (United States)

    Kim, Eun-Sook; Kim, Jung-Ae; Lee, Eui-Kyung

    2017-08-01

    Since the positive-list system was introduced, concerns have been raised over restricting access to new cancer drugs in Korea. Policy changes in the decision-making process, such as risk-sharing agreement and the waiver of pharmacoeconomic data submission, were implemented to improve access to oncology medicines, and other factors are also involved in the reimbursement for cancer drugs. The aim of this study is to investigate the reimbursement listing determinants of new cancer drugs in Korea. All cancer treatment appraisals of Health Insurance Review and Assessment during 2007-2016 were analyzed based on 13 independent variables (comparative effectiveness, cost-effectiveness, drug-price comparison, oncology-specific policy, and innovation such as new mode of action). Univariate and multivariate logistic analyses were conducted. Of 58 analyzed submissions, 40% were listed in the national reimbursement formulary. In univariate analysis, four variables were related to listing: comparative effectiveness, drug-price comparison, new mode of action, and risk-sharing agreement. In multivariate logistic analysis, three variables significantly increased the likelihood of listing: clinical improvement, below alternative's price, and risk-sharing arrangement. Cancer drug's listing increased from 17% to 47% after risk-sharing agreement implementation. Clinical improvement, cost-effectiveness, and RSA application are critical to successful national reimbursement listing.

  18. Preparation of magnetic core-mesoporous shell microspheres with C8-modified interior pore-walls and their application in selective enrichment and analysis of mouse brain peptidome.

    Science.gov (United States)

    Liu, Shasha; Li, Yan; Deng, Chunhui; Mao, Yu; Zhang, Xiangmin; Yang, Pengyuan

    2011-12-01

    In this paper, magnetic mesoporous silica microspheres with C8-modified interior pore-walls were prepared through a facile one-pot sol-gel coating strategy, and were successfully applied for selective enrichment of endogenous peptides in mouse brain for peptidome analysis. Through the one-pot sol-gel approach with surfactant (CTAB) as a template, tetraethyl orthosilicate (TEOS) and n-ctyltriethoxysilane (C8TEOS) as the precursors, C8-modified magnetic mesoporous microspheres (C8-Fe(3)O(4)@mSiO(2)) consisting magnetic core and mesoporous silica shell with C8-groups exposed in the mesopore channels were synthesized. The obtained microspheres possess highly open mesopores of 3.4 nm, high surface area (162.5 m(2)/g), large pore volume (0.17 cm(3)/g), excellent magnetic responsivity (56.3 emu/g) and good dispersibility in aqueous solution. Based on the abundant surface silanol groups, functional C8 groups and the strong magnetic responsivity of the core-shell C8-Fe(3) O(4) @mSiO(2) microspheres, efficient and fast enrichment of peptides was achieved. Additionally, the C8-Fe(3)O(4)@mSiO(2) microspheres exhibit excellent performance in selective enrichment of endogenous peptides from complex samples that are consist of peptides, large proteins and other compounds, including human serum and mouse brain followed by automated nano-LC-ESI-MS/MS analysis. These results indicate C8-Fe(3)O(4)@mSiO(2) microspheres would be a potential candidate for endogenous peptides enrichment and biomarkers discovery in peptidome analysis.

  19. Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; Suk Ha Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop.Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers.In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice

  20. Statistical analysis of large passwords lists, used to optimize brute force attacks

    CSIR Research Space (South Africa)

    Van Heerden, RP

    2009-03-01

    Full Text Available computer illiterate users now use computers • Computer processing power has increased by at least 500 fold (Geer 2005) 2.2.2 UK Web passwords Stuart Brown compiled a list of the most popular passwords used for various web sites. The top 10 passwords... comprise 6.5% of all the passwords used (Brown 2006). The top ten passwords were: • 123 • password • liverpool • letmein (“let me in”) • 123456 • qwerty • charlie • monkey • arsenal • thomas Some area-specific passwords (liverpool and arsenal...

  1. Selected Ratio and Bankruptcy Early-Warning Method Analysis of Competitiveness of Wood Sector Companies Listed on Warsaw Stock Exchange

    Directory of Open Access Journals (Sweden)

    Justyna Biernacka

    2012-09-01

    Full Text Available This paper presents the analysis of economic conditions of wood sector companies listed on the Warsaw Stock Exchange. Among many measures of ratio analysis, the three most frequently used groups of indicators - profitability, debt and liquidity were selected. For a comprehensive presentation of the situation of each company, the Mączyńska & Zawadzki’s model was used as the bankruptcy early warning method. Two furniture industry companies, two wood-based panel industry companies, two pulp and paper industry entities, a representative of sawmilling industry and a company of wood-based panels and furniture industry were analyzed. The analysis showed that companies with stabile position in the market have the best economic conditions, and these were namely the pulp and paper industry and furniture industry.

  2. 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.

  3. Secondary analysis of publicly available data reveals superoxide and oxygen radical pathways are enriched for associations between type 2 diabetes and low-frequency variants.

    Science.gov (United States)

    Yazdanpanah, Mojgan; Chen, Chuhua; Graham, Jinko

    2013-11-01

    Genome-wide association studies explain at most 5%-10% of the heritable components of type 2 diabetes. Some of the "missing type 2 diabetes heritability" could be explained by low-frequency variants. We examined the associations between low-frequency variants and type 2 diabetes, using data from 2538 diabetic and 2977 nondiabetic subjects in the publicly available database of Genotypes and Phenotypes. We applied two approaches. First, we combined information from all low-frequency (1%-5%) variants at a locus in a gene-centric analysis of associations with diabetes. Next, we searched for gene ontology (GO) biological processes that were enriched for gene-centric associations, after correcting for multiple testing to control the false discovery rate (FDR). We found three GO biological processes that were significantly enriched for associations to diabetes: "response to superoxide" (FDR-adjusted p=2.7×10(-3)), "response to oxygen radical" (FDR-adjusted p=2.7×10(-3)), and "heart contraction" (FDR-adjusted p=2.6×10(-2)). There were three genes that contributed to "response to superoxide" and "oxygen radical" pathways, including the SOD1 gene. Gene-centric tests of association with low-frequency variants, followed by analysis to evaluate which biological pathways are enriched for these associations has the potential to recover, at least some proportion of, the "missing heritability" of type 2 diabetes.

  4. Analysis of the performance of fuel cells PWR with a single enrichment and radial distribution of enrichments; Analisis del desempeno de celdas combustibles PWR con un solo enriquecimiento y con distribucion radial de enriquecimientos

    Energy Technology Data Exchange (ETDEWEB)

    Vargas, S.; Gonzalez, J. A.; Alonso, G.; Del Valle, E. [IPN, Escuela Superior de Fisica y Matematicas, Av. IPN s/n, Col. Lindavista, Mexico D.F. 07738 (Mexico); Xolocostli M, J. V. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico)]. e-mail: nolosesamuel@prodigy.net.mx

    2008-07-01

    One of the main challenges in the design of fuel assemblies is the efficient use of uranium achieving burnt homogeneous of the fuel rods as well as the burnt maximum possible of the same ones to the unload. In the case of the assemblies type PWR has been decided actually for fuel assemblies with a single radial enrichment. The present work has like effect to show the because of this decision, reason why a comparison of the neutronic performance of two fuel cells takes place with the same enrichment average but one of them with radial distribution of enrichment and the other with a single enrichment equal to the average. The results shown in the present study of the behavior of the neutron flow as well as the power distribution through of assembly sustain the because of a single radial enrichment. (Author)

  5. Analysis of the performance of fuel cells BWR with a single enrichment and radial distribution of enrichments; Analisis del desempeno de celdas combustibles BWR con un solo enriquecimiento y con distribucion radial de enriquecimientos

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, J. A.; Vargas, S.; Alonso, G.; Del Valle, E. [IPN, Escuela Superior de Fisica y Matematicas, Av. IPN s/n, Col. Lindavista, Mexico D. F. 07738 (Mexico); Xolocostli M, J. V. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico)]. e-mail: govaj666@hotmail.com

    2008-07-01

    The efficient use of the fuel is one of the objectives in the assemblies design of type BWR. The present tendency in the assemblies design of type BWR is through a radial distribution of enrichments. The present work has like object showing the because of this decision, for what a comparison of the neutronic performance of two fuel cells with the same enrichment average but one of them with radial distribution of enrichment and the other with a single enrichment equal to the average. The cells were analyzed with the CASMO-4 code and the obtained results of the behavior of the neutron flow and the power sustain the because of the radial distribution of enrichments. (Author)

  6. Analysis of the medicine list essential for eyes in China%中国眼科基本药物目录探析

    Institute of Scientific and Technical Information of China (English)

    辛红霞; 刘伟; 王利杰

    2009-01-01

    Objective The national essential medicine select system is the core of Chinese medicine policy.How to select drugs fundamental for eyes scientifically is an important ring in establishing the Chinese essential drug system.The present study attempted to compare the National Essential Medicines List and National Essential Insurance List of China with that of the WHO in order to provide reasonable evidence for the adjustment of a new National Essential Medicines List of China. MethodsThe WHO Essential Medicine List (15th edition,Version in 2007),National Essential Medicine List (Version in 2009,China),2009 National Essential Medicine List Chemical Medicine Name (Version in 2009) and National Essential Insurance List of China (Version in 2004) were reviewed.The similarity and difference in the category and number of drugs in the National Essential Medicines List and National Essential Insurance List between China and WHO were compared and analyzed.A descriptive method was adopted to analyze the sorts and numbers of eye drugs in the lists mentioned above.The analysis of drug price was based on the summary sheet from Zhejiang Province. ResultsLittle difference was found in the numbers of eye drugs between the National Essential Medicines List of China and WHO Essential Medicines List.Differences in the sorts of eye drugs were observed in the lists,especially between the National Essential Medicines List of China and WHO Essential Medicines List.Except for levofloxacin,all of the drugs in the National Essential Medicine List of China were included in the National Essential Insurance List of China.ConclusionThe selecting principle and renewing procedure of the National Essential Medicines List and National Essential Insurance List of China should be further improved in China based on the list from WHO.More attention should be paid to the standard,dosage form,affordability,maneuverability etc.during the selecting procedure of eye essential drugs.%目的 比较中国(2009

  7. Physico-chemical quality and homogeneity of folic acid and iron in enriched flour using principal component analysis.

    Science.gov (United States)

    Soeiro, Bruno T; Boen, Thaís R; Wagner, Roger; Lima-Pallone, Juliana A

    2009-01-01

    The aim of the present work was to determine parameters of the corn and wheat flour matrix, such as protein, lipid, moisture, ash and carbohydrates, folic acid and iron contents. Three principal components explained 91% of the total variance. Wheat flours were characterized by high protein and moisture content. On the other hand, the corn flours had the greater carbohydrates, lipids and folic acid levels. The concentrations of folic acid were lower than the issued value for wheat flours. Nevertheless, corn flours presented extremely high values. The iron concentration was higher than that recommended in Brazilian legislation. Poor homogenization of folic acid and iron was observed in enriched flours. This study could be useful to help the governmental authorities in the enriched food programs evaluation.

  8. 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.

  9. Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John; Smith, Richard D.; Metz, Thomas O.

    2007-06-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resulted in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.

  10. 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.

  11. Evaluation of metal enrichment and trophic status on the basis of biogeochemical analysis of shelf sediments of the southeastern Arabian Sea, India

    Science.gov (United States)

    Cheriyan, Eldhose; Sreekanth, Athira; Mrudulrag, S. K.; Sujatha, C. H.

    2015-10-01

    The present study investigated the distribution of environmentally relevant metals and organic matter in the shelf sediments of the southeastern Arabian Sea using biogeochemical proxies for the assessment of environmental quality and trophic status. The distribution of metals in the study site followed the order: Fe>Mg>Pb>Ni>Mn>Co>Cu>Zn>Cd. High biological productivity associated with upwelling leads to significant accumulation of Cd higher than crustal abundance in the shelf region. The enrichment factor (EF) of metals demonstrate enrichment of Pb and Co which suggests the anthropogenic influence and not redox conditions. The sediment quality guidelines (SQG) in comparison with metal concentration revealed adverse effects, possibly occurring in marine benthic species. The spatial trend of metal enrichment along transects is appreciably controlled by the adsorption to fine grained sediments. The multivariate statistical analyses, such as correlations and principal component analysis (PCA) clearly indicated the control of texture, association of clay minerals in the degree of trace metal (Cd, Pb, Ni and Co) contamination from anthropogenic as well as natural sources. Low levels of Zn, preferably display scavenging by Fe/Mn metal oxides. Biochemical descriptors in sediments indicated meso-oligotrophic conditions prevailing in the summer monsoon. The ratios among various biogeochemical parameters such as total organic carbon/total nitrogen (TOC/TNcontamination from a potential fishery zone of Indian exclusive economic zone.

  12. Facile synthesis of Cu(2+)-modified mesoporous silica-coated magnetic graphene composite for enrichment of microcystin-LR followed by mass spectrometry analysis.

    Science.gov (United States)

    Liu, Shasha; Deng, Chunhui; Zhang, Xiangmin

    2016-07-01

    MCs is a group of potent hepatotoxic peptides produced by cyanobacterial in eutrophic water, among which microcystin-LR is the most abundant and toxic. Long-time accumulation of even trace dosage from drinking water would cause significantly hepatic injury to animal and humans. Here we reported a novel Cu(2+)-modified mesoporous silica coated magnetic graphene composite (magG@mSiO2@-Cu(2+)) through mild sol-gel process and surface modification. Next, the composites were successfully applied for enrichment and separation of microcystin-LR followed by MALDI-TOF MS analysis based on the virtues of excellent hydrophilicity, high surface area (261cm(2)g(-1)), sensitively magnetic separation property, accessible porosity (3.10nm) and large amount of modified Cu(2+) ions. Even performed in a lower concentration (0.5μg/L), at which microcystin-LR could not be detected directly, after treatment with the composites the S/N ratio could appear to be 82.93. Furthermore, the novel composites also exhibited high enrichment efficiency in real water sample. It provided a sensitive and efficient technique for enrichment and detection of microcystin-LR and developed a potent method for separation of pollutant in contaminated water.

  13. The Protection of Children’s Privacy in Večernji List and Jutarnji List 2010-2013: A Comparative Analysis

    OpenAIRE

    Lana Ciboci

    2014-01-01

    According to research conducted in 2010 and 2011 (Ciboci et. al., 2011; Vlainić, 2012) children's rights are often violated in Croatian daily newspapers. Since then, the public worked hard on the promotion and protection of children's rights, particularly in the media. The legal protection of children's privacy in the media was increased, as well. The aim of this study is to determine whether the policy of reporting on children in the two most read Croatian daily newspapers - Večernji list an...

  14. ANALYSIS OF HEDGING DETERMINANTS WITH FOREIGN CURRENCY DERIVATIVE INSTRUMENTS ON COMPANIES LISTED ON BEI PERIOD 2012-2015

    Directory of Open Access Journals (Sweden)

    Gatot Nazir Ahmad

    2015-09-01

    Full Text Available This study is conducted to see the effect of the company's firm size, growth opportunities, leverage and liquidity on the decision of hedging with foreign currency derivative instruments on manufacturing companies listed on the Indonesian Stock Exchange (BEI period 2012-2015. The Data that is used on this study is a set of data panel with purposive sampling method, and the criteria for the sample is: (1 manufacturing companies listed on the Stock Exchange period 2012 to 2015, (2 manufacturing companies that has transaction exposure ( liabilities and / or assets denominated in foreign currency, (3 manufacturing companies that has the data is needed for this study. The total sample of this study is 106 companies or 424 observation within 4 years. The Data analysis technique that is used on this study is logistic regression with z-statistic as hypotheses testing to test the regression coefficient with an alpha of 5%. The study result shows that firm size, growth opportunities and liquidity positively and Significantly Affect the decision of hedging with foreign currency derivative instruments, while leverage negatively and insignificantly Affect the decision of hedging with foreign currency derivative instruments.

  15. Econometric analysis on the impact of macroeconomic variables toward financial performance: A case of Malaysian public listed logistics companies

    Science.gov (United States)

    Zakariah, Sahidah; Pyeman, Jaafar; Ghazali, Rahmat; Rahman, Ibrahim A.; Rashid, Ahmad Husni Mohd; Shamsuddin, Sofian

    2014-12-01

    The primary concern of this study is to analyse the impact against macroeconomic variables upon the financial performance, particularly in the case of public listed logistics companies in Malaysia. This study incorporated five macroeconomic variables and four proxies of financial performance. The macroeconomic variables selected are gross domestic product (GDP), total trade (XM), foreign direct investment (FDI), inflation rate (INF), and interest rate (INT). This study is extended to the usage of ratio analysis to predict financial performance in relation to the changes upon macroeconomic variables. As such, this study selected four (4) ratios as proxies to financial performance, which is Operating Profit Margin (OPM), Net Profit Margin (NPM), Return on Asset (ROA), Return on Equity (ROE). The findings of this study may appear non-controversial to some, but it resulted in the following important consensus; (1) GDP is found to be highly impacting NPM and least of ROA, (2) XM has high positive impact on OPM and least on ROE, (3) FDI appear to have insignificant impact towards NPM, and (4) INF and INT show similar negative impact on financial performance, precisely highly negative on OPM and least on ROA. Such findings also conform to the local logistic industry settings, specifically in regards to public listed logistics companies in relation to its financial performance.

  16. Value added analysis and its distribution: a study on BOVESPA-listed banks using ANOVA

    Directory of Open Access Journals (Sweden)

    Leonardo José Seixas Pinto

    2013-05-01

    Full Text Available The value added generated by the financial institutions listed on BOVESPA and its distribution in the years between 2007 to 2011 are the subject of this research which shows how banks divided his wealth with the people, government, third parties and shareholders. Through the use of ANOVA test average in the companies that took part in this research concluded that: (a the average value added of foreign banks differs from national banks. (b The remuneration policy of equity foreign banks differs from national banks. (c The policy of distribution of value added to employees of foreign banks Santander and HSBC differs from the other banks. (d Taxes paid to the government have equal means with the exception of Santander. (e Although curious, Banco Itau and Banco do Brazil is equal in all analyzes in the distribution of value added since it is a private and one public. It appears this way a policy unequal distribution of wealth generation and foreign banks compared with the national public and private banks.

  17. Audit fees: an analysis of the family and nonfamily business listed on the BM&FBovespa

    Directory of Open Access Journals (Sweden)

    Franciele Beck

    2015-08-01

    Full Text Available Objective – Examine the relationship between audit fees and the quality of financial information in familiar and non-familiar companies listed on the BM&FBovespa. Design/methodology/approach – Descriptive, documentary research with application of average test and linear regression model, using data from 2009, 2010 and 2011 of a sample of 133 family businesses and 128 non-familiar BM&FBovespa. The basis for the study was Ghosh and Tang (2015. Findings - The findings indicate a rejection of the hypothesis through the average test and regression model, in which the variable dependent (family firms was not statistically significant. This result differs from that obtained by Ghosh and Tang (2015 and makes inference to the characteristics of the companies and the Brazilian market. Practical implications – Enabled the discussion on the relationship between audit fees and the structure of ownership and control of Brazilian companies, going through the theme of quality of financial information. It also helped the identification of key explanatory variables for audit fees. In family firms included: size, foreign-sales, mergers and/or acquisitions (M&A, Big Four, and in non-family firms: size, regulation, busy-season, Big Four and auditor-tenure.

  18. Whole-Transcriptome RNA-seq, Gene Set Enrichment Pathway Analysis, and Exon Coverage Analysis of Two Plastid RNA Editing Mutants.

    Science.gov (United States)

    Hackett, Justin B; Lu, Yan

    2017-04-07

    In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed two plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the beta subunit of cytochrome b559, an essential component of PSII. The accD gene encodes the beta subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly up-regulated in both orrm6 mutants. The up-regulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.

  19. Selective Enrichment and MALDI-TOF MS Analysis of Small Molecule Compounds with Vicinal Diols by Boric Acid-Functionalized Graphene Oxide

    Science.gov (United States)

    Zhang, Jing; Zheng, Xiaoling; Ni, Yanli

    2015-08-01

    In this study, a 4-vinylphenylboronic acid-functionalized graphene oxide (GO) material was prepared via atom-transfer radical polymerization (ATRP) method and applied for the first time as a novel matrix for the selective enrichment and analysis of small-molecule compounds with vicinal diols, which have been the focus of intense research in the field of life science, by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in positive-ion mode. There are two main factors playing a decisive role in assisting laser D/I process comparing to some traditional matrices: (1) GO provides π-conjugated system by itself for laser absorption and energy transfer; (2) the modified 4-vinylphenylboronic acid can selectively capture small-molecule compounds with vicinal diols. The results demonstrate that the novel material has distinct advantages over previously reported matrices in enriching and assisting the highly efficient ionization of target molecules for mass spectrometry analysis. This work indicates a new application branch for graphene-based matrices and provides an alternative solution for small-molecules analysis.

  20. Comparative Analysis of 16S rRNA and amoA Genes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

    Science.gov (United States)

    Xu, Mouzhong; Schnorr, Jon; Keibler, Brandon

    2012-01-01

    We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the “root” clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized. PMID:22267662

  1. Regulation signature of miR-143 and miR-26 in porcine Salmonella infection identified by binding site enrichment analysis.

    Science.gov (United States)

    Yao, Min; Gao, Weihua; Tao, Hengxun; Yang, Jun; Liu, Guoping; Huang, Tinghua

    2016-04-01

    Salmonella infects many vertebrate species, and pigs colonized with Salmonella are typically Salmonella carriers. Transcriptomic analysis of the response to Salmonella infection in whole blood has been reported for the pig. The objective of this study is to identify the important miRNAs involved in Salmonella infection using binding site enrichment analysis. We predicted porcine microRNA (miRNA) binding sites in the 3' UTR of protein-coding genes for all miRNA families. Based on those predictions, we analyzed miRNA-binding sites for mRNAs expressed in peripheral blood to investigate the functional importance of miRNAs in Salmonella infection in pig. Enrichment analysis revealed that binding sites of five miRNAs (including miR-143, -9839, -26, -2483, and -4335) were significantly over represented for the differentially expressed gene sets. Real-time PCR results indicated that selected members of this miRNA group (miR-143, -26, and -4335) were differentially expressed in whole blood after Salmonella inoculation. The luciferase reporter assay showed that ATP6V1A and IL13RA1 were targets of miR-143 and that miR-26 regulates BINP3L and ARL6IP6. The results strongly suggest that miR-143 and miR-26 play important regulatory roles in the development of Salmonella infection in pig.

  2. A cluster analysis method for identification of subpopulations of cells in flow cytometric list-mode arrays

    Science.gov (United States)

    Li, Z. K.

    1985-01-01

    A specialized program was developed for flow cytometric list-mode data using an heirarchical tree method for identifying and enumerating individual subpopulations, the method of principal components for a two-dimensional display of 6-parameter data array, and a standard sorting algorithm for characterizing subpopulations. The program was tested against a published data set subjected to cluster analysis and experimental data sets from controlled flow cytometry experiments using a Coulter Electronics EPICS V Cell Sorter. A version of the program in compiled BASIC is usable on a 16-bit microcomputer with the MS-DOS operating system. It is specialized for 6 parameters and up to 20,000 cells. Its two-dimensional display of Euclidean distances reveals clusters clearly, as does its 1-dimensional display. The identified subpopulations can, in suitable experiments, be related to functional subpopulations of cells.

  3. The fuzzy line between needs, coverage, and excess in the Mexican Formulary List: an example of qualitative market width analysis.

    Science.gov (United States)

    Rico-Alba, Israel; Figueras, Albert

    2013-04-01

    To assess the rationality of the Mexican Formulary List (MEX-LIST). MEX-LIST was compared with the World Health Organization Essential Medicines List (WHO-LIST) to identify drugs classified as unmet needs. For the MEX-LIST rationality evaluation, the assessment of a non-sponsored, systematic and unbiased source (Prescrire Journal) was used for medicines not listed in WHO-LIST. The rating scale of Prescrire classifies medicines as Bravo, Real Advance, Offers an Advance, Possibly Helpful, Nothing New (NN), Judgment Reserved (JR), or Not Acceptable (NA) depending on their comparative therapeutic value. The NN, JR, and NA categories of medicines are further classified as non-added value. The MEX-LIST contains 771 medicines, which is 2.4-fold more than the WHO-LIST (n = 321). Up to 236 medicines in the MEX-LIST perfectly match the WHO-LIST medicines, 40 could be considered as reasonable substitutes, but 45 (14.0 %) present in the WHO-LIST are not present in the MEX-LIST, including an oversupply of 495 medicines. Rationality level could be analyzed for 353 of these: 43.1 % (n = 152) were classified as NN, 12.2 % (n = 43) as NA, and 6.2 % (n = 22) as JR due to limited available information. In summary, 61.5 % of the evaluated medicines present in the MEX-LIST but not included in the WHO-LIST (n = 217) can be considered drugs that do not add substantial therapeutic benefits, this accounts for 28.1 % of the medicines in the MEX-LIST. MEX-LIST is characterized by a twofold irrationality in that essential medicines to treat prevalent diseases are missing and medicines without any rational added value are in oversupply. This type of study can be easily applied to other countries with the aim of providing a forum for further discussion and improvement of the medicines offered by their national formularies.

  4. Learning From Experience: Qualitative Analysis to Develop a Cognitive Task List for Vaginal Breech Deliveries.

    Science.gov (United States)

    Secter, Michael B; Simpson, Andrea N; Gurau, David; Snelgrove, John W; Hodges, Ryan; Mocarski, Eva; Pittini, Richard; Windrim, Rory; Higgins, Mary

    2015-11-01

    Objectif : De nos jours, dans le domaine de l’obstétrique, il est difficile d’acquérir les compétences cliniques nécessaires à la tenue d’un accouchement vaginal du siège (AVS) en toute sûreté. Des stratégies pédagogiques novatrices sont requises, puisque l’exposition des stagiaires en obstétrique à l’AVS demeure limitée. Cette étude avait pour objectif d’identifier, au moyen de démonstrations filmées par des spécialistes, les compétences verbales et non verbales nécessaires à la prise en charge de l’AVS. Méthodes : Les membres du personnel infirmier de la salle de travail et d’accouchement de trois importants hôpitaux universitaires ont identifié les cliniciens qu’ils considéraient comme étant compétents en matière d’AVS. Les obstétriciens les plus souvent identifiés ont été conviés à participer à l’étude. Les participants ont été filmés alors qu’ils procédaient à un AVS sur un simulateur d’accouchement; à ces occasions, nous leur avons également demandé de nous entretenir de leur évaluation et de leur technique, ainsi que de nous fournir des conseils cliniques issus de leur expérience. Deux membres de l’étude ont passé en revue toutes les vidéos et ont documenté les composantes verbales et non verbales de l’évaluation, les ont groupées en thèmes communs et en ont rédigé une synthèse. Cette synthèse a été transmise à tous les participants et a été analysée par des obstétriciens expérimentés de l’étranger. Résultats : Dix-sept cliniciens ont été identifiés; 12 (70 %) ont consenti à participer à l’étude. Parmi les thèmes identifiés, on trouvait les suivants : évaluation méticuleuse et counseling prégrossesse; rôles de l’équipe multidisciplinaire; nécessité d’une communication attentive et adéquate avec les parents; techniques d’accouchement particulières; et documentation et soins postpartum. Une liste des tâches cliniques a été g

  5. Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease

    Directory of Open Access Journals (Sweden)

    Wang Bin

    2011-03-01

    Full Text Available Abstract Background HIV preferentially infects CD4+ T cells, and the functional impairment and numerical decline of CD4+ and CD8+ T cells characterize HIV disease. The numerical decline of CD4+ and CD8+ T cells affects the optimal ratio between the two cell types necessary for immune regulation. Therefore, this work aimed to define the genomic basis of HIV interactions with the cellular transcriptome of both CD4+ and CD8+ T cells. Results Genome-wide transcriptomes of primary CD4+ and CD8+ T cells from HIV+ patients were analyzed at different stages of HIV disease using Illumina microarray. For each cell subset, pairwise comparisons were performed and differentially expressed (DE genes were identified (fold change >2 and B-statistic >0 followed by quantitative PCR validation. Gene ontology (GO analysis of DE genes revealed enriched categories of complement activation, actin filament, proteasome core and proton-transporting ATPase complex. By gene set enrichment analysis (GSEA, a network of enriched pathways functionally connected by mitochondria was identified in both T cell subsets as a transcriptional signature of HIV disease progression. These pathways ranged from metabolism and energy production (TCA cycle and OXPHOS to mitochondria meditated cell apoptosis and cell cycle dysregulation. The most unique and significant feature of our work was that the non-progressing status in HIV+ long-term non-progressors was associated with MAPK, WNT, and AKT pathways contributing to cell survival and anti-viral responses. Conclusions These data offer new comparative insights into HIV disease progression from the aspect of HIV-host interactions at the transcriptomic level, which will facilitate the understanding of the genetic basis of transcriptomic interaction of HIV in vivo and how HIV subverts the human gene machinery at the individual cell type level.

  6. Has the impact of rising CO2 on plants been exaggerated by meta-analysis of free air CO2 enrichment studies?

    Directory of Open Access Journals (Sweden)

    Matthew Haworth

    2016-08-01

    Full Text Available Meta-analysis is extensively used to synthesise the results of free air CO2 enrichment (FACE studies to produce an average effect size, which is then used to model likely plant response to rising [CO2]. The efficacy of meta-analysis is reliant upon the use of data that characterises the range of responses to a given factor. Previous meta-analyses of the effect of FACE on plants have not incorporated the potential impact of reporting bias in skewing data. By replicating the methodology of these meta-analytic studies, we demonstrate that meta-analysis of FACE has likely exaggerated the effect size of elevated [CO2] on plants by 20 to 40%; having significant implications for predictions of food security and vegetation response to climate change. Incorporation of the impact of reporting bias did not affect the significance or the direction of the [CO2] effect.

  7. Has the Impact of Rising CO2 on Plants been Exaggerated by Meta-Analysis of Free Air CO2 Enrichment Studies?

    Science.gov (United States)

    Haworth, Matthew; Hoshika, Yasutomo; Killi, Dilek

    2016-01-01

    Meta-analysis is extensively used to synthesize the results of free air CO2 enrichment (FACE) studies to produce an average effect size, which is then used to model likely plant response to rising [CO2]. The efficacy of meta-analysis is reliant upon the use of data that characterizes the range of responses to a given factor. Previous meta-analyses of the effect of FACE on plants have not incorporated the potential impact of reporting bias in skewing data. By replicating the methodology of these meta-analytic studies, we demonstrate that meta-analysis of FACE has likely exaggerated the effect size of elevated [CO2] on plants by 20 to 40%; having significant implications for predictions of food security and vegetation response to climate change. Incorporation of the impact of reporting bias did not affect the significance or the direction of the [CO2] effect.

  8. Recalcitrance and structural analysis by water-only flowthrough pretreatment of (13)C enriched corn stover stem.

    Science.gov (United States)

    Foston, Marcus; Trajano, Heather L; Samuel, Reichel; Wyman, Charles E; He, Jian; Ragauskas, Arthur J

    2015-12-01

    This study presents high temperature water-only continuous flowthrough pretreatment coupled with nuclear magnetic resonance (NMR) as a promising analytical tool to examine the plant cell wall, to understand its recalcitrance (i.e., cell wall resistance to deconstruction), and to probe the chemistry occurring during batch pretreatment of biomass. (13)C-enriched corn stover stems were pretreated at 170°C for 60min with a hot-water flow rate of 20mL/min to control fractionation of the cell wall. This approach helped elucidate the nature of plant cell wall chemical recalcitrance and biomass pretreatment chemistry by tracking cell wall fragmentation as a function of time. Fractions of the reactor effluent were collected in a time-resolved fashion and characterized by various NMR techniques to determine the degree and sequence of fragments released, as well as, the chemical composition, molecular structure, and relative molecular weight of those released fragments.

  9. Cluster Analysis of Flow Cytometric List Mode Data on a Personal Computer

    NARCIS (Netherlands)

    Bakker Schut, Tom C.; Bakker schut, T.C.; de Grooth, B.G.; Greve, Jan

    1993-01-01

    A cluster analysis algorithm, dedicated to analysis of flow cytometric data is described. The algorithm is written in Pascal and implemented on an MS-DOS personal computer. It uses k-means, initialized with a large number of seed points, followed by a modified nearest neighbor technique to reduce

  10. Comparative analysis of tertiary alcohol esterase activity in bacterial strains isolated from enrichment cultures and from screening strain libraries.

    Science.gov (United States)

    Herter, Susanne; Nguyen, Giang-Son; Thompson, Mark L; Steffen-Munsberg, Fabian; Schauer, Frieder; Bornscheuer, Uwe T; Kourist, Robert

    2011-05-01

    The preparation of enantiopure tertiary alcohols is of great contemporary interest due to the application of these versatile building blocks in organic synthesis and as precursors towards high value pharmaceutical compounds. Herein, we describe two approaches taken towards the discovery of novel biocatalysts for the synthesis of these valuable compounds. The first approach was initiated with screening of 47 bacterial strains for hydrolytic activity towards the simple tertiary alcohol ester tert-butyl acetate. In conjunction, a second method focussed on the isolation of strains competent for growth on tert-butyl acetate as the sole source of carbon and energy. From functional screening, 10 Gram-positive Actinomycetes showed hydrolytic activity, whilst enrichment selection resulted in the identification of 14 active strains, of which five belong to the Gram-negative cell-wall type. Bacterial strains obtained from both approaches were viable for enantioselective hydrolysis of pyridine substituted tertiary alcohol esters in addition to bulky aliphatic and keto-derived substrates from the same class. Activity towards each of the test substrates was uncovered, with promising enantioselectivities of up to E = 71 in the hydrolysis of a para-substituted pyridine tertiary alcohol ester using a strain of Rhodococcus ruber. Interestingly strains of Microbacterium and Alcaligenes sp. gave opposite enantiopreference in the hydrolysis of a meta-substituted pyridine tertiary alcohol ester with E values of 17 and 54. These approaches show that via both possibilities, screening established strain collections and performing enrichment selection, it is possible to identify novel species which show activity towards sterically challenging substrates.

  11. Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Sample ontology, GOstat and ontology term enrichment Data detail Data name Sample on...tology, GOstat and ontology term enrichment DOI 10.18908/lsdba.nbdc01389-006.V002 Version V2 10.18908/lsdba....t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

  12. What Technology Skills Do Developers Need? A Text Analysis of Job Listings in Library and Information Science (LIS from Jobs.code4lib.org

    Directory of Open Access Journals (Sweden)

    Monica Maceli

    2015-09-01

    Full Text Available Technology plays an indisputably vital role in library and information science (LIS work; this rapidly moving landscape can create challenges for practitioners and educators seeking to keep pace with such change.  In pursuit of building our understanding of currently sought technology competencies in developer-oriented positions within LIS, this paper reports the results of a text analysis of a large collection of job listings culled from the Code4lib jobs website.  Beginning over a decade ago as a popular mailing list covering the intersection of technology and library work, the Code4lib organization's current offerings include a website that collects and organizes LIS-related technology job listings.  The results of the text analysis of this dataset suggest the currently vital technology skills and concepts that existing and aspiring practitioners may target in their continuing education as developers.

  13. Portable microcomputer for the analysis of plutonium gamma-ray spectra. Volume II. Software description and listings. [IAEAPU

    Energy Technology Data Exchange (ETDEWEB)

    Ruhter, W.D.

    1984-05-01

    A portable microcomputer has been developed and programmed for the International Atomic Energy Agency (IAEA) to perform in-field analysis of plutonium gamma-ray spectra. The unit includes a 16-bit LSI-11/2 microprocessor, 32-K words of memory, a 20-character display for user prompting, a numeric keyboard for user responses, and a 20-character thermal printer for hard-copy output of results. The unit weights 11 kg and has dimensions of 33.5 x 30.5 x 23.0 cm. This compactness allows the unit to be stored under an airline seat. Only the positions of the 148-keV /sup 241/Pu and 208-keV /sup 237/U peaks are required for spectral analysis that gives plutonium isotopic ratios and weight percent abundances. Volume I of this report provides a detailed description of the data analysis methodology, operation instructions, hardware, and maintenance and troubleshooting. Volume II describes the software and provides software listings.

  14. Evolving Lists

    Institute of Scientific and Technical Information of China (English)

    JOEI; VILLARAMA

    2009-01-01

    More than two years ago, I wrote a list of the top 10 reasons I love living in China. It was published in a local expats’ magazine and somebody from a radio station spotted it and invited me to talk about the article on the air, a hilarious, comedic if not surreal experience for any foreigner.

  15. Comparative analysis of clinical-scale IFN-gamma positive T-cell enrichment using partially and fully integrated platforms

    Directory of Open Access Journals (Sweden)

    Christoph Priesner

    2016-09-01

    Full Text Available Background and aims. The infusion of enriched CMV-specific donor T-cells appears to be a suitable alternative for the treatment of drug resistant CMV reactivation or de novo infection after both solid organ and hematopoietic stem cell transplantation. Antiviral lymphocytes can be selected from apheresis products using the CliniMACS Cytokine-Capture-System® either with the well-established CliniMACS® Plus (Plus device or with its more versatile successor CliniMACS Prodigy® (Prodigy. Methods. Manufacturing of CMV-specific T-cells was carried out with the Prodigy and Plus in parallel starting with 0.8-1*109 leukocytes collected by lymphapheresis (n=3 and using the MACS GMP PepTivator® HCMVpp65 for antigenic re-stimulation. Target and non-target cells were quantified by a newly developed single-platform assessment and gating strategy using positive (CD3/CD4/CD8/CD45/IFN-gamma, negative (CD14/CD19/CD56, and dead cell (7-AAD discriminators. Results. Both devices produced largely similar results for target cell viabilities: 37.2%-52.2% (Prodigy vs. 51.1%-62.1% (Plus CD45+/7-AAD- cells. Absolute numbers of isolated target cells were 0.1-3.8*106 viable IFN-gamma+ CD3+ cells. The corresponding proportions of IFN-gamma+ CD3+ cells ranged between 19.2% and 95.1% among total CD3+ cells and represented recoveries of 41.9%-87.6%. Within two parallel processes predominantly IFN-gamma+ CD3+CD8+ cytotoxic T-cells were enriched compared to one process that yielded a higher amount of IFN-gamma+ CD3+CD4+ helper T lymphocytes. T-cell purity was higher for the Prodigies products that displayed a lower content of contaminating IFN-gamma- T-cells (3.6%-20.8% compared to the Plus products (19.9%-80.0%. Conclusions. The manufacturing process on the Prodigy saved both process and hands-on time due to its higher process integration and ability for unattended operation. Although the usage of both instruments yielded comparable results, the lower content of residual IFN

  16. Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer.

    Directory of Open Access Journals (Sweden)

    Kazuhide Watanabe

    Full Text Available BACKGROUND: Deregulation of canonical Wnt/CTNNB1 (beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are highly frequent in colon cancer and cause aberrant stabilization of CTNNB1, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of CTNNB1 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of CTNNB1 in colon cancer cells. RESULTS: We observed 3629 CTNNB1 binding peaks across the genome and a significant correlation between CTNNB1 binding and knockdown-induced gene expression change. Our integrative analysis led to the discovery of a direct Wnt target signature composed of 162 genes. Gene ontology analysis of this signature revealed a significant enrichment of Wnt pathway genes, suggesting multiple feedback regulations of the pathway. We provide evidence that this gene signature partially overlaps with the Lgr5+ intestinal stem cell signature, and is significantly enriched in normal intestinal stem cells as well as in clinical colorectal cancer samples. Interestingly, while the expression of the CTNNB1 target gene set does not correlate with survival, elevated expression of negative feedback regulators within the signature predicts better prognosis. CONCLUSION: Our data provide a genome-wide view of chromatin occupancy and gene regulation of Wnt/CTNNB1 signaling in colon cancer cells.

  17. Selective enrichment and ultrasensitive identification of trace peptides in proteome analysis using transient capillary isotachophoresis/zone electrophoresis coupled with nano-ESI-MS.

    Science.gov (United States)

    An, Yanming; Cooper, Jonathan W; Balgley, Brian M; Lee, Cheng S

    2006-09-01

    Besides the complexity in protein samples of biological origin, probably the greatest challenge presently facing comprehensive proteome analysis is related to the large variation of protein relative abundances (>6 orders of magnitude), having potential biological significance in mammalian systems. As demonstrated in this work, transient capillary ITP/zone electrophoresis (CITP/CZE) provides selective analyte enrichment through electrokinetic stacking and extremely high resolving power toward protein and peptide mixtures. The result of the CITP process is that major components may be diluted, but trace compounds are concentrated. The on-column transition of CITP to CZE minimizes additional band broadening while providing superior analyte resolution. Online coupling of transient CITP/CZE with nano-ESI-MS allows ultrasensitive detection of trace peptides at levels of subnanomolar concentration or subfemtomole mass in complex peptide mixtures. More importantly, selective enrichment of trace peptides enables the identification and sequence analysis of low-abundance peptides co-migrated with highly abundant species at a concentration ratio of 1:500,000. The combined CITP/CZE-nano-ESI-MS system is demonstrated to be at least one to two orders of magnitude more sensitive than that attained in conventional electrophoretic and chromatographic-based proteome technologies over a wide dynamic concentration range, potentially allowing comprehensive analysis of protein profiles within a small cell population and limited tissue samples using conventional mass spectrometers. Furthermore, the speed of CITP/CZE separation and the lack of column equilibration in CITP/CZE not only improve the throughput of proteome analysis, but also facilitate its seamless integration with other separation technologies in a multidimensional protein identification platform.

  18. EnviroAtlas - NatureServe Analysis of Imperiled or Federally Listed Species by HUC-12 for the Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset includes analysis by NatureServe of species that are Imperiled (G1/G2) or Listed under the U.S. Endangered Species Act (ESA) by 12-digit...

  19. Development of Nonword and Irregular Word Lists for Australian Grade 3 Students Using Rasch Analysis

    Science.gov (United States)

    Callinan, Sarah; Cunningham, Everarda; Theiler, Stephen

    2014-01-01

    Many tests used in educational settings to identify learning difficulties endeavour to pick up only the lowest performers. Yet these tests are generally developed within a Classical Test Theory (CTT) paradigm that assumes that data do not have significant skew. Rasch analysis is more tolerant of skew and was used to validate two newly developed…

  20. Metabolic Biomarkers and Neurodegeneration: A Pathway Enrichment Analysis of Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis.

    Science.gov (United States)

    Kori, Medi; Aydın, Busra; Unal, Semra; Arga, Kazim Yalcin; Kazan, Dilek

    2016-11-01

    Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) lack robust diagnostics and prognostic biomarkers. Metabolomics is a postgenomics field that offers fresh insights for biomarkers of common complex as well as rare diseases. Using data on metabolite-disease associations published in the previous decade (2006-2016) in PubMed, ScienceDirect, Scopus, and Web of Science, we identified 101 metabolites as putative biomarkers for these three neurodegenerative diseases. Notably, uric acid, choline, creatine, L-glutamine, alanine, creatinine, and N-acetyl-L-aspartate were the shared metabolite signatures among the three diseases. The disease-metabolite-pathway associations pointed out the importance of membrane transport (through ATP binding cassette transporters), particularly of arginine and proline amino acids in all three neurodegenerative diseases. When disease-specific and common metabolic pathways were queried by using the pathway enrichment analyses, we found that alanine, aspartate, glutamate, and purine metabolism might act as alternative pathways to overcome inadequate glucose supply and energy crisis in neurodegeneration. These observations underscore the importance of metabolite-based biomarker research in deciphering the elusive pathophysiology of neurodegenerative diseases. Future research investments in metabolomics of complex diseases might provide new insights on AD, PD, and ALS that continue to place a significant burden on global health.

  1. Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences

    Directory of Open Access Journals (Sweden)

    Jacob D. Galson

    2015-12-01

    Full Text Available Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

  2. Synthesis of Bismuth-Nanoparticle-Enriched Nanoporous Carbon on Graphene for Efficient Electrochemical Analysis of Heavy-Metal Ions.

    Science.gov (United States)

    Cui, Lin; Wu, Jie; Ju, Huangxian

    2015-08-03

    A BiNPs@NPCGS nanocomposite was designed for highly efficient detection of multiple heavy-metal ions by in situ synthesis of bismuth-nanoparticle (BiNP)-enriched nanoporous carbon (NPS) on graphene sheet (GS). The NPCGS was prepared by pyrolysis of zeolitic imidazolate framework-8 (ZIF-8) nanocrystals deposited on graphene oxide and displayed a high surface area of 1251 m(2)  g(-1) and a pore size of 3.4 nm. BiNPs were deposited on NPCGS in situ by chemical reduction of Bi(3+) with NaBH4 . Due to the restrictive effect of the pore/surface structure of NPCGS, the BiNPs were uniform and well dispersed on the NPCGS. The BiNPs@NPCGS showed good conductivity and high effective area, and the presence of BiNPs allowed it to act as an efficient material for anodic-stripping voltammetric detection of heavy-metal ions. Under optimized conditions, the BiNPs@NPCGS-based sensor could simultaneously determine Pb(2+) and Cd(2+) with detection limits of 3.2 and 4.1 nM, respectively. Moreover, the proposed sensor could also differentiate Tl(+) from Pb(2+) and Cd(2+). Owing to its advantages of simple preparation, environmental friendliness, high surface area, and fast electron-transfer ability, BiNPs@NPCGS showed promise for practical application in sensing heavy-metal ions.

  3. EMPIRICAL ANALYSIS OF THE PROFITABILITY AND INDEBTEDNESS IN LISTED COMPANIES – EVIDENCE FROM THE FEDERATION OF BIH

    Directory of Open Access Journals (Sweden)

    Dragan Gabrić

    2015-11-01

    Full Text Available Research on relationship between profitability and indebtedness is an interesting scientific and professional question because it is the basic criterion of performance and security in business. The aim of this paper is to examine and determine the level of correlation between profitability and indebtedness, and to research the differences in the level of indebtedness regarding company's profitability. The secondary data for the purposes of the empirical research were collected through the analysis of publicly available financial statements on a sample of companies listed on the quotation and free primary market on the Sarajevo Stock Exchange in the period from 2010. to 2013. The results of the correlation analysis indicate that there is a negative correlation between profitability indicators and indebtedness indicators within the researched companies in the observed period, which was specially indicated through the Total debt in the number of years and Interest coverage ratio. The results of testing the difference in indicators of indebtedness regarding profitability indicate that there is a difference in the indebtedness indicators measured by the Total debt in the number of years and Interest coverage ratio, between the companies that achieved positive financial result and the companies that achieved negative financial result.

  4. Finding needles in a haystack: application of network analysis and target enrichment studies for the identification of potential anti-diabetic phytochemicals.

    Science.gov (United States)

    Fayaz, Shaik M; Suvanish Kumar, Valsala S; Rajanikant, Krishnamurthy G

    2014-01-01

    Diabetes mellitus is a debilitating metabolic disorder and remains a significant threat to public health. Herbal medicines have been proven to be effective anti-diabetic agents compared to synthetic drugs in terms of side effects. However, the complexity in their chemical constituents and mechanism of action, hinder the effort to discover novel anti-diabetic drugs. Hence, understanding the biological and chemical basis of pharmacological action of phytochemicals is essential for the discovery of potential anti-diabetic drugs. Identifying important active compounds, their protein targets and the pathways involved in diabetes would serve this purpose. In this context, the present study was aimed at exploring the mechanism of action of anti-diabetic plants phytochemicals through network and chemical-based approaches. This study also involves a focused and constructive strategy for preparing new effective anti-diabetic formulations. Further, a protocol for target enrichment was proposed, to identify novel protein targets for important active compounds. Therefore, the successive use of network analysis combined with target enrichment studies would accelerate the discovery of potential anti-diabetic phytochemicals.

  5. Finding needles in a haystack: application of network analysis and target enrichment studies for the identification of potential anti-diabetic phytochemicals.

    Directory of Open Access Journals (Sweden)

    Shaik M Fayaz

    Full Text Available Diabetes mellitus is a debilitating metabolic disorder and remains a significant threat to public health. Herbal medicines have been proven to be effective anti-diabetic agents compared to synthetic drugs in terms of side effects. However, the complexity in their chemical constituents and mechanism of action, hinder the effort to discover novel anti-diabetic drugs. Hence, understanding the biological and chemical basis of pharmacological action of phytochemicals is essential for the discovery of potential anti-diabetic drugs. Identifying important active compounds, their protein targets and the pathways involved in diabetes would serve this purpose. In this context, the present study was aimed at exploring the mechanism of action of anti-diabetic plants phytochemicals through network and chemical-based approaches. This study also involves a focused and constructive strategy for preparing new effective anti-diabetic formulations. Further, a protocol for target enrichment was proposed, to identify novel protein targets for important active compounds. Therefore, the successive use of network analysis combined with target enrichment studies would accelerate the discovery of potential anti-diabetic phytochemicals.

  6. Prolonged applied potential to anode facilitate selective enrichment of bio-electrochemically active Proteobacteria for mediating electron transfer: microbial dynamics and bio-catalytic analysis.

    Science.gov (United States)

    Kannaiah Goud, R; Mohan, S Venkata

    2013-06-01

    Prolonged application of poised potential to anode was evaluated to understand the influence of applied potentials [500 mV (E500); 1000 mV (E1000); 2000 mV (E2000)] on bio-electrogenic activity of microbial fuel cell (MFC) and the resulting dynamics in microbial community in comparison to control operation. E1000 system documented higher electrogenic activity (309 mW/m(2)) followed by E500 (143 mW/m(2)), E2000 (112 mW/m(2)) and control (65 mW/m(2)) operations. The improved power output at optimum applied potential (1000mV) might be attributed to the enrichment of electrochemically active bacteria majorly belonging to the phylum Proteobacteria with less extent of Firmicutes which helped in effective electron (mediated) transfer through release of exogenous shuttlers. Improved bio-electrogenic activity due to enrichment at 1000mV applied potential also correlated well with the observed cyctochrome-c peaks on the voltamatogram, lower ion ohmic losses and bio-electro kinetic analysis. Electric-shock at higher applied potential (E2000) resulted in the survival of less number of microbial species leading to lower electrogenesis.

  7. Check list and zoogeographic analysis of the scale insect fauna (Hemiptera: Coccomorpha) of Greece.

    Science.gov (United States)

    Pellizzari, Giuseppina; Chadzidimitriou, Evangelia; Milonas, Panagiotis; Stathas, George J; Kozár, Ferenc

    2015-09-02

    This paper presents an updated checklist of the Greek scale insect fauna and the results of the first zoogeographic analysis of the Greek scale insect fauna. According to the latest data, the scale insect fauna of the whole Greek territory includes 207 species; of which 187 species are recorded from mainland Greece and the minor islands, whereas only 87 species are known from Crete. The most rich families are the Diaspididae (with 86 species), followed by Coccidae (with 35 species) and Pseudococcidae (with 34 species). In this study the results of a zoogeographic analysis of scale insect fauna from mainland Greece and Crete are also presented. Five species, four from mainland Greece and one from Crete are considered to be endemic. Comparison with the scale insect fauna of other countries is provided.

  8. 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.

  9. Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets

    Directory of Open Access Journals (Sweden)

    De Hertogh Benoît

    2010-10-01

    Full Text Available Abstract Background Microarray data is frequently used to characterize the expression profile of a whole genome and to compare the characteristics of that genome under several conditions. Geneset analysis methods have been described previously to analyze the expression values of several genes related by known biological criteria (metabolic pathway, pathology signature, co-regulation by a common factor, etc. at the same time and the cost of these methods allows for the use of more values to help discover the underlying biological mechanisms. Results As several methods assume different null hypotheses, we propose to reformulate the main question that biologists seek to answer. To determine which genesets are associated with expression values that differ between two experiments, we focused on three ad hoc criteria: expression levels, the direction of individual gene expression changes (up or down regulation, and correlations between genes. We introduce the FAERI methodology, tailored from a two-way ANOVA to examine these criteria. The significance of the results was evaluated according to the self-contained null hypothesis, using label sampling or by inferring the null distribution from normally distributed random data. Evaluations performed on simulated data revealed that FAERI outperforms currently available methods for each type of set tested. We then applied the FAERI method to analyze three real-world datasets on hypoxia response. FAERI was able to detect more genesets than other methodologies, and the genesets selected were coherent with current knowledge of cellular response to hypoxia. Moreover, the genesets selected by FAERI were confirmed when the analysis was repeated on two additional related datasets. Conclusions The expression values of genesets are associated with several biological effects. The underlying mathematical structure of the genesets allows for analysis of data from several genes at the same time. Focusing on expression

  10. Making Lists, Enlisting Scientists

    DEFF Research Database (Denmark)

    Jensen, Casper Bruun

    2011-01-01

    was the indicator conceptualised? How were notions of scientific knowledge and collaboration inscribed and challenged in the process? The analysis shows a two-sided process in which scientists become engaged in making lists but which is simultaneously a way for research policy to enlist scientists. In conclusion...

  11. The rise of non-financial performance measures in annual reports. An analysis of ATX-listed companies

    Directory of Open Access Journals (Sweden)

    Juergen Muehlbacher

    2016-05-01

    Full Text Available Purpose of the article: In the past, annual reports only include financial measures. More recently, this shareholder value approach has been criticized of leading to a strategic short-term orientation. Consequently, the use of strategic performance measurement systems (SPMSs, namely the Balanced Scorecard (BSC, is proposed to communicate non-financial measures to investors and stakeholders. Besides the distribution of critical information, the disclosure of non-financial measures should strengthen the employee's commitment to the long-term strategy. The purpose of the article is thus to reveal whether Austrian companies disclose their strategic performance measures in their annual reports. Methodology/methods: Two observation points, 2002 and 2012, were chosen to analyse the annual reports of companies listed on the ATX. This period of time allows to observe changes as well as new trends. The annual reports have been downloaded from the company’s homepage or received via email or post. A document and content analysis, followed by a frequency analysis, has been applied to identify several non-financial measures with regard to the following BSC derived perspectives: Customer perspective, internal business perspective and innovation and learning perspective. Scientific aim: The scientific aim of the following study is to examine the extent, to which non-financial performance measures are displayed in annual reports. Findings: The analysis of the annual reports showed a tremendous increase of non-financial measures in the time period between 2002 and 2012, which solely arose from the augmented disclosure activities of the innovation and learning perspective. On the other hand, the customer and internal perspective decreased in importance. Moreover, the top ten measures in 2002 have changed and are dominated by diversity and environmental issues in the year 2012. Conclusions: Similar findings in the literature as well as the influence of legal

  12. Rapid fingerprinting of sterols and related compounds in vegetable and animal oils and phytosterol enriched- margarines by transmission mode direct analysis in real time mass spectrometry.

    Science.gov (United States)

    Alberici, Rosana M; Fernandes, Gabriel D; Porcari, Andréia M; Eberlin, Marcos N; Barrera-Arellano, Daniel; Fernández, Facundo M

    2016-11-15

    Plant-derived sterols, often referred to as phytosterols, are important constituents of plant membranes where they assist in maintaining phospholipid bilayer stability. Consumption of phytosterols has been suggested to positively affect human health by reducing cholesterol levels in blood via inhibition of its absorption in the small intestine, thus protecting against heart attack and stroke. Sterols are challenging analytes for mass spectrometry, since their low polarity makes them difficult to ionize by both electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), typically requiring derivatization steps to overcome their low ionization efficiencies. We present a fast and reliable method to characterize the composition of phytosterols in vegetable oils and enriched margarines. The method requires no derivatization steps or sample extraction procedures thanks to the use of transmission mode direct analysis in real time mass spectrometry (TM-DART-MS). Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. 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

  14. A Growth Evaluation and Analysis of Companies Listed on GEM%我国创业板上市公司成长性评价分析

    Institute of Scientific and Technical Information of China (English)

    阮青松; 常乐

    2012-01-01

    Scientific evaluation of GEM listing companies' growth is an important precondition for the healthy development of China's GEM. Taking 183 companies listed on China's GEM as a sample, this article constructs a system of growth-evaluating indexes for GEM listing companies by theoretical analysis and makes an empirical research using factor analysis model. The results show that company' s capacity of risk-controlling, profitability, growth rate, operational efficiency and capacity of innovating mainly reflect the growth of companies listed on GEM.%科学地评价创业板上市公司的成长性是我国创业板市场健康发展的重要前提,通过理论分析构建了创业板上市公司成长性评价指标体系,并以在我国创业板上市的183家公司为样本,采用因子分析模型进行实证分析.研究结果表明:公司的风险控制能力、盈利能力、成长速度、经营效率和创新能力是创业板上市公司成长性的主要体现.

  15. Pathways targeted by antidiabetes drugs are enriched for multiple genes associated with type 2 diabetes risk.

    Science.gov (United States)

    Segrè, Ayellet V; Wei, Nancy; Altshuler, David; Florez, Jose C

    2015-04-01

    Genome-wide association studies (GWAS) have uncovered >65 common variants associated with type 2 diabetes (T2D); however, their relevance for drug development is not yet clear. Of note, the first two T2D-associated loci (PPARG and KCNJ11/ABCC8) encode known targets of antidiabetes medications. We therefore tested whether other genes/pathways targeted by antidiabetes drugs are associated with T2D. We compiled a list of 102 genes in pathways targeted by marketed antidiabetic medications and applied Gene Set Enrichment Analysis (MAGENTA [Meta-Analysis Gene-set Enrichment of variaNT Associations]) to this gene set, using available GWAS meta-analyses for T2D and seven quantitative glycemic traits. We detected a strong enrichment of drug target genes associated with T2D (P = 2 × 10(-5); 14 potential new associations), primarily driven by insulin and thiazolidinedione (TZD) targets, which was replicated in an independent meta-analysis (Metabochip). The glycemic traits yielded no enrichment. The T2D enrichment signal was largely due to multiple genes of modest effects (P = 4 × 10(-4), after removing known loci), highlighting new associations for follow-up (ACSL1, NFKB1, SLC2A2, incretin targets). Furthermore, we found that TZD targets were enriched for LDL cholesterol associations, illustrating the utility of this approach in identifying potential side effects. These results highlight the potential biomedical relevance of genes revealed by GWAS and may provide new avenues for tailored therapy and T2D treatment design. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  16. Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists

    Directory of Open Access Journals (Sweden)

    Masseroli Marco

    2007-03-01

    Full Text Available Abstract Background The increasing protein family and domain based annotations constitute important information to understand protein functions and gain insight into relations among their codifying genes. To allow analyzing of gene proteomic annotations, we implemented novel modules within GFINDer, a Web system we previously developed that dynamically aggregates functional and phenotypic annotations of user-uploaded gene lists and allows performing their statistical analysis and mining. Results Exploiting protein information in Pfam and InterPro databanks, we developed and added in GFINDer original modules specifically devoted to the exploration and analysis of functional signatures of gene protein products. They allow annotating numerous user-classified nucleotide sequence identifiers with controlled information on related protein families, domains and functional sites, classifying them according to such protein annotation categories, and statistically analyzing the obtained classifications. In particular, when uploaded nucleotide sequence identifiers are subdivided in classes, the Statistics Protein Families&Domains module allows estimating relevance of Pfam or InterPro controlled annotations for the uploaded genes by highlighting protein signatures significantly more represented within user-defined classes of genes. In addition, the Logistic Regression module allows identifying protein functional signatures that better explain the considered gene classification. Conclusion Novel GFINDer modules provide genomic protein family and domain analyses supporting better functional interpretation of gene classes, for instance defined through statistical and clustering analyses of gene expression results from microarray experiments. They can hence help understanding fundamental biological processes and complex cellular mechanisms influenced by protein domain composition, and contribute to unveil new biomedical knowledge about the codifying genes.

  17. MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Steffen Sass

    2015-12-01

    Full Text Available MicroRNAs represent ~22 nt long endogenous small RNA molecules that have been experimentally shown to regulate gene expression post-transcriptionally. One main interest in miRNA research is the investigation of their functional roles, which can typically be accomplished by identification of mi-/mRNA interactions and functional annotation of target gene sets. We here present a novel method “miRlastic”, which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network. For the network inference, we applied linear regression modeling with elastic net regularization on matched microRNA and messenger RNA expression profiling data to perform feature selection on prior knowledge from sequence-based target prediction resources. The novelty of miRlastic inference originates in predicting data-driven intra-transcriptome regulatory relationships through feature selection. With synthetic data, we showed that miRlastic outperformed commonly used methods and was suitable even for low sample sizes. To gain insight into the functional role of miRNAs and to determine joint functional properties of miRNA clusters, we introduced a local enrichment analysis procedure. The principle of this procedure lies in identifying regions of high functional similarity by evaluating the shortest paths between genes in the network. We can finally assign functional roles to the miRNAs by taking their regulatory relationships into account. We thoroughly evaluated miRlastic on a cohort of head and neck cancer (HNSCC patients provided by The Cancer Genome Atlas. We inferred an mi-/mRNA regulatory network for human papilloma virus (HPV-associated miRNAs in HNSCC. The resulting network best enriched for experimentally validated miRNA-target interaction, when compared to common methods. Finally, the local enrichment step identified two functional

  18. A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Lun-Ching Chang

    Full Text Available Large scale gene expression (transcriptome analysis and genome-wide association studies (GWAS for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases. In support of the superior discriminative power of this novel approach, we observed no significant enrichment for GWAS-related genes in coexpression modules extracted from single studies or in meta-modules using gene expression data from non-psychiatric control subjects. Genes in the identified module encode proteins implicated in neuronal signaling and structure, including glutamate metabotropic receptors (GRM1, GRM7, GABA receptors (GABRA2, GABRA4, and neurotrophic and development-related proteins [BDNF, reelin (RELN, Ephrin receptors (EPHA3, EPHA5]. These results are consistent with the current understanding of molecular mechanisms of MDD and provide a set of putative interacting molecular partners, potentially reflecting components of a functional module across cells and biological pathways that are synchronously recruited in MDD, other brain disorders and MDD-related illnesses. Collectively, this study demonstrates the importance of integrating transcriptome data, gene

  19. A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies.

    Science.gov (United States)

    Chang, Lun-Ching; Jamain, Stephane; Lin, Chien-Wei; Rujescu, Dan; Tseng, George C; Sibille, Etienne

    2014-01-01

    Large scale gene expression (transcriptome) analysis and genome-wide association studies (GWAS) for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD) and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases. In support of the superior discriminative power of this novel approach, we observed no significant enrichment for GWAS-related genes in coexpression modules extracted from single studies or in meta-modules using gene expression data from non-psychiatric control subjects. Genes in the identified module encode proteins implicated in neuronal signaling and structure, including glutamate metabotropic receptors (GRM1, GRM7), GABA receptors (GABRA2, GABRA4), and neurotrophic and development-related proteins [BDNF, reelin (RELN), Ephrin receptors (EPHA3, EPHA5)]. These results are consistent with the current understanding of molecular mechanisms of MDD and provide a set of putative interacting molecular partners, potentially reflecting components of a functional module across cells and biological pathways that are synchronously recruited in MDD, other brain disorders and MDD-related illnesses. Collectively, this study demonstrates the importance of integrating transcriptome data, gene coexpression modules

  20. Special Analysis: 2017-001 Disposal of Drums Containing Enriched Uranium in Pit 38 at Technical Area 54, Area G

    Energy Technology Data Exchange (ETDEWEB)

    Birdsell, Kay Hanson [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stauffer, Philip H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); French, Sean B. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-06-05

    Los Alamos National Laboratory (LANL) generates radioactive waste as a result of various activities. Operational waste is generated from a wide variety of research and development activities including nuclear weapons development, energy production, and medical research. Environmental restoration (ER), and decontamination and decommissioning (D&D) waste is generated as contaminated sites and facilities at LANL undergo cleanup or remediation. The majority of this waste is low-level radioactive waste (LLW) and is disposed of at the Technical Area 54 (TA-54), Area G disposal facility. This special analysis, SA 2017-001, evaluates the potential impacts of disposing of this waste in Pit 38 at Area G based on the assumptions that form the basis of the Area G PA/CA. Section 2 describes the methods used to conduct the analysis; the results of the evaluation are provided in Section 3; and conclusions and recommendations are provided in Section 4.

  1. List based prefetch

    Energy Technology Data Exchange (ETDEWEB)

    Boyle, Peter; Christ, Norman; Gara, Alan; Kim, Changhoan; Mawhinney, Robert; Ohmacht, Martin; Sugavanam, Krishnan

    2014-08-12

    A list prefetch engine improves a performance of a parallel computing system. The list prefetch engine receives a current cache miss address. The list prefetch engine evaluates whether the current cache miss address is valid. If the current cache miss address is valid, the list prefetch engine compares the current cache miss address and a list address. A list address represents an address in a list. A list describes an arbitrary sequence of prior cache miss addresses. The prefetch engine prefetches data according to the list, if there is a match between the current cache miss address and the list address.

  2. Comparability of Accounting Choices in Future Valuation of Investment Properties: An Analysis of Brazilian and Portuguese Listed Companies

    Directory of Open Access Journals (Sweden)

    Flaida Êmine Alves de Souza

    2015-08-01

    Full Text Available One of the main purposes for adopting the International Financial Reporting Standards (IFRS is the quest for comparability between financial statements within the same country, over time, and between different countries. IFRS have the feature of allowing accounting choices in most of their standards. However, the existence of such flexibility in the process for recognizing, measuring, and disclosing as sets and liabilities may impact on comparability. IFRS have been criticized both due to their accounting choices and the adoption of the fair value paradigm. This article examines these two issues, investigating the choice of the cost model versus the choice of the fair value model for investment properties (IPs, an option guaranteed under the terms of the International Accounting Standard (IAS 40. This research aimed to identify the comparability degree and the factors that determine the accounting choices made by managers of IPs, in Brazilian and Portuguese listed companies, within the periods from 2010 to 2012. Comparability, within and between countries, was identified by the T-index and the search for the determining factors of accounting choices made by managers was performed by means of a logistic re gression analysis. As a result, it was found that, despite the accounting choices allowed by IAS 40, there was a mean comparability between the accounting practices of firms in these countries, but showing a decrease in the index over the years. The explanatory factors identified were auditing by one of the big four (PricewaterhouseCoopers, Deloitte Touche Tohmatsu, KPMG, or Ernst & Young, companies' indeb tedness, relative importance of IPs' balance, net profit, and less experience of Brazil in using the fair value method to appraise IPs.

  3. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

    Science.gov (United States)

    Kotera, Masaaki; Nishimura, Yosuke; Nakagawa, Zen-ichi; Muto, Ai; Moriya, Yuki; Okamoto, Shinobu; Kawashima, Shuichi; Katayama, Toshiaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2014-12-01

    Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

  4. Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

    Science.gov (United States)

    Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

    2013-08-01

    Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association

  5. On-plate-selective enrichment of glycopeptides using boronic acid-modified gold nanoparticles for direct MALDI-QIT-TOF MS analysis.

    Science.gov (United States)

    Tang, Jia; Liu, Yingchao; Qi, Dawei; Yao, Guoping; Deng, Chunhui; Zhang, Xiangmin

    2009-11-01

    In this study, an on-plate-selective enrichment method is developed for fast and efficient glycopeptide investigation. Gold nanoparticles were first spotted and sintered on a stainless-steel plate, then modified with 4-mercaptophenylboronic acid to provide porous substrate with large specific surface and dual functions. These spots were used to selectively capture glycopeptides from peptide mixtures and the captured target peptides could be analyzed by MALDI-MS simply by deposition of 2,5-dihydroxybenzoic acid matrix. Horseradish peroxidase was employed as a standard glycoprotein to investigate the enrichment efficiency. In this way, the enrichment, washing and detection steps can all be fulfilled on a single MALDI target plate. The relatively small sample amount needed, low detection limit and rapid selective enrichment have made this on-plate strategy promising for online enrichment of glycopeptides, which could be applied in high-throughput proteome research.

  6. Analysis, biomedicine, collaboration, and determinism challenges and guidance: wish list for biopharmaceuticals on the interface of computing and statistics.

    Science.gov (United States)

    Goodman, Arnold F

    2011-11-01

    I have personally witnessed processing advance from desk calculators and mainframes, through timesharing and PCs, to supercomputers and cloud computing. I have also witnessed resources grow from too little data into almost too much data, and from theory dominating data into data beginning to dominate theory while needing new theory. Finally, I have witnessed problems advance from simple in a lone discipline into becoming almost too complex in multiple disciplines, as well as approaches evolve from analysis driving solutions into solutions by data mining beginning to drive the analysis itself. How we do all of this has transitioned from competition overcoming collaboration into collaboration starting to overcome competition, as well as what is done being more important than how it is done has transitioned into how it is done becoming as important as what is done. In addition, what or how we do it being more important than what or how we should actually do it has shifted into what or how we should do it becoming just as important as what or how we do it, if not more so. Although we have come a long way in both our methodology and technology, are they sufficient for our current or future complex and multidisciplinary problems with their massive databases? Since the apparent answer is not a resounding yes, we are presented with tremendous challenges and opportunities. This personal perspective adapts my background and experience to be appropriate for biopharmaceuticals. In these times of exploding change, informed perspectives on what challenges should be explored with accompanying guidance may be even more valuable than the far more typical literature reviews in conferences and journals of what has already been accomplished without challenges or guidance. Would we believe that an architect who designs a skyscraper determines the skyscraper's exact exterior, interior and furnishings or only general characteristics? Why not increase dependability of conclusions in

  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.

    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.

  8. 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.

  9. Components of complex lipid biosynthetic pathways in developing castor (Ricinus communis) seeds identified by MudPIT analysis of enriched endoplasmic reticulum.

    Science.gov (United States)

    Brown, Adrian P; Kroon, Johan T M; Topping, Jennifer F; Robson, Joanne L; Simon, William J; Slabas, Antoni R

    2011-08-05

    Ricinoleic acid is a feedstock for nylon-11 (N11) synthesis which is currently obtained from castor (Ricinus communis) oil. Production of this fatty acid in a temperate oilseed crop is of great commercial interest, but the highest reported level in transgenic plant oils is 30%, below the 90% observed in castor and insufficient for commercial exploitation. To identify castor oil-biosynthetic enzymes and inform strategies to improve ricinoleic acid yields, we performed MudPIT analysis on endoplasmic reticulum (ER) purified from developing castor bean endosperm. Candidate enzymes for all steps of triacylglycerol synthesis were identified among 72 proteins in the data set related to complex-lipid metabolism. Previous reported proteomic data from oilseeds had not included any membrane-bound enzyme that might incorporate ricinoleic acid into oil. Analysis of enriched ER enabled determination of which protein isoforms for these enzymes were in developing castor seed. To complement this data, quantitative RT-PCR experiments with castor seed and leaf RNA were performed for orthologues of Arabidopsis oil-synthetic enzymes, determining which were highly expressed in the seed. These data provide important information for further manipulation of ricinoleic acid content in oilseeds and peptide data for future quantification strategies.

  10. Application of porous metal enrichment probe sampling to single cell analysis using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS).

    Science.gov (United States)

    Fu, Qiang; Tang, Jun; Cui, Meng; Xing, Junpeng; Liu, Zhiqiang; Liu, Shuying

    2016-01-01

    There is an increasing need for analyzing metabolism in a single cell, which is important to understand the nature of cellular heterogeneity, disease, growth and specialization, etc. However, single cell analysis is often challenging for the traces of samples. In the present study, porous metal enrichment probe sampling combined with matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) has been applied for in situ analysis of live onion epidemic cell. Porous probe, treated by corroding copper wire with HCl, was directly inserted into a single cell to get cell solution. A self-made linear actuator was enough to control the penetration of probe into the target cell accurately. Then samples on the tip of probe were eluted and detected by a commercial MALDI-TOF-MS directly. The formation of porous microstructure on the probe surface increased the adsorptive capacity of cell solution. The sensitivity of porous probe sampling was 6 times higher than uncorroded probes generally. This method provides a sensitive and convenient way for the sampling and detection of single cell solution. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Inferring time-variable effects of nutrient enrichment on marine ecosystems using inverse modelling and ecological network analysis.

    Science.gov (United States)

    Luong, Anh D; De Laender, Frederik; Olsen, Yngvar; Vadstein, Olav; Dewulf, Jo; Janssen, Colin R

    2014-09-15

    We combined data from an outdoor mesocosm experiment with carbon budget modelling and an ecological network analysis to assess the effects of continuous nutrient additions on the structural and functional dynamics of a marine planktonic ecosystem. The food web receiving no nutrient additions was fuelled by detritus, as zooplankton consumed 7.2 times more detritus than they consumed algae. Nutrient supply instantly promoted herbivory so that it was comparable to detritivory at the highest nutrient addition rate. Nutrient-induced food web restructuring reduced carbon cycling and decreased the average number of compartments a unit flow of carbon crosses before dissipation. Also, the efficiency of copepod production, the link to higher trophic levels harvestable by man, was lowered up to 35 times by nutrient addition, but showed signs of recovery after 9 to 11 days. The dependency of the food web on exogenous input was not changed by the nutrient additions.

  12. Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum

    Directory of Open Access Journals (Sweden)

    Ke Tao

    2011-12-01

    Full Text Available Abstract Background Sesame (Sesamum indicum is one of the most important oilseed crops with high oil contents and rich nutrient value. However, genetic improvement efforts in sesame could not get benefit from molecular biology technology due to poor DNA and RNA sequence resources. In this study, we carried out a large scale of expressed sequence tags (ESTs sequencing from developing sesame seeds and further conducted analysis on seed storage products-related genes. Results A normalized and full-length enriched cDNA library from 5 ~ 30 days old immature seeds was constructed and randomly sequenced, leading to generation of 41,248 expressed sequence tags (ESTs which then formed 4,713 contigs and 27,708 singletons with 44.9% uniESTs being putative full-length open reading frames. Approximately 26,091 of all these uniESTs have significant matches to the counterparts in Nr database of GenBank, and 21,628 of them were assigned to one or more Gene ontology (GO terms. Homologous genes involved in oil biosynthesis were identified including some conservative transcription factors regulating oil biosynthesis such as LEAFY COTYLEDON1 (LEC1, PICKLE (PKL, WRINKLED1 (WRI1 and majority of them were found for the first time in sesame seeds. One hundred and 17 ESTs were identified possibly involved in biosynthesis of sesame lignans, sesamin and sesamolin. In total, 9,347 putative functional genes from developing seeds were identified, which accounts for one third of total genes in the sesame genome. Further analysis of the uniESTs identified 1,949 non-redundant simple sequence repeats (SSRs. Conclusions This study has provided an overview of genes expressed during sesame seed development. This collection of sesame full-length cDNAs covered a wide variety of genes in seeds, in particular, candidate genes involved in biosynthesis of sesame oils and lignans. These EST sequences enriched with full length will contribute to comparative genomic studies on sesame and

  13. Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum).

    Science.gov (United States)

    Ke, Tao; Dong, Caihua; Mao, Han; Zhao, Yingzhong; Chen, Hong; Liu, Hongyan; Dong, Xuyan; Tong, Chaobo; Liu, Shengyi

    2011-12-24

    Sesame (Sesamum indicum) is one of the most important oilseed crops with high oil contents and rich nutrient value. However, genetic improvement efforts in sesame could not get benefit from molecular biology technology due to poor DNA and RNA sequence resources. In this study, we carried out a large scale of expressed sequence tags (ESTs) sequencing from developing sesame seeds and further conducted analysis on seed storage products-related genes. A normalized and full-length enriched cDNA library from 5 ~ 30 days old immature seeds was constructed and randomly sequenced, leading to generation of 41,248 expressed sequence tags (ESTs) which then formed 4,713 contigs and 27,708 singletons with 44.9% uniESTs being putative full-length open reading frames. Approximately 26,091 of all these uniESTs have significant matches to the counterparts in Nr database of GenBank, and 21,628 of them were assigned to one or more Gene ontology (GO) terms. Homologous genes involved in oil biosynthesis were identified including some conservative transcription factors regulating oil biosynthesis such as LEAFY COTYLEDON1 (LEC1), PICKLE (PKL), WRINKLED1 (WRI1) and majority of them were found for the first time in sesame seeds. One hundred and 17 ESTs were identified possibly involved in biosynthesis of sesame lignans, sesamin and sesamolin. In total, 9,347 putative functional genes from developing seeds were identified, which accounts for one third of total genes in the sesame genome. Further analysis of the uniESTs identified 1,949 non-redundant simple sequence repeats (SSRs). This study has provided an overview of genes expressed during sesame seed development. This collection of sesame full-length cDNAs covered a wide variety of genes in seeds, in particular, candidate genes involved in biosynthesis of sesame oils and lignans. These EST sequences enriched with full length will contribute to comparative genomic studies on sesame and other oilseed plants and serve as an abundant

  14. pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis

    Science.gov (United States)

    Rahmati, Sara; Abovsky, Mark; Pastrello, Chiara; Jurisica, Igor

    2017-01-01

    Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. ‘pathway orphans’. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, ‘core pathways’, with physical protein–protein interactions to predict biologically relevant protein–pathway associations, referred to as ‘extended pathways’. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5732 pathway orphans. PathDIP (http://ophid.utoronto.ca/pathdip) annotates 17 070 protein-coding genes with 4678 pathways, and provides multiple query, analysis and output options. PMID:27899558

  15. Simultaneous analysis of folic acid and pantothenic acid in foods enriched with vitamins by stable isotope dilution assays

    Energy Technology Data Exchange (ETDEWEB)

    Rychlik, Michael

    2003-10-24

    Folic and pantothenic acid were quantified in multivitamin products by stable isotope dilution assays using [{sup 2}H{sub 4}]folic acid and [{sup 13}C{sub 3},{sup 15}N]pantothenic acid as the internal standards. Detection was achieved by liquid chromatography/mass spectrometry which enabled unequivocal determination of the vitamins. Due to the very simple extraction procedure, analysis of the vitamins was completed within 2 h. When analyzing multivitamin sweets, the intra-assay and inter-assay coefficient of variation was 3.2% (n=5) and 3.1% (n=5) for folic acid and 4.5% (n=5) as well as 6.5% (n=7) for pantothenic acid, respectively. Along with the precision data, recovery values of 99.4% for folic acid and 103% for pantothenic acid at addition levels of 6 mg/kg and 600 {mu}g/kg, respectively, to starch products proved the accuracy of the new method. Application of the stable isotope dilution assay to fruit juices, whey products, cereals, sweets, pharmaceuticals, wheat flour and salt fortified with one or both vitamins revealed that for the majority of products the labeled pantothenic acid contents were exceeded by about 30%, whereas for folic acid also significantly lower contents than the label claim were found.

  16. Lipidomics analysis reveals efficient storage of hepatic triacylglycerides enriched in unsaturated fatty acids after one bout of exercise in mice.

    Directory of Open Access Journals (Sweden)

    Chunxiu Hu

    Full Text Available BACKGROUND: Endurance exercise induces lipolysis, increases circulating concentrations of free fatty acids (FFA and the uptake and oxidation of fatty acids in the working muscle. Less is known about the regulation of lipid metabolism in the liver during and post-exercise. METHODOLOGY/PRINCIPAL FINDINGS: We performed an ultra fast liquid chromatography-mass spectrometry (UFLC-MS based lipidomics analysis of liver tissue samples obtained from C57Bl/6J mice immediately after a 60 min treadmill run of moderate intensity, and after 3 h of recovery. The PLS-DA scores plot for 115 quantified lipid molecular species revealed a clear separation of the hepatic lipid profile of sedentary from recovering mice, but not from mice immediately after running. 21 lipid species were considered to be most responsible for the difference in the hepatic lipid profiles, including 17 triacylglycerides (TG, one lysophosphatidylcholine (LPC and three phosphatidylcholines (PC. TG species were found to be more abundant in the recovery phase, while PC species were decreased. The degree of accumulation of individual TG species correlated well with the amount of theoretical energy stored whereas no increase was found for TG species containing only saturated or one monounsaturated fatty acid. Total liver TG content as assayed by an enzymatic method was increased to 163% in the recovery phase, while it was significantly decreased in skeletal muscle by the exercise bout and remained less in the recovery phase. Results from fasted and refed mice indicate that fasting-induced lipolysis was associated with a pronounced accumulation of hepatic TG, which is reversed by refeeding for 5 h. Thus food intake per se did not elevate hepatic TG. CONCLUSION: These data indicate that high availability of FFA induced by endurance exercise or fasting resulted in a transient hepatic TG accumulation, while muscle TG content was decreased during exercise presumably due to increased muscle fatty

  17. Preparation of C₁₈-functionalized magnetic polydopamine microspheres for the enrichment and analysis of alkylphenols in water samples.

    Science.gov (United States)

    Wang, Xianying; Deng, Chunhui

    2016-02-01

    In this work, C18-functionalized magnetic polydopamine microspheres (Fe3O4@PDA@C18) were successfully synthesized and applied to the analysis of alkylphenols in water samples. The magnetic Fe3O4 particles coated with hydrophilic surface were synthesized via a solvothermal reaction and the self-polymerization of dopamine. And then the C18 groups were fabricated by a silylanization method. Benefit from the merits of Fe3O4 particles, polydopamine coating and C18 groups, the Fe3O4@PDA@C18 material possessed several properties of super magnetic responsiviness, good water dispersibility, π-electron system and hydrophobic C18 groups. Thus, the materials had great potential to be developed as the adsorbent for the magnetic solid-phase extraction (MSPE) technique. Here, we selected three kinds of alkylphenols (4-tert-octylphenol, 4-n-nonylphenol, 4-n-octylphenol) to be the target analyst for evaluating the performance of the prepared material. In this study, various extraction parameters were investigated and optimized, such as pH values of water sample solution, amount of adsorbents, adsorption and desorption time, the species of desorption solution. Meanwhile, the method validations were studied, including linearity, limit of detection and method precision. From the results, Fe3O4@PDA@C18 composites were successfully applied as the adsorbents for the extraction of alkylphenols in water samples. The proposed material provided an approach for a simple, rapid magnetic solid-phase extraction for hydrophobic compounds in environmental samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. An optimized protocol for the generation and functional analysis of human mast cells from CD34(+) enriched cell populations.

    Science.gov (United States)

    Yin, Yuzhi; Bai, Yun; Olivera, Ana; Desai, Avanti; Metcalfe, Dean D

    2017-09-01

    The culture of mast cells from human tissues such a cord blood, peripheral blood or bone marrow aspirates has advanced our understanding of human mast cells (huMC) degranulation, mediator production and response to pharmacologic agents. However, existing methods for huMC culture tend to be laborious and expensive. Combining technical approaches from several of these protocols, we designed a simplified and more cost effective approach to the culture of mast cells from human cell populations including peripheral blood and cryopreserved cells from lymphocytapheresis. On average, we reduced by 30-50 fold the amount of culture media compared to our previously reported method, while the total MC number generated by this method (2.46±0.63×10(6) vs. 2.4±0.28×10(6), respectively, from 1.0×10(8) lymphocytapheresis or peripheral blood mononuclear blood cells [PBMCs]) was similar to our previous method (2.36±0.70×10(6)), resulting in significant budgetary savings. In addition, we compared the yield of huMCs with or without IL-3 added to early cultures in the presence of stem cell factor (SCF) and interlukin-6 (IL-6) and found that the total MC number generated, while higher with IL-3 in the culture, did not reach statistical significance, suggesting that IL-3, often recommended in the culture of huMCs, is not absolutely required. We then performed a functional analysis by flow cytometry using standard methods and which maximized the data we could obtain from cultured cells. We believe these approaches will allow more laboratories to culture and examine huMC behavior going forward. Published by Elsevier B.V.

  19. Molecular cloning and expression analysis of the retinoid X receptor (RXR) gene in golden pompano Trachinotus ovatus fed Artemia nauplii with different enrichments.

    Science.gov (United States)

    Yang, Qibin; Zheng, Panlong; Ma, Zhenhua; Li, Tao; Jiang, Shigui; Qin, Jian G

    2015-12-01

    The retinoid X receptors (RXRs) are involved in the skeletal development and other biological process such as blood vessel formation and metabolism. Partial sequences of RXRα and β genes were obtained, and their expressions were quantified on golden pompano Trachinotus ovatus at 28 days post hatching (DPH) to explore the molecular response to nutritional manipulation in fish larvae. As live food, Artemia nauplii were separately enriched with Nannochloropsis and Algamac 3080 and non-enriched Artemia nauplii (control) for fish feeding. The expressions of RXRs were detected in the embryos and fish larvae at early stages, suggesting that the skeletal development in golden pompano initiated before yolk re-sorption completion. Fish fed non-enriched Artemia nauplii ended up with higher jaw malformation. The highest specific growth rate was obtained when fish were fed with the Artemia nauplii enriched with Algamac 3080, and the lowest growth rate was observed when fish were fed with unenriched Artemia nauplii. The highest survival was obtained when fish were fed with non-enriched or Nannochloropsis-enriched Artemia nauplii. This study indicates that the use of enriched formula for Artemia nauplii can significantly affect the expression levels of RXRs and jaw malformation of golden pompano larvae, but there is no clear correlation between RXRs expressions and malformation rates when fish are subjected to nutrient challenge.

  20. Metamnemonic Control Over the Discriminability of Memory Evidence: A Signal Detection Analysis of Warning Effects in the Associative List Paradigm

    Science.gov (United States)

    Starns, Jeffrey J.; Lane, Sean M.; Alonzo, Jill D.; Roussel, Cristine C.

    2007-01-01

    According to signal detection theory (SDT), retrieval warnings may decrease false memory in the associative list paradigm either by inducing a conservative criterion shift or by decreasing the amount of evidence that critical theme words were studied. Fitting a SDT model to 12 existing datasets revealed suggestive evidence that warnings impact…

  1. A Randomized Wait-List Controlled Analysis of the Implementation Integrity of Team-Initiated Problem Solving Processes

    Science.gov (United States)

    Newton, J. Stephen; Horner, Robert H.; Algozzine, Bob; Todd, Anne W.; Algozzine, Kate

    2012-01-01

    Members of Positive Behavior Interventions and Supports (PBIS) teams from 34 elementary schools participated in a Team-Initiated Problem Solving (TIPS) Workshop and follow-up technical assistance. Within the context of a randomized wait-list controlled trial, team members who were the first recipients of the TIPS intervention demonstrated greater…

  2. How does family control influence firm strategy and performance? A meta-analysis of US publicly-listed firms

    NARCIS (Netherlands)

    van Essen, M.|info:eu-repo/dai/nl/357514491; Carney, M.; Gedajlovic, E.; Heugens, P.P.M.A.R.

    Empirical Research Question/Issue A contentious and prominent research question in the management literature is whether publicly listed family firms (FFs) outperform other types of corporations. Through a research synthesis of all available studies on the performance of US FFs, we address this

  3. How does family control influence firm strategy and performance? A meta-analysis of US publicly-listed firms

    NARCIS (Netherlands)

    van Essen, M.; Carney, M.; Gedajlovic, E.; Heugens, P.P.M.A.R.

    2015-01-01

    Empirical Research Question/Issue A contentious and prominent research question in the management literature is whether publicly listed family firms (FFs) outperform other types of corporations. Through a research synthesis of all available studies on the performance of US FFs, we address this quest

  4. Efficacy of glutamine-enriched enteral feeding formulae in critically ill patients: a systematic review and meta-analysis of randomized controlled trials.

    Science.gov (United States)

    Mottaghi, Azadeh; Yeganeh, Maryam Zarif; Golzarand, Mahdieh; Jambarsang, Sara; Mirmiran, Parvin

    2016-01-01

    Critically ill patients usually suffer from catabolic stress that could lead to malnutrition and nutritional support therefore is essential to maintain lean body mass, improve metabolic and immune response and decrease rate of mortality and comorbidity in these patients. This meta-analysis was aimed to evaluate effect of glutamineenriched enteral nutrition in critically ill patients. In order to obtain randomized clinical trial studies (RCTs), international databases including MEDLINE and Google scholar and also electronic resources in Iran, including IRAN MEDEX, IRAN DOC, SID, Magiran were systematically searched without language and publication restriction before December 2014. The final included number of studies for meta-analysis was 10. The methodological quality of eligible studies was assessed by four investigators using the Jadad 5-point scale, a scale containing three items describing randomization, blinding and fate of participants. We analyzed data from the included studies using STATA version 12.0, and calculated a pooled odds ratio for dichotomous data and mean differences for continuous data with 95% confidence intervals (CIs). There was no significant difference in mortality in elevated pooled odds ratios (p-value=0.070). A funnel plot was drawn for evaluation of publication bias, but none was found. The fixed effect model shows significant reduction in gut permeability in who received enteral feeding enriched with glutamine (-0.84, 95% CI=-1.25 to -0.44), moreover the funnel plot did not show publication bias. Based on the available data, our meta-analysis showed that enteral glutamine (Gln) supplementation increased mortality rate, though non-significantly, but decreased gut permeability significantly.

  5. Algebraic comparison of partial lists in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Giuseppe Jurman

    Full Text Available The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or to a meta-analysis comparison, it is often the case that sets of alternative feature lists (possibly of different lengths are obtained, instead of just one list. Here we introduce a method, based on permutations, for studying the variability between lists ("list stability" in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated by finding and comparing gene profiles on a large prostate cancer dataset, consisting of two cohorts of patients from different countries, for a total of 455 samples.

  6. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

    Science.gov (United States)

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-03-09

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in L-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport--NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885--were also expressed at significantly higher levels in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, L-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.

  7. Principal component analysis of the effects of environmental enrichment and (--epigallocatechin-3-gallate on age-associated learning deficits in a mouse model of Down syndrome

    Directory of Open Access Journals (Sweden)

    Silvina eCatuara-Solarz

    2015-12-01

    Full Text Available Down syndrome (DS individuals present increased risk for Alzheimer disease (AD neuropathology and AD-type dementia. Here, we investigated the use of green tea extracts containing (--epigallocatechin-3-gallate (EGCG, as co-adjuvant to enhance the effects of environmental enrichment (EE in Ts65Dn mice, a segmental trisomy model of DS that partially mimics DS/AD pathology, at the age of initiation of cognitive decline. Classical repeated measures ANOVA showed that combined EE-EGCG treatment was more efficient than EE or EGCG alone to improve specific spatial learning related variables. Using principal component analysis (PCA we found that several spatial learning parameters contributed similarly to a first PC and explained a large proportion of the variance among groups, thus representing a composite learning measure. This PC1 revealed that EGCG or EE alone had no significant effect. However, combined EE-EGCG significantly ameliorated learning alterations of middle age Ts65Dn mice. Interestingly, PCA revealed an increased variability along learning sessions with good and poor learners in Ts65Dn, and this stratification did not disappear upon treatments. Our results suggest that combining EE and EGCG represents a viable therapeutic approach for amelioration of age-related cognitive decline in DS, although its efficacy may vary across individuals.

  8. 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.

  9. Production of structured lipids by acidolysis of an EPA-enriched fish oil and caprylic acid in a packed bed reactor: analysis of three different operation modes.

    Science.gov (United States)

    González Moreno, P A; Robles Medina, A; Camacho Rubio, F; Camacho Páez, B; Molina Grima, E

    2004-01-01

    Structured triacylglycerols (ST) enriched in eicosapentaenoic acid (EPA) in position 2 of the triacylglycerol (TAG) backbone were synthesized by acidolysis of a commercially available EPA-rich oil (EPAX4510, 40% EPA) and caprylic acid (CA), catalyzed by the 1,3-specific immobilized lipase Lipozyme IM. The reaction was carried out in a packed bed reactor (PBR) operating in two ways: (1) by recirculating the reaction mixture from the exit of the bed to the substrate reservoir (discontinuous mode) and (2) in continuous mode, directing the product mixture leaving the PBR to a product reservoir. By operating in these two ways and using a simple kinetic model, representative values for the apparent kinetic constants (kX) for each fatty acid (native, Li or odd, M) were obtained. The kinetic model assumes that the rate of incorporation of a fatty acid into TAG per amount of enzyme, rX (mole/(h g lipase)) is proportional to the extent of the deviation from the equilibrium for each fatty acid (i.e., the difference of concentration between the fatty acid in the triacylglycerol and the concentration of the same fatty acid in the triacylglycerol once the equilibrium of the acidolysis reaction is reached). The model allows comparing the two operating modes through the processing intensity, defined as mLt/(V[TG]0) and mL/(q[TG]0), for the discontinuous and continuous operation modes, respectively. In discontinuous mode, ST with 59.5% CA and 9.6% EPA were obtained. In contrast, a ST with 51% CA and 19.6% EPA were obtained when using the continuous operation mode. To enhance the CA incorporation when operating in continuous mode, a two-step acidolysis reaction was performed (third operation mode). This continuous two-step process yields a ST with a 64% CA and a 15% EPA. Finally, after purifying the above ST in a preparative silica gel column, impregnated with boric acid, a ST with 66.9% CA and 19.6% EPA was obtained. The analysis by reverse phase and Ag+ liquid chromatography of

  10. An integrated sample pretreatment platform for quantitative N-glycoproteome analysis with combination of on-line glycopeptide enrichment, deglycosylation and dimethyl labeling

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Yejing; Qu, Yanyan; Jiang, Hao; Wu, Qi [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); University of the Chinese Academy of Sciences, Beijing 100039 (China); Zhang, Lihua, E-mail: lihuazhang@dicp.ac.cn [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Yuan, Huiming [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Zhou, Yuan [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); University of the Chinese Academy of Sciences, Beijing 100039 (China); Zhang, Xiaodan; Zhang, Yukui [National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China)

    2014-06-23

    Highlights: • An integrated platform for quantitative N-glycoproteome analysis was established. • On-line enrichment, deglycosylation and labeling could be achieved within 160 min. • A N{sub 2}-assisted interface was applied to improve the compatibility of the platform. • The platform exhibited improved quantification accuracy, precision and throughput. - Abstract: Relative quantification of N-glycoproteomes shows great promise for the discovery of candidate biomarkers and therapeutic targets. The traditional protocol for quantitative analysis of glycoproteomes is usually off-line performed, and suffers from long sample preparation time, and the risk of sample loss or contamination due to manual manipulation. In this study, a novel integrated sample preparation platform for quantitative N-glycoproteome analysis was established, with combination of online N-glycopeptide capture by a HILIC column, sample buffer exchange by a N{sub 2}-assisted HILIC–RPLC interface, deglycosylation by a hydrophilic PNGase F immobilized enzymatic reactor (hIMER) and solid dimethyl labeling on a C18 precolumn. To evaluate the performance of such a platform, two equal aliquots of immunoglobulin G (IgG) digests were sequentially pretreated, followed by MALDI-TOF MS analysis. The signal intensity ratio of heavy/light (H/L) labeled deglycosylated peptides with the equal aliquots was 1.00 (RSD = 6.2%, n = 3), much better than those obtained by the offline protocol, with H/L ratio as 0.76 (RSD = 11.6%, n = 3). Additionally, the total on-line sample preparation time was greatly shortened to 160 min, much faster than that of offline approach (24 h). Furthermore, such an integrated pretreatment platform was successfully applied to analyze the two kinds of hepatocarcinoma ascites syngeneic cell lines with high (Hca-F) and low (Hca-P) lymph node metastasis rates. For H/L labeled Hca-P lysates with the equal aliquots, 99.6% of log 2 ratios (H/L) of quantified glycopeptides ranged from −1

  11. Positional enrichment by proton analysis (PEPA). A one-dimensional {sup 1}H-NMR approach for {sup 13}C stable isotope tracer studies in metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Vinaixa, Maria; Yanes, Oscar [Department of Electronic Engineering-Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus (Spain); Rodriguez, Miguel A.; Capellades, Jordi [Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus (Spain); Aivio, Suvi; Stracker, Travis H. [Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (Spain); Gomez, Josep; Canyellas, Nicolau [Department of Electronic Engineering-, Universitat Rovira i Virgili, Tarragona (Spain)

    2017-03-20

    A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of {sup 13}C-satellite peaks using 1D-{sup 1}H-NMR spectra. In comparison with {sup 13}C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of {sup 13}C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment. Altogether, PEPA provides a novel framework for extending the high-throughput of {sup 1}H-NMR metabolic profiling to stable isotope tracing in metabolomics, facilitating and complementing the information derived from 2D-NMR experiments and expanding the range of isotopically enriched metabolites detected in cellular extracts. (copyright 2017 The Authors. Published by Wiley-VCH Verlag GmbH and Co. KGaA.)

  12. 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.

  13. 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.

  14. 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

  15. POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.

    Science.gov (United States)

    Shameer, Khader; Naika, Mahantesha Bn; Mathew, Oommen K; Sowdhamini, Ramanathan

    2014-01-01

    Biological enrichment analysis using gene ontology (GO) provides a global overview of the functional role of genes or proteins identified from large-scale genomic or proteomic experiments. Phenomic enrichment analysis of gene lists can provide an important layer of information as well as cellular components, molecular functions, and biological processes associated with gene lists. Plant phenomic enrichment analysis will be useful for performing new experiments to better understand plant systems and for the interpretation of gene or proteins identified from high-throughput experiments. Plant ontology (PO) is a compendium of terms to define the diverse phenotypic characteristics of plant species, including plant anatomy, morphology, and development stages. Adoption of this highly useful ontology is limited, when compared to GO, because of the lack of user-friendly tools that enable the use of PO for statistical enrichment analysis. To address this challenge, we introduce Plant Ontology Enrichment Analysis Server (POEAS) in the public domain. POEAS uses a simple list of genes as input data and performs enrichment analysis using Ontologizer 2.0 to provide results in two levels, enrichment results and visualization utilities, to generate ontological graphs that are of publication quality. POEAS also offers interactive options to identify user-defined background population sets, various multiple-testing correction methods, different enrichment calculation methods, and resampling tests to improve statistical significance. The availability of such a tool to perform phenomic enrichment analyses using plant genes as a complementary resource will permit the adoption of PO-based phenomic analysis as part of analytical workflows. POEAS can be accessed using the URL http://caps.ncbs.res.in/poeas.

  16. 上市公司盈余调节手段的分析%Analysis of Means of Regulation of Listed Companies Earnings

    Institute of Scientific and Technical Information of China (English)

    胡星辉

    2011-01-01

    上市公司盈余管理的目的是为了完成或超过市场对它的盈利预期或风险效应,从而提高股票价值。本文从会计政策的选择、经营中关联交易的规划和非经营性损益等方面对上市公司盈余调节的手段进行了分析,其目的是使其遵守国家有关法律法规政策,减少上市公司的风险。%Management of earnings of listed companies is intended to complete or exceed its earnings expecta- tions or market risk effect, thereby enhancing shareholder value. In this paper, the choice of accounting policies, business plans and related party transactions in non-operating gains and losses in terms of surplus agricultural listed companies regulated by means of the analysis, the aim is to make it comply with relevant state laws and regulations and policies to reduce the risk of a listed company

  17. 78 FR 17942 - Request To Amend a License To Export High-Enriched Uranium

    Science.gov (United States)

    2013-03-25

    ... COMMISSION Request To Amend a License To Export High-Enriched Uranium Pursuant to 10 CFR 110.70 (b) ``Public... Security material (High- kilograms U-235 LVR-15 Research will ultimately Administration. Enriched Uranium... medical isotope March 11, 2013 uranium) the list of production at the XSNM3622/02 research...

  18. 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…

  19. 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

  20. Gene and protein analysis of brain derived neurotrophic factor expression in relation to neurological recovery induced by an enriched environment in a rat stroke model.

    Science.gov (United States)

    Hirata, Kenji; Kuge, Yuji; Yokota, Chiaki; Harada, Akina; Kokame, Koichi; Inoue, Hiroyasu; Kawashima, Hidekazu; Hanzawa, Hiroko; Shono, Yuji; Saji, Hideo; Minematsu, Kazuo; Tamaki, Nagara

    2011-05-20

    Although an enriched environment enhances functional recovery after ischemic stroke, the mechanism underlying this effect remains unclear. We previously reported that brain derived neurotrophic factor (BDNF) gene expression decreased in rats housed in an enriched environment for 4 weeks compared to those housed in a standard cage for the same period. To further clarify the relationship between the decrease in BDNF and functional recovery, we investigated the effects of differential 2-week housing conditions on the mRNA of BDNF and protein levels of proBDNF and mature BDNF (matBDNF). After transient occlusion of the right middle cerebral artery of male Sprague-Dawley rats, we divided the rats into two groups: (1) an enriched group housed multiply in large cages equipped with toys, and (2) a standard group housed alone in small cages without toys. Behavioral tests before and after 2-week differential housing showed better neurological recovery in the enriched group than in the standard group. Synaptophysin immunostaining demonstrated that the density of synapses in the peri-infarct area was increased in the enriched group compared to the standard group, while infarct volumes were not significantly different. Real-time reverse transcription polymerase chain reaction, Western blotting and immunostaining all revealed no significant difference between the groups. The present results suggest that functional recovery cannot be ascribed to an increase in matBDNF or a decrease in proBDNF but rather to other underlying mechanisms.

  1. Analysis of Short Tandem Repeat and Single Nucleotide Polymorphism Loci From Single-Source Samples Using a Custom HaloPlex Target Enrichment System Panel.

    Science.gov (United States)

    Wendt, Frank R; Zeng, Xiangpei; Churchill, Jennifer D; King, Jonathan L; Budowle, Bruce

    2016-06-01

    Short tandem repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short tandem repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE. With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing custom-selected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 short tandem repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment.

  2. Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria.

    Science.gov (United States)

    Bozinovski, Dragana; Taubert, Martin; Kleinsteuber, Sabine; Richnow, Hans-Hermann; von Bergen, Martin; Vogt, Carsten; Seifert, Jana

    2014-10-01

    This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation.

  3. Phylogenetic analysis and arsenate reduction effect of the arsenic-reducing bacteria enriched from contaminated soils at an abandoned smelter site

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xuexia; JIA Yongfeng; WANG Xin; XU Liying

    2008-01-01

    Microbial reduction of As(V) (i.e., arsenate) plays an important role in arsenic (As) mobilization in aqueous environment. In this study, we investigated As(Ⅴ) reduction characteristics of the bacteria enriched from the arsenic-contaminated soil at an abandoned smelter site. It was found that As(Ⅴ) was completely reduced to As(Ⅲ) (i.e., arsenite) in 21 h. After 3-d incubation, a yellow solid was precipitated and the concentration of As(Ⅲ) decreased sharply. After 150 h incubation, ca. 65% of soluble arsenic was removed from the solution. The analysis of the precipitate by scanning electron microscopy and energy dispersive spectrometer (SEM-EDS) and X-ray diffraction (XRD) revealed that the main component was crystalline arsenic sulfide (ASS). Microbial mediated reduction and mobilization of adsorbed As(Ⅴ) on ferric hydroxide was also examined. In the microcosm slurry experiment, ca. 53% of the adsorbed As(V) was reduced to As(Ⅲ) by the bacteria, which resulted in an appreciable release of arsenic into aqueous phase. The released arsenic was present predominantly as As(Ⅲ). The microbial diversity was analyzed by 16S rDNA-dependent molecular phylogeny. A near-full-length 16S rDNA gene clone library was constructed. The 197 clones were analyzed using RFLP (restriction fragment length polymorphism) and 72 OTUs were obtained, which contributed 51% of the content for total clone number in six OTUs. Six bacterial clones in these six OTUs were selected for sequencing and the sequenced clones were found to belong to the group Caloramator, Clostridium, and Bacillus.

  4. MGA: A gamma-ray spectrum analysis code for determining plutonium isotopic abundances. Volume 3, FORTRAN listing of the GA code

    Energy Technology Data Exchange (ETDEWEB)

    Gunnink, R

    1991-09-01

    Nondestructive measurements of x-ray and gamma-ray emissions can be used to determine the abundances of various actinides in a sample. Volume 1 of this report describes the methods and algorithms we have developed to determine the relative isotopic abundances of actinides in a sample, by analyzing gamma-ray spectra obtained using germanium detector systems. Volume 2 is a guide to using the MGA (Multiple Group Analysis) computer program we have written to perform plutonium isotopic analyses. This report contains a listing of the FORTRAN instructions of the code.

  5. R&D Investment and The Performance of Firms:Empirical Analysis Based on Listed SMEs’ Data

    Institute of Scientific and Technical Information of China (English)

    Li; Xianzhen; Wu; Jinxi

    2011-01-01

    Based on 122 listed SMEs in Shenzhen Securities,this study evaluates the current situation of SMEsR&D investment and estimates R&D rate of return by using Cobb-Douglas production function as econometric studies of the contribution of R&D.The main findings are that the science-based sectors with the highest R&D intensity have a relatively low rate of return to R&D,the very traditional industries have the lowest return.Finally,we give some explanations to these findings.

  6. Comparison of psychological placebo and waiting list control conditions in the assessment of cognitive behavioral therapy for the treatment of generalized anxiety disorder: a meta-analysis.

    Science.gov (United States)

    Zhu, Zhipei; Zhang, Li; Jiang, Jiangling; Li, Wei; Cao, Xinyi; Zhou, Zhirui; Zhang, Tiansong; Li, Chunbo

    2014-12-01

    There is ongoing debate about the efficacy of placebos in the treatment of mental disorders. In randomized control trials (RCTs) about the treatment of generalized anxiety disorder, the administration of a psychological placebo or placement on a waiting list are the two most common control conditions. But there has never been a systematic comparison of the clinical effect of these different strategies. Compare the change in symptom severity among individuals treated with cognitive behavioral therapy, provided a psychological placebo, or placed on a waiting list using data from RCTs on generalized anxiety disorder. The following databases were searched for RCTs on generalized anxiety disorder: PubMed, PsycInfo, EMBASE, The Cochrane Library, CNKI, Chongqing VIP, Wanfang, Chinese Biological Medical Literature Database, and Taiwan Electronic Periodical Services. Studies were selected based on pre-defined inclusion and exclusion criteria and the quality of each included study - based on the risk of bias and the level of evidence - was formally assessed. Meta-analysis was conducted using RevMan5.3 and network meta-analyses comparing the three groups were conducted using R. Twelve studies with a combined sample size of 531 were included in the analysis. Compared to either control method (placebo or waiting list), cognitive behavioral therapy was more effective for generalized anxiety disorder. Provision of a psychological placebo was associated with a significantly greater reduction of symptoms than placement on a waiting list. Eight of the studies were classified as 'high risk of bias', and the overall level of evidence was classified as 'moderate', indicating that further research could change the overall results of the meta-analysis. RCTs about the treatment of generalized anxiety disorders are generally of moderate quality; they indicate the superiority of CBT but the results cannot, as yet, be considered robust. There is evidence of a non-negligible treatment effect

  7. Conservation Status of Marine Biodiversity in Oceania: An Analysis of Marine Species on the IUCN Red List of Threatened Species

    Directory of Open Access Journals (Sweden)

    Beth A. Polidoro

    2011-01-01

    Full Text Available Given the economic and cultural dependence on the marine environment in Oceania and a rapidly expanding human population, many marine species populations are in decline and may be vulnerable to extinction from a number of local and regional threats. IUCN Red List assessments, a widely used system for quantifying threats to species and assessing species extinction risk, have been completed for 1190 marine species in Oceania to date, including all known species of corals, mangroves, seagrasses, sea snakes, marine mammals, sea birds, sea turtles, sharks, and rays present in Oceania, plus all species in five important perciform fish groups. Many of the species in these groups are threatened by the modification or destruction of coastal habitats, overfishing from direct or indirect exploitation, pollution, and other ecological or environmental changes associated with climate change. Spatial analyses of threatened species highlight priority areas for both site- and species-specific conservation action. Although increased knowledge and use of newly available IUCN Red List assessments for marine species can greatly improve conservation priorities for marine species in Oceania, many important fish groups are still in urgent need of assessment.

  8. GLANET: genomic loci annotation and enrichment tool.

    Science.gov (United States)

    Otlu, Burçak; Firtina, Can; Keles, Sündüz; Tastan, Oznur

    2017-09-15

    Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET . Tutorials are provided at https://glanet.readthedocs.org . burcak@ceng.metu.edu.tr or oznur.tastan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online.

  9. Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth.

    Science.gov (United States)

    Davis, Richard V N; Lamont, Susan J; Rothschild, Max F; Persia, Michael E; Ashwell, Chris M; Schmidt, Carl J

    2015-01-01

    Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers) exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used RNA-seq to compare the transcriptomes of a modern and a legacy broiler line to identify differentially enriched genes in the breast muscle at days 6 and 21 post-hatch. Among the 15,945 genes analyzed, 10,841 were expressed at greater than 0.1 RPKM. At day 6 post-hatch 189 genes, including several regulators of myogenic growth and development, were differentially enriched between the two lines. The transcriptional profiles between lines at day 21 post-hatch identify 193 genes differentially enriched and still include genes associated with myogenic growth. This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2) and negative (MSTN, ACE) myogenic growth regulators may help explain the differences underlying the enhanced growth characteristics of the modern broilers.

  10. Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth.

    Directory of Open Access Journals (Sweden)

    Richard V N Davis

    Full Text Available Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used RNA-seq to compare the transcriptomes of a modern and a legacy broiler line to identify differentially enriched genes in the breast muscle at days 6 and 21 post-hatch. Among the 15,945 genes analyzed, 10,841 were expressed at greater than 0.1 RPKM. At day 6 post-hatch 189 genes, including several regulators of myogenic growth and development, were differentially enriched between the two lines. The transcriptional profiles between lines at day 21 post-hatch identify 193 genes differentially enriched and still include genes associated with myogenic growth. This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2 and negative (MSTN, ACE myogenic growth regulators may help explain the differences underlying the enhanced growth characteristics of the modern broilers.

  11. Ado-lists: A new concept for Stata

    OpenAIRE

    Jann, Ben

    2007-01-01

    A new command called adolist is presented. adolist is a tool to create, install, and uninstall lists of user ado-packages (“adolists”). For example, adolist can create a list of all user packages installed on a system and then install the same packages on another system. Moreover, ado-list can be used to put together thematic lists of packages such as, say, a list on income inequality analysis or time-series add-ons, or the list of “41 user ados everyone should know”. Such lists can then be s...

  12. MCNP5 CRITICALITY VALIDATION AND BIAS FOR INTERMEDIATE ENRICHED URANIUM SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    FINFROCK SH

    2009-12-10

    The purpose of this analysis is to validate the Monte Carlo N-Particle 5 (MCNP5) code Version 1.40 (LA-UR-03-1987, 2005) and its cross-section database for k-code calculations of intermediate enriched uranium systems on INTEL{reg_sign} processor based PC's running any version of the WINDOWS operating system. Configurations with intermediate enriched uranium were modeled with the moderator range of 39 {le} H/Fissile {le} 1438. See Table 2-1 for brief descriptions of selected cases and Table 3-1 for the range of applicability for this validation. A total of 167 input cases were evaluated including bare and reflected systems in a single body or arrays. The 167 cases were taken directly from the previous (Version 4C [Lan 2005]) validation database. Section 2.0 list data used to calculate k-effective (k{sub eff}) for the 167 experimental criticality benchmark cases using the MCNP5 code v1.40 and its cross section database. Appendix B lists the MCNP cross-section database entries validated for use in evaluating the intermediate enriched uranium systems for criticality safety. The dimensions and atom densities for the intermediate enriched uranium experiments were taken from NEA/NSC/DOC(95)03, September 2005, which will be referred to as the benchmark handbook throughout the report. For these input values, the experimental benchmark k{sub eff} is approximately 1.0. The MCNP validation computer runs ran to an accuracy of approximately {+-} 0.001. For the cases where the reported benchmark k{sub eff} was not equal to 1.0000 the MCNP calculational results were normalized. The difference between the MCNP validation computer runs and the experimentally measured k{sub eff} is the MCNP5 v1.40 bias. The USLSTATS code (ORNL 1998) was utilized to perform the statistical analysis and generate an acceptable maximum k{sub eff} limit for calculations of the intermediate enriched uranium type systems.

  13. 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.

  14. Cost-analysis of the WHO Essential Medicines List in A Resource-Limited Setting: Experience from A District Hospital in India.

    Science.gov (United States)

    Alvarez-Uria, Gerardo; Thomas, Dixon; Zachariah, Seeba; Byram, Rajarajeshwari; Kannan, Shanmugamari

    2014-05-01

    The World Health Organization (WHO) has been publishing the essential medicines list (EML) since 1977. The EML includes the most efficacious, safe and cost-effective drugs for the most relevant public health conditions worldwide. The WHO performs a cost-effectiveness analysis within each therapeutic group, but very little is known about which therapeutic groups are costliest for hospitals that adopt the WHO EML concept. In this study, we have described the annual consumption of medicines in a district hospital in India, that limited the list of available drugs according to the WHO EML concept. Only 21 drugs constituted 50% of the hospital spending. Anti-infective medicines accounted for 41% of drug spending, especially antiretrovirals which were used to treat HIV infection. Among other therapeutic groups, insulin had the highest impact on the hospital budget. We identified medicines used in perinatal care, which included anti-D immunoglobulin and lung surfactants, that were used rarely, but bore a relatively high cost burden. The results of this study indicate that, in district that adopt the WHO EML, antiretrovirals and antibiotics were the top therapeutic groups for the drug hospital budgets.

  15. Voluntary Financial Reporting on the Internet: Analysis of the Practice of Stock-Market Listed Croatian and Slovene Joint Stock Companies

    Directory of Open Access Journals (Sweden)

    Ivica Pervan

    2006-03-01

    Full Text Available An investigation into Internet financial reporting carried out in June 2005 that focused on stock-market listed Croatian and Slovene joint-stock companies has two basic aspects, comparative and explanatory. The comparative aspect of the research showed that Slovene corporations have a statistically significant higher level of financial reporting (as measured with IFR score. The average IFR score for 55 corporate entities from Croatia came to just 6.85, while the average IFR score for 30 Slovene firms was 17.63. The second aspect of the investigation was explanatory, and at the level of each state and sample the intention was to find the variables that affect IFR scores significantly. With respect to the Croatian sample it was shown that the IFR score was statistically significantly and positively correlated with size, profitability, number of shareholders, and amount of traffic on the stock markets. Then regression analysis showed that majority foreign ownership had a positive effect on the IFR score. A statistically significant but negative correlation was established for two sectors, tourism and marine transport. For the Slovene sample, comprising 30 firms, the size, profitability and number of stockholders were not significant variables. However, official listing, proportion of market capitalisation and ratio of market to book values of shares were statistically significantly and positively correlated with the IFR score. Only one sector, transport, was significantly and negatively correlated with the IFR score.

  16. Analysis on the environmental information disclosure of Chinese coal listed companies%煤炭行业上市公司环境信息披露研究

    Institute of Scientific and Technical Information of China (English)

    李强; 朱杨慧; 冯波

    2013-01-01

    Using content analysis method,this paper studies the quantity and quality of envi-ronmental information disclosure of Chinese coal listed companies from 2008 to 201 1 It analyzes the reasons of quantitative fluctuation Then,it makes comparison of quality with SINOPEC from integrity,readability,comparability and objectivity Finally,it gives some suggestions to improve the environmental information disclosure of coal listed companies.%采用内容分析法,对煤炭行业上市公司2008-2011年环境信息披露的数量和质量进行研究,剖析其数量上发生波动的可能原因,并从完整性、可读性、可比性和客观性4个方面与同属能源行业的中国石化进行质量比较,最后提出完善煤炭行业上市公司环境信息披露的对策。

  17. A Neutronic Analysis of TRU Recycling in PWRs Loaded with MOX-UE Fuel (MOX with U-235 Enriched U Support)

    Energy Technology Data Exchange (ETDEWEB)

    G. Youinou; S. Bays

    2009-05-01

    This report presents the results of a study dealing with the homogeneous recycling of either Pu or Pu+Np or Pu+Np+Am or Pu+Np+Am+Cm in PWRs using MOX-UE fuel, i.e. standard MOX fuel with a U235 enriched uranium support instead of the standard tail uranium (0.25%) for standard MOX fuel. This approach allows to multirecycle Pu or TRU (Pu+MA) as long as U235 is available, by keeping the Pu or TRU content in the fuel constant and at a value ensuring a negative moderator void coefficient (i.e. the loss of the coolant brings imperatively the reactor to a subcritical state). Once this value is determined, the U235 enrichment of the MOX-UE fuel is adjusted in order to reach the target burnup (51 GWd/t in this study).

  18. Analysis of tank 51H (HTF-51-15-77) subsurface supernatant sample in support of enrichment and corrosion control programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-08-18

    This report provides the results of analyses on Tank 51H subsurface supernatant liquid sample in support of the Enrichment Control Program (ECP) and the Corrosion Control Program (CCP). The purpose of the ECP sample taken from Tank 51H in early June was to determine if the later decants would be “acceptable feed” to the 2H and 3H evaporator systems.

  19. Analysis of tank 51H (HTF-51-15-77) subsurface supernatant sample in support of enrichment and corrosion control programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-08-18

    This report provides the results of analyses on Tank 51H subsurface supernatant liquid sample in support of the Enrichment Control Program (ECP) and the Corrosion Control Program (CCP).The purpose of the ECP sample taken from Tank 51H in early June was to determine if the later decants would be “acceptable feed” to the 2H and 3H evaporator systems.

  20. Analysis of tank 4 (FTF-4-15-22, 23) surface and subsurface supernatant samples in support of enrichment control, corrosion control and evaporator feed qualification programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-09-09

    This report provides the results of analyses on Savannah River Site Tank 4 surface and subsurface supernatant liquid samples in support of the Enrichment Control Program (ECP), the Corrosion Control Program (CCP) and the Evaporator Feed Qualification (EFQ) Program. The purpose of the ECP sample taken from Tank 4 in August 2015 was to determine if the supernatant liquid would be “acceptable feed” to the 2H and 3H evaporator systems.

  1. Quantifying protein synthesis and degradation in Arabidopsis by dynamic 13CO2 labeling and analysis of enrichment in individual amino acids in their free pools and in protein.

    Science.gov (United States)

    Ishihara, Hirofumi; Obata, Toshihiro; Sulpice, Ronan; Fernie, Alisdair R; Stitt, Mark

    2015-05-01

    Protein synthesis and degradation represent substantial costs during plant growth. To obtain a quantitative measure of the rate of protein synthesis and degradation, we supplied (13)CO2 to intact Arabidopsis (Arabidopsis thaliana) Columbia-0 plants and analyzed enrichment in free amino acids and in amino acid residues in protein during a 24-h pulse and 4-d chase. While many free amino acids labeled slowly and incompletely, alanine showed a rapid rise in enrichment in the pulse and a decrease in the chase. Enrichment in free alanine was used to correct enrichment in alanine residues in protein and calculate the rate of protein synthesis. The latter was compared with the relative growth rate to estimate the rate of protein degradation. The relative growth rate was estimated from sequential determination of fresh weight, sequential images of rosette area, and labeling of glucose in the cell wall. In an 8-h photoperiod, protein synthesis and cell wall synthesis were 3-fold faster in the day than at night, protein degradation was slow (3%-4% d(-1)), and flux to growth and degradation resulted in a protein half-life of 3.5 d. In the starchless phosphoglucomutase mutant at night, protein synthesis was further decreased and protein degradation increased, while cell wall synthesis was totally inhibited, quantitatively accounting for the inhibition of growth in this mutant. We also investigated the rates of protein synthesis and degradation during leaf development, during growth at high temperature, and compared synthesis rates of Rubisco large and small subunits of in the light and dark.

  2. Hydrography - Integrated List Attaining

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This layer shows only attaining segments of the Integrated List. The Streams Integrated List represents stream assessments in an integrated format for the Clean...

  3. National List of Beaches

    Data.gov (United States)

    U.S. Environmental Protection Agency — EPA has published a list of coastal recreation waters adjacent to beaches (or similar points of access) used by the public in the U.S. The list, required by the...

  4. Acronym master list

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    This document is a master list of acronyms and other abbreviations that are used by or could be useful to, the personnel at Los Alamos National Laboratory. Many specialized and well-known abbreviations are not included in this list.

  5. 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.

  6. Development for analysis system of rods enrichment of nuclear fuels; Desarrollo de un sistema de analisis de enriquecimiento de barras de combustible nuclear

    Energy Technology Data Exchange (ETDEWEB)

    Rojas C, E.L

    1998-11-01

    Nuclear industry is strongly regulated all over the world and quality assurance is important in every nuclear installation or process related with it. Nuclear fuel manufacture is not the exception. ININ was committed to manufacture four nuclear fuel bundles for the CFE nucleo electric station at Laguna Verde, Veracruz, under General Electric specifications and fulfilling all the requirements of this industry. One of the quality control requisites in nuclear fuel manufacture deals with the enrichment of the pellets inside the fuel bundle rods. To achieve the quality demanded in this aspect, the system described in this work was developed. With this system, developed at ININ it is possible to detect enrichment spikes since 0.4 % in a column of pellets with a 95 % confidence interval and to identify enrichment differences greater than 0.2 % e between homogeneous segments, also with a 95 % confidence interval. ININ delivered the four nuclear fuel bundles to CFE and these were introduced in the core of the nuclear reactor of Unit 1 in the fifth cycle. Nowadays they are producing energy and have shown a correct mechanical performance and neutronic behavior. (Author)

  7. 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...

  8. ChIP-Enrich: gene set enrichment testing for ChIP-seq data.

    Science.gov (United States)

    Welch, Ryan P; Lee, Chee; Imbriano, Paul M; Patil, Snehal; Weymouth, Terry E; Smith, R Alex; Scott, Laura J; Sartor, Maureen A

    2014-07-01

    Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with the presence of one or more peaks and because many biologically defined gene sets have an excess of genes with longer or shorter gene locus lengths. Unlike alternative methods, ChIP-Enrich can account for the wide range of gene locus length-to-peak presence relationships (observed in ENCODE ChIP-seq data sets). We show that ChIP-Enrich has a well-calibrated type I error rate using permuted ENCODE ChIP-seq data sets; in contrast, two commonly used gene set enrichment methods, Fisher's exact test and the binomial test implemented in Genomic Regions Enrichment of Annotations Tool (GREAT), can have highly inflated type I error rates and biases in ranking. We identify DNA-binding proteins, including CTCF, JunD and glucocorticoid receptor α (GRα), that show different enrichment patterns for peaks closer to versus further from transcription start sites. We also identify known and potential new biological functions of GRα. ChIP-Enrich is available as a web interface (http://chip-enrich.med.umich.edu) and Bioconductor package. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. 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

  10. 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...

  11. Investigação da qualidade de farinhas enriquecidas utilizando Análise por Componentes Principais (PCA Enriched flour quality investigation using Principal Component Analysis (PCA

    Directory of Open Access Journals (Sweden)

    Bruno Thiago Soeiro

    2010-09-01

    that corn and wheat flours have to be fortified with folic acid and iron. The main objective of this work was to investigate some enriched flour characteristics using Principal Component Analysis (PCA. Wheat and corn flours presented, on average, acceptable centesimal composition according to the Brazilian Legislation. For the wheat flours investigated, the folic acid concentration was, on average, close to the expected value. Corn flours contained higher amount of vitamin. For both types of flour, the iron content exceeded the label claim of the products. Parameters, such as folic acid, iron, protein, lipids, moisture, ash, and carbohydrates content were present in 30 flour packages purchased from the local market. A matrix with 30 rows and 7 columns was organized and the data was autoscaled. The first information observed was an expected discrimination according to the type of flour. The wheat flours were characterized by high protein, moisture, and ash content. On the other hand, the corn flours had high iron, carbohydrates, lipids, and folic acid. Another important observation was related to the package type. It was noted that the flours packed in plastic bags had less folic acid (152 µg.100 g-1, on average than those packed in paper (259 µg.100 g-1, on average bags. This behavior is probably due to the light incidence during the storage period. This study can be useful to help the governmental authorities in the enriched food program evaluation. In this case, it will be possible to set suitable rules for appropriate food packaging.

  12. List scheduling revisited

    NARCIS (Netherlands)

    Schutten, Johannes M.J.

    1996-01-01

    We consider the problem of scheduling n jobs on m identical parallel machines to minimize a regular cost function. The standard list scheduling algorithm converts a list into a feasible schedule by focusing on the job start times. We prove that list schedules are dominant for this type of problem.

  13. Retail Shopping Lists

    DEFF Research Database (Denmark)

    Schmidt, Marcus

    2012-01-01

    The paper addresses consumers' shopping lists. The current study is based on a survey of 871 lists collected at retail grocery stores. Most items on shopping lists appear on the product category level rather than the brand level. The importance of the brand level varies considerably across product....... The paper ends with a discussion and with suggestions for future research....

  14. Implementation and analysis of list mode algorithm using tubes of response on a dedicated brain and breast PET

    Energy Technology Data Exchange (ETDEWEB)

    Moliner, L. [Instituto de Instrumentación para Imagen Molecular (I3M). Centro Mixto UPV-CSIC-CIEMAT. Camino de Vera s/n, 46022 Valencia (Spain); Correcher, C. [ONCOVISION (GEM-Imaging S.A.), 46012 Valencia (Spain); González, A.J., E-mail: agonzalez@i3m.upv.es [Instituto de Instrumentación para Imagen Molecular (I3M). Centro Mixto UPV-CSIC-CIEMAT. Camino de Vera s/n, 46022 Valencia (Spain); Conde, P.; Hernández, L.; Orero, A.; Rodríguez-Álvarez, M.J.; Sánchez, F.; Soriano, A.; Vidal, L.F.; Benlloch, J.M. [Instituto de Instrumentación para Imagen Molecular (I3M). Centro Mixto UPV-CSIC-CIEMAT. Camino de Vera s/n, 46022 Valencia (Spain)

    2013-02-21

    In this work we present an innovative algorithm for the reconstruction of PET images based on the List-Mode (LM) technique which improves their spatial resolution compared to results obtained with current MLEM algorithms. This study appears as a part of a large project with the aim of improving diagnosis in early Alzheimer disease stages by means of a newly developed hybrid PET-MR insert. At the present, Alzheimer is the most relevant neurodegenerative disease and the best way to apply an effective treatment is its early diagnosis. The PET device will consist of several monolithic LYSO crystals coupled to SiPM detectors. Monolithic crystals can reduce scanner costs with the advantage to enable implementation of very small virtual pixels in their geometry. This is especially useful for LM reconstruction algorithms, since they do not need a pre-calculated system matrix. We have developed an LM algorithm which has been initially tested with a large aperture (186 mm) breast PET system. Such an algorithm instead of using the common lines of response, incorporates a novel calculation of tubes of response. The new approach improves the volumetric spatial resolution about a factor 2 at the border of the field of view when compared with traditionally used MLEM algorithm. Moreover, it has also shown to decrease the image noise, thus increasing the image quality.

  15. Efficient somatic embryogenesis and molecular marker based analysis as effective tools for conservation of red-listed plant Commiphora wightii

    Directory of Open Access Journals (Sweden)

    ASHOK KUMAR PARMAR

    2014-08-01

    Full Text Available A refined and high efficiency protocol for in vitro regeneration of Commiphora wightii, a red-listed medicinal plant of medicinal importance, has been developed through optimized somatic embryogenesis pathway. Cultures from immature fruits were induced and proliferated on B5 medium supplemented with 2.26 µM 2,4-D. Embryogenic calli were obtained and then maintained for extended periods by alternately subculturing on modified MS medium supplemented with 1.11 µM BAP, 0.57 µM IBA and with 0.5% activated charcoal or without PGR every 3-4 weeks. Cyclic embryogenesis was obtained. Late torpedo and early cotyledonary stages somatic embryos were regularly harvested from PGR-free modified MS medium. It was found that percent moisture available in culture containers play a critical role in maturation and subsequent germination of somatic embryos of C. wighti. Maximum germination of more than 80% was achieved through media recycling. Somatic embryo derived plants (emblings were acclimatized. After 5 months, acclimatized plants were out-planted in experimental field. These morphologically normal plants have been surviving for over 3 years. Molecular polymorphism was clearly evident when these plants were tested using RAPD primers, making the plants suitable for use in its species restoration program.

  16. 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.

  17. Coupling of metal-organic frameworks-containing monolithic capillary-based selective enrichment with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for efficient analysis of protein phosphorylation.

    Science.gov (United States)

    Li, Daojin; Yin, Danyang; Chen, Yang; Liu, Zhen

    2017-05-19

    Protein phosphorylation is a major post-translational modification, which plays a vital role in cellular signaling of numerous biological processes. Mass spectrometry (MS) has been an essential tool for the analysis of protein phosphorylation, for which it is a key step to selectively enrich phosphopeptides from complex biological samples. In this study, metal-organic frameworks (MOFs)-based monolithic capillary has been successfully prepared as an effective sorbent for the selective enrichment of phosphopeptides and has been off-line coupled with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for efficient analysis of phosphopeptides. Using š-casein as a representative phosphoprotein, efficient phosphorylation analysis by this off-line platform was verified. Phosphorylation analysis of a nonfat milk sample was also demonstrated. Through introducing large surface areas and highly ordered pores of MOFs into monolithic column, the MOFs-based monolithic capillary exhibited several significant advantages, such as excellent selectivity toward phosphopeptides, superb tolerance to interference and simple operation procedure. Because of these highly desirable properties, the MOFs-based monolithic capillary could be a useful tool for protein phosphorylation analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. ANALYSIS OF EFFECT OF PROFITABILITY, ASSETS STRUCTURE, SIZE OF COMPANIES, AND LIQUIDITY TO CAPITAL STRUCTURES IN MINING COMPANIES LISTED IN INDONESIA STOCK EXCHANGE PERIOD 2012 - 2015

    Directory of Open Access Journals (Sweden)

    Gatot Nazir Ahmad

    2017-09-01

    Full Text Available The purpose of this study is to analyze the effect of profitability, structure assets, firm size and liquidity to the capital structure of mining companies listed on the Indonesia Stock Exchange for the period 2012-2015. Sampling technique using purpose sampling. Data analysis technique used in this research is panel data regression. The results showed that partially profitability had negative and significant effect to capital structure, asset structure had positive and significant effect to capital structure, firm size had positive and significant effect to capital structure, and liquidity had negative and significant effect to capital structure. Simultaneously profitability, asset structure, firm size and liquidity have a significant effect on capital structure.

  19. The Fermi All-Sky Variability Analysis: A List of Flaring Gamma-Ray Sources and the Search for Transients in our Galaxy

    Science.gov (United States)

    Ackermann, M.; Ajello, M.; Albert, A.; Allafort, A.; Antolini, E.; Baldini, L.; Ballet, J.; Barbiellini, G; Bastieri, D.; Bechtol, K.; Bellazzini, R.; Blandford, R. D.; Bloom, E. D.; Brandt, T. J.; Ferrara, E. C.; Guiriec, S.; Harding, A. K.; Hays, E.; Hewitt, J.; McEnery, J. E.; Nemmen, R.; Perkins, J. S.; Scargle, J. D; Thompson, D. J.; Troja, E.

    2013-01-01

    In this paper, we present the Fermi All-sky Variability Analysis (FAVA), a tool to systematically study the variability of the gamma-ray sky measured by the Large Area Telescope on board the Fermi Gamma-ray Space Telescope.For each direction on the sky, FAVA compares the number of gamma-rays observed in a given time window to the number of gamma-rays expected for the average emission detected from that direction. This method is used in weekly time intervals to derive a list of 215 flaring gamma-ray sources. We proceed to discuss the 27 sources found at Galactic latitudes smaller than 10 and show that, despite their low latitudes, most of them are likely of extragalactic origin.

  20. THE FERMI ALL-SKY VARIABILITY ANALYSIS: A LIST OF FLARING GAMMA-RAY SOURCES AND THE SEARCH FOR TRANSIENTS IN OUR GALAXY

    Energy Technology Data Exchange (ETDEWEB)

    Ackermann, M. [Deutsches Elektronen Synchrotron DESY, D-15738 Zeuthen (Germany); Ajello, M. [Space Sciences Laboratory, 7 Gauss Way, University of California, Berkeley, CA 94720-7450 (United States); Albert, A. [Department of Physics, Center for Cosmology and Astro-Particle Physics, The Ohio State University, Columbus, OH 43210 (United States); Allafort, A.; Bechtol, K.; Blandford, R. D.; Bloom, E. D.; Bottacini, E. [W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305 (United States); Antolini, E.; Bonamente, E. [Dipartimento di Fisica, Universita degli Studi di Perugia, I-06123 Perugia (Italy); Baldini, L. [Universita di Pisa and Istituto Nazionale di Fisica Nucleare, Sezione di Pisa, I-56127 Pisa (Italy); Ballet, J. [Laboratoire AIM, CEA-IRFU/CNRS/Universite Paris Diderot, Service d' Astrophysique, CEA Saclay, F-91191 Gif sur Yvette (France); Barbiellini, G. [Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, I-34127 Trieste (Italy); Bastieri, D. [Istituto Nazionale di Fisica Nucleare, Sezione di Padova, I-35131 Padova (Italy); Bellazzini, R.; Bregeon, J. [Istituto Nazionale di Fisica Nucleare, Sezione di Pisa, I-56127 Pisa (Italy); Bouvier, A. [Santa Cruz Institute for Particle Physics, Department of Physics and Department of Astronomy and Astrophysics, University of California at Santa Cruz, Santa Cruz, CA 95064 (United States); Brandt, T. J. [NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Brigida, M. [Dipartimento di Fisica ' ' M. Merlin' ' dell' Universita e del Politecnico di Bari, I-70126 Bari (Italy); Bruel, P., E-mail: majello@slac.stanford.edu, E-mail: allafort@stanford.edu, E-mail: rolf.buehler@desy.de [Laboratoire Leprince-Ringuet, Ecole polytechnique, CNRS/IN2P3, Palaiseau (France); and others

    2013-07-01

    In this paper, we present the Fermi All-sky Variability Analysis (FAVA), a tool to systematically study the variability of the gamma-ray sky measured by the Large Area Telescope on board the Fermi Gamma-ray Space Telescope. For each direction on the sky, FAVA compares the number of gamma-rays observed in a given time window to the number of gamma-rays expected for the average emission detected from that direction. This method is used in weekly time intervals to derive a list of 215 flaring gamma-ray sources. We proceed to discuss the 27 sources found at Galactic latitudes smaller than 10 Degree-Sign and show that, despite their low latitudes, most of them are likely of extragalactic origin.

  1. STOCK PERFORMANCE ANALYSIS OF LISTED ENTITIES AT THE BUCHAREST STOCK EXCHANGE. CASE STUDY ON THE ENERGY AND RELATED UTILITIES SECTOR COMPANIES

    Directory of Open Access Journals (Sweden)

    Ioana Anghel

    2016-12-01

    Full Text Available Financial performance, as a multi-criteria economic category, constitutes a current topic broadly investigated by authors and experts in finance, financial management, accounting, evaluation and general management. In this ever more competitive capital market, because investors are increasingly better informed, it becomes essential for a company to know and periodically evaluate its stock performance in order to compare it at economic branch level. This present research study analyses six companies that activate in the energy and related utilities sector, listed at the Bucharest Stock Exchange, between 2004 and 2015, with the aim of identifying branch similarities regarding the evolution of the key stock growth ratios and indicators used in stock performance analysis. Furthermore, the authors deemed appropriate to correlate their results with the evolution of the main rates of return of the same companies

  2. Queuing for coronary angiography during severe supply-demand mismatch in a US public hospital: analysis of a waiting list registry.

    Science.gov (United States)

    Rosanio, S; Tocchi, M; Cutler, D; Uretsky, B F; Stouffer, G A; deFilippi, C R; MacInerney, E J; Runge, S R; Aaron, J; Otero, J; Garg, S; Runge, M S

    1999-07-14

    Adverse cardiac events have been reported in patients waiting for either coronary surgery or angioplasty. However, data on the risk of adverse events while awaiting coronary angiography are limited, and none are available from a US population. To quantify cardiac outcomes in patients waiting for elective coronary angiography. Observational cohort study of 381 adult outpatients (mean [SD] age, 55 [12] years; 64% male; 61% white) on a waiting list for coronary angiography at a US tertiary care public teaching hospital during 1993-1994. Rates of cardiac death, nonfatal myocardial infarction, and hospitalizations for unstable angina or heart failure as a function of amount of time spent on a waiting list. Sixty-six patients were dropped from the waiting list but were included in the study analysis. During a mean (SD) follow-up of 8.4 (6.5) months, cardiac death, myocardial infarction, and hospitalization occurred in 6 (1.6%), 4 (1.0%), and 26 (6.8%) patients, respectively. The probability of events was minimal in the first 2 weeks and increased steadily between 3 and 13 weeks. By Cox multivariate analysis, 2 variables independently identified an increased risk of adverse events: a strongly positive treadmill exercise electrocardiogram or positive stress imaging result at referral (odds ratio [OR], 2.32; 95% confidence interval [CI], 1.22-4.16; P=.01) and the use of 2 to 3 anti-ischemic medications (OR, 1.98; 95% CI, 1.19-3.96; P=.04). Among 311 patients who ultimately underwent angiography, those with adverse events had a higher prevalence of coronary disease (96% vs 60%; P<.001), more frequently required revascularization (93% vs 53%; P<.001), and had longer hospital stays (mean [SD], 6.2 [4.3] vs 1.3 [0.7] days; P=.001). Our data suggest that in a cohort referred for coronary angiography, delaying the procedure places some patients at risk for death, myocardial infarction, unplanned hospitalization, a longer hospital stay, and, potentially, a poorer prognosis. Waits

  3. 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.

  4. Title III List of Lists -- Data Tool

    Data.gov (United States)

    U.S. Environmental Protection Agency — This list was prepared to help firms handling chemicals determine whether they need to submit reports under sections 302, 304, or 313 of the Emergency Planning and...

  5. 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

  6. Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

    Science.gov (United States)

    Boltaña, Sebastian; Castellana, Barbara; Goetz, Giles; Tort, Lluis; Teles, Mariana; Mulero, Victor; Novoa, Beatriz; Figueras, Antonio; Goetz, Frederick W.; Gallardo-Escarate, Cristian; Planas, Josep V.; Mackenzie, Simon

    2017-01-01

    This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene

  7. Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

    Directory of Open Access Journals (Sweden)

    Sebastian Boltaña

    2017-02-01

    Full Text Available This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS and peptidoglycan (PGN. Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs, carrier proteins/membrane transport (approximately 15%, effectors/modulators and cell communication (approximately 11%, nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5% and intracellular transducers/signal transduction (approximately 5%. Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ that provides a platform enriched for the study

  8. Magnetic nanoparticles of nitrogen enriched carbon (mnNEC) for analysis of pesticides and metabolites in zebrafish by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Zhou, Youe; Xia, Qian; Ding, Mengjie; Kageruka, Hubert; Jiang, Haiying; Jiang, Yan; Jing, Huifen; Xiao, Xiao; Zhong, Hongying

    2013-02-01

    Nanosized carbon based sorbents have been widely used for separation, enrichment and desalting of biological samples because of their distinguished characteristics. In this work, magnetic nanoparticles of nitrogen enriched carbon (mnNEC) have been developed for enrichment of organochlorine pesticide DDT and metabolite DDE that have been accumulated in zebrafish during the course of environmental exposure. Polymerization of pyrrole was performed in the aqueous suspension of Fe(3)O(4) nanoparticles. Resultant core-shell nanoparticules coated with polypyrrole were then subjected to a process of carbonization under high temperature and nitrogen atmospheric condition. The presence of nitrogen atoms in carbon nanoparticles increases the hydrophilicity and dispersability in aqueous samples. It has been experimentally demonstrated that mnNEC can be effectively dispersed in aqueous samples and rapidly isolated by the application of an external magnetic field. Recoveries of DDT and DDE from water range from 90% to 102% and 85-97% respectively. In combination with Selected Ion Monitoring (SIM) experiments of gas chromatography-mass spectrometry, the detection limit can be down to low ng/mL level. By using mnNEC approach, two interesting results have been found for zebrafish with 60 days exposure to DDT (1 μg/l). (1) There is higher concentration of DDT (37-143 ng/g) and DDE (173-1108 ng/g) in male zebrafish body tissues than that of female (7-52 ng/g and 146-362 ng/g for DDT and DDE respectively). (2) There is high ratio of DDE/DDT for both female and male zebrafish, implying high environmental persistence and ongoing bioaccumulation.

  9. Comparative analysis of spectra of the background of the proportional counter filled with Kr, enriched in Kr-78, and with Kr of natural content

    OpenAIRE

    Gavriljuk, Yu. M.; Gavrin, V. N.; Gangapshev, A. M.; Kazalov, V. V.; Kuzminov, V. V.; Panasenko, S. I.; Ratkevich, S. S.

    2007-01-01

    The results of the experiment searching for 2K-capture with large low-background proportional counter are presented. The comparison of spectra of the background of the proportional counter filled with Kr enriched in $^{78}$Kr (8400 hr) and with natural Kr (3039 hr) is given. A new limit on the half-life of $^{78}$Kr with regard to 2K-capture, T$_{1/2}\\geq2.0\\cdot10^{21}$ yrs (95% C.L.) has been obtained.

  10. Carbon dioxide enrichment: Data on the response of cotton to varying CO sub 2 , irrigation, and nitrogen

    Energy Technology Data Exchange (ETDEWEB)

    Sepanski, R.J. (Tennessee Univ., Knoxville, TN (United States). Energy, Environment and Resources Center); Kimball, B.A.; Mauney, J.R.; La Morte, R.L.; Guinn, G.; Nakayama, F.S.; Radin, J.W.; Mitchell, S.T.; Parker, L.L.; Peresta, G.J.; Nixon, P.E. III; Savoy, B.; Harris, S.M.; MacDonald, R.; Pros, H.; Martinez, J. (Agricultural Research Service, Phoenix, AZ (United States)); Lakatos, E.A. (Arizona Univ., Tucs

    1992-06-01

    This document presents results from field CO{sub 2}-enrichment experiments conducted over five consecutive growing seasons, 1983--1987. These results comprise data concerning the effects of continuous CO{sub 2} enrichment on the growth of cotton under optimal and limiting levels of water and nitrogen. Unlike many prior C0{sub 2} enrichment experiments in growth chambers or greenhouses, these studies were conducted on field-planted cotton at close to natural conditions using the open-top chamber approach. Measurements were made on a variety of crop response variables at intervals during the growing season and upon crop harvest. The initial experiment examined the effects of varying C0{sub 2} concentration only. In the following two seasons, the interactive effects of C0{sub 2} concentration and water availability were studied. In the final two seasons, the effects of the three-way interaction between C0{sub 2} concentration, water availability, and nitrogen fertility were investigated. The data comprise three types of information: identification variables (such as year, institution and situ codes, and treatment regimens), intermediate growth measurements (such as plant height, leaf area index, number of flowers, and dry weight of leaves) taken at various times during the growing season, and crop harvest results (such as lint yield, seed yield, and total aboveground dry biomass). They are available free of charge as a numeric data package (NAP) from the Carbon Dioxide Information Analysis Center. The NAP consists of this document and a magnetic tape (or a floppy diskette, upon request) containing machine-readable files. This document provides sample listings of the CO{sub 2} enrichment response data as they appear on the magnetic tape or floppy diskette and provides detailed descriptions of the design and methodology of these experiments, as well as a complete hard copy listing of all of the data in the form of a supplemental text provided as an appendix.

  11. Carbon dioxide enrichment: Data on the response of cotton to varying CO{sub 2}, irrigation, and nitrogen

    Energy Technology Data Exchange (ETDEWEB)

    Sepanski, R.J. [Tennessee Univ., Knoxville, TN (United States). Energy, Environment and Resources Center; Kimball, B.A.; Mauney, J.R.; La Morte, R.L.; Guinn, G.; Nakayama, F.S.; Radin, J.W.; Mitchell, S.T.; Parker, L.L.; Peresta, G.J.; Nixon, P.E. III; Savoy, B.; Harris, S.M.; MacDonald, R.; Pros, H.; Martinez, J. [Agricultural Research Service, Phoenix, AZ (United States); Lakatos, E.A. [Arizona Univ., Tucson, AZ (United States). Dept. of Soil and Water Science

    1992-06-01

    This document presents results from field CO{sub 2}-enrichment experiments conducted over five consecutive growing seasons, 1983--1987. These results comprise data concerning the effects of continuous CO{sub 2} enrichment on the growth of cotton under optimal and limiting levels of water and nitrogen. Unlike many prior C0{sub 2} enrichment experiments in growth chambers or greenhouses, these studies were conducted on field-planted cotton at close to natural conditions using the open-top chamber approach. Measurements were made on a variety of crop response variables at intervals during the growing season and upon crop harvest. The initial experiment examined the effects of varying C0{sub 2} concentration only. In the following two seasons, the interactive effects of C0{sub 2} concentration and water availability were studied. In the final two seasons, the effects of the three-way interaction between C0{sub 2} concentration, water availability, and nitrogen fertility were investigated. The data comprise three types of information: identification variables (such as year, institution and situ codes, and treatment regimens), intermediate growth measurements (such as plant height, leaf area index, number of flowers, and dry weight of leaves) taken at various times during the growing season, and crop harvest results (such as lint yield, seed yield, and total aboveground dry biomass). They are available free of charge as a numeric data package (NAP) from the Carbon Dioxide Information Analysis Center. The NAP consists of this document and a magnetic tape (or a floppy diskette, upon request) containing machine-readable files. This document provides sample listings of the CO{sub 2} enrichment response data as they appear on the magnetic tape or floppy diskette and provides detailed descriptions of the design and methodology of these experiments, as well as a complete hard copy listing of all of the data in the form of a supplemental text provided as an appendix.

  12. Reduced enrichment for research and test reactors: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    1988-05-01

    The international effort to develop new research reactor fuel materials and designs based on the use of low-enriched uranium, instead of highly-enriched uranium, has made much progress during the eight years since its inception. To foster direct communication and exchange of ideas among the specialist in this area, the Reduced Enrichment Research and Test Reactor (RERTR) Program, at the Argonne National Laboratory, sponsored this meeting as the ninth of a series which began in 1978. All previous meetings of this series are listed on the facing page. The focus of this meeting was on the LEU fuel demonstration which was in progress at the Oak Ridge Research (ORR) reactor, not far from where the meeting was held. The visit to the ORR, where a silicide LEU fuel with 4.8 g A/cm/sup 3/ was by then in routine use, illustrated how far work has progressed.

  13. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353.

    Science.gov (United States)

    Cho, Sung Mi; Jeoung, Sae Chae; Song, Ji-Young; Kupriyanova, Elena V; Pronina, Natalia A; Lee, Bong-Woo; Jo, Seong-Whan; Park, Beom-Seok; Choi, Sang-Bong; Song, Ji-Joon; Park, Youn-Il

    2015-11-20

    Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found.

  14. Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa.

    Science.gov (United States)

    Hutcheon, Kate; McLaughlin, Eileen A; Stanger, Simone J; Bernstein, Ilana R; Dun, Matthew D; Eamens, Andrew L; Nixon, Brett

    2017-08-17

    Post-testicular sperm maturation and storage within the epididymis is a key determinant of gamete quality and fertilization competence. Here we demonstrate that mouse spermatozoa possess a complex small non-protein-coding RNA (sRNA) profile, the composition of which is markedly influenced by their epididymal transit. Thus, although miRNAs are highly represented in the spermatozoa of the proximal epididymis, this sRNA class is largely diminished in mature spermatozoa of the distal epididymis. Coincident with this, a substantial enrichment in Piwi-interacting RNA (piRNA) abundance in cauda spermatozoa was detected. Further, features of cauda piRNAs, including; predominantly 29-31 nts in length; preference for uracil at their 5' terminus; no adenine enrichment at piRNA nt 10, and; predominantly mapping to intergenic regions of the mouse genome, indicate that these piRNAs are generated by the PIWIL1-directed primary piRNA production pathway. Accordingly, PIWIL1 was detected via immunoblotting and mass spectrometry in epididymal spermatozoa. These data provide insight into the complexity and dynamic nature of the sRNA profile of spermatozoa and raise the intriguing prospect that piRNAs are generated in situ in maturing spermatozoa. Such information is of particular interest in view of the potential role for paternal sRNAs in influencing conception, embryo development and intergenerational inheritance.

  15. Analysis of organizational options for the uranium enrichment enterprise in relation to asset divesture. [BPA; TVA; SYNFUELS; CONRAIL; British TELECOM; COMSTAT

    Energy Technology Data Exchange (ETDEWEB)

    Harrer, B.J.; Hattrup, M.P.; Dase, J.E.; Nicholls, A.K.

    1986-08-01

    This report presents a comparison of the characteristics of some prominent examples of independent government corporations and agencies with respect to the Department of Energy's (DOE) uranium enrichment enterprise. The six examples studied were: the Bonneville Power Administration (BPA); the Tennessee Valley Authority (TVA); the Synthetic Fuels Corporation (SYNFUELS); the Consolidated Rail Corporation (CONRAIL); the British Telecommunications Corporation (British TELECOM); and the Communications Satellite Organization (COMSAT), in order of decreasing levels of government ownership and control. They range from BPA, which is organized as an agency within DOE, to COMSAT, which is privately owned and free from almost all regulations common to government agencies. Differences in the degree of government involvement in these corporations and in many other characteristics serve to illustrate that there are no accepted standards for defining the characteristics of government corporations. Thus, historical precedent indicates considerable flexibility would be available in the development of enabling legislation to reorganize the enrichment enterprise as a government corporation or independent government agency.

  16. Analysis of organizational options for the uranium enrichment enterprise in relation to asset divesture. [BPA; TVA; SYNFUELS; CONRAIL; British TELECOM; COMSTAT

    Energy Technology Data Exchange (ETDEWEB)

    Harrer, B.J.; Hattrup, M.P.; Dase, J.E.; Nicholls, A.K.

    1986-08-01

    This report presents a comparison of the characteristics of some prominent examples of independent government corporations and agencies with respect to the Department of Energy's (DOE) uranium enrichment enterprise. The six examples studied were: the Bonneville Power Administration (BPA); the Tennessee Valley Authority (TVA); the Synthetic Fuels Corporation (SYNFUELS); the Consolidated Rail Corporation (CONRAIL); the British Telecommunications Corporation (British TELECOM); and the Communications Satellite Organization (COMSAT), in order of decreasing levels of government ownership and control. They range from BPA, which is organized as an agency within DOE, to COMSAT, which is privately owned and free from almost all regulations common to government agencies. Differences in the degree of government involvement in these corporations and in many other characteristics serve to illustrate that there are no accepted standards for defining the characteristics of government corporations. Thus, historical precedent indicates considerable flexibility would be available in the development of enabling legislation to reorganize the enrichment enterprise as a government corporation or independent government agency.

  17. Long term analysis of the biomass content in the feed of a waste-to-energy plant with oxygen-enriched combustion air.

    Science.gov (United States)

    Fellner, Johann; Cencic, Oliver; Zellinger, Günter; Rechberger, Helmut

    2011-10-01

    Thermal utilization of municipal solid waste and commercial wastes has become of increasing importance in European waste management. As waste materials are generally composed of fossil and biogenic materials, a part of the energy generated can be considered as renewable and is thus subsidized in some European countries. Analogously, CO(2) emissions of waste incinerators are only partly accounted for in greenhouse gas inventories. A novel approach for determining these fractions is the so-called balance method. In the present study, the implementation of the balance method on a waste-to-energy plant using oxygen-enriched combustion air was investigated. The findings of the 4-year application indicate on the one hand the general applicability and robustness of the method, and on the other hand the importance of reliable monitoring data. In particular, measured volume flows of the flue gas and the oxygen-enriched combustion air as well as corresponding O(2) and CO(2) contents should regularly be validated. The fraction of renewable (biogenic) energy generated throughout the investigated period amounted to between 27 and 66% for weekly averages, thereby denoting the variation in waste composition over time. The average emission factor of the plant was approximately 45 g CO(2) MJ(-1) energy input or 450 g CO(2) kg(-1) waste incinerated. The maximum error of the final result was about 16% (relative error), which was well above the error (<8%) of the balance method for plants with conventional oxygen supply.

  18. Analysis of the effects of Stillwater NWR proposed water management on Newlands Project Operations and Truckee River listed species

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — In response to a change in Stillwater NWR Complex purposes, an analysis was performed to evaluate potential impacts to endangered species and Newlands Project...

  19. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

    This paper describes a frame-based integration of the three GO subontologies, the Chemicals of Biological Interest ontology (ChEBI), and the Cell Type Ontology (CTO) in which relationships between elements of the ontologies are modeled in a way that better captures the relational semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions of the form (subject, relationship, object) by identifying patterns in GO terms, mapping these patterns and subpatterns to relationships, matching concepts to these patterns and subpatterns, and integrating these assertions into the ontologies. Using this methodology, a large number of reliable assertions linking previously unlinked OBO terms using a wide variety of specific, hierarchically arranged relationships were created: A predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid; a further 429 assertions (corresponding to 6% of the matching terms) were manually created, resulting in an initial set of 4,497 assertions. Furthermore, this methodology programmatically integrates assertions into a base ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels. Such an integration is absent from previous compositional efforts, and we argue its necessity for the creation of coherent biological ontologies when linking previously unlinked terms. PMID:17011833

  20. Earthquake forecast enrichment scores

    Directory of Open Access Journals (Sweden)

    Christine Smyth

    2012-03-01

    Full Text Available The Collaboratory for the Study of Earthquake Predictability (CSEP is a global project aimed at testing earthquake forecast models in a fair environment. Various metrics are currently used to evaluate the submitted forecasts. However, the CSEP still lacks easily understandable metrics with which to rank the universal performance of the forecast models. In this research, we modify a well-known and respected metric from another statistical field, bioinformatics, to make it suitable for evaluating earthquake forecasts, such as those submitted to the CSEP initiative. The metric, originally called a gene-set enrichment score, is based on a Kolmogorov-Smirnov statistic. Our modified metric assesses if, over a certain time period, the forecast values at locations where earthquakes have occurred are significantly increased compared to the values for all locations where earthquakes did not occur. Permutation testing allows for a significance value to be placed upon the score. Unlike the metrics currently employed by the CSEP, the score places no assumption on the distribution of earthquake occurrence nor requires an arbitrary reference forecast. In this research, we apply the modified metric to simulated data and real forecast data to show it is a powerful and robust technique, capable of ranking competing earthquake forecasts.

  1. City model enrichment

    Science.gov (United States)

    Smart, Philip D.; Quinn, Jonathan A.; Jones, Christopher B.

    The combination of mobile communication technology with location and orientation aware digital cameras has introduced increasing interest in the exploitation of 3D city models for applications such as augmented reality and automated image captioning. The effectiveness of such applications is, at present, severely limited by the often poor quality of semantic annotation of the 3D models. In this paper, we show how freely available sources of georeferenced Web 2.0 information can be used for automated enrichment of 3D city models. Point referenced names of prominent buildings and landmarks mined from Wikipedia articles and from the OpenStreetMaps digital map and Geonames gazetteer have been matched to the 2D ground plan geometry of a 3D city model. In order to address the ambiguities that arise in the associations between these sources and the city model, we present procedures to merge potentially related buildings and implement fuzzy matching between reference points and building polygons. An experimental evaluation demonstrates the effectiveness of the presented methods.

  2. Extreme enrichment of Se, Te, PGE and Au in Cu sulfide microdroplets: evidence from LA-ICP-MS analysis of sulfides in the Skaergaard Intrusion, east Greenland

    Science.gov (United States)

    Holwell, David A.; Keays, Reid R.; McDonald, Iain; Williams, Megan R.

    2015-12-01

    The Platinova Reef, in the Skaergaard Intrusion, east Greenland, is an example of a magmatic Cu-PGE-Au sulfide deposit formed in the latter stages of magmatic differentiation. As is characteristic with such deposits, it contains a low volume of sulfide, displays peak metal offsets and is Cu rich but Ni poor. However, even for such deposits, the Platinova Reef contains extremely low volumes of sulfide and the highest Pd and Au tenor sulfides of any magmatic ore deposit. Here, we present the first LA-ICP-MS analyses of sulfide microdroplets from the Platinova Reef, which show that they have the highest Se concentrations (up to 1200 ppm) and lowest S/Se ratios (190-700) of any known magmatic sulfide deposit and have significant Te enrichment. In addition, where sulfide volume increases, there is a change from high Pd-tenor microdroplets trapped in situ to larger, low tenor sulfides. The transition between these two sulfide regimes is marked by sharp peaks in Au, and then Te concentration, followed by a wider peak in Se, which gradually decreases with height. Mineralogical evidence implies that there is no significant post-magmatic hydrothermal S loss and that the metal profiles are essentially a function of magmatic processes. We propose that to generate these extreme precious and semimetal contents, the sulfides must have formed from an anomalously metal-rich package of magma, possibly formed via the dissolution of a previously PGE-enriched sulfide. Other processes such as kinetic diffusion may have also occurred alongside this to produce the ultra-high tenors. The characteristic metal offset pattern observed is largely controlled by partitioning effects, producing offset peaks in the order Pt+Pd>Au>Te>Se>Cu that are entirely consistent with published D values. This study confirms that extreme enrichment in sulfide droplets can occur in closed-system layered intrusions in situ, but this will characteristically form ore deposits that are so low in sulfide that they do

  3. Identifying What Student Affairs Professionals Value: A Mixed Methods Analysis of Professional Competencies Listed in Job Descriptions

    Science.gov (United States)

    Hoffman, John L.; Bresciani, Marilee J.

    2012-01-01

    This mixed method study explored the professional competencies that administrators expect from entry-, mid-, and senior-level professionals as reflected in 1,759 job openings posted in 2008. Knowledge, skill, and dispositional competencies were identified during the qualitative phase of the study. Statistical analysis of the prevalence of…

  4. Probiotic-enriched foods and dietary supplement containing SYNBIO positively affects bowel habits in healthy adults: an assessment using standard statistical analysis and Support Vector Machines.

    Science.gov (United States)

    Silvi, Stefania; Verdenelli, M Cristina; Cecchini, Cinzia; Coman, M Magdalena; Bernabei, M Simonetta; Rosati, Jessica; De Leone, Renato; Orpianesi, Carla; Cresci, Alberto

    2014-12-01

    A randomised, double-blind, placebo-controlled, parallel group study assessed in healthy adults how daily consumption of the probiotic combination SYNBIO®, administered in probiotic-enriched foods or in a dietary supplement, affected bowel habits. Primary and secondary outcomes gave the overall assessment of bowel well-being, while a Psychological General Well-Being Index compiled by participants estimated the health-related quality of life as well as the gastrointestinal tolerance determined with the Gastrointestinal Symptom Rating Scale. Support Vector Machine models for classification problems were used to validate the total outcomes on bowel well-being. SYNBIO® consumption improved bowel habits of volunteers consuming the probiotic foods or capsules, while the same effects were not registered in the control groups. The recovery of probiotic bacteria from the faeces of a cohort of 100 subjects for each supplemented group showed the persistence of strains in the gastrointestinal tract.

  5. A Regulatory Analysis and Reassessment of U.S. Environmental Protection Agency Listed Hazardous Waste Numbers for Applicability to the INTEC Liquid Waste System

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, K.L.; Venneman, T.E.

    1998-12-01

    This report concludes that there are four listed hazardous waste numbers (F001, F002, F005, and U134) applicable to the waste in the Process Equipment Waste Evaporator (PEWE) liquid waste system at the Idaho National Engineering and Environmental Laboratory. The chemical constituents associated with these listed hazardous waste numbers, including those listed only for ignitability are identified. The RCRA Part A permit application hazardous waste numbers identify chemical constituents that may be treated or stored by the PEWE liquid waste system either as a result of a particular characteristic (40 CFR, Subpart C) or as a result of a specific process (40 CFR 261, Subpart D). The RCRA Part A permit application for the PEWE liquid waste system identifies the universe of Environmental Protection Agency (EPA) hazardous waste numbers [23 characteristic (hazardous waste codes) numbers and 105 listed numbers (four F-listed hazardous waste numbers, 20 P-listed hazardous waste numbers, and 81 U-listed hazardous waste numbers)] deemed acceptable for storage and treatment. This evaluation, however, identifies only listed wastes (and their chemical constituents) that have actually entered the PEWE liquid waste system and would, therefore, be assigned to the PEWE liquids and treatment residuals.

  6. 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.

  7. 我国银行类上市公司现金流量表分析%Our bank listing corporation cash flow analysis

    Institute of Scientific and Technical Information of China (English)

    董文杰; 毛春梅

    2014-01-01

    目前我国A股市场中严格以银行类上市公司有16家,通过对其中的四家公司2013年度的现金流量表进行结构分析,使用报表的数据来源于国泰安数据库,文章通过本期的现金流入、流出和结余情况,利用公式比率分析方法,选取一些指标,并对其进行估计和评价该银行的资产的流动性、获取现金能力和发展能力。%At present, China's A share market strictly to bank listing corporation 16, carries on the structure analysis of the four company one of the 2013 annual cash flow statement, using the report data from the Tai'an database, we through this period cash inflow, outflow and balances, analysis using the formula ratio, selecting some index, and makes evaluation and liquidity, the evaluation of the bank's assets to obtain cash ability and development ability of the.

  8. LINGUISTIC REPRESENTATION OF THE CONCEPT «MARRIAGE» IN THE METRIC BOOKS: THE OFFICIAL LIST ANALYSIS METHOD

    Directory of Open Access Journals (Sweden)

    Anna Evgenyevna Belkova

    2013-11-01

    Full Text Available Object: This article identifies the characteristics of metric books of the Tyumen Clerical Board dated back to the XIX century understanding them as official texts belonging to a particular genre; it also describes the lexical units representing the concept of marriage from the subtexts of metric books.Method / methodology of work. Methodological approaches in the present article are coherent with the methods of official text analysis elaborated by V.Y.Deryaginum (1980 (units of lingvotextological analysis are word combinations, sentence models with more or less settled lexical composition; O.V.Barakova (2003 (considers official texts as polysubtextual structures, provides the analysis of the style-forming lexical-and-phraseological means suitable for reconstruction of the linguistic worldview.Results. The linguistic worldview fragments constituting the marriage concept of the linguistic worldview are not voluntary within the framework of the the metric records. They function as a part of certain subtexts (formulas. The linguistic worldview fragments form lexemes and clichéd combinations accompanying concepts reflecting typical life situations. Variability of the registration forms in many respects depended on the competence of the clerk.Scope of the results application. Practical significance of the research is that its results find application in the University practice: when designing courses on the history of Russian literary language, special courses and seminars on onomastics, historical stylistics, linguistic source studies, linguistic study of local lore.DOI: http://dx.doi.org/10.12731/2218-7405-2013-8-36

  9. Analysis financing preference of listing Corporation in China based on the pecking order theory%基于顺序融资理论浅析我国上市公司的融资偏好

    Institute of Scientific and Technical Information of China (English)

    张丽; 杨增亮

    2014-01-01

    顺序融资理论是一种新的资本结构理论。本文通过我国和美国的上市公司融资顺序的国内外比较分析,指出我国上市公司融资偏好差异的原因,提出通过大力发展上市公司债券市场、培育健康股票市场的发展、改善我国上市公司的内源融资顺序的措施,以促进我国上市公司的完善发展。%the pecking order theory is a new theory of capital structure .In this paper , by China and America listing Corporation financing order of domestic and international comparative analysis , points out the reasons for the differences of the financing preference of Chinese listing Corporation , then listing Corporation proposed through the development of bond market , cultivating a healthy development of the stock market , improve China's listing Cor-poration of endogenous financing order measures , in order to promote the development of China's listing Corporation .

  10. Analysis of the antibacterial list in the 2012 edition of the national essential medicines list%2012年版《国家基本药物目录》的抗菌药物目录分析

    Institute of Scientific and Technical Information of China (English)

    陈志东

    2013-01-01

      目的:对2012年版《国家基本药物目录》的抗菌药物目录进行分析。方法:通过对2012年版和2009年版《国家基本药物目录》、《WHO基本药物目录》中的抗菌药物目录及30个省市抗菌药物分级目录比较,分析2012年版《国家基本药物目录》的抗菌药物目录特点、不足及其对医疗机构和制药企业产生的影响。结果:2012年版《国家基本药物目录》的抗菌药物目录在2009年版基础上,增加了品种和剂型,并对某些品种的化学成分和规格作了严格限制。但新增品种、剂型和规格仍欠合理,医疗机构对抗菌药物的分级也与《国家基本药物目录》对抗菌药物的分级存在差异,一些制药企业的抗菌药物产品与《国家基本药物目录》的规定不完全一致。结论:《国家基本药物目录》的抗菌药物品种、剂型和规格的合理性有待提高,医疗机构的抗菌药物分级目录需要调整,一些制药企业抗菌药物产品的销售困难增加。%ABSTRACT Objective: To analyze the antibacterial list in the 2012 edition of the national essential medicines list (NEML). Methods:The antibacterial lists in the 2012 and 2009 editions of NEMLs were compared with WHO model list of essential medicines and antibacterial formulary restriction (AFR) lists of 30 provinces and municipalities in China so as to analyze their characteristics, insufficiencies and influences on medical institutions and pharmaceutical companies. Results:The antibacterial species and dosage forms were increased in 2012, and the chemical compositions and specifications of some antibacterial species were strictly limited however it was not very appropriate in some newly added antibacterial species, dosage forms and specifications. There were some differences in AFR between medical institutions and NEML in 2012, and some antibacterials produced by some pharmaceutical companies were not in fully accord

  11. Predictive Power and Value Relevance of Comprehensive Income Statement: an analysis of Brazilian companies listed on the BM&FBovespa

    Directory of Open Access Journals (Sweden)

    Marcello Angotti

    2016-09-01

    Full Text Available The study aimed to analyze if the information about comprehensive income (CI and its individual components have predictive power to determine the Operating Cash Flow of the subsequent period (OCFt+1 at the Brazilian capital market companies. The research methodology has used financial data collected from Economatica® and CVM databases. The sample selection was performed considering the availability of variables: OCFt+1 and share prices. The period analyzed comprehended the years 2012-2014. It were used quantitative valuation techniques, establishing two moments of study: the first moment by testing the hypothesis that CI has greater predictive power than Net Income (NI for forecasting OCFt+1 (528 firms/years; and the second moment by testing the hypothesis that CI and its components have a value relevance at the Brazilian capital market (605 firms/years. The results suggest that the analysis of the consolidated CI individually would not be incremental for forecasting OCFt+1. However, an increase was observed in the predictive capacity for OCFt+1, with the inclusion of Other Comprehensive Income (OCI. Could not be verified, with aggregate disruption of the individual items of OCI, incremental capacity to determine the OCFt+1. It was observed that the Equity and NI have value relevance, but that is not confirmed to consolidated CI. Added to that, only the cash flow hedge was significant to explain the market value of the company, indicating there is informational benefit to stakeholders that employ the CI in their analysis.

  12. Listed But Less Profitable

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    For the first time in the last three years, China’s listed companies reported lower profit growth By October 31, most of the companies listed in China’s A-share market had published their performance for the third quarter. Reports or corporate ann

  13. Interest Check List.

    Science.gov (United States)

    Bureau of Employment Security (DOL), Washington, DC.

    The original edition of the Department of Labor Interest Check List aims at helping students decide what kinds of work they would like and lists activities that are found in a broad range of industries and occupations. The student is advised to read each of approximately 175 items and indicate how he feels about the activity described by placing a…

  14. Scientific Serial Lists

    Directory of Open Access Journals (Sweden)

    Dana L. Roth

    1972-03-01

    Full Text Available This article describes the need for user-oriented serial lists and the development of such a list in the California Institute of Technology library. The results of conversion from EAM to EDP equipment and subsequent utilization of COM (Computer-Output-Microfilm is reported.

  15. In my Wish List, an Automated Tool for Fail-Secure Design Analysis: an Alloy-Based Feasibility Draft

    Directory of Open Access Journals (Sweden)

    Gurvan Le Guernic

    2014-05-01

    Full Text Available A system is said to be fail-secure, sometimes confused with fail-safe, if it maintains its security requirements even in the event of some faults. Fail-secure analyses are required by some validation schemes, such as some Common Criteria or NATO certifications. However, it is an aspect of security which as been overlooked by the community. This paper attempts to shed some light on the fail-secure field of study by: giving a definition of fail-secure as used in those certification schemes, and emphasizing the differences with fail-safe; and exhibiting a first feasibility draft of a fail-secure design analysis tool based on the Alloy model checker.

  16. The Politics of Security Lists

    NARCIS (Netherlands)

    de Goede, M.; Sullivan, G.

    2016-01-01

    The List, one of the most archaic means of written enumeration and classification, has made a forceful recurrence in the post-9/11 global security landscape. From terrorist sanctions lists and No-Fly lists to "kill-lists" for drone warfare; from the privately compiled lists of risky banking clients

  17. Comparative proteomic analysis of a membrane-enriched fraction from flag leaves reveals responses to chemical hybridization agent SQ-1 in wheat

    Directory of Open Access Journals (Sweden)

    Qilu eSong

    2015-08-01

    Full Text Available The induction of wheat male fertile lines by using the chemical hybridizing agent SQ-1 (CHA-SQ-1 is an effective approach in the utilization of heterosis; however, the molecular basis of male fertility remains unknown. Wheat flag leaves are the initial receptors of CHA-SQ-1 and their membrane structure plays a vital role in response to CHA-SQ-1 stress. To investigate the response of wheat flag leaves to CHA-SQ-1 stress, we compared their quantitative proteomic profiles in the absence and presence of CHA-SQ-1. Our results indicated that wheat flag leaves suffered oxidative stress during CHA-SQ-1 treatments. Leaf O2-, H2O2, and malonaldehyde levels were significantly increased within 10 h after CHA-SQ-1 treatment, while the activities of major antioxidant enzymes such as superoxide dismutase, catalase, and guaiacol peroxidase were significantly reduced. Proteome profiles of membrane-enriched fraction showed a change in the abundance of a battery of membrane proteins involved in multiple biological processes. These variable proteins mainly impaired photosynthesis, ATP synthesis protein mechanisms and were involved in the response to stress. These results provide an explanation of the relationships between membrane proteomes and anther abortion and the practical application of CHA for hybrid breeding.

  18. Oxidation in fish-oil-enriched mayonnaise 2 : Assessment of the efficacy of different tocopherol antioxidant systems by discriminant partial least squares regression analysis

    DEFF Research Database (Denmark)

    Jacobsen, Charlotte; Hartvigsen, Karsten; Lund, Pia

    2000-01-01

    Oxidative protection of mayonnaises with 16% fish oil was studied during cold storage (5 degrees C) after supplementation with different tocopherol systems: the ternary antioxidant system ascorbic acid, lecithin and tocopherol (A/L/T), and two commercial mixtures, an oil-soluble (Toco 70) prepara......Oxidative protection of mayonnaises with 16% fish oil was studied during cold storage (5 degrees C) after supplementation with different tocopherol systems: the ternary antioxidant system ascorbic acid, lecithin and tocopherol (A/L/T), and two commercial mixtures, an oil-soluble (Toco 70......) preparation and a water-soluble (Grindox 1032) preparation, The physical structure of the fish-oil-enriched mayonnaise was manipulated by adding extra emulsifier (Panodan TR) with the purpose of investigating whether or not this affected the antioxidative activity of the tocopherol mixtures. A number....... The rheological and structural properties of the mayonnaise were also affected by the addition of extra emulsifier, but this did not influence the formation of fishy and rancid off-flavours. Addition of the A system caused the immediate formation of distinct fish; and rancid off-flavours in the fresh mayonnaises...

  19. Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds.

    Science.gov (United States)

    Chen, Lei; Zhang, Yu-Hang; Zheng, Mingyue; Huang, Tao; Cai, Yu-Dong

    2016-12-01

    Compound-protein interactions play important roles in every cell via the recognition and regulation of specific functional proteins. The correct identification of compound-protein interactions can lead to a good comprehension of this complicated system and provide useful input for the investigation of various attributes of compounds and proteins. In this study, we attempted to understand this system by extracting properties from both proteins and compounds, in which proteins were represented by gene ontology and KEGG pathway enrichment scores and compounds were represented by molecular fragments. Advanced feature selection methods, including minimum redundancy maximum relevance, incremental feature selection, and the basic machine learning algorithm random forest, were used to analyze these properties and extract core factors for the determination of actual compound-protein interactions. Compound-protein interactions reported in The Binding Databases were used as positive samples. To improve the reliability of the results, the analytic procedure was executed five times using different negative samples. Simultaneously, five optimal prediction methods based on a random forest and yielding maximum MCCs of approximately 77.55 % were constructed and may be useful tools for the prediction of compound-protein interactions. This work provides new clues to understanding the system of compound-protein interactions by analyzing extracted core features. Our results indicate that compound-protein interactions are related to biological processes involving immune, developmental and hormone-associated pathways.

  20. Analysis on China's Real Estate Listing Corporation Profitability%我国房地产上市公司盈利能力分析

    Institute of Scientific and Technical Information of China (English)

    栾云凤

    2014-01-01

    Nowadays, the discussion about the real estate bubble have become more and more intense, the development trend is relates to the whole industrial structure strategy adjustment, the national economy stable and healthy development of the possibility of major issues. This paper selects the financial data of 2010-2012 years, through several important indicators of China’s real estate listing, analysis on corporation profitability, summed up the future development of China’s real estate in-dustry.%现阶段关于房地产泡沫化的讨论越演越烈,其发展趋势是否稳定涉及到整个产业结构战略调整能否顺利进行,国民经济可否稳定健康发展等重大问题。笔者选取2010—2012年相关财务数据,通过几项重要指标对我国房地产上市公司盈利能力进行分析,由此总结出我国房地产行业发展前景。

  1. WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis.

    Science.gov (United States)

    Glez-Peña, Daniel; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

    2009-07-01

    WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources. While the user can specify new gene sets of interest by following a simple four-step wizard, the tool is able to run several queries in parallel. Every time a new set is generated, it is automatically added to the private gene-set cart and the user is notified by an e-mail containing a direct link to the new set stored in the server. WhichGenes provides functionalities to edit, delete and rename existing sets as well as the capability of generating new ones by combining previous existing sets (intersection, union and difference operators). The user can export his sets configuring the output format and selecting among multiple gene identifiers. In addition to the user-friendly environment, WhichGenes allows programmers to access its functionalities in a programmatic way through a Representational State Transfer web service. WhichGenes front-end is freely available at http://www.whichgenes.org/, WhichGenes API is accessible at http://www.whichgenes.org/api/.

  2. Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS.

    Science.gov (United States)

    Nordhoff, M; Tominski, C; Halama, M; Byrne, J M; Obst, M; Kleindienst, S; Behrens, S; Kappler, A

    2017-07-01

    Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats.IMPORTANCE Most described nitrate

  3. Financial analysis of phosphate chemical industry listed companies in China%我国磷化工行业上市公司财务分析

    Institute of Scientific and Technical Information of China (English)

    张海波; 刘颖

    2012-01-01

    从财务的角度,对我国磷化工行业主要上市公司2006--2010年度的财务报表分别从偿债能力、营运能力、盈利能力和发展能力四个方面进行了分析。分析结果表明,兴发集团在最近5年内对流动资产的管理水平是同类企业中最高的,偿债能力在不断提高,权益净利率保持稳定,企业的规模也在不断扩大。此外,杜邦分析体系分析表明,兴发集团的权益净利率的波动主要受销售净利率的影响。%Based on financial perspective, 2006--2010 annual financial statement of main listed company of phosphate chemical industry in China are analyzed from the debt paying ability, operation ability, profitability and development ability. The analysis results show that, in recent five years management level of current assets in Xingfa Group is the highest, its solvency is ceaselessly risen, the return rate on equity is stable and the enterprise scale is expanding continually. In addition, the DuPont analysis system shows that the return rate on equity of Xingfa Group is mainly affected by the sales net rates.

  4. Analysis of glycoprotein E-selectin ligANDs on human and mouse marrow cells enriched for hematopoietic stem/progenitor cells

    KAUST Repository

    Merzaban, Jasmeen S.

    2011-06-09

    Although well recognized that expression of E-selectin on marrow microvessels mediates osteotropism of hematopoietic stem/progenitor cells (HSPCs), our knowledge regarding the cognate E-selectin ligand(s) on HSPCs is incomplete. Flow cytometry using E-selectin-Ig chimera (E-Ig) shows that human marrow cells enriched for HSPCs (CD34+ cells) display greater E-selectin binding than those obtained from mouse (lin-/Sca-1+/c-kit+ [LSK] cells). To define the relevant glycoprotein E-selectin ligands, lysates from human CD34+ and KG1a cells and from mouse LSK cells were immunoprecipitated using E-Ig and resolved byWestern blot using E-Ig. In both human and mouse cells, E-selectin ligand reactivity was observed at ∼ 120- to 130-kDa region, which contained two E-selectin ligands, the P-selectin glycoprotein ligand- 1 glycoform "CLA," and CD43. Human, but not mouse, cells displayed a prominent ∼ 100-kDa band, exclusively comprising the CD44 glycoform "HCELL."E-Ig reactivity was most prominent on CLA in mouse cells and on HCELL in human cells. To further assess HCELL\\'s contribution to E-selectin adherence, complementary studies were performed to silence (via CD44 siRNA) or enforce its expression (via exoglycosylation). Under physiologic shear conditions, CD44/HCELL-silenced human cells showed striking decreases (> 50%) in E-selectin binding. Conversely, enforced HCELL expression of LSK cells profoundly increased E-selectin adherence, yielding > 3-fold more marrow homing in vivo. These data define the key glycoprotein E-selectin ligands of human and mouse HSPCs, unveiling critical species-intrinsic differences in both the identity and activity of these structures. © 2011 by The American Society of Hematology.

  5. Production of Fission Product 99Mo using High-Enriched Uranium Plates in Polish Nuclear Research Reactor MARIA: Technology and Neutronic Analysis

    Directory of Open Access Journals (Sweden)

    Jaroszewicz Janusz

    2014-07-01

    Full Text Available The main objective of 235U irradiation is to obtain the 99mTc isotope, which is widely used in the domain of medical diagnostics. The decisive factor determining its availability, despite its short lifetime, is a reaction of radioactive decay of 99Mo into 99mTc. One of the possible sources of molybdenum can be achieved in course of the 235U fission reaction. The paper presents activities and the calculation results obtained upon the feasibility study on irradiation of 235U targets for production of 99Mo in the MARIA research reactor. Neutronic calculations and analyses were performed to estimate the fission products activity for uranium plates irradiated in the reactor. Results of dummy targets irradiation as well as irradiation uranium plates have been presented. The new technology obtaining 99Mo is based on irradiation of high-enriched uranium plates in standard reactor fuel channel and calculation of the current fission power generation. Measurements of temperatures and the coolant flow in the molybdenum installation carried out in reactor SAREMA system give online information about the current fission power generated in uranium targets. The corrective factors were taken into account as the heat generation from gamma radiation from neighbouring fuel elements as well as heat exchange between channels and the reactor pool. The factors were determined by calibration measurements conducted with aluminium mock-up of uranium plates. Calculations of fuel channel by means of REBUS code with fine mesh structure and libraries calculated by means of WIMS-ANL code were performed.

  6. Construction of a full-length enriched cDNA library and preliminary analysis of expressed sequence tags from Bengal Tiger Panthera tigris tigris.

    Science.gov (United States)

    Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2013-05-24

    In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers.

  7. Exosome enrichment of human serum using multiple cycles of centrifugation.

    Science.gov (United States)

    Kim, Jeongkwon; Tan, Zhijing; Lubman, David M

    2015-09-01

    In this work, we compared the use of repeated cycles of centrifugation at conventional speeds for enrichment of exosomes from human serum compared to the use of ultracentrifugation (UC). After removal of cells and cell debris, a speed of 110 000 × g or 40 000 × g was used for the UC or centrifugation enrichment process, respectively. The enriched exosomes were analyzed using the bicinchoninic acid assay, 1D gel separation, transmission electron microscopy, Western blotting, and high-resolution LC-MS/MS analysis. It was found that a five-cycle repetition of UC or centrifugation is necessary for successful removal of nonexosomal proteins in the enrichment of exosomes from human serum. More significantly, 5× centrifugation enrichment was found to provide similar or better performance than 5× UC enrichment in terms of enriched exosome protein amount, Western blot band intensity for detection of CD-63, and numbers of identified exosome-related proteins and cluster of differentiation (CD) proteins. A total of 478 proteins were identified in the LC-MS/MS analyses of exosome proteins obtained from 5× UCs and 5× centrifugations including many important CD membrane proteins. The presence of previously reported exosome-related proteins including key exosome protein markers demonstrates the utility of this method for analysis of proteins in human serum.

  8. The Financial Evaluation of Pharmaceutical Listed Firms Based on Factor Analysis and Cluster Analysis%基于因子分析和聚类分析的医药上市公司财务评价

    Institute of Scientific and Technical Information of China (English)

    潘欣; 郭继荣

    2016-01-01

    Medical and health system reform has entered into the phase of the deepwater area in our country. Because of the characteristics of high technology, high investment, high return and high risk, and big policy-effected, pharmaceutical listed firms are facing more serious financial risk than generally listed ones. The study of pharmaceutical listed firms’ financial risk evaluation is of great significance. Factor analysis by numerous correlation dimension reduction to the original index condensed into a few factors can generalize data information, and then get firms’ composite scores through the statistical analysis, which overcomes the artificial randomness to determine the weight. Factor scores and comprehensive scores of pharmaceutical manufacturing firms uniting factor analysis and cluster analysis is beneficial to the comprehensive, objective and accurate evaluation of the firms’ financial situation.%我国医疗卫生体制改革已经进入深水区阶段,由于高技术、高投入、高回报、高风险和受政策冲击大等特性的影响,医药上市公司较一般上市公司面临着更加严峻的财务风险,研究医药上市公司的财务风险评价具有重要意义。因子分析通过降维把众多具有相关性的原始指标浓缩成少数几个能高度概括数据信息的因子,通过统计分析可以得到公司综合得分,克服了人为确定权数的随意性。通过综合聚类分析和因子分析得到的医药制造公司的因子得分和综合得分情况,有利于全面、客观、准确地评价公司的财务状况。

  9. DETERMINING CARBON—13 ENRICHMENT USING LOW ENERGY PROTONS

    Institute of Scientific and Technical Information of China (English)

    张维成; 晁致远; 等

    1995-01-01

    The proton-capture reactions 12C(p,γ)13N and 13C(P,γ)14N have been studied to determine 13C enrichments.The system has been calibrated by measuring the gamma-rays yield from the 12C(p,γ)13N and 13C(p,γ)14N reactions as a function of known 13C enrichment.This technique is applicable to the analysis of samples with 13C enrichments between 1% and 90%.

  10. Environmental enrichment on the behavior and welfare of cockatiels (Nymphicus hollandicus

    Directory of Open Access Journals (Sweden)

    V.D.L. Assis

    2016-06-01

    Full Text Available ABSTRACT This study evaluated the influence of physical environmental enrichment on the behavior of cockatiels (Nymphicus hollandicus. Eighteen birds, nine males and nine females, were monitored in environments enriched with wooden sticks and bead rings and in non-enriched environments, in a completely randomized design. Behavioral categories were grouped into locomotion, maintenance, rest, feed, undesirable activities, and interaction with environmental enrichment. Data were analyzed using descriptive analysis of behaviors to produce the ethogram and percentage comparison of frequency values for behavior analysis. Environmental enrichment positively influenced behavioral categories and some behavioral activities of birds.

  11. BiNGO及DAVID在miR-155靶基因富集分析中的应用%Application of BiNGO and DAVID in Biological Enrichment Analysis of miR-155 Target Genes

    Institute of Scientific and Technical Information of China (English)

    杨蓉; 蔡琳

    2012-01-01

    目的 通过对预测得到的miR-155靶基因进行生物信息学分析,探索和比较DAVID(Database for Annotation,Visualization and Integrated Discovery)及BiNGO(Biological Networks Gene Ontology tool)软件在基因本体(GO)及生物学通路富集分析中的应用,以期为miR-155靶基因的实验验证及生物学功能的研究提供理论指导.方法 利用TargetScan 6.0预测得到的miR-155靶基因作为分析的基因集合,通过BiNGO及DAVID对这个靶基因集合进行GO富集分析和生物通路富集分析,并对两个软件的富集分析结果进行比较和分析.结果 miR-155的预测靶基因集合分别富集在转录调控活性、蛋白激酶活性等分子功能上和代谢调控、转录调控、高分子生物合成、基因表达调控及信号转导等生物学过程中(P<0.01);进一步分析显示该基因集合在KEGG代谢通路数据库中,显著富集于T细胞受体信号通路、B细胞受体信号通路、MAPK信号通路、ErbB信号通路等7个信号通路和结直肠癌、急慢性髓性白血病等7个疾病通路中(P<0.05).结论 BiNGO和DAVID软件在miRNAs靶基因富集分析中各有优势,可以结合两个软件的分析结果对miRNAs靶基因集合进行生物学描述,为进一步的功能研究提供生物信息学指导.%Objective To explore and compare the DAVID (Database for Annotation, Visualization and Integrated Discovery) and BiNGO software for bioinformatics analysis through the Gene Ontology and biological pathway enrichment analysis of targets of miR-155,in order to provide theoretical guidance for experimental validation of miR-155 target genes and biological functions. Methods TargetScan 6. 0 algorithm was used to predict target genes of miR-155 , and the result as gene set was analyzed by DAVID and BiNGO software. The differences of enrichment analysis result between DAVID and BiNGO were compared. Results The gene set was mostly enriched in transcriptional regulation activity protein

  12. Priority List : Beaver Creek

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Priority list of water rights at Beaver Creek owned by the State of Colorado or federal Fish and Wildlife. This document also has designs for Parshall flumes and...

  13. Blazar Monitoring List

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a compilation of sources in major blazar monitoring programs. This list contains all blazars known to be regularly monitored, plus all the MOJAVE- &...

  14. Contaminant Candidate List 3

    Data.gov (United States)

    U.S. Environmental Protection Agency — CCL 3 is a list of contaminants that are currently not subject to any proposed or promulgated national primary drinking water regulations, that are known or...

  15. Contaminant Candidate List 1

    Data.gov (United States)

    U.S. Environmental Protection Agency — CCL 1 is a list of contaminants that are currently not subject to any proposed or promulgated national primary drinking water regulations, that are known or...

  16. Contaminant Candidate List 2

    Data.gov (United States)

    U.S. Environmental Protection Agency — CCL 2 is a list of contaminants that are currently not subject to any proposed or promulgated national primary drinking water regulations, that are known or...

  17. License Address List

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Address list generated from National Saltwater Angler Registry. Used in conjunction with an address-based sample as per survey design.

  18. Green Power Partner List

    Science.gov (United States)

    The U.S. EPA's Green Power Partnership is a voluntary program designed to reduce the environmental impact of electricity generation by promoting renewable energy. There are thousands of Green Power Partners, all listed on this page.

  19. Retrofitting Listed Buildings

    DEFF Research Database (Denmark)

    Rasmussen, Torben Valdbjørn

    2011-01-01

    The paper presents a case study where the energy demand for a listed building constructed in 1900 is reduced. Many older buildings are listed and have restrictions that include the entire building or that include only its exterior. For the building presented, only its exterior facade is listed....... The paper demonstrates measures for the improvement of the thermal insulation of the building with solid brick walls. Durable customised measures are shown. The customised measures are required not to change the overall exterior architecture as the building is considered to contribute to the uniqueness...... of the local urban environment and therefore listed. The reduced energy demand, related to individual measures, is estimated and building physics requirements are addressed together with the economic options for evaluating the profitability....

  20. PSCID List - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PSCDB PSCID List Data detail Data name PSCID List DOI 10.18908/lsdba.nbdc01636-001 Descripti...on of data contents The list of PSCID and common elements of each entry Data file File name: pscdb_pscid_lis... acquisition method PDB Data analysis method - Number of data entries 839 entries Data item Description PSCI...nd-binding sites About This Database Database Description Download License Update History of This Database Site Policy | Contact Us PSCID List - PSCDB | LSDB Archive ...

  1. Goat production check list

    DEFF Research Database (Denmark)

    Henriksen, Jørgen; Nielsen, Mette Benedicte Olaf; Madsen, Jørgen

    2009-01-01

    This check list, financed by DanChurchAid, highlights all issues should be carefully investigated before investing in distribution of goats and in interventions to assist poor rural communities to improve their livelihood through goat production.......This check list, financed by DanChurchAid, highlights all issues should be carefully investigated before investing in distribution of goats and in interventions to assist poor rural communities to improve their livelihood through goat production....

  2. Goat production check list

    DEFF Research Database (Denmark)

    Henriksen, Jørgen; Nielsen, Mette Benedicte Olaf; Madsen, Jørgen

    2009-01-01

    This check list, financed by DanChurchAid, highlights all issues should be carefully investigated before investing in distribution of goats and in interventions to assist poor rural communities to improve their livelihood through goat production.......This check list, financed by DanChurchAid, highlights all issues should be carefully investigated before investing in distribution of goats and in interventions to assist poor rural communities to improve their livelihood through goat production....

  3. 2011年版《印度国家基本药物目录》简析%Brief Analysis of Indian Essential Drug List (2011 Version)

    Institute of Scientific and Technical Information of China (English)

    徐巧玲; 李春潇; 胡欣

    2012-01-01

    OBJECTIVE: To provide reference for the formulation of Essential Drug List in China. METHODS: The literature study was conducted about design, establishment and utilization of the list. The experience of Indian Essential Drug List (2011 version), I.e. "Indian National Free Drug Program List", was summarized. RESULTS & CONCLUSION: Indian Essential Drug List (2011 version) is conducted transparently and rationally. The regulations about drug use contribute to rational drug use in medical institutions. The list is an important link among Indian essential medicine policy systems. We should pay attention to the few shortcomings of the formulation of the list%目的:为我国国家基本药物目录制定提供借鉴.方法:采用文献研究法对2011年版《印度国家基本药物目录》(NLEM2011,即印度“全民免费药物计划”目录)在设计、制定、适用等方面进行资料整理,并进行评价,总结其在目录制定方面的经验.结果与结论:NLEM2011编订过程透明化程度较高,决策合理;药物限定了使用医疗卫生机构的范围,有助于合理用药.该目录已成为印度基本药物政策体系间的重要纽带,其优点值得我国借鉴;同时,其不足也值得我国相关政府部门和学者注意.

  4. The Analysis on the Effect of the New Policy of Listed Companies Withdrawing from Shanghai and Shenzhen Stock Exchanges on Listed Companies%沪深交易所上市公司退市政策新风向对上市公司的影响分析

    Institute of Scientific and Technical Information of China (English)

    闫恺媛

    2012-01-01

    本文在深入剖析上海证券交易所《关于完善上海证券交易所上市公司退市制度的方案(征求意见稿)》和深圳证券交易所《关于改进和完善主板、中小企业板上市公司退市制度的方案(征求意见稿)》的基础上,对陕西省上市公司的相关退市风险和存在问题提出了可行对策和政策建议,为促进和引导资本市场健康有序发展提供参考。%On the basis of the deep analysis on the "the Program (draft) on Improving the System of Listed Companies Withdrawing from Shanghai Stock Exchange" published by Shanghai Stock Exchange and "Program (draft) on Improving and Perfecting Companies Listed on the Motherboard and the SME Board Delisting System" published by Shenzhen Stock Exchange, the paper presents delisting risk and problems of the 38 listed companies in Shaanxi province and puts forward feasible strategies and policy recommendations in order to strive to further standardize and guide the healthy and orderly development of Shaanxi capital markets.

  5. 影响上市公司资本结构的因素分析%Analysis of Factors Affecting the Structure of Listed Companies

    Institute of Scientific and Technical Information of China (English)

    苏剑

    2012-01-01

    以2006年深圳证券交易所上市的发行A股的公司作为研究样本,首先利用因子分析的方法从15个分别代表破产成本、代理成本以及节税效果的财务指标中选取了6个能够对资本结构决策产生影响的因子,然后运用多元回归分析证明这6个因子都对资本结构具有显著影响。分析发现,样本企业的融资行为基本遵循了融资优序理论所定义的先内部资金后外部资金的融资顺序。这也说明即使中国的资本市场尚待完善,中国企业的融资原则也已经与国际资本市场的惯例接轨。%It is exemplified that the sample data of companies is listed on Shenzhen Stock Exchange by the factor analysis in 2006.First,six indicators are selected from fifteen financial ones representing bankruptcy costs,agency costs and controlled tax effect.Then,it is found that the sample of companies can follow principles of the pecking order theory and show that although Chinese capital market has many matters,Chinese enterprises have already accepted the principle of international capital markets.

  6. 上市商业银行利率风险实证分析%The Empirical Analysis on the Interest Rate Risk of Listed Commercial Banks

    Institute of Scientific and Technical Information of China (English)

    王丽春

    2014-01-01

    本文以16家上市商业银行在2007~2011年的年报数据为基础,运用RSG模型进行了横向分析与纵向比较,得出我国国有控股商业银行在规避利率风险方面落后于新兴股份制银行,倾向于延续原来的融资缺口状况,并且存在“短借长贷”问题,致使其在利率波动中蒙受较大损失,而部分股份制银行灵活运用缺口管理策略值得借鉴。%Taking the annual report data of 16 listed commercial banks from 2007 to 2011 as the foundation, using RSG model, the paper makes the lateral analysis and longitudinal comparison, and draws the conclusion that China’s state-owned commercial banks are dropped behind the emerging joint-stock banks in the aspect of avoiding the interest rate risk, tend to continue the original fi-nancing gap, and have the problems of“borrowing for a short term and lending for a long term”, which make state-owned commer-cial banks be subject to the large losses in the interest rate fluctuation. Therefore, the flexible gap management strategy of the joint-stock banks is worth using for reference.

  7. China listed company overseas acquits ion performance analysis%中国上市公司海外并购绩效分析

    Institute of Scientific and Technical Information of China (English)

    徐静

    2012-01-01

    This study,using a sample of 210 Chinese listed companies' data,which take cross-border MA between 2005-2009,examines the performance change of the acquiring firms from post-merger period to pre-merger period.Using accounting indicators analysis to analyse the long term performance of the companies,we find that the overall samples' performances have suggested an insignificantly decrease.Additionally,the study suggests that it would be easier for Chinese companies to merge with enterprises in Hong Kong and Taiwan than with pure overseas companies.In conclusion,depending on their practical circumstances,Chinese companies have to be very cautious with every step in acquiring overseas companies,starting from the easiest one,in order to improve success rate.%本文利用2005~2009年间进行海外并购的210家中国上市公司的数据,检验了我国上市公司进行海外并购前后绩效的变化情况。利用会计指标法研究公司并购后的长期绩效发现,并购后整体样本绩效出现了不显著的先降后升的情况。另外,对港澳台资企业的并购比对单纯的外国企业的并购更容易取得成功。结合企业面临的现实条件,中国企业对待海外并购应抱审慎的态度,先易后难,以提高成功率。

  8. Switch-like genes populate cell communication pathways and are enriched for extracellular proteins

    Directory of Open Access Journals (Sweden)

    Tozeren Aydin

    2008-01-01

    Full Text Available Abstract Background Recent studies have placed gene expression in the context of distribution profiles including housekeeping, graded, and bimodal (switch-like. Single-gene studies have shown bimodal expression results from healthy cell signaling and complex diseases such as cancer, however developing a comprehensive list of human bimodal genes has remained a major challenge due to inherent noise in human microarray data. This study presents a two-component mixture analysis of mouse gene expression data for genes on the Affymetrix MG-U74Av2 array for the detection and annotation of switch-like genes. Two-component normal mixtures were fit to the data to identify bimodal genes and their potential roles in cell signaling and disease progression. Results Seventeen percent of the genes on the MG-U74Av2 array (1519 out of 9091 were identified as bimodal or switch-like. KEGG pathways significantly enriched for bimodal genes included ECM-receptor interaction, cell communication, and focal adhesion. Similarly, the GO biological process "cell adhesion" and cellular component "extracellular matrix" were significantly enriched. Switch-like genes were found to be associated with such diseases as congestive heart failure, Alzheimer's disease, arteriosclerosis, breast neoplasms, hypertension, myocardial infarction, obesity, rheumatoid arthritis, and type I and type II diabetes. In diabetes alone, over two hundred bimodal genes were in a different mode of expression compared to normal tissue. Conclusion This research identified and annotated bimodal or switch-like genes in the mouse genome using a large collection of microarray data. Genes with bimodal expression were enriched within the cell membrane and extracellular environment. Hundreds of bimodal genes demonstrated alternate modes of expression in diabetic muscle, pancreas, liver, heart, and adipose tissue. Bimodal genes comprise a candidate set of biomarkers for a large number of disease states because

  9. Enrichment and purification of proteins of Haemophilus influenzae by chromatofocusing.

    Science.gov (United States)

    Fountoulakis, M; Langen, H; Gray, C; Takács, B

    1998-05-15

    Haemophilus influenzae is a bacterium of pharmaceutical interest of which the entire genome has been sequenced. Identification of low-abundance proteins in a two-dimensional map is important for the detection of new drug targets. We applied chromatography on Polybuffer Exchanger (chromatofocusing) in order to fractionate and enrich H. influenzae proteins, possibly low-copy-number gene products, from larger volumes. Two proteins, major ferric iron-binding protein (HI0097) and 5'-nucleotidase (HI0206) were obtained in pure form and hypothetical protein HI0052 was purified to near homogeneity by this single purification step. Four other proteins, aspartate ammonia lyase (HI0534), peptidase D (HI0675), elongation factor Ts (HI0914) and 5-methyltetrahydropteroyltriglutamate methyltransferase (HI1702), were strongly enriched so that chromatography on Polybuffer Exchanger can be used as an initial step for their isolation. Approximately 125 proteins were identified in the fractions collected from the column. Seventy of these were for the first time identified after chromatography on Polybuffer Exchanger. The proteins enriched by the chromatofocusing step include both low-abundance as well as high-copy-number gene products. They do not belong to a single protein class and the majority of them are enzymes with various functions. The results include a list and a two-dimensional map of the proteins enriched by chromatofocusing. They may be useful in the search of drug targets and in the design of purification protocols for the isolation of homologous proteins from related microorganisms.

  10. 中国企业境外上市分析报告研究%Analysis Report on Chinese Enterprises Overseas Listing

    Institute of Scientific and Technical Information of China (English)

    阿茹娜

    2012-01-01

    中国已有一千多家企业成功境外上市.国内企业通过境外上市,不仅解决了融资需求,而且引入了现代企业管理理念和制度,有效地扩大了企业知名度,进一步推动了企业国际战略的实施.本文阐述了国内企业选择境外上市的现状,分析了境外上市过程中产生的问题及其原因,并就我国企业境外上市提出相关建议.%There are more than one thousand enterprises had listed in the overseas market until today. Through overseas listing, domestic enterprises can solve financing needs, introduce modem enterprise management concepts and systems and expand the corporate reputation effectively, all those promote the implementation of corporate international strategy. This paper describes the present situation of domestic enterprises overseas listing, analyzes the problems and causes in listed process and puts forward relevant recommendations for overseas listing of Chinese enterprises.

  11. 基于邮件列表商务营销的分析与研究%BASED ON THE EMAIL LIST MARKETING ANALYSIS AND RESEARCH

    Institute of Scientific and Technical Information of China (English)

    张华南

    2012-01-01

    In the electronic commerce marketing, email list has a strong pertinence,marketing effect is outstanding characteristics are widely used, the mailing list is the user voluntary subscription to the premise, for the user to provide valuable information,at the same time with a number of related business information, to achieve the purpose of network marketing. Good use of mailing lists that business marketing tool, for mailing lists are created ,information publishing and management and mailing list business marketing strategy have in-depth study.%在电子商务营销中,电子邮件列表具有针对性强,营销效果出色的特点得到广泛应用,邮件列表是在用户自愿订阅的前提下,为用户提供有价值的信息,同时附带一定数量与之相关的商业信息,达到网络营销的目的。利用好邮件列表这一商务营销工具,需对邮件列表的创建,信息的发布与管理以及邮件列表商务营销策略有深入的研究。

  12. 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.

  13. 31 CFR 540.316 - Uranium enrichment.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process...

  14. Nutritional Properties of Enriched Local Complementary Flours

    Directory of Open Access Journals (Sweden)

    W.R. Compaoré

    2011-02-01

    Full Text Available This study aimed to identify the nutritional, functional, sensory and microbiological profile of experimental nutritional flours, produced with local products in Burkina Faso. The raw materials included maize (Zea mays, millet (Pennisetum glaucum and rice (Oryza sativa. Local ingredients were pulps of Adansonia digitata and Parkia biglobosa and seeds of Cucurbita maxima and Moringa oleifera. Three formula were developed, the first (F1 with maize, the second (F2 with rice and the last (F3 with millet. Each of these cereals was mixed with predetermined portions of seeds and pulps in order to obtain enriched flour. Nutritional, microbiological and functional analysis and the acceptability criteria of these enriched flours were assessed and compared to Misola (F4, the existing local complementary flour. The fat content of experimental flours were respectively in the first (F1, second (F2 and third formula (F3 15.91±0.01%, 11.82±0.02% and 17.02±0.02%. The carbohydrate range was 65.46±0.06%, 70.81±0.01% and 64.51±0.01% for F1, F2 and F3, while the energetic value is higher than recommended (453.07±0.05, 424.56±0.03 and 458.96±0.05 kcal respectively for F1, F2 and F3. Functional characteristics indicated the good viscosity (117, 119 and 121 mm/30 sec for F1, F2 and F3 least gelation (9, 6 and 7% and water absorption capacity (2, 4 and 1 g/g. Trained sensory evaluation panellists gore the enriched flour porridge a score of acceptable. These enriched flours have great potential as a weaning food in resource-poor and technologically under-developed countries.

  15. On-line solid-phase enrichment coupled to packed reactor flow injection analysis in a green analytical procedure to determine low levels of folic acid using fluorescence detection

    Directory of Open Access Journals (Sweden)

    Emara Samy

    2012-12-01

    Full Text Available Abstract Background Analysis of folic acid (FA is not an easy task because of its presence in lower concentrations, its lower stability under acidic conditions, and its sensitiveness against light and high temperature. The present study is concerned with the development and validation of an automated environmentally friendly pre-column derivatization combined by solid-phase enrichment (SPEn to determine low levels of FA. Results Cerium (IV trihydroxyhydroperoxide (CTH as a packed oxidant reactor has been used for oxidative cleavage of FA into highly fluorescent product, 2-amino-4-hydroxypteridine-6-carboxylic acid. FA was injected into a carrier stream of 0.04 M phosphate buffer, pH 3.4 at a flow-rate of 0.25 mL/min. The sample zone containing the analyte was passed through the CTH reactor thermostated at 40°C, and the fluorescent product was trapped and enriched on a head of small ODS column (10 mm x 4.6 mm i.d., 5 μm particle size. The enriched product was then back-flush eluted by column-switching from the small ODS column to the detector with a greener mobile phase consisting of ethanol and phosphate buffer (0.04M, pH 3.4 in the ratio of 5:95 (v/v. The eluent was monitored fluorimetrically at emission and excitation wavelengths of 463 and 367 nm, respectively. The calibration graph was linear over concentrations of FA in the range of 1.25-50 ng/mL, with a detection limit of 0.49 ng/mL. Conclusion A new simple and sensitive green analytical procedure including on-line pre-column derivatization combined by SPEn has been developed for the routine quality control and dosage form assay of FA at very low concentration level. The method was a powerful analytical technique that had excellent sensitivity, sufficient accuracy and required relatively simple and inexpensive instrumentation.

  16. A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia.

    LENUS (Irish Health Repository)

    Jia, Peilin

    2012-02-01

    After the recent successes of genome-wide association studies (GWAS), one key challenge is to identify genetic variants that might have a significant joint effect on complex diseases but have failed to be identified individually due to weak to moderate marginal effect. One popular and effective approach is gene set based analysis, which investigates the joint effect of multiple functionally related genes (eg, pathways). However, a typical gene set analysis method is biased towards long genes, a problem that is especially severe in psychiatric diseases.

  17. Comparative Analysis of the Development of Agricultural Listed Companies%农业类上市公司发展状况比较

    Institute of Scientific and Technical Information of China (English)

    秦志岗; 傅立民; 马晨; 黎东升

    2011-01-01

    在中国证监会行业划分的基础上,将农副产品加工业和食品制造业上市公司也一并纳入农业类上市公司的范畴.分析了农业类上市公司发展差距,主要表现在,群体数量少、发展不快、成长能力不强、合规性较差、地域分布不均衡.造成这种局面的内因在于农业类上市公司本身的弱质性和发展动力不足,外因在于资本的逐利性和国家政策扶持不够均衡,因此,加快农业类上市公司发展速度的重心是内强素质,外争政策.提出了农业类上市公司发展的政策思路.%On the basis of industry division of China's Securities Regulatory Commission, listed companies in the processing industry of agroproducts and food production have also been incorporated in the category of agricultural listed companies. Developmental discrepancy of agricultural listed companies is analyzed, whose main manifestations are small population quantity, slow development, weak growing capacity, relatively poor rationality and unhalanced regional distribution. The internal canses of this kind of situations lie in the weak quality and inadequate developmental driving force of agricultural listed companies, while the external cause are the capital chasing and unbalanced political support of the country. Therefore, the key of quickening the development of agricultural listed companies is inner power and external competition. Thus, the political thought of the development of agricultural listed companies is proposed.

  18. 酿酒造酒业上市公司盈利能力分析%Profitability Analysis of Wine Industry Listed Companies

    Institute of Scientific and Technical Information of China (English)

    谢淑萍; 顾洪梅; 汪蓉

    2014-01-01

    Carrying out factor analysis of the profitability of wine industry listed companies by means of financial data of A shares of Shen-zhen and Shanghai in 2012, the results show that the influence factors are total assets, total asset turnover, equity concentration, and the operating cash flow per share. The greater size of the company and the greater natural logarithm of total assets mean the comprehensive profitability is stronger;the greater turnover and the faster speed also mean the profitability is stronger;which reflects the operating margin is closely related with total asset turnover, that is the faster speed of total assets will occupy less resources, produce great value and in-crease operating margin significantly, while the operating margin and the total asset turnover are both closely related with the profitability. The listed companies should control the scale and improve the total asset turnover and comprehensive profitability, control ownership con-centration, keep a moderate amount of cash and improve the operating flexibility.%通过选取深市和沪市2012年A股酿酒造酒业上市公司的财务数据,对酿酒造酒业上市公司的盈利能力进行因子分析。分析结果显示影响酿酒造酒业上市公司盈利能力的主要因素是总资产、总资产周转率、股权集中度和每股经营现金流量。公司的规模越大即总资产的自然对数越大,则公司的综合盈利能力越强;总资产周转率越大,总资产周转速度越快,则公司的综合盈利能力越强;总资产周转率越快,公司的经营盈利能力就越强,这体现出营业毛利率与其总资产周转率密切相关,总资产周速度快,占用的资源少,产生的价值大,营业毛利率将显著提高,而营业毛利率与盈利能力密切相关,总资产周转率与综合盈利能力亦密切相关。为提高酿酒造酒业上市公司的盈利能力,应控制公司规模,提高公司总资产周

  19. [Analysis of the nominations of acupuncture and moxibustion of traditional Chinese medicine for inscription on the Representative List of the Intangible Cultural Heritage of Humanity].

    Science.gov (United States)

    Zhu, Bin; Huang, Long-Xiang; Yang, Jin-Sheng; Zhang, Li; Wang, Ying-Ying; Zhao, Jing-Sheng; Wu, Zhong-Chao; Gang, Wei-Juan

    2011-03-01

    The definition of intangible cultural heritage and the Representative List of the Intangible Cultural Heritage of Humanity in Convention for Safeguarding of the Intangible Cultural Heritage is discussed. Nominations of elements should be prepared in accordence with the Guidelines provided in each section. The explaination methods and the determining process of the Nominations for Acupuncture and Moxibustion on the Representative List are analyzed, such as the name of the element, characteristics, identification and definition, value and safeguarding measures, photos and video of the element. The Nominations should be prepared according to the Convention and Guidelines closedly and focus on discussing the cultural, the content, the communities and individuals, safeguarding measures of element.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Ming Yi

    Full Text Available 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.

  2. Nematode Indicators of Organic Enrichment

    NARCIS (Netherlands)

    Ferris, H.; Bongers, A.M.T.

    2006-01-01

    The organisms of the soil food web, dependent on resources from plants or on amendment from other sources, respond characteristically to enrichment of their environment by organic matter. Primary consumers of the incoming substrate, including bacteria, fungi, plant-feeding nematodes, annelids, and

  3. Nematode Indicators of Organic Enrichment

    NARCIS (Netherlands)

    Ferris, H.; Bongers, A.M.T.

    2006-01-01

    The organisms of the soil food web, dependent on resources from plants or on amendment from other sources, respond characteristically to enrichment of their environment by organic matter. Primary consumers of the incoming substrate, including bacteria, fungi, plant-feeding nematodes, annelids, and s

  4. Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue

    OpenAIRE

    2006-01-01

    Background Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and microarray analysis is a useful approach to reduce the overall effort needed to identify genes associated with quantitative traits of interest. Results We constructed a full-lengt...

  5. Implementation Recommendations for MOSAIC: A Workflow Architecture for Analytic Enrichment. Analysis and Recommendations for the Implementation of a Cohesive Method for Orchestrating Analytics in a Distributed Model

    Science.gov (United States)

    2011-02-01

    recognition and genre detection. This analytic work must happen before any of the active workflows execute on the incoming document, so it is...documents of a particular language or genre and this information must be made available to all of them up front. Any further or deeper analysis should...of the structure of an Item to us, but still leaves the location of the document text a mystery . We did some exploring by using the GUI to create a

  6. Characterization of regional cold-hydrothermal inflows enriched in arsenic and associated trace-elements in the southern part of the Duero Basin (Spain), by multivariate statistical analysis.

    Science.gov (United States)

    Giménez-Forcada, Elena; Vega-Alegre, Marisol; Timón-Sánchez, Susana

    2017-09-01

    Naturally occurring arsenic in groundwater exceeding the limit for potability has been reported along the southern edge of the Cenozoic Duero Basin (CDB) near its contact with the Spanish Central System (SCS). In this area, spatial variability of arsenic is high, peaking at 241μg/L. Forty-seven percent of samples collected contained arsenic above the maximum allowable concentration for drinking water (10μg/L). Correlations of As with other hydrochemical variables were investigated using multivariate statistical analysis (Hierarchical Cluster Analysis, HCA and Principal Component Analysis, PCA). It was found that As, V, Cr and pH are closely related and that there were also close correlations with temperature and Na(+). The highest concentrations of arsenic and other associated Potentially Toxic Geogenic Trace Elements (PTGTE) are linked to alkaline NaHCO3 waters (pH≈9), moderate oxic conditions and temperatures of around 18°C-19°C. The most plausible hypothesis to explain the high arsenic concentrations is the contribution of deeper regional flows with a significant hydrothermal component (cold-hydrothermal waters), flowing through faults in the basement rock. Water mixing and water-rock interactions occur both in the fissured aquifer media (igneous and metasedimentary bedrock) and in the sedimentary environment of the CDB, where agricultural pollution phenomena are also active. A combination of multivariate statistical tools and hydrochemical analysis enabled the distribution pattern of dissolved As and other PTGTE in groundwaters in the study area to be interpreted, and their most likely origin to be established. This methodology could be applied to other sedimentary areas with similar characteristics and problems. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. The path analysis of private enterprises' listing on stock market%民营矿业企业上市融资可选路径分析

    Institute of Scientific and Technical Information of China (English)

    罗月庭; 易聪华

    2011-01-01

    Either from the point of recent internal need of realizing value of mineral resources to get fast development or from the view of future development strategy of China's mining industry the access system to be set up. Being listed companies, to private mining enterprises) has become an important and urgent phasal development target. This article compared domestic A-share listing's standard and its related influence on private mining enterprises with HKMB listing in order to provide some alternative for the listing of China's private mining enterprises.%无论从目前中国民营矿业企业自身快速发展实现矿产资源价值的内在需求,还是从未来中国矿业的整体发展战略及其可能建立的准入制度来看,成为上市公司都将成为民营矿业企业的一个非常重要且急迫的阶段性发展目标.本文通过对比分析国内A股上市与香港主板上市对于矿业企业的规范要求及其相关影响,以期为中国民营矿业企业上市融资提供一些可供选择的路径.

  8. Frequency Analysis of the Words in the Academic Word List (AWL) and Non-AWL Content Words in Applied Linguistics Research Papers

    Science.gov (United States)

    Vongpumivitch, Viphavee; Huang, Ju-yu; Chang, Yu-Chia

    2009-01-01

    This study is a corpus-based lexical study that aims to explore the use of words in Coxhead's (2000) Academic Word List (AWL) in journal articles in the field of applied linguistics. A 1.5 million-word corpus called the Applied Linguistics Research Articles Corpus (ALC) was created for this study. The corpus consists of 200 research articles that…

  9. Analysis of the Operating Performance of Listed Companies Based on Equity Incentive Mechanism%基于股权激励机制的上市公司经营绩效分析

    Institute of Scientific and Technical Information of China (English)

    白天

    2016-01-01

    Through empirical analysis of the listed companies which have implemented encouragement scheme of the stock option, this article studies the function of equity incentive mechanism, and comes to the conclusion that the shareholding ratio of the enterprise manager has nothing to do with the enterprise performance. The conclusion shows that there is no obvious positive correlation relationship between the equity incentive mechanism of listed company and operation performance. Finally, through simple analysis of the state-owned listed companies in China, suggestions are proposed from the restriction and deficiency of capital market, professional manager market and corporate governance.%本文通过对目前已经实施股权激励方案上市公司的实证分析,研究股权激励机制的作用,得出企业经理人的持股比例与企业业绩不相关的结论。结论显示:我国上市公司股权激励机制与经营绩效之间不存在显著正相关关系。最后通过对我国国有上市公司的简单分析,从资本市场、职业经理人市场、公司治理方面的制约与缺陷提出建言。

  10. Liste des intrants 2015

    OpenAIRE

    Speiser, Bernhard; Tamm, Lucius; Maurer, Veronika; Berner, Alfred; Schneider, Claudia; Chevillat, Véronique

    2015-01-01

    La liste des intrants contient tous les produits phytosanitaires, les engrais, les substrats du commerce, les produits de lutte contre les mouches des étables, les agents d'ensilage, les aliments minéraux et complémentaires, les produits pour la désinfection des stabulations et les produits contre les maladies des abeilles autorisés pour l'agriculture biologique. Cette liste est contraignante pour les producteurs de Bio Suisse. Sur les fermes Bio Suisse, seuls les produits mentionnés sont aut...

  11. STAFF VACANCY LIST

    CERN Multimedia

    Human Resources Division

    2002-01-01

    For economy reasons, it has been decided to stop printing and distributing this list to Staff Members. It can be found on the Web (LIST). Divisional Administrative Officers will receive an updated printed copy on a monthly basis and are asked to display this in a public place in their division. Copies will also be posted on the notice boards of the Administration Building (No. 60) in the glass-fronted cabinet (close to the lifts) and also on the notice board close to the Post Office. A copy will also be given to the Reception (Building No. 33). Human Resources Division Tel. 74606

  12. An Empirical Analysis of the Factors That Affect the Capital Structure of Listed Companies of Coal Industry%煤炭行业上市公司资本结构影响因素的实证分析

    Institute of Scientific and Technical Information of China (English)

    刘晓; 韩丽红

    2012-01-01

    With 29 listed companies of coal industry in Shanghai and Shenzhen as samples, by adopting factor analysis and multiple linear regression, this paper carries out an empirical analysis to the factors that affect listed companies" capital structure of coal industry. The result shows that the influence of asset liquidity, growth and prof- itability on capital structure is rather remarkable and the influence of enterprise scale, non - debt tax shield and collateral value of assets on the capital structure of listed eompanied is not so remarkable. In addition, there exists positive relation between its growth, non - debt tax shield , collateral value of asset and the listed companies" asset structure. And the rest variables shows negative relationship.%以沪深两市29家煤炭行业上市公司为研究样本,采用因子分析和多元回归方法对煤炭行业上市公司资本结构的影响因素进行了实证研究,分析结果显示:资产流动性、成长性和盈利能力对资本结构的影响比较显著,企业规模、非债务税盾以及资产担保价值对上市公司资本结构的影响并不显著。并且成长性、非债务税盾、资产担保价值与公司的资本结构成正相关关系,其余变量则呈负相关关系。

  13. Work-family enrichment and psychological health

    Directory of Open Access Journals (Sweden)

    Ameeta Jaga

    2013-03-01

    Full Text Available Orientation: This study examines the beneficial aspects of the interface between work and family and its relationships with psychological health from a positive psychology perspective.Research purpose: The objective of this study was to investigate whether work-family enrichment helps to predict psychological health, specifically increased subjective well-being and decreased feelings of emotional exhaustion and depression.Motivation for the study: The burgeoning literature on the work-family interface contains little on the potentially positive benefits of maintaining work and family roles.Research approach, design and method: The authors used a descriptive research design. Employees in two national organisations in the financial retail and logistics industries completed a self-administered survey questionnaire. The authors analysed responses from those who reported both family and work responsibilities (N = 160.Main findings: Consistent with previous research, factor analysis revealed two distinct directions of work-family enrichment: from work to family (W2FE and from family to work (F2WE. Multiple regression analysis showed that F2WE explained a significant proportion of the variance in subjective wellbeing, whilst W2FE explained a significant proportion of the variance in depression and emotional exhaustion.Practical/managerial implications: The findings of this study revealed the individual and organisational benefits of fostering work-family enrichment. Contributions/value add: This study presents empirical evidence for the need to focus on the positive aspects of the work-family interface, provides further support for a positive organisational psychology perspective in organisations and hopefully will encourage further research on interventions in organisations and families.

  14. List coloring with requests

    OpenAIRE

    Dvořák, Zdeněk; Norin, Sergey; Postle, Luke

    2016-01-01

    Let G be a graph with a list assignment L. Suppose a preferred color is given for some of the vertices; how many of these preferences can be respected when L-coloring G? We explore several natural questions arising in this context, and propose directions for further research.

  15. The Christmas list

    CERN Multimedia

    James Gillies

    2010-01-01

    List making seems to be among mankind’s favourite activities, particularly as the old year draws to a close and the new one begins. It seems that we all want to know what the top 100 annoying pop songs are, who are the world’s most embarrassing people and what everyone’s been watching on TV. The transition from 2009 to 2010 was no different, but some of the latest batch of lists have a few surprising entries. According to the Global Language Monitor, ‘twitter’ was the top word of 2009. No surprises there, but ‘hadron’ came in at number 8 on the list. ‘King of pop’ was top phrase, according to the same source, but ‘god particle’ came in at number 10. And while ‘Barack Obama’ was the name of the year, ‘Large Hadron Collider’ came in at number four. The Global Language Monitor was not the only organization whose lists included particle physics references. &ls...

  16. Iterative List Decoding

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom; Hjaltason, Johan

    2005-01-01

    We analyze the relation between iterative decoding and the extended parity check matrix. By considering a modified version of bit flipping, which produces a list of decoded words, we derive several relations between decodable error patterns and the parameters of the code. By developing a tree...... of codewords at minimal distance from the received vector, we also obtain new information about the code....

  17. Water Conservation Resource List.

    Science.gov (United States)

    NJEA Review, 1981

    1981-01-01

    Alarmed by the growing water shortage, the New Jersey State Office of Dissemination has prepared this annotated list of free or inexpensive instructional materials for teaching about water conservation, K-l2. A tipsheet for home water conservation is appended. (Editor/SJL)

  18. An analysis of audit committee effectiveness at the largest listed companies in South Africa from a CFO and audit committee perspective

    Directory of Open Access Journals (Sweden)

    Ben Marx

    2009-12-01

    Full Text Available Purpose: The purpose of the study is to investigate and analyse the effective functioning of audit committees at the largest listed companies in South Africa.Problem investigated: The modern audit committee is often seen as the panacea of the corporate world and as such is looked upon to cure all the financial reporting and control-related problems of entities. Audit committees are, however, not always as effective as they are held to be, as is evidenced by the many well-known corporate scandals and business failures that occurred where audit committees existed and fraudulent financial reporting, audit failures, internal control breakdowns and other irregularities prevailed. The modern audit committee will be of value only if it is properly constituted, is functioning effectively and if its role is clearly understood by all the parties concerned. The research problem investigated stems precisely from this issue, and the paper therefore aims to analyse the effective functioning of the audit committees at the largest listed companies in South Africa. Methodology: The study empirically tested the audit committee practices at the largest listed companies in South Africa. This was done through questionnaires addressed to the CFOs and audit committee chairs. Findings: The study found that audit committees at the largest listed companies in South Africa are well established, properly constituted, have the authority and resources to effectively discharge their responsibilities and consist of members who act independently and who have the right mix of appropriate experience, financial literacy and financial expertise amongst their members. The audit committee's role was found to be generally well understood and supported by the board and the Chief Financial Officers. It was further found that the audit committees are effective in discharging their oversight responsibilities on the board's behalf, with the only real exception being their effectiveness

  19. DNA Microarray and Gene Ontology Enrichment Analysis Reveals That a Mutation in opsX Affects Virulence and Chemotaxis in Xanthomonas oryzae pv. oryzae

    Directory of Open Access Journals (Sweden)

    Hong-Il Kim

    2016-06-01

    Full Text Available Xanthomonas oryzae pv. oryzae (Xoo causes bacterial leaf blight (BLB in rice (Oryza sativa L.. In this study, we investigated the effect of a mutation in opsX (XOO1056, which encodes a saccharide biosynthesis regulatory protein, on the virulence and bacterial chemotaxis of Xoo. We performed DNA microarray analysis, which showed that 63 of 2,678 genes, including genes related to bacterial motility (flagellar and chemotaxis proteins were significantly downregulated (<−2 log₂ fold changes by the mutation in opsX. Indeed, motility assays showed that the mutant strain was nonmotile on semisolid agar swarm plates. In addition, a mutant strain (opsX::Tn5 showed decreased virulence against the susceptible rice cultivar, IR24. Quantitative real-time RT-PCR reaction was performed to confirm the expression levels of these genes, including those related to flagella and chemotaxis, in the opsX mutant. Our findings revealed that mutation of opsX affects both virulence and bacterial motility. These results will help to improve our understanding of Xoo and provide insight into Xoo-rice interactions.

  20. Reduced retinal microvascular density, improved forepaw reach, comparative microarray and gene set enrichment analysis with c-jun targeting DNA enzyme.

    Directory of Open Access Journals (Sweden)

    Cecilia W S Chan

    Full Text Available Retinal neovascularization is a critical component in the pathogenesis of common ocular disorders that cause blindness, and treatment options are limited. We evaluated the therapeutic effect of a DNA enzyme targeting c-jun mRNA in mice with pre-existing retinal neovascularization. A single injection of Dz13 in a lipid formulation containing N-[1-(2,3-dioleoyloxypropyl]-N,N,N-trimethylammonium methyl-sulfate and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine inhibited c-Jun expression and reduced retinal microvascular density. The DNAzyme inhibited retinal microvascular density as effectively as VEGF-A antibodies. Comparative microarray and gene expression analysis determined that Dz13 suppressed not only c-jun but a range of growth factors and matrix-degrading enzymes. Dz13 in this formulation inhibited microvascular endothelial cell proliferation, migration and tubule formation in vitro. Moreover, animals treated with Dz13 sensed the top of the cage in a modified forepaw reach model, unlike mice given a DNAzyme with scrambled RNA-binding arms that did not affect c-Jun expression. These findings demonstrate reduction of microvascular density and improvement in forepaw reach in mice administered catalytic DNA.

  1. Data on regulation of the gene for the adipocyte-enriched micropeptide Adig/Smaf1 by qPCR analysis and luciferase reporter assay

    Directory of Open Access Journals (Sweden)

    Gang Ren

    2016-12-01

    Full Text Available This article describes qPCR analysis for the Adig/Smaf1 gene in multiple in vitro adipocyte differentiation models including white and brown adipogenesis, cell lines and primary cultures. The article also contains qPCR data for transcript levels of Adig/Smaf1 in a wide panel of murine tissues. Expression of Adig/Smaf1 transcript in white and brown adipose tissue in fasted and refed mice is reported and also data for Adig/Smaf1 transcript expression in genetically obese ob/ob mice. Data on the effects of siRNA-mediated knockdown of Srebp1c on Adig/Smaf1 transcript levels in 3T3-L1 adipocytes are shown. Luciferase reporter assays provide data for regulation of an ~ 2 kb fragment of the 5′ flanking region of Adig/Smaf1 gene by PPARγ/RXRα. This data is related to a research article describing Adig/Smaf1 protein expression, “Expression, regulation and functional assessment of the 80 amino acid Small Adipocyte Factor 1 (Smaf1 protein in adipocytes” (G. Ren, P. Eskandari, S. Wang, C.M. Smas, 2016 [1].

  2. 中国上市银行竞争力评价体系构建及其实证分析%The Construction and Empirical Analysis of Competitiveness Evaluation System of China's Listed Banks

    Institute of Scientific and Technical Information of China (English)

    张柏伊; 苏建斌

    2015-01-01

    The competitiveness of listed banks is directly related to the level of competition of the whole bank sys-tem in china. However, China has not formed a unit and sound competitive evaluation system of listed bank yet. A per-fect evaluation system should follow the comprehensive,operational,scientific and hierarchy principle,and should also cover the evaluation index of the scale,profitable potential,liquidity risk, asset quality and growth ability. The writers build the competitive evaluation system of China's listed bank which is based on the above principles and evaluation in-dex,and choose six representative listed banks to analyze these six banks' competitiveness. After analysis,the writers hope to promote the competitiveness of listed banks in china through pointing out the strengths and weaknesses of these six listed banks.%上市银行的竞争力直接关系到我国银行业整体的竞争力水平。然而,目前我国尚未形成统一完善的上市银行竞争力评价体系。一个健全的评价体系应遵循全面性、可操作性、科学性以及结构层次性原则,涵盖规模性、盈利能力、流动性风险、资产质量以及成长能力等评价指标。根据上述原则和评价指标来构建我国上市银行竞争力评价体系,并选取了6家具有代表性的上市银行来对其竞争力进行分析,指出其在竞争力方面的优势及缺陷,以期能够促进我国上市银行竞争力的全面提升。

  3. Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Eduardo Pérez-Palma

    Full Text Available Genome-wide association studies (GWAS have successfully identified several risk loci for Alzheimer's disease (AD. Nonetheless, these loci do not explain the entire susceptibility of the disease, suggesting that other genetic contributions remain to be identified. Here, we performed a meta-analysis combining data of 4,569 individuals (2,540 cases and 2,029 healthy controls derived from three publicly available GWAS in AD and replicated a broad genomic region (>248,000 bp associated with the disease near the APOE/TOMM40 locus in chromosome 19. To detect minor effect size contributions that could help to explain the remaining genetic risk, we conducted network-based pathway analyses either by extracting gene-wise p-values (GW, defined as the single strongest association signal within a gene, or calculated a more stringent gene-based association p-value using the extended Simes (GATES procedure. Comparison of these strategies revealed that ontological sub-networks (SNs involved in glutamate signaling were significantly overrepresented in AD (p<2.7×10(-11, p<1.9×10(-11; GW and GATES, respectively. Notably, glutamate signaling SNs were also found to be significantly overrepresented (p<5.1×10(-8 in the Alzheimer's disease Neuroimaging Initiative (ADNI study, which was used as a targeted replication sample. Interestingly, components of the glutamate signaling SNs are coordinately expressed in disease-related tissues, which are tightly related to known pathological hallmarks of AD. Our findings suggest that genetic variation within glutamate signaling contributes to the remaining genetic risk of AD and support the notion that functional biological networks should be targeted in future therapies aimed to prevent or treat this devastating neurological disorder.

  4. Enrichment of lanthanides in aragonite

    Institute of Scientific and Technical Information of China (English)

    瞿成利; 路波; 刘刚

    2009-01-01

    Using the constant addition technique,the coprecipitation of lanthanum,gadolinium,and lutetium with aragonite in seawater was experimentally investigated at 25 ℃.Their concentrations in aragonite overgrowths were determined by inductive coupled plasma mass spectrometer.All these lanthanides were strongly enriched in aragonite overgrowths.The amount of lanthanum,gadolinium,and lutetium incorporated into aragonite accounted for 57%-99%,50%-89%,and 40%-91% of their initial total amount,respectively.With the in...

  5. Enrichment and aggression in primates.

    Science.gov (United States)

    Honess, P E; Marin, C M

    2006-01-01

    There is considerable evidence that primates housed under impoverished conditions develop behavioural abnormalities, including, in the most extreme example, self-harming behaviour. This has implications for all contexts in which primates are maintained in captivity from laboratories to zoos since by compromising the animals' psychological well-being and allowing them to develop behavioural abnormalities their value as appropriate educational and research models is diminished. This review examines the extensive body of literature documenting attempts to improve living conditions with a view to correcting behavioural abnormalities and housing primates in such a way that they are encouraged to exhibit a more natural range and proportion of behaviours, including less self-directed and social aggression. The results of housing, feeding, physical, sensory and social enrichment efforts are examined with specific focus on their effect on aggressive behaviour and variation in their use and efficacy. It is concluded that while inappropriate or poorly distributed enrichment may encourage aggressive competition, enrichment that is species, sex, age and background appropriate can dramatically reduce aggression, can eliminate abnormal behaviour and substantially improve the welfare of primates maintained in captivity.

  6. Functionalized periodic mesoporous organosilicas for enhanced and selective peptide enrichment.

    Science.gov (United States)

    Wan, Jingjing; Qian, Kun; Zhang, Jun; Liu, Fang; Wang, Yunhua; Yang, Pengyuan; Liu, Baohong; Yu, Chengzhong

    2010-05-18

    The analysis of peptides by the mass spectrometry (MS) technique is important in modern life science. The enrichment of peptides can increase the detection efficiency and is sometimes indispensable for collecting the information on proteins with low-abundance. Herein, we first report that functionalized periodic mesoporous organosilica (PMO) materials have a superior peptide enrichment property. It is demonstrated that the PMO materials with an organo-bridged (-CH(2)-) hybrid wall composition display a highly enhanced peptide enrichment ability compared to the pure silica material (SBA-15) with similar mesostructured parameters and morphology. More importantly, by surface modification of PMO with amino groups (denoted NH(2)-PMO), PMO and NH(2)-PMO with opposite charged surfaces (-25.2 and +39.0 mV, respectively) show selective affinities for positively and negatively charged peptides, respectively. By directly adding PMO, NH(2)-PMO as well as pure silica materials to the peptides solution with a low concentration (1-2 fmol/microL), 36 and 28 peptides can be detected from the BSA digestion in the presence of PMO and NH(2)-PMO, respectively, while only 6 and 4 are monitored in the case of SBA-15 enrichment and from solution without enrichment, respectively. Moreover, 69.4% (25 of 36) of enriched peptides by PMO have pI > or = 6 and 80% (21 of 28) of enriched peptides by NH(2)-PMO possess pI PMO and PMO enrichment together, 51 peptides can be identified with a MOWSE score of 333. It is also noted that similar conclusions can also be obtained from the peptides solution originated from other proteins. This might be an important contribution to the understanding of the interaction between peptides and porous hosts, and the proposed method is promising for the development of both material science and biotechnology.

  7. The nature of mathematical enrichment: a case study of implementation

    Directory of Open Access Journals (Sweden)

    Jennifer Susan Piggott

    2007-12-01

    Full Text Available This paper reports a framework for describing the nature of mathematics enrichment that emerged from a case study based on the work of the NRICH Project (www.nrich.maths.org team when producing “mathematics enrichment trails” (an ordered set of related mathematics problems and support materials. A range of data sources, including the trails, trail development sessions, related literature and the views of colleagues were used to inform the findings. The data were analysed using NVivo and involved the development of two complementary coding systems. One, drawn from the data itself, gave evidence of views of the content aspects of mathematical enrichment. The other, specifically designed and informed by the literature, was used to aid the analysis of the roles of teaching and learning inherent in views of enrichment described by participants. The framework describes the content of an enrichment curriculum as well as implications for teaching and learning, the experiences of learners and the features of settings where this occurs. To support this, some detail is provided on the role, nature and purpose of problem-solving and what constitutes a good problem. While emerging from a particular context, the framework highlights the need for debate concerning the audience for mathematics enrichment, particularly in questioning the commonly held belief that its value is in supporting the needs of the mathematically most able. The framework also has potential value through offering a focus for debate within the wider community concerning the nature of mathematics enrichment and as a reference point for evaluating the potential of existing or new curriculum to deliver mathematics enrichment.

  8. Analysis of Tank 38H (HTF-38-15-119, 127) Surface, Subsurface and Tank 43H (HTF-43-15-116, 117 and 118) Surface, Feed Pump Suction and Jet Suction Subsurface Supernatant Samples in Support of Enrichment, Corrosion Control and Salt Batch Planning Programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-12-17

    Compositional feed limits have been established to ensure that a nuclear criticality event for the 2H and 3H Evaporators is not possible. The Enrichment Control Program (ECP) requires feed sampling to determine the equivalent enriched uranium content prior to transfer of waste other than recycle transfers (requires sampling to determine the equivalent enriched uranium at two locations in Tanks 38H and 43H every 26 weeks) The Corrosion Control Program (CCP) establishes concentration and temperature limits for key constituents and periodic sampling and analysis to confirm that waste supernate is within these limits. This report provides the results of analyses on Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the ECP, the CCP, and the Salt Batch 10 Planning Program.

  9. The status quo of China’s listed companies based on the statistical analysis%基于统计分析法的我国上市公司发展现状分析

    Institute of Scientific and Technical Information of China (English)

    曾妮妮; 永春芳

    2015-01-01

    分析1990—2013年我国上市公司数量和股票交易额的时间序列数据,结果表明我国上市公司数量呈线性增长,股票交易额呈指数增长;搜集、整理全国2489家上市公司所属省份、行业及2013年年度的主要财务指标,分别从地域分布、行业分布和行业竞争力分析,研究表明我国上市公司地域分布差异大,行业分布不均匀,金融业,制造业,房地产业和信息传输、软件和信息技术服务业竞争力较强,而农、林、牧、渔业,建筑业及住宿和餐饮业竞争力较弱,针对现状提出相关建议。%First of all,the article analysis the number of China’s listed companies and the amount of stock trading in1990—2013.Results show that the number of listed companies in China is on a linear growth trend,the stock traded exponential growth trend;Second,the paper collect the industries and the provinces what 2 489 listed companies across the country belong to and sort out the annual main financial indicators of the listed companies in2013.Then respectively from the regional distribution,industry distribution and the industry competitiveness analysis,Studies have shown that China’s listed companies have large difference of regional distribution and their industry distribution is not uniform.At the same time,the results found that competitiveness of finance,manufacturing,real estate and information transmission,software and information technology service industry is stronger .But competitiveness of farming,forestry,animal husbandry, fisheries,construction and accommodation and catering industry is weak.And then some thinking is triggered by the results .Finally in view of some thoughts on the corresponding Suggestions are put forward .

  10. An Enrichment Factor Analysis of the Pollution Elements in PM10 Emission Sources in Longyan City%龙岩市PM10排放源污染元素富集因子分析

    Institute of Scientific and Technical Information of China (English)

    房春生; 魏强; 杨萌尧; 王菊; 陈克华; 肖忠慎

    2012-01-01

    以福建省A层土壤元素背景值作为参考背景值,以Ti作为参考元素,应用富集因子分析方法对龙岩市内6种PM10主要排放源(道路尘、扬尘、钢铁厂尘、水泥厂尘、机动车尾气尘、燃煤尘)的污染元素进行了分析。分析结果表明,龙岩市各PM10排放源均存在着不同程度的污染元素富集污染现象,这些元素的富集污染程度易受人类活动的影响,并经过长时间的积累在城区内富集,使得城区内PM10的污染现象突出。研究结果为龙岩市大气环境治理提供了科学依据,有利于区域大气环境质量的改善。%The pollution elements of the six major emission sources in Longyan City have been analyzed by enrichment factor. These sources are road dust, fugitive dust, steel and iron plant dust, cement factory dust, vehicle exhaust dust and coal dust. The background value of the Strata A soil element in Fujian Province and Ti element are selected as reference during the analysis. It shows that the pollution elements in these emission sources are enriched to certain extent, and it is susceptible to the human activity. The accumulation of these pollution elements in a long duration makes PM10 a serious pollution in the urban center. The research provides a scientific basis for the air environment control and is helpful for improving the environmental air quality.

  11. Enriching Music and Language Arts Experiences

    Science.gov (United States)

    Flohr, John W.

    2006-01-01

    The article focuses on enriching music and language arts experiences of students. Music can enrich literature and language arts, poetry, theater arts, transitions, science, and math, as well as help meet special learner needs. A well-understood example of enrichment is the alphabet song. A music or classroom teacher using the alphabet song helps…

  12. How Did the IGM Become Enriched?

    CERN Document Server

    Aguirre, A; Aguirre, Anthony; Schaye, Joop

    2006-01-01

    The enrichment of the intergalactic medium with heavy elements is a process that lies at the nexus of poorly-understood aspects of physical cosmology. We review current understanding of the processes that may remove metals from galaxies, the basic predictions of these models, the key observational constraints on enrichment, and how intergalactic enrichment may be used to test cosmological simulations.

  13. Analysis of Tank 38H (HTF-38-15-47, 49) and Tank 43H (HTF-43-15-51, 53) surface and subsurface supernatant samples in support of enrichment and corrosion control programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-06-30

    This report provides the results of analyses on Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the Enrichment Control Program (ECP) and the Corrosion Control Program (CCP).

  14. Analysis of Tank 38H (HTF-38-14-150, 151) and Tank 43H (HTF- 43-14-152, 53) Surface and Subsurface Supernatant Samples in Support of Enrichment Control, Corrosion Control and Sodium Aluminosilicate Formation Potential Programs

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-01-14

    This report provides the results of analyses on Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the Enrichment Control Program (ECP), the Corrosion Control Program and Sodium Aluminosilicate Formation Potential in the Evaporator.

  15. Developing an evidence-based list of journals for nursing.

    Science.gov (United States)

    Sherwill-Navarro, Pamela; Kennedy, Joy C; Allen, Margaret Peg

    2014-04-01

    The Nursing and Allied Health Resources Section (NAHRS) of the Medical Library Association created the 2012 NAHRS Selected List of Nursing Journals to assist librarians with collection development and to provide nurses and librarians with data on nursing and interdisciplinary journals to assist their decisions about where to submit articles for publication. This list is a continuation and expansion of a list initially known as the Key Nursing Journals list. It compares database coverage and full-text options for each title and includes an analysis of the number of evidence-based, research, and continuing education articles.

  16. 中国上市银行流动性影响因素分析%Analysis on the Factors of the Liquidity of Chinese Listed Bank

    Institute of Scientific and Technical Information of China (English)

    赵庆

    2013-01-01

    Liquidity is the life of banking .Maintaining a moderate liquidity is important for the assets safety and op-erating efficiency of banks .So, banks should pay attention to the liquidity's risk.Then the working of determining what factors influence the listed bank liquidity is particularly important .By taking indexes such as monetary sup-ply, macro economic situation , inflation, monetary policy, capital market conditions as macro factors and taking in-dexes such as bank credit assets safety status , profitability , asset scale , bank debt scale , commercial bank net in-terest income level , competitive ability , risk index , bad debt reserve as micro factors , grey relational analysis method is used to study their influences to liquidity from the perspectives of macro economic environment and micro management .It is found that the degree of influence on individual banks and the banking industry is not the same .%流动性是银行业生命。保持适度的流动性,对于维护银行资产的安全性、提高银行经营效益具有十分重要的作用,因此,防范流动性风险是每一家银行所必须注意的问题。那么判断哪些因素对于上市银行流动性起到主要影响的工作便显得尤为紧要。采用灰色关联分析方法,从宏观经济环境因素和银行微观经营因素角度出发,选取表征货币供给情况、宏观经济情况、通货膨胀水平、货币政策和资本市场状况的宏观经济因素变量和表征银行信贷资产安全状况指标、银行盈利能力指标、银行资产规模指标、银行负债规模指标、商业银行净利息收人水平、银行抵御风险能力指标、银行竞争能力指标及贷款呆账准备金的银行微观因素来分析对银行流动性影响,发现其对各个银行及银行业的影响程度不尽相同。

  17. A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities

    CERN Document Server

    Soneson, Charlotte

    2011-01-01

    Analysis of multivariate data sets from e.g. microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of the obtained gene lists with respect to sampling variations, which may partly be due to the functional redundancy among genes, implying that multiple genes can play exchangeable roles in the cell. In this paper we use the concept of exchangeability of random variables to model this functional redundancy and thereby account for the instability attributable to sampling variations. We present a flexible framework to incorporate the exchangeability into the representation of lists. The proposed framework supports straightforward robust comparison between any two lists. It can also be used to generate new, more stable gene rankings incorporating more information from the experimental data. Using a microarray data set from lung cancer patients we show that the proposed method prov...

  18. The Comparative Analysis on the Development of Fixed Satellite Services Operators in Asia-Pacific--Comparisons between Listed and Non-Listed Companies%亚太地区固定卫星服务运营商发展比较分析

    Institute of Scientific and Technical Information of China (English)

    闫钊

    2015-01-01

    Asia-Pacific is the most fiercely competitive market of the global fixed satellite services (FSS) industry. More than half of the operators provide services in this area. In recent years, as more and more operators in the world anticipate launching new satellites to meet growing demand in this emerging market. Chinese FSS industry, while maintaining fast and stable development, is facing more and more iferce challenge and competition. Therefore, the comparative analysis on the FSS Operators is quite necessary. By using the methods of comparative analysis, this paper compares the development index of FSS operators in Asia-Pacific, and then offers some suggestions to the Chinese FSS operators on the basis of the comparative analysis results between listed and non-listed companies.%亚太地区是全球固定卫星服务业竞争最为激烈的市场,全球超过一半的运营商在该地区开展业务。近年来,我国固定卫星服务业在保持平稳较快发展的同时,也面临着全球新一轮卫星资源建设高峰和市场竞争进一步加剧等挑战,对竞争对手进行研究十分必要。本文运用比较分析法,对亚太地区固定卫星服务运营商发展指标进行了比较,最后基于非上市公司与上市公司的比较分析结果,为我国运营商提出了一些启示性的建议。

  19. Analysis on the Deffiences Between Project List Pricing And Ration Pricing%分析工程量清单计价与按定额计价的差异性

    Institute of Scientific and Technical Information of China (English)

    杨朝; 董培桢

    2009-01-01

    通过对工程量清单计价与按定额计价的差异进行剖析,全面分析新的计价方式下的计价思路,同时推行工程量清单计价的意义和必要性.%Discuss on the pricing ideas under the new pricing method and the necessity of promoting engineering bill pricing through analysis on the deffiences between project list Pricing and rationprieing.

  20. International measures project for rational energy use (Survey project of the analysis tool of Asian energy consumption efficiency). List of errata; 1998 nendo kokusai energy shiyo gorika nado taisaku jigyo seigohyo. Asia energy shohi koritsuka bunseki tool chosa jigyo

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    The list of errata was prepared for the data book of the international measures project for rational energy use (Survey project of the analysis tool of Asian energy consumption efficiency). Corrected pages of the data book 1 (1990) are as follows: 187-190, 223-226, 259-262, 295- 298, 369-370, 387-388 and 405-406 on Malaysian data. Corrected pages of the data book 2 (1985) are as follows: 102-105 on Chinese data, 154 on common data, and 187-190, 223-226, 259-262, 295-298, 369-370, 387-388 and 405-406 on Malaysian data. (NEDO)