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Sample records for integrative omics approach

  1. Using omics and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases

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    Eria Alaide Rebollar

    2016-02-01

    Full Text Available Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called omics, are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the K-S Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.

  2. A retrospective likelihood approach for efficient integration of multiple omics factors in case-control association studies.

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    Balliu, Brunilda; Tsonaka, Roula; Boehringer, Stefan; Houwing-Duistermaat, Jeanine

    2015-03-01

    Integrative omics, the joint analysis of outcome and multiple types of omics data, such as genomics, epigenomics, and transcriptomics data, constitute a promising approach for powerful and biologically relevant association studies. These studies often employ a case-control design, and often include nonomics covariates, such as age and gender, that may modify the underlying omics risk factors. An open question is how to best integrate multiple omics and nonomics information to maximize statistical power in case-control studies that ascertain individuals based on the phenotype. Recent work on integrative omics have used prospective approaches, modeling case-control status conditional on omics, and nonomics risk factors. Compared to univariate approaches, jointly analyzing multiple risk factors with a prospective approach increases power in nonascertained cohorts. However, these prospective approaches often lose power in case-control studies. In this article, we propose a novel statistical method for integrating multiple omics and nonomics factors in case-control association studies. Our method is based on a retrospective likelihood function that models the joint distribution of omics and nonomics factors conditional on case-control status. The new method provides accurate control of Type I error rate and has increased efficiency over prospective approaches in both simulated and real data. © 2015 Wiley Periodicals, Inc.

  3. Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study.

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    Saw, Woei-Yuh; Tantoso, Erwin; Begum, Husna; Zhou, Lihan; Zou, Ruiyang; He, Cheng; Chan, Sze Ling; Tan, Linda Wei-Lin; Wong, Lai-Ping; Xu, Wenting; Moong, Don Kyin Nwe; Lim, Yenly; Li, Bowen; Pillai, Nisha Esakimuthu; Peterson, Trevor A; Bielawny, Tomasz; Meikle, Peter J; Mundra, Piyushkumar A; Lim, Wei-Yen; Luo, Ma; Chia, Kee-Seng; Ong, Rick Twee-Hee; Brunham, Liam R; Khor, Chiea-Chuen; Too, Heng Phon; Soong, Richie; Wenk, Markus R; Little, Peter; Teo, Yik-Ying

    2017-09-21

    The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.The Singapore Genome Variation projects characterized the genetics of Singapore's Chinese, Malay, and Indian populations. The Singapore Integrative Omics Study introduced here goes further in providing multi-omic measurements in individuals from these populations, including genetic, transcriptome, lipidome, and lifestyle data, and will facilitate the study of common diseases in Asian communities.

  4. Integrative Analysis of Omics Big Data.

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    Yu, Xiang-Tian; Zeng, Tao

    2018-01-01

    The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations.Data integration is an effective concept to solve the complex problem or understand the complicate system. Several benchmark studies have revealed the heterogeneity and trade-off that existed in the analysis of omics data. Integrative analysis can combine and investigate many datasets in a cost-effective reproducible way. Current integration approaches on biological data have two modes: one is "bottom-up integration" mode with follow-up manual integration, and the other one is "top-down integration" mode with follow-up in silico integration.This paper will firstly summarize the combinatory analysis approaches to give candidate protocol on biological experiment design for effectively integrative study on genomics and then survey the data fusion approaches to give helpful instruction on computational model development for biological significance detection, which have also provided newly data resources and analysis tools to support the precision medicine dependent on the big biomedical data. Finally, the problems and future directions are highlighted for integrative analysis of omics big data.

  5. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants

    Czech Academy of Sciences Publication Activity Database

    Großkinsky, D.K.; Syaifullah, S. J.; Roitsch, Thomas

    2017-01-01

    Roč. 99, č. 99 (2017), s. 1-20 ISSN 0022-0957 R&D Projects: GA MŠk(CZ) LO1415 Institutional support: RVO:67179843 Keywords : integrated approaches * multi-omics * phenomics * plant development * plant–environment interactions * plant phenotyping * plant physiology * plant senescence * senescence programme * systems biology Subject RIV: EH - Ecology, Behaviour OBOR OECD: Environmental sciences (social aspects to be 5.7) Impact factor: 5.830, year: 2016

  6. An integrative -omics approach to identify functional sub-networks in human colorectal cancer.

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    Rod K Nibbe

    2010-01-01

    Full Text Available Emerging evidence indicates that gene products implicated in human cancers often cluster together in "hot spots" in protein-protein interaction (PPI networks. Additionally, small sub-networks within PPI networks that demonstrate synergistic differential expression with respect to tumorigenic phenotypes were recently shown to be more accurate classifiers of disease progression when compared to single targets identified by traditional approaches. However, many of these studies rely exclusively on mRNA expression data, a useful but limited measure of cellular activity. Proteomic profiling experiments provide information at the post-translational level, yet they generally screen only a limited fraction of the proteome. Here, we demonstrate that integration of these complementary data sources with a "proteomics-first" approach can enhance the discovery of candidate sub-networks in cancer that are well-suited for mechanistic validation in disease. We propose that small changes in the mRNA expression of multiple genes in the neighborhood of a protein-hub can be synergistically associated with significant changes in the activity of that protein and its network neighbors. Further, we hypothesize that proteomic targets with significant fold change between phenotype and control may be used to "seed" a search for small PPI sub-networks that are functionally associated with these targets. To test this hypothesis, we select proteomic targets having significant expression changes in human colorectal cancer (CRC from two independent 2-D gel-based screens. Then, we use random walk based models of network crosstalk and develop novel reference models to identify sub-networks that are statistically significant in terms of their functional association with these proteomic targets. Subsequently, using an information-theoretic measure, we evaluate synergistic changes in the activity of identified sub-networks based on genome-wide screens of mRNA expression in CRC

  7. Integrated omics analysis of specialized metabolism in medicinal plants.

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    Rai, Amit; Saito, Kazuki; Yamazaki, Mami

    2017-05-01

    Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  8. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants.

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    Großkinsky, Dominik K; Syaifullah, Syahnada Jaya; Roitsch, Thomas

    2018-02-12

    The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses

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    Cristiana Gomes De Oliveira Dal'molin

    2016-08-01

    Full Text Available The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica, as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S.italica. mRNA, protein and metabolite abundances, were measured in mature and immature stem/leaf phytomers and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME. Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study

  10. Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses.

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    de Oliveira Dal'Molin, Cristiana G; Orellana, Camila; Gebbie, Leigh; Steen, Jennifer; Hodson, Mark P; Chrysanthopoulos, Panagiotis; Plan, Manuel R; McQualter, Richard; Palfreyman, Robin W; Nielsen, Lars K

    2016-01-01

    The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica), as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S. italica. mRNA, protein, and metabolite abundances, were measured in mature and immature stem/leaf phytomers, and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME). Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin, and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study, we demonstrated

  11. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

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    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics's usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics. © The Author(s) 2015. Published by Oxford University Press.

  12. Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an IntegratedOmics Approach

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    Stephen R. Lindemann

    2017-06-01

    Full Text Available The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

  13. Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).

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    Zeng, Irene Sui Lan; Lumley, Thomas

    2018-01-01

    Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. The intriguing findings from the review are that the methods used are generalizable to other disciplines with complex systematic structure, and the integrated omics is part of an integrated information science which has collated and integrated different types of information for inferences and decision making. We review the statistical learning methods of exploratory and supervised learning from 42 publications. We also discuss the strengths and limitations of the extended principal component analysis, cluster analysis, network analysis, and regression methods. Statistical techniques such as penalization for sparsity induction when there are fewer observations than the number of features and using Bayesian approach when there are prior knowledge to be integrated are also included in the commentary. For the completeness of the review, a table of currently available software and packages from 23 publications for omics are summarized in the appendix.

  14. Air Force Research Laboratory Integrated Omics Research

    Science.gov (United States)

    2015-10-01

    fuel exposures and cognitive fatigue. 15. SUBJECT TERMS biomonitoring, omics, metabonomics, proteomics, genomics, epigenetics, biomarker, toxin...biomarker discovery in a number of toxicology and human performance projects, including jet fuel exposures and cognitive fatigue. INTRODUCTION One of...chemical exposure for U.S. and NATO military personnel46; inhalation and dermal have been shown to represent the primary routes of exposure47 This

  15. Trends in the Evolution of Snake Toxins Underscored by an Integrative Omics Approach to Profile the Venom of the Colubrid Phalotris mertensi.

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    Campos, Pollyanna Fernandes; Andrade-Silva, Débora; Zelanis, André; Paes Leme, Adriana Franco; Rocha, Marisa Maria Teixeira; Menezes, Milene Cristina; Serrano, Solange M T; Junqueira-de-Azevedo, Inácio de Loiola Meirelles

    2016-08-16

    Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of snake toxins were based on data from a minor parcel of the clade. Here, we investigated the proteins of the totally unknown venom from Phalotris mertensi (Dipsadinae subfamily), in order to obtain a detailed profile of its toxins and to appreciate evolutionary tendencies occurring in colubrid venoms. By means of integrated omics and functional approaches, including RNAseq, Sanger sequencing, high-resolution proteomics, recombinant protein production, and enzymatic tests, we verified an active toxic secretion containing up to 21 types of proteins. A high content of Kunitz-type proteins and C-type lectins were observed, although several enzymatic components such as metalloproteinases and an L-amino acid oxidase were also present in the venom. Interestingly, an arguable venom component of other species was demonstrated as a true venom protein and named svLIPA (snake venom acid lipase). This finding indicates the importance of checking the actual protein occurrence across species before rejecting genes suggested to code for toxins, which are relevant for the discussion about the early evolution of reptile venoms. Moreover, trends in the evolution of some toxin classes, such as simplification of metalloproteinases and rearrangements of Kunitz and Wap domains, parallel similar phenomena observed in other venomous snake families and provide a broader picture of toxin evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002

    OpenAIRE

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present Cyan...

  17. Integration, warehousing, and analysis strategies of Omics data.

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    Gedela, Srinubabu

    2011-01-01

    "-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence information. To explore a genome and downstream molecular processes, we need umpteen results at the various levels of cellular organization by utilizing different experimental designs, data analysis strategies and methodologies. Here comes the need for controlled vocabularies and data integration to annotate, store, and update the flow of experimental data. This chapter explores key methodologies to merge Omics data by semantic data carriers, discusses controlled vocabularies as eXtensible Markup Languages (XML), and provides practical guidance, databases, and software links supporting the integration of Omics data.

  18. How integration of global omics-data could help preparing for pandemics - a scent of influenza

    NARCIS (Netherlands)

    Bos, Lieuwe D. J.; de Jong, Menno D.; Sterk, Peter J.; Schultz, Marcus J.

    2014-01-01

    Pandemics caused by novel emerging or re-emerging infectious diseases could lead to high mortality and morbidity world-wide when left uncontrolled. In this perspective, we evaluate the possibility of integration of global omics-data in order to timely prepare for pandemics. Such an approach requires

  19. Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems.

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    Ma, Tianle; Zhang, Aidong

    2017-01-01

    Omic data analyses pose great informatics challenges. As an emerging subfield of bioinformatics, omics informatics focuses on analyzing multi-omic data efficiently and effectively, and is gaining momentum. There are two underlying trends in the expansion of omics informatics landscape: the explosion of scattered individual omics informatics tools with each of which focuses on a specific task in both single- and multi- omic settings, and the fast-evolving integrated software platforms such as workflow management systems that can assemble multiple tools into pipelines and streamline integrative analysis for complicated tasks. In this survey, we give a holistic view of omics informatics, from scattered individual informatics tools to integrated workflow management systems. We not only outline the landscape and challenges of omics informatics, but also sample a number of widely used and cutting-edge algorithms in omics data analysis to give readers a fine-grained view. We survey various workflow management systems (WMSs), classify them into three levels of WMSs from simple software toolkits to integrated multi-omic analytical platforms, and point out the emerging needs for developing intelligent workflow management systems. We also discuss the challenges, strategies and some existing work in systematic evaluation of omics informatics tools. We conclude by providing future perspectives of emerging fields and new frontiers in omics informatics.

  20. Integrating Multi-omic features exploiting Chromosome Conformation Capture data

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    Ivan eMerelli

    2015-02-01

    Full Text Available The representation, integration and interpretation of omic data is a complex task, in particular considering the huge amount of information that is daily produced in molecular biology laboratories all around the world. The reason is that sequencing data regarding expression profiles, methylation patterns, and chromatin domains is difficult to harmonize in a systems biology view, since genome browsers only allow coordinate-based representations, discarding functional clusters created by the spatial conformation of the DNA in the nucleus. In this context, recent progresses in high throughput molecular biology techniques and bioinformatics have provided insights into chromatin interactions on a larger scale and offer a formidable support for the interpretation of multi-omic data. In particular, a novel sequencing technique called Chromosome Conformation Capture (3C allows the analysis of the chromosome organization in the cell’s natural state. While performed genome wide, this technique is usually called Hi-C. Inspired by service applications such as Google Maps, we developed NuChart, an R package that integrates Hi-C data to describe the chromosomal neighbourhood starting from the information about gene positions, with the possibility of mapping on the achieved graphs genomic features such as methylation patterns and histone modifications, along with expression profiles. In this paper we show the importance of the NuChart application for the integration of multi-omic data in a systems biology fashion, with particular interest in cytogenetic applications of these techniques. Moreover, we demonstrate how the integration of multi-omic data can provide useful information in understanding why genes are in certain specific positions inside the nucleus and how epigenetic patterns correlate with their expression.

  1. Omics approaches in fish quality and safety

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    Maria Lúcia Guerra Monteiro

    2017-05-01

    Full Text Available Omics is a new technology that uses genomics, proteomics, and metabolomics to investigate metabolites from foods. The global demand for fish has shown a progressive increase because it is a significant source of high quality protein, polyunsaturated fatty acids, especially omega-3, and essential minerals. However, there are barriers in the fishery production chain such as lack of standardization, knowledge, and technology transfer to industry. Moreover, fish effective monitoring is difficult due to restricted quality parameters and analytical methods determined by current Brazilian legislation. This review details the limiting chemical parameters and recent advances in analytical procedures for fish quality determination. To improve fish quality monitoring, total volatile basic nitrogen (TVB-N, trimethylamine (TMA, ammonia, pH, and biogenic amines values should be revised and established by fish category and/or type of fish product. On the other hand, protein carbonyl concentration, free fatty acids (FFAs, peroxide values (POV, and thiobarbituric acid reactive substances (TBARS should be included in the national legislation. Simultaneously, the official authorities should take into account effective, practical, and low cost analytical methodologies, which lead to faster results in order to facilitate and enhance the quality control of the products from the fish production chain, ensuring the consumer’s health. Moreover, analytical techniques for the identification of fish species must be introduced in the Brazilian legislation in order to avoid illegal substitutions and negative impacts to consumers.

  2. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro

    2016-01-01

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  3. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru

    2016-11-29

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  4. Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

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    Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

    2016-02-01

    Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

  5. Omics Approach to Identify Factors Involved in Brassica Disease Resistance.

    Science.gov (United States)

    Francisco, Marta; Soengas, Pilar; Velasco, Pablo; Bhadauria, Vijai; Cartea, Maria E; Rodríguez, Victor M

    2016-01-01

    Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, forage and ornamental. Damage caused by pathogens attack affects negatively various aspects of plant growth, development, and crop productivity. Over the last few decades, advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to biotic stress conditions. In this regard, various 'omics' technologies enable qualitative and quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. In this review, we have described advances in 'omic' tools (genomics, transcriptomics, proteomics and metabolomics) in the view of conventional and modern approaches being used to elucidate the molecular mechanisms that underlie Brassica disease resistance.

  6. Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    Directory of Open Access Journals (Sweden)

    Ravi Ramesh Pathak

    2014-04-01

    Full Text Available Assimilation and integration of “omics” technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular information at the organismic level, forming the foundation of systems biology. Research in pulmonary biology/medicine has necessitated integration of omics, network, systems and computational biology data to differentially diagnose, interpret, and prognosticate pulmonary diseases, facilitating improvement in therapy and treatment modalities. This review describes how to leverage this emerging technology in understanding pulmonary diseases at the systems level -called a “systomic” approach. Considering the operational wholeness of cellular and organ systems, diseased genome, proteome, and the metabolome needs to be conceptualized at the systems level to understand disease pathogenesis and progression. Currently available omics technology and resources require a certain degree of training and proficiency in addition to dedicated hardware and applications, making them relatively less user friendly for the pulmonary biologist and clinicians. Herein, we discuss the various strategies, computational tools and approaches required to study pulmonary diseases at the systems level for biomedical scientists and clinical researchers.

  7. Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration.

    Science.gov (United States)

    Cambiaghi, Alice; Ferrario, Manuela; Masseroli, Marco

    2017-05-01

    Metabolomics is a rapidly growing field consisting of the analysis of a large number of metabolites at a system scale. The two major goals of metabolomics are the identification of the metabolites characterizing each organism state and the measurement of their dynamics under different situations (e.g. pathological conditions, environmental factors). Knowledge about metabolites is crucial for the understanding of most cellular phenomena, but this information alone is not sufficient to gain a comprehensive view of all the biological processes involved. Integrated approaches combining metabolomics with transcriptomics and proteomics are thus required to obtain much deeper insights than any of these techniques alone. Although this information is available, multilevel integration of different 'omics' data is still a challenge. The handling, processing, analysis and integration of these data require specialized mathematical, statistical and bioinformatics tools, and several technical problems hampering a rapid progress in the field exist. Here, we review four main tools for number of users or provided features (MetaCoreTM, MetaboAnalyst, InCroMAP and 3Omics) out of the several available for metabolomic data analysis and integration with other 'omics' data, highlighting their strong and weak aspects; a number of related issues affecting data analysis and integration are also identified and discussed. Overall, we provide an objective description of how some of the main currently available software packages work, which may help the experimental practitioner in the choice of a robust pipeline for metabolomic data analysis and integration. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. Longitudinal Omics Modelling and Integration in Clinical Metabonomics Research: challenges in childhood metabolic health research

    Directory of Open Access Journals (Sweden)

    Peter eSperisen

    2015-08-01

    Full Text Available Systems biology is an important approach for deciphering the complex processes in health maintenance and the etiology of metabolic diseases. Such integrative methodologies will help better understand the molecular mechanisms involved in growth and development throughout childhood, and consequently will result in new insights about metabolic and nutritional requirements of infants, children and adults. To achieve this, a better understanding of the physiological processes at anthropometric, cellular and molecular level for any given individual is needed. In this respect, novel omics technologies in combination with sophisticated data modelling techniques are key. Due to the highly complex network of influential factors determining individual trajectories, it becomes imperative to develop proper tools and solutions that will comprehensively model biological information related to growth and maturation of our body functions. The aim of this review and perspective is to evaluate, succinctly, promising data analysis approaches to enable data integration for clinical research, with an emphasis on the longitudinal component. Approaches based on empirical and mechanistic modelling of omics data are essential to leverage findings from high dimensional omics datasets and enable biological interpretation and clinical translation. On the one hand, empirical methods, which provide quantitative descriptions of patterns in the data, are mostly used for exploring and mining datasets. On the other hand, mechanistic models are based on an understanding of the behavior of a system’s components and condense information about the known functions, allowing robust and reliable analyses to be performed by bioinformatics pipelines and similar tools. Herein, we will illustrate current examples, challenges and perspectives in the applications of empirical and mechanistic modelling in the context of childhood metabolic health research.

  9. Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.

    Science.gov (United States)

    Guirro, Maria; Costa, Andrea; Gual-Grau, Andreu; Mayneris-Perxachs, Jordi; Torrell, Helena; Herrero, Pol; Canela, Núria; Arola, Lluís

    2018-02-10

    Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Evaluation of O2PLS in Omics data integration

    NARCIS (Netherlands)

    el Bouhaddani, S.; Houwing-Duistermaat, Jeanine; Salo, Perttu; Perola, Markus; Jongbloed, G.; Uh, Hae-Won

    2016-01-01

    Background
    Rapid computational and technological developments made large amounts of omics data available in different biological levels. It is becoming clear that simultaneous data analysis methods are needed for better interpretation and understanding of the underlying systems biology.

  11. A fully Bayesian latent variable model for integrative clustering analysis of multi-type omics data.

    Science.gov (United States)

    Mo, Qianxing; Shen, Ronglai; Guo, Cui; Vannucci, Marina; Chan, Keith S; Hilsenbeck, Susan G

    2018-01-01

    Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data. Therefore, the aim of this article is to develop a fully Bayesian latent variable method (called iClusterBayes) that can jointly model omics data of continuous and discrete data types for identification of tumor subtypes and relevant omics features. Specifically, the proposed method uses a few latent variables to capture the inherent structure of multiple omics data sets to achieve joint dimension reduction. As a result, the tumor samples can be clustered in the latent variable space and relevant omics features that drive the sample clustering are identified through Bayesian variable selection. This method significantly improve on the existing integrative clustering method iClusterPlus in terms of statistical inference and computational speed. By analyzing TCGA and simulated data sets, we demonstrate the excellent performance of the proposed method in revealing clinically meaningful tumor subtypes and driver omics features. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Machine Learning Approaches to Increasing Value of Spaceflight Omics Databases

    Science.gov (United States)

    Gentry, Diana

    2017-01-01

    The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may

  13. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction.

    Science.gov (United States)

    Dimitrakopoulos, Lampros; Prassas, Ioannis; Diamandis, Eleftherios P; Charames, George S

    2017-09-01

    The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype. Proteomics holds the potential to bridge the gap between genotype and phenotype, because the powerful analytical tool of mass spectrometry has reached a point of maturity to serve this purpose effectively. This integration of "omics" data has given birth to the novel field of onco-proteogenomics, which has much to offer to precision medicine and personalized patient management. Here, we review briefly how each "omics" technology has individually contributed to cancer research, discuss technological and computational advances that have contributed to the realization of onco-proteogenomics, and summarize current and future translational applications.

  14. Time to "go large" on biofilm research: advantages of an omics approach.

    Science.gov (United States)

    Azevedo, Nuno F; Lopes, Susana P; Keevil, Charles W; Pereira, Maria O; Vieira, Maria J

    2009-04-01

    In nature, the biofilm mode of life is of great importance in the cell cycle for many microorganisms. Perhaps because of biofilm complexity and variability, the characterization of a given microbial system, in terms of biofilm formation potential, structure and associated physiological activity, in a large-scale, standardized and systematic manner has been hindered by the absence of high-throughput methods. This outlook is now starting to change as new methods involving the utilization of microtiter-plates and automated spectrophotometry and microscopy systems are being developed to perform large-scale testing of microbial biofilms. Here, we evaluate if the time is ripe to start an integrated omics approach, i.e., the generation and interrogation of large datasets, to biofilms--"biofomics". This omics approach would bring much needed insight into how biofilm formation ability is affected by a number of environmental, physiological and mutational factors and how these factors interplay between themselves in a standardized manner. This could then lead to the creation of a database where biofilm signatures are identified and interrogated. Nevertheless, and before embarking on such an enterprise, the selection of a versatile, robust, high-throughput biofilm growing device and of appropriate methods for biofilm analysis will have to be performed. Whether such device and analytical methods are already available, particularly for complex heterotrophic biofilms is, however, very debatable.

  15. Next Generation "Omics" Approaches in the "Fight" against Blood Doping.

    Science.gov (United States)

    Wang, Guan; Karanikolou, Antonia; Verdouka, Ioanna; Friedmann, Theodore; Pitsiladis, Yannis

    2017-01-01

    Despite being prohibited by the World Anti-Doping Agency (WADA), blood manipulations such as the use of recombinant human erythropoietin and blood transfusions are a well-known method used by athletes to enhance performance. Direct detection of illicit blood manipulation has been partially successful due to the short detection window of the substances/methods, sample collection timing, and the use of sophisticated masking strategies. In response, WADA introduced the athlete biological passport (ABP) in 2009, which is an individualised longitudinal monitoring approach that tests primarily haematologic biomarkers of doping in order to identify atypical variability in response(s) in athletes, highlighting a potential doping violation. Although the implementation of the ABP has been an encouraging step forward in the quest for clean/drug-free sport, this detection method has some limitations. To reduce the risk of being detected by the ABP method, athletes are now resorting to microdoses of prohibited blood boosting substances to prevent abnormal fluctuations in haematologic biomarkers, thereby reducing the sensitivity of the ABP detection method. Recent studies from numerous laboratories, including our own, have confirmed the potential of transcriptomic microarrays, which can reveal distinct changes in gene expression after blood manipulations, to enhance the ABP. There is, therefore, an urgent need to intensify research efforts that involve transcriptomics and other state-of-the-art molecular methods, collectively known as "omics", e.g., proteomics (proteins) and metabolomics (metabolites), in order to identify new and even more robust molecular signatures of blood manipulation that can be used in combination with the ABP and, intriguingly, even as a stand-alone test. © 2017 S. Karger AG, Basel.

  16. MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

    Science.gov (United States)

    Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

    2016-03-18

    Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

  17. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

    Directory of Open Access Journals (Sweden)

    Muneer A. Malla

    2018-06-01

    Full Text Available Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

  18. Utilization of Different Omic Approaches to Unravel Stress Response Mechanisms in the Parasite Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Shruti Nagaraja

    2018-02-01

    Full Text Available During its life cycle, the unicellular parasite Entamoeba histolytica is challenged by a wide variety of environmental stresses, such as fluctuation in glucose concentration, changes in gut microbiota composition, and the release of oxidative and nitrosative species from neutrophils and macrophages. The best mode of survival for this parasite is to continuously adapt itself to the dynamic environment of the host. Our ability to study the stress-induced responses and adaptive mechanisms of this parasite has been transformed through the development of genomics, proteomics or metabolomics (omics sciences. These studies provide insights into different facets of the parasite's behavior in the host. However, there is a dire need for multi-omics data integration to better understand its pathogenic nature, ultimately paving the way to identify new chemotherapeutic targets against amebiasis. This review provides an integration of the most relevant omics information on the mechanisms that are used by E. histolytica to resist environmental stresses.

  19. Multi-omic data integration enables discovery of hidden biological regularities

    DEFF Research Database (Denmark)

    Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

    2016-01-01

    Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi- level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration...... of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome- scale models, based on genomic and bibliomic data......, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can...

  20. Genome scale models of yeast: towards standardized evaluation and consistent omic integration

    DEFF Research Database (Denmark)

    Sanchez, Benjamin J.; Nielsen, Jens

    2015-01-01

    Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published and are curre......Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published...... in which all levels of omics data (from gene expression to flux) have been integrated in yeast GEMs. Relevant conclusions and current challenges for both GEM evaluation and omic integration are highlighted....

  1. An integrative omics perspective for the analysis of chemical signals in ecological interactions.

    Science.gov (United States)

    Brunetti, A E; Carnevale Neto, F; Vera, M C; Taboada, C; Pavarini, D P; Bauermeister, A; Lopes, N P

    2018-03-05

    All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals. Technological and intellectual advances in the last two decades have enabled chemical signals analyses at several molecular levels, including gene expression, molecular diversity, and receptor affinity. These advances have also deepened our understanding of nature to encompass interactions at multiple organism levels across different taxa. This tutorial review describes the most recent analytical developments in 'omics' technologies (i.e., genomics, transcriptomics, proteomics, and metabolomics) and provide recent examples of its application in studies of chemical signals. We highlight how studies have integrated an enormous amount of information generated from different omics disciplines into one publicly available platform. In addition, we stress the importance of considering different signal modalities and an evolutionary perspective to establish a comprehensive understanding of chemical communication.

  2. Investigation of Aspergillus fumigatus biofilm formation by various omics approaches

    Directory of Open Access Journals (Sweden)

    Laetitia eMuszkieta

    2013-02-01

    Full Text Available In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF. This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown biofilm-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between biofilm and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro biofilm growth, we utilized microarray, RNA-sequencing and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three omics methods. We will discuss the advantages and limitations of each method and their complementarity.

  3. Robust Selection Algorithm (RSA) for Multi-Omic Biomarker Discovery; Integration with Functional Network Analysis to Identify miRNA Regulated Pathways in Multiple Cancers.

    Science.gov (United States)

    Sehgal, Vasudha; Seviour, Elena G; Moss, Tyler J; Mills, Gordon B; Azencott, Robert; Ram, Prahlad T

    2015-01-01

    MicroRNAs (miRNAs) play a crucial role in the maintenance of cellular homeostasis by regulating the expression of their target genes. As such, the dysregulation of miRNA expression has been frequently linked to cancer. With rapidly accumulating molecular data linked to patient outcome, the need for identification of robust multi-omic molecular markers is critical in order to provide clinical impact. While previous bioinformatic tools have been developed to identify potential biomarkers in cancer, these methods do not allow for rapid classification of oncogenes versus tumor suppressors taking into account robust differential expression, cutoffs, p-values and non-normality of the data. Here, we propose a methodology, Robust Selection Algorithm (RSA) that addresses these important problems in big data omics analysis. The robustness of the survival analysis is ensured by identification of optimal cutoff values of omics expression, strengthened by p-value computed through intensive random resampling taking into account any non-normality in the data and integration into multi-omic functional networks. Here we have analyzed pan-cancer miRNA patient data to identify functional pathways involved in cancer progression that are associated with selected miRNA identified by RSA. Our approach demonstrates the way in which existing survival analysis techniques can be integrated with a functional network analysis framework to efficiently identify promising biomarkers and novel therapeutic candidates across diseases.

  4. IPF-LASSO: Integrative L1-Penalized Regression with Penalty Factors for Prediction Based on Multi-Omics Data

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    Anne-Laure Boulesteix

    2017-01-01

    Full Text Available As modern biotechnologies advance, it has become increasingly frequent that different modalities of high-dimensional molecular data (termed “omics” data in this paper, such as gene expression, methylation, and copy number, are collected from the same patient cohort to predict the clinical outcome. While prediction based on omics data has been widely studied in the last fifteen years, little has been done in the statistical literature on the integration of multiple omics modalities to select a subset of variables for prediction, which is a critical task in personalized medicine. In this paper, we propose a simple penalized regression method to address this problem by assigning different penalty factors to different data modalities for feature selection and prediction. The penalty factors can be chosen in a fully data-driven fashion by cross-validation or by taking practical considerations into account. In simulation studies, we compare the prediction performance of our approach, called IPF-LASSO (Integrative LASSO with Penalty Factors and implemented in the R package ipflasso, with the standard LASSO and sparse group LASSO. The use of IPF-LASSO is also illustrated through applications to two real-life cancer datasets. All data and codes are available on the companion website to ensure reproducibility.

  5. Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

    Science.gov (United States)

    Vijayakumar, Supreeta; Conway, Max; Lió, Pietro; Angione, Claudio

    2017-05-30

    Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees. Driven by this analogy, we here present a 'forest' of principal methods used for constraint-based modelling in systems biology. This provides a tree-based view of methods available to prospective modellers, also available in interactive version at http://modellingmetabolism.net, where it will be kept updated with new methods after the publication of the present manuscript. Our updated classification of existing methods and tools highlights the most promising in the different branches, with the aim to develop a vision of how existing methods could hybridize and become more complex. We then provide the first hands-on tutorial for multi-objective optimization of metabolic models in R. We finally discuss the implementation of multi-view machine learning approaches in poly-omic integration. Throughout this work, we demonstrate the optimization of trade-offs between multiple metabolic objectives, with a focus on omic data integration through machine learning. We anticipate that the combination of a survey, a perspective on multi-view machine learning and a step-by-step R tutorial should be of interest for both the beginner and the advanced user. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Integration of omic networks in a developmental atlas of maize.

    Science.gov (United States)

    Walley, Justin W; Sartor, Ryan C; Shen, Zhouxin; Schmitz, Robert J; Wu, Kevin J; Urich, Mark A; Nery, Joseph R; Smith, Laurie G; Schnable, James C; Ecker, Joseph R; Briggs, Steven P

    2016-08-19

    Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide scale. To enable network reconstructions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. Networks in which nodes are genes connected on the basis of highly correlated expression patterns of mRNAs were very different from networks that were based on coexpression of proteins. Roughly 85% of highly interconnected hubs were not conserved in expression between RNA and protein networks. However, networks from either data type were enriched in similar ontological categories and were effective in predicting known regulatory relationships. Integration of mRNA, protein, and phosphoprotein data sets greatly improved the predictive power of GRNs. Copyright © 2016, American Association for the Advancement of Science.

  7. VitisNet: "Omics" integration through grapevine molecular networks.

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    Jérôme Grimplet

    Full Text Available BACKGROUND: Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet. METHODOLOGY/PRINCIPAL FINDINGS: The sequences from the Vitis vinifera (cv. Pinot Noir PN40024 genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 "Metabolic", 15 "Genetic Information Processing", 12 "Environmental Information Processing", 3 "Cellular Processes", 21 "Transport", and 80 "Transcription Factors". The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment. CONCLUSIONS/SIGNIFICANCE: VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome

  8. Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses

    Directory of Open Access Journals (Sweden)

    Alejandra Serrano

    2017-09-01

    Full Text Available Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I, lag (II, and ripening (III, in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation and biotic (fungi and viruses stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support

  9. Integrative set enrichment testing for multiple omics platforms

    Directory of Open Access Journals (Sweden)

    Poisson Laila M

    2011-11-01

    Full Text Available Abstract Background Enrichment testing assesses the overall evidence of differential expression behavior of the elements within a defined set. When we have measured many molecular aspects, e.g. gene expression, metabolites, proteins, it is desirable to assess their differential tendencies jointly across platforms using an integrated set enrichment test. In this work we explore the properties of several methods for performing a combined enrichment test using gene expression and metabolomics as the motivating platforms. Results Using two simulation models we explored the properties of several enrichment methods including two novel methods: the logistic regression 2-degree of freedom Wald test and the 2-dimensional permutation p-value for the sum-of-squared statistics test. In relation to their univariate counterparts we find that the joint tests can improve our ability to detect results that are marginal univariately. We also find that joint tests improve the ranking of associated pathways compared to their univariate counterparts. However, there is a risk of Type I error inflation with some methods and self-contained methods lose specificity when the sets are not representative of underlying association. Conclusions In this work we show that consideration of data from multiple platforms, in conjunction with summarization via a priori pathway information, leads to increased power in detection of genomic associations with phenotypes.

  10. A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.

    Science.gov (United States)

    You, Qi; Yan, Hengyu; Liu, Yue; Yi, Xin; Zhang, Kang; Xu, Wenying; Su, Zhen

    2017-05-01

    The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.

  11. A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera

    Directory of Open Access Journals (Sweden)

    Pastor Jullian Fabres

    2017-06-01

    Full Text Available Vitis vinifera (grapevine is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple ‘omics’ can give us the opportunity to better understand how plants modulate their response to different environments. However, ‘omics’ technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different ‘omic’ results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.

  12. ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Ogata

    Full Text Available Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char to microbial composition and degradation (E-class, and makes possible the understanding of relationships between molecular and microbial elements (HetMap. This website is available to the public domain at: https://database.riken.jp/ecomics/.

  13. 'Omics' approaches in tomato aimed at identifying candidate genes ...

    African Journals Online (AJOL)

    adriana

    2013-12-04

    Dec 4, 2013 ... approaches could be combined in order to identify candidate genes for the genetic control of ascorbic ..... applied to other traits under the complex control of many ... Engineering increased vitamin C levels in ... Chem. Biol. 13:532–538. Giovannucci E, Rimm EB, Liu Y, Stampfer MJ, Willett WC (2002). A.

  14. Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.

    Directory of Open Access Journals (Sweden)

    Matthew Ruffalo

    2015-12-01

    Full Text Available Development of high-throughput monitoring technologies enables interrogation of cancer samples at various levels of cellular activity. Capitalizing on these developments, various public efforts such as The Cancer Genome Atlas (TCGA generate disparate omic data for large patient cohorts. As demonstrated by recent studies, these heterogeneous data sources provide the opportunity to gain insights into the molecular changes that drive cancer pathogenesis and progression. However, these insights are limited by the vast search space and as a result low statistical power to make new discoveries. In this paper, we propose methods for integrating disparate omic data using molecular interaction networks, with a view to gaining mechanistic insights into the relationship between molecular changes at different levels of cellular activity. Namely, we hypothesize that genes that play a role in cancer development and progression may be implicated by neither frequent mutation nor differential expression, and that network-based integration of mutation and differential expression data can reveal these "silent players". For this purpose, we utilize network-propagation algorithms to simulate the information flow in the cell at a sample-specific resolution. We then use the propagated mutation and expression signals to identify genes that are not necessarily mutated or differentially expressed genes, but have an essential role in tumor development and patient outcome. We test the proposed method on breast cancer and glioblastoma multiforme data obtained from TCGA. Our results show that the proposed method can identify important proteins that are not readily revealed by molecular data, providing insights beyond what can be gleaned by analyzing different types of molecular data in isolation.

  15. An approach for optimally extending mathematical models of signaling networks using omics data.

    Science.gov (United States)

    Bianconi, Fortunato; Patiti, Federico; Baldelli, Elisa; Crino, Lucio; Valigi, Paolo

    2015-01-01

    Mathematical modeling is a key process in Systems Biology and the use of computational tools such as Cytoscape for omics data processing, need to be integrated in the modeling activity. In this paper we propose a new methodology for modeling signaling networks by combining ordinary differential equation models and a gene recommender system, GeneMANIA. We started from existing models, that are stored in the BioModels database, and we generated a query to use as input for the GeneMANIA algorithm. The output of the recommender system was then led back to the kinetic reactions that were finally added to the starting model. We applied the proposed methodology to EGFR-IGF1R signal transduction network, which plays an important role in translational oncology and cancer therapy of non small cell lung cancer.

  16. Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    NARCIS (Netherlands)

    Ribeiro de Jesus, P.R.

    2015-01-01

    Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    by Paulo Roberto Ribeiro de Jesus

    The main objective of this thesis was to provide a detailed

  17. A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits.

    Science.gov (United States)

    Yan, Kang K; Zhao, Hongyu; Pang, Herbert

    2017-12-06

    High-throughput sequencing data are widely collected and analyzed in the study of complex diseases in quest of improving human health. Well-studied algorithms mostly deal with single data source, and cannot fully utilize the potential of these multi-omics data sources. In order to provide a holistic understanding of human health and diseases, it is necessary to integrate multiple data sources. Several algorithms have been proposed so far, however, a comprehensive comparison of data integration algorithms for classification of binary traits is currently lacking. In this paper, we focus on two common classes of integration algorithms, graph-based that depict relationships with subjects denoted by nodes and relationships denoted by edges, and kernel-based that can generate a classifier in feature space. Our paper provides a comprehensive comparison of their performance in terms of various measurements of classification accuracy and computation time. Seven different integration algorithms, including graph-based semi-supervised learning, graph sharpening integration, composite association network, Bayesian network, semi-definite programming-support vector machine (SDP-SVM), relevance vector machine (RVM) and Ada-boost relevance vector machine are compared and evaluated with hypertension and two cancer data sets in our study. In general, kernel-based algorithms create more complex models and require longer computation time, but they tend to perform better than graph-based algorithms. The performance of graph-based algorithms has the advantage of being faster computationally. The empirical results demonstrate that composite association network, relevance vector machine, and Ada-boost RVM are the better performers. We provide recommendations on how to choose an appropriate algorithm for integrating data from multiple sources.

  18. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

    Directory of Open Access Journals (Sweden)

    Peter B McGarvey

    2009-09-01

    Full Text Available The NIAID (National Institute for Allergy and Infectious Diseases Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1 The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells infected by different bacterial (Bacillus anthracis and Salmonella typhimurium and viral (orthopox pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2 The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3 Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and

  19. An integrative 'omics' solution to the detection of recombinant human erythropoietin and blood doping.

    Science.gov (United States)

    Pitsiladis, Yannis P; Durussel, Jérôme; Rabin, Olivier

    2014-05-01

    Administration of recombinant human erythropoietin (rHumanEPO) improves sporting performance and hence is frequently subject to abuse by athletes, although rHumanEPO is prohibited by the WADA. Approaches to detect rHumanEPO doping have improved significantly in recent years but remain imperfect. A new transcriptomic-based longitudinal screening approach is being developed that has the potential to improve the analytical performance of current detection methods. In particular, studies are being funded by WADA to identify a 'molecular signature' of rHumanEPO doping and preliminary results are promising. In the first systematic study to be conducted, the expression of hundreds of genes were found to be altered by rHumanEPO with numerous gene transcripts being differentially expressed after the first injection and further transcripts profoundly upregulated during and subsequently downregulated up to 4 weeks postadministration of the drug; with the same transcriptomic pattern observed in all participants. The identification of a blood 'molecular signature' of rHumanEPO administration is the strongest evidence to date that gene biomarkers have the potential to substantially improve the analytical performance of current antidoping methods such as the Athlete Biological Passport for rHumanEPO detection. Given the early promise of transcriptomics, research using an 'omics'-based approach involving genomics, transcriptomics, proteomics and metabolomics should be intensified in order to achieve improved detection of rHumanEPO and other doping substances and methods difficult to detect such a recombinant human growth hormone and blood transfusions.

  20. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

    Science.gov (United States)

    Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

    2017-01-01

    Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

  1. Integrative omic analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

    Directory of Open Access Journals (Sweden)

    Gage eKoehler

    2015-10-01

    Full Text Available To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative omic approaches were applied to Fragaria × ananassa Duch. ‘Korona’. Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1 to 10 days of cold (2°C exposure. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine, pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold.Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.

  2. Integrative analysis of multiple diverse omics datasets by sparse group multitask regression

    Directory of Open Access Journals (Sweden)

    Dongdong eLin

    2014-10-01

    Full Text Available A variety of high throughput genome-wide assays enable the exploration of genetic risk factors underlying complex traits. Although these studies have remarkable impact on identifying susceptible biomarkers, they suffer from issues such as limited sample size and low reproducibility. Combining individual studies of different genetic levels/platforms has the promise to improve the power and consistency of biomarker identification. In this paper, we propose a novel integrative method, namely sparse group multitask regression, for integrating diverse omics datasets, platforms and populations to identify risk genes/factors of complex diseases. This method combines multitask learning with sparse group regularization, which will: 1 treat the biomarker identification in each single study as a task and then combine them by multitask learning; 2 group variables from all studies for identifying significant genes; 3 enforce sparse constraint on groups of variables to overcome the ‘small sample, but large variables’ problem. We introduce two sparse group penalties: sparse group lasso and sparse group ridge in our multitask model, and provide an effective algorithm for each model. In addition, we propose a significance test for the identification of potential risk genes. Two simulation studies are performed to evaluate the performance of our integrative method by comparing it with conventional meta-analysis method. The results show that our sparse group multitask method outperforms meta-analysis method significantly. In an application to our osteoporosis studies, 7 genes are identified as significant genes by our method and are found to have significant effects in other three independent studies for validation. The most significant gene SOD2 has been identified in our previous osteoporosis study involving the same expression dataset. Several other genes such as TREML2, HTR1E and GLO1 are shown to be novel susceptible genes for osteoporosis, as confirmed

  3. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

    Science.gov (United States)

    Fitó, Montserrat; Melander, Olle; Martínez, José Alfredo; Toledo, Estefanía; Carpéné, Christian; Corella, Dolores

    2016-01-01

    Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition. PMID:27598147

  4. Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

    Directory of Open Access Journals (Sweden)

    Silva Holtfreter

    2016-03-01

    Full Text Available Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.

  5. Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

    Science.gov (United States)

    Holtfreter, Silva; Kolata, Julia; Stentzel, Sebastian; Bauerfeind, Stephanie; Schmidt, Frank; Sundaramoorthy, Nandakumar; Bröker, Barbara M.

    2016-01-01

    Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control. PMID:28248221

  6. A semantic web framework to integrate cancer omics data with biological knowledge.

    Science.gov (United States)

    Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

    2012-01-25

    The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

  7. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food.

    Science.gov (United States)

    Ferri, Emanuele; Galimberti, Andrea; Casiraghi, Maurizio; Airoldi, Cristina; Ciaramelli, Carlotta; Palmioli, Alessandro; Mezzasalma, Valerio; Bruni, Ilaria; Labra, Massimo

    2015-01-01

    In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

  8. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

    Directory of Open Access Journals (Sweden)

    Emanuele Ferri

    2015-01-01

    Full Text Available In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR and Mass Spectroscopy (MS were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

  9. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

    Science.gov (United States)

    Ferri, Emanuele; Airoldi, Cristina; Ciaramelli, Carlotta; Palmioli, Alessandro; Bruni, Ilaria

    2015-01-01

    In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling. PMID:26783518

  10. An OMIC approach to elaborate the antibacterial mechanisms of different alkaloids.

    Science.gov (United States)

    Avci, Fatma Gizem; Sayar, Nihat Alpagu; Sariyar Akbulut, Berna

    2018-05-01

    Plant-derived substances have regained interest in the fight against antibiotic resistance owing to their distinct antimicrobial mechanisms and multi-target properties. With the recent advances in instrumentation and analysis techniques, OMIC approaches are extensively used for target identification and elucidation of the mechanism of phytochemicals in drug discovery. In the current study, RNA sequencing based transcriptional profiling together with global differential protein expression analysis was used to comparatively elaborate the activities and the effects of the plant alkaloids boldine, bulbocapnine, and roemerine along with the well-known antimicrobial alkaloid berberine in Bacillus subtilis cells. The transcriptomic findings were validated by qPCR. Images from scanning electron microscope were obtained to visualize the effects on the whole-cells. The results showed that among the three selected alkaloids, only roemerine possessed antibacterial activity. Unlike berberine, which is susceptible to efflux through multidrug resistance pumps, roemerine accumulated in the cells. This in turn resulted in oxidative stress and building up of reactive oxygen species, which eventually deregulated various pathways such as iron uptake. Treatment with boldine or bulbocapnine slightly affected various metabolic pathways but has not changed the growth patterns at all. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

    Directory of Open Access Journals (Sweden)

    Peter E Larsen

    2016-01-01

    Full Text Available In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree and Laccaria bicolor (mycorrhizal fungi interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

  12. A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System

    Directory of Open Access Journals (Sweden)

    David J. Beale

    2017-03-01

    Full Text Available A multi-omics approach was applied to an urban river system (the Brisbane River (BR, Queensland, Australia in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS of the V5–V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem. Sites sampled represented the transition from less affected (upstream to polluted (downstream environments along the BR. Chemometric analysis of the combined datasets indicated a clear separation between the sampled environments. Burkholderiales and Cyanobacteria were common key factors for differentiation of pristine waters. Increased sugar alcohol and short-chain fatty acid production was observed by Actinomycetales and Rhodospirillaceae that are known to form biofilms in urban polluted and brackish waters. Results from this study indicate that a multi-omics approach enables a deep understanding of the health of an aquatic ecosystem, providing insight into the bacterial diversity present and the metabolic output of the population when exposed to environmental contaminants.

  13. Improving stability of prediction models based on correlated omics data by using network approaches.

    Directory of Open Access Journals (Sweden)

    Renaud Tissier

    Full Text Available Building prediction models based on complex omics datasets such as transcriptomics, proteomics, metabolomics remains a challenge in bioinformatics and biostatistics. Regularized regression techniques are typically used to deal with the high dimensionality of these datasets. However, due to the presence of correlation in the datasets, it is difficult to select the best model and application of these methods yields unstable results. We propose a novel strategy for model selection where the obtained models also perform well in terms of overall predictability. Several three step approaches are considered, where the steps are 1 network construction, 2 clustering to empirically derive modules or pathways, and 3 building a prediction model incorporating the information on the modules. For the first step, we use weighted correlation networks and Gaussian graphical modelling. Identification of groups of features is performed by hierarchical clustering. The grouping information is included in the prediction model by using group-based variable selection or group-specific penalization. We compare the performance of our new approaches with standard regularized regression via simulations. Based on these results we provide recommendations for selecting a strategy for building a prediction model given the specific goal of the analysis and the sizes of the datasets. Finally we illustrate the advantages of our approach by application of the methodology to two problems, namely prediction of body mass index in the DIetary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome study (DILGOM and prediction of response of each breast cancer cell line to treatment with specific drugs using a breast cancer cell lines pharmacogenomics dataset.

  14. Making the Most of Omics for Symbiosis Research

    Science.gov (United States)

    Chaston, J.; Douglas, A.E.

    2012-01-01

    Omics, including genomics, proteomics and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites etc. into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally-sophisticated downstream analyses are essential to reveal interactions not evident to visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies – long lists of factors – into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses. PMID:22983030

  15. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches.

    Science.gov (United States)

    Papadimitriou, Konstantinos; Zoumpopoulou, Georgia; Foligné, Benoit; Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie

    2015-01-01

    Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer's health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut-brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

  16. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

    Directory of Open Access Journals (Sweden)

    Konstantinos ePapadimitriou

    2015-02-01

    Full Text Available Over the past decades the food industry has been revolutionized towards the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut-brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

  17. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

    Science.gov (United States)

    Papadimitriou, Konstantinos; Zoumpopoulou, Georgia; Foligné, Benoit; Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie

    2015-01-01

    Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms. PMID:25741323

  18. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.

    NARCIS (Netherlands)

    Emond-Rheault, Jean-Guillaume; Jeukens, Julie; Freschi, Luca; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Colavecchio, Anna; Barrere, Virginie; Cadieux, Brigitte; Arya, Gitanjali; Bekal, Sadjia; Berry, Chrystal; Burnett, Elton; Cavestri, Camille; Chapin, Travis K; Crouse, Alanna; Daigle, France; Danyluk, Michelle D; Delaquis, Pascal; Dewar, Ken; Doualla-Bell, Florence; Fliss, Ismail; Fong, Karen; Fournier, Eric; Franz, Eelco; Garduno, Rafael; Gill, Alexander; Gruenheid, Samantha; Harris, Linda; Huang, Carol B; Huang, Hongsheng; Johnson, Roger; Joly, Yann; Kerhoas, Maud; Kong, Nguyet; Lapointe, Gisèle; Larivière, Line; Loignon, Stéphanie; Malo, Danielle; Moineau, Sylvain; Mottawea, Walid; Mukhopadhyay, Kakali; Nadon, Céline; Nash, John; Ngueng Feze, Ida; Ogunremi, Dele; Perets, Ann; Pilar, Ana V; Reimer, Aleisha R; Robertson, James; Rohde, John; Sanderson, Kenneth E; Song, Lingqiao; Stephan, Roger; Tamber, Sandeep; Thomassin, Paul; Tremblay, Denise; Usongo, Valentine; Vincent, Caroline; Wang, Siyun; Weadge, Joel T; Wiedmann, Martin; Wijnands, Lucas; Wilson, Emily D; Wittum, Thomas; Yoshida, Catherine; Youfsi, Khadija; Zhu, Lei; Weimer, Bart C; Goodridge, Lawrence; Levesque, Roger C

    2017-01-01

    The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided

  19. Omics Research on the International Space Station

    Science.gov (United States)

    Love, John

    2015-01-01

    The International Space Station (ISS) is an orbiting laboratory whose goals include advancing science and technology research. Completion of ISS assembly ushered a new era focused on utilization, encompassing multiple disciplines such as Biology and Biotechnology, Physical Sciences, Technology Development and Demonstration, Human Research, Earth and Space Sciences, and Educational Activities. The research complement planned for upcoming ISS Expeditions 45&46 includes several investigations in the new field of omics, which aims to collectively characterize sets of biomolecules (e.g., genomic, epigenomic, transcriptomic, proteomic, and metabolomic products) that translate into organismic structure and function. For example, Multi-Omics is a JAXA investigation that analyzes human microbial metabolic cross-talk in the space ecosystem by evaluating data from immune dysregulation biomarkers, metabolic profiles, and microbiota composition. The NASA OsteoOmics investigation studies gravitational regulation of osteoblast genomics and metabolism. Tissue Regeneration uses pan-omics approaches with cells cultured in bioreactors to characterize factors involved in mammalian bone tissue regeneration in microgravity. Rodent Research-3 includes an experiment that implements pan-omics to evaluate therapeutically significant molecular circuits, markers, and biomaterials associated with microgravity wound healing and tissue regeneration in bone defective rodents. The JAXA Mouse Epigenetics investigation examines molecular alterations in organ specific gene expression patterns and epigenetic modifications, and analyzes murine germ cell development during long term spaceflight. Lastly, Twins Study ("Differential effects of homozygous twin astronauts associated with differences in exposure to spaceflight factors"), NASA's first foray into human omics research, applies integrated analyses to assess biomolecular responses to physical, physiological, and environmental stressors associated

  20. Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities.

    Science.gov (United States)

    Campos, Nádia A; Panis, Bart; Carpentier, Sebastien C

    2017-01-01

    One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.

  1. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

    Directory of Open Access Journals (Sweden)

    Jean-Guillaume Emond-Rheault

    2017-06-01

    Full Text Available The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS, at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.

  2. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

    Directory of Open Access Journals (Sweden)

    Jasmine Chong

    2017-11-01

    Full Text Available The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies. In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation analysis to metabolic network-based modeling approaches. Throughout the process, we strive to present a unified conceptual framework for multi-omics integration and interpretation, as well as point out potential future directions.

  3. From data to knowledge: The future of multi-omics data analysis for the rhizosphere

    Energy Technology Data Exchange (ETDEWEB)

    Allen White, Richard; Borkum, Mark I.; Rivas-Ubach, Albert; Bilbao, Aivett; Wendler, Jason P.; Colby, Sean M.; Köberl, Martina; Jansson, Christer

    2017-06-01

    The rhizosphere is the interface between a plant's roots and its surrounding soil. The rhizosphere microbiome, a complex microbial ecosystem, nourishes the terrestrial biosphere. Integrated multi-omics is a modern approach to systems biology that analyzes and interprets the datasets of multiple -omes of both individual organisms and multi-organism communities and consortia. The successful usage and application of integrated multi-omics to rhizospheric science is predicated upon the availability of rhizosphere-specific data, metadata and software. This review analyzes the availability of multi-omics data, metadata and software for rhizospheric science, identifying potential issues, challenges and opportunities.

  4. Harnessing Integrative Omics to Facilitate Molecular Imaging of the Human Epidermal Growth Factor Receptor Family for Precision Medicine.

    Science.gov (United States)

    Pool, Martin; de Boer, H Rudolf; Hooge, Marjolijn N Lub-de; van Vugt, Marcel A T M; de Vries, Elisabeth G E

    2017-01-01

    Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents. Using the human epidermal growth factor receptor (HER) family as a model in (pre)clinical studies, we illustrate how molecular imaging may be employed to characterize whole body target expression as well as monitor drug effectiveness and the emergence of tumor resistance. We further discuss how an integrative omics discovery platform could guide the selection of 'effect sensors' - new molecular imaging targets - which are dynamic markers that indicate treatment effectiveness or resistance.

  5. The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.

    Directory of Open Access Journals (Sweden)

    Shingo Miyauchi

    Full Text Available Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1 simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases; 2 the key role of lytic polysaccharide monooxygenases (LPMO; 3 the early transcriptional regulation of lignin active peroxidases; 4 the induction of detoxification processes dealing with biomass-derived compounds; and 5 the frequent attachments of the carbohydrate binding module 1 (CBM1 to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various

  6. Clinical multi-omics strategies for the effective cancer management.

    Science.gov (United States)

    Yoo, Byong Chul; Kim, Kyung-Hee; Woo, Sang Myung; Myung, Jae Kyung

    2017-08-15

    Cancer is a global health issue as a multi-factorial complex disease, and early detection and novel therapeutic strategies are required for more effective cancer management. With the development of systemic analytical -omics strategies, the therapeutic approach and study of the molecular mechanisms of carcinogenesis and cancer progression have moved from hypothesis-driven targeted investigations to data-driven untargeted investigations focusing on the integrated diagnosis, treatment, and prevention of cancer in individual patients. Predictive, preventive, and personalized medicine (PPPM) is a promising new approach to reduce the burden of cancer and facilitate more accurate prognosis, diagnosis, as well as effective treatment. Here we review the fundamentals of, and new developments in, -omics technologies, together with the key role of a variety of practical -omics strategies in PPPM for cancer treatment and diagnosis. In this review, a comprehensive and critical overview of the systematic strategy for predictive, preventive, and personalized medicine (PPPM) for cancer disease was described in a view of cancer prognostic prediction, diagnostics, and prevention as well as cancer therapy and drug responses. We have discussed multi-dimensional data obtained from various resources and integration of multisciplinary -omics strategies with computational method which could contribute the more effective PPPM for cancer. This review has provided the novel insights of the current applications of each and combined -omics technologies, which showed their powerful potential for the establishment of PPPM for cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 'Omics' Approaches to Understanding Interstitial Cystitis/Painful Bladder Syndrome/Bladder Pain Syndrome

    Directory of Open Access Journals (Sweden)

    Sungyong You

    2012-12-01

    Full Text Available Recent efforts in the generation of large genomics, transcriptomics, proteomics, metabolomics and other types of 'omics' data sets have provided an unprecedentedly detailed view of certain diseases, however to date most of this literature has been focused on malignancy and other lethal pathological conditions. Very little intensive work on global profiles has been performed to understand the molecular mechanism of interstitial cystitis/painful bladder syndrome/bladder pain syndrome (IC/PBS/BPS, a chronic lower urinary tract disorder characterized by pelvic pain, urinary urgency and frequency, which can lead to long lasting adverse effects on quality of life. A lack of understanding of molecular mechanism has been a challenge and dilemma for diagnosis and treatment, and has also led to a delay in basic and translational research focused on biomarker and drug discovery, clinical therapy, and preventive strategies against IC/PBS/BPS. This review describes the current state of 'omics' studies and available data sets relevant to IC/PBS/BPS, and presents opportunities for new research directed at understanding the pathogenesis of this complex condition.

  8. Fluxomics - connecting 'omics analysis and phenotypes.

    Science.gov (United States)

    Winter, Gal; Krömer, Jens O

    2013-07-01

    In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies. © 2012 John Wiley & Sons Ltd and Society for Applied Microbiology.

  9. MADMAX - Management and analysis database for multiple ~omics experiments

    NARCIS (Netherlands)

    Lin, K.; Kools, H.J.; Groot, de P.J.; Gavai, A.K.; Basnet, R.K.; Bonnema, A.B.; Visser, R.G.F.; Leunissen, J.

    2011-01-01

    The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is

  10. Cancer panomics: computational methods and infrastructure for integrative analysis of cancer high-throughput "omics" data

    DEFF Research Database (Denmark)

    Brunak, Søren; De La Vega, Francisco M.; Rätsch, Gunnar

    2014-01-01

    Targeted cancer treatment is becoming the goal of newly developed oncology medicines and has already shown promise in some spectacular cases such as the case of BRAF kinase inhibitors in BRAF-mutant (e.g. V600E) melanoma. These developments are driven by the advent of high-throughput sequencing......, which continues to drop in cost, and that has enabled the sequencing of the genome, transcriptome, and epigenome of the tumors of a large number of cancer patients in order to discover the molecular aberrations that drive the oncogenesis of several types of cancer. Applying these technologies...... in the clinic promises to transform cancer treatment by identifying therapeutic vulnerabilities of each patient's tumor. These approaches will need to address the panomics of cancer--the integration of the complex combination of patient-specific characteristics that drive the development of each person's tumor...

  11. [Progress in omics research of Aspergillus niger].

    Science.gov (United States)

    Sui, Yufei; Ouyang, Liming; Lu, Hongzhong; Zhuang, Yingping; Zhang, Siliang

    2016-08-25

    Aspergillus niger, as an important industrial fermentation strain, is widely applied in the production of organic acids and industrial enzymes. With the development of diverse omics technologies, the data of genome, transcriptome, proteome and metabolome of A. niger are increasing continuously, which declared the coming era of big data for the research in fermentation process of A. niger. The data analysis from single omics and the comparison of multi-omics, to the integrations of multi-omics based on the genome-scale metabolic network model largely extends the intensive and systematic understanding of the efficient production mechanism of A. niger. It also provides possibilities for the reasonable global optimization of strain performance by genetic modification and process regulation. We reviewed and summarized progress in omics research of A. niger, and proposed the development direction of omics research on this cell factory.

  12. Evaluation of a non-targeted "Omic"' approach in the safety assessment of genetically modified plants

    DEFF Research Database (Denmark)

    Metzdorff, Stine Broeng; Kok, E. J.; Knuthsen, Pia

    2006-01-01

    -time PCR, and High Performance Liquid Chromatography. Analysis by cDNA microarray was used as a non-targeted approach for the identification of potential unintended effects caused by the transformation. The results revealed that, although the transgenic lines possessed different types of integration events...... has the potential to become a useful tool for screening of unintended effects, but state that it is crucial to have substantial information on the natural variation in traditional crops in order to be able to interpret "ornics" data correctly within the framework of food safety assessment strategies...

  13. Omics strategies for revealing Yersinia pestis virulence

    Science.gov (United States)

    Yang, Ruifu; Du, Zongmin; Han, Yanping; Zhou, Lei; Song, Yajun; Zhou, Dongsheng; Cui, Yujun

    2012-01-01

    Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis. PMID:23248778

  14. Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model

    NARCIS (Netherlands)

    Davidov, E.; Clish, C.B.; Oresic, M.; Meys, M.; Stochaj, W.; Snell, P.; Lavine, G.; Londo, T.R.; Adourian, A.; Zhang, X.; Johnston, M.; Morel, N.; Marple, E.W.; Plasterer, T.N.; Neumann, E.; Verheij, E.; Vogels, J.T.W.E.; Havekes, L.M.; Greef, J. van der; Naylor, S.

    2004-01-01

    Multitiered quantitative analysis of biological systems is rapidly becoming the desired approach to study hierarchical functional interactions between proteins and metabolites. We describe here a novel systematic approach to analyze organisms with complex metabolic regulatory networks. By using

  15. Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.

    Science.gov (United States)

    Phan, John H; Quo, Chang F; Cheng, Chihwen; Wang, May Dongmei

    2012-01-01

    This paper reviews challenges and opportunities in multiscale data integration for biomedical informatics. Biomedical data can come from different biological origins, data acquisition technologies, and clinical applications. Integrating such data across multiple scales (e.g., molecular, cellular/tissue, and patient) can lead to more informed decisions for personalized, predictive, and preventive medicine. However, data heterogeneity, community standards in data acquisition, and computational complexity are big challenges for such decision making. This review describes genomic and proteomic (i.e., molecular), histopathological imaging (i.e., cellular/tissue), and clinical (i.e., patient) data; it includes case studies for single-scale (e.g., combining genomic or histopathological image data), multiscale (e.g., combining histopathological image and clinical data), and multiscale and multiplatform (e.g., the Human Protein Atlas and The Cancer Genome Atlas) data integration. Numerous opportunities exist in biomedical informatics research focusing on integration of multiscale and multiplatform data.

  16. AucPR: an AUC-based approach using penalized regression for disease prediction with high-dimensional omics data.

    Science.gov (United States)

    Yu, Wenbao; Park, Taesung

    2014-01-01

    It is common to get an optimal combination of markers for disease classification and prediction when multiple markers are available. Many approaches based on the area under the receiver operating characteristic curve (AUC) have been proposed. Existing works based on AUC in a high-dimensional context depend mainly on a non-parametric, smooth approximation of AUC, with no work using a parametric AUC-based approach, for high-dimensional data. We propose an AUC-based approach using penalized regression (AucPR), which is a parametric method used for obtaining a linear combination for maximizing the AUC. To obtain the AUC maximizer in a high-dimensional context, we transform a classical parametric AUC maximizer, which is used in a low-dimensional context, into a regression framework and thus, apply the penalization regression approach directly. Two kinds of penalization, lasso and elastic net, are considered. The parametric approach can avoid some of the difficulties of a conventional non-parametric AUC-based approach, such as the lack of an appropriate concave objective function and a prudent choice of the smoothing parameter. We apply the proposed AucPR for gene selection and classification using four real microarray and synthetic data. Through numerical studies, AucPR is shown to perform better than the penalized logistic regression and the nonparametric AUC-based method, in the sense of AUC and sensitivity for a given specificity, particularly when there are many correlated genes. We propose a powerful parametric and easily-implementable linear classifier AucPR, for gene selection and disease prediction for high-dimensional data. AucPR is recommended for its good prediction performance. Beside gene expression microarray data, AucPR can be applied to other types of high-dimensional omics data, such as miRNA and protein data.

  17. Molecular characterization of breast cancer cell lines through multiple omic approaches.

    Science.gov (United States)

    Smith, Shari E; Mellor, Paul; Ward, Alison K; Kendall, Stephanie; McDonald, Megan; Vizeacoumar, Frederick S; Vizeacoumar, Franco J; Napper, Scott; Anderson, Deborah H

    2017-06-05

    in common or unique ways. These two new kinase or "Kin-OMIC" analyses add another dimension of important data about these frequently used breast cancer cell lines. This will assist researchers in selecting the most appropriate cell lines to use for breast cancer studies and provide context for the interpretation of the emerging results.

  18. Integrating multiple omics to unravel mechanisms of Cyclosporin A induced hepatotoxicity in vitro

    NARCIS (Netherlands)

    Hof, Van den W.F.P.M.; Ruiz Aracama, Ainhoa; Summeren, Van Anke; Jennen, D.G.J.; Gaj, Stan; Coonen, M.L.J.; Brauers, Karen; Wodzig, W.K.W.H.; Delft, van J.H.M.; Kleinjans, J.C.S.

    2015-01-01

    In order to improve attrition rates of candidate-drugs there is a need for a better understanding of the mechanisms underlying drug-induced hepatotoxicity. We aim to further unravel the toxicological response of hepatocytes to a prototypical cholestatic compound by integrating transcriptomic and

  19. Multi-Omics Research Trends in Sepsis: A Bibliometric, Comparative Analysis Between the United States, the European Union 28 Member States, and China.

    Science.gov (United States)

    Evangelatos, Nikolaos; Satyamoorthy, Kapaettu; Levidou, Georgia; Bauer, Pia; Brand, Helmut; Kouskouti, Christina; Lehrach, Hans; Brand, Angela

    2018-03-01

    "-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China. Using a 5-year longitudinal bibliometric study design from 2011 to 2015, we analyzed the sepsis-related research articles in English language that included at least one or multi-omics technologies in publicly available form in Medline (free full texts). We found that the United States has had the lead (almost one-third of publications) in the inclusion of an "-omics" or multi-omics technology in sepsis within the study period. However, both China and the EU-28 displayed a significant increase in the number of publications that employed one or more types of "-omics" research (p < 0.005), while the EU-28 displayed a significant increase especially in multi-omics research articles in sepsis (p < 0.05). Notably, more than half of the multi-omics research studies in the sepsis knowledge domain had a university or government/state funding source. Among the multi-omics research publications in sepsis, the combination of genomics and transcriptomics was the most frequent (40.5%), followed by genomics and proteomics (20.4%). We suggest that the lead of the United States in the field of "-omics" and multi-omics research in sepsis is likely at stake, with both the EU-28 and China rapidly increasing their research capacity. Moreover, "triple omics" that combine genomics, proteomics, and metabolomics analyses appear to be uncommon in sepsis, and yet much needed for triangulation of systems science data. These observations

  20. Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data.

    Science.gov (United States)

    Tomescu, Oana A; Mattanovich, Diethard; Thallinger, Gerhard G

    2014-01-01

    Technological improvements have shifted the focus from data generation to data analysis. The availability of large amounts of data from transcriptomics, protemics and metabolomics experiments raise new questions concerning suitable integrative analysis methods. We compare three integrative analysis techniques (co-inertia analysis, generalized singular value decomposition and integrative biclustering) by applying them to gene and protein abundance data from the six life cycle stages of Plasmodium falciparum. Co-inertia analysis is an analysis method used to visualize and explore gene and protein data. The generalized singular value decomposition has shown its potential in the analysis of two transcriptome data sets. Integrative Biclustering applies biclustering to gene and protein data. Using CIA, we visualize the six life cycle stages of Plasmodium falciparum, as well as GO terms in a 2D plane and interpret the spatial configuration. With GSVD, we decompose the transcriptomic and proteomic data sets into matrices with biologically meaningful interpretations and explore the processes captured by the data sets. IBC identifies groups of genes, proteins, GO Terms and life cycle stages of Plasmodium falciparum. We show method-specific results as well as a network view of the life cycle stages based on the results common to all three methods. Additionally, by combining the results of the three methods, we create a three-fold validated network of life cycle stage specific GO terms: Sporozoites are associated with transcription and transport; merozoites with entry into host cell as well as biosynthetic and metabolic processes; rings with oxidation-reduction processes; trophozoites with glycolysis and energy production; schizonts with antigenic variation and immune response; gametocyctes with DNA packaging and mitochondrial transport. Furthermore, the network connectivity underlines the separation of the intraerythrocytic cycle from the gametocyte and sporozoite stages

  1. Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment.

    Science.gov (United States)

    Daddiego, Loretta; Bianco, Linda; Capodicasa, Cristina; Carbone, Fabrizio; Dalmastri, Claudia; Daroda, Lorenza; Del Fiore, Antonella; De Rossi, Patrizia; Di Carli, Mariasole; Donini, Marcello; Lopez, Loredana; Mengoni, Alessio; Paganin, Patrizia; Perrotta, Gaetano; Bevivino, Annamaria

    2018-01-01

    Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  2. Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach

    Directory of Open Access Journals (Sweden)

    Maciej M. Lalowski

    2018-04-01

    Full Text Available The heart of a newborn mouse has an exceptional capacity to regenerate from myocardial injury that is lost within the first week of its life. In order to elucidate the molecular mechanisms taking place in the mouse heart during this critical period we applied an untargeted combinatory multiomics approach using large-scale mass spectrometry-based quantitative proteomics, metabolomics and mRNA sequencing on hearts from 1-day-old and 7-day-old mice. As a result, we quantified 1.937 proteins (366 differentially expressed, 612 metabolites (263 differentially regulated and revealed 2.586 differentially expressed gene loci (2.175 annotated genes. The analyses pinpointed the fructose-induced glycolysis-pathway to be markedly active in 1-day-old neonatal mice. Integrated analysis of the data convincingly demonstrated cardiac metabolic reprogramming from glycolysis to oxidative phosphorylation in 7-days old mice, with increases of key enzymes and metabolites in fatty acid transport (acylcarnitines and β-oxidation. An upsurge in the formation of reactive oxygen species and an increase in oxidative stress markers, e.g., lipid peroxidation, altered sphingolipid and plasmalogen metabolism were also evident in 7-days mice. In vitro maintenance of physiological fetal hypoxic conditions retained the proliferative capacity of cardiomyocytes isolated from newborn mice hearts. In summary, we provide here a holistic, multiomics view toward early postnatal changes associated with loss of a tissue regenerative capacity in the neonatal mouse heart. These results may provide insight into mechanisms of human cardiac diseases associated with tissue regenerative incapacity at the molecular level, and offer a prospect to discovery of novel therapeutic targets.

  3. toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.

    Science.gov (United States)

    Rhee, David B; Croken, Matthew McKnight; Shieh, Kevin R; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron

    2015-01-01

    Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community. © The Author(s) 2015. Published by Oxford University Press.

  4. "Omics" of maize stress response for sustainable food production: opportunities and challenges.

    Science.gov (United States)

    Gong, Fangping; Yang, Le; Tai, Fuju; Hu, Xiuli; Wang, Wei

    2014-12-01

    Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.

  5. RGmatch: matching genomic regions to proximal genes in omics data integration

    Directory of Open Access Journals (Sweden)

    Pedro Furió-Tarí

    2016-11-01

    Full Text Available Abstract Background The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. Results In this work we review the tools that are publicly available for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gene, transcript, or exon level, applying a set of rules to annotate each region-gene association with the region location within the gene. RGmatch can be applied to any organism as long as genome annotation is available. Furthermore, we qualitatively and quantitatively compare RGmatch to other tools. Conclusions RGmatch simplifies the association of a genomic region with its closest gene. At the same time, it is a powerful tool because the rules used to annotate these associations are very easy to modify according to the researcher’s specific interests. Some important differences between RGmatch and other similar tools already in existence are RGmatch’s flexibility, its wide range of user options, compatibility with any annotatable organism, and its comprehensive and user-friendly output.

  6. Omics Advances in Ecotoxicology.

    Science.gov (United States)

    Zhang, Xiaowei; Xia, Pu; Wang, Pingping; Yang, Jianghu; Baird, Donald J

    2018-04-03

    Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.

  7. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

    Directory of Open Access Journals (Sweden)

    Diogo M O Ogawa

    Full Text Available We propose the technique of biogeochemical typing (BGC typing as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES; and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR spectroscopy and proton nuclear magnetic resonance (1H-NMR all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that

  8. Metabolomics and Integrative Omics for the Development of Thai Traditional Medicine

    Science.gov (United States)

    Khoomrung, Sakda; Wanichthanarak, Kwanjeera; Nookaew, Intawat; Thamsermsang, Onusa; Seubnooch, Patcharamon; Laohapand, Tawee; Akarasereenont, Pravit

    2017-01-01

    In recent years, interest in studies of traditional medicine in Asian and African countries has gradually increased due to its potential to complement modern medicine. In this review, we provide an overview of Thai traditional medicine (TTM) current development, and ongoing research activities of TTM related to metabolomics. This review will also focus on three important elements of systems biology analysis of TTM including analytical techniques, statistical approaches and bioinformatics tools for handling and analyzing untargeted metabolomics data. The main objective of this data analysis is to gain a comprehensive understanding of the system wide effects that TTM has on individuals. Furthermore, potential applications of metabolomics and systems medicine in TTM will also be discussed. PMID:28769804

  9. Omics and Environmental Science Genomic Approaches With Natural Fish Populations From Polluted Environments

    Science.gov (United States)

    Bozinovic, Goran; Oleksiak, Marjorie F.

    2010-01-01

    Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways while population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a pre-determined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complimentary studies. However, while these genomic approaches are immensely powerful for identifying candidate gene and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains. PMID:21072843

  10. Integration a functional approach

    CERN Document Server

    Bichteler, Klaus

    1998-01-01

    This book covers Lebesgue integration and its generalizations from Daniell's point of view, modified by the use of seminorms. Integrating functions rather than measuring sets is posited as the main purpose of measure theory. From this point of view Lebesgue's integral can be had as a rather straightforward, even simplistic, extension of Riemann's integral; and its aims, definitions, and procedures can be motivated at an elementary level. The notion of measurability, for example, is suggested by Littlewood's observations rather than being conveyed authoritatively through definitions of (sigma)-algebras and good-cut-conditions, the latter of which are hard to justify and thus appear mysterious, even nettlesome, to the beginner. The approach taken provides the additional benefit of cutting the labor in half. The use of seminorms, ubiquitous in modern analysis, speeds things up even further. The book is intended for the reader who has some experience with proofs, a beginning graduate student for example. It might...

  11. Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction.

    Science.gov (United States)

    Liu, Cong; Wang, Xujun; Genchev, Georgi Z; Lu, Hui

    2017-07-15

    New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge. There is also a shortage of computational tools for predicting cancer prognosis by using supervised learning methods. The current standard approach is to fit a Cox regression model by concatenating the different types of omics data in a linear manner, while penalty could be added for feature selection. A more powerful approach, however, would be to incorporate data by considering relationships among omics datatypes. Here we developed two methods: a SKI-Cox method and a wLASSO-Cox method to incorporate the association among different types of omics data. Both methods fit the Cox proportional hazards model and predict a risk score based on mRNA expression profiles. SKI-Cox borrows the information generated by these additional types of omics data to guide variable selection, while wLASSO-Cox incorporates this information as a penalty factor during model fitting. We show that SKI-Cox and wLASSO-Cox models select more true variables than a LASSO-Cox model in simulation studies. We assess the performance of SKI-Cox and wLASSO-Cox using TCGA glioblastoma multiforme and lung adenocarcinoma data. In each case, mRNA expression, methylation, and copy number variation data are integrated to predict the overall survival time of cancer patients. Our methods achieve better performance in predicting patients' survival in glioblastoma and lung adenocarcinoma. Copyright © 2017. Published by Elsevier

  12. Omics Approaches for Identifying Physiological Adaptations to Genome Instability in Aging.

    Science.gov (United States)

    Edifizi, Diletta; Schumacher, Björn

    2017-11-04

    DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage. The insulin-like signalling pathway has been implicated in a DNA damage response (DDR) network that includes epidermal growth factor (EGF)-, AMP-activated protein kinases (AMPK)- and the target of rapamycin (TOR)-like signalling pathways, which are known regulators of growth, metabolism, and stress responses. The same pathways, together with the autophagy-mediated proteostatic response and the decline in energy metabolism have also been found to be similarly regulated during natural aging, suggesting striking parallels in the physiological adaptation upon persistent DNA damage due to DNA repair defects and long-term low-level DNA damage accumulation occurring during natural aging. These insights will be an important starting point to study the interplay between signalling networks involved in progeroid syndromes that are caused by DNA repair deficiencies and to gain new understanding of the consequences of DNA damage in the aging process.

  13. Omics Approaches for Identifying Physiological Adaptations to Genome Instability in Aging

    Directory of Open Access Journals (Sweden)

    Diletta Edifizi

    2017-11-01

    Full Text Available DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage. The insulin-like signalling pathway has been implicated in a DNA damage response (DDR network that includes epidermal growth factor (EGF-, AMP-activated protein kinases (AMPK- and the target of rapamycin (TOR-like signalling pathways, which are known regulators of growth, metabolism, and stress responses. The same pathways, together with the autophagy-mediated proteostatic response and the decline in energy metabolism have also been found to be similarly regulated during natural aging, suggesting striking parallels in the physiological adaptation upon persistent DNA damage due to DNA repair defects and long-term low-level DNA damage accumulation occurring during natural aging. These insights will be an important starting point to study the interplay between signalling networks involved in progeroid syndromes that are caused by DNA repair deficiencies and to gain new understanding of the consequences of DNA damage in the aging process.

  14. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    Science.gov (United States)

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  15. Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional Omics.

    Science.gov (United States)

    Liu, Lin; Gong, Weili; Sun, Xiaomeng; Chen, Guanjun; Wang, Lushan

    2018-02-07

    Byproducts of food processing can be utilized for the production of high-value-added enzyme cocktails. In this study, we utilized integrated functional omics technology to analyze composition and functional characteristics of extracellular enzymes produced by Aspergillus niger grown on food processing byproducts. The results showed that oligosaccharides constituted by arabinose, xylose, and glucose in wheat bran were able to efficiently induce the production of extracellular enzymes of A. niger. Compared with other substrates, wheat bran was more effective at inducing the secretion of β-glucosidases from GH1 and GH3 families, as well as >50% of proteases from A1-family aspartic proteases. Compared with proteins induced by single wheat bran or soybean dregs, the protein yield induced by their mixture was doubled, and the time required to reach peak enzyme activity was shortened by 25%. This study provided a technical platform for the complex formulation of various substrates and functional analysis of extracellular enzymes.

  16. Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach.

    Science.gov (United States)

    Ali, Mehreen; Khan, Suleiman A; Wennerberg, Krister; Aittokallio, Tero

    2018-04-15

    Proteomics profiling is increasingly being used for molecular stratification of cancer patients and cell-line panels. However, systematic assessment of the predictive power of large-scale proteomic technologies across various drug classes and cancer types is currently lacking. To that end, we carried out the first pan-cancer, multi-omics comparative analysis of the relative performance of two proteomic technologies, targeted reverse phase protein array (RPPA) and global mass spectrometry (MS), in terms of their accuracy for predicting the sensitivity of cancer cells to both cytotoxic chemotherapeutics and molecularly targeted anticancer compounds. Our results in two cell-line panels demonstrate how MS profiling improves drug response predictions beyond that of the RPPA or the other omics profiles when used alone. However, frequent missing MS data values complicate its use in predictive modeling and required additional filtering, such as focusing on completely measured or known oncoproteins, to obtain maximal predictive performance. Rather strikingly, the two proteomics profiles provided complementary predictive signal both for the cytotoxic and targeted compounds. Further, information about the cellular-abundance of primary target proteins was found critical for predicting the response of targeted compounds, although the non-target features also contributed significantly to the predictive power. The clinical relevance of the selected protein markers was confirmed in cancer patient data. These results provide novel insights into the relative performance and optimal use of the widely applied proteomic technologies, MS and RPPA, which should prove useful in translational applications, such as defining the best combination of omics technologies and marker panels for understanding and predicting drug sensitivities in cancer patients. Processed datasets, R as well as Matlab implementations of the methods are available at https://github.com/mehr-een/bemkl-rbps. mehreen

  17. ShockOmics: multiscale approach to the identification of molecular biomarkers in acute heart failure induced by shock.

    Science.gov (United States)

    Aletti, Federico; Conti, Costanza; Ferrario, Manuela; Ribas, Vicent; Bollen Pinto, Bernardo; Herpain, Antoine; Post, Emiel; Romay Medina, Eduardo; Barlassina, Cristina; de Oliveira, Eliandre; Pastorelli, Roberta; Tedeschi, Gabriella; Ristagno, Giuseppe; Taccone, Fabio S; Schmid-Schönbein, Geert W; Ferrer, Ricard; De Backer, Daniel; Bendjelid, Karim; Baselli, Giuseppe

    2016-01-28

    The ShockOmics study (ClinicalTrials.gov identifier NCT02141607) is a multicenter prospective observational trial aimed at identifying new biomarkers of acute heart failure in circulatory shock, by means of a multiscale analysis of blood samples and hemodynamic data from subjects with circulatory shock. Ninety septic shock and cardiogenic shock patients will be recruited in three intensive care units (ICU) (Hôpital Erasme, Université Libre de Bruxelles, Belgium; Hospital Universitari Mutua Terrassa, Spain; Hôpitaux Universitaires de Genève, Switzerland). Hemodynamic signals will be recorded every day for up to seven days from shock diagnosis (time T0). Clinical data and blood samples will be collected for analysis at: i) T1  5 and lactate levels ≥ 2 mmol/L. The exclusion criteria are: expected death within 24 h since ICU admission; > 4 units of red blood cells or >1 fresh frozen plasma transfused; active hematological malignancy; metastatic cancer; chronic immunodepression; pre-existing end stage renal disease requiring renal replacement therapy; recent cardiac surgery; Child-Pugh C cirrhosis; terminal illness. Enrollment will be preceded by the signature of the Informed Consent by the patient or his/her relatives and by the physician in charge. Three non-shock control groups will be included in the study: a) healthy blood donors (n = 5); b) septic patients (n = 10); c) acute myocardial infarction or patients with prolonged acute arrhythmia (n = 10). The hemodynamic data will be downloaded from the ICU monitors by means of dedicated software. The blood samples will be utilized for transcriptomics, proteomics and metabolomics ("-omics") analyses. ShockOmics will provide new insights into the pathophysiological mechanisms underlying shock as well as new biomarkers for the timely diagnosis of cardiac dysfunction in shock and quantitative indices for assisting the therapeutic management of shock patients.

  18. Omics-based approaches reveal phospholipids remodeling of Rhizopus oryzae responding to furfural stress for fumaric acid-production from xylose.

    Science.gov (United States)

    Pan, Xinrong; Liu, Huanhuan; Liu, Jiao; Wang, Cheng; Wen, Jianping

    2016-12-01

    In order to relieve the toxicity of furfural on Rhizopus oryzae fermentation, the molecular mechanism of R. oryzae responding to furfural stress for fumaric acid-production was investigated by omics-based approaches. In metabolomics analysis, 29 metabolites including amino acid, sugars, polyols and fatty acids showed significant changes for maintaining the basic cell metabolism at the cost of lowering fumaric acid production. To further uncover the survival mechanism, lipidomics was carried out, revealing that phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and polyunsaturated acyl chains might be closely correlated with R. oryzae's adapting to furfural stress. Based on the above omics analysis, lecithin, inositol and soybean oil were exogenously supplemented separately with an optimized concentration in the presence of furfural, which increased fumaric acid titer from 5.78g/L to 10.03g/L, 10.05g/L and 12.13g/L (increased by 73.5%, 73.8% and 110%, respectively). These findings provide a methodological guidance for hemicellulose-fumaric acid development. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations

    Directory of Open Access Journals (Sweden)

    Abdellah Tebani

    2016-09-01

    Full Text Available The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  20. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations.

    Science.gov (United States)

    Tebani, Abdellah; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

    2016-09-14

    The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM) are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  1. A practical data processing workflow for multi-OMICS projects.

    Science.gov (United States)

    Kohl, Michael; Megger, Dominik A; Trippler, Martin; Meckel, Hagen; Ahrens, Maike; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-Claudius; Baba, Hideo A; Sitek, Barbara; Schlaak, Jörg F; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin

    2014-01-01

    Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post

  2. A conceptual model for translating omic data into clinical action

    Directory of Open Access Journals (Sweden)

    Timothy M Herr

    2015-01-01

    Full Text Available Genomic, proteomic, epigenomic, and other "omic" data have the potential to enable precision medicine, also commonly referred to as personalized medicine. The volume and complexity of omic data are rapidly overwhelming human cognitive capacity, requiring innovative approaches to translate such data into patient care. Here, we outline a conceptual model for the application of omic data in the clinical context, called "the omic funnel." This model parallels the classic "Data, Information, Knowledge, Wisdom pyramid" and adds context for how to move between each successive layer. Its goal is to allow informaticians, researchers, and clinicians to approach the problem of translating omic data from bench to bedside, by using discrete steps with clearly defined needs. Such an approach can facilitate the development of modular and interoperable software that can bring precision medicine into widespread practice.

  3. EXPOsOMICS: final policy workshop and stakeholder consultation.

    Science.gov (United States)

    Turner, Michelle C; Vineis, Paolo; Seleiro, Eduardo; Dijmarescu, Michaela; Balshaw, David; Bertollini, Roberto; Chadeau-Hyam, Marc; Gant, Timothy; Gulliver, John; Jeong, Ayoung; Kyrtopoulos, Soterios; Martuzzi, Marco; Miller, Gary W; Nawrot, Timothy; Nieuwenhuijsen, Mark; Phillips, David H; Probst-Hensch, Nicole; Samet, Jonathan; Vermeulen, Roel; Vlaanderen, Jelle; Vrijheid, Martine; Wild, Christopher; Kogevinas, Manolis

    2018-02-15

    The final meeting of the EXPOsOMICS project "Final Policy Workshop and Stakeholder Consultation" took place 28-29 March 2017 to present the main results of the project and discuss their implications both for future research and for regulatory and policy activities. This paper summarizes presentations and discussions at the meeting related with the main results and advances in exposome research achieved through the EXPOsOMICS project; on other parallel research initiatives on the study of the exposome in Europe and in the United States and their complementarity to EXPOsOMICS; lessons learned from these early studies on the exposome and how they may shape the future of research on environmental exposure assessment; and finally the broader implications of exposome research for risk assessment and policy development on environmental exposures. The main results of EXPOsOMICS in relation to studies of the external exposome and internal exposome in relation to both air pollution and water contaminants were presented as well as new technologies for environmental health research (adductomics) and advances in statistical methods. Although exposome research strengthens the scientific basis for policy development, there is a need in terms of showing added value for public health to: improve communication of research results to non-scientific audiences; target research to the broader landscape of societal challenges; and draw applicable conclusions. Priorities for future work include the development and standardization of methodologies and technologies for assessing the external and internal exposome, improved data sharing and integration, and the demonstration of the added value of exposome science over conventional approaches in answering priority policy questions.

  4. An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity.

    Science.gov (United States)

    Qiao, Qin; Le Manach, Séverine; Huet, Hélène; Duvernois-Berthet, Evelyne; Chaouch, Soraya; Duval, Charlotte; Sotton, Benoit; Ponger, Loïc; Marie, Arul; Mathéron, Lucrèce; Lennon, Sarah; Bolbach, Gérard; Djediat, Chakib; Bernard, Cécile; Edery, Marc; Marie, Benjamin

    2016-12-01

    Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L -1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L -1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L -1  MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a

  5. Omics studies of citrus, grape and rosaceae fruit trees.

    Science.gov (United States)

    Shiratake, Katsuhiro; Suzuki, Mami

    2016-01-01

    Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

  6. Integrated multi-omics analysis supports role of lysophosphatidylcholine and related glycerophospholipids in the Lotus japonicus-Glomus intraradices mycorrhizal symbiosis.

    Science.gov (United States)

    Vijayakumar, Vinod; Liebisch, Gerhard; Buer, Benjamin; Xue, Li; Gerlach, Nina; Blau, Samira; Schmitz, Jessica; Bucher, Marcel

    2016-02-01

    Interaction of plant roots with arbuscular mycorrhizal fungi (AMF) is a complex trait resulting in cooperative interactions among the two symbionts including bidirectional exchange of resources. To study arbuscular mycorrhizal symbiosis (AMS) trait variation in the model plant Lotus japonicus, we performed an integrated multi-omics analysis with a focus on plant and fungal phospholipid (PL) metabolism and biological significance of lysophosphatidylcholine (LPC). Our results support the role of LPC as a bioactive compound eliciting cellular and molecular response mechanisms in Lotus. Evidence is provided for large interspecific chemical diversity of LPC species among mycorrhizae with related AMF species. Lipid, gene expression and elemental profiling emphasize the Lotus-Glomus intraradices interaction as distinct from other arbuscular mycorrhizal (AM) interactions. In G. intraradices, genes involved in fatty acid (FA) elongation and biosynthesis of unsaturated FAs were enhanced, while in Lotus, FA synthesis genes were up-regulated during AMS. Furthermore, FAS protein localization to mitochondria suggests FA biosynthesis and elongation may also occur in AMF. Our results suggest the existence of interspecific partitioning of PL resources for generation of LPC and novel candidate bioactive PLs in the Lotus-G. intraradices symbiosis. Moreover, the data advocate research with phylogenetically diverse Glomeromycota species for a broader understanding of the molecular underpinnings of AMS. © 2015 John Wiley & Sons Ltd.

  7. Visual comparative omics of fungi for plant biomass deconstruction

    Directory of Open Access Journals (Sweden)

    Shingo Miyauchi

    2016-08-01

    Full Text Available Wood-decay fungi are able to decompose plant cell wall components such as cellulose, hemicelluloses and lignin. Such fungal capabilities may be exploited for the enhancement of directed enzymatic degradation of recalcitrant plant biomass. The comparative analysis of wood-decay fungi using a multi-omics approach gives not only new insights into the strategies for decomposing complex plant materials but also basic knowledge for the design of combinations of enzymes for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT, to simplify the analysis and interpretation of transcriptomic and secretomic data. The ABCDEFGT workflow is primarily constructed of self-organizing maps for grouping genes with similar transcription patterns and an overlay with secreted proteins. The ABCDEFGT workflow produces simple graphic outputs of genome-wide transcriptomes and secretomes. It enables visual inspection without a priori of the omics data, facilitating discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data showed a global overlap, confirming the pertinence of the genome-wide approach to study the fungal biological responses to the carbon sources. Our method was compared to a recently-developed clustering method in order to assess the biological relevance of the method and ease of interpretation. Our approach provided a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of enzymes participating in the decomposition of cellulose, hemicellulose and lignin such as Lytic Polysaccharide Monooxygenases (LPMO, modular enzymes associated with a cellulose binding module

  8. A Multi-omics Approach to Understand the Microbial Transformation of Lignocellulosic Materials in the Digestive System of the Wood-Feeding Beetle Odontotaenius disjunctus

    Science.gov (United States)

    Ceja Navarro, J. A.; Karaoz, U.; White, R. A., III; Lipton, M. S.; Adkins, J.; Mayali, X.; Blackwell, M.; Pett-Ridge, J.; Brodie, E.; Hao, Z.

    2015-12-01

    Odontotaenius disjuctus is a wood feeding beetle that processes large amounts of hardwoods and plays an important role in forest carbon cycling. In its gut, plant material is transformed into simple molecules by sequential processing during passage through the insect's digestive system. In this study, we used multiple 'omics approaches to analyze the distribution of microbial communities and their specific functions in lignocellulose deconstruction within the insect's gut. Fosmid clones were selected and sequenced from a pool of clones based on their expression of plant polymer degrading enzymes, allowing the identification of a wide range of carbohydrate degrading enzymes. Comparison of metagenomes of all gut regions demonstrated the distribution of genes across the beetle gut. Cellulose, starch, and xylan degradation genes were particularly abundant in the midgut and posterior hindgut. Genes involved in hydrogenotrophic production of methane and nitrogenases were more abundant in the anterior hindgut. Assembled contigs were binned into 127 putative genomes representing Bacteria, Archaea, Fungi and Nematodes. Eleven complete genomes were reconstructed allowing to identify linked functions/traits, including organisms with cellulosomes, and a combined potential for cellulose, xylan and starch hydrolysis and nitrogen fixation. A metaproteomic study was conducted to test the expression of the pathways identified in the metagenomic study. Preliminary analyses suggest enrichment of pathways related to hemicellulosic degradation. A complete xylan degradation pathway was reconstructed and GC-MS/MS based metabolomics identified xylobiose and xylose as major metabolite pools. To relate microbial identify to function in the beetle gut, Chip-SIP isotope tracing was conducted with RNA extracted from beetles fed 13C-cellulose. Multiple 13C enriched bacterial groups were detected, mainly in the midgut. Our multi-omics approach has allowed us to characterize the contribution of

  9. Research on inbreeding in the 'omic' era

    DEFF Research Database (Denmark)

    Kristensen, Torsten N; Pedersen, Kamilla S; Vermeulen, Cornelis J

    2010-01-01

    Developments in molecular and systems biology have enabled novel approaches to be used in the study of inbreeding. Mechanistic and functional studies using ‘omic' technologies can increase the understanding of the consequences of inbreeding, from the level of DNA to that of population growth...

  10. Contributions of polyunsaturated fatty acids (PUFA) on cerebral neurobiology: an integrated omics approach with epigenomic focus

    Science.gov (United States)

    2016-12-01

    increase in N-3/n-6 fatty acid ratio reduces maternal obesity - associated inflammation and limits adverse developmental programming in mice. PLoS One...reduced transcriptional expressions. The majority of miRNAs overexpressed by BLD are associated with Alzheimer’s and schizophrenia. BLD implicated long-term...requires choline, other methyl donors and sufficient amounts of energy [7,8]. Hence, foods enriched with or deprived of such supplements enable control of

  11. Evaluating the antidiabetic effects of Chinese herbal medicine: Xiao-Ke-An in 3T3-L1 cells and KKAy mice using both conventional and holistic omics approaches.

    Science.gov (United States)

    Yang, Zhenzhong; Wang, Linli; Zhang, Feng; Li, Zheng

    2015-08-13

    Xiao-Ke-An (XKA) is a Chinese medicine widely used for treating type 2 diabetes mellitus (T2D). It is composed of eight herbal medicines traditionally used for T2D, including Rehmannia glutinosa Libosch, Anemarrhena asphodeloides Bunge, Coptis chinensis Franch, etc. The aim of the present study was to investigate the antidiabetic effects of XKA with both conventional and holistic omics approaches. The antidiabetic effect of XKA was first investigated in 3T3-L1 cells to study the effect of XKA on adipogenesis in vitro. Oil Red O staining was performed to determine the lipid accumulation. The intracellular total cholesterol (TC) and triglyceride (TG) contents in XKA treated 3T3-L1 cells were also evaluated. The therapeutic effects of XKA was further evaluated in KKAy mice with both conventional and holistic omics approaches. Body weight, fasting and non-fasting blood glucose, and oral glucose tolerance were measured during the experiment. At the time of sacrifice, serum was collected for the measurement of TG, TC, high-density lipoprotein cholesterol (HDL-c) and low-density lipoprotein cholesterol (LDL-c). The liver, kidney, spleen, pancreas, heart and adipose tissues were harvested and weighted. The liver was used for further microarray experiment. Omics approaches were adopted to evaluate the holistic rebalancing effect of XKA at molecular network level. XKA significantly inhibited adipogenic differentiation, lowered the intracellular TC and TG contents in 3T3-L1 cells. XKA improved the glucose homeostasis and lipid metabolism, ameliorated insulin resistance in KKAy mice. Furthermore, XKA also exhibited effective therapeutic effects by reversing the molecular T2D disease network from an unbalanced state. This study investigated the antidiabetic effects of XKA with both conventional and holistic omics approaches, providing both phenotypic evidence and underlying action mechanisms for the clinical use of XKA treating T2D.

  12. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  13. Expression Profiling of Human Pluripotent Stem Cell-Derived Cardiomyocytes Exposed to Doxorubicin-Integration and Visualization of Multi-Omics Data.

    Science.gov (United States)

    Holmgren, Gustav; Sartipy, Peter; Andersson, Christian X; Lindahl, Anders; Synnergren, Jane

    2018-05-01

    Anthracyclines, such as doxorubicin, are highly efficient chemotherapeutic agents against a variety of cancers. However, anthracyclines are also among the most cardiotoxic therapeutic drugs presently on the market. Chemotherapeutic-induced cardiomyopathy is one of the leading causes of disease and mortality in cancer survivors. The exact mechanisms responsible for doxorubicin-induced cardiomyopathy are not completely known, but the fact that the cardiotoxicity is dose-dependent and that there is a variation in time-to-onset of toxicity, and gender- and age differences suggests that several mechanisms may be involved. In this study, we investigated doxorubicin-induced cardiotoxicity in human pluripotent stem cell-derived cardiomyocytes using proteomics. In addition, different sources of omics data (protein, mRNA, and microRNA) from the same experimental setup were further combined and analyzed using newly developed methods to identify differential expression in data of various origin and types. Subsequently, the results were integrated in order to generate a combined visualization of the findings. In our experimental model system, we exposed cardiomyocytes derived from human pluripotent stem cells to doxorubicin for up to 2 days, followed by a wash-out period of additionally 12 days. Besides an effect on the cell morphology and cardiomyocyte functionality, the data show a strong effect of doxorubicin on all molecular levels investigated. Differential expression patterns that show a linkage between the proteome, transcriptome, and the regulatory microRNA network, were identified. These findings help to increase the understanding of the mechanisms behind anthracycline-induced cardiotoxicity and suggest putative biomarkers for this condition.

  14. Analysis of integrated multiple 'omics' datasets reveals the mechanisms of initiation and determination in the formation of tuberous roots in Rehmannia glutinosa.

    Science.gov (United States)

    Li, Mingjie; Yang, Yanhui; Li, Xinyu; Gu, Li; Wang, Fengji; Feng, Fajie; Tian, Yunhe; Wang, Fengqing; Wang, Xiaoran; Lin, Wenxiong; Chen, Xinjian; Zhang, Zhongyi

    2015-09-01

    All tuberous roots in Rehmannia glutinosa originate from the expansion of fibrous roots (FRs), but not all FRs can successfully transform into tuberous roots. This study identified differentially expressed genes and proteins associated with the expansion of FRs, by comparing the tuberous root at expansion stages (initiated tuberous root, ITRs) and FRs at the seedling stage (initiated FRs, IFRs). The role of miRNAs in the expansion of FRs was also explored using the sRNA transcriptome and degradome to identify miRNAs and their target genes that were differentially expressed between ITRs and FRs at the mature stage (unexpanded FRs, UFRs, which are unable to expand into ITRs). A total of 6032 genes and 450 proteins were differentially expressed between ITRs and IFRs. Integrated analyses of these data revealed several genes and proteins involved in light signalling, hormone response, and signal transduction that might participate in the induction of tuberous root formation. Several genes related to cell division and cell wall metabolism were involved in initiating the expansion of IFRs. Of 135 miRNAs differentially expressed between ITRs and UFRs, there were 27 miRNAs whose targets were specifically identified in the degradome. Analysis of target genes showed that several miRNAs specifically expressed in UFRs were involved in the degradation of key genes required for the formation of tuberous roots. As far as could be ascertained, this is the first time that the miRNAs that control the transition of FRs to tuberous roots in R. glutinosa have been identified. This comprehensive analysis of 'omics' data sheds new light on the mechanisms involved in the regulation of tuberous roots formation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  15. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics.

    Science.gov (United States)

    Mudaliar, Manikhandan; Tassi, Riccardo; Thomas, Funmilola C; McNeilly, Tom N; Weidt, Stefan K; McLaughlin, Mark; Wilson, David; Burchmore, Richard; Herzyk, Pawel; Eckersall, P David; Zadoks, Ruth N

    2016-08-16

    Mastitis, inflammation of the mammary gland, is the most common and costly disease of dairy cattle in the western world. It is primarily caused by bacteria, with Streptococcus uberis as one of the most prevalent causative agents. To characterize the proteome during Streptococcus uberis mastitis, an experimentally induced model of intramammary infection was used. Milk whey samples obtained from 6 cows at 6 time points were processed using label-free relative quantitative proteomics. This proteomic analysis complements clinical, bacteriological and immunological studies as well as peptidomic and metabolomic analysis of the same challenge model. A total of 2552 non-redundant bovine peptides were identified, and from these, 570 bovine proteins were quantified. Hierarchical cluster analysis and principal component analysis showed clear clustering of results by stage of infection, with similarities between pre-infection and resolution stages (0 and 312 h post challenge), early infection stages (36 and 42 h post challenge) and late infection stages (57 and 81 h post challenge). Ingenuity pathway analysis identified upregulation of acute phase protein pathways over the course of infection, with dominance of different acute phase proteins at different time points based on differential expression analysis. Antimicrobial peptides, notably cathelicidins and peptidoglycan recognition protein, were upregulated at all time points post challenge and peaked at 57 h, which coincided with 10 000-fold decrease in average bacterial counts. The integration of clinical, bacteriological, immunological and quantitative proteomics and other-omic data provides a more detailed systems level view of the host response to mastitis than has been achieved previously.

  16. Omics and cachexia.

    Science.gov (United States)

    Twelkmeyer, Brigitte; Tardif, Nicolas; Rooyackers, Olav

    2017-05-01

    The purpose of this review is to recapture recent advances in cachexia-related diseases, mainly cancer cachexia, and treatment using genomic, transcriptomics, proteomic, and metabolomics-related techniques. From recent studies in the cancer cachexia field it is clear that the tumor has a direct effect on distant organs via its secretome. The affected pathways on the other hand were largely known from earlier studies with changes in energy-related pathways (mainly lipid metabolism) and the protein degradation pathways. Treatment-oriented studies use mostly rodent models and in-vivo cultures and it is too early for human studies. Omics tools are powerful if used in the right way. Omics research has identified the tumor as an important player in cancer cachexia and some interesting novel treatments have been found in experimental models.

  17. An Integrated Approach to Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 8. An Integrated Approach to Biology. Aniket Bhattacharya. General Article Volume 16 Issue 8 August 2011 pp 742-753. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/016/08/0742-0753 ...

  18. Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates

    Directory of Open Access Journals (Sweden)

    Arike Liisa

    2011-02-01

    Full Text Available Abstract Background Lactococcus lactis is recognised as a safe (GRAS microorganism and has hence gained interest in numerous biotechnological approaches. As it is fastidious for several amino acids, optimization of processes which involve this organism requires a thorough understanding of its metabolic regulations during multisubstrate growth. Results Using glucose limited continuous cultivations, specific growth rate dependent metabolism of L. lactis including utilization of amino acids was studied based on extracellular metabolome, global transcriptome and proteome analysis. A new growth medium was designed with reduced amino acid concentrations to increase precision of measurements of consumption of amino acids. Consumption patterns were calculated for all 20 amino acids and measured carbon balance showed good fit of the data at all growth rates studied. It was observed that metabolism of L. lactis became more efficient with rising specific growth rate in the range 0.10 - 0.60 h-1, indicated by 30% increase in biomass yield based on glucose consumption, 50% increase in efficiency of nitrogen use for biomass synthesis, and 40% reduction in energy spilling. The latter was realized by decrease in the overall product formation and higher efficiency of incorporation of amino acids into biomass. L. lactis global transcriptome and proteome profiles showed good correlation supporting the general idea of transcription level control of bacterial metabolism, but the data indicated that substrate transport systems together with lower part of glycolysis in L. lactis were presumably under allosteric control. Conclusions The current study demonstrates advantages of the usage of strictly controlled continuous cultivation methods combined with multi-omics approach for quantitative understanding of amino acid and energy metabolism of L. lactis which is a valuable new knowledge for development of balanced growth media, gene manipulations for desired product

  19. AucPR: An AUC-based approach using penalized regression for disease prediction with high-dimensional omics data

    OpenAIRE

    Yu, Wenbao; Park, Taesung

    2014-01-01

    Motivation It is common to get an optimal combination of markers for disease classification and prediction when multiple markers are available. Many approaches based on the area under the receiver operating characteristic curve (AUC) have been proposed. Existing works based on AUC in a high-dimensional context depend mainly on a non-parametric, smooth approximation of AUC, with no work using a parametric AUC-based approach, for high-dimensional data. Results We propose an AUC-based approach u...

  20. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology.

    Science.gov (United States)

    Fondi, Marco; Liò, Pietro

    2015-02-01

    Integrated -omics approaches are quickly spreading across microbiology research labs, leading to (i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organization and (ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi -omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists. Copyright © 2015. Published by Elsevier GmbH.

  1. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 3. Untargeted metabolomics.

    Science.gov (United States)

    Thomas, Funmilola Clara; Mudaliar, Manikhandan; Tassi, Riccardo; McNeilly, Tom N; Burchmore, Richard; Burgess, Karl; Herzyk, Pawel; Zadoks, Ruth N; Eckersall, P David

    2016-08-16

    Intramammary infection leading to bovine mastitis is the leading disease problem affecting dairy cows and has marked effects on the milk produced by infected udder quarters. An experimental model of Streptococcus uberis mastitis has previously been investigated for clinical, immunological and pathophysiological alteration in milk, and has been the subject of peptidomic and quantitative proteomic investigation. The same sample set has now been investigated with a metabolomics approach using liquid chromatography and mass spectrometry. The analysis revealed over 3000 chromatographic peaks, of which 690 were putatively annotated with a metabolite. Hierarchical clustering analysis and principal component analysis demonstrated that metabolite changes due to S. uberis infection were maximal at 81 hours post challenge with metabolites in the milk from the resolution phase at 312 hours post challenge being closest to the pre-challenge samples. Metabolic pathway analysis revealed that the majority of the metabolites mapped to carbohydrate and nucleotide metabolism show a decreasing trend in concentration up to 81 hours post-challenge whereas an increasing trend was found in lipid metabolites and di-, tri- and tetra-peptides up to the same time point. The increase in these peptides coincides with an increase in larger peptides found in the previous peptidomic analysis and is likely to be due to protease degradation of milk proteins. Components of bile acid metabolism, linked to the FXR pathway regulating inflammation, were also increased. Metabolomic analysis of the response in milk during mastitis provides an essential component to the full understanding of the mammary gland's response to infection.

  2. Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction.

    Science.gov (United States)

    Yu, Kun-Hsing; Fitzpatrick, Michael R; Pappas, Luke; Chan, Warren; Kung, Jessica; Snyder, Michael

    2017-09-12

    Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information poses an informatics challenge in systematically identifying patterns associated with health outcomes, and no general-purpose data-mining tool exists for physicians, medical researchers, and citizen scientists without significant training in programming and bioinformatics. To bridge this gap, we built the Omics AnalySIs System for PRecision Oncology (OASISPRO), a web-based system to mine the quantitative omics information from The Cancer Genome Atlas (TCGA). This system effectively visualizes patients' clinical profiles, executes machine-learning algorithms of choice on the omics data, and evaluates the prediction performance using held-out test sets. With this tool, we successfully identified genes strongly associated with tumor stage, and accurately predicted patients' survival outcomes in many cancer types, including mesothelioma and adrenocortical carcinoma. By identifying the links between omics and clinical phenotypes, this system will facilitate omics studies on precision cancer medicine and contribute to establishing personalized cancer treatment plans. This web-based tool is available at http://tinyurl.com/oasispro ;source codes are available at http://tinyurl.com/oasisproSourceCode . © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  3. Omics Methods for Probing the Mode of Action of Natural and Synthetic Phytotoxins

    OpenAIRE

    Duke, Stephen O.; Bajsa, Joanna; Pan, Zhiqiang

    2013-01-01

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances ...

  4. Integrating cell biology and proteomic approaches in plants.

    Science.gov (United States)

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-10-03

    Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

  5. Ares I Integrated Test Approach

    Science.gov (United States)

    Taylor, Jim

    2008-01-01

    This slide presentation reviews the testing approach that NASA is developing for the Ares I launch vehicle. NASA is planning a complete series of development, qualification and verification tests. These include: (1) Upper stage engine sea-level and altitude testing (2) First stage development and qualification motors (3) Upper stage structural and thermal development and qualification test articles (4) Main Propulsion Test Article (MPTA) (5) Upper stage green run testing (6) Integrated Vehicle Ground Vibration Testing (IVGVT) and (7) Aerodynamic characterization testing.

  6. Research from the NASA Twins Study and Omics in Support of Mars Missions

    Science.gov (United States)

    Kundrot, C.; Shelhamer, M.; Scott, G.

    2015-01-01

    The NASA Twins Study, NASA's first foray into integrated omic studies in humans, illustrates how an integrated omics approach can be brought to bear on the challenges to human health and performance on a Mars mission. The NASA Twins Study involves US Astronaut Scott Kelly and his identical twin brother, Mark Kelly, a retired US Astronaut. No other opportunity to study a twin pair for a prolonged period with one subject in space and one on the ground is available for the foreseeable future. A team of 10 principal investigators are conducting the Twins Study, examining a very broad range of biological functions including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. A novel aspect of the study is the integrated study of molecular, physiological, cognitive, and microbiological properties. Major sample and data collection from both subjects for this study began approximately six months before Scott Kelly's one year mission on the ISS, continue while Scott Kelly is in flight and will conclude approximately six months after his return to Earth. Mark Kelly will remain on Earth during this study, in a lifestyle unconstrained by this study, thereby providing a measure of normal variation in the properties being studied. An overview of initial results and the future plans will be described as well as the technological and ethical issues raised for spaceflight studies involving omics.

  7. News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.

    Science.gov (United States)

    Deusch, Simon; Tilocca, Bruno; Camarinha-Silva, Amélia; Seifert, Jana

    2015-01-01

    Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about the investigated microbiota. In general, integration of the main Omics-technologies (genomics, transcriptomics, proteomics and metabolomics) in live science promises highly detailed information about the specific research object and helps to understand molecular changes in response to internal and external environmental factors. The microbial communities settled in the mammalian gastrointestinal tract are essential for the host metabolism and have a major impact on its physiology and health. The microbiotas of livestock like chicken, pig and ruminants are becoming a focus of interest for veterinaries, animal nutritionists and microbiologists. While pig is more often used as an animal model for human-related studies, the rumen microbiota harbors a diversity of enzymes converting complex carbohydrates into monomers which bears high potential for biotechnological applications. This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.

  8. Inflammaging and human longevity in the omics era.

    Science.gov (United States)

    Monti, Daniela; Ostan, Rita; Borelli, Vincenzo; Castellani, Gastone; Franceschi, Claudio

    2017-07-01

    Inflammaging is a recent theory of aging originally proposed in 2000 where data and conceptualizations regarding the aging of the immune system (immunosenescence) and the evolution of immune responses from invertebrates to mammals converged. This theory has received an increasing number of citations and experimental confirmations. Here we present an updated version of inflammaging focused on omics data - particularly on glycomics - collected on centenarians, semi-supercentenarians and their offspring. Accordingly, we arrived to the following conclusions: i) inflammaging has a structure where specific combinations of pro- and anti-inflammatory mediators are involved; ii) inflammaging is systemic and more complex than we previously thought, as many organs, tissues and cell types participate in producing pro- and anti-inflammatory stimuli defined "molecular garbage"; iii) inflammaging is dynamic, can be propagated locally to neighboring cells and systemically from organ to organ by circulating products and microvesicles, and amplified by chronic age-related diseases constituting a "local fire", which in turn produces additional inflammatory stimuli and molecular garbage; iv) an integrated Systems Medicine approach is urgently needed to let emerge a robust and highly informative set/combination of omics markers able to better grasp the complex molecular core of inflammaging in elderly and centenarians. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Malaysia implements the integrated approach.

    Science.gov (United States)

    1977-01-01

    Malaysia has implemented an integrated approach in providing family planning services to eligible couples. In 1964 the government of Malaysia adopted a national family planning program, and implementation began in the urban areas and extended into the rural areas. Other agencies are involved in providing family planning services and information including the Federation of Family Planning Associations, the Ministry of Health, the National Family Planning Board, and the Federal Land Development Authority. The number of women practicing contraception has increased from 20,726 in 1967 to 533,646 by 1976. and other methods, 3.9%, respectively. There has been an increase in the percentage of acceptors between ages 15-29 from 56% in 1968 to 71.3% in 1975. The 2nd Malaysian national plan will use a multidisciplinary approach to the problem.

  10. Clustering multilayer omics data using MuNCut.

    Science.gov (United States)

    Teran Hidalgo, Sebastian J; Ma, Shuangge

    2018-03-14

    Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functionalities of omics units, assisting dimension reduction in outcome model building, and others. In the most recent omics studies, a prominent trend is to conduct multilayer profiling, which collects multiple types of genetic, genomic, epigenetic and other measurements on the same subjects. In the literature, clustering methods tailored to multilayer omics data are still limited. Directly applying the existing clustering methods to multilayer omics data and clustering each layer first and then combing across layers are both "suboptimal" in that they do not accommodate the interconnections within layers and across layers in an informative way. In this study, we develop the MuNCut (Multilayer NCut) clustering approach. It is tailored to multilayer omics data and sufficiently accounts for both across- and within-layer connections. It is based on the novel NCut technique and also takes advantages of regularized sparse estimation. It has an intuitive formulation and is computationally very feasible. To facilitate implementation, we develop the function muncut in the R package NcutYX. Under a wide spectrum of simulation settings, it outperforms competitors. The analysis of TCGA (The Cancer Genome Atlas) data on breast cancer and cervical cancer shows that MuNCut generates biologically meaningful results which differ from those using the alternatives. We propose a more effective clustering analysis of multiple omics data. It provides a new venue for jointly analyzing genetic, genomic, epigenetic and other measurements.

  11. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

    Science.gov (United States)

    Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

    2017-10-02

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

  12. Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2017-06-10

    Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker's yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein-protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

  13. Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

    Directory of Open Access Journals (Sweden)

    Malod-Dognin Noël

    2017-06-01

    Full Text Available Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker’s yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein–protein interaction (PPI, co-expression (COEX and genetic interaction (GI data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO. We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

  14. Integrated approaches to perceptual learning.

    Science.gov (United States)

    Jacobs, Robert A

    2010-04-01

    New technologies and new ways of thinking have recently led to rapid expansions in the study of perceptual learning. We describe three themes shared by many of the nine articles included in this topic on Integrated Approaches to Perceptual Learning. First, perceptual learning cannot be studied on its own because it is closely linked to other aspects of cognition, such as attention, working memory, decision making, and conceptual knowledge. Second, perceptual learning is sensitive to both the stimulus properties of the environment in which an observer exists and to the properties of the tasks that the observer needs to perform. Moreover, the environmental and task properties can be characterized through their statistical regularities. Finally, the study of perceptual learning has important implications for society, including implications for science education and medical rehabilitation. Contributed articles relevant to each theme are summarized. Copyright © 2010 Cognitive Science Society, Inc.

  15. DOE systems approach and integration

    International Nuclear Information System (INIS)

    Logan, J.A.

    1987-01-01

    Six sites are now disposing of most of DOE's currently generated waste. These are: Hanford, Idaho National Engineering Laboratory, Los Alamos National Laboratory, the Nevada Test Site, Oak Ridge, and Savannah River. Within DOE, experience with disposal of solid LLW has been that arid site disposal facilities (first four) appear to have performed well, while humid site disposal facilities (last two) have experienced some waste migration. DOE's intent, of course, is to operate all its waste disposal facilities so that public health and safety are not adversely affected. To ensure that this continues to be the case, activities are underway to increase use of waste form stabilization and engineered barriers where appropriate. For the sake of overall economy, these measures are to be applied as and where needed, through use of the systems approach. In this paper the author discusses two topics: the system approach, which DOE has decided to use for resolving waste disposal problems in the management of DOE's low-level wastes; and DOE's intended integration of activities underway at the waste management systems throughout DOE facilities. 2 figures

  16. Omics methods for probing the mode of action of natural phytotoxins

    Science.gov (United States)

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics...

  17. News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals

    Directory of Open Access Journals (Sweden)

    Simon Deusch

    2015-01-01

    This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.

  18. Dissecting Candida albicans Infection from the Perspective of C. albicans Virulence and Omics Approaches on Host–Pathogen Interaction: A Review

    Directory of Open Access Journals (Sweden)

    Voon Kin Chin

    2016-10-01

    Full Text Available Candida bloodstream infections remain the most frequent life-threatening fungal disease, with Candida albicans accounting for 70% to 80% of the Candida isolates recovered from infected patients. In nature, Candida species are part of the normal commensal flora in mammalian hosts. However, they can transform into pathogens once the host immune system is weakened or breached. More recently, mortality attributed to Candida infections has continued to increase due to both inherent and acquired drug resistance in Candida, the inefficacy of the available antifungal drugs, tedious diagnostic procedures, and a rising number of immunocompromised patients. Adoption of animal models, viz. minihosts, mice, and zebrafish, has brought us closer to unraveling the pathogenesis and complexity of Candida infection in human hosts, leading towards the discovery of biomarkers and identification of potential therapeutic agents. In addition, the advancement of omics technologies offers a holistic view of the Candida-host interaction in a non-targeted and non-biased manner. Hence, in this review, we seek to summarize past and present milestone findings on C. albicans virulence, adoption of animal models in the study of C. albicans infection, and the application of omics technologies in the study of Candida–host interaction. A profound understanding of the interaction between host defense and pathogenesis is imperative for better design of novel immunotherapeutic strategies in future.

  19. The nephrologist of tomorrow: towards a kidney-omic future.

    Science.gov (United States)

    Hanna, Mina H; Dalla Gassa, Alessandra; Mayer, Gert; Zaza, Gianluigi; Brophy, Patrick D; Gesualdo, Loreto; Pesce, Francesco

    2017-03-01

    Omics refers to the collective technologies used to explore the roles and relationships of the various types of molecules that make up the phenotype of an organism. Systems biology is a scientific discipline that endeavours to quantify all of the molecular elements of a biological system. Therefore, it reflects the knowledge acquired by omics in a meaningful manner by providing insights into functional pathways and regulatory networks underlying different diseases. The recent advances in biotechnological platforms and statistical tools to analyse such complex data have enabled scientists to connect the experimentally observed correlations to the underlying biochemical and pathological processes. We discuss in this review the current knowledge of different omics technologies in kidney diseases, specifically in the field of pediatric nephrology, including biomarker discovery, defining as yet unrecognized biologic therapeutic targets and linking omics to relevant standard indices and clinical outcomes. We also provide here a unique perspective on the field, taking advantage of the experience gained by the large-scale European research initiative called "Systems Biology towards Novel Chronic Kidney Disease Diagnosis and Treatment" (SysKid). Based on the integrative framework of Systems biology, SysKid demonstrated how omics are powerful yet complex tools to unravel the consequences of diabetes and hypertension on kidney function.

  20. From integrated control to integrated farming, an experimental approach

    NARCIS (Netherlands)

    Vereijken, P.H.

    1989-01-01

    Integrated control or integrated pest management (IPM), as envisaged originally, is not being practised to any large extent in arable farming, notwithstanding considerable research efforts. The reasons for this are discussed. A more basic approach called integrated farming is suggested. Preliminary

  1. Guiding recombinant antivenom development by omics technologies

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard

    2017-01-01

    directed towards the different omics technologies (particularly venomics, antivenomics, and toxicovenomics) that are being used to uncover novel animal toxins, shed light on venom complexity, and provide directions for how to determine the medical relevance of individual toxins within whole venoms. Finally......, endogenous animal proteins with toxin-neutralizing capabilities, and recombinant monoclonal antibodies. Harnessing either of these approaches, antivenom development may benefit from an in-depth understanding of venom compositions and the medical importance of individual venom toxins. Focus is thus also......, techniques for assessing antivenom specificity and cross-reactivity are reviewed, with special focus on antivenomics and high-density peptide microarray technology....

  2. Data integration approaches using ETL

    Directory of Open Access Journals (Sweden)

    Alexandra Maria Ioana FLOREA

    2016-01-01

    Full Text Available Traditional data warehouses and ETL tools have been slowly pushed to expand their limits as big data has become a more and more prominent actor on the analytics stage. This paper analyzes and compares the features of Pentaho Data Integration and Oracle Data Integrator, two of the main data integration platforms. Such tools are relevant in the context of the evolution of the analytics field, which is expanding from classical business intelligence activities to the use and analysis of big data.

  3. Reproducibility and Transparency of Omics Research - Impacts on Human Health Risk Assessment

    Science.gov (United States)

    Omics technologies are becoming more widely used in toxicology, necessitating their consideration in human health hazard and risk assessment programs. Today, risk assessors in the United States Environmental Protection Agency’s Integrated Risk Information System (IRIS) Toxicologi...

  4. Omics methods for probing the mode of action of natural and synthetic phytotoxins.

    Science.gov (United States)

    Duke, Stephen O; Bajsa, Joanna; Pan, Zhiqiang

    2013-02-01

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.

  5. Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

    Science.gov (United States)

    Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

    2017-03-01

    Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Chapter 3: Omics and the Future of Sustainable Biomaterials

    Science.gov (United States)

    Juliet D. Tang; Susan V. Diehl

    2014-01-01

    With global focus on the conversion of biomass into products, fuels, and energy, there is a strong need for information that will lead to new sustainable products, applications, and biotechnological advances. The omics approach to biology is a discovery-driven method that may deliver solutions to these overarching problems. It gives scientists the ability to obtain a...

  7. INTEGRATED EXPERIENCE APPROACH TO LEARNING.

    Science.gov (United States)

    POSTLETHWAIT, S.N.; AND OTHERS

    THE USE OF AUDIOTUTORIAL TECHNIQUES FOR TEACHING INTRODUCTORY COLLEGE BOTANY IS DESCRIBED. SPECIFIC PRACTICES USED AT PURDUE UNIVERSITY TO ILLUSTRATE DIFFERENT FACETS OF THE APPROACH ARE ANALYZED. INCLUDED ARE INDEPENDENT STUDY SESSIONS, SMALL ASSEMBLY SESSIONS, GENERAL ASSEMBLY SESSIONS, AND HOME STUDY SESSIONS. ILLUSTRATIONS AND SPECIFICATIONS…

  8. Integrative approaches to computational biomedicine

    Science.gov (United States)

    Coveney, Peter V.; Diaz-Zuccarini, Vanessa; Graf, Norbert; Hunter, Peter; Kohl, Peter; Tegner, Jesper; Viceconti, Marco

    2013-01-01

    The new discipline of computational biomedicine is concerned with the application of computer-based techniques and particularly modelling and simulation to human health. Since 2007, this discipline has been synonymous, in Europe, with the name given to the European Union's ambitious investment in integrating these techniques with the eventual aim of modelling the human body as a whole: the virtual physiological human. This programme and its successors are expected, over the next decades, to transform the study and practice of healthcare, moving it towards the priorities known as ‘4P's’: predictive, preventative, personalized and participatory medicine.

  9. Integrative medicine approach to chronic pain.

    Science.gov (United States)

    Teets, Raymond Y; Dahmer, Stephen; Scott, Emilie

    2010-06-01

    Chronic pain can be a frustrating condition for patient and clinician. The integrative medicine approach to pain can offer hope, adding safe complementary and alternative medical (CAM) therapies to mitigate pain and suffering. Such CAM therapies include nutrition, supplements and herbs, manual medicine, acupuncture, yoga, and mind-body approaches. The evidence is heterogeneous regarding these approaches, but some evidence suggests efficacy and confirms safety. The integrative medicine approach can be beneficial in a patient with chronic pain. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Statistical inference an integrated approach

    CERN Document Server

    Migon, Helio S; Louzada, Francisco

    2014-01-01

    Introduction Information The concept of probability Assessing subjective probabilities An example Linear algebra and probability Notation Outline of the bookElements of Inference Common statistical modelsLikelihood-based functions Bayes theorem Exchangeability Sufficiency and exponential family Parameter elimination Prior Distribution Entirely subjective specification Specification through functional forms Conjugacy with the exponential family Non-informative priors Hierarchical priors Estimation Introduction to decision theoryBayesian point estimation Classical point estimation Empirical Bayes estimation Comparison of estimators Interval estimation Estimation in the Normal model Approximating Methods The general problem of inference Optimization techniquesAsymptotic theory Other analytical approximations Numerical integration methods Simulation methods Hypothesis Testing Introduction Classical hypothesis testingBayesian hypothesis testing Hypothesis testing and confidence intervalsAsymptotic tests Prediction...

  11. Functional integral approach to classical statistical dynamics

    International Nuclear Information System (INIS)

    Jensen, R.V.

    1980-04-01

    A functional integral method is developed for the statistical solution of nonlinear stochastic differential equations which arise in classical dynamics. The functional integral approach provides a very natural and elegant derivation of the statistical dynamical equations that have been derived using the operator formalism of Martin, Siggia, and Rose

  12. Integration of electronic nose technology with spirometry: validation of a new approach for exhaled breath analysis

    NARCIS (Netherlands)

    de Vries, R.; Brinkman, P.; van der Schee, M. P.; Fens, N.; Dijkers, E.; Bootsma, S. K.; de Jongh, F. H. C.; Sterk, P. J.

    2015-01-01

    New 'omics'-technologies have the potential to better define airway disease in terms of pathophysiological and clinical phenotyping. The integration of electronic nose (eNose) technology with existing diagnostic tests, such as routine spirometry, can bring this technology to 'point-of-care'. We

  13. Toward an Integrated Psychological Approach - Phase II

    International Development Research Centre (IDRC) Digital Library (Canada)

    Trauma, Development and Peacebuilding : Toward an Integrated Psychological Approach - Phase II. Over the past decade, the peace, conflict and development community has begun to question the value of medicalized approaches such as post-traumatic stress disorder (PTSD) in dealing with aftermath of political violence ...

  14. Guiding recombinant antivenom development by omics technologies

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard

    2017-01-01

    , endogenous animal proteins with toxin-neutralizing capabilities, and recombinant monoclonal antibodies. Harnessing either of these approaches, antivenom development may benefit from an in-depth understanding of venom compositions and the medical importance of individual venom toxins. Focus is thus also...... directed towards the different omics technologies (particularly venomics, antivenomics, and toxicovenomics) that are being used to uncover novel animal toxins, shed light on venom complexity, and provide directions for how to determine the medical relevance of individual toxins within whole venoms. Finally......In this review, the different approaches that have been employed with the aim of developing novel antivenoms against animal envenomings are presented and discussed. Reported efforts have focused on the use of innovative immunization strategies, small molecule inhibitors against enzymatic toxins...

  15. OMICs technologies: tools for food science

    National Research Council Canada - National Science Library

    Benkeblia, Noureddine

    2012-01-01

    ... in the transformation from industrial to sustained food technologies and the role of these omics tools to mitigate the growing pressure of limited natural resources and environmental degradation...

  16. Curriculum Integration Using Enterprise Resource Planning: An Integrative Case Approach

    Science.gov (United States)

    Cannon, David M.; Klein, Helen A; Koste, Lori L.; Magal, Simha R.

    2004-01-01

    Efforts to achieve greater curriculum integration in schools of business have included team teaching, student group projects, multidisciplinary cases, and, more recently, the use of enterprise resource planning (ERP) systems. Although these approaches are beneficial, they tend to be implemented on an ad hoc basis rather than through curriculum…

  17. The Use of Omic Technologies Applied to Traditional Chinese Medicine Research

    Directory of Open Access Journals (Sweden)

    Dalinda Isabel Sánchez-Vidaña

    2017-01-01

    Full Text Available Natural products represent one of the most important reservoirs of structural and chemical diversity for the generation of leads in the drug development process. A growing number of researchers have shown interest in the development of drugs based on Chinese herbs. In this review, the use and potential of omic technologies as powerful tools in the modernization of traditional Chinese medicine are discussed. The analytical combination from each omic approach is crucial for understanding the working mechanisms of cells, tissues, organs, and organisms as well as the mechanisms of disease. Gradually, omic approaches have been introduced in every stage of the drug development process to generate high-quality Chinese medicine-based drugs. Finally, the future picture of the use of omic technologies is a promising tool and arena for further improvement in the modernization of traditional Chinese medicine.

  18. CANDU plant life management - An integrated approach

    International Nuclear Information System (INIS)

    Hopkins, J.R.

    1998-01-01

    An integrated approach to plant life management has been developed for CANDU reactors. Strategies, methods, and procedures have been developed for assessment of critical systems structures and components and for implementing a reliability centred maintenance program. A Technology Watch program is being implemented to eliminate 'surprises'. Specific work has been identified for 1998. AECL is working on the integrated program with CANDU owners and seeks participation from other CANDU owners

  19. Integration of metabolomics and transcriptomics in nanotoxicity studies.

    Science.gov (United States)

    Shin, Tae Hwan; Lee, Da Yeon; Lee, Hyeon-Seong; Park, Hyung Jin; Jin, Moon Suk; Paik, Man-Jeong; Manavalan, Balachandran; Mo, Jung-Soon; Lee, Gwang

    2018-01-01

    Biomedical research involving nanoparticles has produced useful products with medical applications. However, the potential toxicity of nanoparticles in biofluids, cells, tissues, and organisms is a major challenge. The '-omics' analyses provide molecular profiles of multifactorial biological systems instead of focusing on a single molecule. The 'omics' approaches are necessary to evaluate nanotoxicity because classical methods for the detection of nanotoxicity have limited ability in detecting miniscule variations within a cell and do not accurately reflect the actual levels of nanotoxicity. In addition, the 'omics' approaches allow analyses of in-depth changes and compensate for the differences associated with high-throughput technologies between actual nanotoxicity and results from traditional cytotoxic evaluations. However, compared with a single omics approach, integrated omics provides precise and sensitive information by integrating complex biological conditions. Thus, these technologies contribute to extended safety evaluations of nanotoxicity and allow the accurate diagnoses of diseases far earlier than was once possible in the nanotechnology era. Here, we review a novel approach for evaluating nanotoxicity by integrating metabolomics with metabolomic profiling and transcriptomics, which is termed "metabotranscriptomics". [BMB Reports 2018; 51(1): 14-20].

  20. The role of the clinician in the multi-omics era: are you ready?

    Science.gov (United States)

    van Karnebeek, Clara D M; Wortmann, Saskia B; Tarailo-Graovac, Maja; Langeveld, Mirjam; Ferreira, Carlos R; van de Kamp, Jiddeke M; Hollak, Carla E; Wasserman, Wyeth W; Waterham, Hans R; Wevers, Ron A; Haack, Tobias B; Wanders, Ronald J A; Boycott, Kym M

    2018-01-23

    Since Garrod's first description of alkaptonuria in 1902, and newborn screening for phenylketonuria introduced in the 1960s, P4 medicine (preventive, predictive, personalized, and participatory) has been a reality for the clinician serving patients with inherited metabolic diseases. The era of high-throughput technologies promises to accelerate its scale dramatically. Genomics, transcriptomics, epigenomics, proteomics, glycomics, metabolomics, and lipidomics offer an amazing opportunity for holistic investigation and contextual pathophysiologic understanding of inherited metabolic diseases for precise diagnosis and tailored treatment. While each of the -omics technologies is important to systems biology, some are more mature than others. Exome sequencing is emerging as a reimbursed test in clinics around the world, and untargeted metabolomics has the potential to serve as a single biochemical testing platform. The challenge lies in the integration and cautious interpretation of these big data, with translation into clinically meaningful information and/or action for our patients. A daunting but exciting task for the clinician; we provide clinical cases to illustrate the importance of his/her role as the connector between physicians, laboratory experts and researchers in the basic, computer, and clinical sciences. Open collaborations, data sharing, functional assays, and model organisms play a key role in the validation of -omics discoveries. Having all the right expertise at the table when discussing the diagnostic approach and individualized management plan according to the information yielded by -omics investigations (e.g., actionable mutations, novel therapeutic interventions), is the stepping stone of P4 medicine. Patient participation and the adjustment of the medical team's plan to his/her and the family's wishes most certainly is the capstone. Are you ready?

  1. Integrated Approach to User Account Management

    Science.gov (United States)

    Kesselman, Glenn; Smith, William

    2007-01-01

    IT environments consist of both Windows and other platforms. Providing user account management for this model has become increasingly diffi cult. If Microsoft#s Active Directory could be enhanced to extend a W indows identity for authentication services for Unix, Linux, Java and Macintosh systems, then an integrated approach to user account manag ement could be realized.

  2. Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

    Science.gov (United States)

    Wu, Yibo; Williams, Evan G.; Dubuis, Sébastien; Mottis, Adrienne; Jovaisaite, Virginija; Houten, Sander M.; Argmann, Carmen A.; Faridi, Pouya; Wolski, Witold; Kutalik, Zoltán; Zamboni, Nicola; Auwerx, Johan; Aebersold, Ruedi

    2014-01-01

    SUMMARY The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome—a subset of the metabolome—and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPRmt). UPRmt shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes. PMID:25215496

  3. Statistical inference an integrated Bayesianlikelihood approach

    CERN Document Server

    Aitkin, Murray

    2010-01-01

    Filling a gap in current Bayesian theory, Statistical Inference: An Integrated Bayesian/Likelihood Approach presents a unified Bayesian treatment of parameter inference and model comparisons that can be used with simple diffuse prior specifications. This novel approach provides new solutions to difficult model comparison problems and offers direct Bayesian counterparts of frequentist t-tests and other standard statistical methods for hypothesis testing.After an overview of the competing theories of statistical inference, the book introduces the Bayes/likelihood approach used throughout. It pre

  4. THE FEMINIST APPROACH TO PSYCHOTHERAPY INTEGRATION

    Directory of Open Access Journals (Sweden)

    Lorena Božac Deležan

    2011-12-01

    Full Text Available The goal of Integrative Psychotherapy is to establish full inner and external contact (Moursund & Erskine, 2004. The most important goal in feminist therapy is the transformation of an individual as well as the transformation of the society as a whole (Herlihy & Corey, 2004. In my work I attempt to integrate both: to help the client establish inner and external contact, but also help him/her to become aware and recognize inner messages connected with his/her gender and replace them with constructive beliefs of his/her own, as well as for him/her to learn, regardless of his/her gender, to trust his/her intuition and experience. In this article I present my approach to integration in psychotherapy and the way I use feminist principles in Integrative Psychotherapy.

  5. Performance improvement integration: a whole systems approach.

    Science.gov (United States)

    Page, C K

    1999-02-01

    Performance improvement integration in health care organizations is a challenge for health care leaders. Required for accreditation by the Joint Commission on Accreditation of Healthcare Organizations (Joint Commission), performance improvement (PI) can be designed as a sustainable model for performance to survive in a turbulent period. Central Baptist Hospital developed a model for PI that focused on strategy established by the leadership team, delineated responsibility through the organizational structure of shared governance, and accountability for outcomes evidenced through the organization's profitability. Such an approach integrated into the culture of the organization can produce positive financial margins, positive customer satisfaction, and commendations from the Joint Commission.

  6. FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.

    Directory of Open Access Journals (Sweden)

    Takeru Uchiyama

    Full Text Available Exponential growth of high-throughput data and the increasing complexity of omics information have been making processing and interpreting biological data an extremely difficult and daunting task. Here we developed FuncTree (http://bioviz.tokyo/functree, a web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data. FuncTree allows user to map their omics data onto the "Functional Tree map", a predefined circular dendrogram, which represents the hierarchical relationship of all known biological functions defined in the KEGG database. This novel visualization method allows user to overview the broad functionality of their data, thus allowing a more accurate and comprehensive understanding of the omics information. FuncTree provides extensive customization and calculation methods to not only allow user to directly map their omics data to identify the functionality of their data, but also to compute statistically enriched functions by comparing it to other predefined omics data. We have validated FuncTree's analysis and visualization capability by mapping pan-genomic data of three different types of bacterial genera, metagenomic data of the human gut, and transcriptomic data of two different types of human cell expression. All three mapping strongly confirms FuncTree's capability to analyze and visually represent key functional feature of the omics data. We believe that FuncTree's capability to conduct various functional calculations and visualizing the result into a holistic overview of biological function, would make it an integral analysis/visualization tool for extensive omics base research.

  7. The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.; Köberl, Martina; Bilbao, Aivett; Colby, Sean M.; Hoyt, David W.; Bingol, Kerem; Kim, Young-Mo; Wendler, Jason P.; Hixson, Kim K.; Jansson, Christer

    2017-06-01

    Over the past century, the significance of the rhizosphere as a complex, biological system, comprised of vast, interconnected networks of microbial organisms that interact directly with their plant hosts (e.g., archæa, bacteria, fungi, eukaryotes, and viruses) has been increasingly recognized by the scientific community. Providing a nutritional base to the terrestrial biosphere, the rhizosphere is integral to plant growth, crop production and ecosystem health. Lack of mechanistic understanding of the rhizosphere constitutes a critical knowledge gap, inhibiting our ability to predict and control the terrestrial ecosystem in order to achieve desirable outcomes (e.g., bioenergy production, crop yield maximization, and soilbased carbon sequestration). Application of multi-omics has the potential to significantly advance our knowledge of rhizospheric science. This review covers: cutting- and bleeding-edge, multi-omic techniques and technologies; methods and protocols for specific rhizospheric science questions; and, challenges to be addressed during this century of rhizospheric science.

  8. Introduction to solid mechanics an integrated approach

    CERN Document Server

    Lubliner, Jacob

    2017-01-01

    This expanded second edition presents in one text the concepts and processes covered in statics and mechanics of materials curricula following a systematic, topically integrated approach. Building on the novel pedagogy of fusing concepts covered in traditional undergraduate courses in rigid-body statics and deformable body mechanics, rather than simply grafting them together, this new edition develops further the authors’ very original treatment of solid mechanics with additional figures, an elaboration on selected solved problems, and additional text as well as a new subsection on viscoelasticity in response to students’ feedback. Introduction to Solid Mechanics: An Integrated Approach, Second Edition, offers a holistic treatment of the depth and breadth of solid mechanics and the inter-relationships of its underlying concepts. Proceeding from first principles to applications, the book stands as a whole greater than the sum of its parts.  .

  9. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

    Science.gov (United States)

    Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

    2016-01-01

    We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

  10. Multi-omic integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in Type 2 diabetic obesity.

    Science.gov (United States)

    Rowlands, David S; Page, Rachel A; Sukala, William R; Giri, Mamta; Ghimbovschi, Svetlana D; Hayat, Irum; Cheema, Birinder S; Lys, Isabelle; Leikis, Murray; Sheard, Phillip W; Wakefield, St John; Breier, Bernhard; Hathout, Yetrib; Brown, Kristy; Marathi, Ramya; Orkunoglu-Suer, Funda E; Devaney, Joseph M; Leiken, Benjamin; Many, Gina; Krebs, Jeremy; Hopkins, Will G; Hoffman, Eric P

    2014-10-15

    Epigenomic regulation of the transcriptome by DNA methylation and posttranscriptional gene silencing by miRNAs are potential environmental modulators of skeletal muscle plasticity to chronic exercise in healthy and diseased populations. We utilized transcriptome networks to connect exercise-induced differential methylation and miRNA with functional skeletal muscle plasticity. Biopsies of the vastus lateralis were collected from middle-aged Polynesian men and women with morbid obesity (44 kg/m(2) ± 10) and Type 2 diabetes before and following 16 wk of resistance (n = 9) or endurance training (n = 8). Longitudinal transcriptome, methylome, and microRNA (miRNA) responses were obtained via microarray, filtered by novel effect-size based false discovery rate probe selection preceding bioinformatic interrogation. Metabolic and microvascular transcriptome topology dominated the network landscape following endurance exercise. Lipid and glucose metabolism modules were connected to: microRNA (miR)-29a; promoter region hypomethylation of nuclear receptor factor (NRF1) and fatty acid transporter (SLC27A4), and hypermethylation of fatty acid synthase, and to exon hypomethylation of 6-phosphofructo-2-kinase and Ser/Thr protein kinase. Directional change in the endurance networks was validated by lower intramyocellular lipid, increased capillarity, GLUT4, hexokinase, and mitochondrial enzyme activity and proteome. Resistance training also lowered lipid and increased enzyme activity and caused GLUT4 promoter hypomethylation; however, training was inconsequential to GLUT4, capillarity, and metabolic transcriptome. miR-195 connected to negative regulation of vascular development. To conclude, integrated molecular network modelling revealed differential DNA methylation and miRNA expression changes occur in skeletal muscle in response to chronic exercise training that are most pronounced with endurance training and topographically associated with functional metabolic and

  11. Addressing uncertainties in the ERICA Integrated Approach

    International Nuclear Information System (INIS)

    Oughton, D.H.; Agueero, A.; Avila, R.; Brown, J.E.; Copplestone, D.; Gilek, M.

    2008-01-01

    Like any complex environmental problem, ecological risk assessment of the impacts of ionising radiation is confounded by uncertainty. At all stages, from problem formulation through to risk characterisation, the assessment is dependent on models, scenarios, assumptions and extrapolations. These include technical uncertainties related to the data used, conceptual uncertainties associated with models and scenarios, as well as social uncertainties such as economic impacts, the interpretation of legislation, and the acceptability of the assessment results to stakeholders. The ERICA Integrated Approach has been developed to allow an assessment of the risks of ionising radiation, and includes a number of methods that are intended to make the uncertainties and assumptions inherent in the assessment more transparent to users and stakeholders. Throughout its development, ERICA has recommended that assessors deal openly with the deeper dimensions of uncertainty and acknowledge that uncertainty is intrinsic to complex systems. Since the tool is based on a tiered approach, the approaches to dealing with uncertainty vary between the tiers, ranging from a simple, but highly conservative screening to a full probabilistic risk assessment including sensitivity analysis. This paper gives on overview of types of uncertainty that are manifest in ecological risk assessment and the ERICA Integrated Approach to dealing with some of these uncertainties

  12. Multi-platform ’Omics Analysis of Human Ebola Virus Disease Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Eisfeld, Amie J.; Halfmann, Peter J.; Wendler, Jason P.; Kyle, Jennifer E.; Burnum-Johnson, Kristin E.; Peralta, Zuleyma; Maemura, Tadashi; Walters, Kevin B.; Watanabe, Tokiko; Fukuyama, Satoshi; Yamashita, Makoto; Jacobs, Jon M.; Kim, Young-Mo; Casey, Cameron P.; Stratton, Kelly G.; Webb-Robertson, Bobbie-Jo M.; Gritsenko, Marina A.; Monroe, Matthew E.; Weitz, Karl K.; Shukla, Anil K.; Tian, Mingyuan; Neumann, Gabriele; Reed, Jennifer L.; van Bakel, Harm; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; N' jai, Alhaji; Sahr, Foday; Kawaoka, Yoshihiro

    2017-12-01

    The pathogenesis of human Ebola virus disease (EVD) is complex. EVD is characterized by high levels of virus replication and dissemination, dysregulated immune responses, extensive virus- and host-mediated tissue damage, and disordered coagulation. To clarify how host responses contribute to EVD pathophysiology, we performed multi-platform ’omics analysis of peripheral blood mononuclear cells and plasma from EVD patients. Our results indicate that EVD molecular signatures overlap with those of sepsis, imply that pancreatic enzymes contribute to tissue damage in fatal EVD, and suggest that Ebola virus infection may induce aberrant neutrophils whose activity could explain hallmarks of fatal EVD. Moreover, integrated biomarker prediction identified putative biomarkers from different data platforms that differentiated survivors and fatalities early after infection. This work reveals insight into EVD pathogenesis, suggests an effective approach for biomarker identification, and provides an important community resource for further analysis of human EVD severity.

  13. Integration models: multicultural and liberal approaches confronted

    Science.gov (United States)

    Janicki, Wojciech

    2012-01-01

    European societies have been shaped by their Christian past, upsurge of international migration, democratic rule and liberal tradition rooted in religious tolerance. Boosting globalization processes impose new challenges on European societies, striving to protect their diversity. This struggle is especially clearly visible in case of minorities trying to resist melting into mainstream culture. European countries' legal systems and cultural policies respond to these efforts in many ways. Respecting identity politics-driven group rights seems to be the most common approach, resulting in creation of a multicultural society. However, the outcome of respecting group rights may be remarkably contradictory to both individual rights growing out from liberal tradition, and to reinforced concept of integration of immigrants into host societies. The hereby paper discusses identity politics upturn in the context of both individual rights and integration of European societies.

  14. Introduction to solid mechanics an integrated approach

    CERN Document Server

    Lubliner, Jacob

    2014-01-01

    This textbook presents for the first time in one text the concepts and processes covered in statics and mechanics of materials curricula following a systematic, topically integrated approach. Since the turn of the millennium, it has become common in engineering schools to combine the traditional undergraduate offerings in rigid-body statics (usually called “statics”) and deformable body mechanics (known traditionally as “strength of materials” or, more recently, “mechanics of materials”) into a single, introductory course in solid mechanics. Many textbooks for the new course sequentially meld pieces of existing, discrete books—sometimes, but not always, acknowledging the origin—into two halves covering Statics and Mechanics of Materials. In this volume, Professors Lubliner and Papadopoulos methodically combine the essentials of statics and mechanics of materials, illustrating the relationship of concepts throughout, into one "integrated" text. This book also: ·         Offers thorough...

  15. Pedagogic process modeling: Humanistic-integrative approach

    Directory of Open Access Journals (Sweden)

    Boritko Nikolaj M.

    2007-01-01

    Full Text Available The paper deals with some current problems of modeling the dynamics of the subject-features development of the individual. The term "process" is considered in the context of the humanistic-integrative approach, in which the principles of self education are regarded as criteria for efficient pedagogic activity. Four basic characteristics of the pedagogic process are pointed out: intentionality reflects logicality and regularity of the development of the process; discreteness (stageability in dicates qualitative stages through which the pedagogic phenomenon passes; nonlinearity explains the crisis character of pedagogic processes and reveals inner factors of self-development; situationality requires a selection of pedagogic conditions in accordance with the inner factors, which would enable steering the pedagogic process. Offered are two steps for singling out a particular stage and the algorithm for developing an integrative model for it. The suggested conclusions might be of use for further theoretic research, analyses of educational practices and for realistic predicting of pedagogical phenomena. .

  16. FUPOL: an Integrated Approach to Participative Policies

    Directory of Open Access Journals (Sweden)

    Silvana Tomic Rotim

    2014-05-01

    Full Text Available The Future Policy Modelling Project (FUPOL is a research project funded by the 7th framework program of the European Union. Its research focus are new technologies and methods for e-governance, e-participation and policy modelling. The FUPOL consortium consists of partners from European countries, China and Kenya. and comprises innovative multinational companies, leading research institutes, high-level political organizations as well as strong pilot partners. This paper describes the FUPOL new integrated approach to policy design and implementation including also specific examples from real life pilots in cities from different countries. FUPOL consists of an advanced policy lifecycle and an IT-solution with features supporting all phases of the proposed lifecycle. The FUPOL concept and functional modules as well as the technical architecture to achieve such a complete integration are described.

  17. Advances in Ecological Speciation: an integrative approach.

    Science.gov (United States)

    Faria, Rui; Renaut, Sebastien; Galindo, Juan; Pinho, Catarina; Melo-Ferreira, José; Melo, Martim; Jones, Felicity; Salzburger, Walter; Schluter, Dolph; Butlin, Roger

    2014-02-01

    The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference 'Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation. © 2013 John Wiley & Sons Ltd.

  18. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    Science.gov (United States)

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  19. Molecular signatures from omics data: from chaos to consensus.

    Science.gov (United States)

    Sung, Jaeyun; Wang, Yuliang; Chandrasekaran, Sriram; Witten, Daniela M; Price, Nathan D

    2012-08-01

    In the past 15 years, new "omics" technologies have made it possible to obtain high-resolution molecular snapshots of organisms, tissues, and even individual cells at various disease states and experimental conditions. It is hoped that these developments will usher in a new era of personalized medicine in which an individual's molecular measurements are used to diagnose disease, guide therapy, and perform other tasks more accurately and effectively than is possible using standard approaches. There now exists a vast literature of reported "molecular signatures". However, despite some notable exceptions, many of these signatures have suffered from limited reproducibility in independent datasets, insufficient sensitivity or specificity to meet clinical needs, or other challenges. In this paper, we discuss the process of molecular signature discovery on the basis of omics data. In particular, we highlight potential pitfalls in the discovery process, as well as strategies that can be used to increase the odds of successful discovery. Despite the difficulties that have plagued the field of molecular signature discovery, we remain optimistic about the potential to harness the vast amounts of available omics data in order to substantially impact clinical practice. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. DTW4Omics: comparing patterns in biological time series.

    Directory of Open Access Journals (Sweden)

    Rachel Cavill

    Full Text Available When studying time courses of biological measurements and comparing these to other measurements eg. gene expression and phenotypic endpoints, the analysis is complicated by the fact that although the associated elements may show the same patterns of behaviour, the changes do not occur simultaneously. In these cases standard correlation-based measures of similarity will fail to find significant associations. Dynamic time warping (DTW is a technique which can be used in these situations to find the optimal match between two time courses, which may then be assessed for its significance. We implement DTW4Omics, a tool for performing DTW in R. This tool extends existing R scripts for DTW making them applicable for "omics" datasets where thousands entities may need to be compared with a range of markers and endpoints. It includes facilities to estimate the significance of the matches between the supplied data, and provides a set of plots to enable the user to easily visualise the output. We illustrate the utility of this approach using a dataset linking the exposure of the colon carcinoma Caco-2 cell line to oxidative stress by hydrogen peroxide (H2O2 and menadione across 9 timepoints and show that on average 85% of the genes found are not obtained from a standard correlation analysis between the genes and the measured phenotypic endpoints. We then show that when we analyse the genes identified by DTW4Omics as significantly associated with a marker for oxidative DNA damage (8-oxodG, through over-representation, an Oxidative Stress pathway is identified as the most over-represented pathway demonstrating that the genes found by DTW4Omics are biologically relevant. In contrast, when the positively correlated genes were similarly analysed, no pathways were found. The tool is implemented as an R Package and is available, along with a user guide from http://web.tgx.unimaas.nl/svn/public/dtw/.

  1. Use of Metabolomics as a Complementary Omic Approach to Implement Risk Criteria for First-Degree Relatives of Gastric Cancer Patients

    Directory of Open Access Journals (Sweden)

    Giuseppe Corona

    2018-03-01

    Full Text Available A positive family history is a strong and consistently reported risk factor for gastric cancer (GC. So far, it has been demonstrated that serum pepsinogens (PGs, and gastrin 17 (G17 are useful for screening individuals at elevated risk to develop atrophic gastritis but they are suboptimal biomarkers to screen individuals for GC. The main purpose of this study was to investigate serum metabolomic profiles to find additional biomarkers that could be integrated with serum PGs and G17 to improve the diagnosis of GC and the selection of first-degree relatives (FDR at higher risk of GC development. Serum metabolomic profiles included 188 serum metabolites, covering amino acids, biogenic amines, acylcarnitines, phosphatidylcholines, sphingomyelins and hexoses. Serum metabolomic profiles were performed with tandem mass spectrometry using the Biocrates AbsoluteIDQ p180 kit. The initial cohort (training set consisted of n = 49 GC patients and n = 37 FDR. Differential metabolomic signatures among the two groups were investigated by univariate and multivariate partial least square differential analysis. The most significant metabolites were further selected and validated in an independent group of n = 22 GC patients and n = 17 FDR (validation set. Receiver operating characteristic (ROC curves were used to evaluate the diagnostic power and the optimal cut-off for each of the discriminant markers. Multivariate analysis was applied to associate the selected serum metabolites, PGs, G17 and risk factors such as age, gender and Helicobacter pylori (H. pylori infection with the GC and FDR has been performed and an integrative risk prediction algorithm was developed. In the training set, 40 metabolites mainly belonging to phospholipids and acylcarnitines classes were differentially expressed between GC and FDR. Out of these 40 metabolites, 9 were further confirmed in the validation set. Compared with FDR, GC patients were characterized by lower levels of

  2. APPROACH FOR IMPROVING THE INTEGRATED SENSOR ORIENTATION

    Directory of Open Access Journals (Sweden)

    E. Mitishita

    2016-06-01

    Full Text Available The direct determination of exterior orientation parameters (EOP of aerial images via integration of the Inertial Measurement Unit (IMU and GPS is often used in photogrammetric mapping nowadays. The accuracies of the EOP depend on the accurate parameters related to sensors mounting when the job is performed (offsets of the IMU relative to the projection centre and the angles of boresigth misalignment between the IMU and the photogrammetric coordinate system. In principle, when the EOP values do not achieve the required accuracies for the photogrammetric application, the approach, known as Integrated Sensor Orientation (ISO, is used to refine the direct EOP. ISO approach requires accurate Interior Orientation Parameters (IOP and standard deviation of the EOP under flight condition. This paper investigates the feasibility of use the in situ camera calibration to obtain these requirements. The camera calibration uses a small sub block of images, extracted from the entire block. A digital Vexcel UltraCam XP camera connected to APPLANIX POS AVTM system was used to get two small blocks of images that were use in this study. The blocks have different flight heights and opposite flight directions. The proposed methodology improved significantly the vertical and horizontal accuracies of the 3D point intersection. Using a minimum set of control points, the horizontal and vertical accuracies achieved nearly one image pixel of resolution on the ground (GSD. The experimental results are shown and discussed.

  3. Healing and Preventing Pain: Complementary and Integrative Approaches

    Science.gov (United States)

    ... page please turn JavaScript on. Feature: Pain Management Healing and Preventing Pain, Complementary and Integrative Approaches Past ... Pain Management" Articles Putting A Pause In Pain / Healing and Preventing Pain Complementary and Integrative Approaches / Pain ...

  4. A community proposal to integrate proteomics activities in ELIXIR

    NARCIS (Netherlands)

    Vizcaíno, Juan Antonio; Walzer, Mathias; Jiménez, Rafael C; Bittremieux, Wout; Bouyssié, David; Carapito, Christine; Corrales, Fernando; Ferro, Myriam; Heck, Albert J R; Horvatovich, Peter; Hubalek, Martin; Lane, Lydie; Laukens, Kris; Levander, Fredrik; Lisacek, Frederique; Novak, Petr; Palmblad, Magnus; Piovesan, Damiano; Pühler, Alfred; Schwämmle, Veit; Valkenborg, Dirk; van Rijswijk, Merlijn; Vondrasek, Jiri; Eisenacher, Martin; Martens, Lennart; Kohlbacher, Oliver

    2017-01-01

    Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this

  5. Data mining in newt-omics, the repository for omics data from the newt.

    Science.gov (United States)

    Looso, Mario; Braun, Thomas

    2015-01-01

    Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of "omics" studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface ( http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.

  6. 2. Gestaltdrama as an Integrative Psychotherapeutic Approach

    Directory of Open Access Journals (Sweden)

    Polínek Martin Dominik

    2016-03-01

    Full Text Available The following text is an overview study which defines the basic phenomena and effective factors of Gestalt drama and outlines some of the researches carried out in this area by the author during recent years. Gestalt drama is the name of a specific psychotherapeutic approach applied by the author in his practice, which combines Gestalt therapy with expressive approaches (especially with dramatherapy, theatrotherapy and fairytale-therapy. Linking Gestalt therapy and expressive techniques results in a specific psychotherapeutic approach whose versatility and holistic conception makes it suitable not only for psychotherapy but also for self-development of people with special needs, as it has the potential to meet the higher psychological needs even when the lower needs are not sufficiently saturated. The article further presents the interpretation of the partial results of research focusing on the analysis of integration performance where gestaltdrama techniques have been applied. These performances resulted from one-day dramatherapy workshops with clients suffering from mental retardation and with clients with behavioural disorders. This includes the analysis of differences between dramatical expression within the above target groups.

  7. Unsupervised multiple kernel learning for heterogeneous data integration.

    Science.gov (United States)

    Mariette, Jérôme; Villa-Vialaneix, Nathalie

    2018-03-15

    Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account. We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during the TARA Oceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single kernel PCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpretability of the kernel PCA in regards with the original data. Second, the multi-omics breast cancer datasets, provided by The Cancer Genome Atlas, is analysed using a kernel Self-Organizing Maps with both single and multi-omics strategies. The comparison of these two approaches demonstrates the benefit of our integration method to improve the representation of the studied biological system. Proposed methods are available in the R package mixKernel, released on CRAN. It is fully compatible with the mixOmics package and a tutorial describing the approach can be found on mixOmics web site http://mixomics.org/mixkernel/. jerome.mariette@inra.fr or nathalie.villa-vialaneix@inra.fr. Supplementary data are available at Bioinformatics online.

  8. Permutation statistical methods an integrated approach

    CERN Document Server

    Berry, Kenneth J; Johnston, Janis E

    2016-01-01

    This research monograph provides a synthesis of a number of statistical tests and measures, which, at first consideration, appear disjoint and unrelated. Numerous comparisons of permutation and classical statistical methods are presented, and the two methods are compared via probability values and, where appropriate, measures of effect size. Permutation statistical methods, compared to classical statistical methods, do not rely on theoretical distributions, avoid the usual assumptions of normality and homogeneity of variance, and depend only on the data at hand. This text takes a unique approach to explaining statistics by integrating a large variety of statistical methods, and establishing the rigor of a topic that to many may seem to be a nascent field in statistics. This topic is new in that it took modern computing power to make permutation methods available to people working in the mainstream of research. This research monograph addresses a statistically-informed audience, and can also easily serve as a ...

  9. Thermodynamics and statistical mechanics an integrated approach

    CERN Document Server

    Shell, M Scott

    2015-01-01

    Learn classical thermodynamics alongside statistical mechanics with this fresh approach to the subjects. Molecular and macroscopic principles are explained in an integrated, side-by-side manner to give students a deep, intuitive understanding of thermodynamics and equip them to tackle future research topics that focus on the nanoscale. Entropy is introduced from the get-go, providing a clear explanation of how the classical laws connect to the molecular principles, and closing the gap between the atomic world and thermodynamics. Notation is streamlined throughout, with a focus on general concepts and simple models, for building basic physical intuition and gaining confidence in problem analysis and model development. Well over 400 guided end-of-chapter problems are included, addressing conceptual, fundamental, and applied skill sets. Numerous worked examples are also provided together with handy shaded boxes to emphasize key concepts, making this the complete teaching package for students in chemical engineer...

  10. Stakeholder interaction within the ERICA Integrated Approach.

    Science.gov (United States)

    Zinger, I; Oughton, D H; Jones, S R

    2008-09-01

    Within the ERICA project, stakeholder involvement has been addressed within three main areas: generic interactions throughout the project, specific consultation by means of attendance to events and considerations as part of the ERICA Integrated Approach and Assessment Tool. The word stakeholders meant namely any individual or group who may be affected by or have an interest in an issue, and to include experts, lay-people and the public. An End-Users-Group (EUG) was set up to facilitate the two-way dialogue between the ERICA Consortium and stakeholders. The ERICA EUG consisted of representatives of 60 organisations ranging from regulatory bodies, national advisory bodies, academia, non-governmental organisations, industry, consultants and inter-governmental organisations. Stakeholder interaction was included from the very start of the project. Inputs from the EUG were recorded and in most instances incorporated within the development of the project and thus influenced and helped to shape some of the ERICA deliverables.

  11. MODELS OF TECHNOLOGY ADOPTION: AN INTEGRATIVE APPROACH

    Directory of Open Access Journals (Sweden)

    Andrei OGREZEANU

    2015-06-01

    Full Text Available The interdisciplinary study of information technology adoption has developed rapidly over the last 30 years. Various theoretical models have been developed and applied such as: the Technology Acceptance Model (TAM, Innovation Diffusion Theory (IDT, Theory of Planned Behavior (TPB, etc. The result of these many years of research is thousands of contributions to the field, which, however, remain highly fragmented. This paper develops a theoretical model of technology adoption by integrating major theories in the field: primarily IDT, TAM, and TPB. To do so while avoiding mess, an approach that goes back to basics in independent variable type’s development is proposed; emphasizing: 1 the logic of classification, and 2 psychological mechanisms behind variable types. Once developed these types are then populated with variables originating in empirical research. Conclusions are developed on which types are underpopulated and present potential for future research. I end with a set of methodological recommendations for future application of the model.

  12. Integrating systems Approaches into Pharmaceutical Sciences

    DEFF Research Database (Denmark)

    Westerhoff, H.V.; Mosekilde, Erik; Noe, C. R.

    2008-01-01

    During the first week of December 2007, the European Federation for Pharmaceutical Sciences (EUFEPS) and BioSim, the major European Network of Excellence on Systems Biology, held a challenging conference on the use of mathematical models in the drug development process. More precisely, the purpose...... of the conference was to promote the ‘Integration of Systems Approaches into Pharmaceutical Sciences’ in view of optimising the development of new effective drugs. And a challenge this is, considering both the high attrition rates in the pharmaceutical industry and the failure of finding definitive drug solutions...... for many of the diseases that plague mankind today. The conference was co-sponsored by the American College of Clinical Pharmacology, the European Center for Pharmaceutical Medicine, and the Swiss Society of Pharmaceutical Sciences and, besides representatives from the European Regulatory Agencies and FDA...

  13. Systematic Approach to Better Understanding Integration Costs

    Energy Technology Data Exchange (ETDEWEB)

    Stark, Gregory B. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    This research presents a systematic approach to evaluating the costs of integrating new generation and operational procedures into an existing power system, and the methodology is independent of the type of change or nature of the generation. The work was commissioned by the U.S. Department of Energy and performed by the National Renewable Energy Laboratory to investigate three integration cost-related questions: (1) How does the addition of new generation affect a system's operational costs, (2) How do generation mix and operating parameters and procedures affect costs, and (3) How does the amount of variable generation (non-dispatchable wind and solar) impact the accuracy of natural gas orders? A detailed operational analysis was performed for seven sets of experiments: variable generation, large conventional generation, generation mix, gas prices, fast-start generation, self-scheduling, and gas supply constraints. For each experiment, four components of integration costs were examined: cycling costs, non-cycling VO&M costs, fuel costs, and reserves provisioning costs. The investigation was conducted with PLEXOS production cost modeling software utilizing an updated version of the Institute of Electrical and Electronics Engineers 118-bus test system overlaid with projected operating loads from the Western Electricity Coordinating Council for the Sacramento Municipal Utility District, Puget Sound Energy, and Public Service Colorado in the year 2020. The test system was selected in consultation with an industry-based technical review committee to be a reasonable approximation of an interconnection yet small enough to allow the research team to investigate a large number of scenarios and sensitivity combinations. The research should prove useful to market designers, regulators, utilities, and others who want to better understand how system changes can affect production costs.

  14. Quantum gravitation. The Feynman path integral approach

    International Nuclear Information System (INIS)

    Hamber, Herbert W.

    2009-01-01

    The book covers the theory of Quantum Gravitation from the point of view of Feynman path integrals. These provide a manifestly covariant approach in which fundamental quantum aspects of the theory such as radiative corrections and the renormalization group can be systematically and consistently addressed. The path integral method is suitable for both perturbative as well as non-perturbative studies, and is known to already provide a framework of choice for the theoretical investigation of non-abelian gauge theories, the basis for three of the four known fundamental forces in nature. The book thus provides a coherent outline of the present status of the theory gravity based on Feynman's formulation, with an emphasis on quantitative results. Topics are organized in such a way that the correspondence to similar methods and results in modern gauge theories becomes apparent. Covariant perturbation theory are developed using the full machinery of Feynman rules, gauge fixing, background methods and ghosts. The renormalization group for gravity and the existence of non-trivial ultraviolet fixed points are investigated, stressing a close correspondence with well understood statistical field theory models. Later the lattice formulation of gravity is presented as an essential tool towards an understanding of key features of the non-perturbative vacuum. The book ends with a discussion of contemporary issues in quantum cosmology such as scale dependent gravitational constants and quantum effects in the early universe. (orig.)

  15. Linking Ecological, Environmental and Biogeochemical Data with Multi'omics Analysis

    Science.gov (United States)

    Hasler-Sheetal, H.; Castorani, M. C.; Fragner, L.; Zeng, Y.; Holmer, M.; Glud, R. N.; Weckwerth, W.; Canfield, D. E.

    2016-02-01

    The integrated analysis of multi'omics and environmental data provides a holistic understanding of biological processes and has been proven to be challenging. Here we present our research concept for conducting multi-omics experiments and linking them to environmental data. Hypoxia, reduced light availability and species interaction - all amplified by global warming - cause a global decline of seagrasses. Metabolic mechanisms for coping with these global threats are largely unknown and multi'omics approaches can be an important approach for generating this insight. We applied GC, LC-qTOF-MS and bioinformatics to investigate the effects of environmental pressure on metabolites present in seagrasses. In a first experiment we assessed the metabolomics response of the seagrass Zostera marina towards anoxia and showed that photosynthetically derived oxygen could satisfy the oxygen demand in the leaves. But accumulation of fermentation products in the roots showed that the rhizosphere was under anoxic stress. In contrast nocturnal anoxia caused a biphasic shift in the metabolome of roots and leaves. This nocturnal reprogramming of the metabolome under anoxia indicates a mitigation mechanism to avoid the toxic effects. A pathway enrichment analysis proposes the alanine shunt, the GABA shunt and the 2-oxoglutarate shunt as such mitigation mechanisms that alleviate pyruvate levels and lead to carbon and nitrogen storage during anoxia. In a second experiment, varying light exposure and species interaction of Z. marina with the blue mussel Mytilus edulis - a co-occurring species in seagrass systems - resulted in treatment specific metabolic fingerprints in seagrass. Light modified the metabolic fingerprint expressed in Z. marina to the presence of mussels, indicating varying physiological responses to mussels in normal and low light regimes. Multivariate data-analysis indicated light exposure as main driver (45%) and mussel presence as minor driver (13%) for the metabolic

  16. Pressure Shell Approach to Integrated Environmental Protection

    Science.gov (United States)

    Kennedy, Kriss J.

    2011-01-01

    The next generation of exploration mission human systems will require environmental protection such as radiation protection that is effective and efficient. In order to continue human exploration, habitat systems will require special shells to protect astronauts from hostile environments. The Pressure Shell Approach to integrated environmental (radiation) protection is a multi-layer shell that can be used for multifunctional environmental protection. Self-healing, self-repairing nano technologies and sensors are incorporated into the shell. This shell consists of multiple layers that can be tailored for specific environmental protection needs. Mainly, this innovation focuses on protecting crew from exposure to micrometeorites, thermal, solar flares, and galactic cosmic ray (GCR) radiation. The Pressure Shell Approach consists of a micrometeoroid and secondary ejecta protection layer; a thin, composite shell placed in between two layers that is non-structural; an open cavity layer that can be filled with water, regolith, or polyethylene foam; a thicker composite shell that is a structural load bearing that is placed between two layers; and a bladder coating on the interior composite shell. This multi-layer shell creates an effective radiation protection system. Most of its layers can be designed with the materials necessary for specific environments. In situ materials such as water or regolith can be added to the shell design for supplemental radiation protection.

  17. A knowledge integration approach to flood vulnerability

    Science.gov (United States)

    Mazzorana, Bruno; Fuchs, Sven

    2014-05-01

    Understanding, qualifying and quantifying vulnerability is an essential need for implementing effective and efficient flood risk mitigation strategies; in particular if possible synergies between different mitigation alternatives, such as active and passive measures, should be achieved. In order to combine different risk management options it is necessary to take an interdisciplinary approach to vulnerability reduction, and as a result the affected society may be willing to accept a certain degree of self-responsibility. However, due to differing mono-disciplinary approaches and regional foci undertaken until now, different aspects of vulnerability to natural hazards in general and to floods in particular remain uncovered and as a result the developed management options remain sub-optimal. Taking an even more fundamental viewpoint, the empirical vulnerability functions used in risk assessment specifically fail to capture physical principles of the damage-generating mechanisms to the build environment. The aim of this paper is to partially close this gap by discussing a balanced knowledge integration approach which can be used to resolve the multidisciplinary disorder in flood vulnerability research. Modelling techniques such as mathematical-physical modelling of the flood hazard impact to and response from the building envelope affected, and formative scenario analyses of possible consequences in terms of damage and loss are used in synergy to provide an enhanced understanding of vulnerability and to render the derived knowledge into interdisciplinary mitigation strategies. The outlined formal procedure allows for a convincing knowledge alignment of quantified, but partial, information about vulnerability as a result of the application of physical and engineering notions and valuable, but often underspecified, qualitative argumentation strings emerging from the adopted socio-economic viewpoint.

  18. A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.

    Science.gov (United States)

    Gant, Timothy W; Sauer, Ursula G; Zhang, Shu-Dong; Chorley, Brian N; Hackermüller, Jörg; Perdichizzi, Stefania; Tollefsen, Knut E; van Ravenzwaay, Ben; Yauk, Carole; Tong, Weida; Poole, Alan

    2017-12-01

    A generic Transcriptomics Reporting Framework (TRF) is presented that lists parameters that should be reported in 'omics studies used in a regulatory context. The TRF encompasses the processes from transcriptome profiling from data generation to a processed list of differentially expressed genes (DEGs) ready for interpretation. Included within the TRF is a reference baseline analysis (RBA) that encompasses raw data selection; data normalisation; recognition of outliers; and statistical analysis. The TRF itself does not dictate the methodology for data processing, but deals with what should be reported. Its principles are also applicable to sequencing data and other 'omics. In contrast, the RBA specifies a simple data processing and analysis methodology that is designed to provide a comparison point for other approaches and is exemplified here by a case study. By providing transparency on the steps applied during 'omics data processing and analysis, the TRF will increase confidence processing of 'omics data, and regulatory use. Applicability of the TRF is ensured by its simplicity and generality. The TRF can be applied to all types of regulatory 'omics studies, and it can be executed using different commonly available software tools. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

  19. Application of omics data in regulatory toxicology: report of an international BfR expert workshop.

    Science.gov (United States)

    Marx-Stoelting, P; Braeuning, A; Buhrke, T; Lampen, A; Niemann, L; Oelgeschlaeger, M; Rieke, S; Schmidt, F; Heise, T; Pfeil, R; Solecki, R

    2015-11-01

    Advances in omics techniques and molecular toxicology are necessary to provide new perspectives for regulatory toxicology. By the application of modern molecular techniques, more mechanistic information should be gained to support standard toxicity studies and to contribute to a reduction and refinement of animal experiments required for certain regulatory purposes. The relevance and applicability of data obtained by omics methods to regulatory purposes such as grouping of chemicals, mode of action analysis or classification and labelling needs further improvement, defined validation and cautious expert judgment. Based on the results of an international expert workshop organized 2014 by the Federal Institute for Risk Assessment in Berlin, this paper is aimed to provide a critical overview of the regulatory relevance and reliability of omics methods, basic requirements on data quality and validation, as well as regulatory criteria to decide which effects observed by omics methods should be considered adverse or non-adverse. As a way forward, it was concluded that the inclusion of omics data can facilitate a more flexible approach for regulatory risk assessment and may help to reduce or refine animal testing.

  20. Omics approaches to study the oral microbiome

    OpenAIRE

    Belda Ferre, Pedro

    2015-01-01

    Introducción La visión clásica de los microorganismos como agentes infecciosos ha propiciado que se consideren como meros agentes causales de enfermedades. Sin embargo, la larga historia de coexistencia entre microorganismos y los seres humanos, ha hecho que ambos se hayan adaptado mutuamente y coevolucionen (Dubos et al. 1965, McFall-Ngai 2002)⁠. De hecho, en el cuerpo humano habitan 1014 células bacterianas, un orden de magnitud más que células humanas (Savage 1977)⁠. Entre los benefic...

  1. Bioinformatics and biomarker discovery "Omic" data analysis for personalized medicine

    CERN Document Server

    Azuaje, Francisco

    2010-01-01

    This book is designed to introduce biologists, clinicians and computational researchers to fundamental data analysis principles, techniques and tools for supporting the discovery of biomarkers and the implementation of diagnostic/prognostic systems. The focus of the book is on how fundamental statistical and data mining approaches can support biomarker discovery and evaluation, emphasising applications based on different types of "omic" data. The book also discusses design factors, requirements and techniques for disease screening, diagnostic and prognostic applications. Readers are provided w

  2. Mildew-omics: How global analyses aid the understanding of life and evolution of powdery mildews

    Directory of Open Access Journals (Sweden)

    Laurence Veronique Bindschedler

    2016-02-01

    Full Text Available The common powdery mildew plant diseases are caused by ascomycete fungi of the order Erysiphales. Their characteristic life style as obligate biotrophs renders functional analyses in these species challenging, mainly because of experimental constraints to genetic manipulation. Global large-scale (-omics approaches are thus particularly valuable and insightful for the characterisation of the life and evolution of powdery mildews. Here we review the knowledge obtained so far from genomic, transcriptomic and proteomic studies in these fungi. We consider current limitations and challenges regarding these surveys and provide an outlook on desired future investigations on the basis of the various –omics technologies.

  3. Nuclear power programme planning: An integrated approach

    International Nuclear Information System (INIS)

    2001-12-01

    The International Atomic Energy Agency (IAEA) has published material on different policy considerations in the introduction of nuclear power, primarily addressed to top level decision makers in government and industry in Member States. Several Member States and experts recommended to the IAEA to address the aspects of an integrated approach to nuclear power programme planning and to serve as guidance to those countries wishing to embark on a nuclear power programme. As a follow-up, the present publication is primarily intended to serve as guidance for executives and managers in Member States in planning for possible introduction of nuclear power plants in their electricity generating systems. Nuclear power programme planning, as dealt with in this publication, includes all activities that need to be carried out up to a well-founded decision to proceed with a project feasibility study. Project implementation beyond this decision is not in the scope of this publication. Although it is possible to use nuclear energy as a heat source for industrial processes, desalination and other heat applications, it is assumed in this publication that the planning is aimed towards nuclear power for electricity generation. Much of the information given would, however, also be relevant for planning of nuclear reactors for heat production. The publication was prepared within the framework of the IAEA programme on nuclear power planning, implementation and performance as a joint activity of the Nuclear Power Engineering Section and the Planning and Economic Studies Section (Division of Nuclear Power)

  4. Safety in Schools: An Integral Approach

    Science.gov (United States)

    Gairin, Joaquin; Castro, Diego

    2011-01-01

    The present paper summarizes a research project into integral safety in schools. The aims of this particular research are, firstly, to evaluate the degree of integral safety in schools, secondly, to propose means for improving prevention and integral safety systems and thirdly, to identify the characteristics of safety culture. The field work was…

  5. A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Hugh D.; Eisfeld, Amie J.; Sims, Amy; McDermott, Jason E.; Matzke, Melissa M.; Webb-Robertson, Bobbie-Jo M.; Tilton, Susan C.; Tchitchek, Nicholas; Josset, Laurence; Li, Chengjun; Ellis, Amy L.; Chang, Jean H.; Heegel, Robert A.; Luna, Maria L.; Schepmoes, Athena A.; Shukla, Anil K.; Metz, Thomas O.; Neumann, Gabriele; Benecke, Arndt; Smith, Richard D.; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G.; Waters, Katrina M.

    2013-07-25

    Respiratory infections stemming from influenza viruses and the Severe Acute Respiratory Syndrome corona virus (SARS-CoV) represent a serious public health threat as emerging pandemics. Despite efforts to identify the critical interactions of these viruses with host machinery, the key regulatory events that lead to disease pathology remain poorly targeted with therapeutics. Here we implement an integrated network interrogation approach, in which proteome and transcriptome datasets from infection of both viruses in human lung epithelial cells are utilized to predict regulatory genes involved in the host response. We take advantage of a novel “crowd-based” approach to identify and combine ranking metrics that isolate genes/proteins likely related to the pathogenicity of SARS-CoV and influenza virus. Subsequently, a multivariate regression model is used to compare predicted lung epithelial regulatory influences with data derived from other respiratory virus infection models. We predicted a small set of regulatory factors with conserved behavior for consideration as important components of viral pathogenesis that might also serve as therapeutic targets for intervention. Our results demonstrate the utility of integrating diverse ‘omic datasets to predict and prioritize regulatory features conserved across multiple pathogen infection models.

  6. Numerical approach to one-loop integrals

    International Nuclear Information System (INIS)

    Fujimoto, Junpei; Shimizu, Yoshimitsu; Kato, Kiyoshi; Oyanagi, Yoshio.

    1992-01-01

    Two numerical methods are proposed for the calculation of one-loop scalar integrals. In the first method, the singularity is cancelled by the symmetrization of the integrand and the integration is done by a Monte-Carlo method. In the second one, after the transform of the integrand into a standard form, the integral is reduced into a regular numerical integral. These methods provide us practical tools to evaluate one-loop Feynman diagrams with desired numerical accuracy. They are extended to the integral with numerator and the treatment of the one-loop virtual correction to the cross section is also presented. (author)

  7. ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

    Science.gov (United States)

    Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

    2017-08-10

    Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or

  8. An Integrated Computer-Aided Approach for Environmental Studies

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Chen, Fei; Jaksland, Cecilia

    1997-01-01

    A general framework for an integrated computer-aided approach to solve process design, control, and environmental problems simultaneously is presented. Physicochemical properties and their relationships to the molecular structure play an important role in the proposed integrated approach. The sco...... and applicability of the integrated approach is highlighted through examples involving estimation of properties and environmental pollution prevention. The importance of mixture effects on some environmentally important properties is also demonstrated....

  9. CANDU plant life management - An integrated approach

    International Nuclear Information System (INIS)

    Charlebois, P.; Hart, R.S.; Hopkins, J.R.

    1998-01-01

    Commercial versions of CANDU reactors were put into service starting more than 25 years ago. The first unit of Ontario Hydro's Pickering A station was put into service in 1971, and Bruce A in 1977. Most CANDU reactors, however, are only now approaching their mid-life of 15 to 20 years of operation. In particular, the first series of CANDU 6 plants which entered service in the early 1980's were designed for a 30 year life and are now approaching mid life. The current CANDU 6 design is based on a 40 year life as a result of advancement in design and materials through research and development. In order to assure safe and economic operation of these reactors, a comprehensive CANDU Plant Life Management (PLIM) program is being developed from the knowledge gained during the operation of Ontario Hydro's Pickering, Bruce, and Darlington stations, worldwide information from CANDU 6 stations, CANDU research and development programs, and other national and international sources. This integration began its first phase in 1994, with the identification of most of the critical systems structures and components in these stations, and a preliminary assessment of degradation and mechanisms that could affect their fitness for service for their planned life. Most of these preliminary assessments are now complete, together with the production of the first iteration of Life Management Plans for several of the systems and components. The Generic CANDU 6 PLIM program is now reaching its maturity, with formal processes to systematically identify and evaluate the major CSSCs in the station, and a plan to ensure that the plant surveillance, operation, and maintenance programs monitor and control component degradation well within the original design specifications essential for the plant life attainment. A Technology Watch program is being established to ensure that degradation mechanisms which could impact on plant life are promptly investigated and mitigating programs established. The

  10. Global Environmental Change: An integrated modelling approach

    International Nuclear Information System (INIS)

    Den Elzen, M.

    1993-01-01

    Two major global environmental problems are dealt with: climate change and stratospheric ozone depletion (and their mutual interactions), briefly surveyed in part 1. In Part 2 a brief description of the integrated modelling framework IMAGE 1.6 is given. Some specific parts of the model are described in more detail in other Chapters, e.g. the carbon cycle model, the atmospheric chemistry model, the halocarbon model, and the UV-B impact model. In Part 3 an uncertainty analysis of climate change and stratospheric ozone depletion is presented (Chapter 4). Chapter 5 briefly reviews the social and economic uncertainties implied by future greenhouse gas emissions. Chapters 6 and 7 describe a model and sensitivity analysis pertaining to the scientific uncertainties and/or lacunae in the sources and sinks of methane and carbon dioxide, and their biogeochemical feedback processes. Chapter 8 presents an uncertainty and sensitivity analysis of the carbon cycle model, the halocarbon model, and the IMAGE model 1.6 as a whole. Part 4 presents the risk assessment methodology as applied to the problems of climate change and stratospheric ozone depletion more specifically. In Chapter 10, this methodology is used as a means with which to asses current ozone policy and a wide range of halocarbon policies. Chapter 11 presents and evaluates the simulated globally-averaged temperature and sea level rise (indicators) for the IPCC-1990 and 1992 scenarios, concluding with a Low Risk scenario, which would meet the climate targets. Chapter 12 discusses the impact of sea level rise on the frequency of the Dutch coastal defence system (indicator) for the IPCC-1990 scenarios. Chapter 13 presents projections of mortality rates due to stratospheric ozone depletion based on model simulations employing the UV-B chain model for a number of halocarbon policies. Chapter 14 presents an approach for allocating future emissions of CO 2 among regions. (Abstract Truncated)

  11. A management systems approach to pipeline integrity

    Energy Technology Data Exchange (ETDEWEB)

    Abes, J. [CC Technologies Canada, Calgary, AB (Canada)

    2008-07-01

    A management systems approach to pipeline integrity was discussed in terms of accident causation models, lessons from accidents, and management systems. Accident causation models include the Heinrich domino theory; epidemiological models; event chain models; and system-based models. A review of the Bellingham pipeline accident showed that if the pipeline had not been weakened by external damage, it likely would have been able to withstand the pressure that occurred on the day of the rupture, and the accident would not have happened. It was also determined that there was inadequate inspection of excavation work during the water treatment plant project and consequently, there was a failure to identify and repair the damage done to the pipeline. The presentation also addressed other findings, such as inaccurate evaluation of in-line pipeline inspection data; failure to manage and protect the supervisory control and data acquisition system (SCADA); and ineffective management oversight of construction and activation of products terminal. The Carlsbad pipeline explosion was also presented as another example of an accident. Several violations by El Paso were cited, including failure to ensure that qualified personnel performed internal corrosion control procedures; failure to perform necessary tests for corrosion; and failure to follow procedures for continuing surveillance of its facilities. Last, the presentation provided a definition of management systems and discussed the characteristics and elements of a management system. These elements included policy and leadership commitment; organizational structure and responsibilities; management of resources; communication plan; document and records management; operational controls; management of change; and continual improvement. 1 fig.

  12. Integrated NPP life cycle management - Agency's approach

    International Nuclear Information System (INIS)

    Gueorguiev, B.

    2002-01-01

    Full text: The number of nuclear power plants (NPPs) operating in the world has been roughly constant for the past seven years. There are 438 reactors of 353,489 MW(e) capacity in the world and they generated 2448.9 TWh in 2001 giving a total world operating experience with nuclear power of 10,363 years. About 230 units have reached already over 15 years of operation and significant number of these plants are fully depreciated. Share of nuclear power in electricity production sector in Member States utilising nuclear power plants represents a meaningful amount and in 14 countries it exceeds 30%. Therefore, a loss of this share should be covered by new installed capacities either from conventional or alternative sources of electricity generation. Recent forecasts, for nuclear power use over the next two decades range from ∼350 to ∼500 GW(e) worldwide. While assessing the need for any nuclear power related programmes there are several important factors that must be considered since even 350 GW(e) is a very large programme requiring several hundred thousand highly qualified personnel and a substantial infrastructure to assure its continued safe, reliable and cost-effective operation. It is important to assure reliable, safe and economic beneficial performance of the plant, which requires in turn an appropriated management of any activity connected with any taken period of a plant life starting from design and ending by the decided mode of decommissioning. The period between the first and the last payment for the activities connected with the existence of a plant could be defined as a life cycle of the plant. Such integrated approach requires considering the life cycle of the plant in a much broader sense than just operational life and is characterized by the variety of activities and their management represents in a whole a plant life management programme (PLIM). Therefore PLIM could be defined as an aggregate (totality) of technical, financial, economical and

  13. RISK INTEGRATION MECHANISMS AND APPROACHES IN BANKING INDUSTRY

    OpenAIRE

    JIANPING LI; JICHUANG FENG; XIAOLEI SUN; MINGLU LI

    2012-01-01

    Recently, the number of consultative documents and research papers that discuss risk integration has grown considerably. This paper presents a comprehensive review of the work done on risk integration in the banking industry. This survey includes: (1) risk integration methods within regulatory frameworks and the banking industry; (2) challenges of risk integration; (3) risk interaction mechanisms; (4) development of risk integration approaches; (5) risk interaction results: diversification ve...

  14. Novel CNS drug discovery and development approach: model-based integration to predict neuro-pharmacokinetics and pharmacodynamics.

    Science.gov (United States)

    de Lange, Elizabeth C M; van den Brink, Willem; Yamamoto, Yumi; de Witte, Wilhelmus E A; Wong, Yin Cheong

    2017-12-01

    CNS drug development has been hampered by inadequate consideration of CNS pharmacokinetic (PK), pharmacodynamics (PD) and disease complexity (reductionist approach). Improvement is required via integrative model-based approaches. Areas covered: The authors summarize factors that have played a role in the high attrition rate of CNS compounds. Recent advances in CNS research and drug discovery are presented, especially with regard to assessment of relevant neuro-PK parameters. Suggestions for further improvements are also discussed. Expert opinion: Understanding time- and condition dependent interrelationships between neuro-PK and neuro-PD processes is key to predictions in different conditions. As a first screen, it is suggested to use in silico/in vitro derived molecular properties of candidate compounds and predict concentration-time profiles of compounds in multiple compartments of the human CNS, using time-course based physiology-based (PB) PK models. Then, for selected compounds, one can include in vitro drug-target binding kinetics to predict target occupancy (TO)-time profiles in humans. This will improve neuro-PD prediction. Furthermore, a pharmaco-omics approach is suggested, providing multilevel and paralleled data on systems processes from individuals in a systems-wide manner. Thus, clinical trials will be better informed, using fewer animals, while also, needing fewer individuals and samples per individual for proof of concept in humans.

  15. Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics

    NARCIS (Netherlands)

    Wilmes, Anja; Bielow, Chris; Ranninger, Christina; Bellwon, Patricia; Aschauer, Lydia; Limonciel, Alice; Chassaigne, Hubert; Kristl, Theresa; Aiche, Stephan; Huber, Christian G; Guillou, Claude; Hewitt, Philipp; Leonard, Martin O; Dekant, Wolfgang; Bois, Frederic Y; Jennings, Paul

    2015-01-01

    Cisplatin is one of the most widely used chemotherapeutic agents for the treatment of solid tumours. The major dose-limiting factor is nephrotoxicity, in particular in the proximal tubule. Here, we use an integrated omics approach, including transcriptomics, proteomics and metabolomics coupled to

  16. Decomposition approaches to integration without a measure

    Czech Academy of Sciences Publication Activity Database

    Greco, S.; Mesiar, Radko; Rindone, F.; Sipeky, L.

    2016-01-01

    Roč. 287, č. 1 (2016), s. 37-47 ISSN 0165-0114 Institutional support: RVO:67985556 Keywords : Choquet integral * Decision making * Decomposition integral Subject RIV: BA - General Mathematics Impact factor: 2.718, year: 2016 http://library.utia.cas.cz/separaty/2016/E/mesiar-0457408.pdf

  17. An integrated approach to change leadership.

    Science.gov (United States)

    Skelton-Green, Judith; Simpson, Beverley; Scott, Julia

    2007-01-01

    Leading change has become one of the essential core competencies of health professionals today. Since 2001, the authors have been the key designers and facilitators of the Dorothy Wylie Nursing Leadership Institute (DMW-NLI). The background, key characteristics and benefits of the DMW-NLI have been described in detail elsewhere (Simpson et al. 2002). One of the Institute's key features is that participants bring a change initiative that they wish to pursue and - during their time on site - we assist them in developing that project to the point where it has a strong chance of success. When we incorporated this aspect into the DMW-NLI program, we believed that opportunity to apply the learning of the Institute to a desired initiative in the home setting would add significant value, not only to the participants, but also to their sponsoring organizations. Further, it was our hope that we could develop a methodology to advance the change initiative, which would be a valuable tool that participants could use in future change projects.As we looked to the literature, we found no shortage of articles on change theory, as well as numerous tools and techniques for project management. However, we did not find one single approach or methodology that we felt was comprehensive yet concise enough to serve as a practical guide for those who wish to advance a change initiative in their practice settings today. Therefore, we developed an integrated conceptual framework and methodology for leading change initiatives, building on selected current and classic theories of change that are relevant today. Both the framework and methodology have proven very hardy, and will, we believe, be of interest to nurse leaders and other health professionals in leadership roles. This paper will provide a brief overview of relevant background literature on leading change initiatives, introduce the DMW-NLI Change Leadership conceptual framework, describe a number of activities that support the

  18. Unveiling network-based functional features through integration of gene expression into protein networks.

    Science.gov (United States)

    Jalili, Mahdi; Gebhardt, Tom; Wolkenhauer, Olaf; Salehzadeh-Yazdi, Ali

    2018-06-01

    Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies. In this work, we highlight and review the progress, challenges and advantages associated with emerging approaches, integrating gene expression and protein-protein interaction networks to unravel network-based functional features. This includes identifying disease related genes, gene prioritization, clustering protein interactions, developing the modules, extract active subnetworks and static protein complexes or dynamic/temporal protein complexes. We also discuss how these approaches contribute to our understanding of the biology of complex traits and diseases. This article is part of a Special Issue entitled: Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Data Integration The Relational Logic Approach

    CERN Document Server

    Genesereth, Michael

    2010-01-01

    Data integration is a critical problem in our increasingly interconnected but inevitably heterogeneous world. There are numerous data sources available in organizational databases and on public information systems like the World Wide Web. Not surprisingly, the sources often use different vocabularies and different data structures, being created, as they are, by different people, at different times, for different purposes. The goal of data integration is to provide programmatic and human users with integrated access to multiple, heterogeneous data sources, giving each user the illusion of a sin

  20. Polymer reaction engineering, an integrated approach

    NARCIS (Netherlands)

    Meyer, T.; Keurentjes, J.T.F.; Meyer, T.; Keurentjes, J.T.F.

    2005-01-01

    Summary This chapter contains sections titled: Polymer Materials A Short History of Polymer Reaction Engineering The Position of Polymer Reaction Engineering Toward Integrated Polymer Reaction Engineering The Disciplines in Polymer Reaction Engineering The Future: Product-inspired Polymer Reaction

  1. AIM: An Integrated Approach to Organizational Improvement

    Directory of Open Access Journals (Sweden)

    Ronald A. Styron, Jr.

    2016-02-01

    Full Text Available This concept paper is based on the new problem-solving model of Blended Leadership called Alloy Improvement Model (AIM. This model consists of an integration of change theory, leadership theory, and democratic principles and practices to form a comprehensive problem-solving strategy for organizational leaders. The utilization of AIM will assist leaders in moving from problems to solutions while engaging stakeholders in a comprehensive, efficient, inclusive, informative, integrated and transparent process.

  2. Integrated crop protection as a system approach

    OpenAIRE

    Haan, de, J.J.; Wijnands, F.G.; Sukkel, W.

    2005-01-01

    New farming systems in vegetable production are required as demands for high quality products that do not pollute the environment are rising, and production risks are large and incomes low. The methodology of prototyping new systems is described, especially the themes, parameters and target values connected to integrated crop protection. The role of integrated crop protection in prototyping new systems is discussed. The results of twenty years working with this prototyping methodology are pre...

  3. The Impact of Technology Integration through a Transformative Approach

    Science.gov (United States)

    Cubillos, Jo Ann

    2013-01-01

    The integration of technology into classroom instruction in K-12 schools remains problematic. The problems associated with this integration are troubling, as technology integration may change a teacher's pedagogy toward more innovative approaches that increase student achievement. The purpose of this study was to document teachers' experiences as…

  4. Integrating Adult Learning and Technologies for Effective Education: Strategic Approaches

    Science.gov (United States)

    Wang, Victor C. X.

    2010-01-01

    As adult learners and educators pioneer the use of technology in the new century, attention has been focused on developing strategic approaches to effectively integrate adult learning and technology in different learning environments. "Integrating Adult Learning and Technologies for Effective Education: Strategic Approaches" provides innovative…

  5. HeartMath and Ubuntu integral healing approaches for social ...

    African Journals Online (AJOL)

    HeartMath and Ubuntu integral healing approaches for social coherence and physical activity. Stephen D. Edwards. Abstract. This research was motivated by many social health problems confronting planet earth. Its aim is to introduce HeartMath and Ubuntu as complimentary, integral healing approaches for promoting ...

  6. The Intersystem Model of Psychotherapy: An Integrated Systems Treatment Approach

    Science.gov (United States)

    Weeks, Gerald R.; Cross, Chad L.

    2004-01-01

    This article introduces the intersystem model of psychotherapy and discusses its utility as a truly integrative and comprehensive approach. The foundation of this conceptually complex approach comes from dialectic metatheory; hence, its derivation requires an understanding of both foundational and integrational constructs. The article provides a…

  7. Investigation of Integrated Vehicle Health Management Approaches

    Science.gov (United States)

    Paris, Deidre

    2005-01-01

    This report is to present the work that was performed during the summer in the Advance Computing Application office. The NFFP (NASA Faculty Fellow Program) had ten summer faculty members working on IVHM (Integrated Vehicle Health Management) technologies. The objective of this project was two-fold: 1) to become familiar with IVHM concepts and key demonstrated IVHM technologies; and 2) to integrate the research that has been performed by IVHM faculty members into the MASTLAB (Marshall Avionic Software Test Lab). IVHM is a NASA-wide effort to coordinate, integrate and apply advanced software, sensors and design technologies to increase the level of intelligence, autonomy, and health state of future vehicles. IVHM is an important concept because it is consistent with the current plan for NASA to go to the moon, mars, and beyond. In order for NASA to become more involved in deep exploration, avionic systems will need to be highly adaptable and autonomous.

  8. THE FEMINIST APPROACH TO PSYCHOTHERAPY INTEGRATION

    OpenAIRE

    Lorena Božac Deležan

    2011-01-01

    The goal of Integrative Psychotherapy is to establish full inner and external contact (Moursund & Erskine, 2004). The most important goal in feminist therapy is the transformation of an individual as well as the transformation of the society as a whole (Herlihy & Corey, 2004). In my work I attempt to integrate both: to help the client establish inner and external contact, but also help him/her to become aware and recognize inner messages connected with his/her gender and replace them with con...

  9. Design of Integrated Circuits Approaching Terahertz Frequencies

    DEFF Research Database (Denmark)

    Yan, Lei

    In this thesis, monolithic microwave integrated circuits(MMICs) are presented for millimeter-wave and submillimeter-wave or terahertz(THz) applications. Millimeter-wave power generation from solid state devices is not only crucial for the emerging high data rate wireless communications but also...... heterodyne receivers with requirements of room temperature operation, low system complexity, and high sensitivity, monolithic integrated Schottky diode technology is chosen for the implementation of submillimeterwave components. The corresponding subharmonic mixer and multiplier for a THz radiometer system...

  10. Approaches to Integrated Building Design Environments

    DEFF Research Database (Denmark)

    Bagger-Petersen, Susanne C; Andersen, Tom

    1996-01-01

    This report discusses functional requirements and specification which needs to be defined and fulfilled to initiate development of an integrated building design environment. The purpose is to outline specifications for further discussion and development. The report documents the first phase...... in an ongoing project at the Technical University of Denmark. The overall project objective is to provide a theoretically well-founded prototype of an integrated IT-system which can serve as a device of feedback from practice and as a test-bed for the developed concept and architecture....

  11. Field theory a path integral approach

    CERN Document Server

    Das, Ashok

    2006-01-01

    This unique book describes quantum field theory completely within the context of path integrals. With its utility in a variety of fields in physics, the subject matter is primarily developed within the context of quantum mechanics before going into specialized areas.Adding new material keenly requested by readers, this second edition is an important expansion of the popular first edition. Two extra chapters cover path integral quantization of gauge theories and anomalies, and a new section extends the supersymmetry chapter, where singular potentials in supersymmetric systems are described.

  12. Inferring genetic architecture of complex traits using Bayesian integrative analysis of genome and transcriptiome data

    DEFF Research Database (Denmark)

    Ehsani, Alireza; Sørensen, Peter; Pomp, Daniel

    2012-01-01

    Background To understand the genetic architecture of complex traits and bridge the genotype-phenotype gap, it is useful to study intermediate -omics data, e.g. the transcriptome. The present study introduces a method for simultaneous quantification of the contributions from single nucleotide......-modal distribution of genomic values collapses, when gene expressions are added to the model Conclusions With increased availability of various -omics data, integrative approaches are promising tools for understanding the genetic architecture of complex traits. Partitioning of explained variances at the chromosome...

  13. Development of Multisensory Integration Approach Model

    Science.gov (United States)

    Kumar, S. Prasanna; Nathan, B. Sami

    2016-01-01

    Every teacher expects optimum level of processing in mind of them students. The level of processing is mainly depends upon memory process. Most of the students have retrieval difficulties on past learning. Memory difficulties directly related to sensory integration. In these circumstances the investigator made an attempt to construct Multisensory…

  14. The Integration Movement in the Caribbean at Crossroads: Towards a New Approach of Integration

    OpenAIRE

    Uziel Nogueira

    1997-01-01

    The Institute for the Integration of Latin America and the Caribbean (INTAL) has inaugurated a Working Papers Series with the publication of a study by Uziel Nogueira, the Institute's Economist. Entitled "The Integration Movement in the Caribbean at the Crossroads: Towards a New Approach to Integration", the study opens with an overview of the movement towards integration among the English-speaking countries of the Caribbean. It continues with an analysis of the integration process during thi...

  15. An integrative approach to apprehend desistance.

    Science.gov (United States)

    F-Dufour, Isabelle; Brassard, Renée; Martel, Joane

    2015-05-01

    The process underlying desistance is still a strong subject of debate. This article seeks to introduce several core concepts of Archer's morphogenic approach to study how people desist from crime. At first, it discusses the primary existing theories of desistance. Then, this article demonstrates the usefulness of this approach by presenting empirical evidence drawn from semistructured interviews collected with 29 men who desisted from crime in an eastern province of Canada. The study demonstrates how this alternative approach allows for the consolidation of existing knowledge on desistance. Then implication of these findings for both theory and practice are discussed. © The Author(s) 2013.

  16. Integrated approach to economical, reliable, safe nuclear power production

    International Nuclear Information System (INIS)

    1982-06-01

    An Integrated Approach to Economical, Reliable, Safe Nuclear Power Production is the latest evolution of a concept which originated with the Defense-in-Depth philosophy of the nuclear industry. As Defense-in-Depth provided a framework for viewing physical barriers and equipment redundancy, the Integrated Approach gives a framework for viewing nuclear power production in terms of functions and institutions. In the Integrated Approach, four plant Goals are defined (Normal Operation, Core and Plant Protection, Containment Integrity and Emergency Preparedness) with the attendant Functional and Institutional Classifications that support them. The Integrated Approach provides a systematic perspective that combines the economic objective of reliable power production with the safety objective of consistent, controlled plant operation

  17. Omics on bioleaching: current and future impacts.

    Science.gov (United States)

    Martinez, Patricio; Vera, Mario; Bobadilla-Fazzini, Roberto A

    2015-10-01

    Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.

  18. Design of Integrated Circuits Approaching Terahertz Frequencies

    OpenAIRE

    Yan, Lei; Johansen, Tom Keinicke

    2013-01-01

    In this thesis, monolithic microwave integrated circuits(MMICs) are presented for millimeter-wave and submillimeter-wave or terahertz(THz) applications. Millimeter-wave power generation from solid state devices is not only crucial for the emerging high data rate wireless communications but also important for driving THz signal sources. To meet the requirement of high output power, amplifiers based on InP double heterojunction bipolar transistor (DHBT) devices from the III-V Lab in Marcoussic,...

  19. Virtual integration: A game-theoretic approach

    OpenAIRE

    Schorer, Michael

    2014-01-01

    Embedded systems are playing a key role to enable the features of todays cars and other road vehicles. Advances in current hardware platforms of these embedded systems and growing implementation of features in software rather than in new hardware modules lead to new and continuously more complex automotive software systems. The integration process in the course of development of automotive software systems is a crucial and complex phase. An efficient combination of the set of components i...

  20. Concept for integrated environmental monitoring. Scientific approach

    Energy Technology Data Exchange (ETDEWEB)

    Haber, W [comp.; Schoenthaler, K; Kerner, H F; Koeppel, J; Spandau, L

    1998-09-01

    Despite considerable expenditures for environmental protection and intensified efforts in the areas of environmental research and monitoring, environmental damage increasingly occurs, sometimes with global effects, largely due to the lack of early diagnosis. In the past few years various institutions have therefore demanded improvements in environmental monitoring. The Council of Experts on Environmental Issues (`Rat von Sachverstaendigen fuer Umweltfragen`, SRU), in particular, in its `Environmental Report` of 1987 and in its Special Report on `General Ecological Environmental Monitoring` (1990) presented far-reaching demands for a nationwide ecological early warning system which should integrate the various local, regional, national, and even global monitoring levels, and which should encompass an environmental monitoring of entire ecosystems at representative locations. This is aimed at creating the prerequisites for - detection of long-term gradual environmental change, - confirmation of refutation of initial assumptions regarding the causes of these environmental changes, - permitting decisions on preventive actions to stabilize or improve environmental conditions and - making it possible to assess the success of environmental protection policies. This report includes an abbreviated version and documentation of the conference on the `Concept for Integrated Environmental Monitoring` and the final report `Specification of the Concept for Integrated Environmental Monitoring from the Perspective of Nature Conservation`. (orig.)

  1. Integrated care for diabetes - The Singapore Approach

    Directory of Open Access Journals (Sweden)

    Su Qian Yeo

    2012-03-01

    Full Text Available Background The prevalence of diabetes mellitus is 12.7% in Singapore. Managing people with diabetes in the community may be needed to reduce unnecessary utilisation of expensive specialist resources and to reduce hospital waiting times for patients with complications. Care Practice The Singapore General Hospital (SGH Delivering on Target (DOT Programme was launched in 2005 to right-site clinically stable diabetic patients from the hospital to private DOT GPs. The Chronic Disease Management Office (CDMO was established and a fully customised DOT information technology (IT system was developed. Three initiatives were implemented: (i Subsidised Drug Delivery Programme, (ii Diagnostic Tests Incentive Programme, and (iii Allied Healthcare Incentive Programme. Discussion Right-siting was enabled through patient incentives that eased the burden of out-of-pocket expenditure. Right Siting Officers (RSOs maintained a general oversight of the patient pathway. The integrated system supported shared care follow-up by enabling DOT GPs to share updates on the patients' health status with the referring specialists. Conclusion A coherent process across all healthcare providers similar to the SGH DOT Programme may facilitate efforts to shift the care for people with diabetes to the community and to provide integrated care. Successful integration may require incentives for institutional partners and patients.

  2. Integrated Artificial Intelligence Approaches for Disease Diagnostics.

    Science.gov (United States)

    Vashistha, Rajat; Chhabra, Deepak; Shukla, Pratyoosh

    2018-06-01

    Mechanocomputational techniques in conjunction with artificial intelligence (AI) are revolutionizing the interpretations of the crucial information from the medical data and converting it into optimized and organized information for diagnostics. It is possible due to valuable perfection in artificial intelligence, computer aided diagnostics, virtual assistant, robotic surgery, augmented reality and genome editing (based on AI) technologies. Such techniques are serving as the products for diagnosing emerging microbial or non microbial diseases. This article represents a combinatory approach of using such approaches and providing therapeutic solutions towards utilizing these techniques in disease diagnostics.

  3. Alcoholism: integrating approaches to influence policy

    African Journals Online (AJOL)

    Adele

    Most importantly that these disorders are treatable and treatment can be cost effective. It is crucial that we continually challenge our assumptions of best treatment practices. Rehabilitation programs in the. USA have in the last decade radically changed their approach to treatment, providing most treatment in ambulatory reha ...

  4. Founding Editorial: Embryology — An Integrated Approach

    Directory of Open Access Journals (Sweden)

    Michael Richardson

    2001-01-01

    Full Text Available We introduce the Embryology domain of TheScientificWorld and outline the scope and aims. We argue for an interdisciplinary approach to problems in develop-mental biology. Three areas are identified as being of particular relevance to this domain: evolutionary developmental biology, teratology, and descriptive or experimental embryology.

  5. New Theoretical Approach Integrated Education and Technology

    Science.gov (United States)

    Ding, Gang

    2010-01-01

    The paper focuses on exploring new theoretical approach in education with development of online learning technology, from e-learning to u-learning and virtual reality technology, and points out possibilities such as constructing a new teaching ecological system, ubiquitous educational awareness with ubiquitous technology, and changing the…

  6. Integrated approach to transmission services pricing

    International Nuclear Information System (INIS)

    Yu, C.W.; David, A.K.

    1999-01-01

    The paper presents an intuitively logical split between: (a) embedded, (b) operating, and (c) expansion cost based pricing and methodologies for implementation, for transmission services. A conceptually straightforward mechanism for the equitable allocation of transmission network embedded cost recovery based on capacity-use and reliability benefit is proposed, expansion cost is charged on a long-run marginal cost basis and finally, operating cost recovery is based on short-run marginal pricing. This is followed by co-ordinating these alternatives and integrating the pricing mechanisms to achieve appropriate price signals for bulk power users of transmission systems. (author)

  7. Critical Perspectives of Pedagogical Approaches to Reversing the Order of Integration in Double Integrals

    Science.gov (United States)

    Tisdell, Christopher C.

    2017-01-01

    This paper presents some critical perspectives regarding pedagogical approaches to the method of reversing the order of integration in double integrals from prevailing educational literature on multivariable calculus. First, we question the message found in popular textbooks that the traditional process of reversing the order of integration is…

  8. Undergraduate hematology – a more integrated approach

    Directory of Open Access Journals (Sweden)

    Di Carlofelice MA

    2016-11-01

    Full Text Available Matteo A Di Carlofelice,* Jack FT Cope*Faculty of Medicine, Imperial College London, London, UK*These authors contributed equally to this workAs fellow medical students we read with great interest the article by Mandan et al1 proposing a dedicated hematology rotation. The authors highlight a gap in clinical hematology teaching, particularly compared to “conventional rotations”.1 Their suggestion has merits and we agree with most of the points raised; however, propose instead for us to build on current teaching as opposed to establishing a new rotation.The integration of theoretical and practical learning was concluded to be beneficial to both teacher and student by Wrenn and Wrenn.2 In the original article it is mentioned that “clinical experience allows students to comprehend and apply this knowledge in practice, enabling the all-important integration of their learning”.1 As we agree that hematology overlaps with other specialties and therefore requires a thorough understanding, we value how a clinical attachment would be useful to solidify lecture-based teaching.View the original paper by Mandan et al.

  9. Leisure market segmentation : an integrated preferences/constraints-based approach

    NARCIS (Netherlands)

    Stemerding, M.P.; Oppewal, H.; Beckers, T.A.M.; Timmermans, H.J.P.

    1996-01-01

    Traditional segmentation schemes are often based on a grouping of consumers with similar preference functions. The research steps, ultimately leading to such segmentation schemes, are typically independent. In the present article, a new integrated approach to segmentation is introduced, which

  10. SESSION V: INTEGRATED APPROACHES IN LAND AND WATER ...

    African Journals Online (AJOL)

    SESSION V: INTEGRATED APPROACHES IN LAND AND WATER MANAGEMENT RESEARCH/LAND AND WATER MANAGEMENT ECONOMICS AND POLICY - Socioeconomic implications of improved forage species on smallholder farms in Kenya.

  11. Integration of case study approach, project design and computer ...

    African Journals Online (AJOL)

    Integration of case study approach, project design and computer modeling in managerial accounting education ... Journal of Fundamental and Applied Sciences ... in the Laboratory of Management Accounting and Controlling Systems at the ...

  12. Integrated landscape approach : Closing the gap between theory and application

    NARCIS (Netherlands)

    Bürgi, Matthias; Ali, Panna; Chowdhury, Afroza; Heinimann, Andreas; Hett, Cornelia; Kienast, Felix; Mondal, Manoranjan Kumar; Upreti, Bishnu Raj; Verburg, Peter H.

    2017-01-01

    Recently, the integrated landscape approach has gained increasing interest of the scientific community, as well as of organizations active in the field of sustainable development. However, the enthusiastic welcome is challenged by little consensus on theory, terminology and definitions. Moreover,

  13. Path integral approach to multidimensional quantum tunnelling

    International Nuclear Information System (INIS)

    Balantekin, A.B.; Takigawa, N.

    1985-01-01

    Path integral formulation of the coupled channel problem in the case of multidimensional quantum tunneling is presented and two-time influence functionals are introduced. The two-time influence functionals are calculated explicitly for the three simplest cases: Harmonic oscillators linearly or quadratically coupled to the translational motion and a system with finite number of equidistant energy levels linearly coupled to the translational motion. The effects of these couplings on the transmission probability are studied for two limiting cases, adiabatic case and when the internal system has a degenerate energy spectrum. The condition for the transmission probability to show a resonant structure is discussed and exemplified. Finally, the properties of the dissipation factor in the adiabatic limit and its correlation with the friction coefficient in the classically accessible region are studied

  14. Aluminum recycling—An integrated, industrywide approach

    Science.gov (United States)

    Das, Subodh K.; Green, John A. S.; Kaufman, J. Gilbert; Emadi, Daryoush; Mahfoud, M.

    2010-02-01

    The aluminum industry is a leading proponent of global sustainability and strongly advocates the use of recycled metal. As the North American primary aluminum industry continues to move offshore to other geographic areas such as Iceland and the Middle East, where energy is more readily available at lower cost, the importance of the secondary (i.e., recycled metal) market in the U.S. will continue to increase. The purpose of this paper is to take an integrated, industry-wide look at the recovery of material from demolished buildings, shredded automobiles, and aging aircraft, as well as from traditional cans and other rigid containers. Attempts will be made to assess how the different alloys used in these separate markets can be recycled in the most energy-efficient manner.

  15. A boundary integral approach to unstable solidification

    International Nuclear Information System (INIS)

    Strain, J.

    1989-01-01

    We consider the supercooled Stefan problem with a general anisotropic curvature- and velocity-dependent boundary condition on the moving interface. We present numerical methods, based on an integral equation formulation and including a new algorithm for moving curves with curvature-dependent velocity. These methods compute a periodic interface with O(Δt) accuracy, where Δt is the time step. Previous work has been limited to short time spans and achieved slightly less than O(Δt 1/2 ) accuracy. Accurate numerical results are seen to agree with the predictions of linear stability theory. This agreement has eluded previous authors, because their numerical methods suffered from grid effects and their linear stability theory was incorrect. We study the long-time evolution of an unstable interface. Our computations exhibit the beginnings of a sidebranching instability when the boundary condition includes anisotropy and tip-splitting in the isotropic case. copyright 1989 Academic Press, Inc

  16. An integrated approach for prioritized process improvement.

    Science.gov (United States)

    Vanteddu, Gangaraju; McAllister, Charles D

    2014-01-01

    The purpose of this paper is to propose an integrated framework to simultaneously identify and improve healthcare processes that are important from the healthcare provider's and patient's perspectives. A modified quality function deployment (QFD) chart is introduced to the field of healthcare quality assurance. A healthcare service example is used to demonstrate the utility of the proposed chart. The proposed framework is versatile and can be used in a wide variety of healthcare quality improvement contexts, wherein, two different perspectives are needed to be considered for identifying and improving critical healthcare processes. The modified QFD chart used in conjunction with the stacked Pareto chart will facilitate the identification of key performance metrics from the patient's and the hospital's perspectives. Subsequently, the chief contributory factors at different levels are identified in a very efficient manner. Healthcare quality improvement professionals will be able to use the proposed modified QFD chart in association with stacked Pareto chart for effective quality assurance.

  17. Regional Integrated Silvopastoral Approaches to Ecosystem Management Project

    OpenAIRE

    CIPAV (Centre For Research on Sustainable Agricultural Production Systems); CATIE (Centro Agronomico Tropical de Investigacion y Ensenanza); NITLAPAN

    2007-01-01

    Metadata only record The Regional Integrated Silvopastoral Approaches to Ecosystem Management Project introduces the payment for environmental services approach to silvopastoral farmers in Colombia, Costa Rica, and Nicaragua. The objectives of the project are to "demonstrate and measure a) the effects the introduction of payment incentives for environmental services to farmers on their adoption of integrated silvopastoral farming systems in degraded pasture lands; and b) the resulting impr...

  18. Integrative approaches to childhood constipation and encopresis.

    Science.gov (United States)

    Culbert, Timothy P; Banez, Gerard A

    2007-12-01

    Constipation and encopresis (fecal soiling) are common childhood disorders that may lead to significant functional impairment. The etiology and course of constipation and encopresis are increasingly conceptualized from a broad biopsychosocial perspective, and therefore a holistic approach to assessment and treatment is indicated. Many children experience symptoms of chronic constipation and/or encopresis that are only partially responsive to conventional medical therapy. Complementary/alternative therapies can often help in the treatment of constipation/encopresis and are well accepted by patients and families.

  19. Omics: biomedical perspectives and applications

    National Research Council Canada - National Science Library

    Barh, Debmalya; Blum, Kenneth; Madigan, Margaret A

    2012-01-01

    ... by The MathWorks of a particular pedagogical approach or particular use of the MATLAB® software. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2012 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version ...

  20. Approaches to the summability of divergent multidimensional integrals

    International Nuclear Information System (INIS)

    Vainikko, G M; Lifanov, I K

    2003-01-01

    Under discussion are various approaches to the concept of summability (finding the finite part - (f.p.)) of divergent integrals with integrand represented as a product of two functions, one with a parameter-dependent non-integrable singularity at one point of the integration and the other absolutely integrable. A study is made of summability methods which are based on the expansion of the absolutely integrable function in a Taylor series with centre at the singular point (f.p.), on the analytic continuation with respect to the parameter of the singularity (a.f.p.), and on integration by parts (f.p.p.). Formulae of changes of variables in such integrals are presented

  1. Integrating lifestyle approaches into osteoarthritis care

    Directory of Open Access Journals (Sweden)

    Garver MJ

    2015-09-01

    Full Text Available Matthew J Garver,1 Brian C Focht,2 Sarah J Taylor3 1Department of Kinesiology and Nutrition, Abilene Christian University, Abilene, TX, 2Department of Human Sciences, Ohio State University, Columbus, OH, 3School of Occupational Therapy, Texas Woman's University, Dallas, TX, USA Abstract: As the lifetime risk, societal cost, and overall functional impact of osteoarthritis (OA is imposing, it is imperative that clinicians provide an individualized care model for patients. Patients must be offered a multiplicity of care strategies and encouraged to embrace lifestyle approaches for self-managing the effects and symptoms of OA. Certainly, the attitude of the clinician and patient will directly influence receptivity and implementation of lifestyle approaches. This work proposes how the use of structured and routine assessments and cognitive therapy ideologies may complement a comprehensive treatment plan. Assessments described herein include objective and/or self-report measures of physical function, pain, attitude about social support, and sleep quality. Baseline assessments followed by systematic monitoring of the results may give patients and clinicians valuable insight into the effectiveness of the care plan. Empirical evidence from randomized trials with OA patients highlights the effectiveness of cognitive behavioral change strategies for addressing salient concerns for OA (pain control, mobility performance, and sleep quality. Cognitive restructuring can provide patients with renewed power in managing their disease. Cognitive therapy topics discussed presently include: 1 what is OA?, 2 effectiveness of exercise and FITT (frequency, intensity, time, and type principles for OA patients, 3 goal-setting and barriers, and 4 translating to independent care. Woven within the discussion about cognitive therapy are ideas about how the results from baseline assessments and group-mediated dynamics might assist more favorable outcomes. There are a plethora

  2. Integrated microsystems packaging approach with LCP

    Science.gov (United States)

    Jaynes, Paul; Shacklette, Lawrence W.

    2006-05-01

    Within the government communication market there is an increasing push to further miniaturize systems with the use of chip-scale packages, flip-chip bonding, and other advances over traditional packaging techniques. Harris' approach to miniaturization includes these traditional packaging advances, but goes beyond this level of miniaturization by combining the functional and structural elements of a system, thus creating a Multi-Functional Structural Circuit (MFSC). An emerging high-frequency, near hermetic, thermoplastic electronic substrate material, Liquid Crystal Polymer (LCP), is the material that will enable the combination of the electronic circuit and the physical structure of the system. The first embodiment of this vision for Harris is the development of a battlefield acoustic sensor module. This paper will introduce LCP and its advantages for MFSC, present an example of the work that Harris has performed, and speak to LCP MFSCs' potential benefits to miniature communications modules and sensor platforms.

  3. AN INTEGRATED APPROACH FOR LINKED DATA BROWSING

    Directory of Open Access Journals (Sweden)

    W. Beek

    2017-07-01

    Full Text Available The Netherlands' Cadastre, Land Registry and Mapping Agency – in short Kadaster – collects and registers administrative and spatial data on property and the rights involved. Currently, the Kadaster is publishing its geo-spatial data assets as Linked Open Data. The Kadaster manages hundreds of datasets that describe hundreds of millions of geospatial objects, including all Dutch buildings, roads, and forests. The Kadaster exposes this large collection of data to thousands of daily users that operate from within different contexts and that need to be supported in different use cases. Therefore, Kadaster must offer diverse, yet complementary, approaches for browsing and exploring the data it publishes. Specifically, it supports the following paradigms for browsing and exploring its data assets: hierarchical browsing, graph navigation, faceted browsing, and tabular browsing. These paradigms are useful for different tasks, cover different use cases, and are implemented by reusing and/or developing Open Source libraries and applications.

  4. Preregularization and the path integral approach to the chiral anomaly

    International Nuclear Information System (INIS)

    Elias, V.; McKeon, G.; Steele, T.; Mann, R.B.; Treml, T.F.; Sherry, T.N.

    1987-01-01

    We explore the connection between perturbative and non-perturbative (path-integral) approaches to the axial anomaly. In particular, we show how the Jacobian associated with the fermionic measure corresponding to local axial transformations may be calculated directly from shift-of-integration-variable surface terms in four Euclidean dimensions. No regularization (explicit parametrization of UV infinities) is required in this approach, but invariance of the Jacobian under vector gauge transformations (i.e. preregularization) is required to remove a variable-of-integration ambiguity within the expression for the Jacobian of the fermionic measure. (orig.)

  5. The integrated approach methodology for operator information evaluation

    International Nuclear Information System (INIS)

    Stroube, K.; Modarres, M.; Roush, M.; Hunt, N.; Pearce, R.

    1986-01-01

    The Integrated Approach has developed a complete method for evaluating the relative importance of operation information improvements. By use of decision trees the impact of information on success probability of a function or system can be evaluated. This approach couples goal trees and human success likelihoods to estimate anticipated consequences of a given information system

  6. Towards an integrated approach to health and medicine in Africa

    African Journals Online (AJOL)

    2016-08-18

    Aug 18, 2016 ... As such, a social approach to health-seeking behaviour questions how decisions ... In conclusion, the paper proposes that medicine and the humanities should engage seriously .... mental questions: What story does the integration or separation .... approach which has taken an interest in traditional healing.

  7. Learning about the Weather through an Integrated STEM Approach

    Science.gov (United States)

    Serin, Gokhan

    2014-01-01

    Introducing concepts through an integrated science, technology, engineering and mathematics (STEM) approach can promote interest and motivation (Bennett, Lubben and Hogarth, 2007; Bybee, 2010). However, implementing such an approach effectively in a classroom setting, with relevant links, is a challenging task. Some concepts lend themselves more…

  8. An integrated artificial neural networks approach for predicting global radiation

    International Nuclear Information System (INIS)

    Azadeh, A.; Maghsoudi, A.; Sohrabkhani, S.

    2009-01-01

    This article presents an integrated artificial neural network (ANN) approach for predicting solar global radiation by climatological variables. The integrated ANN trains and tests data with multi layer perceptron (MLP) approach which has the lowest mean absolute percentage error (MAPE). The proposed approach is particularly useful for locations where no available measurement equipment. Also, it considers all related climatological and meteorological parameters as input variables. To show the applicability and superiority of the integrated ANN approach, monthly data were collected for 6 years (1995-2000) in six nominal cities in Iran. Separate model for each city is considered and the quantity of solar global radiation in each city is calculated. Furthermore an integrated ANN model has been introduced for prediction of solar global radiation. The acquired results of the integrated model have shown high accuracy of about 94%. The results of the integrated model have been compared with traditional angstrom's model to show its considerable accuracy. Therefore, the proposed approach can be used as an efficient tool for prediction of solar radiation in the remote and rural locations with no direct measurement equipment.

  9. Integrated, regional approach to risk management of industrial systems

    International Nuclear Information System (INIS)

    Chakraborty, S.

    1992-01-01

    This paper focuses on the following four main issues: (1) necessity for an integrated, regional approach to risk management of industrial systems; (2) principles of risk management; (3) integrated approach and overall methodology; and (4) implementation of risk management strategies on a regional basis. The U.N. Interagency project on risk management for large industrial areas, which is a pioneer type of international initiative for an integrated approach to risk management, is discussed in this context. Another encouraging activity for further development of overall methodologies for risk management is the ongoing project on the risk and safety of technical systems at the Swiss Federal Institute of Technology in Aurich. The concept of integral risk management takes into account multidimensional factors including technical, economic, political, social, and ethical considerations to allow a well-balanced decision-making process

  10. Assessment of berberine as a multi-target antimicrobial: a multi-omics study for drug discovery and repositioning.

    Science.gov (United States)

    Karaosmanoglu, Kubra; Sayar, Nihat Alpagu; Kurnaz, Isil Aksan; Akbulut, Berna Sariyar

    2014-01-01

    Postgenomics drug development is undergoing major transformation in the age of multi-omics studies and drug repositioning. Rather than applications solely in personalized medicine, omics science thus additionally offers a better understanding of a broader range of drug targets and drug repositioning. Berberine is an isoquinoline alkaloid found in many medicinal plants. We report here a whole genome microarray study in tandem with proteomics techniques for mining the plethora of targets that are putatively involved in the antimicrobial activity of berberine against Escherichia coli. We found DNA replication/repair and transcription to be triggered by berberine, indicating that nucleic acids, in general, are among its targets. Our combined transcriptomics and proteomics multi-omics findings underscore that, in the presence of berberine, cell wall or cell membrane transport and motility-related functions are also specifically regulated. We further report a general decline in metabolism, as seen by repression of genes in carbohydrate and amino acid metabolism, energy production, and conversion. An involvement of multidrug efflux pumps, as well as reduced membrane permeability for developing resistance against berberine in E. coli was noted. Collectively, these findings offer original and significant leads for omics-guided drug discovery and future repositioning approaches in the postgenomics era, using berberine as a multi-omics case study.

  11. Recent developments in the path integral approach to anomalies

    International Nuclear Information System (INIS)

    Fujikawa, Kazuo.

    1986-08-01

    After a brief summary of the path integral approach to anomalous identities, some of the recent developments in this approach are discussed. The topics discussed include (i) Construction of the effective action by means of the covariant current, (ii) Gauss law constraint in anomalous gauge theories, (iii) Path integral approach to anomalies in superconformal transformations, (iv) Conformal and ghost number anomalies in string theory in analogy with the instanton calculation, (v) Covariant local Lorentz anomaly and its connection with the mathematical construction of the consistent anomaly. (author)

  12. High resolution integral holography using Fourier ptychographic approach.

    Science.gov (United States)

    Li, Zhaohui; Zhang, Jianqi; Wang, Xiaorui; Liu, Delian

    2014-12-29

    An innovative approach is proposed for calculating high resolution computer generated integral holograms by using the Fourier Ptychographic (FP) algorithm. The approach initializes a high resolution complex hologram with a random guess, and then stitches together low resolution multi-view images, synthesized from the elemental images captured by integral imaging (II), to recover the high resolution hologram through an iterative retrieval with FP constrains. This paper begins with an analysis of the principle of hologram synthesis from multi-projections, followed by an accurate determination of the constrains required in the Fourier ptychographic integral-holography (FPIH). Next, the procedure of the approach is described in detail. Finally, optical reconstructions are performed and the results are demonstrated. Theoretical analysis and experiments show that our proposed approach can reconstruct 3D scenes with high resolution.

  13. Serial-omics characterization of equine urine.

    Directory of Open Access Journals (Sweden)

    Min Yuan

    Full Text Available Horse urine is easily collected and contains molecules readily measurable using mass spectrometry that can be used as biomarkers representative of health, disease or drug tampering. This study aimed at analyzing microliter levels of horse urine to purify, identify and quantify proteins, polar metabolites and non-polar lipids. Urine from a healthy 12 year old quarter horse mare on a diet of grass hay and vitamin/mineral supplements with limited pasture access was collected for serial-omics characterization. The urine was treated with methyl tert-butyl ether (MTBE and methanol to partition into three distinct layers for protein, non-polar lipid and polar metabolite content from a single liquid-liquid extraction and was repeated two times. Each layer was analyzed by high performance liquid chromatography-high resolution tandem mass spectrometry (LC-MS/MS to obtain protein sequence and relative protein levels as well as identify and quantify small polar metabolites and lipids. The results show 46 urine proteins, many related to normal kidney function, structural and circulatory proteins as well as 474 small polar metabolites but only 10 lipid molecules. Metabolites were mostly related to urea cycle and ammonia recycling as well as amino acid related pathways, plant diet specific molecules, etc. The few lipids represented triglycerides and phospholipids. These data show a complete mass spectrometry based-omics characterization of equine urine from a single 333 μL mid-stream urine aliquot. These omics data help serve as a baseline for healthy mare urine composition and the analyses can be used to monitor disease progression, health status, monitor drug use, etc.

  14. Single-cell technologies in environmental omics

    KAUST Repository

    Kodzius, Rimantas; Gojobori, Takashi

    2015-01-01

    Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.

  15. Single-cell technologies in environmental omics

    KAUST Repository

    Kodzius, Rimantas

    2015-10-22

    Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.

  16. A new Gauss quadrature for multicentre integrals over STOs in the Gaussian integral transform approach

    International Nuclear Information System (INIS)

    Bouferguene, Ahmed

    2005-01-01

    When computing multicentre integrals over Slater-type orbitals (STOs) by means of the Shavitt and Karplus Gaussian integral transforms (Shavitt and Karplus 1962 J. Chem. Phys. 36 550), one usually ends up with a multiple integral of the form ∫ 0 1 du ∫ 0 1 dv ...∫ 0 ∞ dz F(u, v, ..., z) (Shavitt and Karplus 1965 J. Chem. Phys. 43 398) in which all the integrals are inter-related. The most widely used approach for computing such an integral is to apply a product of Gauss-Legendre quadratures for the integrals over [0, 1] while the semi-infinite term is evaluated by a special procedure. Although numerous approaches have been developed to accurately perform the integration over [0, ∞) efficiently, it is the aim of this work to add a new tool that could be of some benefit in carrying out the hard task of multicentre integrals over STOs. The new approach relies on a special Gauss quadrature referred to as Gauss-Bessel to accurately evaluate the semi-infinite integral of interest. In this work, emphasis is put on accuracy rather than efficiency since its aim is essentially to bring a proof of concept showing that Gauss-Bessel quadrature can successfully be applied in the context of multicentre integrals over STOs. The obtained accuracy is comparable to that obtained with other methods available in the literature

  17. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L. Exposed to Water Deficit

    Directory of Open Access Journals (Sweden)

    Stefania Savoi

    2017-07-01

    Full Text Available Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  18. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit.

    Science.gov (United States)

    Savoi, Stefania; Wong, Darren C J; Degu, Asfaw; Herrera, Jose C; Bucchetti, Barbara; Peterlunger, Enrico; Fait, Aaron; Mattivi, Fulvio; Castellarin, Simone D

    2017-01-01

    Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis -regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  19. Integrated Giant Magnetoresistance Technology for Approachable Weak Biomagnetic Signal Detections.

    Science.gov (United States)

    Shen, Hui-Min; Hu, Liang; Fu, Xin

    2018-01-07

    With the extensive applications of biomagnetic signals derived from active biological tissue in both clinical diagnoses and human-computer-interaction, there is an increasing need for approachable weak biomagnetic sensing technology. The inherent merits of giant magnetoresistance (GMR) and its high integration with multiple technologies makes it possible to detect weak biomagnetic signals with micron-sized, non-cooled and low-cost sensors, considering that the magnetic field intensity attenuates rapidly with distance. This paper focuses on the state-of-art in integrated GMR technology for approachable biomagnetic sensing from the perspective of discipline fusion between them. The progress in integrated GMR to overcome the challenges in weak biomagnetic signal detection towards high resolution portable applications is addressed. The various strategies for 1/ f noise reduction and sensitivity enhancement in integrated GMR technology for sub-pT biomagnetic signal recording are discussed. In this paper, we review the developments of integrated GMR technology for in vivo/vitro biomagnetic source imaging and demonstrate how integrated GMR can be utilized for biomagnetic field detection. Since the field sensitivity of integrated GMR technology is being pushed to fT/Hz 0.5 with the focused efforts, it is believed that the potential of integrated GMR technology will make it preferred choice in weak biomagnetic signal detection in the future.

  20. Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network

    Science.gov (United States)

    Yao, Qianlan; Xu, Yanjun; Yang, Haixiu; Shang, Desi; Zhang, Chunlong; Zhang, Yunpeng; Sun, Zeguo; Shi, Xinrui; Feng, Li; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

    2015-01-01

    The identification of disease-related metabolites is important for a better understanding of metabolite pathological processes in order to improve human medicine. Metabolites, which are the terminal products of cellular regulatory process, can be affected by multi-omic processes. In this work, we propose a powerful method, MetPriCNet, to predict and prioritize disease candidate metabolites based on integrated multi-omics information. MetPriCNet prioritized candidate metabolites based on their global distance similarity with seed nodes in a composite network, which integrated multi-omics information from the genome, phenome, metabolome and interactome. After performing cross-validation on 87 phenotypes with a total of 602 metabolites, MetPriCNet achieved a high AUC value of up to 0.918. We also assessed the performance of MetPriCNet on 18 disease classes and found that 4 disease classes achieved an AUC value over 0.95. Notably, MetPriCNet can also predict disease metabolites without known disease metabolite knowledge. Some new high-risk metabolites of breast cancer were predicted, although there is a lack of known disease metabolite information. A predicted disease metabolic landscape was constructed and analyzed based on the results of MetPriCNet for 87 phenotypes to help us understand the genetic and metabolic mechanism of disease from a global view. PMID:26598063

  1. A design approach for integrating thermoelectric devices using topology optimization

    DEFF Research Database (Denmark)

    Soprani, Stefano; Haertel, Jan Hendrik Klaas; Lazarov, Boyan Stefanov

    2016-01-01

    Efficient operation of thermoelectric devices strongly relies on the thermal integration into the energy conversion system in which they operate. Effective thermal integration reduces the temperature differences between the thermoelectric module and its thermal reservoirs, allowing the system...... to operate more efficiently. This work proposes and experimentally demonstrates a topology optimization approach as a design tool for efficient integration of thermoelectric modules into systems with specific design constraints. The approach allows thermal layout optimization of thermoelectric systems...... for different operating conditions and objective functions, such as temperature span, efficiency, and power recoveryrate. As a specific application, the integration of a thermoelectric cooler into the electronics section ofa downhole oil well intervention tool is investigated, with the objective of minimizing...

  2. Science Teachers’ Pedagogical Content Knowledge and Integrated Approach

    Science.gov (United States)

    Adi Putra, M. J.; Widodo, A.; Sopandi, W.

    2017-09-01

    The integrated approach refers to the stages of pupils’ psychological development. Unfortunately, the competences which are designed into the curriculum is not appropriate with the child development. This Manuscript presents PCK (pedagogical content knowledge) of teachers who teach science content utilizing an integrated approach. The data has been collected by using CoRe, PaP-eR, and interviews from six elementary teachers who teach science. The paper informs that high and stable teacher PCKs have an impact on how teachers present integrated teaching. Because it is influenced by the selection of important content that must be submitted to the students, the depth of the content, the reasons for choosing the teaching procedures and some other things. So for teachers to be able to integrate teaching, they should have a balanced PCK.

  3. Are we closer to the vision? A proposed framework for incorporating omics into environmental assessments.

    Science.gov (United States)

    Martyniuk, Christopher J

    2018-04-01

    Environmental science has benefited a great deal from omics-based technologies. High-throughput toxicology has defined adverse outcome pathways (AOPs), prioritized chemicals of concern, and identified novel actions of environmental chemicals. While many of these approaches are conducted under rigorous laboratory conditions, a significant challenge has been the interpretation of omics data in "real-world" exposure scenarios. Clarity in the interpretation of these data limits their use in environmental monitoring programs. In recent years, one overarching objective of many has been to address fundamental questions concerning experimental design and the robustness of data collected under the broad umbrella of environmental genomics. These questions include: (1) the likelihood that molecular profiles return to a predefined baseline level following remediation efforts, (2) how reference site selection in an urban environment influences interpretation of omics data and (3) what is the most appropriate species to monitor in the environment from an omics point of view. In addition, inter-genomics studies have been conducted to assess transcriptome reproducibility in toxicology studies. One lesson learned from inter-genomics studies is that there are core molecular networks that can be identified by multiple laboratories using the same platform. This supports the idea that "omics-networks" defined a priori may be a viable approach moving forward for evaluating environmental impacts over time. Both spatial and temporal variability in ecosystem structure is expected to influence molecular responses to environmental stressors, and it is important to recognize how these variables, as well as individual factor (i.e. sex, age, maturation), may confound interpretation of network responses to chemicals. This mini-review synthesizes the progress made towards adopting these tools into environmental monitoring and identifies future challenges to be addressed, as we move into the next

  4. An integrated lean-methods approach to hospital facilities redesign.

    Science.gov (United States)

    Nicholas, John

    2012-01-01

    Lean production methods for eliminating waste and improving processes in manufacturing are now being applied in healthcare. As the author shows, the methods are appropriate for redesigning hospital facilities. When used in an integrated manner and employing teams of mostly clinicians, the methods produce facility designs that are custom-fit to patient needs and caregiver work processes, and reduce operational costs. The author reviews lean methods and an approach for integrating them in the redesign of hospital facilities. A case example of the redesign of an emergency department shows the feasibility and benefits of the approach.

  5. Multi-omic profiling of EPO producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    Heterologous protein production in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied to characterize the physiological impact of erythropoietin production, and discover production bottlenecks, ...

  6. Multi-omic profiling of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    2015-01-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied...

  7. A Key Event Path Analysis Approach for Integrated Systems

    Directory of Open Access Journals (Sweden)

    Jingjing Liao

    2012-01-01

    Full Text Available By studying the key event paths of probabilistic event structure graphs (PESGs, a key event path analysis approach for integrated system models is proposed. According to translation rules concluded from integrated system architecture descriptions, the corresponding PESGs are constructed from the colored Petri Net (CPN models. Then the definitions of cycle event paths, sequence event paths, and key event paths are given. Whereafter based on the statistic results after the simulation of CPN models, key event paths are found out by the sensitive analysis approach. This approach focuses on the logic structures of CPN models, which is reliable and could be the basis of structured analysis for discrete event systems. An example of radar model is given to characterize the application of this approach, and the results are worthy of trust.

  8. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

    Science.gov (United States)

    Hultman, Jenni; Waldrop, Mark P; Mackelprang, Rachel; David, Maude M; McFarland, Jack; Blazewicz, Steven J; Harden, Jennifer; Turetsky, Merritt R; McGuire, A David; Shah, Manesh B; VerBerkmoes, Nathan C; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K

    2015-05-14

    Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

  9. Deciphering functional diversification within the lichen microbiota by meta-omics.

    Science.gov (United States)

    Cernava, Tomislav; Erlacher, Armin; Aschenbrenner, Ines Aline; Krug, Lisa; Lassek, Christian; Riedel, Katharina; Grube, Martin; Berg, Gabriele

    2017-07-19

    Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.

  10. Integrated Approaches to Occupational Health and Safety: A Systematic Review.

    Science.gov (United States)

    Cooklin, A; Joss, N; Husser, E; Oldenburg, B

    2017-09-01

    The study objective was to conduct a systematic review of the effectiveness of integrated workplace interventions that combine health promotion with occupational health and safety. Electronic databases (n = 8), including PsychInfo and MEDLINE, were systematically searched. Studies included were those that reported on workplace interventions that met the consensus definition of an "integrated approach," published in English, in the scientific literature since 1990. Data extracted were occupation, worksite, country, sample size, intervention targets, follow-up period, and results reported. Quality was assessed according to American College of Occupational and Environmental Medicine Practice Guidelines. Heterogeneity precluded formal meta-analyses. Results were classified according to the outcome(s) assessed into five categories (health promotion, injury prevention, occupational health and safety management, psychosocial, and return-on-investment). Narrative synthesis of outcomes was performed. A total of 31 eligible studies were identified; 23 (74%) were (quasi-)experimental trials. Effective interventions were most of those aimed at improving employee physical or mental health. Less consistent results were reported from integrated interventions targeting occupational health and safety management, injury prevention, or organizational cost savings. Integrated approaches have been posed as comprehensive solutions to complex issues. Empirical evidence, while still emerging, provides some support for this. Continuing investment in, and evaluation of, integrated approaches are worthwhile.

  11. Safety Concepts in Structural Glass Engineering : Towards an Integrated Approach

    NARCIS (Netherlands)

    Bos, F.P.

    2009-01-01

    This dissertation proposes the Integrated Approach to Structural Glass Safety, based on four clearly defined element safety properties, damage sensitivity, relative resistance, redundancy, and fracture mode. The Element Safety Diagram (ESD) is introduced to provide an easy-to-read graphical

  12. Towards an integrated approach in supporting microbiological food safety decisions

    DEFF Research Database (Denmark)

    Havelaar, A.H.; Braunig, J.; Christiansen, K.

    2007-01-01

    an integrated scientific approach combining veterinary and medical epidemiology, risk assessment for the farm-to-fork food chain as well as agricultural and health economy. Scientific advice is relevant in all stages of the policy cycle: to assess the magnitude of the food safety problem, to define...

  13. Recent changes in Central European landscapes: An integrative ecological approach

    Czech Academy of Sciences Publication Activity Database

    Těšitel, Jan; Kučera, Tomáš

    2005-01-01

    Roč. 24, č. 1 (2005), s. 3-6 ISSN 1335-342X Institutional research plan: CEZ:AV0Z60870520 Keywords : integrative ecological approach * transdisciplinarity * interdisciplinarity * landscape ecology Subject RIV: DO - Wilderness Conservation Impact factor: 0.085, year: 2005

  14. Child Psychotherapy, Child Analysis, and Medication: A Flexible, Integrative Approach.

    Science.gov (United States)

    Whitman, Laura

    2015-01-01

    For children with moderate to severe emotional or behavioral problems, the current approach in child psychiatry is to make an assessment for the use of both psychotherapy and medication. This paper describes integration of antidepressants and stimulants with psychoanalytically oriented techniques.

  15. An Integrated Approach to Indoor and Outdoor Localization

    Science.gov (United States)

    2017-04-17

    TITLE AND SUBTITLE An Integrated Approach to Indoor and Outdoor Localization 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-12-1-0299 5c.   PROGRAM ELEMENT...Distribution approved for public release. Figure 5: A flowchart of the method of computing an initial position estimate by comparing a single WiFi scan

  16. Availability objectives integration to design. The CIDEM approach

    International Nuclear Information System (INIS)

    Degrave, C.; Martin-Onraet, M.

    1994-01-01

    Considering the operation experience feedback from its nuclear park and from foreign parks, and considering new approaches and design tools such as concurrent engineering, total quality, etc., EDF (Electricite de France) has decided to start the CIDEM approach (integration of availability, operating experience feedback and maintenance into design), an analytical and systematical study process for new projects (REP2000 (or PWR2000)), in order to optimize as much as possible the design phase while integrating maintenance, availability and safety objectives, with the view of a minimized kWh cost. This process, already used in other industries, employs concepts such as RAM (Reliability Availability Maintainability), RCM (Reliability Centered Maintenance) and ILS (Integrated Logistic Support). The availability and maintenance scheduling studies for the REP2000 project are detailed. 10 fig., 6 tab

  17. Framework for the quantitative weight-of-evidence analysis of 'omics data for regulatory purposes.

    Science.gov (United States)

    Bridges, Jim; Sauer, Ursula G; Buesen, Roland; Deferme, Lize; Tollefsen, Knut E; Tralau, Tewes; van Ravenzwaay, Ben; Poole, Alan; Pemberton, Mark

    2017-12-01

    A framework for the quantitative weight-of-evidence (QWoE) analysis of 'omics data for regulatory purposes is presented. The QWoE framework encompasses seven steps to evaluate 'omics data (also together with non-'omics data): (1) Hypothesis formulation, identification and weighting of lines of evidence (LoEs). LoEs conjoin different (types of) studies that are used to critically test the hypothesis. As an essential component of the QWoE framework, step 1 includes the development of templates for scoring sheets that predefine scoring criteria with scores of 0-4 to enable a quantitative determination of study quality and data relevance; (2) literature searches and categorisation of studies into the pre-defined LoEs; (3) and (4) quantitative assessment of study quality and data relevance using the respective pre-defined scoring sheets for each study; (5) evaluation of LoE-specific strength of evidence based upon the study quality and study relevance scores of the studies conjoined in the respective LoE; (6) integration of the strength of evidence from the individual LoEs to determine the overall strength of evidence; (7) characterisation of uncertainties and conclusion on the QWoE. To put the QWoE framework in practice, case studies are recommended to confirm the relevance of its different steps, or to adapt them as necessary. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Predictive analytics of environmental adaptability in multi-omic network models.

    Science.gov (United States)

    Angione, Claudio; Lió, Pietro

    2015-10-20

    Bacterial phenotypic traits and lifestyles in response to diverse environmental conditions depend on changes in the internal molecular environment. However, predicting bacterial adaptability is still difficult outside of laboratory controlled conditions. Many molecular levels can contribute to the adaptation to a changing environment: pathway structure, codon usage, metabolism. To measure adaptability to changing environmental conditions and over time, we develop a multi-omic model of Escherichia coli that accounts for metabolism, gene expression and codon usage at both transcription and translation levels. After the integration of multiple omics into the model, we propose a multiobjective optimization algorithm to find the allowable and optimal metabolic phenotypes through concurrent maximization or minimization of multiple metabolic markers. In the condition space, we propose Pareto hypervolume and spectral analysis as estimators of short term multi-omic (transcriptomic and metabolic) evolution, thus enabling comparative analysis of metabolic conditions. We therefore compare, evaluate and cluster different experimental conditions, models and bacterial strains according to their metabolic response in a multidimensional objective space, rather than in the original space of microarray data. We finally validate our methods on a phenomics dataset of growth conditions. Our framework, named METRADE, is freely available as a MATLAB toolbox.

  19. The Twins Study: NASA's First Foray into 21st Century Omics Research

    Science.gov (United States)

    Kundrot, C. E.; Shelhamer, M.; Scott, G. B. I.

    2015-01-01

    The full array of 21st century omics-based research methods should be intelligently employed to reduce the health and performance risks that astronauts will be exposed to during exploration missions beyond low Earth Orbit. In March of 2015, US Astronaut Scott Kelly will launch to the International Space Station for a one year mission while his twin brother, Mark Kelly, a retired US Astronaut, remains on the ground. This situation presents an extremely rare flight opportunity to perform an integrated omics-based demonstration pilot study involving identical twin astronauts. A group of 10 principal investigators has been competitively selected, funded, and teamed together to form the Twins Study. A very broad range of biological function are being examined including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. The plans for the Twins Study and an overview of initial results will be described as well as the technological and ethical issues raised for such spaceflight studies. An anticipated outcome of the Twins Study is that it will place NASA on a trajectory of using omics-based information to develop precision countermeasures for individual astronauts.

  20. Integrating radiology vertically into an undergraduate medical education curriculum: a triphasic integration approach

    Directory of Open Access Journals (Sweden)

    Al Qahtani F

    2014-06-01

    Full Text Available Fahd Al Qahtani,1 Adel Abdelaziz2,31Radiology Department, Faculty of Medicine, Al-Baha University, Al-Baha, Saudi Arabia; 2Medical Education Development Unit, Faculty of Medicine, Al-Baha University, Al-Baha, Saudi Arabia; 3Medical Education Department, Faculty of Medicine, Suez Canal University, Ismailia, EgyptAbstract: Fulfilling the goal of integrating radiology into undergraduate medical curricula is a real challenge due to the enduring faith assuming that traditional medical disciplines are worthy of consuming the available study time. In this manner, radiology is addressed occasionally and with relevance to these traditional disciplines. In Al-Baha University Faculty of Medicine, Al-Baha, Saudi Arabia, efforts have been made to integrate radiology vertically and in a structured manner into the undergraduate curriculum from the first year to the sixth year. For achieving convenient integration of radiology, a triphasic approach to integration is adopted. This approach consists of the integration of radiology foundations into the basic sciences phase, development of a distinct 4-week module in year 4, and finally, integration of clinical applications of radiology in the clinical phase modules. Feedback of students and inferences obtained through assessment and program evaluation are in favor of this approach to integration. Minor reform and some improvement related to time allocated and content balancing are still indicated.Keywords: radiology foundations, radiology module, students assessment

  1. The use of 'Omics technology to rationally improve industrial mammalian cell line performance.

    Science.gov (United States)

    Lewis, Amanda M; Abu-Absi, Nicholas R; Borys, Michael C; Li, Zheng Jian

    2016-01-01

    Biologics represent an increasingly important class of therapeutics, with 7 of the 10 top selling drugs from 2013 being in this class. Furthermore, health authority approval of biologics in the immuno-oncology space is expected to transform treatment of patients with debilitating and deadly diseases. The growing importance of biologics in the healthcare field has also resulted in the recent approvals of several biosimilars. These recent developments, combined with pressure to provide treatments at lower costs to payers, are resulting in increasing need for the industry to quickly and efficiently develop high yielding, robust processes for the manufacture of biologics with the ability to control quality attributes within narrow distributions. Achieving this level of manufacturing efficiency and the ability to design processes capable of regulating growth, death and other cellular pathways through manipulation of media, feeding strategies, and other process parameters will undoubtedly be facilitated through systems biology tools generated in academic and public research communities. Here we discuss the intersection of systems biology, 'Omics technologies, and mammalian bioprocess sciences. Specifically, we address how these methods in conjunction with traditional monitoring techniques represent a unique opportunity to better characterize and understand host cell culture state, shift from an empirical to rational approach to process development and optimization of bioreactor cultivation processes. We summarize the following six key areas: (i) research applied to parental, non-recombinant cell lines; (ii) systems level datasets generated with recombinant cell lines; (iii) datasets linking phenotypic traits to relevant biomarkers; (iv) data depositories and bioinformatics tools; (v) in silico model development, and (vi) examples where these approaches have been used to rationally improve cellular processes. We critically assess relevant and state of the art research

  2. Critical perspectives of pedagogical approaches to reversing the order of integration in double integrals

    Science.gov (United States)

    Tisdell, Christopher C.

    2017-11-01

    This paper presents some critical perspectives regarding pedagogical approaches to the method of reversing the order of integration in double integrals from prevailing educational literature on multivariable calculus. First, we question the message found in popular textbooks that the traditional process of reversing the order of integration is necessary when solving well-known problems. Second, we illustrate that the method of integration by parts can be directly applied to many of the classic pedagogical problems in the literature concerning double integrals, without taking the well-worn steps associated with reversing the order of integration. Third, we examine the benefits and limitations of such a method. In our conclusion, we advocate for integration by parts to be a part of the pedagogical conversation in the learning and teaching of double integral methods; and call for more debate around its use in the learning and teaching of other areas of mathematics. Finally, we emphasize the need for critical approaches in the pedagogy of mathematics more broadly.

  3. Science of Integrated Approaches to Natural Resources Management

    Science.gov (United States)

    Tengberg, Anna; Valencia, Sandra

    2017-04-01

    To meet multiple environmental objectives, integrated programming is becoming increasingly important for the Global Environmental Facility (GEF), the financial mechanism of the multilateral environmental agreements, including the United Nations Convention to Combat Desertification (UNCCD). Integration of multiple environmental, social and economic objectives also contributes to the achievement of the Sustainable Development Goals (SDGs) in a timely and cost-effective way. However, integration is often not well defined. This paper therefore focuses on identifying key aspects of integration and assessing their implementation in natural resources management (NRM) projects. To that end, we draw on systems thinking literature, and carry out an analysis of a random sample of GEF integrated projects and in-depth case studies demonstrating lessons learned and good practices in addressing land degradation and other NRM challenges. We identify numerous challenges and opportunities of integrated approaches that need to be addressed in order to maximise the catalytic impact of the GEF during problem diagnosis, project design, implementation and governance. We highlight the need for projects to identify clearer system boundaries and main feedback mechanisms within those boundaries, in order to effectively address drivers of environmental change. We propose a theory of change for Integrated Natural Resources Management (INRM) projects, where short-term environmental and socio-economic benefits will first accrue at the local level. Implementation of improved INRM technologies and practices at the local level can be extended through spatial planning, strengthening of innovation systems, and financing and incentive mechanisms at the watershed and/or landscape/seascape level to sustain and enhance ecosystem services at larger scales and longer time spans. We conclude that the evolving scientific understanding of factors influencing social, technical and institutional innovations and

  4. Integrated systems approach to meet the insider threat

    International Nuclear Information System (INIS)

    Barnes, L.D.

    1985-01-01

    This paper describes an approach to mitigating the insider threat by integrating and supplementing existing data systems and procedures without placing an undue burden on plant management and operating personnel. Nuclear facilities have plans to deal with any forseeable chain of events, and long-term records of activities are maintained to verify that the requirements are met. The integrated systems approach proposed in this paper does not change established facility practices; rather, the approach attempts to utilize the information generated by the system. This will provide real-time interaction between the documented work permits, the operating procedure system, and the security system so that controlled access authorizations are based on a need to enter and access is limited to specific times and places

  5. Posterior Approach to Kidney Dissection: An Old Surgical Approach for Integrated Medical Curricula

    Science.gov (United States)

    Daly, Frank J.; Bolender, David L.; Jain, Deepali; Uyeda, Sheryl; Hoagland, Todd M.

    2015-01-01

    Integrated medical curricular changes are altering the historical regional anatomy approach to abdominal dissection. The renal system is linked physiologically and biochemically to the cardiovascular and respiratory systems; yet, anatomists often approach the urinary system as part of the abdomen and pelvic regions. As part of an integrated…

  6. Graph-based sequence annotation using a data integration approach.

    Science.gov (United States)

    Pesch, Robert; Lysenko, Artem; Hindle, Matthew; Hassani-Pak, Keywan; Thiele, Ralf; Rawlings, Christopher; Köhler, Jacob; Taubert, Jan

    2008-08-25

    The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara-Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.

  7. Spatial Data Integration Using Ontology-Based Approach

    Science.gov (United States)

    Hasani, S.; Sadeghi-Niaraki, A.; Jelokhani-Niaraki, M.

    2015-12-01

    In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

  8. SPATIAL DATA INTEGRATION USING ONTOLOGY-BASED APPROACH

    Directory of Open Access Journals (Sweden)

    S. Hasani

    2015-12-01

    Full Text Available In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

  9. Abelian Chern endash Simons theory. II. A functional integral approach

    International Nuclear Information System (INIS)

    Manoliu, M.

    1998-01-01

    Following Witten, [Commun. Math. Phys. 21, 351 endash 399 (1989)] we approach the Abelian quantum Chern endash Simons (CS) gauge theory from a Feynman functional integral point of view. We show that for 3-manifolds with and without a boundary the formal functional integral definitions lead to mathematically proper expressions that agree with the results from the rigorous construction [J. Math. Phys. 39, 170 endash 206 (1998)] of the Abelian CS topological quantum field theory via geometric quantization. copyright 1998 American Institute of Physics

  10. Dynamic integration of residential building design and green energies : the Bireth approach : building integrated renewable energy total harvest approach

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, K.P. [Hong Kong Univ., Hong Kong (China). Dept. of Architecture; Luk, C.L.P. [Chu Hai College of Higher Education, Hong Kong (China). Dept. of Architecture; Wong, S.T. [Hong Kong Univ., Hong Kong (China). Div. of Arts and Humanities, SPACE; Chung, S.L.; Fung, K.S.; Leung, M.F. [Hong Kong Inst. of Vocational Education, Hong Kong (China)

    2006-07-01

    Renewable energy sources that are commonly used in buildings include solar energy, wind energy and rainwater collection. High quality environmentally responsive residential buildings are designed to provide good insulation in winter and solar shading in summer. However, this study demonstrated that the green energy design in residential buildings is not usually well integrated. For example, windows with clear double or triple glazed glass, allow good penetration of sunlight during the day in winter, but are not further dynamically insulated for when the sun goes down to avoid heat loss from the building. Additionally, good solar static shading devices often block much needed daylight on cloudy winter days. These examples emphasize the lack of an integrated approach to gain the best advantage of green energies and to minimize energy costs in residential buildings. This study addressed issues facing the integrated approach with particular reference to the design of a small residential building in rural Beijing. The design included a new approach for interpreting a traditional Beijing court yard house in the modern Beijing rural context, while integrating multi-responding innovative green energy applications derived from first principles. This paper also presented a proposal for a village house in Hong Kong to harvest as much renewable energies as possible, primarily wind energy and solar energy, that come into contact with the building. The purpose was to work towards a renewable energy approach for buildings, namely the Bireth approach, which will benefit practically all houses by making them zero energy houses. The paper described the feasibility of integrating renewable energies in buildings to fulfill performance requirements such improving ventilation, providing warm interiors, drying clothes, or storing solar and wind energies into power batteries. The challenges facing the development of a proposed micro solar hot air turbine were also presented. 15 refs., 6

  11. A design approach for integrating thermoelectric devices using topology optimization

    International Nuclear Information System (INIS)

    Soprani, S.; Haertel, J.H.K.; Lazarov, B.S.; Sigmund, O.; Engelbrecht, K.

    2016-01-01

    Highlights: • The integration of a thermoelectric (TE) cooler into a robotic tool is optimized. • Topology optimization is suggested as design tool for TE integrated systems. • A 3D optimization technique using temperature dependent TE properties is presented. • The sensitivity of the optimization process to the boundary conditions is studied. • A working prototype is constructed and compared to the model results. - Abstract: Efficient operation of thermoelectric devices strongly relies on the thermal integration into the energy conversion system in which they operate. Effective thermal integration reduces the temperature differences between the thermoelectric module and its thermal reservoirs, allowing the system to operate more efficiently. This work proposes and experimentally demonstrates a topology optimization approach as a design tool for efficient integration of thermoelectric modules into systems with specific design constraints. The approach allows thermal layout optimization of thermoelectric systems for different operating conditions and objective functions, such as temperature span, efficiency, and power recovery rate. As a specific application, the integration of a thermoelectric cooler into the electronics section of a downhole oil well intervention tool is investigated, with the objective of minimizing the temperature of the cooled electronics. Several challenges are addressed: ensuring effective heat transfer from the load, minimizing the thermal resistances within the integrated system, maximizing the thermal protection of the cooled zone, and enhancing the conduction of the rejected heat to the oil well. The design method incorporates temperature dependent properties of the thermoelectric device and other materials. The 3D topology optimization model developed in this work was used to design a thermoelectric system, complete with insulation and heat sink, that was produced and tested. Good agreement between experimental results and

  12. An integrated approach towards future ballistic neck protection materials selection.

    Science.gov (United States)

    Breeze, John; Helliker, Mark; Carr, Debra J

    2013-05-01

    Ballistic protection for the neck has historically taken the form of collars attached to the ballistic vest (removable or fixed), but other approaches, including the development of prototypes incorporating ballistic material into the collar of an under body armour shirt, are now being investigated. Current neck collars incorporate the same ballistic protective fabrics as the soft armour of the remaining vest, reflecting how ballistic protective performance alone has historically been perceived as the most important property for neck protection. However, the neck has fundamental differences from the thorax in terms of anatomical vulnerability, flexibility and equipment integration, necessitating a separate solution from the thorax in terms of optimal materials selection. An integrated approach towards the selection of the most appropriate combination of materials to be used for each of the two potential designs of future neck protection has been developed. This approach requires evaluation of the properties of each potential material in addition to ballistic performance alone, including flexibility, mass, wear resistance and thermal burden. The aim of this article is to provide readers with an overview of this integrated approach towards ballistic materials selection and an update of its current progress in the development of future ballistic neck protection.

  13. Incorporation of omics analyses into artificial gravity research for space exploration countermeasure development.

    Science.gov (United States)

    Schmidt, Michael A; Goodwin, Thomas J; Pelligra, Ralph

    The next major steps in human spaceflight include flyby, orbital, and landing missions to the Moon, Mars, and near earth asteroids. The first crewed deep space mission is expected to launch in 2022, which affords less than 7 years to address the complex question of whether and how to apply artificial gravity to counter the effects of prolonged weightlessness. Various phenotypic changes are demonstrated during artificial gravity experiments. However, the molecular dynamics (genotype and molecular phenotypes) that underlie these morphological, physiological, and behavioral phenotypes are far more complex than previously understood. Thus, targeted molecular assessment of subjects under various G conditions can be expected to miss important patterns of molecular variance that inform the more general phenotypes typically being measured. Use of omics methods can help detect changes across broad molecular networks, as various G-loading paradigms are applied. This will be useful in detecting off-target, or unanticipated effects of the different gravity paradigms applied to humans or animals. Insights gained from these approaches may eventually be used to inform countermeasure development or refine the deployment of existing countermeasures. This convergence of the omics and artificial gravity research communities may be critical if we are to develop the proper artificial gravity solutions under the severely compressed timelines currently established. Thus, the omics community may offer a unique ability to accelerate discovery, provide new insights, and benefit deep space missions in ways that have not been previously considered.

  14. Path-integral approach to resonant electron-molecule scattering

    International Nuclear Information System (INIS)

    Winterstetter, M.; Domcke, W.

    1993-01-01

    A path-integral formulation of resonant electron-molecule scattering is developed within the framework of the projection-operator formalism of scattering theory. The formation and decay of resonances is treated in real time as a quantum-mechanical electronic-tunneling process, modified by the coupling of the electronic motion with the nuclear degrees of freedom. It is shown that the electronic continuum can be summed over in the path-integral formulation, resulting formally in the path integral for an effective two-state system with coupling to vibrations. The harmonic-oscillator approximation is adopted for the vibrational motion in the present work. Approximation methods are introduced which render the numerical evaluation of the sum over paths feasible for up to ∼10 3 elementary time slices. The theory is numerically realized for simple but nontrivial models representing the 2 Π g d-wave shape resonance in e - +N 2 collisions and the 2 Σ u + p-wave shape resonance in e - +H 2 collisions, respectively. The accuracy of the path-integral results is assessed by comparison with exact numerical reference data for these models. The essential virtue of the path-integral approach is the fact that the computational effort scales at most linearly with the number of vibrational degrees of freedom. The path-integral method is thus well suited to treat electron collisions with polyatomic molecules and molecular aggregates

  15. Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Geng, Peng; Zhang, Liang; Shi, Gui Yang

    2017-05-01

    Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.

  16. Babenko’s Approach to Abel’s Integral Equations

    Directory of Open Access Journals (Sweden)

    Chenkuan Li

    2018-03-01

    Full Text Available The goal of this paper is to investigate the following Abel’s integral equation of the second kind: y ( t + λ Γ ( α ∫ 0 t ( t − τ α − 1 y ( τ d τ = f ( t , ( t > 0 and its variants by fractional calculus. Applying Babenko’s approach and fractional integrals, we provide a general method for solving Abel’s integral equation and others with a demonstration of different types of examples by showing convergence of series. In particular, we extend this equation to a distributional space for any arbitrary α ∈ R by fractional operations of generalized functions for the first time and obtain several new and interesting results that cannot be realized in the classical sense or by the Laplace transform.

  17. Drugs of Abuse and Addiction: An integrated approach to teaching.

    Science.gov (United States)

    Miller, Lindsey N; Mercer, Susan L

    2017-05-01

    To describe the design, implementation, and student perceptions of a Drugs of Abuse and Addiction elective course utilizing an integrated teaching model. Third-year pharmacy students enrolled in the two credit hour elective. Teaching methodology included didactic lecture, journal club, simulated addiction assignment with reflection, debates, external speakers, site visit to a residential drug court program and research paper with presentation. A course objective survey was administered upon course completion. All students strongly agreed that having science- and clinical-based faculty members develop and deliver course content was beneficial. Additionally, all students agree to strongly agree that their research project helped them integrate and comprehend the science and practice surrounding drugs of abuse and addiction. Students enjoyed an integrated teaching approach and multiple teaching methodologies leading to increased engagement and enhancement of student learning. Course enrollment was beneficial for personalized learning, but limited student perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. The Integrated Approach to the Accident Evaluation for Advanced LWRs

    International Nuclear Information System (INIS)

    Oriolo, F.; Paci, S.

    1998-01-01

    The present paper discusses some relevant phenomena occurring in advanced LWRs during postulated accident scenarios. In particular, the operation of ESF is the starting point for analysis of those phenomena that cause the mutual influence between PS and containment in these plants. As a consequence, it is highlighted as accident analyses which treat PS and containment phenomena completely separated may be not adequate when applied to innovate reactors. Exemplified thermal-hydraulic analysis are presented for AP600 and SBWR, using the FUMO integrated model, for highlight accident evolution taking into account these interactions. The architecture of this integrated code is presented highlighting the importance of an integrated approach to the safety analysis in innovative reactors. (author)

  19. Systems Approaches: A Global and Historical Perspective on Integrative Medicine

    Science.gov (United States)

    2012-01-01

    The globalization of healing systems is a dance of cultural awareness and cultural dominance that has arisen throughout history. With the development of greater communication and interest in whole-systems approaches to healing, the opportunity for the development of a global perspective on healing has emerged with new life force. The birth of integrative holistic healing systems in the West, such as naturopathic, homeopathic, anthroposophic, integral and functional medicine, and others, echoes the ocean of wisdom present in traditional healing systems, such as traditional Chinese medicine (TCM) and Ayurveda. In working to integrate the lessons from these systems, we see the inextricable link between man and the natural world, we work to understand the root cause of disease, we focus on the whole person to return balance, and we use empiric observation in large populations over time to grasp the interrelationships inherent in the whole-systems view of illness and wellness. PMID:24278794

  20. Integrated Transport Planning Framework Involving Combined Utility Regret Approach

    DEFF Research Database (Denmark)

    Wang, Yang; Monzon, Andres; Di Ciommo, Floridea

    2014-01-01

    Sustainable transport planning requires an integrated approach involving strategic planning, impact analysis, and multicriteria evaluation. This study aimed at relaxing the utility-based decision-making assumption by newly embedding anticipated-regret and combined utility regret decision mechanisms...... in a framework for integrated transport planning. The framework consisted of a two-round Delphi survey, integrated land use and transport model for Madrid, and multicriteria analysis. Results show that (a) the regret-based ranking has a similar mean but larger variance than the utility-based ranking does, (b......) the least-regret scenario forms a compromise between the desired and the expected scenarios, (c) the least-regret scenario can lead to higher user benefits in the short term and lower user benefits in the long term, (d) the utility-based, the regret-based, and the combined utility- and regret...

  1. RISK MANAGEMENT: AN INTEGRATED APPROACH TO RISK MANAGEMENT AND ASSESSMENT

    OpenAIRE

    Szabo Alina

    2012-01-01

    Purpose: The objective of this paper is to offer an overview over risk management cycle by focusing on prioritization and treatment, in order to ensure an integrated approach to risk management and assessment, and establish the ‘top 8-12’ risks report within the organization. The interface with Internal Audit is ensured by the implementation of the scoring method to prioritize risks collected from previous generated risk report. Methodology/approach: Using evidence from other research in ...

  2. Flexible Web services integration: a novel personalised social approach

    Science.gov (United States)

    Metrouh, Abdelmalek; Mokhati, Farid

    2018-05-01

    Dynamic composition or integration remains one of the key objectives of Web services technology. This paper aims to propose an innovative approach of dynamic Web services composition based on functional and non-functional attributes and individual preferences. In this approach, social networks of Web services are used to maintain interactions between Web services in order to select and compose Web services that are more tightly related to user's preferences. We use the concept of Web services community in a social network of Web services to reduce considerably their search space. These communities are created by the direct involvement of Web services providers.

  3. A manufacturable process integration approach for graphene devices

    Science.gov (United States)

    Vaziri, Sam; Lupina, Grzegorz; Paussa, Alan; Smith, Anderson D.; Henkel, Christoph; Lippert, Gunther; Dabrowski, Jarek; Mehr, Wolfgang; Östling, Mikael; Lemme, Max C.

    2013-06-01

    In this work, we propose an integration approach for double gate graphene field effect transistors. The approach includes a number of process steps that are key for future integration of graphene in microelectronics: bottom gates with ultra-thin (2 nm) high-quality thermally grown SiO2 dielectrics, shallow trench isolation between devices and atomic layer deposited Al2O3 top gate dielectrics. The complete process flow is demonstrated with fully functional GFET transistors and can be extended to wafer scale processing. We assess, through simulation, the effects of the quantum capacitance and band bending in the silicon substrate on the effective electric fields in the top and bottom gate oxide. The proposed process technology is suitable for other graphene-based devices such as graphene-based hot electron transistors and photodetectors.

  4. The integrated approach to teaching programming in secondary school

    Directory of Open Access Journals (Sweden)

    Martynyuk A.A.

    2018-02-01

    Full Text Available the article considers an integrated approach to teaching programming with the use of technologies of computer modeling and 3D-graphics, allowing to improve the quality of education. It is shown that this method will allow you to systematize knowledge, improve the level of motivation through the inclusion of relevant technologies, to develop skills of project activities, to strengthen interdisciplinary connections, and promotes professional and personal self-determination of students of secondary school.

  5. Graph-based sequence annotation using a data integration approach

    Directory of Open Access Journals (Sweden)

    Pesch Robert

    2008-06-01

    Full Text Available The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.

  6. Workplace mental health: developing an integrated intervention approach

    Science.gov (United States)

    2014-01-01

    Background Mental health problems are prevalent and costly in working populations. Workplace interventions to address common mental health problems have evolved relatively independently along three main threads or disciplinary traditions: medicine, public health, and psychology. In this Debate piece, we argue that these three threads need to be integrated to optimise the prevention of mental health problems in working populations. Discussion To realise the greatest population mental health benefits, workplace mental health intervention needs to comprehensively 1) protect mental health by reducing work–related risk factors for mental health problems; 2) promote mental health by developing the positive aspects of work as well as worker strengths and positive capacities; and 3) address mental health problems among working people regardless of cause. We outline the evidence supporting such an integrated intervention approach and consider the research agenda and policy developments needed to move towards this goal, and propose the notion of integrated workplace mental health literacy. Summary An integrated approach to workplace mental health combines the strengths of medicine, public health, and psychology, and has the potential to optimise both the prevention and management of mental health problems in the workplace. PMID:24884425

  7. [Integrative approach in the psychotherapy of borderline personality disorder].

    Science.gov (United States)

    Kuritárné Szabó, Ildikó

    2012-01-01

    In the last 20 years six psychotherapy methods have been developed specifically for borderline personality disorder. Solid RCT evidences suggests the efficacy of all the methods. Roughly equivalent improvement was obtained from the different types of psychotherapies. Today we have reached a new phase of the borderline "psychotherapy boom", the integrative approach. According to the integrative treatment advocates we should not choose among these effective treatments but we can incorporate in the therapy all the components that work. The integrative approach uses general factors common to all effective therapies, combined with specific treatment techniques taken from different therapies in order to treat the given patient's psychopathology. These common factors are: coherent framework; attention to strategies for building strong positive alliance and maintaining patient motivation; creating a safe and structured therapeutic environment; clear treatment frame; transparency of the goals and roles; focus upon presenting problems; higher level therapeutic activity; here-and-now focus; and facilitating self-reflection. Treatment focuses on change while maintaining a validating and supportive stance. General strategies can be supplemented by more specific techniques such as cognitive-behavioral interventions for reducing maladaptive behavior, training for developing emotion regulation skills and interpersonal skills coming from dialectical behavior therapy. Methods drawn from psychodynamic approaches can be used for the modification of underlying interpersonal cognitive-emotional schemas.

  8. Integration of distributed system simulation tools for a holistic approach to integrated building and system design

    NARCIS (Netherlands)

    Radosevic, M.; Hensen, J.L.M.; Wijsman, A.J.T.M.; Hensen, J.L.M.; Lain, M.

    2004-01-01

    Advanced architectural developments require an integrated approach to design where simulation tools available today deal. only with a small subset of the overall problem. The aim of this study is to enable run time exchange of necessary data at suitable frequency between different simulation

  9. An integrated approach for integrated intelligent instrumentation and control system (I3CS)

    International Nuclear Information System (INIS)

    Jung, C.H.; Kim, J.T.; Kwon, K.C.

    1997-01-01

    Nuclear power plants to guarantee the safety of public should be designed to reduce the operator intervention resulting in operating human errors, identify the process states in transients, and aid to make a decision of their tasks and guide operator actions. For the sake of this purpose, MMIS(MAN-Machine Interface System) in NPPs should be the integrated top-down approach tightly focused on the function-based task analysis including an advanced digital technology, an operator support function, and so on. The advanced I and C research team in KAERI has embarked on developing an Integrated Intelligent Instrumentation and Control System (I 3 CS) for Korea's next generation nuclear power plants. I 3 CS bases the integrated top-down approach on the function-based task analysis, modern digital technology, standardization and simplification, availability and reliability, and protection of investment. (author). 4 refs, 6 figs

  10. An integrated approach for integrated intelligent instrumentation and control system (I{sup 3}CS)

    Energy Technology Data Exchange (ETDEWEB)

    Jung, C H; Kim, J T; Kwon, K C [Korea Atomic Energy Research Inst., Yusong, Taejon (Korea, Republic of)

    1997-07-01

    Nuclear power plants to guarantee the safety of public should be designed to reduce the operator intervention resulting in operating human errors, identify the process states in transients, and aid to make a decision of their tasks and guide operator actions. For the sake of this purpose, MMIS(MAN-Machine Interface System) in NPPs should be the integrated top-down approach tightly focused on the function-based task analysis including an advanced digital technology, an operator support function, and so on. The advanced I and C research team in KAERI has embarked on developing an Integrated Intelligent Instrumentation and Control System (I{sup 3}CS) for Korea`s next generation nuclear power plants. I{sup 3}CS bases the integrated top-down approach on the function-based task analysis, modern digital technology, standardization and simplification, availability and reliability, and protection of investment. (author). 4 refs, 6 figs.

  11. Validation of standard operating procedures in a multicenter retrospective study to identify -omics biomarkers for chronic low back pain.

    Directory of Open Access Journals (Sweden)

    Concetta Dagostino

    Full Text Available Chronic low back pain (CLBP is one of the most common medical conditions, ranking as the greatest contributor to global disability and accounting for huge societal costs based on the Global Burden of Disease 2010 study. Large genetic and -omics studies provide a promising avenue for the screening, development and validation of biomarkers useful for personalized diagnosis and treatment (precision medicine. Multicentre studies are needed for such an effort, and a standardized and homogeneous approach is vital for recruitment of large numbers of participants among different centres (clinical and laboratories to obtain robust and reproducible results. To date, no validated standard operating procedures (SOPs for genetic/-omics studies in chronic pain have been developed. In this study, we validated an SOP model that will be used in the multicentre (5 centres retrospective "PainOmics" study, funded by the European Community in the 7th Framework Programme, which aims to develop new biomarkers for CLBP through three different -omics approaches: genomics, glycomics and activomics. The SOPs describe the specific procedures for (1 blood collection, (2 sample processing and storage, (3 shipping details and (4 cross-check testing and validation before assays that all the centres involved in the study have to follow. Multivariate analysis revealed the absolute specificity and homogeneity of the samples collected by the five centres for all genetics, glycomics and activomics analyses. The SOPs used in our multicenter study have been validated. Hence, they could represent an innovative tool for the correct management and collection of reliable samples in other large-omics-based multicenter studies.

  12. How can design approaches be integrated into entrepreneurship education?

    DEFF Research Database (Denmark)

    Færgemann, Helle Meibom; Nørgård, Rikke Toft; Robinson, Sarah

    reflection about the intention and how the elements fit with the entrepreneurship field. The proposed process model presented (Fig 3) primarily has potential to strengthen the awareness of the need to alternate between divergence and convergence many times through an entrepreneurial process. Apart from......Questions we care about: When educating students through entrepreneurship we are interested in how can design approaches and processes be integrated into Entrepreneurship Education and what effect does this have on entrepreneurial learning? Approach: This is a conceptual paper which draws on data...... from a classic entrepreneurship course (mix of for- and through-approach) as well as a classic design course. Furthermore data from the iterative development of an entrepreneurship course with substantial design elements is a key data source. Overall, products and processes in the course have been...

  13. Integration of expression data in genome-scale metabolic network reconstructions

    Directory of Open Access Journals (Sweden)

    Anna S. Blazier

    2012-08-01

    Full Text Available With the advent of high-throughput technologies, the field of systems biology has amassed an abundance of omics data, quantifying thousands of cellular components across a variety of scales, ranging from mRNA transcript levels to metabolite quantities. Methods are needed to not only integrate this omics data but to also use this data to heighten the predictive capabilities of computational models. Several recent studies have successfully demonstrated how flux balance analysis (FBA, a constraint-based modeling approach, can be used to integrate transcriptomic data into genome-scale metabolic network reconstructions to generate predictive computational models. In this review, we summarize such FBA-based methods for integrating expression data into genome-scale metabolic network reconstructions, highlighting their advantages as well as their limitations.

  14. RISK MANAGEMENT: AN INTEGRATED APPROACH TO RISK MANAGEMENT AND ASSESSMENT

    Directory of Open Access Journals (Sweden)

    Szabo Alina

    2012-12-01

    Full Text Available Purpose: The objective of this paper is to offer an overview over risk management cycle by focusing on prioritization and treatment, in order to ensure an integrated approach to risk management and assessment, and establish the ‘top 8-12’ risks report within the organization. The interface with Internal Audit is ensured by the implementation of the scoring method to prioritize risks collected from previous generated risk report. Methodology/approach: Using evidence from other research in the area and the professional expertise, this article outlines an integrated approach to risk assessment and risk management reporting processes, by separating the risk in two main categories: strategic and operational risks. The focus is on risk prioritization and scoring; the final output will comprise a mix of strategic and operational (‘top 8-12’ risks, which should be used to establish the annual Internal Audit plan. Originality/value: By using an integrated approach to risk assessment and risk management will eliminate the need for a separate Internal Audit risk assessment over prevailing risks. It will reduce the level of risk assessment overlap by different functions (Tax, Treasury, Information System over the same risk categories as a single methodology, is used and will align timings of risk assessment exercises. The risk prioritization by usage of risk and control scoring criteria highlights the combination between financial and non-financial impact criteria allowing risks that do not naturally lend themselves to a financial amount to be also assessed consistently. It is emphasized the usage of score method to prioritize the risks included in the annual audit plan in order to increase accuracy and timelines.

  15. Auditory-Verbal Music Play Therapy: An Integrated Approach (AVMPT).

    Science.gov (United States)

    Mohammad Esmaeilzadeh, Sahar; Sharifi, Shahla; Tayarani Niknezhad, Hamid

    2013-09-01

    Hearing loss occurs when there is a problem with one or more parts of the ear or ears and causes children to have a delay in the language-learning process. Hearing loss affects children's lives and their development. Several approaches have been developed over recent decades to help hearing-impaired children develop language skills. Auditory-verbal therapy (AVT) is one such approach. Recently, researchers have found that music and play have a considerable effect on the communication skills of children, leading to the development of music therapy (MT) and play therapy (PT). There have been several studies which focus on the impact of music on hearing-impaired children. The aim of this article is to review studies conducted in AVT, MT, and PT and their efficacy in hearing-impaired children. Furthermore, the authors aim to introduce an integrated approach of AVT, MT, and PT which facilitates language and communication skills in hearing-impaired children. In this article we review studies of AVT, MT, and PT and their impact on hearing-impaired children. To achieve this goal, we searched databases and journals including Elsevier, Chor Teach, and Military Psychology, for example. We also used reliable websites such as American Choral Directors Association and Joint Committee on Infant Hearing websites. The websites were reviewed and key words in this article used to find appropriate references. Those articles which are related to ours in content were selected. VT, MT, and PT enhance children's communication and language skills from an early age. Each method has a meaningful impact on hearing loss, so by integrating them we have a comprehensive method in order to facilitate communication and language learning. To achieve this goal, the article offers methods and techniques to perform AVT and MT integrated with PT leading to an approach which offers all advantages of these three types of therapy.

  16. A path integral approach to the Hodgkin-Huxley model

    Science.gov (United States)

    Baravalle, Roman; Rosso, Osvaldo A.; Montani, Fernando

    2017-11-01

    To understand how single neurons process sensory information, it is necessary to develop suitable stochastic models to describe the response variability of the recorded spike trains. Spikes in a given neuron are produced by the synergistic action of sodium and potassium of the voltage-dependent channels that open or close the gates. Hodgkin and Huxley (HH) equations describe the ionic mechanisms underlying the initiation and propagation of action potentials, through a set of nonlinear ordinary differential equations that approximate the electrical characteristics of the excitable cell. Path integral provides an adequate approach to compute quantities such as transition probabilities, and any stochastic system can be expressed in terms of this methodology. We use the technique of path integrals to determine the analytical solution driven by a non-Gaussian colored noise when considering the HH equations as a stochastic system. The different neuronal dynamics are investigated by estimating the path integral solutions driven by a non-Gaussian colored noise q. More specifically we take into account the correlational structures of the complex neuronal signals not just by estimating the transition probability associated to the Gaussian approach of the stochastic HH equations, but instead considering much more subtle processes accounting for the non-Gaussian noise that could be induced by the surrounding neural network and by feedforward correlations. This allows us to investigate the underlying dynamics of the neural system when different scenarios of noise correlations are considered.

  17. Optimal Integration of Intermittent Renewables: A System LCOE Stochastic Approach

    Directory of Open Access Journals (Sweden)

    Carlo Lucheroni

    2018-03-01

    Full Text Available We propose a system level approach to value the impact on costs of the integration of intermittent renewable generation in a power system, based on expected breakeven cost and breakeven cost risk. To do this, we carefully reconsider the definition of Levelized Cost of Electricity (LCOE when extended to non-dispatchable generation, by examining extra costs and gains originated by the costly management of random power injections. We are thus lead to define a ‘system LCOE’ as a system dependent LCOE that takes properly into account intermittent generation. In order to include breakeven cost risk we further extend this deterministic approach to a stochastic setting, by introducing a ‘stochastic system LCOE’. This extension allows us to discuss the optimal integration of intermittent renewables from a broad, system level point of view. This paper thus aims to provide power producers and policy makers with a new methodological scheme, still based on the LCOE but which updates this valuation technique to current energy system configurations characterized by a large share of non-dispatchable production. Quantifying and optimizing the impact of intermittent renewables integration on power system costs, risk and CO 2 emissions, the proposed methodology can be used as powerful tool of analysis for assessing environmental and energy policies.

  18. An integrated approach to evaluate food antioxidant capacity.

    Science.gov (United States)

    Sun, T; Tanumihardjo, S A

    2007-11-01

    Many methods are available for determining food antioxidant capacity, which is an important topic in food and nutrition research and marketing. However, the results and inferences from different methods may vary substantially because each complex chemical reaction generates unique values. To get a complete and dynamic picture of the ranking of food antioxidant capacity, relative antioxidant capacity index (RACI), a hypothetical concept, is created from the perspective of statistics by integrating the antioxidant capacity values generated from different in vitro methods. RACI is the mean value of standard scores transformed from the initial data generated with different methods for each food item. By comparing the antioxidant capacity of 20 commonly consumed vegetables in the U.S. market that were measured with 7 chemical methods, we demonstrated that the RACI correlated strongly with each method. The significant correlation of RACI with an independent data set further confirmed that RACI is a valid tool to assess food antioxidant capacity. The key advantage of this integrated approach is that RACI is in a numerical scale with no units and has consistent agreement with chemical methods. Although it is a relative index and may not represent a specific antioxidant property of different food items, RACI provides a reasonably accurate rank of antioxidant capacity among foods. Therefore, it can be used as an integrated approach to evaluate food antioxidant capacity.

  19. Studying integrated health care systems with a structurationist approach

    Science.gov (United States)

    Demers, Louis; Arseneault, Stéphane; Couturier, Yves

    2010-01-01

    Introduction To implement an integrated health care system is not an easy task and to ensure its sustainability is yet more difficult. Aim Discuss how a structurationist approach can shed light on the stakes of these processes and guide the managers of such endeavours. Theory and method Structuration theory [1] has been used by numerous authors to cast new light on complex organizational phenomena. One of the central tenets of this theory is that social systems, such as integrated health care systems, are recurrent social practices across time-space and are characterized by structural properties which simultaneously constrain and enable the constitutive social actors who reproduce and transform the system through their practices. We will illustrate our theoretical standpoint with empirical material gathered during the study of an integrated health care system for the frail elderly in Quebec, Canada. This system has been implemented in 1997 and is still working well in 2010. Results and conclusion To implement an integrated health care system that is both effective and sustainable, its managers must shrewdly allow for the existing system and progressively introduce changes in the way managers and practitioners at work in the system view their role and act on a daily basis.

  20. Design of pressure vessels using shape optimization: An integrated approach

    Energy Technology Data Exchange (ETDEWEB)

    Carbonari, R.C., E-mail: ronny@usp.br [Department of Mechatronic Engineering, Escola Politecnica da Universidade de Sao Paulo, Av. Prof. Mello Moraes, 2231 Sao Paulo, SP 05508-900 (Brazil); Munoz-Rojas, P.A., E-mail: pablo@joinville.udesc.br [Department of Mechanical Engineering, Universidade do Estado de Santa Catarina, Bom Retiro, Joinville, SC 89223-100 (Brazil); Andrade, E.Q., E-mail: edmundoq@petrobras.com.br [CENPES, PDP/Metodos Cientificos, Petrobras (Brazil); Paulino, G.H., E-mail: paulino@uiuc.edu [Newmark Laboratory, Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Av., Urbana, IL 61801 (United States); Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 158 Mechanical Engineering Building, 1206 West Green Street, Urbana, IL 61801-2906 (United States); Nishimoto, K., E-mail: knishimo@usp.br [Department of Naval Architecture and Ocean Engineering, Escola Politecnica da Universidade de Sao Paulo, Av. Prof. Mello Moraes, 2231 Sao Paulo, SP 05508-900 (Brazil); Silva, E.C.N., E-mail: ecnsilva@usp.br [Department of Mechatronic Engineering, Escola Politecnica da Universidade de Sao Paulo, Av. Prof. Mello Moraes, 2231 Sao Paulo, SP 05508-900 (Brazil)

    2011-05-15

    Previous papers related to the optimization of pressure vessels have considered the optimization of the nozzle independently from the dished end. This approach generates problems such as thickness variation from nozzle to dished end (coupling cylindrical region) and, as a consequence, it reduces the optimality of the final result which may also be influenced by the boundary conditions. Thus, this work discusses shape optimization of axisymmetric pressure vessels considering an integrated approach in which the entire pressure vessel model is used in conjunction with a multi-objective function that aims to minimize the von-Mises mechanical stress from nozzle to head. Representative examples are examined and solutions obtained for the entire vessel considering temperature and pressure loading. It is noteworthy that different shapes from the usual ones are obtained. Even though such different shapes may not be profitable considering present manufacturing processes, they may be competitive for future manufacturing technologies, and contribute to a better understanding of the actual influence of shape in the behavior of pressure vessels. - Highlights: > Shape optimization of entire pressure vessel considering an integrated approach. > By increasing the number of spline knots, the convergence stability is improved. > The null angle condition gives lower stress values resulting in a better design. > The cylinder stresses are very sensitive to the cylinder length. > The shape optimization of the entire vessel must be considered for cylinder length.

  1. Integrating availability and maintenance objectives in plant design. EDF approach

    International Nuclear Information System (INIS)

    Degrave, Claude; Martin-Onraet, Michel

    1995-01-01

    Energy self sufficiency is a major strategic necessity for France. Regarding the fossil fuels power, competitiveness of nuclear energy is a key goal for Electricite de France. Accordingly, for future nuclear power plants to remain competitive, it is necessary to maintain the kWh production costs of the future units at a level close to those of the latest units under construction (N4 series), while raising the safety level. EDF therefore decided to implement an analytical and systematic process for study of the new projects to optimize the design by integration of the maintenance (durations, costs), availability and radiation exposure goals from the related operating experience. This approach, CIDEM (French acronym for Design Integrating Availability, operating Experience and Maintenance) aims at a single goal: to minimize the kWh production cost incorporating investment, operation and fuel costs, allowing for the operating experience from French and foreign units. The implementation of the CIDEM process constitutes for EDF a new approach to the study of the new Nuclear Power Plant projects. The competitivity of nuclear energy greatly depends on the success of such an approach. The studies conducted in the availability field have already highlighted a number of critical points and have made it possible to define the corresponding goal allocations and to establish a first series of structuring specifications for the project. (J.P.N.)

  2. Ray-based approach to integrated 3D visual communication

    Science.gov (United States)

    Naemura, Takeshi; Harashima, Hiroshi

    2001-02-01

    For a high sense of reality in the next-generation communications, it is very important to realize three-dimensional (3D) spatial media, instead of existing 2D image media. In order to comprehensively deal with a variety of 3D visual data formats, the authors first introduce the concept of "Integrated 3D Visual Communication," which reflects the necessity of developing a neutral representation method independent of input/output systems. Then, the following discussions are concentrated on the ray-based approach to this concept, in which any visual sensation is considered to be derived from a set of light rays. This approach is a simple and straightforward to the problem of how to represent 3D space, which is an issue shared by various fields including 3D image communications, computer graphics, and virtual reality. This paper mainly presents the several developments in this approach, including some efficient methods of representing ray data, a real-time video-based rendering system, an interactive rendering system based on the integral photography, a concept of virtual object surface for the compression of tremendous amount of data, and a light ray capturing system using a telecentric lens. Experimental results demonstrate the effectiveness of the proposed techniques.

  3. Sustainable solid waste management: An integrated approach for Asian countries

    International Nuclear Information System (INIS)

    Shekdar, Ashok V.

    2009-01-01

    Solid waste management (SWM) has been an integral part of every human society. The approaches for SWM should be compatible with the nature of a given society, and, in this regard, Asian countries are no exception. In keeping with global trends, the systems are being oriented to concentrate on sustainability issues; mainly through the incorporation of 3R (reduce, reuse and recycle) technologies. However, degree and nature of improvements toward sustainability are varying and depend on the economic status of a country. High-income countries like Japan and South Korea can afford to spend more to incorporate 3R technologies. Most of the latest efforts focus on 'Zero Waste' and/or 'Zero Landfilling' which is certainly expensive for weaker economies such as those of India or Indonesia. There is a need to pragmatically assess the expectations of SWM systems in Asian countries. Hence, in this paper, we analyze the situation in different Asian countries, and explore future trends. We conceptually evaluate issues surrounding the sustainability of SWM. We propose a multi-pronged integrated approach for improvement that achieves sustainable SWM in the context of national policy and legal frameworks, institutional arrangement, appropriate technology, operational and financial management, and public awareness and participation. In keeping with this approach, a generic action plan has been proposed that could be tailored to suit a situation in a particular country. Our proposed concept and action plan framework would be useful across a variety of country-specific scenarios

  4. Ortho-perio integrated approach in periodontally compromised patients

    Science.gov (United States)

    Ramachandra, C. S.; Shetty, Pradeep Chandra; Rege, Sanyukta; Shah, Chitrang

    2011-01-01

    It is an undisputed fact that sound and strong periodontal health is a must in patients seeking orthodontic treatment. Does this mean that we are going to deny orthodontic treatment for those adults whose number is rising, more often secondary to periodontal deterioration and pathological migration of teeth resulting in aesthetic and functional problems? Need of the hour is to have an integrated approach where in periodontal treatment precedes orthodontic treatment to restore periodontal health. Orthodontic treatment should be performed under strict plaque control measures to place the teeth in a structurally balanced and functionally efficient position. Aim of this article is to familiarize the practicing clinicians both in the field of orthodontics and periodontics with current thoughts and successful clinical techniques used in the field of periodontology to regenerate lost periodontal structures. Furthermore, it aims to integrate such techniques into the orthodontic treatment of patients with severe bone loss. PMID:22368371

  5. HOLISTIC VISION: INTEGRATIVE APPROACH IN GUIDANCE AND COUNSELING SERVICES

    Directory of Open Access Journals (Sweden)

    Ade Hidayat

    2016-06-01

    Full Text Available Abstract: The philosophical issues in Guidance and Counseling especially in epistemological discourse have made paradigmatic friction that pointed by some issues from therapeutic-clinical to comprehensive way with preventive development prespective approach. It was also caused by the wider friction where quantum physic has remove classic Newtonian one, then the influence has generally removed another disciplines, where Guidance and Counseling in one of them. Through the comprehensive paradigm, Guidance dan Counseling need to take prepare the expert in order to capable to develop integrated and comprehensive thinking awareness. It means the Guidance and Counseling holistic vision is urged. Through the holistic vision, all of the competency of student is noticed integrally, such as intellectual, emotional, social, physical, artistic, creativity, ecological awareness, and spiritual competencies.Keywords: Ecoliteracy, Holictic Vision, Guidance and Counseling of Comprehensive.

  6. CSR Integration into the Financial Economy: A Conceptual Approach

    Directory of Open Access Journals (Sweden)

    Georgiana - Loredana FRECEA

    2016-06-01

    Full Text Available Corporate social responsibility is a complex concept and its design integrates economic, social and environmental issues, pointing out the operational effects on a voluntary basis. It is considered a strategic point in the actual evolution of the economy, due to the financial market dynamism, being identified a critical correlation between financial crises and corporate social responsibility. The main purpose of this paper is to synthesize, through a literature review, the multiple dimensions of CSR, with a special emphasis on the theoretical approach. In order to provide a coherent overview on the banking CSR, it will be proposed a division of the CSR theories according to: (1 the ethical approach, (2 the stakeholders approach, and (3 the corporate governance approach. The major aim of this paper is to fill a gap in the theoretical approach of the CSR for the banking system, due to the necessity to unify the CSR reporting elements in order to find a balance between the bank’s organizational structure and their legitimacy to operate on the financial market.

  7. The disposition of nuclear waste: an integrated international approach

    International Nuclear Information System (INIS)

    Waltar, A.E.

    2001-01-01

    This paper proposes the establishment of a new, globally integrated approach for dealing with spent nuclear fuel (SNF), high-level waste, and plutonium supplies. The end product is envisioned to be a new global agency (tentatively called the International Nuclear Waste Authority, or INWA), which would have the authority to establish and enforce all nuclear waste disposal standards and subsequently execute all financial arrangements appropriate for obtaining full-scale global implementation. We suggest the IAEA as the logical existing organization to facilitate generating the structure for the INWA. (author)

  8. The state-level approach: moving beyond integrated safeguards

    International Nuclear Information System (INIS)

    Tape, James W.

    2008-01-01

    The concept of a State-Level Approach (SLA) for international safeguards planning, implementation, and evaluation was contained in the Conceptual Framework for Integrated Safeguards (IS) agreed in 2002. This paper describes briefly the key elements of the SLA, including State-level factors and high-level safeguards objectives, and considers different cases in which application of the SLA methodology could address safeguards for 'suspect' States, 'good' States, and Nuclear Weapons States hosting fuel cycle centers. The continued use and further development of the SLA to customize safeguards for each State, including for States already under IS, is seen as central to effective and efficient safeguards for an expanding nuclear world.

  9. Integrated approach to yoga therapy and autism spectrum disorders

    Directory of Open Access Journals (Sweden)

    Shantha Radhakrishna

    2010-01-01

    Full Text Available A specially designed Integrated Approach to Yoga Therapy module was applied to Autism Spectrum Disorders over a period of two academic years. Despite low numbers (six in each arm, consistency and magnitude of effects make the findings significant. Parental participation, allowing firm guidance to be given to each child, resulted in significant improvements in imitation and other skills, and in behavior at home and family relationships. We hypothesize that guided imitation of therapist body positions stimulated mirror neuron activation, resulting in improved sense of self.

  10. The Need for Integrated Approaches in Metabolic Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

    2016-08-15

    This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must b e considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

  11. Integrated care: wellness-oriented peer approaches: a key ingredient for integrated care.

    Science.gov (United States)

    Swarbrick, Margaret A

    2013-08-01

    People with lived experience of mental illness have become leaders of an influential movement to help the mental health system embrace the notion of whole health and wellness in the areas of advocacy, policy, and care delivery. Wellness-oriented peer approaches delivered by peer-support whole-health specialists and wellness coaches can play an important role in integrated care models. This column examines the wellness definitions and peer models and some specific benefits and tensions between the peer-oriented wellness approach and the medical model. These models can work in unison to improve health and wellness among people with mental and substance use disorders.

  12. Advanced multiresponse process optimisation an intelligent and integrated approach

    CERN Document Server

    Šibalija, Tatjana V

    2016-01-01

    This book presents an intelligent, integrated, problem-independent method for multiresponse process optimization. In contrast to traditional approaches, the idea of this method is to provide a unique model for the optimization of various processes, without imposition of assumptions relating to the type of process, the type and number of process parameters and responses, or interdependences among them. The presented method for experimental design of processes with multiple correlated responses is composed of three modules: an expert system that selects the experimental plan based on the orthogonal arrays; the factor effects approach, which performs processing of experimental data based on Taguchi’s quality loss function and multivariate statistical methods; and process modeling and optimization based on artificial neural networks and metaheuristic optimization algorithms. The implementation is demonstrated using four case studies relating to high-tech industries and advanced, non-conventional processes.

  13. Integrated Approaches for the Study of Real Mineral Flotation Systems

    Directory of Open Access Journals (Sweden)

    Andrea Gerson

    2013-01-01

    Full Text Available It is more common than not, for mineral processing studies to proceed via the examination of model flotation systems with the resulting data often lacking statistical verification. The resultant concentrates and tails may then be subjected to a restricted range of analyses, for diagnosis of the flotation behavior variations observed, that themselves bias the outcomes. For instance surface analysis may be undertaken without reference to solution speciation, or liberation may be studied but surface speciation may not be taken into account. We propose an integrated approach whereby firstly the flotation data are vigorously scrutinized and the mineralogy, liberation, surface and solution speciation are examined in parallel to establish a chemical over view of the system. It is proposed that to make progress in the understanding of flotation systems, in terms of the minerals chemistry, that a multi-dimensional analytical approach is utilized and that the focus shifts towards the analysis of real ores and industrial flotation systems.

  14. Struggling against suicide: the need for an integrative approach.

    Science.gov (United States)

    De Leo, Diego

    2002-01-01

    Transcultural comparisons would be beneficial for both our understanding of suicide phenomena and the setting up of preventative strategies. Changes in attitude throughout history, gender and age differences, socio-economic factors, influence of race and ethnicity, and the impact of religion are among the aspects mentioned in this article. All of them can actually have a considerable effect on suicide rates, and all of them should be taken into account when interpreting suicide trends and designing antisuicide strategies. In fact, both risk and protective factors may vary remarkably in different cultures. The need for an integrative approach is evident today more than ever, and this fact calls for more concerted and coordinated, multidisciplinary approaches to suicide prevention.

  15. An integrative approach to research of deforestation under concession management

    International Nuclear Information System (INIS)

    Hepner, G.F.; Walker, R.T.

    1991-01-01

    A methodological approach integrating questionnaire research of tropical foresters with analyses of the actual patterns of concession logging and land use activities portrayed on various types of satellite imagery is discussed. The imagery analysis is necessary to: document the location place and magnitude of forest utilization and change in concession areas; confirm that responses vis-a-vis deforestation in the questionnaire correspond to observable behaviors as evidenced by the actual patterns of logging activities; and document the postharvest land utilization and conversion to other land uses. It is argued that this approach will link the process and pattern of logging activities to reveal the main factors leading to deforestation under the concession system of management. 20 refs

  16. An integrated modeling approach to age invariant face recognition

    Science.gov (United States)

    Alvi, Fahad Bashir; Pears, Russel

    2015-03-01

    This Research study proposes a novel method for face recognition based on Anthropometric features that make use of an integrated approach comprising of a global and personalized models. The system is aimed to at situations where lighting, illumination, and pose variations cause problems in face recognition. A Personalized model covers the individual aging patterns while a Global model captures general aging patterns in the database. We introduced a de-aging factor that de-ages each individual in the database test and training sets. We used the k nearest neighbor approach for building a personalized model and global model. Regression analysis was applied to build the models. During the test phase, we resort to voting on different features. We used FG-Net database for checking the results of our technique and achieved 65 percent Rank 1 identification rate.

  17. Auditory-Verbal Music Play Therapy: An Integrated Approach (AVMPT

    Directory of Open Access Journals (Sweden)

    Sahar Mohammad Esmaeilzadeh

    2013-10-01

    Full Text Available Introduction: Hearing loss occurs when there is a problem with one or more parts of the ear or ears and causes children to have a delay in the language-learning process. Hearing loss affects children's lives and their development. Several approaches have been developed over recent decades to help hearing-impaired children develop language skills. Auditory-verbal therapy (AVT is one such approach. Recently, researchers have found that music and play have a considerable effect on the communication skills of children, leading to the development of music therapy (MT and play therapy (PT. There have been several studies which focus on the impact of music on hearing-impaired children. The aim of this article is to review studies conducted in AVT, MT, and PT and their efficacy in hearing-impaired children. Furthermore, the authors aim to introduce an integrated approach of AVT, MT, and PT which facilitates language and communication skills in hearing-impaired children.   Materials and Methods: In this article we review studies of AVT, MT, and PT and their impact on hearing-impaired children. To achieve this goal, we searched databases and journals including Elsevier, Chor Teach, and Military Psychology, for example. We also used reliable websites such as American Choral Directors Association and Joint Committee on Infant Hearing websites. The websites were reviewed and key words in this article used to find appropriate references. Those articles which are related to ours in content were selected.    Results: Recent technologies have brought about great advancement in the field of hearing disorders. Now these impairments can be detected at birth, and in the majority of cases, hearing impaired children can develop fluent spoken language through audition. According to researches on the relationship between hearing impaired children’s communication and language skills and different approaches of therapy, it is known that learning through listening and

  18. An integrated Boltzmann+hydrodynamics approach to heavy ion collisions

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, Hannah

    2009-04-22

    In this thesis the first fully integrated Boltzmann+hydrodynamics approach to relativistic heavy ion reactions has been developed. After a short introduction that motivates the study of heavy ion reactions as the tool to get insights about the QCD phase diagram, the most important theoretical approaches to describe the system are reviewed. The hadron-string transport approach that this work is based on is the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) approach. Predictions for the charged particle multiplicities at LHC energies are made. The next step is the development of a new framework to calculate the baryon number density in a transport approach. Time evolutions of the net baryon number and the quark density have been calculated at AGS, SPS and RHIC energies. Studies of phase diagram trajectories using hydrodynamics are performed. The hybrid approach that has been developed as the main part of this thesis is based on the UrQMD transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. The full (3+1) dimensional ideal relativistic one fluid dynamics evolution is solved using the SHASTA algorithm. Three different equations of state have been used, namely a hadron gas equation of state without a QGP phase transition, a chiral EoS and a bag model EoS including a strong first order phase transition. For the freeze-out transition from hydrodynamics to the cascade calculation two different set-ups are employed. The parameter dependences of the model are investigated and the time evolution of different quantities is explored. The hybrid model calculation is able to reproduce the experimentally measured integrated as well as transverse momentum dependent v{sub 2} values for charged particles. The multiplicity and mean transverse mass excitation function is calculated for pions, protons and kaons in the energy range from E{sub lab}=2-160 A GeV. The HBT correlation of the negatively charged pion source

  19. An integrated Boltzmann+hydrodynamics approach to heavy ion collisions

    International Nuclear Information System (INIS)

    Petersen, Hannah

    2009-01-01

    In this thesis the first fully integrated Boltzmann+hydrodynamics approach to relativistic heavy ion reactions has been developed. After a short introduction that motivates the study of heavy ion reactions as the tool to get insights about the QCD phase diagram, the most important theoretical approaches to describe the system are reviewed. The hadron-string transport approach that this work is based on is the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) approach. Predictions for the charged particle multiplicities at LHC energies are made. The next step is the development of a new framework to calculate the baryon number density in a transport approach. Time evolutions of the net baryon number and the quark density have been calculated at AGS, SPS and RHIC energies. Studies of phase diagram trajectories using hydrodynamics are performed. The hybrid approach that has been developed as the main part of this thesis is based on the UrQMD transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. The full (3+1) dimensional ideal relativistic one fluid dynamics evolution is solved using the SHASTA algorithm. Three different equations of state have been used, namely a hadron gas equation of state without a QGP phase transition, a chiral EoS and a bag model EoS including a strong first order phase transition. For the freeze-out transition from hydrodynamics to the cascade calculation two different set-ups are employed. The parameter dependences of the model are investigated and the time evolution of different quantities is explored. The hybrid model calculation is able to reproduce the experimentally measured integrated as well as transverse momentum dependent v 2 values for charged particles. The multiplicity and mean transverse mass excitation function is calculated for pions, protons and kaons in the energy range from E lab =2-160 A GeV. The HBT correlation of the negatively charged pion source created in

  20. The transformative potential of an integrative approach to pregnancy.

    Science.gov (United States)

    Eidem, Haley R; McGary, Kriston L; Capra, John A; Abbot, Patrick; Rokas, Antonis

    2017-09-01

    Complex traits typically involve diverse biological pathways and are shaped by numerous genetic and environmental factors. Pregnancy-associated traits and pathologies are further complicated by extensive communication across multiple tissues in two individuals, interactions between two genomes-maternal and fetal-that obscure causal variants and lead to genetic conflict, and rapid evolution of pregnancy-associated traits across mammals and in the human lineage. Given the multi-faceted complexity of human pregnancy, integrative approaches that synthesize diverse data types and analyses harbor tremendous promise to identify the genetic architecture and environmental influences underlying pregnancy-associated traits and pathologies. We review current research that addresses the extreme complexities of traits and pathologies associated with human pregnancy. We find that successful efforts to address the many complexities of pregnancy-associated traits and pathologies often harness the power of many and diverse types of data, including genome-wide association studies, evolutionary analyses, multi-tissue transcriptomic profiles, and environmental conditions. We propose that understanding of pregnancy and its pathologies will be accelerated by computational platforms that provide easy access to integrated data and analyses. By simplifying the integration of diverse data, such platforms will provide a comprehensive synthesis that transcends many of the inherent challenges present in studies of pregnancy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Integrative biology approach identifies cytokine targeting strategies for psoriasis.

    Science.gov (United States)

    Perera, Gayathri K; Ainali, Chrysanthi; Semenova, Ekaterina; Hundhausen, Christian; Barinaga, Guillermo; Kassen, Deepika; Williams, Andrew E; Mirza, Muddassar M; Balazs, Mercedesz; Wang, Xiaoting; Rodriguez, Robert Sanchez; Alendar, Andrej; Barker, Jonathan; Tsoka, Sophia; Ouyang, Wenjun; Nestle, Frank O

    2014-02-12

    Cytokines are critical checkpoints of inflammation. The treatment of human autoimmune disease has been revolutionized by targeting inflammatory cytokines as key drivers of disease pathogenesis. Despite this, there exist numerous pitfalls when translating preclinical data into the clinic. We developed an integrative biology approach combining human disease transcriptome data sets with clinically relevant in vivo models in an attempt to bridge this translational gap. We chose interleukin-22 (IL-22) as a model cytokine because of its potentially important proinflammatory role in epithelial tissues. Injection of IL-22 into normal human skin grafts produced marked inflammatory skin changes resembling human psoriasis. Injection of anti-IL-22 monoclonal antibody in a human xenotransplant model of psoriasis, developed specifically to test potential therapeutic candidates, efficiently blocked skin inflammation. Bioinformatic analysis integrating both the IL-22 and anti-IL-22 cytokine transcriptomes and mapping them onto a psoriasis disease gene coexpression network identified key cytokine-dependent hub genes. Using knockout mice and small-molecule blockade, we show that one of these hub genes, the so far unexplored serine/threonine kinase PIM1, is a critical checkpoint for human skin inflammation and potential future therapeutic target in psoriasis. Using in silico integration of human data sets and biological models, we were able to identify a new target in the treatment of psoriasis.

  2. The meaning of integrated care: a systems approach

    Directory of Open Access Journals (Sweden)

    Lars Edgren

    2008-10-01

    Full Text Available Introduction: Organizations can be regarded as systems. The traditional model of systems views them as machines. This seems to be insufficient when it comes to understanding and organizing complex tasks. To better understand integrated care we should approach organizations as constantly changing living organisms, where many agents are interconnected in so-called Complex Adaptive Systems (CAS. Theory and discussion: The term “complex” emphasizes that the necessary competence to perform a task is not owned by any one part, but comes as a result of co-operation within the system. “Adaptive” means that system change occurs through successive adaptations. A CAS consists of several subsystems called agents, which act in dependence of one another. Examples would be the ant-hill, the human immune defence, the financial market and the surgical operating theatre team. Studying a CAS, the focus is on the interaction and communication between agents. Although these thoughts are not new, the CAS-approach has not yet been widely applied to the management of integrated care. This helps the management to understand why the traditional top down way of managing, following the machine model thinking, may meet with problems in interdependent organizations with complex tasks. Conclusion: When we perceive health and social services as CASs we should gain more insight into the processes that go on within and between organizations and how top management, for example within a hospital, in fact executes its steering function.

  3. Integrated approach to assess ecosystem health in harbor areas.

    Science.gov (United States)

    Bebianno, M J; Pereira, C G; Rey, F; Cravo, A; Duarte, D; D'Errico, G; Regoli, F

    2015-05-01

    Harbors are critical environments with strategic economic importance but with potential environmental impact: health assessment criteria are a key issue. An ecosystem health status approach was carried out in Portimão harbor as a case-study. Priority and specific chemical levels in sediments along with their bioavailability in mussels, bioassays and a wide array of biomarkers were integrated in a biomarker index (IBR index) and the overall data in a weight of evidence (WOE) model. Metals, PAHs, PCBs and HCB were not particularly high compared with sediment guidelines and standards for dredging. Bioavailability was evident for Cd, Cu and Zn. Biomarkers proved more sensitive namely changes of antioxidant responses, metallothioneins and vittellogenin-like proteins. IBR index indicated that site 4 was the most impacted area. Assessment of the health status by WOE approach highlighted the importance of integrating sediment chemistry, bioaccumulation, biomarkers and bioassays and revealed that despite some disturbance in the harbor area, there was also an impact of urban effluents from upstream. Environmental quality assessment in harbors. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. An integrative approach to inferring biologically meaningful gene modules

    Directory of Open Access Journals (Sweden)

    Wang Kai

    2011-07-01

    Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

  5. Integrated variable projection approach (IVAPA) for parallel magnetic resonance imaging.

    Science.gov (United States)

    Zhang, Qiao; Sheng, Jinhua

    2012-10-01

    Parallel magnetic resonance imaging (pMRI) is a fast method which requires algorithms for the reconstructing image from a small number of measured k-space lines. The accurate estimation of the coil sensitivity functions is still a challenging problem in parallel imaging. The joint estimation of the coil sensitivity functions and the desired image has recently been proposed to improve the situation by iteratively optimizing both the coil sensitivity functions and the image reconstruction. It regards both the coil sensitivities and the desired images as unknowns to be solved for jointly. In this paper, we propose an integrated variable projection approach (IVAPA) for pMRI, which integrates two individual processing steps (coil sensitivity estimation and image reconstruction) into a single processing step to improve the accuracy of the coil sensitivity estimation using the variable projection approach. The method is demonstrated to be able to give an optimal solution with considerably reduced artifacts for high reduction factors and a low number of auto-calibration signal (ACS) lines, and our implementation has a fast convergence rate. The performance of the proposed method is evaluated using a set of in vivo experiment data. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Optimizing Groundwater Monitoring Networks Using Integrated Statistical and Geostatistical Approaches

    Directory of Open Access Journals (Sweden)

    Jay Krishna Thakur

    2015-08-01

    Full Text Available The aim of this work is to investigate new approaches using methods based on statistics and geo-statistics for spatio-temporal optimization of groundwater monitoring networks. The formulated and integrated methods were tested with the groundwater quality data set of Bitterfeld/Wolfen, Germany. Spatially, the monitoring network was optimized using geo-statistical methods. Temporal optimization of the monitoring network was carried out using Sen’s method (1968. For geostatistical network optimization, a geostatistical spatio-temporal algorithm was used to identify redundant wells in 2- and 2.5-D Quaternary and Tertiary aquifers. Influences of interpolation block width, dimension, contaminant association, groundwater flow direction and aquifer homogeneity on statistical and geostatistical methods for monitoring network optimization were analysed. The integrated approach shows 37% and 28% redundancies in the monitoring network in Quaternary aquifer and Tertiary aquifer respectively. The geostatistical method also recommends 41 and 22 new monitoring wells in the Quaternary and Tertiary aquifers respectively. In temporal optimization, an overall optimized sampling interval was recommended in terms of lower quartile (238 days, median quartile (317 days and upper quartile (401 days in the research area of Bitterfeld/Wolfen. Demonstrated methods for improving groundwater monitoring network can be used in real monitoring network optimization with due consideration given to influencing factors.

  7. An Integrated Approach for RNA-seq Data Normalization.

    Science.gov (United States)

    Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

    2016-01-01

    DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

  8. Integrated System Health Management: Foundational Concepts, Approach, and Implementation.

    Science.gov (United States)

    Figueroa, Fernando; Schmalzel, John; Walker, Mark; Venkatesh, Meera; Kapadia, Ravi; Morris, Jon; Turowski, Mark; Smith, Harvey

    2009-01-01

    Implementation of integrated system health management (ISHM) capability is fundamentally linked to the management of data, information, and knowledge (DIaK) with the purposeful objective of determining the health of a system. It is akin to having a team of experts who are all individually and collectively observing and analyzing a complex system, and communicating effectively with each other in order to arrive to an accurate and reliable assessment of its health. We present concepts, procedures, and a specific approach as a foundation for implementing a credible ISHM capability. The capability stresses integration of DIaK from all elements of a system. The intent is also to make possible implementation of on-board ISHM capability, in contrast to a remote capability. The information presented is the result of many years of research, development, and maturation of technologies, and of prototype implementations in operational systems (rocket engine test facilities). The paper will address the following topics: 1. ISHM Model of a system 2. Detection of anomaly indicators. 3. Determination and confirmation of anomalies. 4. Diagnostic of causes and determination of effects. 5. Consistency checking cycle. 6. Management of health information 7. User Interfaces 8. Example implementation ISHM has been defined from many perspectives. We define it as a capability that might be achieved by various approaches. We describe a specific approach that has been matured throughout many years of development, and pilot implementations. ISHM is a capability that is achieved by integrating data, information, and knowledge (DIaK) that might be distributed throughout the system elements (which inherently implies capability to manage DIaK associated with distributed sub-systems). DIaK must be available to any element of a system at the right time and in accordance with a meaningful context. ISHM Functional Capability Level (FCL) is measured by how well a system performs the following

  9. Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks.

    Science.gov (United States)

    Fearnley, Liam G; Inouye, Michael

    2016-10-01

    Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology. © The Author 2016. Published by Oxford University Press on behalf of the International Epidemiological Association.

  10. The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology

    DEFF Research Database (Denmark)

    Kildegaard, Helene Faustrup; Baycin-Hizal, Deniz; Lewis, Nathan

    2013-01-01

    into mathematical models that describe CHO phenotypes will provide crucial biotechnology insights. As ‘omics technologies and computational systems biology mature, genome-scale approaches will lead to major innovations in cell line development and metabolic engineering, thereby improving protein production......Chinese hamster ovary (CHO) cells are the primary factories for biopharmaceuticals because of their capacity to correctly fold and post-translationally modify recombinant proteins compatible with humans. New opportunities are arising to enhance these cell factories, especially since the CHO-K1 cell...

  11. Challenges and opportunities for integrating lake ecosystem modelling approaches

    Science.gov (United States)

    Mooij, Wolf M.; Trolle, Dennis; Jeppesen, Erik; Arhonditsis, George; Belolipetsky, Pavel V.; Chitamwebwa, Deonatus B.R.; Degermendzhy, Andrey G.; DeAngelis, Donald L.; Domis, Lisette N. De Senerpont; Downing, Andrea S.; Elliott, J. Alex; Ruberto, Carlos Ruberto; Gaedke, Ursula; Genova, Svetlana N.; Gulati, Ramesh D.; Hakanson, Lars; Hamilton, David P.; Hipsey, Matthew R.; Hoen, Jochem 't; Hulsmann, Stephan; Los, F. Hans; Makler-Pick, Vardit; Petzoldt, Thomas; Prokopkin, Igor G.; Rinke, Karsten; Schep, Sebastiaan A.; Tominaga, Koji; Van Dam, Anne A.; Van Nes, Egbert H.; Wells, Scott A.; Janse, Jan H.

    2010-01-01

    A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative

  12. An integrative approach to cultural competence in the psychiatric curriculum.

    Science.gov (United States)

    Fung, Kenneth; Andermann, Lisa; Zaretsky, Ari; Lo, Hung-Tat

    2008-01-01

    As it is increasingly recognized that cultural competence is an essential quality for any practicing psychiatrist, postgraduate psychiatry training programs need to incorporate cultural competence training into their curricula. This article documents the unique approach to resident cultural competence training being developed in the Department of Psychiatry at the University of Toronto, which has the largest residency training program in North America and is situated in an ethnically diverse city and country. The authors conducted a systematic review of cultural competence by searching databases including PubMed, PsycINFO, PsycArticles, CINAHL, Social Science Abstracts, and Sociological Abstracts; by searching government and professional association publications; and through on-site visits to local cross-cultural training programs. Based on the results of the review, a resident survey, and a staff retreat, the authors developed a deliberate "integrative" approach with a mindful, balanced emphasis on both generic and specific cultural competencies. Learning objectives were derived from integrating the seven core competencies of a physician as defined by the Canadian Medical Education Directions for Specialists (CanMEDS) roles framework with the tripartite model of attitudes, knowledge, and skills. The learning objectives and teaching program were further integrated across different psychiatric subspecialties and across the successive years of residency. Another unique strategy used to foster curricular and institutional change was the program's emphasis on evaluation, making use of insights from modern educational theories such as formative feedback and blueprinting. Course evaluations of the core curriculum from the first group of residents were positive. The authors propose that these changes to the curriculum may lead to enhanced cultural competence and clinical effectiveness in health care.

  13. Methods to isolate a large amount of generative cells, sperm cells and vegetative nuclei from tomato pollen for omics analysis

    Directory of Open Access Journals (Sweden)

    Yunlong eLu

    2015-06-01

    Full Text Available The development of sperm cells from microspores involves a set of finely regulated molecular and cellular events and the coordination of these events. The mechanisms underlying these events and their interconnections remain a major challenge. Systems analysis of genome-wide molecular networks and functional modules with high-throughput omics approaches is crucial for understanding the mechanisms; however, this study is hindered because of the difficulty in isolating a large amount of cells of different types, especially generative cells (GCs, from the pollen. Here, we optimized the conditions of tomato pollen germination and pollen tube growth to allow for long-term growth of pollen tubes in vitro with sperm cells (SCs generated in the tube. Using this culture system, we developed methods for isolating GCs, SCs and vegetative-cell nuclei (VN from just-germinated tomato pollen grains and growing pollen tubes and their purification by Percoll density gradient centrifugation. The purity and viability of isolated GCs and SCs were confirmed by microscopy examination and fluorescein diacetate staining, respectively, and the integrity of VN was confirmed by propidium iodide staining. We could obtain about 1.5 million GCs and 2.0 million SCs each from 180 mg initiated pollen grains, and 10 million VN from 270 mg initiated pollen grains germinated in vitro in each experiment. These methods provide the necessary preconditions for systematic biology studies of SC development and differentiation in higher plants.

  14. Methods to isolate a large amount of generative cells, sperm cells and vegetative nuclei from tomato pollen for "omics" analysis.

    Science.gov (United States)

    Lu, Yunlong; Wei, Liqin; Wang, Tai

    2015-01-01

    The development of sperm cells (SCs) from microspores involves a set of finely regulated molecular and cellular events and the coordination of these events. The mechanisms underlying these events and their interconnections remain a major challenge. Systems analysis of genome-wide molecular networks and functional modules with high-throughput "omics" approaches is crucial for understanding the mechanisms; however, this study is hindered because of the difficulty in isolating a large amount of cells of different types, especially generative cells (GCs), from the pollen. Here, we optimized the conditions of tomato pollen germination and pollen tube growth to allow for long-term growth of pollen tubes in vitro with SCs generated in the tube. Using this culture system, we developed methods for isolating GCs, SCs and vegetative cell nuclei (VN) from just-germinated tomato pollen grains and growing pollen tubes and their purification by Percoll density gradient centrifugation. The purity and viability of isolated GCs and SCs were confirmed by microscopy examination and fluorescein diacetate staining, respectively, and the integrity of VN was confirmed by propidium iodide staining. We could obtain about 1.5 million GCs and 2.0 million SCs each from 180 mg initiated pollen grains, and 10 million VN from 270 mg initiated pollen grains germinated in vitro in each experiment. These methods provide the necessary preconditions for systematic biology studies of SC development and differentiation in higher plants.

  15. Tropical forest carbon assessment: integrating satellite and airborne mapping approaches

    International Nuclear Information System (INIS)

    Asner, Gregory P

    2009-01-01

    Large-scale carbon mapping is needed to support the UNFCCC program to reduce deforestation and forest degradation (REDD). Managers of forested land can potentially increase their carbon credits via detailed monitoring of forest cover, loss and gain (hectares), and periodic estimates of changes in forest carbon density (tons ha -1 ). Satellites provide an opportunity to monitor changes in forest carbon caused by deforestation and degradation, but only after initial carbon densities have been assessed. New airborne approaches, especially light detection and ranging (LiDAR), provide a means to estimate forest carbon density over large areas, which greatly assists in the development of practical baselines. Here I present an integrated satellite-airborne mapping approach that supports high-resolution carbon stock assessment and monitoring in tropical forest regions. The approach yields a spatially resolved, regional state-of-the-forest carbon baseline, followed by high-resolution monitoring of forest cover and disturbance to estimate carbon emissions. Rapid advances and decreasing costs in the satellite and airborne mapping sectors are already making high-resolution carbon stock and emissions assessments viable anywhere in the world.

  16. An integrated approach to determine phenomenological equations in metallic systems

    Science.gov (United States)

    Ghamarian, Iman

    It is highly desirable to be able to make predictions of properties in metallic materials based upon the composition of the material and the microstructure. Unfortunately, the complexity of real, multi-component, multi-phase engineering alloys makes the provision of constituent-based (i.e., composition or microstructure) phenomenological equations extremely difficult. Due to these difficulties, qualitative predictions are frequently used to study the influence of microstructure or composition on the properties. Neural networks were used as a tool to get a quantitative model from a database. However, the developed model is not a phenomenological model. In this study, a new method based upon the integration of three separate modeling approaches, specifically artificial neural networks, genetic algorithms, and monte carlo was proposed. These three methods, when coupled in the manner described in this study, allows for the extraction of phenomenological equations with a concurrent analysis of uncertainty. This approach has been applied to a multi-component, multi-phase microstructure exhibiting phases with varying spatial and morphological distributions. Specifically, this approach has been applied to derive a phenomenological equation for the prediction of yield strength in alpha+beta processed Ti-6-4. The equation is consistent with not only the current dataset but also, where available, the limited information regarding certain parameters such as intrinsic yield strength of pure hexagonal close-packed alpha titanium.

  17. Finding Practical Approaches to Integrated Water Resources Management

    Directory of Open Access Journals (Sweden)

    John Butterworth

    2010-02-01

    Full Text Available Integrated Water Resources Management (IWRM has often been interpreted and implemented in a way that is only really suited to countries with the most developed water infrastructures and management capacities. While sympathetic to many of the criticisms levelled at the IWRM concept and recognising the often disappointing levels of adoption, this paper and the series of papers it introduces identify some alternative ways forward in a developmental context that place more emphasis on the practical in-finding solutions to water scarcity. A range of lighter, more pragmatic and context-adapted approaches, strategies and entry points are illustrated with examples from projects and initiatives in mainly 'developing' countries. The authors argue that a more service-orientated (WASH, irrigation and ecosystem services, locally rooted and balanced approach to IWRM that better matches contexts and capacities should build on such strategies, in addition to the necessary but long-term policy reforms and river basin institution-building at higher levels. Examples in this set of papers not only show that the 'lighter', more opportunistic and incremental approach has potential as well as limitations but also await wider piloting and adoption.

  18. Contingent approach to Internet-based supply network integration

    Science.gov (United States)

    Ho, Jessica; Boughton, Nick; Kehoe, Dennis; Michaelides, Zenon

    2001-10-01

    The Internet is playing an increasingly important role in enhancing the operations of supply networks as many organizations begin to recognize the benefits of Internet- enabled supply arrangements. However, the developments and applications to-date do not extend significantly beyond the dyadic model, whereas the real advantages are to be made with the external and network models to support a coordinated and collaborative based approach. The DOMAIN research group at the University of Liverpool is currently defining new Internet- enabled approaches to enable greater collaboration across supply chains. Different e-business models and tools are focusing on different applications. Using inappropriate e- business models, tools or techniques will bring negative results instead of benefits to all the tiers in the supply network. Thus there are a number of issues to be considered before addressing Internet based supply network integration, in particular an understanding of supply chain management, the emergent business models and evaluating the effects of deploying e-business to the supply network or a particular tier. It is important to utilize a contingent approach to selecting the right e-business model to meet the specific supply chain requirements. This paper addresses the issues and provides a case study on the indirect materials supply networks.

  19. Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery.

    Science.gov (United States)

    Huo, Zhiguang; Tseng, George

    2017-06-01

    Cancer subtypes discovery is the first step to deliver personalized medicine to cancer patients. With the accumulation of massive multi-level omics datasets and established biological knowledge databases, omics data integration with incorporation of rich existing biological knowledge is essential for deciphering a biological mechanism behind the complex diseases. In this manuscript, we propose an integrative sparse K -means (is- K means) approach to discover disease subtypes with the guidance of prior biological knowledge via sparse overlapping group lasso. An algorithm using an alternating direction method of multiplier (ADMM) will be applied for fast optimization. Simulation and three real applications in breast cancer and leukemia will be used to compare is- K means with existing methods and demonstrate its superior clustering accuracy, feature selection, functional annotation of detected molecular features and computing efficiency.

  20. Improved bacteriophage genome data is necessary for integrating viral and bacterial ecology.

    Science.gov (United States)

    Bibby, Kyle

    2014-02-01

    The recent rise in "omics"-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases-currently, only 0.001% of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.

  1. Systems approaches to integrated solid waste management in developing countries

    International Nuclear Information System (INIS)

    Marshall, Rachael E.; Farahbakhsh, Khosrow

    2013-01-01

    Highlights: ► Five drivers led developed countries to current solid waste management paradigm. ► Many unique factors challenge developing country solid waste management. ► Limited transferability of developed country approaches to developing countries. ► High uncertainties and decision stakes call for post-normal approaches. ► Systems thinking needed for multi-scale, self-organizing eco-social waste systems. - Abstract: Solid waste management (SWM) has become an issue of increasing global concern as urban populations continue to rise and consumption patterns change. The health and environmental implications associated with SWM are mounting in urgency, particularly in the context of developing countries. While systems analyses largely targeting well-defined, engineered systems have been used to help SWM agencies in industrialized countries since the 1960s, collection and removal dominate the SWM sector in developing countries. This review contrasts the history and current paradigms of SWM practices and policies in industrialized countries with the current challenges and complexities faced in developing country SWM. In industrialized countries, public health, environment, resource scarcity, climate change, and public awareness and participation have acted as SWM drivers towards the current paradigm of integrated SWM. However, urbanization, inequality, and economic growth; cultural and socio-economic aspects; policy, governance, and institutional issues; and international influences have complicated SWM in developing countries. This has limited the applicability of approaches that were successful along the SWM development trajectories of industrialized countries. This review demonstrates the importance of founding new SWM approaches for developing country contexts in post-normal science and complex, adaptive systems thinking

  2. Systems approaches to integrated solid waste management in developing countries

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, Rachael E., E-mail: rmarsh01@uoguelph.ca [School of Engineering, University of Guelph, Albert A. Thornbrough Building, Guelph, ON, Canada N1G 2W1 (Canada); Farahbakhsh, Khosrow, E-mail: khosrowf@uoguelph.ca [School of Engineering, University of Guelph, Albert A. Thornbrough Building, Guelph, ON, Canada N1G 2W1 (Canada)

    2013-04-15

    Highlights: ► Five drivers led developed countries to current solid waste management paradigm. ► Many unique factors challenge developing country solid waste management. ► Limited transferability of developed country approaches to developing countries. ► High uncertainties and decision stakes call for post-normal approaches. ► Systems thinking needed for multi-scale, self-organizing eco-social waste systems. - Abstract: Solid waste management (SWM) has become an issue of increasing global concern as urban populations continue to rise and consumption patterns change. The health and environmental implications associated with SWM are mounting in urgency, particularly in the context of developing countries. While systems analyses largely targeting well-defined, engineered systems have been used to help SWM agencies in industrialized countries since the 1960s, collection and removal dominate the SWM sector in developing countries. This review contrasts the history and current paradigms of SWM practices and policies in industrialized countries with the current challenges and complexities faced in developing country SWM. In industrialized countries, public health, environment, resource scarcity, climate change, and public awareness and participation have acted as SWM drivers towards the current paradigm of integrated SWM. However, urbanization, inequality, and economic growth; cultural and socio-economic aspects; policy, governance, and institutional issues; and international influences have complicated SWM in developing countries. This has limited the applicability of approaches that were successful along the SWM development trajectories of industrialized countries. This review demonstrates the importance of founding new SWM approaches for developing country contexts in post-normal science and complex, adaptive systems thinking.

  3. The Site Approach - Lessons Learned from the Integrated Safeguards Approach for JNC-1

    International Nuclear Information System (INIS)

    Kikuchi, M.; Iso, S.; Tomine, K.; Hirato, Y.; Namekawa, M.; Takasugi, N.; Watanabe, M.; Tsutaki, Y.; Asano, T.; Nagatani, T.; Ninagawa, J.; Fujiwara, S.; Takahashi, S.; Kimura, T.; Kodani, Y.; Fukuhara, J.; Miyaji, N.; Kawakami, Y.; Koizumi, A.; Yamazaki, Y.; Nishinosono, S.; Sasaki, K.

    2010-01-01

    Integrated safeguards approaches for specific sites are recognized important elements in the design of a State-level approach under the concept of grouping facilities. Japan and the IAEA agreed further improvement of integrated safeguards implementation in effective and efficient manner, particularly at large complex nuclear sites in Japan. Japan and the IAEA developed the integrated safeguards approach for specific sites defined at Article 18 of Additional Protocol. In 2008, the IAEA started the three-year test implementation of JNC-1 site approach for improving the effectiveness and efficiency of the safeguards implementation of UDU material handling facilities. Japan and IAEA agreed to adopt the sector concept in order to make clear of subjected nuclear material to be verified. The sector is defined as spatial assignment that treats the same material stratum beyond MBAs in the site. The arrangement of MBAs and related material balance calculations as well as statistical analysis is maintained as a fundamental safeguards measure. At the boundaries of each sector, appropriate unattended NDA system and/or C/S system are installed, and material flows across the boundaries are verified by the system or attendance of resident inspectors. For inventory verification of the nuclear material stayed in sectors, an appropriate numbers of randomly scheduled inspections will be implemented. IAEA can access to the randomly selected sectors within 2 hours after notification. NRTA based on frequent operator's declaration will be performed for achievement of timeliness detection goal. The JNC-1 site approach has been implemented under the enhanced co-operation between the IAEA and SSAC through joint use of equipment and arrangements for DA analysis. Especially, national inspectors are working with IAEA together for coordination with operators. Because NMCC lab analyses all DA samples taken from facilities and the analysis results will be shared by the IAEA, certain numbers of DA

  4. An integrated view of complex landscapes: a big data-model integration approach to trans-disciplinary science

    Science.gov (United States)

    The Earth is a complex system comprised of many interacting spatial and temporal scales. Understanding, predicting, and managing for these dynamics requires a trans-disciplinary integrated approach. Although there have been calls for this integration, a general approach is needed. We developed a Tra...

  5. Linking Science and Language Arts: A Review of the Literature Which Compares Integrated versus Non-Integrated Approaches

    Science.gov (United States)

    Bradbury, Leslie U.

    2014-01-01

    The purpose of this paper is to review the literature published during the last 20 years that investigates the impact of approaches that describe themselves as integrating science and language arts on student learning and/or attitude at the elementary level. The majority of papers report that integrated approaches led to greater student…

  6. An integrated MCDM approach to green supplier selection

    Directory of Open Access Journals (Sweden)

    Morteza Yazdani

    2014-06-01

    Full Text Available Supplier selection management has been considered as an important subject for industrial organizations. In order to remain on the market, to gain profitability and to retain competitive advantage, business units need to establish an integrated and structured supplier selection system. In addition, environmental protection problems have been big solicitudes for organizations to consider green approach in supplier selection problem. However, finding proper suppliers involves several variables and it is critically a complex process. In this paper, the main attention is focused on finding the right supplier based on fuzzy multi criteria decision making (MCDM process. The weights of criteria are calculated by analytical hierarchical process (AHP and the final ranking is achieved by fuzzy technique for order preference by similarity to an ideal solution (TOPSIS. TOPSIS advantage among the other similar methods is to obtain the best solution close to ideal solution. The paper attempts to express better understanding by an example of an automobile manufacturing supply chain.

  7. Modeling fabrication of nuclear components: An integrative approach

    Energy Technology Data Exchange (ETDEWEB)

    Hench, K.W.

    1996-08-01

    Reduction of the nuclear weapons stockpile and the general downsizing of the nuclear weapons complex has presented challenges for Los Alamos. One is to design an optimized fabrication facility to manufacture nuclear weapon primary components in an environment of intense regulation and shrinking budgets. This dissertation presents an integrative two-stage approach to modeling the casting operation for fabrication of nuclear weapon primary components. The first stage optimizes personnel radiation exposure for the casting operation layout by modeling the operation as a facility layout problem formulated as a quadratic assignment problem. The solution procedure uses an evolutionary heuristic technique. The best solutions to the layout problem are used as input to the second stage - a simulation model that assesses the impact of competing layouts on operational performance. The focus of the simulation model is to determine the layout that minimizes personnel radiation exposures and nuclear material movement, and maximizes the utilization of capacity for finished units.

  8. Path integral approach to electron scattering in classical electromagnetic potential

    International Nuclear Information System (INIS)

    Xu Chuang; Feng Feng; Li Ying-Jun

    2016-01-01

    As is known to all, the electron scattering in classical electromagnetic potential is one of the most widespread applications of quantum theory. Nevertheless, many discussions about electron scattering are based upon single-particle Schrodinger equation or Dirac equation in quantum mechanics rather than the method of quantum field theory. In this paper, by using the path integral approach of quantum field theory, we perturbatively evaluate the scattering amplitude up to the second order for the electron scattering by the classical electromagnetic potential. The results we derive are convenient to apply to all sorts of potential forms. Furthermore, by means of the obtained results, we give explicit calculations for the one-dimensional electric potential. (paper)

  9. Infectious diseases in oyster aquaculture require a new integrated approach.

    Science.gov (United States)

    Pernet, Fabrice; Lupo, Coralie; Bacher, Cédric; Whittington, Richard J

    2016-03-05

    Emerging diseases pose a recurrent threat to bivalve aquaculture. Recently, massive mortality events in the Pacific oyster Crassostrea gigas associated with the detection of a microvariant of the ostreid herpesvirus 1 (OsHV-1µVar) have been reported in Europe, Australia and New Zealand. Although the spread of disease is often viewed as a governance failure, we suggest that the development of protective measures for bivalve farming is presently held back by the lack of key scientific knowledge. In this paper, we explore the case for an integrated approach to study the management of bivalve disease, using OsHV-1 as a case study. Reconsidering the key issues by incorporating multidisciplinary science could provide a holistic understanding of OsHV-1 and increase the benefit of research to policymakers. © 2016 The Author(s).

  10. CLARM: An integrative approach for functional modules discovery

    KAUST Repository

    Salem, Saeed M.; Alroobi, Rami; Banitaan, Shadi; Seridi, Loqmane; Brewer, James E.; Aljarah, Ibrahim

    2011-01-01

    Functional module discovery aims to find well-connected subnetworks which can serve as candidate protein complexes. Advances in High-throughput proteomic technologies have enabled the collection of large amount of interaction data as well as gene expression data. We propose, CLARM, a clustering algorithm that integrates gene expression profiles and protein protein interaction network for biological modules discovery. The main premise is that by enriching the interaction network by adding interactions between genes which are highly co-expressed over a wide range of biological and environmental conditions, we can improve the quality of the discovered modules. Protein protein interactions, known protein complexes, and gene expression profiles for diverse environmental conditions from the yeast Saccharomyces cerevisiae were used for evaluate the biological significance of the reported modules. Our experiments show that the CLARM approach is competitive to wellestablished module discovery methods. Copyright © 2011 ACM.

  11. Strategic Technology Investment Analysis: An Integrated System Approach

    Science.gov (United States)

    Adumitroaie, V.; Weisbin, C. R.

    2010-01-01

    Complex technology investment decisions within NASA are increasingly difficult to make such that the end results are satisfying the technical objectives and all the organizational constraints. Due to a restricted science budget environment and numerous required technology developments, the investment decisions need to take into account not only the functional impact on the program goals, but also development uncertainties and cost variations along with maintaining a healthy workforce. This paper describes an approach for optimizing and qualifying technology investment portfolios from the perspective of an integrated system model. The methodology encompasses multi-attribute decision theory elements and sensitivity analysis. The evaluation of the degree of robustness of the recommended portfolio provides the decision-maker with an array of viable selection alternatives, which take into account input uncertainties and possibly satisfy nontechnical constraints. The methodology is presented in the context of assessing capability development portfolios for NASA technology programs.

  12. Engineering systems reliability, safety, and maintenance an integrated approach

    CERN Document Server

    Dhillon, B S

    2017-01-01

    Today, engineering systems are an important element of the world economy and each year billions of dollars are spent to develop, manufacture, operate, and maintain various types of engineering systems around the globe. Many of these systems are highly sophisticated and contain millions of parts. For example, a Boeing jumbo 747 is made up of approximately 4.5 million parts including fasteners. Needless to say, reliability, safety, and maintenance of systems such as this have become more important than ever before.  Global competition and other factors are forcing manufacturers to produce highly reliable, safe, and maintainable engineering products. Therefore, there is a definite need for the reliability, safety, and maintenance professionals to work closely during design and other phases. Engineering Systems Reliability, Safety, and Maintenance: An Integrated Approach eliminates the need to consult many different and diverse sources in the hunt for the information required to design better engineering syste...

  13. An integrated approach to route selection in slurry pipeline design

    Energy Technology Data Exchange (ETDEWEB)

    Betinol, Roy G.; Altmann, Nara [Brass Chile S.A., Santiago (Chile)

    2009-12-19

    The pressure to get engineering projects done and constructed as fast as possible in order to take advantage of the high prices in metals and petrochemicals has been driving companies to skip the conceptual phase and go straight into basic engineering with cost estimates in the level of 15% accuracy. By-passing early engineering and demanding higher cost estimating accuracy is a contradiction. In most cases, savings made on capital investment is much higher had money been spent in conceptual studies which allow for the optimal solution to be found. This paper reviews one of the key aspects in conceptual engineering of slurry pipeline designs: route selection. This activity is often overlooked, causing capital cost and operating difficulties to rise unnecessarily. This paper describes and gives example on how an integrated client/engineering company's approach to route selection can produce significant savings in pipeline construction and operating costs. (author)

  14. Science based integrated approach to advanced nuclear fuel development - vision, approach, and overview

    Energy Technology Data Exchange (ETDEWEB)

    Unal, Cetin [Los Alamos National Laboratory; Pasamehmetoglu, Kemal [IDAHO NATIONAL LAB; Carmack, Jon [IDAHO NATIONAL LAB

    2010-01-01

    Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Rcactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems is critical. In order to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. The purpose of this paper is to identify the modeling and simulation approach in order to deliver predictive tools for advanced fuels development. The coordination between experimental nuclear fuel design, development technical experts, and computational fuel modeling and simulation technical experts is a critical aspect of the approach and naturally leads to an integrated, goal-oriented science-based R & D approach and strengthens both the experimental and computational efforts. The Advanced Fuels Campaign (AFC) and Nuclear Energy Advanced Modeling and Simulation (NEAMS) Fuels Integrated Performance and Safety Code (IPSC) are working together to determine experimental data and modeling needs. The primary objective of the NEAMS fuels IPSC project is to deliver a coupled, three-dimensional, predictive computational platform for modeling the fabrication and both normal and abnormal operation of nuclear fuel pins and assemblies, applicable to both existing and future reactor fuel designs. The science based program is pursuing the development of an integrated multi-scale and multi-physics modeling and simulation platform for nuclear fuels. This overview paper discusses the vision, goals and approaches how to develop and implement the new approach.

  15. Science based integrated approach to advanced nuclear fuel development - vision, approach, and overview

    International Nuclear Information System (INIS)

    Unal, Cetin; Pasamehmetoglu, Kemal; Carmack, Jon

    2010-01-01

    Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Rcactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems is critical. In order to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. The purpose of this paper is to identify the modeling and simulation approach in order to deliver predictive tools for advanced fuels development. The coordination between experimental nuclear fuel design, development technical experts, and computational fuel modeling and simulation technical experts is a critical aspect of the approach and naturally leads to an integrated, goal-oriented science-based R and D approach and strengthens both the experimental and computational efforts. The Advanced Fuels Campaign (AFC) and Nuclear Energy Advanced Modeling and Simulation (NEAMS) Fuels Integrated Performance and Safety Code (IPSC) are working together to determine experimental data and modeling needs. The primary objective of the NEAMS fuels IPSC project is to deliver a coupled, three-dimensional, predictive computational platform for modeling the fabrication and both normal and abnormal operation of nuclear fuel pins and assemblies, applicable to both existing and future reactor fuel designs. The science based program is pursuing the development of an integrated multi-scale and multi-physics modeling and simulation platform for nuclear fuels. This overview paper discusses the vision, goals and approaches how to develop and implement the new approach.

  16. A novel virtual hub approach for multisource downstream service integration

    Science.gov (United States)

    Previtali, Mattia; Cuca, Branka; Barazzetti, Luigi

    2016-08-01

    A large development of downstream services is expected to be stimulated starting from earth observations (EO) datasets acquired by Copernicus satellites. An important challenge connected with the availability of downstream services is the possibility for their integration in order to create innovative applications with added values for users of different categories level. At the moment, the world of geo-information (GI) is extremely heterogeneous in terms of standards and formats used, thus preventing a facilitated access and integration of downstream services. Indeed, different users and data providers have also different requirements in terms of communication protocols and technology advancement. In recent years, many important programs and initiatives have tried to address this issue even on trans-regional and international level (e.g. INSPIRE Directive, GEOSS, Eye on Earth and SEIS). However, a lack of interoperability between systems and services still exists. In order to facilitate the interaction between different downstream services, a new architectural approach (developed within the European project ENERGIC OD) is proposed in this paper. The brokering-oriented architecture introduces a new mediation layer (the Virtual Hub) which works as an intermediary to bridge the gaps linked to interoperability issues. This intermediation layer de-couples the server and the client allowing a facilitated access to multiple downstream services and also Open Data provided by national and local SDIs. In particular, in this paper an application is presented integrating four services on the topic of agriculture: (i) the service given by Space4Agri (providing services based on MODIS and Landsat data); (ii) Gicarus Lab (providing sample services based on Landsat datasets) and (iii) FRESHMON (providing sample services for water quality) and services from a several regional SDIs.

  17. An integrated approach for multi-level sample size determination

    International Nuclear Information System (INIS)

    Lu, M.S.; Teichmann, T.; Sanborn, J.B.

    1997-01-01

    Inspection procedures involving the sampling of items in a population often require steps of increasingly sensitive measurements, with correspondingly smaller sample sizes; these are referred to as multilevel sampling schemes. In the case of nuclear safeguards inspections verifying that there has been no diversion of Special Nuclear Material (SNM), these procedures have been examined often and increasingly complex algorithms have been developed to implement them. The aim in this paper is to provide an integrated approach, and, in so doing, to describe a systematic, consistent method that proceeds logically from level to level with increasing accuracy. The authors emphasize that the methods discussed are generally consistent with those presented in the references mentioned, and yield comparable results when the error models are the same. However, because of its systematic, integrated approach the proposed method elucidates the conceptual understanding of what goes on, and, in many cases, simplifies the calculations. In nuclear safeguards inspections, an important aspect of verifying nuclear items to detect any possible diversion of nuclear fissile materials is the sampling of such items at various levels of sensitivity. The first step usually is sampling by ''attributes'' involving measurements of relatively low accuracy, followed by further levels of sampling involving greater accuracy. This process is discussed in some detail in the references given; also, the nomenclature is described. Here, the authors outline a coordinated step-by-step procedure for achieving such multilevel sampling, and they develop the relationships between the accuracy of measurement and the sample size required at each stage, i.e., at the various levels. The logic of the underlying procedures is carefully elucidated; the calculations involved and their implications, are clearly described, and the process is put in a form that allows systematic generalization

  18. Trends in scenario development methodologies and integration in NUMO's approach

    International Nuclear Information System (INIS)

    Ebashi, Takeshi; Ishiguro, Katsuhiko; Wakasugi, Keiichiro; Kawamura, Hideki; Gaus, Irina; Vomvoris, Stratis; Martin, Andrew J.; Smith, Paul

    2011-01-01

    The development of scenarios for quantitative or qualitative analysis is a key element of the assessment of the safety of geological disposal systems. As an outcome of an international workshop attended by European and the Japanese implementers, a number of features common to current methodologies could be identified, as well as trends in their evolution over time. In the late nineties, scenario development was often described as a bottom-up process, whereby scenarios were said to be developed in essence from FEP databases. Nowadays, it is recognised that, in practice, the approaches actually adopted are better described as top-down or 'hybrid', taking as their starting point an integrated (top-down) understanding of the system under consideration including uncertainties in initial state, sometimes assisted by the development of 'storyboards'. A bottom-up element remains (hence the term 'hybrid') to the extent that FEP databases or FEP catalogues (including interactions) are still used, but the focus is generally on completeness checking, which occurs parallel to the main assessment process. Recent advances focus on the consistent treatment of uncertainties throughout the safety assessment and on the integration of operational safety and long term safety. (author)

  19. Family welfare programme calls for an integrated approach.

    Science.gov (United States)

    Singh, P N

    3 phases can be identified in India's family planning program in the 4 decades since the country achieved its independence: a stage designed to improve the infrastructure of family planning; a phase of integration of different health and family welfare services; and an attempt of community involvement and universal coverage. At this time there is a widespread infrastructure and a growing awareness of family planning services. The birthrate has declined from 41.2/1000 in the 1960s to 33.3/1000 in the 1980s; the mortality rate declined from 27.4 to 14.2. The current facilities of family welfare services are inadequate, particularly in rural areas. The present provision of auxiliary nurse midwives (ANMS) at the rate of 1/5000 can cover effectively only 1/3 of eligible couples. Further, in rural areas, communication and motivational efforts are lacking as well as easy availability of personnel and medical supplies. Finally, about 40% of the rural population lives below the poverty line and have not reached the economic threshold which is essential for adoption of the small family norm. The primary issue is to deal with the problem of social development. The emphasis needs to be on an integrated and package approach to economic progress and social transformation coupled with the family planning program. The best way to bring about the needed socioeconomic change is to provide educational and gainful employment opportunities.

  20. An integrated approach of composting methodologies for solid waste management

    Directory of Open Access Journals (Sweden)

    K. Kumaresan

    2016-03-01

    Full Text Available Organic fraction of solid waste, which upon degradation produces foul smell and generates pathogens, if not properly managed. Composting is not a method of waste disposal but it is a method of waste recycling and used for agricultural purposes. An integrated approach of composting methodology was tested for municipal solid waste management. Solid waste first was composted and after 22 days, was further processed by vermicomposting. Samples were routinely taken for analysis of carbon, nitrogen, moisture content, pH and temperature to determine the quality of composting. Decrease in moisture content to 32.1 %, relative decrease in carbon and nitrogen content were also observed. Among the different types of treatment, municipal solid waste + activated sludge integration showed promising results, followed by vermicomposting municipal solid waste + activated sludge combination, compared to the combinations of dried activated sludge, municipal solid waste + activated sludge semisolid and municipal solid waste + sewage water. Thus, windrow composting followed by vermicomposting gave a better result than other methods. Thus this method would serve as a potential alternative for solid waste management.

  1. An integrated approach of composting methodologies for solid waste management

    International Nuclear Information System (INIS)

    Kumaresan, K.; Balan, R.; Sridhar, A.; Aravind, J.; Kanmani, P.

    2016-01-01

    Organic fraction of solid waste, which upon degradation produces foul smell and generates pathogens, if not properly managed. Composting is not a method of waste disposal but it is a method of waste recycling and used for agricultural purposes. An integrated approach of composting methodology was tested for municipal solid waste management. Solid waste first was composted and after 22 days, was further processed by vermicomposting. Samples were routinely taken for analysis of carbon, nitrogen, moisture content, p H and temperature to determine the quality of composting. Decrease in moisture content to 32.1 %, relative decrease in carbon and nitrogen content were also observed. Among the different types of treatment, municipal solid waste + activated sludge integration showed promising results, followed by vermicomposting municipal solid waste + activated sludge combination, compared to the combinations of dried activated sludge, municipal solid waste + activated sludge semisolid and municipal solid waste + sewage water. Thus, windrow composting followed by vermicomposting gave a better result than other methods. Thus this method would serve as a potential alternative for solid waste management.

  2. Computational approaches to standard-compliant biofilm data for reliable analysis and integration.

    Science.gov (United States)

    Sousa, Ana Margarida; Ferreira, Andreia; Azevedo, Nuno F; Pereira, Maria Olivia; Lourenço, Anália

    2012-12-01

    The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. Nowadays, biofilm studies are heterogeneous and data-intensive, encompassing different levels of analysis. Computational modelling of biofilm studies has become thus a requirement to make sense of these vast and ever-expanding biofilm data volumes. The rationale of the present work is a machine-readable format for representing biofilm studies and supporting biofilm data interchange and data integration. This format is supported by the Biofilm Science Ontology (BSO), the first ontology on biofilms information. The ontology is decomposed into a number of areas of interest, namely: the Experimental Procedure Ontology (EPO) which describes biofilm experimental procedures; the Colony Morphology Ontology (CMO) which characterises morphologically microorganism colonies; and other modules concerning biofilm phenotype, antimicrobial susceptibility and virulence traits. The overall objective behind BSO is to develop semantic resources to capture, represent and share data on biofilms and related experiments in a regularized fashion manner. Furthermore, the present work also introduces a framework in assistance of biofilm data interchange and analysis - BiofOmics (http://biofomics.org) - and a public repository on colony morphology signatures - MorphoCol (http://stardust.deb.uminho.pt/morphocol).

  3. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

    2016-01-01

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  4. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  5. An integrated approach for facilities planning by ELECTRE method

    Science.gov (United States)

    Elbishari, E. M. Y.; Hazza, M. H. F. Al; Adesta, E. Y. T.; Rahman, Nur Salihah Binti Abdul

    2018-01-01

    Facility planning is concerned with the design, layout, and accommodation of people, machines and activities of a system. Most of the researchers try to investigate the production area layout and the related facilities. However, few of them try to investigate the relationship between the production space and its relationship with service departments. The aim of this research to is to integrate different approaches in order to evaluate, analyse and select the best facilities planning method that able to explain the relationship between the production area and other supporting departments and its effect on human efforts. To achieve the objective of this research two different approaches have been integrated: Apple’s layout procedure as one of the effective tools in planning factories, ELECTRE method as one of the Multi Criteria Decision Making methods (MCDM) to minimize the risk of getting poor facilities planning. Dalia industries have been selected as a case study to implement our integration the factory have been divided two main different area: the whole facility (layout A), and the manufacturing area (layout B). This article will be concerned with the manufacturing area layout (Layout B). After analysing the data gathered, the manufacturing area was divided into 10 activities. There are five factors that the alternative were compared upon which are: Inter department satisfactory level, total distance travelled for workers, total distance travelled for the product, total time travelled for the workers, and total time travelled for the product. Three different layout alternatives have been developed in addition to the original layouts. Apple’s layout procedure was used to study and evaluate the different alternatives layouts, the study and evaluation of the layouts was done by calculating scores for each of the factors. After obtaining the scores from evaluating the layouts, ELECTRE method was used to compare the proposed alternatives with each other and with

  6. Project INTEGRATE - a common methodological approach to understand integrated health care in Europe

    Directory of Open Access Journals (Sweden)

    Lucinda Cash-Gibson

    2014-12-01

    Full Text Available Background: The use of case studies in health services research has proven to be an excellent methodology for gaining in-depth understanding of the organisation and delivery of health care. This is particularly relevant when looking at the complexity of integrated healthcare programmes, where multifaceted interactions occur at the different levels of care and often without a clear link between the interventions (new and/or existing and their impact on outcomes (in terms of patients health, both patient and professional satisfaction and cost-effectiveness. Still, integrated care is seen as a core strategy in the sustainability of health and care provision in most societies in Europe and beyond. More specifically, at present, there is neither clear evidence on transferable factors of integrated care success nor a method for determining how to establish these specific success factors. The drawback of case methodology in this case, however, is that the in-depth results or lessons generated are usually highly context-specific and thus brings the challenge of transferability of findings to other settings, as different health care systems and different indications are often not comparable. Project INTEGRATE, a European Commission-funded project, has been designed to overcome these problems; it looks into four chronic conditions in different European settings, under a common methodology framework (taking a mixed-methods approach to try to overcome the issue of context specificity and limited transferability. The common methodological framework described in this paper seeks to bring together the different case study findings in a way that key lessons may be derived and transferred between countries, contexts and patient-groups, where integrated care is delivered in order to provide insight into generalisability and build on existing evidence in this field.Methodology: To compare the different integrated care experiences, a mixed-methods approach has

  7. Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era.

    Science.gov (United States)

    Moroz, Leonid L

    2015-12-01

    The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  8. GeneLab: A Systems Biology Platform for Spaceflight Omics Data

    Science.gov (United States)

    Reinsch, Sigrid S.; Lai, San-Huei; Chen, Rick; Thompson, Terri; Berrios, Daniel; Fogle, Homer; Marcu, Oana; Timucin, Linda; Chakravarty, Kaushik; Coughlan, Joseph

    2015-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and

  9. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

    Energy Technology Data Exchange (ETDEWEB)

    Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.; Casey, Cameron P.; Stratton, Kelly G.; Gonzalez, Juan F.; Habyarimana, Fabien; Negretti, Nicholas M.; Sims, Amy C.; Chauhan, Sadhana; Thackray, Larissa B.; Halfmann, Peter J.; Walters, Kevin B.; Kim, Young-Mo; Zink, Erika M.; Nicora, Carrie D.; Weitz, Karl K.; Webb-Robertson, Bobbie-Jo M.; Nakayasu, Ernesto S.; Ahmer, Brian; Konkel, Michael E.; Motin, Vladimir; Baric, Ralph S.; Diamond, Michael S.; Kawaoka, Yoshihiro; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.

    2017-01-01

    The continued emergence and spread of infectious agents is of increasing concern due to increased population growth and the associated increased livestock production to meet food demands, increased urbanization and land-use changes, and greater travel. A systems biology approach to infectious disease research can significantly advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can only take place subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. Partial inactivation was observed for pathogens without exposed lipid membranes including 99.99% inactivation of community-associated methicillin-resistant Staphylococcus aureus, 99.6% and >99% inactivation of Clostridium difficile spores and vegetative cells, respectively, and 50% inactivation of adenovirus type 5. To demonstrate that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses, we highlight select proteomics, metabolomics and lipidomics data from human epithelial lung cells infected with wild-type and mutant forms of influenza H7N9. We believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics

  10. The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

    Directory of Open Access Journals (Sweden)

    Poblete-Castro Ignacio

    2012-03-01

    Full Text Available Abstract Background Pseudomonas putida KT2442 is a natural producer of polyhydroxyalkanoates (PHAs, which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made biopolymers. However, despite the substantial body of work on PHA production by P. putida strains, it is not yet clear how the bacterium re-arranges its whole metabolism when it senses the limitation of nitrogen and the excess of fatty acids as carbon source, to result in a large accumulation of PHAs within the cell. In the present study we investigated the metabolic response of KT2442 using a systems biology approach to highlight the differences between single- and multiple-nutrient-limited growth in chemostat cultures. Results We found that 26, 62, and 81% of the cell dry weight consist of PHA under conditions of carbon, dual, and nitrogen limitation, respectively. Under nitrogen limitation a specific PHA production rate of 0.43 (g·(g·h-1 was obtained. The residual biomass was not constant for dual- and strict nitrogen-limiting growth, showing a different feature in comparison to other P. putida strains. Dual limitation resulted in patterns of gene expression, protein level, and metabolite concentrations that substantially differ from those observed under exclusive carbon or nitrogen limitation. The most pronounced differences were found in the energy metabolism, fatty acid metabolism, as well as stress proteins and enzymes belonging to the transport system. Conclusion This is the first study where the interrelationship between nutrient limitations and PHA synthesis has been investigated under well-controlled conditions using a system level approach. The knowledge generated will be of great assistance for the development of bioprocesses and further metabolic engineering work in this versatile organism to both enhance and diversify the industrial production of PHAs.

  11. Integrated Management System as constituent of balanced development approach

    International Nuclear Information System (INIS)

    Pasternak, J.

    2005-01-01

    Globalization of the economy makes RAFAKO S.A. react promptly and efficiently to what goes on in the surrounding world. The way this company is organized and managed constitutes the fundamental condition for success and it is this subject that the authors have concentrated on. The restructuring process of the company started in 1998. A business management structure was established and individual fields of activity, as profit or cost centers for budgeting and reporting, were separated. Employment rationalization was started, labour valuation system, its effectiveness and a new payment policy were implemented. In accordance with the stipulation resulting from standard PN-EN ISO 9000:2001, process-like approach to management was assumed. This paper presents the process based approach to management and elements of project management at RAFAKO S.A. The experiences in project management, originating from the history of this company, facilitated considerably the first stages of process management implementation. A brief description of budget planning technique and elements of cost account, as well as how the budget and account are interpreted in the Integrated Management System were presented. (author)

  12. Distortion-Free Watermarking Approach for Relational Database Integrity Checking

    Directory of Open Access Journals (Sweden)

    Lancine Camara

    2014-01-01

    Full Text Available Nowadays, internet is becoming a suitable way of accessing the databases. Such data are exposed to various types of attack with the aim to confuse the ownership proofing or the content protection. In this paper, we propose a new approach based on fragile zero watermarking for the authentication of numeric relational data. Contrary to some previous databases watermarking techniques which cause some distortions in the original database and may not preserve the data usability constraints, our approach simply seeks to generate the watermark from the original database. First, the adopted method partitions the database relation into independent square matrix groups. Then, group-based watermarks are securely generated and registered in a trusted third party. The integrity verification is performed by computing the determinant and the diagonal’s minor for each group. As a result, tampering can be localized up to attribute group level. Theoretical and experimental results demonstrate that the proposed technique is resilient against tuples insertion, tuples deletion, and attributes values modification attacks. Furthermore, comparison with recent related effort shows that our scheme performs better in detecting multifaceted attacks.

  13. Social Network Analysis and Nutritional Behavior: An Integrated Modeling Approach.

    Science.gov (United States)

    Senior, Alistair M; Lihoreau, Mathieu; Buhl, Jerome; Raubenheimer, David; Simpson, Stephen J

    2016-01-01

    Animals have evolved complex foraging strategies to obtain a nutritionally balanced diet and associated fitness benefits. Recent research combining state-space models of nutritional geometry with agent-based models (ABMs), show how nutrient targeted foraging behavior can also influence animal social interactions, ultimately affecting collective dynamics and group structures. Here we demonstrate how social network analyses can be integrated into such a modeling framework and provide a practical analytical tool to compare experimental results with theory. We illustrate our approach by examining the case of nutritionally mediated dominance hierarchies. First we show how nutritionally explicit ABMs that simulate the emergence of dominance hierarchies can be used to generate social networks. Importantly the structural properties of our simulated networks bear similarities to dominance networks of real animals (where conflicts are not always directly related to nutrition). Finally, we demonstrate how metrics from social network analyses can be used to predict the fitness of agents in these simulated competitive environments. Our results highlight the potential importance of nutritional mechanisms in shaping dominance interactions in a wide range of social and ecological contexts. Nutrition likely influences social interactions in many species, and yet a theoretical framework for exploring these effects is currently lacking. Combining social network analyses with computational models from nutritional ecology may bridge this divide, representing a pragmatic approach for generating theoretical predictions for nutritional experiments.

  14. Data integration, systems approach and multilevel description of complex biosystems

    International Nuclear Information System (INIS)

    Hernández-Lemus, Enrique

    2013-01-01

    Recent years have witnessed the development of new quantitative approaches and theoretical tenets in the biological sciences. The advent of high throughput experiments in genomics, proteomics and electrophysiology (to cite just a few examples) have provided the researchers with unprecedented amounts of data to be analyzed. Large datasets, however can not provide the means to achieve a complete understanding of the underlying biological phenomena, unless they are supplied with a solid theoretical framework and with proper analytical tools. It is now widely accepted that by using and extending some of the paradigmatic principles of what has been called complex systems theory, some degree of advance in this direction can be attained. We will be presenting ways in which by using data integration techniques (linear, non-linear, combinatorial, graphical), multidimensional-multilevel descriptions (multifractal modeling, dimensionality reduction, computational learning), as well as an approach based in systems theory (interaction maps, probabilistic graphical models, non-equilibrium physics) have allowed us to better understand some problems in the interface of Statistical Physics and Computational Biology

  15. Karet KB and jamu: an integrated approach to condom marketing.

    Science.gov (United States)

    Piet, D L; Hendrata, L

    1974-01-01

    The development of an out-of-clinic method for marketing condoms in Indonesia is described. A jamu company (jamu referes to any herbal medicant, many of which are related to sexual activity, whose use is firmly integrated into the Indonesian way of life) was contracted by the private, non-profit Prosperous Indonesia Foundation (YIS) to distribute condoms as a jamu item. The condoms are donated to YIS by the U.S. Agency for International Development, and are retailed at 20 rupees for a package of 3, with a profit of 4 rupees for the retailer. Mobile promotional/sales units are the most effective means for selling the devices. The approach appeals to the cultural and sexual character of the people. The media is used extensively to promote condoms and family planning. Although it is too early to assess the impact of the program, it is anticipated that this novel approach will spread the use of condoms to all areas of Indonesia.

  16. Phytoremediation of coal mine spoil dump through integrated biotechnological approach

    Energy Technology Data Exchange (ETDEWEB)

    Juwarkar, A.A.; Jambhulkar, H.P. [National Environmental Engineering Research Institute, Nagpur (India)

    2008-07-15

    Field experiment was conducted on mine spoil dump on an area of 10 ha, to restore the fertility and productivity of the coal mine spoil dump using integrated biotechnological approach. The approach involves use of effluent treatment plant sludge (ETP sludge), as an organic amendment, biofertilizers and mycorrihzal fungi along with suitable plant species. The results of the study indicated that amendment with effluent treatment plant sludge (ETP sludge), at 50 ton/ha improved the physico-chemical properties of coal mine spoil. Due to biofertilizer inoculation different microbial groups such as Rhizobium, Azotobacter and VAM spores, which were practically absent in mine spoil improved greatly. Inoculation of biofertilizer and application of ETP sludge helped in reducing the toxicity of heavy metals such as chromium, zinc, copper, iron, manganese lead, nickel and cadmium, which were significantly reduced to 41%, 43%, 37%, 37%, 34%, 39%, 37% and 40%, respectively, due to the increased organic matter content in the ETP sludge and its alkaline pH (8.10-8.28), at which the metals gets immobilized and translocation of metals is arrested. Thus, amendment and biofertilizer application provided better supportive material for anchorage and growth of the plant on coal mine spoil dump.

  17. Integrated approach for coastal hazards and risks in Sri Lanka

    Science.gov (United States)

    Garcin, M.; Desprats, J. F.; Fontaine, M.; Pedreros, R.; Attanayake, N.; Fernando, S.; Siriwardana, C. H. E. R.; de Silva, U.; Poisson, B.

    2008-06-01

    The devastating impact of the tsunami of 26 December 2004 on the shores of the Indian Ocean recalled the importance of knowledge and the taking into account of coastal hazards. Sri Lanka was one of the countries most affected by this tsunami (e.g. 30 000 dead, 1 million people homeless and 70% of the fishing fleet destroyed). Following this tsunami, as part of the French post-tsunami aid, a project to establish a Geographical Information System (GIS) on coastal hazards and risks was funded. This project aims to define, at a pilot site, a methodology for multiple coastal hazards assessment that might be useful for the post-tsunami reconstruction and for development planning. This methodology could be applied to the whole coastline of Sri Lanka. The multi-hazard approach deals with very different coastal processes in terms of dynamics as well as in terms of return period. The first elements of this study are presented here. We used a set of tools integrating a GIS, numerical simulations and risk scenario modelling. While this action occurred in response to the crisis caused by the tsunami, it was decided to integrate other coastal hazards into the study. Although less dramatic than the tsunami these remain responsible for loss of life and damage. Furthermore, the establishment of such a system could not ignore the longer-term effects of climate change on coastal hazards in Sri Lanka. This GIS integrates the physical and demographic data available in Sri Lanka that is useful for assessing the coastal hazards and risks. In addition, these data have been used in numerical modelling of the waves generated during periods of monsoon as well as for the December 2004 tsunami. Risk scenarios have also been assessed for test areas and validated by field data acquired during the project. The results obtained from the models can be further integrated into the GIS and contribute to its enrichment and to help in better assessment and mitigation of these risks. The coastal

  18. Integrated approach for coastal hazards and risks in Sri Lanka

    Directory of Open Access Journals (Sweden)

    M. Garcin

    2008-06-01

    Full Text Available The devastating impact of the tsunami of 26 December 2004 on the shores of the Indian Ocean recalled the importance of knowledge and the taking into account of coastal hazards. Sri Lanka was one of the countries most affected by this tsunami (e.g. 30 000 dead, 1 million people homeless and 70% of the fishing fleet destroyed. Following this tsunami, as part of the French post-tsunami aid, a project to establish a Geographical Information System (GIS on coastal hazards and risks was funded. This project aims to define, at a pilot site, a methodology for multiple coastal hazards assessment that might be useful for the post-tsunami reconstruction and for development planning. This methodology could be applied to the whole coastline of Sri Lanka.

    The multi-hazard approach deals with very different coastal processes in terms of dynamics as well as in terms of return period. The first elements of this study are presented here. We used a set of tools integrating a GIS, numerical simulations and risk scenario modelling. While this action occurred in response to the crisis caused by the tsunami, it was decided to integrate other coastal hazards into the study. Although less dramatic than the tsunami these remain responsible for loss of life and damage. Furthermore, the establishment of such a system could not ignore the longer-term effects of climate change on coastal hazards in Sri Lanka.

    This GIS integrates the physical and demographic data available in Sri Lanka that is useful for assessing the coastal hazards and risks. In addition, these data have been used in numerical modelling of the waves generated during periods of monsoon as well as for the December 2004 tsunami. Risk scenarios have also been assessed for test areas and validated by field data acquired during the project. The results obtained from the models can be further integrated into the GIS and contribute to its enrichment and to help in better assessment and mitigation

  19. Omics-bioinformatics in the context of clinical data

    NARCIS (Netherlands)

    Mayer, Gert; Heinze, Georg; Mischak, Harald; Hellemons, Merel E; Heerspink, Hiddo J Lambers; Bakker, Stephan J L; de Zeeuw, Dick; Haiduk, Martin; Rossing, Peter; Oberbauer, Rainer

    2011-01-01

    The Omics revolution has provided the researcher with tools and methodologies for qualitative and quantitative assessment of a wide spectrum of molecular players spanning from the genome to the meta-bolome level. As a consequence, explorative analysis (in contrast to purely hypothesis driven

  20. Role of omics techniques in the toxicity testing of nanoparticles

    Directory of Open Access Journals (Sweden)

    Eleonore Fröhlich

    2017-11-01

    Full Text Available Abstract Nanotechnology is regarded as a key technology of the twenty-first century. Despite the many advantages of nanotechnology it is also known that engineered nanoparticles (NPs may cause adverse health effects in humans. Reports on toxic effects of NPs relay mainly on conventional (phenotypic testing but studies of changes in epigenome, transcriptome, proteome, and metabolome induced by NPs have also been performed. NPs most relevant for human exposure in consumer, health and food products are metal, metal oxide and carbon-based NPs. They were also studied quite frequently with omics technologies and an overview of the study results can serve to answer the question if screening for established targets of nanotoxicity (e.g. cell death, proliferation, oxidative stress, and inflammation is sufficient or if omics techniques are needed to reveal new targets. Regulated pathways identified by omics techniques were confirmed by phenotypic assays performed in the same study and comparison of particle types and cells by the same group indicated a more cell/organ-specific than particle specific regulation pattern. Between different studies moderate overlap of the regulated pathways was observed and cell-specific regulation is less obvious. The lack of standardization in particle exposure, in omics technologies, difficulties to translate mechanistic data to phenotypes and comparison with human in vivo data currently limit the use of these technologies in the prediction of toxic effects by NPs.

  1. 'Omic' genetic technologies for herbal medicines in psychiatry.

    Science.gov (United States)

    Sarris, Jerome; Ng, Chee Hong; Schweitzer, Isaac

    2012-04-01

    The field of genetics, which includes the use of 'omic' technologies, is an evolving area of science that has emerging application in phytotherapy. Omic studies include pharmacogenomics, proteomics and metabolomics. Herbal medicines, as monotherapies, or complex formulations such as traditional Chinese herbal prescriptions, may benefit from omic studies, and this new field may be termed 'herbomics'. Applying herbomics in the field of psychiatry may provide answers about which herbal interventions may be effective for individuals, which genetic processes are triggered, and the subsequent neurochemical pathways of activity. The use of proteomic technology can explore the differing epigenetic effects on neurochemical gene expression between individual herbs, isolated constituents and complex formulae. The possibilities of side effects or insufficient response to the herb can also be assessed via pharmacogenomic analysis of polymorphisms of cytochrome P450 liver enzymes or P-glycoprotein. While another novel application of omic technology is for the validation of the concept of synergy in individual herbal extracts and prescriptive formulations. Chronic administration of psychotropic herbal medicines may discover important effects on chromatin remodelling via modification of histone and DNA methylation. This paper focuses on the emerging field of herbomics, and is to our knowledge the first publication to explore this in the area of psychiatry. Copyright © 2011 John Wiley & Sons, Ltd.

  2. Social network approaches to leadership: an integrative conceptual review.

    Science.gov (United States)

    Carter, Dorothy R; DeChurch, Leslie A; Braun, Michael T; Contractor, Noshir S

    2015-05-01

    Contemporary definitions of leadership advance a view of the phenomenon as relational, situated in specific social contexts, involving patterned emergent processes, and encompassing both formal and informal influence. Paralleling these views is a growing interest in leveraging social network approaches to study leadership. Social network approaches provide a set of theories and methods with which to articulate and investigate, with greater precision and rigor, the wide variety of relational perspectives implied by contemporary leadership theories. Our goal is to advance this domain through an integrative conceptual review. We begin by answering the question of why-Why adopt a network approach to study leadership? Then, we offer a framework for organizing prior research. Our review reveals 3 areas of research, which we term: (a) leadership in networks, (b) leadership as networks, and (c) leadership in and as networks. By clarifying the conceptual underpinnings, key findings, and themes within each area, this review serves as a foundation for future inquiry that capitalizes on, and programmatically builds upon, the insights of prior work. Our final contribution is to advance an agenda for future research that harnesses the confluent ideas at the intersection of leadership in and as networks. Leadership in and as networks represents a paradigm shift in leadership research-from an emphasis on the static traits and behaviors of formal leaders whose actions are contingent upon situational constraints, toward an emphasis on the complex and patterned relational processes that interact with the embedding social context to jointly constitute leadership emergence and effectiveness. (c) 2015 APA, all rights reserved.

  3. Growing trend of CE at the omics level: the frontier of systems biology.

    Science.gov (United States)

    Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

    2010-01-01

    In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

  4. The human gut microbiome and its dysfunctions through the meta-omics prism.

    Science.gov (United States)

    Mondot, Stanislas; Lepage, Patricia

    2016-05-01

    The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual). It is now acknowledged that the microbiota has coevolved with its host to achieve a symbiotic relationship, leading to physiological homeostasis. The gut microbiota ensures vital functions, such as food digestibility, maturation of the host immune system, and protection against pathogens. Over the last few decades, the gut microbiota has also been associated with numerous diseases, such as inflammatory bowel disease, irritable bowel syndrome, obesity, and metabolic diseases. In most of these pathologies, a microbial dysbiosis has been found, indicating shifts in the taxonomic composition of the gut microbiota and changes in its functionality. Our understanding of the influence of the gut microbiota on human health is still growing. Working with microorganisms residing in the gut is challenging since most of them are anaerobic and a vast majority (approximately 75%) are uncultivable to date. Recently, a wide range of new approaches (meta-omics) has been developed to bypass the uncultivability and reveal the intricate mechanisms that sustain gut microbial homeostasis. After a brief description of these approaches (metagenomics, metatranscriptomics, metaproteomics, and metabolomics), this review will discuss the importance of considering the gut microbiome as a structured ecosystem and the use of meta-omics to decipher dysfunctions of the gut microbiome in diseases. © 2016 New York Academy of Sciences.

  5. Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent

    International Nuclear Information System (INIS)

    Zhang, Yan; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang

    2014-01-01

    Highlights: • Mice exposed to mixed chemical wastewater and its treated effluent for 90 days. • Hepatic transcriptomic alterations were analyzed by digital gene expression. • Serum metabolomic alterations were analyzed by proton nuclear magnetic resonance. • The water samples induced disruption of lipid metabolism and hepatotoxicity. • Omics approaches are valuable to evaluate the complicated toxicity of wastewater. - Abstract: Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ( 1 H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE

  6. Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yan; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang, E-mail: hqren@nju.edu.cn

    2014-05-01

    Highlights: • Mice exposed to mixed chemical wastewater and its treated effluent for 90 days. • Hepatic transcriptomic alterations were analyzed by digital gene expression. • Serum metabolomic alterations were analyzed by proton nuclear magnetic resonance. • The water samples induced disruption of lipid metabolism and hepatotoxicity. • Omics approaches are valuable to evaluate the complicated toxicity of wastewater. - Abstract: Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ({sup 1}H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE.

  7. A new, integrated, approach to mineralization-based CCS

    Energy Technology Data Exchange (ETDEWEB)

    Hunwick, R.J. [Integrated Carbon Sequestration Pty Ltd., Lindfield, NSW (Australia)

    2009-11-15

    Mineralization is an attractive concept for carbon capture and storage as it can avoid some of the potential public acceptance problems of geosequestering pressurised CO{sub 2}. But there are major cost and energy penalty concerns. A new integrated approach to mineralisation, avoiding the intermediate step of CO{sub 2} extraction and promising considerable benefits, is outlined here. The ICS process integrates two operation in the first, an ammonia-rich aqueous solution of ammonium bicarbonate is used to scrub carbon dioxide from flue gases to form a solution enriched in carbon dioxide. In the second, pretreated serpentinite or other suitable ultramafic rock is blended directly into this rich solution prior to the mixture being held under controlled conditions in a purpose-built reactor. The silicate minerals react with ammonium carbonate to form magnesium carbonate and silica, thereby directly removing frrm solution the carbon dioxide that was absorbed in the flue gas scrubbers as insoluble precipitates. The capture solution is regenerated for its recycle to the flue gas scrubbers. Trials at Lucas Hights have demonstrated the direct conversion of silicates to magnesite, and work continues to establish optimum conditions for this reaction to allow a continuous pilot plant to be designed. Their thermodynamic modeling has confirmed the energy efficiency of the process. Pre-feasibility studies into retrofitting ICS to major existing coal-fired power stations to capture at least 90% of their carbon dioxide emissions suggest a total cost of US$50 to capture and store each tonne of the gas permanently. Since the tonnage of rock required for this mineralisation process is six times the tonnage of coal to be fired in the host power station logic dictates that any new power station should be nearer the rock deposit than the coal field that furnishes its fuel. 2 figs.

  8. Inspector training for VIFM equipment - An integrated approach

    International Nuclear Information System (INIS)

    Truong, Q.S. Bob; Keeffe, R.; Ellacott, T.; Desson, K.; Herber, N.

    2001-01-01

    Full text: The VXI Integrated Fuel Monitor (VIFM) was developed by the Canadian Safeguards Support Program (CSSP) as a generic radiation monitor for safeguards applications. The VIFM equipment features a modular design, where a single cabinet can house several instruments such as bundle counters, core discharge monitors, Yes/No monitors, and other devices. VIFM can also be used in a stand-alone, transportable mode, with a detector connected to a single VIFM module linked to a laptop computer. VIFM equipment is currently in use at CANDU nuclear generating stations in several countries. Because each facility may have a different combination of detectors, the training program has been designed to reflect the modular nature of VIFM. Introductory material is generic and applies to any facility. More advanced material is carefully compartmentalized to allow IAEA Inspectors to concentrate their efforts in areas that concern them. Advanced material is available in a just-in-time reference format that simplifies rapid access to detailed information. A number of training resources have been developed, including multimedia and video material on CD-ROMs. This material has been designed to operate on a laptop computer, allowing inspectors to review and refresh their knowledge at any time - for example, during inspection trips. Although each of these resources is useful in its own right, the CSSP is developing an integrated approach to inspector training that combines all of these elements in a new way calculated to produce better training results than in the past. This new training approach features a two-day workshop preceded by a period of CD-ROM-based self-paced study. After the workshop, participants are able to make use of printed and CD-ROM-based reference materials for just-in-time 'refreshers'. Each step in this integrated approach to training will be described in the presentation. Briefly, the steps are as follows. A multimedia computer-based training package is made

  9. Biomass gasification systems for residential application: An integrated simulation approach

    International Nuclear Information System (INIS)

    Prando, Dario; Patuzzi, Francesco; Pernigotto, Giovanni; Gasparella, Andrea; Baratieri, Marco

    2014-01-01

    The energy policy of the European member States is promoting high-efficiency cogeneration systems by means of the European directive 2012/27/EU. Particular facilitations have been implemented for the small-scale and micro-cogeneration units. Furthermore, the directive 2010/31/EU promotes the improvement of energy performance of buildings and use of energy from renewable sources for the building sector. In this scenario, systems based on gasification are considered a promising technological solution when dealing with biomass and small scale systems. In this paper, an integrated approach has been implemented to assess the energy performance of combined heat and power (CHP) systems based on biomass gasification and installed in residential blocks. The space-heating loads of the considered building configurations have been simulated by means of EnergyPlus. The heat load for domestic hot water demand has been calculated according to the average daily profiles suggested by the Italian and European technical standards. The efficiency of the whole CHP system has been evaluated supplementing the simulation of the gasification stage with the energy balance of the cogeneration set (i.e., internal combustion engine) and implementing the developed routines in the Matlab-Simulink environment. The developed model has been used to evaluate the primary energy saving (PES) of the CHP system compared to a reference case of separate production of heat and power. Economic analyses are performed either with or without subsidizations for the generated electricity. The results highlight the capability of the integrated approach to estimate both energy and economic performances of CHP systems applied to the residential context. Furthermore, the importance of the generated heat valorisation and the proper system sizing have been discussed. - Highlights: • CHP system based on biomass gasification to meet household energy demand is studied. • Influence of CHP size and operation time on

  10. A Triangular Approach to Integrate Research, Education and Practice in Higher Engineering Education

    Science.gov (United States)

    Heikkinen, Eetu-Pekka; Jaako, Juha; Hiltunen, Jukka

    2017-01-01

    Separate approaches in engineering education, research and practice are not very useful when preparing students for working life; instead, integration of education, research and industrial practices is needed. A triangular approach (TA) as a method to accomplish this integration and as a method to provide students with integrated expertise is…

  11. Interventions to promote an integrated approach to public health problems : an application to childhood obesity

    NARCIS (Netherlands)

    Hendriks, Anna-Marie; Gubbels, Jessica S; De Vries, Nanne K.; Seidell, Jaap C; Kremers, Stef P J; Jansen, Maria W J

    2012-01-01

    Experts stress the need to bring the childhood obesity epidemic under control by means of an integrated approach. The implementation of such an approach requires the development of integrated enabling policies on public health by local governments. A prerequisite for developing such integrated

  12. Approaches to cancer assessment in EPA's Integrated Risk Information System.

    Science.gov (United States)

    Gehlhaus, Martin W; Gift, Jeffrey S; Hogan, Karen A; Kopylev, Leonid; Schlosser, Paul M; Kadry, Abdel-Razak

    2011-07-15

    The U.S. Environmental Protection Agency's (EPA) Integrated Risk Information System (IRIS) Program develops assessments of health effects that may result from chronic exposure to chemicals in the environment. The IRIS database contains more than 540 assessments. When supported by available data, IRIS assessments provide quantitative analyses of carcinogenic effects. Since publication of EPA's 2005 Guidelines for Carcinogen Risk Assessment, IRIS cancer assessments have implemented new approaches recommended in these guidelines and expanded the use of complex scientific methods to perform quantitative dose-response assessments. Two case studies of the application of the mode of action framework from the 2005 Cancer Guidelines are presented in this paper. The first is a case study of 1,2,3-trichloropropane, as an example of a chemical with a mutagenic mode of carcinogenic action thus warranting the application of age-dependent adjustment factors for early-life exposure; the second is a case study of ethylene glycol monobutyl ether, as an example of a chemical with a carcinogenic action consistent with a nonlinear extrapolation approach. The use of physiologically based pharmacokinetic (PBPK) modeling to quantify interindividual variability and account for human parameter uncertainty as part of a quantitative cancer assessment is illustrated using a case study involving probabilistic PBPK modeling for dichloromethane. We also discuss statistical issues in assessing trends and model fit for tumor dose-response data, analysis of the combined risk from multiple types of tumors, and application of life-table methods for using human data to derive cancer risk estimates. These issues reflect the complexity and challenges faced in assessing the carcinogenic risks from exposure to environmental chemicals, and provide a view of the current trends in IRIS carcinogenicity risk assessment. Copyright © 2011. Published by Elsevier Inc.

  13. Towards an integrated approach to health and medicine in Africa.

    Science.gov (United States)

    Batisai, Kezia

    2016-12-01

    This article frames the intersections of medicine and humanities as intrinsic to understanding the practice of health care in Africa. Central to this manuscript, which draws on empirical findings on the interplay between HIV and AIDS and alternative medicine in Zimbabwe is the realisation that very limited research has been undertaken to examine 'HIV/AIDS patient behaviour' with respect to choice of therapy on the continent [Bene, M. & Darkoh, M. B. K. (2014). The Constraints of Antiretroviral Uptake in Rural Areas: The Case of Thamaga and Surrounding Villages, Botswana. Journal of Social Aspects of HIV/AIDS, 11(1), 167-177. doi: 10.1080/17290376.2014.972057 ; Chavunduka, G. (1998). Professionalisation of Traditional Medicine in Zimbabwe, Harare, Jongwe Printers; O'Brien, S. & Broom, A. (2014). HIV in (and out of) the Clinic: Biomedicine, Traditional Medicine and Spiritual Healing in Harare. Journal of Social Aspects of HIV/AIDS, 11(1), 94-104. doi: 10.1080/17290376.2014.938102 ]. As such, a social approach to health-seeking behaviour questions how decisions about alternative therapies including herbal remedies, traditional healing and faith healing are made. The paper unpacks the realities around how people living with HIV and AIDS - who span different age groups and profess various religious backgrounds, faced with an insurmountable health challenge against a background of limited resources and no cure for the virus - often experience shifts in health-seeking behaviour. Grappling with seemingly simple questions about 'when, where and how to seek medical attention', the paper provides pointers to therapy choices and health-seeking behaviour; and it serves as a route into deeper and intense healthcare practice explorations. In conclusion, the paper proposes that medicine and the humanities should engage seriously with those social aspects of HIV and AIDS which call for an integrated approach to healthcare practice in Africa. If combined, medicine and the humanities

  14. Approaches to cancer assessment in EPA's Integrated Risk Information System

    International Nuclear Information System (INIS)

    Gehlhaus, Martin W.; Gift, Jeffrey S.; Hogan, Karen A.; Kopylev, Leonid; Schlosser, Paul M.; Kadry, Abdel-Razak

    2011-01-01

    The U.S. Environmental Protection Agency's (EPA) Integrated Risk Information System (IRIS) Program develops assessments of health effects that may result from chronic exposure to chemicals in the environment. The IRIS database contains more than 540 assessments. When supported by available data, IRIS assessments provide quantitative analyses of carcinogenic effects. Since publication of EPA's 2005 Guidelines for Carcinogen Risk Assessment, IRIS cancer assessments have implemented new approaches recommended in these guidelines and expanded the use of complex scientific methods to perform quantitative dose-response assessments. Two case studies of the application of the mode of action framework from the 2005 Cancer Guidelines are presented in this paper. The first is a case study of 1,2,3-trichloropropane, as an example of a chemical with a mutagenic mode of carcinogenic action thus warranting the application of age-dependent adjustment factors for early-life exposure; the second is a case study of ethylene glycol monobutyl ether, as an example of a chemical with a carcinogenic action consistent with a nonlinear extrapolation approach. The use of physiologically based pharmacokinetic (PBPK) modeling to quantify interindividual variability and account for human parameter uncertainty as part of a quantitative cancer assessment is illustrated using a case study involving probabilistic PBPK modeling for dichloromethane. We also discuss statistical issues in assessing trends and model fit for tumor dose-response data, analysis of the combined risk from multiple types of tumors, and application of life-table methods for using human data to derive cancer risk estimates. These issues reflect the complexity and challenges faced in assessing the carcinogenic risks from exposure to environmental chemicals, and provide a view of the current trends in IRIS carcinogenicity risk assessment.

  15. Integrated approach in the treatment of metabolic syndrome

    Directory of Open Access Journals (Sweden)

    2014-03-01

    Full Text Available The Goal of this study was to investigate the efficacy of the integrated approach for the treatment of metabolic syndrome (MS aiming to correct all of its components versus standard therapy using clinical outcomes (BMI, waist circumference, blood pressure, lipid levels, assessment of psychological status (Beck Depression Inventory, and quality of life (SF-36. Methods: A total of 60 patients with MS were included in the study. The study group (30 subjects mean age 41.0±11 years, women - 23 (76.7%, men - 7 (23.3% received the complex therapy of MS - pharmacotherapy of obesity (orlistat and insulin resistance (metformin, lipid-lowering therapy (statins or fibrates, antihypertensive therapy. Control group (30 patients mean age 43.4±9.5 years, women - 26 (86.7%, men - 4 (13.3% was treated with statins or fibrates and received antihypertensive therapy when needed. At the inclusion in the study and after 6 months of therapy all patients underwent clinical and laboratory investigation, assessment of depression and quality of life. Results: We found a more significant reduction of all clinical outcomes (body weight, blood pressure, improvement in glucose and lipid metabolism, a significant decrease in the prevalence and severity of the depression, and an improvement in the quality of life in patients of study group compared with standard therapy. Conclusion: Complex treatment of the MS, including pharmacotherapy of obesity (orlistat, Xenical and insulin resistance (metformin, Glucophage is characterized by a greater clinical efficacy compared with standard therapy.

  16. Climate change and local pollution effects. An integrated approach

    International Nuclear Information System (INIS)

    Aaheim, H.A.; Kristin, A.; Seip, H.M.

    1999-01-01

    Few studies on measures for mitigation of damage caused by man-made emissions to the environment have tried to consider all major effects. We illustrate the importance of an integrated approach by estimating costs and benefits of a proposed energy saving program for Hungary, originally designed to reduce CO 2 emissions. The dominant benefit of implementing the program is likely to be reduced health damage from local pollutants. Also reduced costs of material damage and to a lesser extent vegetation damage contribute to make the net benefit considerable. Compared to the reduction in these local and regional effects, the benefits from reducing greenhouse gases are likely to be minor. Since local effects in general occur much earlier after measures have been implemented than effects of increased emissions of greenhouse gases, inclusion of local effects makes evaluation of climate policy less dependent on the choice of discount rate. In our opinion, similar results are likely for many measures originally designed to reduce emissions of greenhouse gases particularly in some areas in developing countries with high local pollution levels. Main uncertainties in the analysis, e.g. in the relationships between damage and pollution level, are discussed. 72 refs

  17. Evolutionary algorithms approach for integrated bioenergy supply chains optimization

    International Nuclear Information System (INIS)

    Ayoub, Nasser; Elmoshi, Elsayed; Seki, Hiroya; Naka, Yuji

    2009-01-01

    In this paper, we propose an optimization model and solution approach for designing and evaluating integrated system of bioenergy production supply chains, SC, at the local level. Designing SC that simultaneously utilize a set of bio-resources together is a complicated task, considered here. The complication arises from the different nature and sources of bio-resources used in bioenergy production i.e., wet, dry or agriculture, industrial etc. Moreover, the different concerns that decision makers should take into account, to overcome the tradeoff anxieties of the socialists and investors, i.e., social, environmental and economical factors, was considered through the options of multi-criteria optimization. A first part of this research was introduced in earlier research work explaining the general Bioenergy Decision System gBEDS [Ayoub N, Martins R, Wang K, Seki H, Naka Y. Two levels decision system for efficient planning and implementation of bioenergy production. Energy Convers Manage 2007;48:709-23]. In this paper, brief introduction and emphasize on gBEDS are given; the optimization model is presented and followed by a case study on designing a supply chain of nine bio-resources at Iida city in the middle part of Japan.

  18. Reclamation of coal mine spoil dump through integrated biotechnological approach

    International Nuclear Information System (INIS)

    Juwarkar, A.S.; Thawale, P.R.; Mowade, S.; Shrivastava, S.; Deshbhratar, P.B.; Juwarkar, A.

    1994-01-01

    Laboratory and field studies were carried out to restore the fertility and productivity of coal mine spoil using primary clarifier sludge from paper mill effluent treatment plant and use of specialised culture of biofertilizers and mycorrhizal fungi. Plants namely Tectona grandis, Delbergia sissoo, Gmelina arporea, Emblica officinalis and Cassia seamea were grown. Sludge amendment enhanced the survival rate of plants to 80% compared to 20% in unamended spoil. Plants grown on unamended spoil showed stunted growth. Growth of plants increased by 188-484% when sludge was applied at the rate of 100 tonnes per hectare. At 100 tones per hectare sludge amendment, biofertilizer and mycorrhizae treatment there were 83.7 nodules in shishum as against only 4.6 nodules in case of spoil alone. Further root length was 276% and 281% more respectively in case of shishum and teak. Inoculation of plant saplings with respective biofertilizers and mycorrhizae further increased the plant growth by 144-198%. At Durgapur coal mine, 56,000 saplings of Tectona grandis, Gmelina arporea, Delbergia sissoo, Emblica officinalis, Azadirachta indica, Acacia ariculiformis, Prosopis etc were successfully planted on spoil dump using integrated biotechnological approach. 10 refs., 5 tabs

  19. Photonic integrated circuits : a new approach to laser technology

    NARCIS (Netherlands)

    Piramidowicz, R.; Stopinski, S.T.; Lawniczuk, K.; Welikow, K.; Szczepanski, P.; Leijtens, X.J.M.; Smit, M.K.

    2012-01-01

    In this work a brief review on photonic integrated circuits (PICs) is presented with a specific focus on integrated lasers and amplifiers. The work presents the history of development of the integration technology in photonics and its comparison to microelectronics. The major part of the review is

  20. Building Thematic and Integrated Services for European Solid Earth Sciences: the EPOS Integrated Approach

    Science.gov (United States)

    Harrison, M.; Cocco, M.

    2017-12-01

    EPOS (European Plate Observing System) has been designed with the vision of creating a pan-European infrastructure for solid Earth science to support a safe and sustainable society. In accordance with this scientific vision, the EPOS mission is to integrate the diverse and advanced European Research Infrastructures for solid Earth science relying on new e-science opportunities to monitor and unravel the dynamic and complex Earth System. EPOS will enable innovative multidisciplinary research for a better understanding of the Earth's physical and chemical processes that control earthquakes, volcanic eruptions, ground instability and tsunami as well as the processes driving tectonics and Earth's surface dynamics. To accomplish its mission, EPOS is engaging different stakeholders, to allow the Earth sciences to open new horizons in our understanding of the planet. EPOS also aims at contributing to prepare society for geo-hazards and to responsibly manage the exploitation of geo-resources. Through integration of data, models and facilities, EPOS will allow the Earth science community to make a step change in developing new concepts and tools for key answers to scientific and socio-economic questions concerning geo-hazards and geo-resources as well as Earth sciences applications to the environment and human welfare. The research infrastructures (RIs) that EPOS is coordinating include: i) distributed geophysical observing systems (seismological and geodetic networks); ii) local observatories (including geomagnetic, near-fault and volcano observatories); iii) analytical and experimental laboratories; iv) integrated satellite data and geological information services; v) new services for natural and anthropogenic hazards; vi) access to geo-energy test beds. Here we present the activities planned for the implementation phase focusing on the TCS, the ICS and on their interoperability. We will discuss the data, data-products, software and services (DDSS) presently under

  1. A generic, time-resolved, integrated digital image correlation, identification approach

    NARCIS (Netherlands)

    Hoefnagels, J.P.M.; Neggers, J.; Blaysat, Benoît; Hild, François; Geers, M.G.D.; Jin, H.; Sciammarella, C.; Yoshida, S.; Lamberti, L.

    2015-01-01

    A generic one-step Integrated Digital Image Correlation (I-DIC) inverse parameter identification approach is introduced that enables direct identification of constitutive model parameters by intimately integrating a Finite Elements Method (FEM) with Digital Image Correlation (DIC), directly

  2. Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology

    Directory of Open Access Journals (Sweden)

    Caryn N. Oates

    2016-11-01

    Full Text Available Gall-inducing insects are capable of exerting a high level of control over their hosts’ cellular machinery to the extent that the plant’s development, metabolism, chemistry, and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review, we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However, understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance.

  3. Omics approaches to study host-microbiota interactions

    NARCIS (Netherlands)

    Baarlen, van P.; Kleerebezem, M.; Wells, J.

    2013-01-01

    The intestinal microbiota has profound effects on our physiology and immune system and disturbances in the equilibrium between microbiota and host have been observed in many disorders. Here we discuss the possibilities to further our understanding of how microbiota impacts on human health and

  4. 'Omics' approaches in tomato aimed at identifying candidate genes ...

    African Journals Online (AJOL)

    adriana

    2013-12-04

    Dec 4, 2013 ... importance for human health and nutrition. This species has ... function to genes, proteins and metabolites is still a daunting task. Major challenges ... relation of the expression pattern of genes with the accu- mulation pattern of ..... M, Gordon JS, Rose, JKC, Martin G, Tanksley SD, Bouzayen M,. Jahn MM ...

  5. 'Omics' approaches in tomato aimed at identifying candidate genes ...

    African Journals Online (AJOL)

    Tomato (Solanum lycopersicum) is one of the most important vegetables in the world with significant importance for human health and nutrition. This species has long served as model system for plant genetics, development, physiology, pathology, and fleshy fruit ripening, resulting in the accumulation of many genetic and ...

  6. OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

    Science.gov (United States)

    Zhou, Guangyan; Xia, Jianguo

    2018-06-07

    Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

  7. Integrating physical and financial approaches to manage environmental financial risk

    Science.gov (United States)

    Characklis, Gregory; Meyer, Eliot; Foster, Benjamin

    2017-04-01

    Physical and/or engineered solutions have long been used to manage risks associated with adverse environmental events. Examples include reservoirs as a tool for mitigating drought-related supply risk, levees for managing flood risk and dredging of inland waterways to ensure navigability during low flow periods. These measures can reduce many types of risk (e.g., loss of life), but are often employed as a means of protecting against financial losses. When the focus is on managing environmental financial risk, physical solutions can be effective, but also costly. In many cases, non-physical tools can provide a less expensive means of managing financial risk, with these often taking the form of financial instruments such as hedging contracts, contingency funds or insurance. Some of these instruments, such as flood insurance, are widely available, but historically many environmental financial risks have been managed primarily (or solely) via physical solutions without much consideration of alternatives, thereby opening opportunities for innovation in developing financial solutions. Recent research has demonstrated that financial instruments can play a significant role in managing drought-related financial risk in sectors as diverse as water utilities, energy generation and inland navigation. Nonetheless, this work has largely considered the use of these instruments within systems in which physical solutions are already in place (but failing to achieve desired performance). The next step in the evolution of managing environmental financial risk involves developing methods for designing risk management strategies that do not assume an established physical system. Here the goal is to identify the relative role that physical solutions and financial instruments should play as they are integrated into a comprehensive risk management strategy. This is not a straightforward challenge as one approach reduces the risk of financial losses and the other redistributes those losses

  8. Towards an integrated approach to health and medicine in Africa

    Directory of Open Access Journals (Sweden)

    Kezia Batisai

    2016-01-01

    Full Text Available This article frames the intersections of medicine and humanities as intrinsic to understanding the practice of health care in Africa. Central to this manuscript, which draws on empirical findings on the interplay between HIV and AIDS and alternative medicine in Zimbabwe is the realisation that very limited research has been undertaken to examine ‘HIV/AIDS patient behaviour’ with respect to choice of therapy on the continent [Bene, M. & Darkoh, M. B. K. (2014. The Constraints of Antiretroviral Uptake in Rural Areas: The Case of Thamaga and Surrounding Villages, Botswana. SAHARA-J: Journal of Social Aspects of HIV/AIDS, 11(1, 167–177. doi:10.1080/17290376.2014.972057; Chavunduka, G. (1998. Professionalisation of Traditional Medicine in Zimbabwe, Harare, Jongwe Printers; O’Brien, S. & Broom, A. (2014. HIV in (and out of the Clinic: Biomedicine, Traditional Medicine and Spiritual Healing in Harare. SAHARA-J: Journal of Social Aspects of HIV/AIDS, 11(1, 94–104. doi:10.1080/17290376.2014.938102]. As such, a social approach to health-seeking behaviour questions how decisions about alternative therapies including herbal remedies, traditional healing and faith healing are made. The paper unpacks the realities around how people living with HIV and AIDS – who span different age groups and profess various religious backgrounds, faced with an insurmountable health challenge against a background of limited resources and no cure for the virus – often experience shifts in health-seeking behaviour. Grappling with seemingly simple questions about ‘when, where and how to seek medical attention’, the paper provides pointers to therapy choices and health-seeking behaviour; and it serves as a route into deeper and intense healthcare practice explorations. In conclusion, the paper proposes that medicine and the humanities should engage seriously with those social aspects of HIV and AIDS which call for an integrated approach to healthcare practice in

  9. Inviscid/Boundary-Layer Aeroheating Approach for Integrated Vehicle Design

    Science.gov (United States)

    Lee, Esther; Wurster, Kathryn E.

    2017-01-01

    A typical entry vehicle design depends on the synthesis of many essential subsystems, including thermal protection system (TPS), structures, payload, avionics, and propulsion, among others. The ability to incorporate aerothermodynamic considerations and TPS design into the early design phase is crucial, as both are closely coupled to the vehicle's aerodynamics, shape and mass. In the preliminary design stage, reasonably accurate results with rapid turn-representative entry envelope was explored. Initial results suggest that for Mach numbers ranging from 9-20, a few inviscid solutions could reasonably sup- port surface heating predictions at Mach numbers variation of +/-2, altitudes variation of +/-10 to 20 kft, and angle-of-attack variation of +/- 5. Agreement with Navier-Stokes solutions was generally found to be within 10-15% for Mach number and altitude, and 20% for angle of attack. A smaller angle-of-attack increment than the 5 deg around times for parametric studies and quickly evolving configurations are necessary to steer design decisions. This investigation considers the use of an unstructured 3D inviscid code in conjunction with an integral boundary-layer method; the former providing the flow field solution and the latter the surface heating. Sensitivity studies for Mach number, angle of attack, and altitude, examine the feasibility of using this approach to populate a representative entry flight envelope based on a limited set of inviscid solutions. Each inviscid solution is used to generate surface heating over the nearby trajectory space. A subset of a considered in this study is recommended. Results of the angle-of-attack sensitivity studies show that smaller increments may be needed for better heating predictions. The approach is well suited for application to conceptual multidisciplinary design and analysis studies where transient aeroheating environments are critical for vehicle TPS and thermal design. Concurrent prediction of aeroheating

  10. Mediterranean Storms: An Integrated Approach of Risk Management

    Science.gov (United States)

    Karageorgou, H.; Riza, E.; Linos, A.; Papanikolaou, D.

    2010-09-01

    Disaster by UN definition is "a serious disruption of the functioning of a community or a society, involving widespread human, material, economic, or environmental losses and impacts, which exceeds the ability of the affected community or society to cope using only its own resources". Mediterranean storms induce flash floods caused by excessive amounts of rainfall within a short lasting period of time. The intensity and duration of precipitation, region geomorphology, urbanization and different governmental emergency management structures trigger different consequences between Mediterranean countries. The integrated approach in management of storm risk represents a holistic perspective including interactions between government, science and technology institutions, developing agencies, private sector, NGOs and public. Local authorities and national government are responsible for the design, preparation and decision on storm risk management policies and strategies considering scientific risk identifying, assessing and understanding. Efficient governance management requires satisfied response to early warning systems, functionality of the affected systems upon which society depends and appropriate focus on variable interest, beliefs, values and ideologies between social groups. Also an appropriate balancing of benefits and costs in an efficient and equitable manner is important for the governance risk management. Natural sciences in corporation with the engineering science have developed effective early prediction, warning and monitoring systems on storm and flood risk. The health sciences use prediction systems for health related hazards and consequences and the social sciences research estimates the human resilience during disasters and the factors which affect and determine the human behavior. Also social sciences survey the response of public to early warning messages, the appropriate communicative methods to distributing messages and mechanisms to improve public

  11. Rationale for an integrated approach to genetic epidemiology.

    Science.gov (United States)

    Laberge, Claude M; Knoppers, Bartha Maria

    1992-10-01

    Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....

  12. PHWR Fuel - an integrated approach in Indian context

    Energy Technology Data Exchange (ETDEWEB)

    Jayaraj, R.N. [Nuclear Fuel Complex, Dept. of Atomic Energy, Hyderabad (India)

    2008-07-01

    The nuclear power programme in India is based on a three-stage approach in which the Pressurized Heavy Water Reactors (PHWR) forms the backbone of the first stage. Over the years, apart from gaining expertise in design, construction and operation of PHWRs, innovative fuel designs and manufacturing technologies have also been evolved. Presently, thirteen PHWR 220 units and two PHWR 540 units are in operation. Three more PHWR 220 units are in the advanced stage of construction. In addition, the PHWR power generation programme envisages construction of eight more PHWR 700 units. Nuclear Fuel Complex (NFC) at Hyderabad, established in early 70s, is the only manufacturer of fuel and reactor core structurals for all the PHWRs in India. Since inception, the thrust has been on indigenous development of technology in the areas of production processes, equipment manufacture and quality assurance programmes. Commensurate with the PHWR programme, NFC has expanded its production capacities and has fabricated more than 380,000 fuel bundles since inception. Towards optimization of uranium resources and implementation of 'closed fuel cycle' concept, large quantities of reprocessed uranium fuel bundles have been manufactured and introduced in the initial cores of PHWRs. In recent times, NFC introduced several modifications in the production processes like vapour ammonia precipitation for UO{sub 2} powder production, advanced resistance welding controls and improved versions of welding machines, which all have facilitated in improving the quality and productivity of the fuel. Superior quality control systems like spectrophotometric determination of SSA of UO{sub 2} powders, machine vision systems for pellet inspection, thermography for evaluating weld integrity, etc. has channelised NDT techniques into fuel production lines. The paper summarizes various improvements carried out in the design and manufacture of PHWR fuel. New concepts evolved in high burn-up fuels and

  13. PHWR Fuel - an integrated approach in Indian context

    International Nuclear Information System (INIS)

    Jayaraj, R.N.

    2008-01-01

    The nuclear power programme in India is based on a three-stage approach in which the Pressurized Heavy Water Reactors (PHWR) forms the backbone of the first stage. Over the years, apart from gaining expertise in design, construction and operation of PHWRs, innovative fuel designs and manufacturing technologies have also been evolved. Presently, thirteen PHWR 220 units and two PHWR 540 units are in operation. Three more PHWR 220 units are in the advanced stage of construction. In addition, the PHWR power generation programme envisages construction of eight more PHWR 700 units. Nuclear Fuel Complex (NFC) at Hyderabad, established in early 70s, is the only manufacturer of fuel and reactor core structurals for all the PHWRs in India. Since inception, the thrust has been on indigenous development of technology in the areas of production processes, equipment manufacture and quality assurance programmes. Commensurate with the PHWR programme, NFC has expanded its production capacities and has fabricated more than 380,000 fuel bundles since inception. Towards optimization of uranium resources and implementation of 'closed fuel cycle' concept, large quantities of reprocessed uranium fuel bundles have been manufactured and introduced in the initial cores of PHWRs. In recent times, NFC introduced several modifications in the production processes like vapour ammonia precipitation for UO 2 powder production, advanced resistance welding controls and improved versions of welding machines, which all have facilitated in improving the quality and productivity of the fuel. Superior quality control systems like spectrophotometric determination of SSA of UO 2 powders, machine vision systems for pellet inspection, thermography for evaluating weld integrity, etc. has channelised NDT techniques into fuel production lines. The paper summarizes various improvements carried out in the design and manufacture of PHWR fuel. New concepts evolved in high burn-up fuels and development of state

  14. Financial Integration and Financial Crisis: Croatia Approaching the EMU

    Directory of Open Access Journals (Sweden)

    Dražen Derado

    2009-09-01

    Full Text Available The breakdown of command economies has significantly increased growth potentials all over Europe and opened up prospects for economic development. Encouraged by that, the EU embarked on the process of deeper economic integration. Its main aspects – economic liberalization and monetary integration – coincided with the worldwide globalization of trade and capital flows. As a laggard country in the process of economic integration, Croatia is in a particularly difficult position – besides soaring trade deficit, it is highly indebted and strongly dependant upon foreign capital. Appreciating theoretical inferences and empirical evidence on monetary integration, while taking reference to the realized level of international financial integration and external vulnerability, the aim of the paper is to find out if Croatia fulfils the criteria for successful monetary integration.

  15. Integrated approach to hazardous and radioactive waste remediation

    International Nuclear Information System (INIS)

    Hyde, R.A.; Reece, W.J.

    1994-01-01

    The US Department of Energy Office of Technology Development is supporting the demonstration, and evaluation of a suite of waste retrieval technologies. An integration of leading-edge technologies with commercially available baseline technologies will form a comprehensive system for effective and efficient remediation of buried waste throughout the complex of DOE nuclear facilities. This paper discusses the complexity of systems integration, addressing organizational and engineering aspects of integration as well as the impact of human operators, and the importance of using integrated systems in remediating buried hazardous and radioactive waste

  16. New Approaches to Aluminum Integral Foam Production with Casting Methods

    Directory of Open Access Journals (Sweden)

    Ahmet Güner

    2015-08-01

    Full Text Available Integral foam has been used in the production of polymer materials for a long time. Metal integral foam casting systems are obtained by transferring and adapting polymer injection technology. Metal integral foam produced by casting has a solid skin at the surface and a foam core. Producing near-net shape reduces production expenses. Insurance companies nowadays want the automotive industry to use metallic foam parts because of their higher impact energy absorption properties. In this paper, manufacturing processes of aluminum integral foam with casting methods will be discussed.

  17. -Omic and Electronic Health Record Big Data Analytics for Precision Medicine.

    Science.gov (United States)

    Wu, Po-Yen; Cheng, Chih-Wen; Kaddi, Chanchala D; Venugopalan, Janani; Hoffman, Ryan; Wang, May D

    2017-02-01

    Rapid advances of high-throughput technologies and wide adoption of electronic health records (EHRs) have led to fast accumulation of -omic and EHR data. These voluminous complex data contain abundant information for precision medicine, and big data analytics can extract such knowledge to improve the quality of healthcare. In this paper, we present -omic and EHR data characteristics, associated challenges, and data analytics including data preprocessing, mining, and modeling. To demonstrate how big data analytics enables precision medicine, we provide two case studies, including identifying disease biomarkers from multi-omic data and incorporating -omic information into EHR. Big data analytics is able to address -omic and EHR data challenges for paradigm shift toward precision medicine. Big data analytics makes sense of -omic and EHR data to improve healthcare outcome. It has long lasting societal impact.

  18. -Omic and Electronic Health Records Big Data Analytics for Precision Medicine

    Science.gov (United States)

    Wu, Po-Yen; Cheng, Chih-Wen; Kaddi, Chanchala D.; Venugopalan, Janani; Hoffman, Ryan; Wang, May D.

    2017-01-01

    Objective Rapid advances of high-throughput technologies and wide adoption of electronic health records (EHRs) have led to fast accumulation of -omic and EHR data. These voluminous complex data contain abundant information for precision medicine, and big data analytics can extract such knowledge to improve the quality of health care. Methods In this article, we present -omic and EHR data characteristics, associated challenges, and data analytics including data pre-processing, mining, and modeling. Results To demonstrate how big data analytics enables precision medicine, we provide two case studies, including identifying disease biomarkers from multi-omic data and incorporating -omic information into EHR. Conclusion Big data analytics is able to address –omic and EHR data challenges for paradigm shift towards precision medicine. Significance Big data analytics makes sense of –omic and EHR data to improve healthcare outcome. It has long lasting societal impact. PMID:27740470

  19. Integrated assessment of the global warming problem. A decision-analytical approach

    International Nuclear Information System (INIS)

    Van Lenthe, J.; Hendrickx, L.; Vlek, C.A.J.

    1995-01-01

    The project on the title subject aims at developing a policy-oriented methodology for the integrated assessment of the global warming problem. Decision analysis in general and influence diagrams in particular appear to constitute an appropriate integrated assessment methodology. The influence-diagram approach is illustrated at a preliminary integrated modeling of the global warming problem. In next stages of the research, attention will be shifted from the methodology of integrated assessment to the contents of integrated models. 4 figs., 5 refs

  20. Effects of radiation on model plant rice - OMICS: Recent progress and future prospects

    International Nuclear Information System (INIS)

    Rakwal, Randeep; Shibato, Junko; Agrawal, Ganesh Kumar; Imanaka, Tetsuji; Fukutani, Satoshi; Tamogami, Shigeru; Endo, Satoru; Sahoo, Sarat Kumar; Kimura, Shinzo

    2011-01-01

    This is the age of functional genomics, where genomes to high-throughput technologies and to the phenotype are making inroads into various biological questions and problems. In this report, I along with my co-workers will present an outline into the omics approaches, focusing on the global gene expression profiling (DNA microarray technique), plants and the environment, and culminating in the use of genomics to analyze the effects of radiation on plant life. For this, rice (Oryza sativa L.) geonome model and monocot cereal crop plant will be used as an example. It is our hope that use of both model and non-model plants in conjunction with high-throughput transcriptomics approaches will lead the way for unraveling radiation responses in plants, setting the stage for further research on this important aspect of our environment with direct and indirect impact on human life and civilization. (author)

  1. Using the integrated rural mobility and access (IRMA) approach in prospering rural South Africa

    CSIR Research Space (South Africa)

    Chakwizira, J

    2008-11-01

    Full Text Available settlements implications of current rural development approaches are outlined. The potential and impact of the integrated rural mobility and access approach (IRMA) in unlocking socio-economic and spatial livelihood opportunities are discussed. In this regard...

  2. Introduction: Integration as a three-way process approach?

    NARCIS (Netherlands)

    Garcés-Mascareñas, B.; Penninx, R.; Garcés-Mascareñas, B.; Penninx, R.

    2016-01-01

    This chapter introduces the topic of this volume, which is the recent departure from viewing integration as a strictly two-way process (between migrants and the receiving society) to acknowledge the potential role that countries of origin might play in support of the integration process. It traces

  3. A stochastic-programming approach to integrated asset and liability ...

    African Journals Online (AJOL)

    This increase in complexity has provided an impetus for the investigation into integrated asset- and liability-management frameworks that could realistically address dynamic portfolio allocation in a risk-controlled way. In this paper the authors propose a multi-stage dynamic stochastic-programming model for the integrated ...

  4. 'Omics investigations of HIV and SIV pathogenesis and innate immunity.

    Science.gov (United States)

    Palermo, Robert E; Fuller, Deborah H

    2013-01-01

    In the 30 years since the advent of the AIDS epidemic, the biomedical community has put forward a battery of molecular therapies that are based on the accumulated knowledge of a limited number of viral targets. Despite these accomplishments, the community still confronts unanswered foundational questions about HIV infection. What are the cellular or biomolecular processes behind HIV pathogenesis? Can we elucidate the characteristics that distinguish those individuals who are naturally resistant to either infection or disease progression? The discovery of simian immunodeficiency viruses (SIVs) and the ensuing development of in vivo, nonhuman primate (NHP) infection models was a tremendous advance, especially in abetting the exploration of vaccine strategies. And while there have been numerous NHP infection models and vaccine trials performed, fundamental questions remain regarding host-virus interactions and immune correlates of protection. These issues are, perhaps, most starkly illustrated with the appreciation that many species of African nonhuman primates are naturally infected with strains of SIV that do not cause any appreciable disease while replicating to viral loads that match or exceed those seen with pathogenic SIV infections in Asian species of nonhuman primates. The last decade has seen the establishment of high-throughput molecular profiling tools, such as microarrays for transcriptomics, SNP arrays for genome features, and LC-MS techniques for proteins or metabolites. These provide the capacity to interrogate a biological model at a comprehensive, systems level, in contrast to historical approaches that characterized a few genes or proteins in an experiment. These methods have already had revolutionary impacts in understanding human diseases originating within the host genome such as genetic disorders and cancer, and the methods are finding increasing application in the context of infectious disease. We will provide a review of the use of such 'omics

  5. Genelab: Scientific Partnerships and an Open-Access Database to Maximize Usage of Omics Data from Space Biology Experiments

    Science.gov (United States)

    Reinsch, S. S.; Galazka, J..; Berrios, D. C; Chakravarty, K.; Fogle, H.; Lai, S.; Bokyo, V.; Timucin, L. R.; Tran, P.; Skidmore, M.

    2016-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. The GeneLab Data System (GLDS) is NASA's premier open-access omics data platform for biological experiments. GLDS houses standards-compliant, high-throughput sequencing and other omics data from spaceflight-relevant experiments. The GeneLab project at NASA-Ames Research Center is developing the database, and also partnering with spaceflight projects through sharing or augmentation of experiment samples to expand omics analyses on precious spaceflight samples. The partnerships ensure that the maximum amount of data is garnered from spaceflight experiments and made publically available as rapidly as possible via the GLDS. GLDS Version 1.0, went online in April 2015. Software updates and new data releases occur at least quarterly. As of October 2016, the GLDS contains 80 datasets and has search and download capabilities. Version 2.0 is slated for release in September of 2017 and will have expanded, integrated search capabilities leveraging other public omics databases (NCBI GEO, PRIDE, MG-RAST). Future versions in this multi-phase project will provide a collaborative platform for omics data analysis. Data from experiments that explore the biological effects of the spaceflight environment on a wide variety of model organisms are housed in the GLDS including data from rodents, invertebrates, plants and microbes. Human datasets are currently limited to those with anonymized data (e.g., from cultured cell lines). GeneLab ensures prompt release and open access to high-throughput genomics, transcriptomics, proteomics, and metabolomics data from spaceflight and ground-based simulations of microgravity, radiation or other space environment factors. The data are meticulously curated to assure that accurate experimental and sample processing metadata are included with each data set. GLDS download volumes indicate strong

  6. A system and approach for total pipeline integrity management

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Todd; Neidhardt, Dietmar [Tuboscope Pipeline Services, Houston, TX (United States); Gonzalez, Oscar [Tuboscope Mexico S.A. de C.V., Mexico, D.F. (Mexico)

    2005-07-01

    Pipeline rehabilitation and maintenance decisions are made using a wide variety of data, criteria, and expertise. The goal is to arrive at an optimal plan that considers risk and best return on Repair and Maintenance (R and M) expenditures for aging pipeline systems in both regulated and non-regulated environments. In order to achieve these goals, historical, operations, and assessment data is gathered, aligned and integrated as part of a baseline assessment. Integrity threats are identified based on operations and industry experience, and combined with potential consequences to public safety, the environment, and business to clearly delineate high risk exposure segments in the system. Integrity assessments are conducted in a prioritized manner, using the most appropriate technology and methods to address the threats. These include In Line Inspection technologies: MFL, Deformation, UT, INS (combinations thereof), Direct Assessment for EC and SCC threats, Hydro testing, and other indirect methods. From these results, decisions are made and R and M plans developed. To arrive at an optimal R and M plan, proper use of existing data, new integrity assessment data, and decision risk models is required. This paper presentation will detail the tactical aspect of an effective integrity management platform. Experience in decision support, operations priorities and execution of a rehabilitation plan using LinaView Pro{sup TM} integrity management system with risk-based integrity tools and maintenance planning will be presented. A process overview, results, and benefits will be given using these examples from operating oil and gas transmission pipelines. (author)

  7. A Neo-Rawlsian Approach to Residential Integration

    Directory of Open Access Journals (Sweden)

    Kevin J. Brown

    2013-08-01

    Full Text Available Over the past 40 years, the United States has engaged in various policies to integrate otherwise segregated black and white households within a shared space. However, little work has been done to fully articulate a moral argument for residential integration among black and white households. This paper offers what I refer to as the normative argument, which possesses two morally-impelled arguments for residential integration. Since the ethical appeal to integrate is often couched in the language of justice, I begin with a framework—based upon the work of the late philosopher John Rawls—for considering the moral aspects of residential integration. However, I go on to point out intractable problems related to the Rawlsian framework that would fail to flesh out all ethical considerations of the normative argument. From here, I provide a revised, or neo-Rawlsian, framework for understanding residential integration which addresses the aforementioned problems. This exercise is both important and necessary for the future of residential mixing, as better understanding the moral and ethical attributes of this discussion is, perhaps, the best means to lubricate the fundamental shift from 'spatial' to 'social' integration.

  8. The mercury burden of the Czech population: An integrated approach.

    Science.gov (United States)

    Puklová, Vladimíra; Krsková, Andrea; Cerná, Milena; Cejchanová, Mája; Rehůrková, Irena; Ruprich, Jirí; Kratzer, Karel; Kubínová, Růzena; Zimová, Magdaléna

    2010-07-01

    In this paper an integrated approach in assessment of the population exposure from various sources of total mercury (THg) oral intake in the Czech Republic is presented. The information on total mercury levels in diet, drinking water, surface urban soil and body fluids and tissues stem from the Czech national Environmental Health Monitoring System (EHMS) operated since 1994. The THg concentration was determined by the special atomic absorption spectrophotometer AMA 254. The data on THg content in food from the sales network were collected in 12 cities. The estimated average dietary intake representing more than 95% of weight of usual diet composition ranged 1-2% of the JECFA/FAO WHO provisional tolerable weekly intake (PTWI) value for total mercury (5 microg/kg b.w./week). Data on drinking water quality stem from the nationwide monitoring database. The content of THg in drinking water is generally low; only 0.2% of the Czech population supplied with drinking water from the distribution networks (total of 92% of the population) has a mercury intake from drinking water higher than 1% PTWI and not exceeding 5% PTWI. The estimation of potential mercury intake by unintentional consumption of soil in small children was based on THg content in surface soil of a total of 324 nursery schools in 24 cities and towns. Median value was 0.16 mg/kg. Human biomonitoring was performed in 9 Czech cities. In 2007, the mercury median values in blood of adults (N=412) were 0.85 and 0.89 microg/l in males and in females, respectively; urine median value in adults was 1.10 microg/g creatinine. In 2008, the blood median value in children (N=324) amounted to 0.35 microg/l; urine median value is 0.16 microg/g creatinine. In children's hair the median THg value was 0.18 microg/g. The correlation between fish consumption and blood THg levels was observed in both adults and children. Also the biomonitoring outputs did not reveal a substantial burden of the population. Copyright 2010 Elsevier

  9. PNAUM: integrated approach to Pharmaceutical Services, Science, Technology and Innovation.

    Science.gov (United States)

    Gadelha, Carlos Augusto Grabois; Costa, Karen Sarmento; Nascimento, José Miguel do; Soeiro, Orlando Mário; Mengue, Sotero Serrate; Motta, Márcia Luz da; Carvalho, Antônio Carlos Campos de

    2016-12-01

    This paper describes the development process of the Pesquisa Nacional sobre Acesso, Utilização e Promoção do Uso Racional de Medicamentos (PNAUM - National Survey on Access, Use and Promotion of Rational Use of Medicines) based on an integrated approach to pharmaceutical services, science, technology and innovation. It starts by contextualizing health and development in Brazil and features elements of the National Policy for Science, Technology and Innovation in Health in Brazil and the National Policy for Pharmaceutical Services. On presenting pharmaceutical policy guidelines, it stresses the lack of nationwide data. This survey, commissioned by the Brazilian Ministry of Health, has two components: household survey and evaluation of pharmaceutical services in primary care. The findings point to perspectives that represent, besides the enhancement of public policy for pharmaceutical services and public health, results of government action aimed at developing the economic and industrial health care complex to improve the health conditions of the Brazilian population. RESUMO O artigo apresenta o processo de construção da Pesquisa Nacional sobre Acesso, Utilização e Promoção do Uso Racional de Medicamento a partir de uma concepção integradora da Assistência Farmacêutica, Ciência, Tecnologia e Inovação. Inicia-se contextualizando a saúde e o desenvolvimento no País e apresenta elementos da Política Nacional de Ciência Tecnologia e Inovação em Saúde no Brasil e da Política Nacional de Assistência Farmacêutica. Ao apresentar as diretrizes das Políticas Farmacêuticas, destaca-se a carência de dados de abrangência nacional. A presente pesquisa, encomendada pelo Ministério da Saúde, foi estruturada em dois componentes: inquérito domiciliar e avaliação dos serviços de assistência farmacêutica na atenção básica. As perspectivas dos resultados representam, além do incremento das políticas públicas farmacêuticas e de saúde p

  10. Integrated Natural Resource Management: Approaches and Lessons from the Himalaya

    Directory of Open Access Journals (Sweden)

    K. G. Saxena

    2002-01-01

    Full Text Available Losses of forest cover, biodiversity, agricultural productivity, and ecosystem services in the Himalayan mountain region are interlinked problems and threats to the sustainable livelihoods of 115 x 106 mountain people as well as the inhabitants of the adjoining Indo-gangetic plains. Until the 1970s, environmental conservation, food security, and rural economic development were treated as independent sectors. The poor outcomes of sector-oriented approaches catalyzed efforts to address environmental and socioeconomic problems concurrently. The identification of "key" natural resource management interventions is an important dimension of integrated management. Projects to rehabilitate the degraded lands that cover 40% of the Indian Himalaya could be key interventions provided that they address both socioeconomic and environmental concerns across spatial and temporal scales. However, projects of this type, e.g., investments in conifer plantations on degraded forest lands, have failed because their designs did not take into account the needs of local residents. This study illustrates a case of land rehabilitation in a small isolated village close to the alpine zone. Vital elements of this project strategy included identifying local perceptions and knowledge and involving the local people in the selection and implementation of the interventions needed to restore the land. Communities were found to be more concerned with the immediate economic benefits from bamboo and medicinal species than the long-term benefits of tree planting. The villagers eventually reached a consensus to plant broadleaved multipurpose trees in association with bamboo and medicinal species. Despite assurances that all the economic benefits from rehabilitation would go to the community, the people would not agree to voluntary labor, although they did absorb significant costs by providing social fencing, farmyard manure, and propagules from community forests. Households shared

  11. Consequence Based Design. An approach for integrating computational collaborative models (Integrated Dynamic Models) in the building design phase

    DEFF Research Database (Denmark)

    Negendahl, Kristoffer

    relies on various advancements in the area of integrated dynamic models. It also relies on the application and test of the approach in practice to evaluate the Consequence based design and the use of integrated dynamic models. As a result, the Consequence based design approach has been applied in five...... and define new ways to implement integrated dynamic models for the following project. In parallel, seven different developments of new methods, tools and algorithms have been performed to support the application of the approach. The developments concern: Decision diagrams – to clarify goals and the ability...... affect the design process and collaboration between building designers and simulationists. Within the limits of applying the approach of Consequence based design to five case studies, followed by documentation based on interviews, surveys and project related documentations derived from internal reports...

  12. Intergovernmental approach of the new liberalism in the development of integration processes

    OpenAIRE

    O. P. Stadnyk; R. Y. Romaniuk

    2013-01-01

    Investigated intergovernmental theory approach to understanding the new liberalism integration processes. Determined the nature of the liberal intergovernmental approach that Andrew Moravchik developed within the new liberalism. Emphasized that the intergovernmental approach of the new liberalism theory considers national preferences in international relations as being primarily determined by domestic political processes. Liberal intergovernmental approach rejects the rhetoric of so­called na...

  13. Web-based approach to the INTEGRAL data

    Czech Academy of Sciences Publication Activity Database

    Münz, F.; Kocka, Matúš

    2009-01-01

    Roč. 18, 3-4 (2009), s. 379-382 ISSN 1392-0049. [INTEGRAL/BART workshop 2009. Karlovy Vary, 26.03.2009-29.03.2009] R&D Projects: GA AV ČR IAA3003206 Grant - others:ESA(XE) ESA-PECS project No. 98023 Institutional research plan: CEZ:AV0Z10030501 Keywords : gamma rays * gursts * INTEGRAL Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 1.032, year: 2009

  14. A path-integral approach to inclusive processes

    International Nuclear Information System (INIS)

    Sukumar, C.V.

    1995-01-01

    The cross section for an inclusive scattering process may be expressed in terms of a double path integral. Evaluation of the double path integral by the stationary-phase approximation yields classical equations of motion for the stationary trajectories and a classical cross section for the inclusive process which depends on the polarization of the initial state. Polarization analyzing powers are calculated from this theory and the results are compared with those obtained in an earlier paper. ((orig.))

  15. A unified approach to stochastic integration on the real line

    DEFF Research Database (Denmark)

    Basse-O'Connor, Andreas; Graversen, Svend-Erik; Pedersen, Jan

    Stochastic integration on the predictable σ-field with respect to σ-finite L0-valued measures, also known as formal semimartingales, is studied. In particular, the triplet of such measures is introduced and used to characterize the set of integrable processes. Special attention is given to Lévy...... processes indexed by the real line. Surprisingly, many of the basic properties break down in this situation compared to the usual R+ case....

  16. A participatory and integrative approach to improve productivity and ergonomics in assembly

    NARCIS (Netherlands)

    Looze, M.P. de; Rhijn, J.W. van; Deursen, J. van; Tuinzaad, G.H.; Reijneveld, C.N.

    2003-01-01

    A participatory and integrative approach was applied to improve the productivity and ergonomics of the assembly lines in two factories, producing magnetic stop valves and office furniture, respectively. Main elements of the approach are the active participation of the company and the integration of

  17. Connecting the Dots Downunder Towards An Integrated Institutional Approach To Digital Content Management

    CERN Document Server

    Harboe-Ree, Cathrine

    2004-01-01

    There is a growing interest among academic institutions in managing institutional digital content produced in and for research, teaching and learning. This article argues for an integrated approach to this activity and examines the role of libraries in facilitating this. It then considers some existing approaches to providing software to support this. Australian initiatives consistent with this integrated model are then discussed.

  18. Exploring EFL Learners' Perceptions of Integrated Skills Approach: A Grounded Theory

    Science.gov (United States)

    Tajzad, Maryam; Ostovar-Namaghi, Seyyed Ali

    2014-01-01

    This qualitative study aims at exploring EFL learners' perceptions of the integrated skills approach to language teaching. To this end, the researchers presented the integrated skills approach to a group of 30 participants and interviewed those who were willing to share their views and experience with the researchers. The researchers used grounded…

  19. The paradigm of consumer-driven and responsive supply chains: An integrated project approach

    NARCIS (Netherlands)

    Zimmermann, K.L.; Lans, van der I.A.

    2009-01-01

    This paper describes an integrated project approach that forms the basis of the studies on consumer-driven in