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Sample records for integrated biochemical analysis

  1. Integration of electrochemistry in micro-total analysis systems for biochemical assays: recent developments.

    Science.gov (United States)

    Xu, Xiaoli; Zhang, Song; Chen, Hui; Kong, Jilie

    2009-11-15

    Micro-total analysis systems (microTAS) integrate different analytical operations like sample preparation, separation and detection into a single microfabricated device. With the outstanding advantages of low cost, satisfactory analytical efficiency and flexibility in design, highly integrated and miniaturized devices from the concept of microTAS have gained widespread applications, especially in biochemical assays. Electrochemistry is shown to be quite compatible with microanalytical systems for biochemical assays, because of its attractive merits such as simplicity, rapidity, high sensitivity, reduced power consumption, and sample/reagent economy. This review presents recent developments in the integration of electrochemistry in microdevices for biochemical assays. Ingenious microelectrode design and fabrication methods, and versatility of electrochemical techniques are involved. Practical applications of such integrated microsystem in biochemical assays are focused on in situ analysis, point-of-care testing and portable devices. Electrochemical techniques are apparently suited to microsystems, since easy microfabrication of electrochemical elements and a high degree of integration with multi-analytical functions can be achieved at low cost. Such integrated microsystems will play an increasingly important role for analysis of small volume biochemical samples. Work is in progress toward new microdevice design and applications.

  2. A modular microfluidic architecture for integrated biochemical analysis.

    Science.gov (United States)

    Shaikh, Kashan A; Ryu, Kee Suk; Goluch, Edgar D; Nam, Jwa-Min; Liu, Juewen; Thaxton, C Shad; Chiesl, Thomas N; Barron, Annelise E; Lu, Yi; Mirkin, Chad A; Liu, Chang

    2005-07-12

    Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.

  3. Biochemical Process Development and Integration | Bioenergy | NREL

    Science.gov (United States)

    Biochemical Process Development and Integration Biochemical Process Development and Integration Our conversion and separation processes to pilot-scale integrated process development and scale up. We also Publications Accounting for all sugar produced during integrated production of ethanol from lignocellulosic

  4. Integrated biochemical, molecular genetic, and bioacoustical analysis of mesoscale variability of the euphausiid Nematoscelis difficilis in the California Current

    Science.gov (United States)

    Bucklin, Ann; Wiebe, Peter H.; Smolenack, Sara B.; Copley, Nancy J.; Clarke, M. Elizabeth

    2002-03-01

    Integrated assessment of the euphausiid Nematoscelis difficilis (Crustacea; Euphausiacea) and the zooplankton assemblage of the California Current was designed to investigate individual, population, and community responses to mesoscale variability in biological and physical characters of the ocean. Zooplankton samples and observational data were collected along a cross-shelf transect of the California Current in association with the California Cooperative Fisheries Investigations (CalCOFI) Survey during October 1996. The transect crossed three domains defined by temperature and salinity: nearshore, mid-Current, and offshore. Individual N. difficilis differed in physiological condition along the transect, with higher size-corrected concentrations of four central metabolic enzymes (citrate synthetase, hexokinase, lactate dehydrogenase (LDH), and phosphoglucose isomerase (PGI)) for euphausiids collected in nearshore waters than in mid-Current and offshore waters. There was little variation in the DNA sequences of the genes encoding PGI and LDH (all DNA changes were either silent or heterozygous base substitutions), suggesting that differences in enzyme concentration did not result from underlying molecular genetic variation. The population genetic makeup of N. difficilis varied from sample to sample based on haplotype frequencies of mitochondrial cytochrome oxidase I (mtCOI; P=0.029). There were significant differences between pooled nearshore and offshore samples, based on allele frequencies at two sites of common substitutions in the mtCOI sequence ( P=0.020 and 0.026). Silhouette and bioacoustical backscattering measurements of the zooplankton assemblage of the top 100 m showed marked diel vertical migration of the scattering layer, of which euphausiids were a small but significant fraction. The biochemical and molecular assays are used as indices of complex physiological (i.e., growth and condition) and genetic (i.e., mortality) processes; the bioacoustical

  5. Radio-metabolite analysis of carbon-11 biochemical partitioning to non-structural carbohydrates for integrated metabolism and transport studies.

    Science.gov (United States)

    Babst, Benjamin A; Karve, Abhijit A; Judt, Tatjana

    2013-06-01

    Metabolism and phloem transport of carbohydrates are interactive processes, yet each is often studied in isolation from the other. Carbon-11 ((11)C) has been successfully used to study transport and allocation processes dynamically over time. There is a need for techniques to determine metabolic partitioning of newly fixed carbon that are compatible with existing non-invasive (11)C-based methodologies for the study of phloem transport. In this report, we present methods using (11)C-labeled CO2 to trace carbon partitioning to the major non-structural carbohydrates in leaves-sucrose, glucose, fructose and starch. High-performance thin-layer chromatography (HPTLC) was adapted to provide multisample throughput, raising the possibility of measuring different tissues of the same individual plant, or for screening multiple plants. An additional advantage of HPTLC was that phosphor plate imaging of radioactivity had a much higher sensitivity and broader range of sensitivity than radio-HPLC detection, allowing measurement of (11)C partitioning to starch, which was previously not possible. Because of the high specific activity of (11)C and high sensitivity of detection, our method may have additional applications in the study of rapid metabolic responses to environmental changes that occur on a time scale of minutes. The use of this method in tandem with other (11)C assays for transport dynamics and whole-plant partitioning makes a powerful combination of tools to study carbohydrate metabolism and whole-plant transport as integrated processes.

  6. Thermodynamic analysis of biochemical systems

    International Nuclear Information System (INIS)

    Yuan, Y.; Fan, L.T.; Shieh, J.H.

    1989-01-01

    Introduction of the concepts of the availability (or exergy), datum level materials, and the dead state has been regarded as some of the most significant recent developments in classical thermodynamics. Not only the available energy balance but also the material and energy balances of a biological system may be established in reference to the datum level materials in the dead state or environment. In this paper these concepts are illustrated with two examples of fermentation and are shown to be useful in identifying sources of thermodynamic inefficiency, thereby leading naturally to the rational definition of thermodynamic efficiency of a biochemical process

  7. Probabilistic sensitivity analysis of biochemical reaction systems.

    Science.gov (United States)

    Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

    2009-09-07

    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

  8. Integrated physiological, biochemical and molecular analysis identifies important traits and mechanisms associated with differential response of rice genotypes to elevated temperature

    Directory of Open Access Journals (Sweden)

    Boghireddy eSailaja

    2015-11-01

    Full Text Available In changing climate, heat stress caused by high temperature poses a serious threat to rice cultivation. A multiple organizational analysis at physiological, biochemical and molecular level is required to fully understand the impact of elevated temperature in rice. This study was aimed at deciphering the elevated temperature response in eleven popular and mega rice cultivars widely grown in India. Physiological and biochemical traits specifically membrane thermostability (MTS, antioxidants, and photosynthesis were studied at vegetative and reproductive phases which were used to establish a correlation with grain yield under stress. Several useful traits in different genotypes were identified which will be important resource to develop high temperature tolerant rice cultivars. Interestingly, Nagina22 emerged as best performer in terms of yield as well as expression of physiological and biochemical traits at elevated temperature. It showed lesser relative injury, lesser reduction in chlorophyll content, increased super oxide dismutase, catalase and peroxidase activity, lesser reduction in net photosynthetic rate (PN, high transpiration rate (E and other photosynthetic/ fluorescence parameters contributing to least reduction in spikelet fertility and grain yield at elevated temperature. Further, expression of 14 genes including heat shock transcription factors and heat shock proteins was analyzed in Nagina22 (tolerant and Vandana (susceptible at flowering phase, strengthening the fact that N22 performs better at molecular level also during elevated temperature. This study shows that elevated temperature response is complex and involves multiple biological processes which are needed to be characterized to address the challenges of future climate extreme conditions.

  9. Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice.

    Science.gov (United States)

    Lakatos, Anita; Goldberg, Natalie R S; Blurton-Jones, Mathew

    2017-03-10

    We previously demonstrated that transplantation of murine neural stem cells (NSCs) can improve motor and cognitive function in a transgenic model of Dementia with Lewy Bodies (DLB). These benefits occurred without changes in human α-synuclein pathology and were mediated in part by stem cell-induced elevation of brain-derived neurotrophic factor (BDNF). However, instrastriatal NSC transplantation likely alters the brain microenvironment via multiple mechanisms that may synergize to promote cognitive and motor recovery. The underlying neurobiology that mediates such restoration no doubt involves numerous genes acting in concert to modulate signaling within and between host brain cells and transplanted NSCs. In order to identify functionally connected gene networks and additional mechanisms that may contribute to stem cell-induced benefits, we performed weighted gene co-expression network analysis (WGCNA) on striatal tissue isolated from NSC- and vehicle-injected wild-type and DLB mice. Combining continuous behavioral and biochemical data with genome wide expression via network analysis proved to be a powerful approach; revealing significant alterations in immune response, neurotransmission, and mitochondria function. Taken together, these data shed further light on the gene network and biological processes that underlie the therapeutic effects of NSC transplantation on α-synuclein induced cognitive and motor impairments, thereby highlighting additional therapeutic targets for synucleinopathies.

  10. Integrating Carbon Nanotubes into Microfluidic Chip for Separating Biochemical Compounds

    DEFF Research Database (Denmark)

    Chen, Miaoxiang Max; Mogensen, Klaus Bo; Bøggild, Peter

    2012-01-01

    We present a new type of device to separate biochemical compounds wherein carbon nanotubes (CNTs) are integrated as chromatographic stationary phase. The CNTs were directly grown on the bottom of microfluidic channels on Si/SiO2 substrates by chemical vapor deposition (CVD). Acetylene was used...... as carbon source and Ni was employed as catalyst. For electrokinetic separations, higher electrical field strength is usually required; therefore, the CNTs were constructed in pillar-array-form by patterning the catalyst layer. Electrical field strength of 2.0 kV/cm has been realized, which is more than one...

  11. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

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    Goutsias John

    2010-11-01

    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

  12. Applied spectrophotometry: analysis of a biochemical mixture.

    Science.gov (United States)

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

  13. Skin biochemical composition analysis by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Patricia Karen; Tosato, Maira Gaspar; Alves, Rani de Souza; Martin, Airton Abrahao; Favero, Priscila Pereira; Raniero, Leandro, E-mail: amartin@univap.br [Laboratorio de Espectroscopia Vibracional Biomedica, Instituto de Pesquisa e Desenvolvimento - IP e D, Universidade do Vale do Paraiba - UniVap, Sao Jose dos Campos, SP (Brazil)

    2012-09-15

    Skin aging is characterized by cellular and molecular alterations. In this context, Confocal Raman spectroscopy was used in vivo to measure these biochemical changes as function of the skin depth. In this study we have tried to correlate spectra from pure amino acids to in vivo spectra from volunteers with different ages. This study was performed on 32 volunteers: 11 from Group A (20-23 years), 11 from Group B (39-42 years) and 10 from Group C (59-62 years). For each group, the Raman spectra were measured on the surface (0 mm), 30 +- 3 mm and 60 +- 3 {mu}m below the surface. The results from intergroup comparisons showed that the oldest group had a prevalence of the tyrosine band, but it also presented a decrease in the band centered at 875 cm{sup -1} of pyrrolidone acid. The amide I band centered at 1637 cm{sup -1} that is attributed to collagen, as well as other proteins and lipid, showed a smaller amount of these biomolecules for Group C, which can be explained by the decrease in collagen concentration as a function of age. (author)

  14. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

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    Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 ...

  15. Biochemical and cytological analysis of five cultivars of Cicer ...

    African Journals Online (AJOL)

    SAM

    2014-03-12

    Mar 12, 2014 ... variability and relatedness, seed storage protein analysis represents a valid alternative to ... Indian Institute of Pulse Research, Kanpur (U.P.) India. During the present study, five accessions were used for biochemical and cytological analysis. The details of five ... using pestle and mortar. 500 ml of protein ...

  16. An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

    Science.gov (United States)

    Wu, Zujian; Pang, Wei; Coghill, George M

    2015-01-01

    Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

  17. Applied Spectrophotometry: Analysis of a Biochemical Mixture

    Science.gov (United States)

    Trumbo, Toni A.; Schultz, Emeric; Borland, Michael G.; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the…

  18. Study on color difference estimation method of medicine biochemical analysis

    Science.gov (United States)

    Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun

    2006-01-01

    The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.

  19. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material ...

  20. National Bioenergy Center - Biochemical Platform Integration Project: Quarterly Update, Winter 2010

    Energy Technology Data Exchange (ETDEWEB)

    Schell, D.

    2011-02-01

    Winter 2011 edition of the National Bioenergy Center's Biochemical Platform Integration Project quarterly newsletter. Issue topics: 33rd Symposium on Biotechnology for Fuels and Chemicals program topic areas; results from reactive membrane extraction of inhibitors from dilute-acid pretreated corn stover; list of 2010 task publications.

  1. Metabologenomics of Phaeochromocytoma and Paraganglioma: An Integrated Approach for Personalised Biochemical and Genetic Testing.

    Science.gov (United States)

    Eisenhofer, Graeme; Klink, Barbara; Richter, Susan; Lenders, Jacques Wm; Robledo, Mercedes

    2017-04-01

    The tremendous advances over the past two decades in both clinical genetics and biochemical testing of chromaffin cell tumours have led to new considerations about how these aspects of laboratory medicine can be integrated to improve diagnosis and management of affected patients. With germline mutations in 15 genes now identified to be responsible for over a third of all cases of phaeochromocytomas and paragangliomas, these tumours are recognised to have one of the richest hereditary backgrounds among all neoplasms. Depending on the mutation, tumours show distinct differences in metabolic pathways that relate to or even directly impact clinical presentation. At the same time, there has been improved understanding about how catecholamines are synthesised, stored, secreted and metabolised by chromaffin cell tumours. Although the tumours may not always secrete catecholamines it has become clear that almost all continuously produce and metabolise catecholamines. This has not only fuelled changes in laboratory medicine, but has also assisted in recognition of genotype-biochemical phenotype relationships important for diagnostics and clinical care. In particular, differences in catecholamine and energy pathway metabolomes can guide genetic testing, assist with test interpretation and provide predictions about the nature, behaviour and imaging characteristics of the tumours. Conversely, results of genetic testing are important for guiding how routine biochemical testing should be employed and interpreted in surveillance programmes for at-risk patients. In these ways there are emerging needs for modern laboratory medicine to seamlessly integrate biochemical and genetic testing into the diagnosis and management of patients with chromaffin cell tumours.

  2. A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-05-01

    Full Text Available Abstract Background Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based sensitivity analysis approach for studying the robustness and fragility properties of biochemical reaction systems under uncertainty in the standard chemical potentials of the activated complexes of the reactions and the standard chemical potentials of the molecular species. In that approach, key sensitivity indices were estimated by Monte Carlo sampling, which is computationally very demanding and impractical for large biochemical reaction systems. Computationally efficient algorithms are needed to make variance-based sensitivity analysis applicable to realistic cellular networks, modeled by biochemical reaction systems that consist of a large number of reactions and molecular species. Results We present four techniques, derivative approximation (DA, polynomial approximation (PA, Gauss-Hermite integration (GHI, and orthonormal Hermite approximation (OHA, for analytically approximating the variance-based sensitivity indices associated with a biochemical reaction system. By using a well-known model of the mitogen-activated protein kinase signaling cascade as a case study, we numerically compare the approximation quality of these techniques against traditional Monte Carlo sampling. Our results indicate that, although DA is computationally the most attractive technique, special care should be exercised when using it for sensitivity analysis, since it may only be accurate at low levels of uncertainty. On the other hand, PA, GHI, and OHA are computationally more demanding than DA but can work well at high levels of uncertainty. GHI results in a slightly better accuracy than PA, but it is more difficult to implement. OHA produces the most accurate approximation results and can be implemented in a straightforward manner. It turns out that the computational cost of the

  3. An electrodynamic preconcentrator integrated thermoelectric biosensor chip for continuous monitoring of biochemical process

    International Nuclear Information System (INIS)

    Choi, Yong-Hwan; Kim, Min-gu; Kang, Dong-Hyun; Sim, Jaesam; Kim, Jongbaeg; Kim, Yong-Jun

    2012-01-01

    This paper proposes an integrated sensor chip for continuous monitoring of a biochemical process. It is composed of a preconcentrator and a thermoelectric biosensor. In the preconcentrator, the concentration of the injected biochemical sample is electrodynamically condensed. Then, in the downstream thermoelectric biosensor, the preconcentrated target molecules react with sequentially injected capture molecules and generate reaction heat. The reaction heat is detected based on the thermoelectric effect, and an integrated split-flow microchannel improves the sensor stability by providing ability to self-compensate thermal noise. These sequential preconcentration and detection processes are performed in completely label-free and continuous conditions and consequently enhance the sensor sensitivity. The performance of the integrated biosensor chip was evaluated at various flow rates and applied voltages. First, in order to verify characteristics of the fabricated preconcentrator, 10 µm -diameter polystyrene (PS) particles were used. The particles were concentrated by applying ac voltage from 0 to 16 V pp at 3 MHz at various flow rates. In the experimental result, approximately 92.8% of concentration efficiency was achieved at a voltage over 16 V pp and at a flow rate below 100 µl h −1 . The downstream thermoelectric biosensor was characterized by measuring reaction heat of biotin–streptavidin interaction. The preconcentrated streptavidin-coated PS particles flow into the reaction chamber and react with titrated biotin. The measured output voltage was 288.2 µV at a flow rate of 100 µl h −1 without preconcentration. However, by using proposed preconcentrator, an output voltage of 812.3 µV was achieved with a 16 V pp -applied preconcentration in the same given sample and flow rate. According to these results, the proposed label-free biomolecular preconcentration and detection technique can be applied in continuous and high-throughput biochemical applications

  4. Integrated genetic analysis microsystems

    International Nuclear Information System (INIS)

    Lagally, Eric T; Mathies, Richard A

    2004-01-01

    With the completion of the Human Genome Project and the ongoing DNA sequencing of the genomes of other animals, bacteria, plants and others, a wealth of new information about the genetic composition of organisms has become available. However, as the demand for sequence information grows, so does the workload required both to generate this sequence and to use it for targeted genetic analysis. Microfabricated genetic analysis systems are well poised to assist in the collection and use of these data through increased analysis speed, lower analysis cost and higher parallelism leading to increased assay throughput. In addition, such integrated microsystems may point the way to targeted genetic experiments on single cells and in other areas that are otherwise very difficult. Concomitant with these advantages, such systems, when fully integrated, should be capable of forming portable systems for high-speed in situ analyses, enabling a new standard in disciplines such as clinical chemistry, forensics, biowarfare detection and epidemiology. This review will discuss the various technologies available for genetic analysis on the microscale, and efforts to integrate them to form fully functional robust analysis devices. (topical review)

  5. Biochemical analysis of CTLA-4 immunoreactive material from human blood

    Directory of Open Access Journals (Sweden)

    Dennert Kate

    2009-09-01

    Full Text Available Abstract Background CTLA-4 was initially described as a membrane-bound molecule that inhibited lymphocyte activation by interacting with B7.1 and B7.2 molecules on antigen presenting cells. Alternative splicing of mRNA encoding the CTLA-4 receptor leads to the production of a molecule (sCTLA-4 that lacks a membrane anchor and is therefore secreted into the extracellular space. Despite studies finding that people with autoimmune disease more frequently express high levels of sCTLA-4 in their blood than apparently healthy people, the significance of these findings is unclear. Methods Molecules isolated from blood using CTLA-4 specific antibodies were analyzed with ligand binding assays, mass spectroscopy, and biochemical fractionation in an effort to increase our understanding of CTLA-4 immunoreactive material. Results Mass spectroscopy analysis of the molecules recognized by multiple CTLA-4-specific antibodies failed to identify any CTLA-4 protein. Even though these molecules bind to the CTLA-4 receptors B7.1 and B7.2, they also exhibit properties common to immunoglobulins. Conclusion We have identified molecules in blood that are recognized by CTLA-4 specific antibodies but also exhibit properties of immunoglobulins. Our data indicates that what has been called sCTLA-4 is not a direct product of the CTLA-4 gene, and that the CTLA-4 protein is not part of this molecule. These results may explain why the relationship of sCTLA-4 to immune system activity has been difficult to elucidate.

  6. Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase.

    Science.gov (United States)

    Guo, Xiao; Niemi, Natalie M; Coon, Joshua J; Pagliarini, David J

    2017-07-14

    The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue ∼50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S. cerevisiae has not been conclusively defined. Here, using comparative mitochondrial phosphoproteomics, analyses of protein-protein interactions by affinity enrichment-mass spectrometry, and in vitro biochemistry, we define Ptc6p as the primary PDC phosphatase in S. cerevisiae Our analyses further suggest additional substrates for related S. cerevisiae phosphatases and describe the overall phosphoproteomic changes that accompany mitochondrial respiratory dysfunction. In summary, our quantitative proteomics and biochemical analyses have identified Ptc6p as the primary-and likely sole- S. cerevisiae PDC phosphatase, closing a key knowledge gap about the regulation of yeast mitochondrial metabolism. Our findings highlight the power of integrative omics and biochemical analyses for annotating the functions of poorly characterized signaling proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Imminent Cardiac Risk Assessment via Optical Intravascular Biochemical Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wetzel, D.; Wetzel, L; Wetzel, M; Lodder, R

    2009-01-01

    Heart disease is by far the biggest killer in the United States, and type II diabetes, which affects 8% of the U.S. population, is on the rise. In many cases, the acute coronary syndrome and/or sudden cardiac death occurs without warning. Atherosclerosis has known behavioral, genetic and dietary risk factors. However, our laboratory studies with animal models and human post-mortem tissue using FT-IR microspectroscopy reveal the chemical microstructure within arteries and in the arterial walls themselves. These include spectra obtained from the aortas of ApoE-/- knockout mice on sucrose and normal diets showing lipid deposition in the former case. Also pre-aneurysm chemical images of knockout mouse aorta walls, and spectra of plaque excised from a living human patient are shown for comparison. In keeping with the theme of the SPEC 2008 conference Spectroscopic Diagnosis of Disease this paper describes the background and potential value of a new catheter-based system to provide in vivo biochemical analysis of plaque in human coronary arteries. We report the following: (1) results of FT-IR microspectroscopy on animal models of vascular disease to illustrate the localized chemical distinctions between pathological and normal tissue, (2) current diagnostic techniques used for risk assessment of patients with potential unstable coronary syndromes, and (3) the advantages and limitations of each of these techniques illustrated with patent care histories, related in the first person, by the physician coauthors. Note that the physician comments clarify the contribution of each diagnostic technique to imminent cardiac risk assessment in a clinical setting, leading to the appreciation of what localized intravascular chemical analysis can contribute as an add-on diagnostic tool. The quality of medical imaging has improved dramatically since the turn of the century. Among clinical non-invasive diagnostic tools, laboratory tests of body fluids, EKG, and physical examination are

  8. Novel method of dual fiber Bragg gratings integrated in fiber ring laser for biochemical sensors

    Science.gov (United States)

    Bui, H.; Pham, T. B.; Nguyen, V. A.; Pham, V. D.; Do, T. C.; Nguyen, T. V.; Hoang, T. H. C.; Le, H. T.; Pham, V. H.

    2018-05-01

    Optical sensors have been shown to be very effective for measuring the toxic content in liquid and air environments. Optical sensors, which operate based on the wavelength shift of the optical signals, require an expensive spectrometer. In this paper, we propose a new configuration of the optical sensor device for measuring wavelength shift without using a spectrometer. This configuration has a large potential for application in biochemical sensing techniques, and comes with a low cost. This configuration uses dual fiber Bragg gratings (FBGs) integrated in a fiber ring laser structure of erbium-doped fiber, in which one FBG is used as a reference to sweep over the applicable spectrum of the etched-Bragg grating. The etched-FBG as a sensing probe is suitable for bio- and/or chemical sensors. The sensitivity and accuracy of the sensor system can be improved by the narrow linewidth of emission spectra from the laser, the best limit of detection of this sensor is 1.5  ×  10‑4 RIU (RIU: refractive index unit), as achieved by the optical sensor using a high resolution spectrometer. This sensor system has been experimentally investigated to detect different types of organic compounds, gasoline, mixing ratios of organic solvents in gasoline, and nitrate concentration in water samples. The experimental results show that this sensing method could determine different mixing ratios of organic solvents with good repeatability, high accuracy, and rapid response: e.g. for ethanol and/or methanol in gasoline RON 92 (RON: research octane number) of 0%–14% v/v, and nitrate in water samples at a low concentration range of 0–50 ppm. These results suggest that the proposed configuration can construct low-cost and accurate biochemical sensors.

  9. Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses.

    Directory of Open Access Journals (Sweden)

    Claire Saulou-Bérion

    Full Text Available For a better understanding of the systemic effect of sub-lethal micromolar concentrations of ionic silver on Escherichia coli, we performed a multi-level characterization of cells under Ag+-mediated stress using an integrative biology approach combining physiological, biochemical and transcriptomic data. Physiological parameters, namely bacterial growth and survival after Ag+ exposure, were first quantified and related to the accumulation of intracellular silver, probed for the first time by nano secondary ion mass spectroscopy at sub-micrometer lateral resolution. Modifications in E. coli biochemical composition were evaluated under Ag+-mediated stress by in situ synchrotron Fourier-transform infrared microspectroscopy and a comprehensive transcriptome response was also determined. Using multivariate statistics, correlations between the physiological parameters, the extracellular concentration of AgNO3 and the intracellular silver content, gene expression profiles and micro-spectroscopic data were investigated. We identified Ag+-dependent regulation of gene expression required for growth (e.g. transporter genes, transcriptional regulators, ribosomal proteins, for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR and for coping with various types of stress (dnaK, pspA, metA,R, oxidoreductase genes. The silver-induced shortening of the acyl chain of fatty acids, mostly encountered in cell membrane, was highlighted by microspectroscopy and correlated with the down-regulated expression of genes involved in fatty acid transport (fadL and synthesis/modification of lipid A (lpxA and arnA. The increase in the disordered secondary structure of proteins in the presence of Ag+ was assessed through the conformational shift shown for amides I and II, and further correlated with the up-regulated expression of peptidase (hfq and chaperone (dnaJ, and regulation of transpeptidase expression (ycfS and ycbB. Interestingly, as these

  10. Silicon-Nitride-based Integrated Optofluidic Biochemical Sensors using a Coupled-Resonator Optical Waveguide

    Directory of Open Access Journals (Sweden)

    Jiawei eWANG

    2015-04-01

    Full Text Available Silicon nitride (SiN is a promising material platform for integrating photonic components and microfluidic channels on a chip for label-free, optical biochemical sensing applications in the visible to near-infrared wavelengths. The chip-scale SiN-based optofluidic sensors can be compact due to a relatively high refractive index contrast between SiN and the fluidic medium, and low-cost due to the complementary metal-oxide-semiconductor (CMOS-compatible fabrication process. Here, we demonstrate SiN-based integrated optofluidic biochemical sensors using a coupled-resonator optical waveguide (CROW in the visible wavelengths. The working principle is based on imaging in the far field the out-of-plane elastic-light-scattering patterns of the CROW sensor at a fixed probe wavelength. We correlate the imaged pattern with reference patterns at the CROW eigenstates. Our sensing algorithm maps the correlation coefficients of the imaged pattern with a library of calibrated correlation coefficients to extract a minute change in the cladding refractive index. Given a calibrated CROW, our sensing mechanism in the spatial domain only requires a fixed-wavelength laser in the visible wavelengths as a light source, with the probe wavelength located within the CROW transmission band, and a silicon digital charge-coupled device (CCD / CMOS camera for recording the light scattering patterns. This is in sharp contrast with the conventional optical microcavity-based sensing methods that impose a strict requirement of spectral alignment with a high-quality cavity resonance using a wavelength-tunable laser. Our experimental results using a SiN CROW sensor with eight coupled microrings in the 680nm wavelength reveal a cladding refractive index change of ~1.3 × 10^-4 refractive index unit (RIU, with an average sensitivity of ~281 ± 271 RIU-1 and a noise-equivalent detection limit (NEDL of 1.8 ×10^-8 RIU ~ 1.0 ×10^-4 RIU across the CROW bandwidth of ~1 nm.

  11. Energy analysis of biochemical conversion processes of biomass to bioethanol

    Energy Technology Data Exchange (ETDEWEB)

    Bakari, M.; Ngadi, M.; Bergthorson, T. [McGill Univ., Ste-Anne-de-Bellevue, PQ (Canada). Dept. of Bioresource Engineering

    2010-07-01

    Bioethanol is among the most promising of biofuels that can be produced from different biomass such as agricultural products, waste and byproducts. This paper reported on a study that examined the energy conversion of different groups of biomass to bioethanol, including lignocelluloses, starches and sugar. Biochemical conversion generally involves the breakdown of biomass to simple sugars using different pretreatment methods. The energy needed for the conversion steps was calculated in order to obtain mass and energy efficiencies for the conversions. Mass conversion ratios of corn, molasses and rice straw were calculated as 0.3396, 0.2300 and 0.2296 kg of bioethanol per kg of biomass, respectively. The energy efficiency of biochemical conversion of corn, molasses and rice straw was calculated as 28.57, 28.21 and 31.33 per cent, respectively. The results demonstrated that lignocelluloses can be efficiently converted with specific microorganisms such as Mucor indicus, Rhizopus oryzae using the Simultaneous Saccharification and Fermentation (SSF) methods.

  12. A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems.

    NARCIS (Netherlands)

    F.J. Bruggeman (Frank); H. Burchard; B. Kooi; B.P. Sommeijer (Ben)

    2006-01-01

    textabstractBiochemical systems are bound by two mathematically-relevant restrictions. First, state variables in such systems represent non-negative quantities, such as concentrations of chemical compounds. Second, biochemical systems conserve mass and energy. Both properties must be reflected in

  13. Resonant-cantilever bio/chemical sensors with an integrated heater for both resonance exciting optimization and sensing repeatability enhancement

    International Nuclear Information System (INIS)

    Yu Haitao; Li Xinxin; Gan Xiaohua; Liu Yongjing; Liu Xiang; Xu Pengcheng; Li Jungang; Liu Min

    2009-01-01

    With an integrated resonance exciting heater and a self-sensing piezoresistor, resonant micro-cantilever bio/chemical sensors are optimally designed and fabricated by micromachining techniques. This study is emphasized on the optimization of the integrated heating resistor. Previous research has put the heater at either the cantilever clamp end, the midpoint or the free end. Aiming at sufficiently high and stable resonant amplitude, our research indicates that the optimized location of the thermal-electric exciting resistor is the clamp end instead of other positions. By both theoretical analysis and resonance experiments where three heating resistors are placed at the three locations of the fabricated cantilever, it is clarified that the clamp end heating provides the most efficient resonance excitation in terms of resonant amplitude, Q-factor and resonance stability. Besides, the optimized combination of dc bias and ac voltage is determined by both analysis and experimental verification. With the optimized heating excitation, the resonant cantilever is used for biotin–avidin-specific detection, resulting in a ±0.1 Hz ultra-low noise floor of the frequency signal and a 130 fg mass resolution. In addition to resonance excitation, the heater is used to heat up the cantilever for speed-up desorption after detection that helps rapid and repeated sensing to chemical vapor. The clamp end is determined (by simulation) as the optimal heating location for uniform temperature distribution on the cantilever. Using the resonant cantilever, a rapid and repeated sensing experiment on dimethyl methylphosphonate (DMMP) vapor shows that a short-period heating at the detection interval significantly quickens the signal recovery and enhances the sensing repeatability

  14. Biochemical parameters in Tubifex tubifex as an integral part of complex sediment toxicity assessment

    Energy Technology Data Exchange (ETDEWEB)

    Smutna, M.; Hilscherova, K.; Paskova, V. [Masaryk Univ., Brno (CZ). RECETOX (Research Centre for Environmental Chemistry and Ecotoxicology); Marsalek, B [Czech Academy of Science, Brno (Czech Republic). Centre for Cyanobacteria and their Toxins

    2008-06-15

    Background, aim, and scope Restoration of lakes and reservoirs with extensive cyanobacterial water bloom often requires evaluation of the sediment quality. Next to the chemical analysis of known pollutants, sediment bioassays should be employed to assess toxicity of the present contaminants and to make predictions of associated risk. Brno reservoir in the Czech Republic is a typical example of water bodies with long-term problems concerning cyanobacterial water blooms. Comprehensive assessment of reservoir sediment quality was conducted since successful reservoir restoration might require sediment removal. An important part of this survey focused on an examination of the utility of Tubifex tubifex and its sublethal biochemical markers for the assessment of direct sediment toxicity. Materials and methods This complex study included chemical analysis of contaminants (heavy metals, organic pollutants), ecotoxicity testing of sediment elutriates (tests with Daphnia magna, Pseudomonas putida, Sinapis alba, Scenedesmus subspicatus), and other parameters. We have tested in more detail the applicability of T. tubifex as a test organism for direct evaluation of contact sediment toxicity. Survival tests after 14 days of exposure were complemented by an assessment of parameters serving as biomarkers for sublethal effects [such as total glutathione content (GSH), activities of the enzymes glutathione transferase (GST), glutathione peroxidase (GPx), and glutathione reductase (GR)]. The data matrix was subjected to multivariate analysis to interpret relationships between different parameters and possible differences among locations. Results The multivariate statistical techniques helped to clearly identify the more contaminated upstream sites and separate them from the less contaminated and reference samples. The data document closer relationships of the detected sediment contamination with results of direct sediment exposure in the T. tubifex test regarding mortality but namely

  15. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory

    Directory of Open Access Journals (Sweden)

    Qian Hong

    2008-05-01

    Full Text Available Abstract Background: Several approaches, including metabolic control analysis (MCA, flux balance analysis (FBA, correlation metric construction (CMC, and biochemical circuit theory (BCT, have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results: In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RT BS and ST BS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion: One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA.

  16. Microfluidic Devices for Chemical and Biochemical Analysis in Microgravity

    Science.gov (United States)

    Roman, Gregory T.; Culbertson, Christopher T.; Meyer, Amanda; Ramsey, J. Michael; Gonda, Steven R.

    2004-01-01

    One often touted benefit of "Lab-on-a-Chip" devices is their potential for use in remote environments. The ultimate remote environment is outer space, and NASA has multiple needs in the area of analytical sensing capability in such an environment. In particular, we are interested in integrating microfluidic devices with NASA bioreactor systems. In such an integrated system, the microfluidic device will serve as a biosensor and be used for both feedback control and for detecting various bioproducts produced by cells cultured in the NASA bioreactors. As a first step in demonstrating the ability of microfluidic devices to operate under the extreme environmental conditions found in outer space, we constructed a portable, battery operated platform for testing under reduced gravity conditions on a NASA KC-135 reduced gravity research aircraft, (AKA "the vomit comet"). The test platform consisted of a microchip, two 0-8kV high voltage power supplies, a high voltage switch, a solid-state diode-pumped green laser, a channel photomultiplier, and an inertial mass measurement unit, all under the control of a laptop computer and powered by 10 D-cell alkaline batteries. Over the course of 4 KC-135 flights, 1817 fast electrophoretic separations of 4 amino acids and/or proteins were performed in a variety of gravitational environments including zero-G, Martian-G, lunar-G, and 2-G. Results from these experiments will be presented and discussed.

  17. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  18. Integrative Analysis of Metabolic Models – from Structure to Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hartmann, Anja, E-mail: hartmann@ipk-gatersleben.de [Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany); Schreiber, Falk [Monash University, Melbourne, VIC (Australia); Martin-Luther-University Halle-Wittenberg, Halle (Germany)

    2015-01-26

    The characterization of biological systems with respect to their behavior and functionality based on versatile biochemical interactions is a major challenge. To understand these complex mechanisms at systems level modeling approaches are investigated. Different modeling formalisms allow metabolic models to be analyzed depending on the question to be solved, the biochemical knowledge and the availability of experimental data. Here, we describe a method for an integrative analysis of the structure and dynamics represented by qualitative and quantitative metabolic models. Using various formalisms, the metabolic model is analyzed from different perspectives. Determined structural and dynamic properties are visualized in the context of the metabolic model. Interaction techniques allow the exploration and visual analysis thereby leading to a broader understanding of the behavior and functionality of the underlying biological system. The System Biology Metabolic Model Framework (SBM{sup 2} – Framework) implements the developed method and, as an example, is applied for the integrative analysis of the crop plant potato.

  19. Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans

    NARCIS (Netherlands)

    Kruse, T.; Pas, van de B.A.; Atteia, A.; Krab, K.; Hagen, W.R.; Goodwin, L.; Chain, P.; Boeren, S.; Maphosa, F.; Schraa, G.; Vos, de W.M.; Oost, van der J.; Smidt, H.; Stams, A.J.M.

    2015-01-01

    Desulfitobacterium dehalogenans is able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components and shotgun proteomics to study elements of the

  20. Biochemical Cardiovascular Risk Factors After Hypertensive Pregnancy Disorders: A Systematic Review and Meta-analysis

    NARCIS (Netherlands)

    Hermes, W.; Ket, J.C.; Pampus, M.G. van; Franx, A.; Veenendaal, M.V.; Kolster, C.; Tamsma, J.T.; Bloemenkamp, K.W.; Ponjee, G.; van der Hout, E.; Ten Horn, H.; Loix, S.; Mol, B.W.; Groot, C.J. de

    2012-01-01

    The objective of this study was to perform a systematic review and meta-analysis of studies assessing biochemical cardiovascular risk factors in women with previous hypertensive pregnancy disorders and women with previous normotensive pregnancies. Data were collected from PubMed and EMBASE (from

  1. Biochemical Cardiovascular Risk Factors After Hypertensive Pregnancy Disorders : A Systematic Review and Meta-analysis

    NARCIS (Netherlands)

    Hermes, Wietske; Ket, Johannes C. F.; van Pampus, Maria G.; Franx, Arie; Veenendaal, Marjolein V. E.; Kolster, Clara; Tamsma, Jouke T.; Bloemenkamp, Kitty W. M.; Ponjee, Gabrielle; van der Hout, Evelien; ten Horn, Hilde; Loix, Stephanie; Mol, Ben Willem; de Groot, Christianne J. M.

    2012-01-01

    The objective of this study was to perform a systematic review and meta-analysis of studies assessing biochemical cardiovascular risk factors in women with previous hypertensive pregnancy disorders and women with previous normotensive pregnancies. Data were collected from PubMed and EMBASE (from

  2. Mosquito salivary gland protein preservation in the field for immunological and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Almeras L

    2011-03-01

    Full Text Available Abstract Mosquito salivary proteins are involved in several biological processes that facilitate their blood feeding and have also been reported to elicit an IgG response in vertebrates. A growing number of studies have focused on this immunological response for its potential use as a biological marker of exposure to arthropod bites. As mosquito saliva collection is extremely laborious and inefficient, most research groups prefer to work on mosquito salivary glands (SGs. Thus, SG protein integrity is a critical factor in obtaining meaningful data from immunological and biochemical analysis. Current methodologies rely on an immediate freezing of SGs after their collection. However, the maintenance of samples in a frozen environment can be hard to achieve in field conditions. In this study, SG proteins from two mosquito species (Aedes aegypti and Anopheles gambiae s.s. stored in different media for 5 days at either +4°C or room temperature (RT were evaluated at the quantitative (i.e., ELISA and qualitative (i.e., SDS-PAGE and immunoblotting levels. Our results indicated that PBS medium supplemented with an anti-protease cocktail seems to be the best buffer to preserve SG antigens for 5 days at +4°C for ELISA analysis. Conversely, cell-lysis buffer (Urea-Thiourea-CHAPS-Tris was best at preventing protein degradation both at +4°C and RT for further qualitative analysis. These convenient storage methods provide an alternative to freezing and are expected to be applicable to other biological samples collected in the field.

  3. The NREL Biochemical and Thermochemical Ethanol Conversion Processes: Financial and Environmental Analysis Comparison

    Directory of Open Access Journals (Sweden)

    Jesse Sky Daystar

    2015-07-01

    Full Text Available The financial and environmental performance of the National Renewable Energy Lab’s (NREL thermochemical and biochemical biofuel conversion processes are examined herein with pine, eucalyptus, unmanaged hardwood, switchgrass, and sweet sorghum. The environmental impacts of the process scenarios were determined by quantifying greenhouse gas (GHG emissions and TRACI impacts. Integrated financial and environmental performance metrics were introduced and used to examine the biofuel production scenarios. The thermochemical and biochemical conversion processes produced the highest financial performance and lowest environmental impacts when paired with pine and sweet sorghum, respectively. The high ash content of switchgrass and high lignin content of loblolly pine lowered conversion yields, resulting in the highest environmental impacts and lowest financial performance for the thermochemical and biochemical conversion processes, respectively. Biofuel produced using the thermochemical conversion process resulted in lower TRACI single score impacts and somewhat lower GHG emissions per megajoule (MJ of fuel than using the biochemical conversion pathway. The cost of carbon mitigation resulting from biofuel production and corresponding government subsidies was determined to be higher than the expected market carbon price. In some scenarios, the cost of carbon mitigation was several times higher than the market carbon price, indicating that there may be other more cost-effective methods of reducing carbon emissions.

  4. Modelling and Analysis of Biochemical Signalling Pathway Cross-talk

    Directory of Open Access Journals (Sweden)

    Robin Donaldson

    2010-02-01

    Full Text Available Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising parallel composition of instances of generic modules (with internal and external labels. Pathways are then composed by (synchronising parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways.

  5. Ultraviolet inactivation of avian sarcoma virus: biological and biochemical analysis

    International Nuclear Information System (INIS)

    Owada, M.; Ihara, S.; Toyoshima, K.; Kozai, Y.; Sugino, Y.

    1976-01-01

    The rate of inactivation by ultraviolet light of the focus-forming capacity of avian sarcoma virus was almost the same as that of the virus-producing capacity, measured as plaque formation. In addition, no significant difference was observed in inactivation of the transforming capacity assayed on C/BE chick embryo fibroblasts (CEF), which carry endogenous avian tumor virus DNA, and on duck embryo fibroblasts (DEF), which are known to be devoid of this DNA. All foci induced by nonirradiated virus produced infectious sarcoma virus, but some of the foci induced by uv-irradiated virus did not produce infectious virus of either transforming or transformation-defective type. The proportion of nonproducer foci was 3.4 times more in DEF than in gs - chf - CEF. RNAs extracted from uv-irradiated virions by sodium dodecyl sulfate (SDS) treatment were found to be composed of 60--70 S and 4 S RNAs by analysis in a sucrose gradient containing 0.5 percent SDS. The large RNA, however, became hydrophobic after irradiation and was sedimented with SDS by addition of one drop of saturated potassium chloride solution. This RNA was not dissociated into 30--40S components by heating at 100 0 for 45 sec, unlike 60--70 S RNA from uv-irradiated virions. After SDS--Pronase treatment, the 60--70 S RNA from uv-irradiated virions no longer had these altered characteristics. Reverse transcriptase activity with the endogenous template decreased in parallel with increase in the uv dose. The reduction rate was similar to that assayed with exogenous template or in the presence of actinomycin D. These data strongly suggest that RNA damage is not the only cause of virus inactivation by uv light

  6. Molecular and biochemical analysis of symbiotic plant receptor kinase complexes

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Douglas R; Riely, Brendan K

    2010-09-01

    -localize (i.e., the flotillin FLOT4) with symbiotic receptor-like proteins. As controls for TAP tag analysis we have generated protein isoforms that carry fluorescent domains (translational fusions to GFP) and these have been used to establish the subcellular location and dynamics of two symbiotic receptors, LYK3 and DMI2. Both proteins localize to membrane microdomains, or putative lipid rafts, and display dynamic behavior following elicitation with the Nod factor ligand. Finally, mass spectrometry of interacting proteins is yielding lists of candidate proteins that we are poised to test using semi-high throughput RNAi technology and Tnt1 knockout collections in Medicago truncatula.

  7. Meta-analysis of the relationship of mycotoxins with biochemical and hematological parameters in broilers.

    Science.gov (United States)

    Andretta, I; Kipper, M; Lehnen, C R; Lovatto, P A

    2012-02-01

    A meta-analysis was carried out to study the association of mycotoxins with hematological and biochemical profiles in broilers. Ninety-eight articles published between 1980 and 2009 were used in the database, totaling 37,371 broilers. The information was selected from the Materials and Methods and Results sections in the selected articles and then tabulated in a database. Meta-analysis followed 3 sequential analyses: graphic, correlation, and variance-covariance. Mycotoxins reduced (P Mycotoxins also altered (P effect was observed on the relationship between the concentration of aflatoxin in diets and the serum concentration of alkaline phosphatase, γ-glutamyl transferase, alanine aminotransferase, and aspartate aminotransferase. The total protein concentration in blood was 18% lower (P mycotoxin and without the additive. The meta-analysis performed in this study allowed us to address and quantify systematically the relationship of mycotoxins with alterations in hematologic and biochemical profiles in broilers.

  8. Biochemical analysis of force-sensitive responses using a large-scale cell stretch device.

    Science.gov (United States)

    Renner, Derrick J; Ewald, Makena L; Kim, Timothy; Yamada, Soichiro

    2017-09-03

    Physical force has emerged as a key regulator of tissue homeostasis, and plays an important role in embryogenesis, tissue regeneration, and disease progression. Currently, the details of protein interactions under elevated physical stress are largely missing, therefore, preventing the fundamental, molecular understanding of mechano-transduction. This is in part due to the difficulty isolating large quantities of cell lysates exposed to force-bearing conditions for biochemical analysis. We designed a simple, easy-to-fabricate, large-scale cell stretch device for the analysis of force-sensitive cell responses. Using proximal biotinylation (BioID) analysis or phospho-specific antibodies, we detected force-sensitive biochemical changes in cells exposed to prolonged cyclic substrate stretch. For example, using promiscuous biotin ligase BirA* tagged α-catenin, the biotinylation of myosin IIA increased with stretch, suggesting the close proximity of myosin IIA to α-catenin under a force bearing condition. Furthermore, using phospho-specific antibodies, Akt phosphorylation was reduced upon stretch while Src phosphorylation was unchanged. Interestingly, phosphorylation of GSK3β, a downstream effector of Akt pathway, was also reduced with stretch, while the phosphorylation of other Akt effectors was unchanged. These data suggest that the Akt-GSK3β pathway is force-sensitive. This simple cell stretch device enables biochemical analysis of force-sensitive responses and has potential to uncover molecules underlying mechano-transduction.

  9. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  10. Biochemical and phyto chemical analysis of dipterygium glaucum collected from Cholistan desert

    International Nuclear Information System (INIS)

    Mehmood, K.; Mehmood, S.; Ramzan, M.

    2010-01-01

    The present study evaluates the Biochemical and phyto chemical analysis of Dipterygium Glaucum from Cholistan desert. Ash contents, carbohydrates, crude fibers, crude fats, were carried out along with the estimation of minerals. Determination of biochemical constituents indicate the presence of total carbohydrates 0.156% (0.174 reducing sugars and O.041 % non reducing),starch contents 0.053%, crude fibers 26.83%, crude fats 13.30% and nitrogen contents 0.0 14%. Concentration of sodium was 3.3%,Potassium 37.6%, lithium 0.1 %, Calcium 0.01 %, Magnesium 0.022%, nickel 0.764%, copper 2.372%, manganese 0.003%, sulphur 0.8%, Phosphorous 1.60%. Moisture and ash contents were 5.60% and 4.75% respectively. alkaloids, glycoside, cardiac glycoside, bound anthraquinones and saponins were present while flavonoids and unbound anthraquinones were absent. no anti bacterial activity was found in this plant extract. (author)

  11. Lab-on-a-chip systems with integrated optics for biochemical applications

    DEFF Research Database (Denmark)

    Mogensen, Klaus Bo; Gustafsson, O; Nunes, Pedro

    2008-01-01

    Two different applications that take advantage of integrated planar waveguides will be shown. The first example is a silicon chips for capillary electrochromatography (CEC), where the fluidic part contains electrically insulated channels with an injection cross and a chromatography column...

  12. Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination.

    Science.gov (United States)

    Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E; Evans, David J

    2016-08-19

    Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3' non-coding region we have further developed a cell-based assay (the 3'CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Biochemical Analysis of Synovial Fluid, Cerebrospinal Fluid and Vitreous Humor at Early Postmortem Intervals in Donkeys

    Directory of Open Access Journals (Sweden)

    Doha Yahia

    2014-01-01

    Full Text Available Biochemical analysis of body fluids after death is a helpful tool in veterinary forensic medicine. Synovial fluid, cerebrospinal fluid (CSF and vitreous humor are easily accessible and well preserved from contamination. Five donkeys (Equus africanus asinus aged 1 - 2 years old were subjected to the study. Samples (Synovial fluid, CSF and vitreous humor were collected before death (antimortem and then at 2, 4, 6, 8, 10 and 12 hours postmortem. Samples were analyzed for glucose, chloride, sodium, magnesium, potassium, enzymes and total protein. Synovial fluid analysis showed that glucose concentration started to decrease at 6 hours postmortem, while magnesium level increased with time. Other parameters were more stable. CSF analysis showed several changes related to time after death as the decrease in glucose and sodium levels, and the increased levels of potassium, magnesium, calcium and total protein. Vitreous analysis revealed a reduction in glucose level and increased potassium and magnesium concentrations. The present study concluded that biochemical analysis of synovial fluid, vitreous humor and CSF can help in determination of time since death in donkeys. This study recommend using CSF for determination of early post-mortem intervals.

  14. Integrated piping structural analysis system

    International Nuclear Information System (INIS)

    Motoi, Toshio; Yamadera, Masao; Horino, Satoshi; Idehata, Takamasa

    1979-01-01

    Structural analysis of the piping system for nuclear power plants has become larger in scale and in quantity. In addition, higher quality analysis is regarded as of major importance nowadays from the point of view of nuclear plant safety. In order to fulfill to the above requirements, an integrated piping structural analysis system (ISAP-II) has been developed. Basic philosophy of this system is as follows: 1. To apply the date base system. All information is concentrated. 2. To minimize the manual process in analysis, evaluation and documentation. Especially to apply the graphic system as much as possible. On the basis of the above philosophy four subsystems were made. 1. Data control subsystem. 2. Analysis subsystem. 3. Plotting subsystem. 4. Report subsystem. Function of the data control subsystem is to control all information of the data base. Piping structural analysis can be performed by using the analysis subsystem. Isometric piping drawing and mode shape, etc. can be plotted by using the plotting subsystem. Total analysis report can be made without the manual process through the reporting subsystem. (author)

  15. Integrated micro-biochemical approach for phytoremediation of cadmium and zinc contaminated soils.

    Science.gov (United States)

    Mani, Dinesh; Kumar, Chitranjan; Patel, Niraj Kumar

    2015-01-01

    The integrated potential of oilcake manure (OM), elemental sulphur (S(0)), Glomus fasciculatum and Pseudomonas putida by growing Helianthus annuus L for phytoremediation of cadmium and zinc contaminated soils was investigated under pot experiment. The integrated treatment (2.5 g kg(-1) OM, 0.8 g kg(-1) S(0) and co-inoculation with G. fasciculatum and P. putida promoted the dry biomass of the plant. The treatment was feasible for enhanced cadmium accumulation up to 6.56 and 5.25 mg kg(-1) and zinc accumulation up to 45.46 and 32.56 mg kg(-1) in root and shoot, respectively, which caused maximum remediation efficiency (0.73 percent and 0.25 percent) and bioaccumulation factor (2.39 and 0.83) for Cd and Zn, respectively showing feasible uptake (in mg kg(-1) dry biomass) of Cd (5.55) and Zn (35.51) at the contaminated site. Thus, authors conclude to integrate oilcake manure, S(0) and microbial co-inoculation for enhanced clean-up of cadmium and zinc-contaminated soils. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

    Science.gov (United States)

    Bowsher, Clive G

    2011-02-15

    Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

  17. The Comparative Analysis of Biochemical Parameters in Patients with Pleural Effusions: A Prospective Study

    Directory of Open Access Journals (Sweden)

    Ali Kutluk

    2016-09-01

    Full Text Available Aim: The differentiation of exudative from transudative effusion is important to lead the clinician in making further biochemical analysis for possible etiology and in choosing the appropriate treatment strategy. The aim of the study is to evaluate the diagnostic value of biochemical parameters together with Light%u2019s criteria to differentiate exudative from transudative effusions. Material and Method: The LDH, total protein, albumin, adenosine deaminase (ADA, apolipoprotein A1, apolipoprotein B, Lipoprotein-A, total cholesterol, HDL-cholesterol, VLDL-cholesterol, LDL-cholesterol, and triglyceride levels of patients with unknown etiology were measured both in plasma and pleural fluid. Mann-Whitney U was used to compare the groups and p < 0.05 was accepted as statistical significance. Sensitivity, specificity, and accuracy were calculated for each biochemical parameter. The ROC analysis was used to estimate the optimum cut-off value for the highest sensitivity and specificity.Results: Pleural LDH (p=0.001, total protein (p=0.001, albumin (p=0.001, triglyceride (p=0.001, total cholesterol (p=0.001, HDL-cholesterol (p=0.042, VLDL-cholesterol (p=0.001, LDL-cholesterol (p=0.001, apolipoprotein A1 (p=0.021, and HDL-cholesterol/LDL-cholesterol ratio (p=0.048 were found significant in differentiating exudative from transudative effusions. Discussion: The study showed that the use of pleural LDH, total cholesterol, and HDL-cholesterol levels together is more significant than Light%u2019s criteria. The sensitivity, specificity, and accuracy of this test were 99%, 94.1%, and 96.2% respectively.

  18. Comparative study of human blood Raman spectra and biochemical analysis of patients with cancer

    Science.gov (United States)

    Shamina, Lyudmila A.; Bratchenko, Ivan A.; Artemyev, Dmitry N.; Myakinin, Oleg O.; Moryatov, Alexander A.; Orlov, Andrey E.; Kozlov, Sergey V.; Zakharov, Valery P.

    2018-04-01

    In this study we measured spectral features of blood by Raman spectroscopy. Correlation of the obtained spectral data and biochemical studies results is investigated. Analysis of specific spectra allows for identification of informative spectral bands proportional to components whose content is associated with body fluids homeostasis changes at various pathological conditions. Regression analysis of the obtained spectral data allows for discriminating the lung cancer from other tumors with a posteriori probability of 88.3%. The potentiality of applying surface-enhanced Raman spectroscopy with utilized experimental setup for further studies of the body fluids component composition was estimated. The greatest signal amplification was achieved for the gold substrate with a surface roughness of 1 μm. In general, the developed approach of body fluids analysis provides the basis of a useful and minimally invasive method of pathologies screening.

  19. A moment-convergence method for stochastic analysis of biochemical reaction networks.

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  20. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jiajun [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Nie, Qing [Department of Mathematics, University of California at Irvine, Irvine, California 92697 (United States); Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Province Key Laboratory of Computational Science and School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  1. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  2. Cantilever-based bio-chemical sensor integrated in a microliquid handling system

    DEFF Research Database (Denmark)

    Thaysen, Jacob; Marie, Rodolphe; Boisen, Anja

    2001-01-01

    The cantilevers have integrated piezoresistive readout which, compared to optical readout, enables simple measurements on even non-transparent liquids, such as blood. First, we introduce a simple theory for using piezoresistive cantilevers as surface stress sensors. Then, the sensor fabrication...... based on conventional microfabrication is described and the sensor characterization is discussed. During the characterization we found a stress sensitivity of (ΔR/R)=4.6:10 -4 (N/m)-1 and a minimum detectable surface stress change of 2.6 mN/m. Aqua regia etch of gold on top of the cantilevers has been...... monitored, and immobilization of single-stranded thiol modified DNA-oligos has been detected by the sensor. Finally, it is demonstrated that it is possible to analyze two samples simultaneously by utilizing the laminar flow in the microliquid handling system....

  3. Analysis of postoperative biochemical values and clinical outcomes after adrenalectomy for primary aldosteronism.

    Science.gov (United States)

    Swearingen, Andrew J; Kahramangil, Bora; Monteiro, Rosebel; Krishnamurthy, Vikram; Jin, Judy; Shin, Joyce; Siperstein, Allan; Berber, Eren

    2018-04-01

    Primary aldosteronism causes hypertension and hypokalemia and is often surgically treatable. Diagnosis includes elevated plasma aldosterone, suppressed plasma renin activity, and elevated aldosterone renin ratio. Adrenalectomy improves hypertension and hypokalemia. Postoperative plasma aldosterone and plasma renin activity may be useful in documenting cure or failure. A retrospective analysis of patients who underwent adrenalectomy for primary aldosteronism from 2010 to 2016 was performed, analyzing preoperative and postoperative plasma aldosterone, plasma renin activity, hypertension, and hypokalemia. The utility of postoperative testing was assessed. Clinical cure was defined as improved hypertension control and resolution of potassium loss. Biochemical cure was defined as aldosterone renin ratio reduction to <23.6. Forty-four patients were included; 20 had plasma aldosterone and plasma renin activity checked on postoperative day 1. In the study, 40/44 (91%) were clinically cured. All clinical failures had of biochemical failure at follow-up. Postoperative day 1aldosterone renin ratio <23.6 had PPV of 95% for clinical cure. Cured patients had mean plasma aldosterone drop of 33.1 ng/dL on postoperative day 1; noncured patient experienced 3.9 ng/dL increase. A cutoff of plasma aldosterone decrease of 10 ng/dL had high positive predictive value for clinical cure. Changes in plasma aldosterone and plasma renin activity after adrenalectomy correlate with improved hypertension and hypokalemia. The biochemical impact of adrenalectomy manifests as early as postoperative day 1. We propose a plasma aldosterone decrease of 10 ng/dL as a criterion to predict clinical cure. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Principal component analysis of tomato genotypes based on some morphological and biochemical quality indicators

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2012-01-01

    Full Text Available This study investigates variability of tomato genotypes based on morphological and biochemical fruit traits. Experimental material is a part of tomato genetic collection from Institute of Filed and Vegetable Crops in Novi Sad, Serbia. Genotypes were analyzed for fruit mass, locule number, index of fruit shape, fruit colour, dry matter content, total sugars, total acidity, lycopene and vitamin C. Minimum, maximum and average values and main indicators of variability (CV and σ were calculated. Principal component analysis was performed to determinate variability source structure. Four principal components, which contribute 93.75% of the total variability, were selected for analysis. The first principal component is defined by vitamin C, locule number and index of fruit shape. The second component is determined by dry matter content, and total acidity, the third by lycopene, fruit mass and fruit colour. Total sugars had the greatest part in the fourth component.

  5. Ultrastructural and biochemical analysis of epidermal xanthophores and dermal chromatophores of the teleost Sparus aurata.

    Science.gov (United States)

    Ferrer, C; Solano, F; Zuasti, A

    1999-04-01

    We have studied the pigmentary system of the teleost Sparus aurata skin by electron microscopy and chromatographic analysis. Under electron microscopy, we found the dermis to contain the three major types of recognized chromatophores: melanophores, xanthophores and iridophores. Melanophores were more abundant in the dorsal region, whereas the iridophores were more abundant in the ventral region. The most important discovery was that of epidermal xanthophores. Epidermal xanthophores were the only chromatophores in the epidermis, something only found in S aurata and in a teleost species living in the Antartic sea. In contrast, the biochemical analysis did not establish any special characteristics: we found pteridine and flavin pigments located mostly in the pigmented dorsal region. Riboflavin and pterin were two of the most abundant coloured pigment types, but other colourless pigments such as xanthopterin and isoxanthopterin were also detected.

  6. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach

    Science.gov (United States)

    2006-02-01

    some variability between protein assay measurements. Using densitometric analysis after 1D-PAGE, microfiltration alone showed an 11 ( 5% sample reduction...KOPETSCH, O., WOSZCZYK, A., et al. (2003). Serum S-100B protein as a molecular marker in severe trau- matic brain injury. Restor . Neurol. Neurosci. 21...proteomics. Implications in the search for preventive initiatives to slow the clinical progression of Alzheimer’s disease dementia. Restor . Neurol. Neurosci

  7. Cluster analysis of the biochemical composition in 53 Sichuan EGCG3"Me tea resources

    Science.gov (United States)

    Li, J. H.; Chen, S. X.; Zhu, M. Z.; Meng, X. L.

    2017-09-01

    The EGCG3"Me contents in the young tea leaves of 102 tea resources in sichuan were analyzed accurately using HPLC-DAD. The results revealed that there was a wide variation in EGCG3"Me levels among different tea resources. The EGCG3"Me content in different tea resources was in a range from 0 to 11.04 mg/g, mean was 2.33 mg/g.53 tea resources contained EGCG3"Me, accounting for 51.96% of the total number of resources survey. Shucha5, Jinguanyin, Chengxi11, Fenghuang-dancong, Chongpi 71-1 were found to contain higher EGCG3"Me content (>10mg/g).Cluster analysis showed that: 53 Sichuan EGCG3"Me tea resources were divided into six groups and the difference was obvious between their biochemical composition; tea resources rich in EGCG3"Me were mainly distributed in Sichuan, Chongqing and Fujian Province, mostly were shrub and mid-leaf, mainly existed in tea resources which were suitable to make green tea, oolong tea. The morphological and biochemical distribution provided a good theoretical basis for selecting and utilizing higher EGCG3"Me resources.

  8. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  9. Integrative Workflows for Metagenomic Analysis

    Directory of Open Access Journals (Sweden)

    Efthymios eLadoukakis

    2014-11-01

    Full Text Available The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS, have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e. Sanger. From a bioinformatic perspective, this boils down to many gigabytes of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control and annotation of metagenomic data, embracing various, major sequencing technologies and applications.

  10. Fourier transform infrared microspectroscopy for the analysis of the biochemical composition of C. elegans worms.

    Science.gov (United States)

    Sheng, Ming; Gorzsás, András; Tuck, Simon

    2016-01-01

    Changes in intermediary metabolism have profound effects on many aspects of C. elegans biology including growth, development and behavior. However, many traditional biochemical techniques for analyzing chemical composition require relatively large amounts of starting material precluding the analysis of mutants that cannot be grown in large amounts as homozygotes. Here we describe a technique for detecting changes in the chemical compositions of C. elegans worms by Fourier transform infrared microspectroscopy. We demonstrate that the technique can be used to detect changes in the relative levels of carbohydrates, proteins and lipids in one and the same worm. We suggest that Fourier transform infrared microspectroscopy represents a useful addition to the arsenal of techniques for metabolic studies of C. elegans worms.

  11. Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals.

    Science.gov (United States)

    Su, Fei; Xu, Ping

    2014-01-29

    Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.

  12. Crystallographic and biochemical analysis of the mouse poly(ADP-ribose glycohydrolase.

    Directory of Open Access Journals (Sweden)

    Zhizhi Wang

    Full Text Available Protein poly(ADP-ribosylation (PARylation regulates a number of important cellular processes. Poly(ADP-ribose glycohydrolase (PARG is the primary enzyme responsible for hydrolyzing the poly(ADP-ribose (PAR polymer in vivo. Here we report crystal structures of the mouse PARG (mPARG catalytic domain, its complexes with ADP-ribose (ADPr and a PARG inhibitor ADP-HPD, as well as four PARG catalytic residues mutants. With these structures and biochemical analysis of 20 mPARG mutants, we provide a structural basis for understanding how the PAR polymer is recognized and hydrolyzed by mPARG. The structures and activity complementation experiment also suggest how the N-terminal flexible peptide preceding the PARG catalytic domain may regulate the enzymatic activity of PARG. This study contributes to our understanding of PARG catalytic and regulatory mechanisms as well as the rational design of PARG inhibitors.

  13. Integrated Radiation Analysis and Design Tools

    Data.gov (United States)

    National Aeronautics and Space Administration — The Integrated Radiation Analysis and Design Tools (IRADT) Project develops and maintains an integrated tool set that collects the current best practices, databases,...

  14. Analysis of gingival pocket microflora and biochemical blood parameters in dogs suffering from periodontal disease.

    Science.gov (United States)

    Polkowska, Izabela; Sobczyńska-Rak, Aleksandra; Gołyńska, Magdalena

    2014-01-01

    Periodontal diseases in dogs are caused by bacteria colonising the oral cavity. The presence of plaque comprising accumulations of aerobic and anaerobic bacteria leads to the development of periodontitis. Due to the fact that in a large percentage of cases periodontal diseases remain undiagnosed, and consequently untreated, they tend to acquire a chronic character, lead to bacteraemia and negatively impact the health of internal organs. The aim of the present study was to perform a qualitative microbiological analysis of gingival pockets and determine the correlations between selected morphological and biochemical blood parameters and the extent periodontal diseases. Twenty-one dogs treated for periodontal diseases were qualified for the study and subsequently divided into two groups: with 3rd and 4th stage of periodontal disease. Swabs from the patients' gingival pockets were taken for bacteriological testing. Blood was tested for parameters including erythrocyte count, haemoglobin concentration, haematocrit values and leukocyte count. Blood serum was analyzed with respect to the concentrations of alanine transaminase (ALT), aspartate transaminase (AspAT/AST) and urea. The microbiological analysis of gingival pockets indicated the presence of numerous pathogens with a growth tendency in bacterial cultures observed in dogs with advanced-stage periodontal disease. The concentration of biochemical blood markers was significantly higher in dogs with 4th stage of periodontal disease, to compared to the 3rd-stage group. Morphological parameters were not significantly different with the exception of haemoglobin concentration, which was lower in dogs with 4th stage disease. In both groups, elevated leukocyte counts were observed. By conducting a detailed microbiological examination, it is possible to provide a better prognosis, plan adequate treatment and monitor dogs treated for peridontopathy. Copyright © 2014 International Institute of Anticancer Research (Dr. John G

  15. Improvement in shelf life of minimally processed cilantro leaves through integration of kinetin pretreatment and packaging interventions: Studies on microbial population dynamics, biochemical characteristics and flavour retention.

    Science.gov (United States)

    Ranjitha, K; Shivashankara, K S; Sudhakar Rao, D V; Oberoi, Harinder Singh; Roy, T K; Bharathamma, H

    2017-04-15

    Effect of integrating optimized combination of pretreatment with packaging on shelf life of minimally processed cilantro leaves (MPCL) was appraised through analysis of their sensory attributes, biochemical characteristics, microbial population and flavour profile during storage. Minimally pretreated cilantro leaves pretreated with 50ppm kinetin and packed in 25μ polypropylene bags showed a shelf life of 21days. Optimized combination helped in efficiently maintaining sensory parameters, flavour profile, and retention of antioxidants in MPCL until 21days. Studies conducted on the effect of optimized combination on microbial population and flavour profile revealed that among different microorganisms, pectinolysers had a significant effect on spoilage of MPCL and their population of ⩽3.59logcfu/g was found to be acceptable. Principal component analysis of headspace volatiles revealed that (E)-2-undecenal, (E)-2-hexadecenal, (E)-2-tetradecenal & (E)-2-tetradecen-1-ol in stored samples clustered with fresh samples and therefore, could be considered as freshness indicators for MPCL. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

    Science.gov (United States)

    Pantazis, Yannis; Katsoulakis, Markos A; Vlachos, Dionisios G

    2013-10-22

    Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data. In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, existing sensitivity analysis approaches such as variants of the finite difference method can have an overwhelming computational cost in models with a high-dimensional parameter space. We develop a sensitivity analysis methodology suitable for complex stochastic reaction networks with a large number of parameters. The proposed approach is based on Information Theory methods and relies on the quantification of information loss due to parameter perturbations between time-series distributions. For this reason, we need to work on path-space, i.e., the set consisting of all stochastic trajectories, hence the proposed approach is referred to as "pathwise". The pathwise sensitivity analysis method is realized by employing the rigorously-derived Relative Entropy Rate, which is directly computable from the propensity functions. A key aspect of the method is that an associated pathwise Fisher Information Matrix (FIM) is defined, which in turn constitutes a gradient-free approach to quantifying parameter sensitivities. The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks. As a gradient-free method, the proposed sensitivity analysis provides a significant advantage when dealing with complex stochastic systems with a large number of parameters. In addition, the knowledge of the structure of the FIM can allow to efficiently address

  17. Integrated minicomputer alpha analysis system

    International Nuclear Information System (INIS)

    Vasilik, D.G.; Coy, D.E.; Seamons, M.; Henderson, R.W.; Romero, L.L.; Thomson, D.A.

    1978-01-01

    Approximately 1,000 stack and occupation air samples from plutonium and uranium facilities at LASL are analyzed daily. The concentrations of radio-nuclides in air are determined by measuring absolute alpha activities of particulates collected on air sample filter media. The Integrated Minicomputer Pulse system (IMPULSE) is an interface between many detectors of extremely simple design and a Digital Equipment Corporation (DEC) PDP-11/04 minicomputer. The detectors are photomultiplier tubes faced with zinc sulfide (ZnS). The average detector background is approximately 0.07 cpm. The IMPULSE system includes two mainframes, each of which can hold up to 64 detectors. The current hardware configuration includes 64 detectors in one mainframe and 40 detectors in the other. Each mainframe contains a minicomputer with 28K words of Random Access Memory. One minicomputer controls the detectors in both mainframes. A second computer was added for fail-safe redundancy and to support other laboratory computer requirements. The main minicomputer includes a dual floppy disk system and a dual DEC 'RK05' disk system for mass storage. The RK05 facilitates report generation and trend analysis. The IMPULSE hardware provides for passage of data from the detectors to the computer, and for passage of status and control information from the computer to the detector stations

  18. A new family of phosphoinositide phosphatases in microorganisms: identification and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Bennett Hayley J

    2010-08-01

    Full Text Available Abstract Background Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virulence of many human pathogens, allowing them to survive and replicate in the host cells. Phosphoinositide phosphatases from bacterial pathogens are therefore key players in this modulation and constitute attractive targets for chemotherapy. MptpB, a virulence factor from Mycobacterium tuberculosis, has phosphoinositide phosphatase activity and a distinct active site P-loop signature HCXXGKDR that shares characteristics with eukaryotic lipid phosphatases and protein tyrosine phosphatases. We used this P-loop signature as a "diagnostic motif" to identify related putative phosphatases with phosphoinositide activity in other organisms. Results We found more than 200 uncharacterised putative phosphatase sequences with the conserved signature in bacteria, with some related examples in fungi and protozoa. Many of the sequences identified belong to recognised human pathogens. Interestingly, no homologues were found in any other organisms including Archaea, plants, or animals. Phylogenetic analysis revealed that these proteins are unrelated to classic eukaryotic lipid phosphatases. However, biochemical characterisation of those from Listeria monocytogenes and Leishmania major, demonstrated that, like MptpB, they have phosphatase activity towards phosphoinositides. Mutagenesis studies established that the conserved Asp and Lys in the P-loop signature (HCXXGKDR are important in catalysis and substrate binding respectively. Furthermore, we provide experimental evidence that the number of basic residues in the P-loop is critical in determining activity towards poly-phosphoinositides. Conclusion This new family of enzymes in microorganisms shows distinct sequence and biochemical characteristics to classic eukaryotic lipid phosphatases

  19. A new family of phosphoinositide phosphatases in microorganisms: identification and biochemical analysis.

    Science.gov (United States)

    Beresford, Nicola J; Saville, Charis; Bennett, Hayley J; Roberts, Ian S; Tabernero, Lydia

    2010-08-02

    Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virulence of many human pathogens, allowing them to survive and replicate in the host cells. Phosphoinositide phosphatases from bacterial pathogens are therefore key players in this modulation and constitute attractive targets for chemotherapy. MptpB, a virulence factor from Mycobacterium tuberculosis, has phosphoinositide phosphatase activity and a distinct active site P-loop signature HCXXGKDR that shares characteristics with eukaryotic lipid phosphatases and protein tyrosine phosphatases. We used this P-loop signature as a "diagnostic motif" to identify related putative phosphatases with phosphoinositide activity in other organisms. We found more than 200 uncharacterised putative phosphatase sequences with the conserved signature in bacteria, with some related examples in fungi and protozoa. Many of the sequences identified belong to recognised human pathogens. Interestingly, no homologues were found in any other organisms including Archaea, plants, or animals. Phylogenetic analysis revealed that these proteins are unrelated to classic eukaryotic lipid phosphatases. However, biochemical characterisation of those from Listeria monocytogenes and Leishmania major, demonstrated that, like MptpB, they have phosphatase activity towards phosphoinositides. Mutagenesis studies established that the conserved Asp and Lys in the P-loop signature (HCXXGKDR) are important in catalysis and substrate binding respectively. Furthermore, we provide experimental evidence that the number of basic residues in the P-loop is critical in determining activity towards poly-phosphoinositides. This new family of enzymes in microorganisms shows distinct sequence and biochemical characteristics to classic eukaryotic lipid phosphatases and they have no homologues in humans. This study provides

  20. A system dynamics model integrating physiology and biochemical regulation predicts extent of crassulacean acid metabolism (CAM) phases.

    Science.gov (United States)

    Owen, Nick A; Griffiths, Howard

    2013-12-01

    A system dynamics (SD) approach was taken to model crassulacean acid metabolism (CAM) expression from measured biochemical and physiological constants. SD emphasizes state-dependent feedback interaction to describe the emergent properties of a complex system. These mechanisms maintain biological systems with homeostatic limits on a temporal basis. Previous empirical studies on CAM have correlated biological constants (e.g. enzyme kinetic parameters) with expression over the CAM diel cycle. The SD model integrates these constants within the architecture of the CAM 'system'. This allowed quantitative causal connections to be established between biological inputs and the four distinct phases of CAM delineated by gas exchange and malic acid accumulation traits. Regulation at flow junctions (e.g. stomatal and mesophyll conductance, and malic acid transport across the tonoplast) that are subject to feedback control (e.g. stomatal aperture, malic acid inhibition of phosphoenolpyruvate carboxylase, and enzyme kinetics) was simulated. Simulated expression for the leaf-succulent Kalanchoë daigremontiana and more succulent tissues of Agave tequilana showed strong correlation with measured gas exchange and malic acid accumulation (R(2)  = 0.912 and 0.937, respectively, for K. daigremontiana and R(2)  = 0.928 and 0.942, respectively, for A. tequilana). Sensitivity analyses were conducted to quantitatively identify determinants of diel CO2 uptake. The transition in CAM expression from low to high volume/area tissues (elimination of phase II-IV carbon-uptake signatures) was achieved largely by the manipulation three input parameters. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  1. Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in flavonoid biosynthetic pathway.

    Directory of Open Access Journals (Sweden)

    Wei Sun

    Full Text Available Chalcone synthase (CHS catalyzes the first committed step in the flavonoid biosynthetic pathway. In this study, the cDNA (FhCHS1 encoding CHS from Freesia hybrida was successfully isolated and analyzed. Multiple sequence alignments showed that both the conserved CHS active site residues and CHS signature sequence were found in the deduced amino acid sequence of FhCHS1. Meanwhile, crystallographic analysis revealed that protein structure of FhCHS1 is highly similar to that of alfalfa CHS2, and the biochemical analysis results indicated that it has an enzymatic role in naringenin biosynthesis. Moreover, quantitative real-time PCR was performed to detect the transcript levels of FhCHS1 in flowers and different tissues, and patterns of FhCHS1 expression in flowers showed significant correlation to the accumulation patterns of anthocyanin during flower development. To further characterize the functionality of FhCHS1, its ectopic expression in Arabidopsis thaliana tt4 mutants and Petunia hybrida was performed. The results showed that overexpression of FhCHS1 in tt4 mutants fully restored the pigmentation phenotype of the seed coats, cotyledons and hypocotyls, while transgenic petunia expressing FhCHS1 showed flower color alteration from white to pink. In summary, these results suggest that FhCHS1 plays an essential role in the biosynthesis of flavonoid in Freesia hybrida and may be used to modify the components of flavonoids in other plants.

  2. Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe

    NARCIS (Netherlands)

    Slawiak, M.; Beckhoven, van J.R.C.M.; Speksnijder, A.G.C.L.; Czajkowski, R.L.; Grabe, G.; Wolf, van der J.M.

    2009-01-01

    Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing

  3. Molecular Analysis, Biochemical Characterization, Antimicrobial Activity, and Immunological Analysis of Proteus mirabilis Isolated from Broilers.

    Science.gov (United States)

    Yeh, Hung-Yueh; Line, John E; Hinton, Arthur

    2018-03-01

    Proteus mirabilis, a Gram-negative bacterium, is ubiquitous in the environment and is considered as the normal microflora in the human gastrointestinal tract. However, this bacterium is an opportunistic pathogen in humans, often causing urinary tract infections. Moreover, Proteus has been frequently isolated from food animals, including poultry. Whether this bacterium contributes to the foodborne illness in humans is unclear. In this report, P. mirabilis isolates recovered from broilers during housing in the units were characterized, their antimicrobial activity was assayed, and broiler immune response to the soluble proteins was determined. Cecal contents and fecal droppings were treated according to the standard protocol for isolation. Speciation based on biochemical reactions and the antimicrobial activity of the isolates were carried out using commercial kits. Immunoblot was assayed to determine immune status of broilers against P. mirabilis. A total of 10 isolates of P. mirabilis were selected for further characterization. These isolates could grow in pH 6.0 and 1% NaCl conditions. They were resistant to sodium lactate, troleandomycin, rifamycin SV, vancomycin, but sensitive to nalidixic acid, cefotaxime and novobiocin. Moreover, the CTX, ACC, CMY-1, BIC, NDM, VEB, qnrB and qnrD genes were detected by PCR amplification in all isolates. Sera from broilers harboring this bacterium reacted to the P. mirabilis soluble proteins, but not from litter- and age-matched P. mirabilis negative and SPF chickens, indicating that this bacterium infected chickens that could have humoral immune response against P. mirabilis. This study provides a rationale for further monitoring P. mirabilis during poultry production to determine whether this bacterium poses potential threats to public health. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

  4. Assessing earthworm and sewage sludge impacts on microbiological and biochemical soil quality using multivariate analysis

    Directory of Open Access Journals (Sweden)

    Hanye Jafari Vafa

    2017-06-01

    Full Text Available Introduction: Land application of organic wastes and biosolids such as municipal sewage sludge has been an important and attractive practice for improving different properties of agricultural soils with low organic matter content in semi-arid regions, due to an increase of soil organic matter level and fertility. However, application of this organic waste may directly or indirectly affect soil bio-indicators such as microbial and enzymatic activities through a change in the activity of other soil organisms such as earthworms. Earthworms are the most important soil saprophagous fauna and much of the faunal biomass is attributed to the presence of these organisms in the soil. Therefore, it is crucial to evaluate the effect of earthworm activity on soil microbial and biochemical attributes, in particularly when soils are amended with urban sewage sludge. The purpose of this study was to evaluate the earthworm effects on biochemical and microbiological properties of a calcareous soil amended with municipal sewage sludge using Factor Analysis (FA. Materials and Methods: In the present study, the experimental treatments were sewage sludge (without and with 1.5% sewage sludge as the first factor and earthworm (no earthworm, Eiseniafoetida from epigeic group, Allolobophracaliginosa from endogeic group and a mixture of the two species as the second factor. The study was setup as 2×4 full factorial experiment arranged in a completely randomized design with three replications for each treatment under greenhouse conditions over 90 days. A calcareous soil from the 0-30 cm layer with clay loam texture was obtained from a farmland field under fallow without cultivation history for ten years. The soil was air-dried and passed through a 2-mm sieve for the experiment. Sewage sludge as the soil organic amendment was collected from Wastewater Treatment Plant in Shahrekord. Sewage sludge was air-dried and grounded to pass through a 1-mm sieve for a uniform mixture

  5. Problems in mathematical analysis III integration

    CERN Document Server

    Kaczor, W J

    2003-01-01

    We learn by doing. We learn mathematics by doing problems. This is the third volume of Problems in Mathematical Analysis. The topic here is integration for real functions of one real variable. The first chapter is devoted to the Riemann and the Riemann-Stieltjes integrals. Chapter 2 deals with Lebesgue measure and integration. The authors include some famous, and some not so famous, integral inequalities related to Riemann integration. Many of the problems for Lebesgue integration concern convergence theorems and the interchange of limits and integrals. The book closes with a section on Fourier series, with a concentration on Fourier coefficients of functions from particular classes and on basic theorems for convergence of Fourier series. The book is primarily geared toward students in analysis, as a study aid, for problem-solving seminars, or for tutorials. It is also an excellent resource for instructors who wish to incorporate problems into their lectures. Solutions for the problems are provided in the boo...

  6. Synthesis of Biochemical Applications on Flow-Based Microfluidic Biochips using Constraint Programming

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2012-01-01

    Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. In this paper we are interested in flow-based biochips, in which the flow of liquid is manipulated using integrated microvalves. By combin...

  7. Biochemical and genetic analysis of the Drk SH2/SH3 adaptor protein of Drosophila.

    Science.gov (United States)

    Raabe, T; Olivier, J P; Dickson, B; Liu, X; Gish, G D; Pawson, T; Hafen, E

    1995-06-01

    The Drk SH3-SH2-SH3 adaptor protein has been genetically identified in a screen for rate-limiting components acting downstream of the Sevenless (Sev) receptor tyrosine kinase in the developing eye of Drosophila. It provides a link between the activated Sev receptor and Sos, a guanine nucleotide release factor that activates Ras1. We have used a combined biochemical and genetic approach to study the interactions between Sev, Drk and Sos. We show that Tyr2546 in the cytoplasmic tail of Sev is required for Drk binding, probably because it provides a recognition site for the Drk SH2 domain. Interestingly, a mutation at this site does not completely block Sev function in vivo. This may suggest that Sev can signal in a Drk-independent, parallel pathway or that Drk can also bind to an intermediate docking protein. Analysis of the Drk-Sos interaction has identified a high affinity binding site for Drk SH3 domains in the Sos tail. We show that the N-terminal Drk SH3 domain is primarily responsible for binding to the tail of Sos in vitro, and for signalling to Ras in vivo.

  8. Biochemical and Molecular Analysis of the Hb Lepore Boston Washington in a Syrian Homozygous Child

    Directory of Open Access Journals (Sweden)

    Monica Pirastru

    2017-01-01

    Full Text Available Hemoglobin (Hb Lepore is composed of two normal α chains and two δβ fusion globins that arise from unequal crossover events between the δ- and β-globin genes. The Hb Lepore is widespread all over the world and in many ethnic groups. It includes some of the few clinically significant Hb variants that are associated with a β-thalassemia phenotype. Here, we describe the first occurrence of Hb Lepore Boston Washington in a Syrian individual. The patient, a 10-year-old child, shows severe anemia with a Hb level of 6.85 g/dL and typical thalassemic red cell indices. The diagnostic procedure implies hematological, biochemical, and molecular analysis, including multiplex ligation-dependent probe amplification (MLPA assay, GAP-PCR, and DNA sequencing. This latter allowed us to define the correct structure of the hybrid δβ-globin gene. The knowledge of the spectrum of mutations associated with different geographical areas is the prerequisite to set up large-scale screening programs and be able to offer genetic counseling to couples at risk.

  9. Seed Biochemical Analysis Based Profiling of Diverse Wheat Genetic Resource from Pakistan

    Science.gov (United States)

    Khalid, Anam; Hameed, Amjad

    2017-01-01

    Wheat is the major nutrient source worldwide. In Pakistan, it has a crucial place in agriculture as well as in national economy. For seed biochemical compositional analysis, wheat germplasm (77 genotypes) was collected from different agro-climatic zones of Pakistan. Significant variation (p sugar was found in Saleem-2000 (29.86 mg/g s. wt.), reducing sugars in Punjab-96 (12.68 mg/g s. wt.), non-reducing sugars in Saleem-2000 (27.33 mg/g s. wt.). However, highest albumins was identified in TC-4928 (352.89 mg/g s. wt.) and globulins in MEXI PAK (252.67 mg/g s. wt.), salt soluble proteins in Faisalabad-2008 (162.44 mg/g s. wt.), and total soluble proteins in Punjab-96 (487.33 mg/g s. wt.) indicating good quality of wheat genotypes as well as good nutritional status. Genotypes which have been ranked high in respective parameter can be employed in breeding to enhance the nutritional quality of wheat. PMID:28775731

  10. Biochemical analysis of the Hormoconis resinae fungal mycelium in the corrosion of aeronautical aluminium alloys

    International Nuclear Information System (INIS)

    Araya, R.; Bobadilla, C.; Vera, R.; Rosales, B. M.

    2007-01-01

    Biochemical analyses of the Hormoconis resinae fungal mycelium would explain behaviour differences of corrosive and non-corrosive strains of Al and its aeronautical alloys. In previous works its aggressiveness had been studied through SEM-EDX surface analysis, electrochemical techniques and immersion testing. In this paper separation of the proteins of the mycelium produced by a non-corrosive strain and its culture along three generations was performed. cultures were prepared in batch in the presence and absence of pure Al and AA 2024, AA 7005 and AA 7075 alloys. The mycelia grown throughout the three generations increasingly recovered usual characteristics at the third replication, included their corrosiveness on Al and its alloys previously shown by all out strains. Among the bio-molecule fractions isolated and analysed during this preliminary study only the proteins revealed changes with the generation grown. When this fungal strain was cultured in the presence of alloy metal sheets electrophoresis of the protean fraction was correlative with the distinct mycelia behaviour observed, including corrosiveness on Al and its alloys. (Author) 30 refs

  11. The Vehicle Integrated Performance Analysis Experience: Reconnecting With Technical Integration

    Science.gov (United States)

    McGhee, D. S.

    2006-01-01

    Very early in the Space Launch Initiative program, a small team of engineers at MSFC proposed a process for performing system-level assessments of a launch vehicle. Aimed primarily at providing insight and making NASA a smart buyer, the Vehicle Integrated Performance Analysis (VIPA) team was created. The difference between the VIPA effort and previous integration attempts is that VIPA a process using experienced people from various disciplines, which focuses them on a technically integrated assessment. The foundations of VIPA s process are described. The VIPA team also recognized the need to target early detailed analysis toward identifying significant systems issues. This process is driven by the T-model for technical integration. VIPA s approach to performing system-level technical integration is discussed in detail. The VIPA process significantly enhances the development and monitoring of realizable project requirements. VIPA s assessment validates the concept s stated performance, identifies significant issues either with the concept or the requirements, and then reintegrates these issues to determine impacts. This process is discussed along with a description of how it may be integrated into a program s insight and review process. The VIPA process has gained favor with both engineering and project organizations for being responsive and insightful

  12. Integrated logistic support analysis system

    International Nuclear Information System (INIS)

    Carnicero Iniguez, E.J.; Garcia de la Sen, R.

    1993-01-01

    Integrating logic support into a system results in a large volume of information having to be managed which can only be achieved with the help of computer applications. Both past experience and growing needs in such tasks have led Emperesarios Agrupados to undertake an ambitious development project which is described in this paper. (author)

  13. Analysis of integrated energy systems

    International Nuclear Information System (INIS)

    Matsuhashi, Takaharu; Kaya, Yoichi; Komiyama, Hiroshi; Hayashi, Taketo; Yasukawa, Shigeru.

    1988-01-01

    World attention is now attracted to the concept of Novel Horizontally Integrated Energy System (NHIES). In NHIES, all fossil fuels are fist converted into CO and H 2 . Potential environmental contaminants such as sulfur are removed during this process. CO turbines are mainly used to generate electric power. Combustion is performed in pure oxygen produced through air separation, making it possible to completely prevent the formation of thermal NOx. Thus, NHIES would release very little amount of such substances that would contribute to acid rain. In this system, the intermediate energy sources of CO, H 2 and O 2 are integrated horizontally. They are combined appropriately to produce a specific form of final energy source. The integration of intermediate energy sources can provide a wide variety of final energy sources, allowing any type of fossil fuel to serve as an alternative to other types of fossil fuel. Another feature of NHIES is the positive use of nuclear fuel to reduce the formation of CO 2 . Studies are under way in Japan to develop a new concept of integrated energy system. These studies are especially aimed at decreased overall efficiency and introduction of new liquid fuels that are high in conversion efficiency. Considerations are made on the final form of energy source, robust control, acid fallout, and CO 2 reduction. (Nogami, K.)

  14. Integrative Analysis of Omics Big Data.

    Science.gov (United States)

    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.

  15. Time from first detectable PSA following radical prostatectomy to biochemical recurrence: A competing risk analysis

    Science.gov (United States)

    de Boo, Leonora; Pintilie, Melania; Yip, Paul; Baniel, Jack; Fleshner, Neil; Margel, David

    2015-01-01

    Introduction: In this study, we estimated the time from first detectable prostate-specific antigen (PSA) following radical prostatectomy (RP) to commonly used definitions of biochemical recurrence (BCR). We also identified the predictors of time to BCR. Methods: We identified subjects who underwent a RP and had an undetectable PSA after surgery followed by at least 1 detectable PSA between 2000 and 2011. The primary outcome was time to BCR (PSA ≥0.2 and successive PSA ≥0.2) and prediction of the rate of PSA rise. Outcomes were calculated using a competing risk analysis, with univariable and multivariable Fine and Grey models. We employed a mixed effect model to test clinical predictors that are associated with the rate of PSA rise. Results: The cohort included 376 patients. The median follow-up from surgery was 60.5 months (interquartile range [IQR] 40.8–91.5) and from detectable PSA was 18 months (IQR 11–32). Only 45.74% (n = 172) had PSA values ≥0.2 ng/mL, while 15.16% (n = 57) reached the PSA level of ≥0.4 ng/mL and rising. On multivariable analysis, the values of the first detectable PSA and pathologic Gleason grade 8 or higher were consistently independent predictors of time to BCR. In the mixed effect model rate, the PSA rise was associated with time from surgery to first detectable PSA, Gleason score, and prostate volume. The main limitation of this study is the large proportion of patients that received treatment without reaching BCR. It is plausible that shorter estimated median times would occur at a centre that does not use salvage therapy at such an early state. Conclusion: The time from first detectable PSA to BCR may be lengthy. Our analyses of the predictors of the rate of PSA rise can help determine a personalized approach for patients with a detectable PSA after surgery. PMID:25624961

  16. Containment integrity analysis under accidents

    International Nuclear Information System (INIS)

    Lin Chengge; Zhao Ruichang; Liu Zhitao

    2010-01-01

    Containment integrity analyses for current nuclear power plants (NPPs) mainly focus on the internal pressure caused by design basis accidents (DBAs). In addition to the analyses of containment pressure response caused by DBAs, the behavior of containment during severe accidents (SAs) are also evaluated for AP1000 NPP. Since the conservatism remains in the assumptions,boundary conditions and codes, margin of the results of containment integrity analyses may be overestimated. Along with the improvements of the knowledge to the phenomena and process of relevant accidents, the margin overrated can be appropriately reduced by using the best estimate codes combined with the uncertainty methods, which could be beneficial to the containment design and construction of large passive plants (LPP) in China. (authors)

  17. Integrative biological analysis for neuropsychopharmacology.

    Science.gov (United States)

    Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

    2014-01-01

    Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

  18. Integrating reliability analysis and design

    International Nuclear Information System (INIS)

    Rasmuson, D.M.

    1980-10-01

    This report describes the Interactive Reliability Analysis Project and demonstrates the advantages of using computer-aided design systems (CADS) in reliability analysis. Common cause failure problems require presentations of systems, analysis of fault trees, and evaluation of solutions to these. Results have to be communicated between the reliability analyst and the system designer. Using a computer-aided design system saves time and money in the analysis of design. Computer-aided design systems lend themselves to cable routing, valve and switch lists, pipe routing, and other component studies. At EG and G Idaho, Inc., the Applicon CADS is being applied to the study of water reactor safety systems

  19. Ixodes ricinus tick lipocalins: identification, cloning, phylogenetic analysis and biochemical characterization.

    Directory of Open Access Journals (Sweden)

    Jérôme Beaufays

    Full Text Available BACKGROUND: During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. METHODOLOGY/PRINCIPAL FINDINGS: Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for "Lipocalin from I. ricinus" and numbered from 1 to 14 (LIR1 to LIR14. According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50-70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. CONCLUSIONS/SIGNIFICANCE: This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C

  20. Diagnosing and quantification of acute alcohol intoxication. Comparison of dual-energy CT with biochemical analysis. Initial experience

    International Nuclear Information System (INIS)

    Korkusuz, H.; Abbas Raschidi, B.; Keese, D.; Kromen, W.; Bauer, R.W.; Vogl, T.J.; Namgaladze, D.

    2012-01-01

    Purpose: To quantify the correlation between fat content of an acute alcohol intoxication and the difference of computer tomography attenuation value in dual-energy CT in comparison to biochemical triglyceride analysis and to evaluate qualitatively the value of DECT in the diagnosis of fatty liver caused by ethanol-dosage in rats. Materials and Methods: DECT at 140 kV and 80 kV was performed on 20 rats before and two days after the administration of 3 ml of 50 % ethanol. The CT attenuation value in the livers at 140 kV, 80 kV and the differences between them in Hounsfield units (ΔH) were collected. Parts of the liver (100 mg) were measured in biochemical triglyceride analysis as the reference standard. A blood sample was also taken to measure specific liver enzymes. Results: Linear correlation between biochemical triglyceride analysis and CT density of ΔH was found (r = 0.949). 140 kV attenuation data were between 44 HU and 61.3 HU, 80 kV attenuation data were between 58.4 HU and 64.7 HU, and ΔH data were between 3.4 HU and 14.4 HU (p ≤ 0.037). The biochemical triglyceride analysis data were between 7.1 mg/g and 41.1 mg/g. The hepatic enzymes serum aspartate (ASAT) aminotransferase and alanine aminotransferase (ALAT) were elevated in all rats. ASAT correlated directly with ΔHU (r = -0.86). Conclusion: DECT provides a non-invasive method to determine and evaluate hepatic fat content after acute alcohol intoxication. It provides the possibility to detect and quantify the hepatic fat content of liver graft. (orig.)

  1. Integrative cluster analysis in bioinformatics

    CERN Document Server

    Abu-Jamous, Basel; Nandi, Asoke K

    2015-01-01

    Clustering techniques are increasingly being put to use in the analysis of high-throughput biological datasets. Novel computational techniques to analyse high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. This book details the complete pathway of cluster analysis, from the basics of molecular biology to the generation of biological knowledge. The book also presents the latest clustering methods and clustering validation, thereby offering the reader a comprehensive review o

  2. [Correlation analysis between biochemical and biophysical markers of endothelium damage in children with diabetes type 1].

    Science.gov (United States)

    Głowińska-Olszewska, Barbara; Urban, Mirosława; Tołwińska, Joanna; Peczyńska, Jadwiga; Florys, Bozena

    2005-01-01

    Endothelial damage is one of the earliest stages in the atherosclerosis process. Adhesion molecules, secreted from dysfunctional endothelial cells are considered as early markers of atherosclerotic disease. Ultrasonographic evaluation of brachial arteries serves to detect biophysical changes in endothelial function, and evaluation of carotid arteries intima-media thickness allows to evaluate the earliest structural changes in the vessels. The aim of the study was to the evaluate levels of selected adhesion molecules (sICAM-1, sVCAM-1, sE-selectin, sP-selectin) and endothelial function with use of brachial artery dilatation study (flow mediated dilation--FMD, nitroglycerine mediated dilation--NTGMD) and IMT in carotid arteries in children and adolescents with diabetes type 1, as well as the correlation analysis between biochemical and biophysical markers of endothelial dysfunction. We studied 76 children and adolescents, with mean age--15.6+/-2.5 years, suffering from diabetes mean 7.8+/-2.8 years, mean HbA1c--8.4+/-1.5%. Control group consisted of 33 healthy children age and gender matched. Adhesion molecules levels were estimated with the use of immunoenzymatic methods (R&D Systems). Endothelial function was evaluated by study of brachial arteries dilation--FMD, NTGMD, with ultrasonographic evaluation (Hewlett Packard Sonos 4500) after Celermajer method, and IMT after Pignoli method. In the study group we found elevated levels of sICAM-1: 309.54+/-64 vs. 277.85+/-52 ng/ml in the control group (p<00.05) and elevated level of sE-selectin: 87.81+/-35 vs. 66.21+/-22 ng/ml (p<00.05). We found significantly impaired FMD in brachial arteries in the study group--7.51+/-4.52 vs. 12.61+/-4.65% (p<00.05) and significantly higher IMT value: 0.51+/-0.07 vs. 0.42+/-0.05 mm (p<00.001). Correlation analysis revealed a significant negative correlation between sE-selectin and FMD - r=-0.33 (p=0.004), and a positive correlation between E-selectin and IMT: r=0.32 (p=0.005). 1. In

  3. Integral data analysis for resonance parameters determination

    International Nuclear Information System (INIS)

    Larson, N.M.; Leal, L.C.; Derrien, H.

    1997-09-01

    Neutron time-of-flight experiments have long been used to determine resonance parameters. Those resonance parameters have then been used in calculations of integral quantities such as Maxwellian averages or resonance integrals, and results of those calculations in turn have been used as a criterion for acceptability of the resonance analysis. However, the calculations were inadequate because covariances on the parameter values were not included in the calculations. In this report an effort to correct for that deficiency is documented: (1) the R-matrix analysis code SAMMY has been modified to include integral quantities of importance, (2) directly within the resonance parameter analysis, and (3) to determine the best fit to both differential (microscopic) and integral (macroscopic) data simultaneously. This modification was implemented because it is expected to have an impact on the intermediate-energy range that is important for criticality safety applications

  4. Time from first detectable PSA following radical prostatectomy to biochemical recurrence: A competing risk analysis

    NARCIS (Netherlands)

    L. De Boo (Leonora); M. Pintilie (Melania); P. Yip (Paul); J. Baniel (Jack); N.E. Fleshner (Neil); D. Margel (David)

    2015-01-01

    textabstractIntroduction: In this study, we estimated the time from first detectable prostate-specific antigen (PSA) following radical prostatectomy (RP) to commonly used definitions of biochemical recurrence (BCR). We also identified the predictors of time to BCR. Methods: We identified subjects

  5. MINERAL AND BIOCHEMICAL ANALYSIS OF VARIOUS PARTS OF CISSUS QUADRANGULARIS LINN

    OpenAIRE

    Udayakumar, R.; Sundaran, M.; Krishna, Raghuram

    2004-01-01

    Ash, minerals and biochemical contents were determined in various parts of root, stem and leaf of Cissus quadrangularis. The maximum ash content was observed in the root. The maximum concentration of carbohydrate and protein in the root and phosphorus, iron, calcium and lipids in the stem were observed.

  6. Microfluidic device for continuous single cells analysis via Raman spectroscopy enhanced by integrated plasmonic nanodimers

    DEFF Research Database (Denmark)

    Perozziello, Gerardo; Candeloro, Patrizio; De Grazia, Antonio

    2016-01-01

    In this work a Raman flow cytometer is presented. It consists of a microfluidic device that takes advantages of the basic principles of Raman spectroscopy and flow cytometry. The microfluidic device integrates calibrated microfluidic channels-where the cells can flow one-by-one -, allowing single...... cell Raman analysis. The microfluidic channel integrates plasmonic nanodimers in a fluidic trapping region. In this way it is possible to perform Enhanced Raman Spectroscopy on single cell. These allow a label-free analysis, providing information about the biochemical content of membrane and cytoplasm...

  7. Preliminary Integrated Safety Analysis Status Report

    International Nuclear Information System (INIS)

    Gwyn, D.

    2001-01-01

    This report provides the status of the potential Monitored Geologic Repository (MGR) Integrated Safety Analysis (EA) by identifying the initial work scope scheduled for completion during the ISA development period, the schedules associated with the tasks identified, safety analysis issues encountered, and a summary of accomplishments during the reporting period. This status covers the period from October 1, 2000 through March 30, 2001

  8. International Space Station Configuration Analysis and Integration

    Science.gov (United States)

    Anchondo, Rebekah

    2016-01-01

    Ambitious engineering projects, such as NASA's International Space Station (ISS), require dependable modeling, analysis, visualization, and robotics to ensure that complex mission strategies are carried out cost effectively, sustainably, and safely. Learn how Booz Allen Hamilton's Modeling, Analysis, Visualization, and Robotics Integration Center (MAVRIC) team performs engineering analysis of the ISS Configuration based primarily on the use of 3D CAD models. To support mission planning and execution, the team tracks the configuration of ISS and maintains configuration requirements to ensure operational goals are met. The MAVRIC team performs multi-disciplinary integration and trade studies to ensure future configurations meet stakeholder needs.

  9. Integrability of dynamical systems algebra and analysis

    CERN Document Server

    Zhang, Xiang

    2017-01-01

    This is the first book to systematically state the fundamental theory of integrability and its development of ordinary differential equations with emphasis on the Darboux theory of integrability and local integrability together with their applications. It summarizes the classical results of Darboux integrability and its modern development together with their related Darboux polynomials and their applications in the reduction of Liouville and elementary integrabilty and in the center—focus problem, the weakened Hilbert 16th problem on algebraic limit cycles and the global dynamical analysis of some realistic models in fields such as physics, mechanics and biology. Although it can be used as a textbook for graduate students in dynamical systems, it is intended as supplementary reading for graduate students from mathematics, physics, mechanics and engineering in courses related to the qualitative theory, bifurcation theory and the theory of integrability of dynamical systems.

  10. Bias due to Preanalytical Dilution of Rodent Serum for Biochemical Analysis on the Siemens Dimension Xpand Plus

    Directory of Open Access Journals (Sweden)

    Jennifer L. Johns

    2018-02-01

    Full Text Available Clinical pathology testing of rodents is often challenging due to insufficient sample volume. One solution in clinical veterinary and exploratory research environments is dilution of samples prior to analysis. However, published information on the impact of preanalytical sample dilution on rodent biochemical data is incomplete. The objective of this study was to evaluate the effects of preanalytical sample dilution on biochemical analysis of mouse and rat serum samples utilizing the Siemens Dimension Xpand Plus. Rats were obtained from end of study research projects. Mice were obtained from sentinel testing programs. For both, whole blood was collected via terminal cardiocentesis into empty tubes and serum was harvested. Biochemical parameters were measured on fresh and thawed frozen samples run straight and at dilution factors 2–10. Dilutions were performed manually, utilizing either ultrapure water or enzyme diluent per manufacturer recommendations. All diluted samples were generated directly from the undiluted sample. Preanalytical dilution caused clinically unacceptable bias in most analytes at dilution factors four and above. Dilution-induced bias in total calcium, creatinine, total bilirubin, and uric acid was considered unacceptable with any degree of dilution, based on the more conservative of two definitions of acceptability. Dilution often caused electrolyte values to fall below assay range precluding evaluation of bias. Dilution-induced bias occurred in most biochemical parameters to varying degrees and may render dilution unacceptable in the exploratory research and clinical veterinary environments. Additionally, differences between results obtained at different dilution factors may confound statistical comparisons in research settings. Comparison of data obtained at a single dilution factor is highly recommended.

  11. Strategic Analysis of Technology Integration at Allstream

    OpenAIRE

    Brown, Jeff

    2011-01-01

    Innovation has been defined as the combination of invention and commercialization. Invention without commercialization is rarely, if ever, profitable. For the purposes of this paper the definition of innovation will be further expanded into the concept of technology integration. Successful technology integration not only includes new technology introduction, but also the operationalization of the new technology within each business unit of the enterprise. This paper conducts an analysis of Al...

  12. Analysis Method for Integrating Components of Product

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jun Ho [Inzest Co. Ltd, Seoul (Korea, Republic of); Lee, Kun Sang [Kookmin Univ., Seoul (Korea, Republic of)

    2017-04-15

    This paper presents some of the methods used to incorporate the parts constituting a product. A new relation function concept and its structure are introduced to analyze the relationships of component parts. This relation function has three types of information, which can be used to establish a relation function structure. The relation function structure of the analysis criteria was established to analyze and present the data. The priority components determined by the analysis criteria can be integrated. The analysis criteria were divided based on their number and orientation, as well as their direct or indirect characteristic feature. This paper presents a design algorithm for component integration. This algorithm was applied to actual products, and the components inside the product were integrated. Therefore, the proposed algorithm was used to conduct research to improve the brake discs for bicycles. As a result, an improved product similar to the related function structure was actually created.

  13. Analysis Method for Integrating Components of Product

    International Nuclear Information System (INIS)

    Choi, Jun Ho; Lee, Kun Sang

    2017-01-01

    This paper presents some of the methods used to incorporate the parts constituting a product. A new relation function concept and its structure are introduced to analyze the relationships of component parts. This relation function has three types of information, which can be used to establish a relation function structure. The relation function structure of the analysis criteria was established to analyze and present the data. The priority components determined by the analysis criteria can be integrated. The analysis criteria were divided based on their number and orientation, as well as their direct or indirect characteristic feature. This paper presents a design algorithm for component integration. This algorithm was applied to actual products, and the components inside the product were integrated. Therefore, the proposed algorithm was used to conduct research to improve the brake discs for bicycles. As a result, an improved product similar to the related function structure was actually created.

  14. Improving Marine Ecosystem Models with Biochemical Tracers

    Science.gov (United States)

    Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

    2018-01-01

    Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

  15. Biofuel and Biochemical Analysis of Amphora coffeaeformis RR03, a Novel Marine Diatom, Cultivated in an Open Raceway Pond

    Directory of Open Access Journals (Sweden)

    Muthu Ganesan Rajaram

    2018-05-01

    Full Text Available (1 Background: To increase the biochemical productivity and to reduce the production cost of microalgal biodiesel, this study aimed to investigate the effects of CO2 on biomass, fatty acids, carbon-hydrogen, and biochemical accumulation of the marine diatom, Amphora coffeaeformis RR03 (A. coffeaeformis RR03. (2 Methods: Fatty acid composition of the dry biomass of A. coffeaeformis RR03 was analysed using Gas chromatography-mass spectrometry (GC-MS. (3 Results: The results showed that A. coffeaeformis RR03 contained high biomass productivity and biochemical composition in different cultivation conditions. A. coffeaeformis RR03 showed maximum growth of 5.2 × 106/mL on 21st day cultivation under CO2 supply. The bio-crude oil production from A. coffeaeformis RR03 was 36.19 megajoule (MJ. GC-MS analysis found that the dry biomass of A. coffeaeformis RR03 contained maximum of 47.72% fatty acids of 16-octadecanoic acid methyl ester (10:12 and 19.58% pentadecanoic acid, 13-methyl-, and methyl ester (9.24. (4 Conclusion: The results of this study may suggest that a novel diatom of A. coffeaeformis RR03 could be a suitable candidate for biocrude production in order to meet the future demand of energy.

  16. An integrated acquisition, display, and analysis system

    International Nuclear Information System (INIS)

    Ahmad, T.; Huckins, R.J.

    1987-01-01

    The design goal of the ND9900/Genuie was to integrate a high performance data acquisition and display subsystem with a state-of-the-art 32-bit supermicrocomputer. This was achieved by integrating a Digital Equipment Corporation MicroVAX II CPU board with acquisition and display controllers via the Q-bus. The result is a tightly coupled processing and analysis system for Pulse Height Analysis and other applications. The system architecture supports distributed processing, so that acquisition and display functions are semi-autonomous, making the VAX concurrently available for applications programs

  17. A detailed radiobiological and dosimetric analysis of biochemical outcomes in a case-control study of permanent prostate brachytherapy patients

    International Nuclear Information System (INIS)

    Butler, Wayne M.; Stewart, Renee R.; Merrick, Gregory S.

    2009-01-01

    The purpose of this study is to determine dosimetric and radiobiological predictors of biochemical control after recalculation of prostate implant dosimetry using updated AAPM Task Group 43 (TG-43) parameters and the radiobiological parameters recommended by TG-137. All biochemical failures among patients implanted with 125 I or 103 Pd sources between 1994 and March 2006 were matched 2:1 with nonfailure controls. The individual matching was by risk group, radionuclide, prescribed dose, and time of implant (one match before and one after the failed patient) resulting in a median follow-up of 10.9 years. Complete dose volume histogram (DVH) data were recalculated for all 55 cases and 110 controls after updating the original source strength by the retrospectively determined ratios of TG-43. Differential DVH data were acquired in 179 increments of prostate volume versus percentage prescribed dose. At each incremental dose level i, the biologically equivalent dose BED i , equivalent uniform dose EUD i , and tumor control probability TCP i were calculated from the implant dose plus any external beam delivered to the patient. Total BED, EUD, and TCP were then derived from the incremental values for comparison with single point dosimetric quality parameters and DVH-based averages. There was no significant difference between failures and controls in terms of total BED (143 vs 142 Gy), EUD (95 vs 94 Gy), or TCP (0.87 vs 0.89). Conditional logistic regression analysis factored out the matching variables and stratified the cohort into each case and its controls, but no radiobiological parameter was predictive of biochemical failure. However, there was a significant difference between radiobiological parameters of 125 I and 103 Pd due to less complete coverage of the target volume by the former isotope. The implant BED and TCP were highly correlated with the D 90 and natural prescription doses and a series of mean DVH-based doses such as the harmonic mean and expressions of the

  18. Abel integral equations analysis and applications

    CERN Document Server

    Gorenflo, Rudolf

    1991-01-01

    In many fields of application of mathematics, progress is crucially dependent on the good flow of information between (i) theoretical mathematicians looking for applications, (ii) mathematicians working in applications in need of theory, and (iii) scientists and engineers applying mathematical models and methods. The intention of this book is to stimulate this flow of information. In the first three chapters (accessible to third year students of mathematics and physics and to mathematically interested engineers) applications of Abel integral equations are surveyed broadly including determination of potentials, stereology, seismic travel times, spectroscopy, optical fibres. In subsequent chapters (requiring some background in functional analysis) mapping properties of Abel integral operators and their relation to other integral transforms in various function spaces are investi- gated, questions of existence and uniqueness of solutions of linear and nonlinear Abel integral equations are treated, and for equatio...

  19. Biochemical and genetic analysis of the Drk SH2/SH3 adaptor protein of Drosophila.

    OpenAIRE

    Raabe, T; Olivier, J P; Dickson, B J; Liu, X; Gish, G D; Pawson, T; Hafen, E

    1995-01-01

    The Drk SH3-SH2-SH3 adaptor protein has been genetically identified in a screen for rate-limiting components acting downstream of the Sevenless (Sev) receptor tyrosine kinase in the developing eye of Drosophila. It provides a link between the activated Sev receptor and Sos, a guanine nucleotide release factor that activates Ras1. We have used a combined biochemical and genetic approach to study the interactions between Sev, Drk and Sos. We show that Tyr2546 in the cytoplasmic tail of Sev is r...

  20. Nonlinear structural analysis using integrated force method

    Indian Academy of Sciences (India)

    A new formulation termed the Integrated Force Method (IFM) was proposed by Patnaik ... nated ``Structure (nY m)'' where (nY m) are the force and displacement degrees of ..... Patnaik S N, Yadagiri S 1976 Frequency analysis of structures.

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

    Science.gov (United States)

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

    2014-12-01

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

  2. Analysis of Technetium Species and Fractions in Natural Seaweed Using Biochemical Separation and ICP-MS Measurement

    DEFF Research Database (Denmark)

    Shi, Keliang; Hou, Xiaolin; Qiao, Jixin

    2016-01-01

    An extremely high accumulation and retention of technetium in marine plants, especially brown seaweed, makes it a unique bioindicator of technetium. In the present work, a novel approach was developed for the speciation analysis of technetium in seaweed, wherein a series of biochemical separations....... Besides the inorganic species of TcO4-, most of technetium (>75%) combined with organic components of seaweed such as algin, cellulose, and pigment. This investigation could provide important fundamental knowledge for studying the processes and mechanisms of 99Tc accumulation in the natural seaweed....

  3. Methods in the use of GC/C/IRMS for the analysis of biochemical and pollutant isotope signatures of compounds

    International Nuclear Information System (INIS)

    Macko, S.A.; Engel, M.H.

    2001-01-01

    The potential for application of GC/C/IRMS analysis to any multitude of environmental, ecological or biochemical research areas is only beginning to be realized. Extension of compound-specific isotope analytical data derived from modern organisms and settings to yield interpretations of ancient depositional environments certainly appears possible. Further application of GC/C/IRMS approaches to understand the cycling of carbon and nitrogen, the identification and alteration of pollutants, or resolve metabolic relationships between compounds in living or extinct organisms are all within the scope of future research. (author)

  4. Aldehyde Dehydrogenases in Arabidopsis thaliana: Biochemical Requirements, Metabolic Pathways, and Functional Analysis.

    Science.gov (United States)

    Stiti, Naim; Missihoun, Tagnon D; Kotchoni, Simeon O; Kirch, Hans-Hubert; Bartels, Dorothea

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) are a family of enzymes which catalyze the oxidation of reactive aldehydes to their corresponding carboxylic acids. Here we summarize molecular genetic and biochemical analyses of selected ArabidopsisALDH genes. Aldehyde molecules are very reactive and are involved in many metabolic processes but when they accumulate in excess they become toxic. Thus activity of aldehyde dehydrogenases is important in regulating the homeostasis of aldehydes. Overexpression of some ALDH genes demonstrated an improved abiotic stress tolerance. Despite the fact that several reports are available describing a role for specific ALDHs, their precise physiological roles are often still unclear. Therefore a number of genetic and biochemical tools have been generated to address the function with an emphasis on stress-related ALDHs. ALDHs exert their functions in different cellular compartments and often in a developmental and tissue specific manner. To investigate substrate specificity, catalytic efficiencies have been determined using a range of substrates varying in carbon chain length and degree of carbon oxidation. Mutational approaches identified amino acid residues critical for coenzyme usage and enzyme activities.

  5. Biochemical impact of soccer: an analysis of hormonal, muscle damage, and redox markers during the season.

    Science.gov (United States)

    Silva, João Renato; Rebelo, António; Marques, Franklim; Pereira, Laura; Seabra, André; Ascensão, António; Magalhães, José

    2014-04-01

    This study aimed to analyze changes in performance, muscle function, and stress-related biochemical markers in professional soccer players (n = 14) at 4 timepoints (3 for performance and 4 for stress-related biochemical markers) during the soccer season [Formula: see text] preseason (E1), midseason (E2), end of the season (E3) [Formula: see text] and after the end of the recovery period (E4). Performance in 5- and 30-m sprints, countermovement jump, and agility, and maximal isokinetic knee extension and knee flexion strength were measured (E1 to E3). We observed increased in-season levels of myoglobin (E2 > E1 and E4; p E1 and E4; p player during the competition period), performance, and hormonal and redox parameters (r = 0.456-0.615; p soccer players face significant changes in biomarkers of physiologic strain (muscle damage and oxidative stress-related markers) during the season, but values return to normal during the off-season. Additionally, MAT influences physical, hormonal, and oxidative stress-related parameters in professional soccer players.

  6. Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28.

    Directory of Open Access Journals (Sweden)

    Bonsu Ku

    Full Text Available Dual-specificity phosphatases (DUSPs constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

  7. A hybrid approach to device integration on a genetic analysis platform

    International Nuclear Information System (INIS)

    Brennan, Des; Justice, John; Aherne, Margaret; Galvin, Paul; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Macek, Milan

    2012-01-01

    Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization. (paper)

  8. Analysis of some biochemical and haematological parameters for Mucuna pruriens (DC) seed powder in male rats.

    Science.gov (United States)

    Chukwudi, Ndukwe Henry; Simeon, Omale; Chinyere, Aguiyi John

    2011-10-01

    The biochemical and haematological effects of the seed powder of Mucuna pruriens in male rats were evaluated to establish some biological properties of this potential biopesticide currently undergoing investigation. The result showed that Mucuna pruriens seed extract produced a significant (p<0.05) increase in white blood cell (WBC) count, as well as in bilirubin concentrations, alkaline phosphatase (ALP), protein and creatinine levels measured. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly reduced (P<0.05) in comparison with the experimental control. PCV, Hb, albumin level and WBC differential counts gave no significant difference between treated and control groups. The results revealed metabolic imbalance in the rats which suggests a mild cholestasis effect of the extract.

  9. Biochemical System Analysis of Lutein Production by Heterotrophic Chlorella pyrenoidosa in a Fermentor

    Directory of Open Access Journals (Sweden)

    Zheng-Yun Wu

    2009-01-01

    Full Text Available Chlorella is a promising alternative source of lutein, as it can be cultivated heterotrophically with high efficiency. In this study, the carotenoids in Chlorella pyrenoidosa heterotrophically cultivated in a 19-litre fermentor have been analyzed and determined by using HPLC and HPLC-MS. A biochemical system theory (BST model was developed for understanding the regulatory features of carotenoid metabolism during the batch cultivation. Factors that influence lutein production by C. pyrenoidosa were discussed based on the model. It shows that low flux for lycopene formation is the major bottleneck for lutein production, while by-product syntheses and inhibitions affect the cellular lutein content much less. However, with further increase of the cellular lutein content, the inhibition on lycopene formation by lutein may become a limiting factor. Although speculative, these results may provide useful information for further elucidation of the regulatory mechanisms of carotenoid biosynthesis in Chlorella and modifying its metabolic network to enhance lutein production.

  10. Biochemical and topological analysis of bovine sperm cells induced by low power laser irradiation

    Science.gov (United States)

    Dreyer, T. R.; Siqueira, A. F. P.; Magrini, T. D.; Fiorito, P. A.; Assumpção, M. E. O. A.; Nichi, M.; Martinho, H. S.; Milazzotto, M. P.

    2011-07-01

    Low-level laser irradiation (LLLI) increases ATP production and energy supply to the cell which could increase sperm motility, acrossomal reaction and consequently the fertilizing potential. The aim of this study was to characterize the biochemical and topological changes induced by low power laser irradiation on bull sperm cells. Post-thawing sperm were irradiated with a 633nm laser with fluence rates of 30, 150 and 300mJ.cm-2 (power of 5mW for 1, 5 and 10minutes, respectively); 45, 230, and 450mJ.cm-2 (7.5mW for 1, 5 and 10 minutes); and 60, 300 and 600mJ.cm-2 (10mW for 1, 5 and 10 minutes). Biochemical and metabolical changes were analyzed by FTIR and flow cytometry; oxygen reactive species production was assessed by TBARS and the morphological changes were evaluated by AFM. Motility had no difference among times or powers of irradiation. Increasing in ROS generation was observed with power of 5mW compared to 7.5 and 10mW, and with 10min of irradiation in comparison with 5 and 1min of irradiation. This higher ROS generation was related to an increase in acrossomal and plasma membrane damage. FTIR results showed that the amount of lipids was inversely proportional to the quantity of ROS generated. AFM images showed morphological differences in plasma/acrossomal membrane, mainly on the equatorial region. We conclude that LLLI is an effective method to induce changes on sperm cell metabolism but more studies are necessary to establish an optimal dose to increase the fertility potential of these cells.

  11. Integrating neural network technology and noise analysis

    International Nuclear Information System (INIS)

    Uhrig, R.E.; Oak Ridge National Lab., TN

    1995-01-01

    The integrated use of neural network and noise analysis technologies offers advantages not available by the use of either technology alone. The application of neural network technology to noise analysis offers an opportunity to expand the scope of problems where noise analysis is useful and unique ways in which the integration of these technologies can be used productively. The two-sensor technique, in which the responses of two sensors to an unknown driving source are related, is used to demonstration such integration. The relationship between power spectral densities (PSDs) of accelerometer signals is derived theoretically using noise analysis to demonstrate its uniqueness. This relationship is modeled from experimental data using a neural network when the system is working properly, and the actual PSD of one sensor is compared with the PSD of that sensor predicted by the neural network using the PSD of the other sensor as an input. A significant deviation between the actual and predicted PSDs indicate that system is changing (i.e., failing). Experiments carried out on check values and bearings illustrate the usefulness of the methodology developed. (Author)

  12. [Integrated health care organizations: guideline for analysis].

    Science.gov (United States)

    Vázquez Navarrete, M Luisa; Vargas Lorenzo, Ingrid; Farré Calpe, Joan; Terraza Núñez, Rebeca

    2005-01-01

    There has been a tendency recently to abandon competition and to introduce policies that promote collaboration between health providers as a means of improving the efficiency of the system and the continuity of care. A number of countries, most notably the United States, have experienced the integration of health care providers to cover the continuum of care of a defined population. Catalonia has witnessed the steady emergence of increasing numbers of integrated health organisations (IHO) but, unlike the United States, studies on health providers' integration are scarce. As part of a research project currently underway, a guide was developed to study Catalan IHOs, based on a classical literature review and the development of a theoretical framework. The guide proposes analysing the IHO's performance in relation to their final objectives of improving the efficiency and continuity of health care by an analysis of the integration type (based on key characteristics); external elements (existence of other suppliers, type of services' payment mechanisms); and internal elements (model of government, organization and management) that influence integration. Evaluation of the IHO's performance focuses on global strategies and results on coordination of care and efficiency. Two types of coordination are evaluated: information coordination and coordination of care management. Evaluation of the efficiency of the IHO refers to technical and allocative efficiency. This guide may have to be modified for use in the Catalan context.

  13. Integrated tools for control-system analysis

    Science.gov (United States)

    Ostroff, Aaron J.; Proffitt, Melissa S.; Clark, David R.

    1989-01-01

    The basic functions embedded within a user friendly software package (MATRIXx) are used to provide a high level systems approach to the analysis of linear control systems. Various control system analysis configurations are assembled automatically to minimize the amount of work by the user. Interactive decision making is incorporated via menu options and at selected points, such as in the plotting section, by inputting data. There are five evaluations such as the singular value robustness test, singular value loop transfer frequency response, Bode frequency response, steady-state covariance analysis, and closed-loop eigenvalues. Another section describes time response simulations. A time response for random white noise disturbance is available. The configurations and key equations used for each type of analysis, the restrictions that apply, the type of data required, and an example problem are described. One approach for integrating the design and analysis tools is also presented.

  14. An integrated system for genetic analysis

    Directory of Open Access Journals (Sweden)

    Duan Xiao

    2006-04-01

    Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

  15. Integrated Reliability and Risk Analysis System (IRRAS)

    International Nuclear Information System (INIS)

    Russell, K.D.; McKay, M.K.; Sattison, M.B.; Skinner, N.L.; Wood, S.T.; Rasmuson, D.M.

    1992-01-01

    The Integrated Reliability and Risk Analysis System (IRRAS) is a state-of-the-art, microcomputer-based probabilistic risk assessment (PRA) model development and analysis tool to address key nuclear plant safety issues. IRRAS is an integrated software tool that gives the user the ability to create and analyze fault trees and accident sequences using a microcomputer. This program provides functions that range from graphical fault tree construction to cut set generation and quantification. Version 1.0 of the IRRAS program was released in February of 1987. Since that time, many user comments and enhancements have been incorporated into the program providing a much more powerful and user-friendly system. This version has been designated IRRAS 4.0 and is the subject of this Reference Manual. Version 4.0 of IRRAS provides the same capabilities as Version 1.0 and adds a relational data base facility for managing the data, improved functionality, and improved algorithm performance

  16. Integrated micro-biochemical approach for phytoremediation of cadmium and lead contaminated soils using Gladiolus grandiflorus L cut flower.

    Science.gov (United States)

    Mani, Dinesh; Kumar, Chitranjan; Patel, Niraj Kumar

    2016-02-01

    The potential of vermicompost, elemental sulphur, Thiobacillus thiooxidans and Pseudomonas putida for phytoremediation is well known individually but their integrated approach has not been discovered so far. The present work highlights the consideration of so far overlooked aspects of their integrated treatment by growing the ornamental plant, Gladiolus grandiflorus L in uncontaminated and sewage-contaminated soils (sulphur-deficient alluvial Entisols, pH 7.6-7.8) for phytoremediation of cadmium and lead under pot experiment. Between vermicompost and elemental sulphur, the response of vermicompost was higher towards improvement in the biometric parameters of plants, whereas the response of elemental sulphur was higher towards enhanced bioaccumulation of heavy metals under soils. The integrated treatment (T7: vermicompost 6g and elemental sulphur 0.5gkg(-1) soil and co-inoculation of the plant with T. thiooxidans and P. putida) was found superior in promoting root length, plant height and dry biomass of the plant. The treatment T7 caused enhanced accumulation of Cd up to 6.96 and 6.45mgkg(-1) and Pb up to 22.6 and 19.9mgkg(-1) in corm and shoot, respectively at the contaminated soil. T7 showed maximum remediation efficiency of 0.46% and 0.19% and bioaccumulation factor of 2.92 and 1.21 and uptake of 6.75 and 21.4mgkg(-1) dry biomass for Cd and Pb respectively in the contaminated soil. The integrated treatment T7 was found significant over the individual treatments to promote plant growth and enhance phytoremediation. Hence, authors conclude to integrate vermicompost, elemental sulphur and microbial co-inoculation for the enhanced clean-up of Cd and Pb-contaminated soils. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Integrity Analysis of Damaged Steam Generator Tubes

    International Nuclear Information System (INIS)

    Stanic, D.

    1998-01-01

    Variety of degradation mechanisms affecting steam generator tubes makes steam generators as one of the critical components in the nuclear power plants. Depending of their nature, degradation mechanisms cause different types of damages. It requires performance of extensive integrity analysis in order to access various conditions of crack behavior under operating and accidental conditions. Development and application of advanced eddy current techniques for steam generator examination provide good characterization of found damages. Damage characteristics (shape, orientation and dimensions) may be defined and used for further evaluation of damage influence on tube integrity. In comparison with experimental and analytical methods, numerical methods are also efficient tools for integrity assessment. Application of finite element methods provides relatively simple modeling of different type of damages and simulation of various operating conditions. The stress and strain analysis may be performed for elastic and elasto-plastic state with good ability for visual presentation of results. Furthermore, the fracture mechanics parameters may be calculated. Results obtained by numerical analysis supplemented with experimental results are the base for definition of alternative plugging criteria which may significantly reduce the number of plugged tubes. (author)

  18. The integrated microbial genome resource of analysis.

    Science.gov (United States)

    Checcucci, Alice; Mengoni, Alessio

    2015-01-01

    Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

  19. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis

    Directory of Open Access Journals (Sweden)

    Jolly Emmitt R

    2005-11-01

    Full Text Available Abstract Background A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. Results Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. Conclusion We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation.

  20. Integrated analysis of genetic data with R

    Directory of Open Access Journals (Sweden)

    Zhao Jing

    2006-01-01

    Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

  1. Advancing Alternative Analysis: Integration of Decision Science

    DEFF Research Database (Denmark)

    Malloy, Timothy F; Zaunbrecher, Virginia M; Batteate, Christina

    2016-01-01

    Decision analysis-a systematic approach to solving complex problems-offers tools and frameworks to support decision making that are increasingly being applied to environmental challenges. Alternatives analysis is a method used in regulation and product design to identify, compare, and evaluate......, and civil society and included experts in toxicology, decision science, alternatives assessment, engineering, and law and policy. Participants were divided into two groups and prompted with targeted questions. Throughout the workshop, the groups periodically came together in plenary sessions to reflect......) engaging the systematic development and evaluation of decision approaches and tools; (2) using case studies to advance the integration of decision analysis into alternatives analysis; (3) supporting transdisciplinary research; and (4) supporting education and outreach efforts....

  2. Biochemical analysis of plant protection afforded by a nonpathogenic endophytic mutant of Colletotrichum magna

    Energy Technology Data Exchange (ETDEWEB)

    Redman, R.S.; Rodriguez, R.J. (Geological Survey, Seattle, WA (United States) Univ. of Washington, Seattle, WA (United States). Dept. of Botany); Clifton, D.R.; Morrel, J.; Brown, G. (Geological Survey, Seattle, WA (United States)); Freeman, S. (Volcani Center, Bet Dagan (Israel). Dept. of Plant Pathology)

    1999-02-01

    A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) plant-defense response were investigated in anthracnose-resistant and-susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h and then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1-colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.

  3. Mixotrophic growth and biochemical analysis of Chlorella vulgaris cultivated with diluted monosodium glutamate wastewater.

    Science.gov (United States)

    Ji, Yan; Hu, Wenrong; Li, Xiuqing; Ma, Guixia; Song, Mingming; Pei, Haiyan

    2014-01-01

    Monosodium glutamate wastewater (MSGW) is a potential medium for microbial cultivation because of containing abundant organic nutrient. This paper seeks to evaluate the feasibility of growing Chlorella vulgaris with MSGW and assess the influence of MSGW concentration on the biomass productivity and biochemical compositions. The MSGW diluted in different concentrations was prepared for microalga cultivation. C. vulgaris growth was greatly promoted with MSGW compared with the inorganic BG11 medium. C. vulgaris obtained the maximum biomass concentration (1.02 g/L) and biomass productivity (61.47 mg/Ld) with 100-time diluted MSGW. The harvested biomass was rich in protein (36.01-50.64%) and low in lipid (13.47-25.4%) and carbohydrate (8.94-20.1%). The protein nutritional quality and unsaturated fatty acids content of algal increased significantly with diluted MSGW. These results indicated that the MSGW is a feasible alternative for mass cultivation of C. vulgaris. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

    Science.gov (United States)

    Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

    2010-12-01

    Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

  5. Integration and segregation in auditory scene analysis

    Science.gov (United States)

    Sussman, Elyse S.

    2005-03-01

    Assessment of the neural correlates of auditory scene analysis, using an index of sound change detection that does not require the listener to attend to the sounds [a component of event-related brain potentials called the mismatch negativity (MMN)], has previously demonstrated that segregation processes can occur without attention focused on the sounds and that within-stream contextual factors influence how sound elements are integrated and represented in auditory memory. The current study investigated the relationship between the segregation and integration processes when they were called upon to function together. The pattern of MMN results showed that the integration of sound elements within a sound stream occurred after the segregation of sounds into independent streams and, further, that the individual streams were subject to contextual effects. These results are consistent with a view of auditory processing that suggests that the auditory scene is rapidly organized into distinct streams and the integration of sequential elements to perceptual units takes place on the already formed streams. This would allow for the flexibility required to identify changing within-stream sound patterns, needed to appreciate music or comprehend speech..

  6. Integrated framework for dynamic safety analysis

    International Nuclear Information System (INIS)

    Kim, Tae Wan; Karanki, Durga R.

    2012-01-01

    In the conventional PSA (Probabilistic Safety Assessment), detailed plant simulations by independent thermal hydraulic (TH) codes are used in the development of accident sequence models. Typical accidents in a NPP involve complex interactions among process, safety systems, and operator actions. As independent TH codes do not have the models of operator actions and full safety systems, they cannot literally simulate the integrated and dynamic interactions of process, safety systems, and operator responses. Offline simulation with pre decided states and time delays may not model the accident sequences properly. Moreover, when stochastic variability in responses of accident models is considered, defining all the combinations for simulations will be cumbersome task. To overcome some of these limitations of conventional safety analysis approach, TH models are coupled with the stochastic models in the dynamic event tree (DET) framework, which provides flexibility to model the integrated response due to better communication as all the accident elements are in the same model. The advantages of this framework also include: Realistic modeling in dynamic scenarios, comprehensive results, integrated approach (both deterministic and probabilistic models), and support for HRA (Human Reliability Analysis)

  7. Integrating health and environmental impact analysis

    DEFF Research Database (Denmark)

    Reis, S; Morris, G.; Fleming, L. E.

    2015-01-01

    which addresses human activity in all its social, economic and cultural complexity. The new approach must be integral to, and interactive, with the natural environment. We see the continuing failure to truly integrate human health and environmental impact analysis as deeply damaging, and we propose...... while equally emphasizing the health of the environment, and the growing calls for 'ecological public health' as a response to global environmental concerns now suffusing the discourse in public health. More revolution than evolution, ecological public health will demand new perspectives regarding...... the interconnections among society, the economy, the environment and our health and well-being. Success must be built on collaborations between the disparate scientific communities of the environmental sciences and public health as well as interactions with social scientists, economists and the legal profession...

  8. Advancing Alternative Analysis: Integration of Decision Science.

    Science.gov (United States)

    Malloy, Timothy F; Zaunbrecher, Virginia M; Batteate, Christina M; Blake, Ann; Carroll, William F; Corbett, Charles J; Hansen, Steffen Foss; Lempert, Robert J; Linkov, Igor; McFadden, Roger; Moran, Kelly D; Olivetti, Elsa; Ostrom, Nancy K; Romero, Michelle; Schoenung, Julie M; Seager, Thomas P; Sinsheimer, Peter; Thayer, Kristina A

    2017-06-13

    Decision analysis-a systematic approach to solving complex problems-offers tools and frameworks to support decision making that are increasingly being applied to environmental challenges. Alternatives analysis is a method used in regulation and product design to identify, compare, and evaluate the safety and viability of potential substitutes for hazardous chemicals. We assessed whether decision science may assist the alternatives analysis decision maker in comparing alternatives across a range of metrics. A workshop was convened that included representatives from government, academia, business, and civil society and included experts in toxicology, decision science, alternatives assessment, engineering, and law and policy. Participants were divided into two groups and were prompted with targeted questions. Throughout the workshop, the groups periodically came together in plenary sessions to reflect on other groups' findings. We concluded that the further incorporation of decision science into alternatives analysis would advance the ability of companies and regulators to select alternatives to harmful ingredients and would also advance the science of decision analysis. We advance four recommendations: a ) engaging the systematic development and evaluation of decision approaches and tools; b ) using case studies to advance the integration of decision analysis into alternatives analysis; c ) supporting transdisciplinary research; and d ) supporting education and outreach efforts. https://doi.org/10.1289/EHP483.

  9. Structural integrity analysis of a steam turbine

    International Nuclear Information System (INIS)

    Villagarcia, Maria P.

    1997-01-01

    One of the most critical components of a power utility is the rotor of the steam turbine. Catastrophic failures of the last decades have promoted the development of life assessment procedures for rotors. The present study requires the knowledge of operating conditions, component geometry, the properties of materials, history of the component, size, location and nature of the existing flaws. The aim of the present work is the obtention of a structural integrity analysis procedure for a steam turbine rotor, taking into account the above-mentioned parameters. In this procedure, a stress thermal analysis by finite elements is performed initially, in order to obtain the temperature and stress distribution for a subsequent analysis by fracture mechanics. The risk of a fast fracture due to flaws in the central zone of the rotor is analyzed. The procedure is applied to an operating turbine: the main steam turbine of the Atucha I nuclear power utility. (author)

  10. A taxonomy of integral reaction path analysis

    Energy Technology Data Exchange (ETDEWEB)

    Grcar, Joseph F.; Day, Marcus S.; Bell, John B.

    2004-12-23

    W. C. Gardiner observed that achieving understanding through combustion modeling is limited by the ability to recognize the implications of what has been computed and to draw conclusions about the elementary steps underlying the reaction mechanism. This difficulty can be overcome in part by making better use of reaction path analysis in the context of multidimensional flame simulations. Following a survey of current practice, an integral reaction flux is formulated in terms of conserved scalars that can be calculated in a fully automated way. Conditional analyses are then introduced, and a taxonomy for bidirectional path analysis is explored. Many examples illustrate the resulting path analysis and uncover some new results about nonpremixed methane-air laminar jets.

  11. The ASDEX integrated data analysis system AIDA

    International Nuclear Information System (INIS)

    Grassie, K.; Gruber, O.; Kardaun, O.; Kaufmann, M.; Lackner, K.; Martin, P.; Mast, K.F.; McCarthy, P.J.; Mertens, V.; Pohl, D.; Rang, U.; Wunderlich, R.

    1989-11-01

    Since about two years, the ASDEX integrated data analysis system (AIDA), which combines the database (DABA) and the statistical analysis system (SAS), is successfully in operation. Besides a considerable, but meaningful, reduction of the 'raw' shot data, it offers the advantage of carefully selected and precisely defined datasets, which are easily accessible for informative tabular data overviews (DABA), and multi-shot analysis (SAS). Even rather complicated, statistical analyses can be performed efficiently within this system. In this report, we want to summarise AIDA's main features, give some details on its set-up and on the physical models which have been used for the derivation of the processed data. We also give short introduction how to use DABA and SAS. (orig.)

  12. Expression analysis and biochemical characterization of beans plants biofortificated with zinc

    Directory of Open Access Journals (Sweden)

    Sandra Pérez Álvarez

    2017-09-01

    Full Text Available The present work was carried out in greenhouse conditions at the Centro de Investigación en Alimentación y Desarrollo AC in Delicias, Chihuahua, México. Four different concentrations (0, 25, 50 and 100 μM L−1 of Zn chelate and sulfate were used to study the antioxidant system of Phaseolus vulgaris L. Three genes related with antioxidant activity [superoxide dismutase (SOD, glutathione peroxidase (GSH-Px and catalase (CAT] were selected for expression study. Results showed that when Zn chelate at 50 and 100 μM L−1 were applied SOD was repressed and GSH-Px expression was low at 0, 25 and 100 μM L−1 while with sulfate form SOD expression was low and GSH-Px expression was strong in all treatment. CAT was highly expressed in all form and treatments. For a biochemical study the same enzymes were spectrophotometrically measured. SOD activity shows differences in both forms of Zn, chelate form was different at 25, 50 and 100 μM L−1 with less activity at 100 μM L−1 and sulfate treatment shows differences in all concentrations used. GSH-Px activity shows significant differences with sulfate form at 25, 50 μM L−1 where at 50 μM the activity was higher and low at 100 μM L−1, CAT does not exhibit significant differences but with chelate treatment at 50–100 μM L−1 the activity was higher compared to sulfate. Finally, to raise the Zn concentration in bean under biofortification program is a promising strategy in cropping systems in order to increase the ingestion of zinc and antioxidant capacity in the general population and provided the benefits that this element offered in human health.

  13. Neuroprotective effect of edaravone in experimental glaucoma model in rats: a immunofluorescence and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Arzu Toruk Aksar

    2015-04-01

    Full Text Available AIM: To evaluate the neuroprotective activity of systemically administered edaravone in early and late stage of experimental glaucoma in rats. METHODS: In this study, 60 Wistar albino rats were used. Experimental glaucoma model was created by injecting hyaluronic acid to the anterior chamber once a week for 6wk in 46 of 60 subjects. Fourteen subjects without any medication were included as control group. Edaravone administered intraperitoneally 3 mg/kg/d to the 15 of 30 subjects starting at the onset of glaucoma induction and also administered intraperitoneally 3 mg/kg/d to the other 15 subjects starting at three weeks after the onset of glaucoma induction. The other 16 subjects who underwent glaucoma induction was administered any therapy. Retinal ganglion cells (RGCs have been marked with dextran tetramethylrhodamine (DTMR retrograde at the end of the sixth week and after 48h, subjects were sacrificed by the method of cardiac perfusion. Alive RGC density was assessed in the whole-mount retina. Whole-mount retinal tissues homogenized and nitric oxide (NO, malondialdehyde (MDA and total antioxidant capacity (TAC values were measured biochemically. RESULTS: RGCs counted with Image-Pro Plus program, in the treatment group were found to be statistically significantly protected, compared to the glaucoma group (Bonferroni, P<0.05. The neuroprotective activity of edaravone was found to be more influential by administration at the start of the glaucoma process. Statistically significant lower NO levels were determined in the glaucoma group comparing treatment groups (Bonferroni, P<0.05. MDA levels were found to be highest in untreated glaucoma group, TAC levels were found to be lower in the glaucoma induction groups than the control group (Bonferroni, P<0.05. CONCLUSION: Systemic administration of Edaravone in experimental glaucoma showed potent neuroprotective activity. The role of oxidative stress causing RGC damage in glaucoma was supported by this

  14. Biochemical analysis of a papain-like protease isolated from the latex of Asclepias curassavica L.

    Science.gov (United States)

    Liggieri, Constanza; Obregon, Walter; Trejo, Sebastian; Priolo, Nora

    2009-02-01

    Most of the species belonging to Asclepiadaceae family usually secrete an endogenous milk-like fluid in a network of laticifer cells in which sub-cellular organelles intensively synthesize proteins and secondary metabolites. A new papain-like endopeptidase (asclepain c-II) has been isolated and characterized from the latex extracted from petioles of Asclepias curassavica L. (Asclepiadaceae). Asclepain c-II was the minor proteolytic component in the latex, but showed higher specific activity than asclepain c-I, the main active fraction previously studied. Both enzymes displayed quite distinct biochemical characteristics, confirming that they are different enzymes. Crude extract was purified by cation exchange chromatography (FPLC). Two active fractions, homogeneous by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and mass spectrometry, were isolated. Asclepain c-II displayed a molecular mass of 23,590 Da, a pI higher than 9.3, maximum proteolytic activity at pH 9.4-10.2, and showed poor thermostability. The activity of asclepain c-II is inhibited by cysteine proteases inhibitors like E-64, but not by any other protease inhibitors such as 1,10-phenantroline, phenylmethanesulfonyl fluoride, and pepstatine. The Nterminal sequence (LPSFVDWRQKGVVFPIRNQGQCGSCWTFSA) showed a high similarity with those of other plant cysteine proteinases. When assayed on N-alpha-CBZ-amino acid-p-nitrophenyl esters, the enzyme exhibited higher preference for the glutamine derivative. Determinations of kinetic parameters were performed with N-alpha-CBZ-L-Gln-p-nitrophenyl ester as substrate: K(m)=0.1634 mM, k(cat)=121.48 s(-1), and k(cat)/K(m)=7.4 x 10(5) s(-1)/mM.

  15. Transcriptome and biochemical analysis of a flower color polymorphism in Silene littorea (Caryophyllaceae

    Directory of Open Access Journals (Sweden)

    Inés eCasimiro-Soriguer

    2016-02-01

    Full Text Available Flower color polymorphisms are widely used as model traits from genetics to ecology, yet determining the biochemical and molecular basis can be challenging. Anthocyanin-based flower color variations can be caused by at least 12 structural and three regulatory genes in the anthocyanin biosynthetic pathway. We use mRNA-Seq to simultaneously sequence and estimate expression of these candidate genes in nine samples of Silene littorea representing three color morphs (dark pink, light pink and white across three developmental stages in hopes of identifying the cause of flower color variation. We identified 29 putative paralogues for the 15 candidate genes in the anthocyanin biosynthetic pathway. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogues, we identified 622 SNPs, yet only nine synonymous SNPs in Ans had allele frequencies that differentiated pigmented petals (dark pink and light pink from white petals. These Ans allele frequency differences were further investigated with an expanded sequencing survey of 38 individuals, yet no SNPs consistently differentiated the color morphs. We also found one locus, F3h1, with strong differential expression between pigmented and white samples (>42x. This may be caused by decreased expression of Myb1a in white petal buds. Myb1a in S. littorea is a regulatory locus closely related to Subgroup 7 Mybs known to regulate F3h and other loci in the first half of the ABP in model species. We then compare the mRNA-Seq results with petal biochemistry which revealed cyanidin as the primary anthocyanin and five flavonoid intermediates. Concentrations of three of the flavonoid intermediates were significantly lower in white petals than in pigmented petals (rutin, quercetin and isovitexin. The biochemistry results for rutin, quercetin, luteolin and apigenin are consistent with the transcriptome results suggesting a blockage at F3h, possibly caused

  16. Analysis of the hematological and biochemical parameters related to lead intoxication.

    Science.gov (United States)

    Yılmaz, Hınç; Keten, Alper; Karacaoğlu, Emre; Tutkun, Engin; Akçan, Ramazan

    2012-11-01

    In parallel with industrial advancements, number of the occupational diseases secondary to chemical exposure is increasing. The chemical agents in the work places affect various organ and tissue systems, leading to chronic diseases. In this study, the cases diagnosed with occupational disease due to exposure to lead were studied and importance of the environmental forensic sciences on this issue was emphasized. A hundred and ninety patients diagnosed with occupational disease related to lead intoxication in Ankara Occupational Diseases Hospital between 01/01/2009 and 31/12/2009 were included in the study. Twenty cases were used as the controls. Sociodemographic characteristics, serum chemical parameters and hematological parameters of the patients were retrospectively assessed. Mean age of the cases included in the study was 35.3±8.69. Hemoglobin (Hb) (p=0.018) and Mean corpuscular volume (MCV) (plead exposure than in the controls. Gamma glutamyl transferase (GGT) was significantly lower in the patients with lead exposure than in the controls (p=0.002), whereas alkaline phosphatase (ALP) was found higher (plead exposure than in the control group (p=0.01), while Thyrotrophin-stimulating hormone (TSH) levels were lower (plead (Pb) was correlated positively with ALP values and negatively with Hb, MCV and TSH. Considering its effects on the biochemical and hematological parameters, a detailed investigation should be carried out in the cases with lead exposure, which occupies an important place among the occupational diseases. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  17. Robot-assisted radical prostatectomy has lower biochemical recurrence than laparoscopic radical prostatectomy: Systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Seon Heui Lee

    2017-05-01

    Full Text Available Purpose: To assess the effectiveness and safety of robot-assisted radical prostatectomy (RARP versus laparoscopic radical prostatectomy (LRP in the treatment of prostate cancer. Materials and Methods: Existing systematic reviews were updated to investigate the effectiveness and safety of RARP. Electronic databases, including Ovid MEDLINE, Ovid Embase, the Cochrane Library, KoreaMed, Kmbase, and others, were searched through July 2014. The quality of the selected systematic reviews was assessed by using the revised assessment of multiple systematic reviews (R-Amstar and the Cochrane Risk of Bias tool. Meta-analysis was performed by using Revman 5.2 (Cochrane Community and Comprehensive Meta-Analysis 2.0 (CMA; Biostat. Cochrane Q and I2 statistics were used to assess heterogeneity. Results: Two systematic reviews and 16 additional studies were selected from a search performed of existing systematic reviews. These included 2 randomized controlled clinical trials and 28 nonrandomized comparative studies. The risk of complications, such as injury to organs by the Clavien-Dindo classification, was lower with RARP than with LRP (relative risk [RR], 0.44; 95% confidence interval [CI], 1.23–0.85; p=0.01. The risk of urinary incontinence was lower (RR, 0.43; 95% CI, 0.31–0.60; p<0.000001 and the potency rate was significantly higher with RARP than with LRP (RR, 1.38; 95% CI, 1.11–1.70; I2 =78%; p=0.003. Regarding positive surgical margins, no significant difference in risk between the 2 groups was observed; however, the biochemical recurrence rate was lower after RARP than after LRP (RR, 0.59; 95% CI, 0.48–0.73; I2 =21%; p<0.00001. Conclusions: RARP appears to be a safe and effective technique compared with LRP with a lower complication rate, better potency, a higher continence rate, and a decreased rate of biochemical recurrence.

  18. Accelerator physics analysis with an integrated toolkit

    International Nuclear Information System (INIS)

    Holt, J.A.; Michelotti, L.; Satogata, T.

    1992-08-01

    Work is in progress on an integrated software toolkit for linear and nonlinear accelerator design, analysis, and simulation. As a first application, ''beamline'' and ''MXYZPTLK'' (differential algebra) class libraries, were used with an X Windows graphics library to build an user-friendly, interactive phase space tracker which, additionally, finds periodic orbits. This program was used to analyse a theoretical lattice which contains octupoles and decapoles to find the 20th order, stable and unstable periodic orbits and to explore the local phase space structure

  19. Effect of Different Fertilization Systems (Chemical, Biological and Integrated( on Nitrogen and Phosphorus Concentration, Biochemical Attributes and Sepals Dry Weight of Roselle (Hibiscus sabdariffa L.

    Directory of Open Access Journals (Sweden)

    roghayeh mohammadpour vashvaei

    2017-12-01

    Full Text Available Introduction Roselle (Hibiscus sabdariffa L. is a subtropical medicinal plant belongs to the Malvaceae family. Roselle sepals are valuable due to its therapeutic properties and culinary uses. During past decades rising cost of chemical inputs and overusing them in conventional farming have caused various environmental issues such as soil and water resources contamination, reduction in food quality production, decreasing soil fertility and biological imbalance in the soil that they impose irreparable damage to ecosystems. Sustainable agriculture which is based on the use of bio-fertilizers with the aim of eliminating or considerably reducing the use of chemical inputs is the optimal solution to overcome these problems. Abo-Baker and Gehan (2011 in their study on the effect of bio-fertilizers in combination with different rates of chemical fertilizers on growth characters, yield component and chemical constituents of roselle demonstrated that the inoculation with the mixture of bio-fertilizers combined with 50 or 100% chemical fertilizers improved, in most cases, growth characters and increased sepal yield or at least did not differ significantly from the control (full recommended dose of NPK alone. These researchers stated that applying 50% of the recommended dose of NPK plus the mixture of bio-fertilizer can save half of the quantity of chemical fertilizers, decrease the production cost and obtain high quality product. The present study was designed to investigate the effect of bio-fertilizers in combination with different doses of chemical fertilizers on the element concentrations, biochemical properties and yield of roselle to find the appropriate integration of them. Material and Methods This experiment was conducted based on a randomized complete block design with three replications, at the Research Station, University of Zabol, during growing season of 2011-2012 and 2012-2013. Experimental treatments were plant nutrition with NPK (220, 130

  20. The Integral A Crux for Analysis

    CERN Document Server

    Krantz, Steven G

    2011-01-01

    This book treats all of the most commonly used theories of the integral. After motivating the idea of integral, we devote a full chapter to the Riemann integral and the next to the Lebesgue integral. Another chapter compares and contrasts the two theories. The concluding chapter offers brief introductions to the Henstock integral, the Daniell integral, the Stieltjes integral, and other commonly used integrals. The purpose of this book is to provide a quick but accurate (and detailed) introduction to all aspects of modern integration theory. It should be accessible to any student who has had ca

  1. Comparative biochemical analysis after steam pretreatment of lignocellulosic agricultural waste biomass from Williams Cavendish banana plant (Triploid Musa AAA group).

    Science.gov (United States)

    Kamdem, Irénée; Jacquet, Nicolas; Tiappi, Florian Mathias; Hiligsmann, Serge; Vanderghem, Caroline; Richel, Aurore; Jacques, Philippe; Thonart, Philippe

    2015-11-01

    The accessibility of fermentable substrates to enzymes is a limiting factor for the efficient bioconversion of agricultural wastes in the context of sustainable development. This paper presents the results of a biochemical analysis performed on six combined morphological parts of Williams Cavendish Lignocellulosic Biomass (WCLB) after steam cracking (SC) and steam explosion (SE) pretreatments. Solid (S) and liquid (L) fractions (Fs) obtained from SC pretreatment performed at 180°C (SLFSC180) and 210°C (SLFSC210) generated, after diluted acid hydrolysis, the highest proportions of neutral sugar (NS) contents, specifically 52.82 ± 3.51 and 49.78 ± 1.39%w/w WCLB dry matter (DM), respectively. The highest proportions of glucose were found in SFSC210 (53.56 ± 1.33%w/w DM) and SFSC180 (44.47 ± 0.00%w/w DM), while the lowest was found in unpretreated WCLB (22.70 ± 0.71%w/w DM). Total NS content assessed in each LF immediately after SC and SE pretreatments was less than 2%w/w of the LF DM, thus revealing minor acid autohydrolysis consequently leading to minor NS production during the steam pretreatment. WCLB subjected to SC at 210 °C (SC210) generated up to 2.7-fold bioaccessible glucan and xylan. SC and SE pretreatments showed potential for the deconstruction of WCLB (delignification, depolymerization, decrystallization and deacetylation), enhancing its enzymatic hydrolysis. The concentrations of enzymatic inhibitors, such as 2-furfuraldehyde and 5-(hydroxymethyl)furfural from LFSC210, were the highest (41 and 21 µg ml(-1), respectively). This study shows that steam pretreatments in general and SC210 in particular are required for efficient bioconversion of WCLB. Yet, biotransformation through biochemical processes (e.g., anaerobic digestion) must be performed to assess the efficiency of these pretreatments. © The Author(s) 2015.

  2. Parallel processing of structural integrity analysis codes

    International Nuclear Information System (INIS)

    Swami Prasad, P.; Dutta, B.K.; Kushwaha, H.S.

    1996-01-01

    Structural integrity analysis forms an important role in assessing and demonstrating the safety of nuclear reactor components. This analysis is performed using analytical tools such as Finite Element Method (FEM) with the help of digital computers. The complexity of the problems involved in nuclear engineering demands high speed computation facilities to obtain solutions in reasonable amount of time. Parallel processing systems such as ANUPAM provide an efficient platform for realising the high speed computation. The development and implementation of software on parallel processing systems is an interesting and challenging task. The data and algorithm structure of the codes plays an important role in exploiting the parallel processing system capabilities. Structural analysis codes based on FEM can be divided into two categories with respect to their implementation on parallel processing systems. The first category codes such as those used for harmonic analysis, mechanistic fuel performance codes need not require the parallelisation of individual modules of the codes. The second category of codes such as conventional FEM codes require parallelisation of individual modules. In this category, parallelisation of equation solution module poses major difficulties. Different solution schemes such as domain decomposition method (DDM), parallel active column solver and substructuring method are currently used on parallel processing systems. Two codes, FAIR and TABS belonging to each of these categories have been implemented on ANUPAM. The implementation details of these codes and the performance of different equation solvers are highlighted. (author). 5 refs., 12 figs., 1 tab

  3. Techno-Economic Analysis of Biochemical Scenarios for Production of Cellulosic Ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Kazi, F. K.; Fortman, J.; Anex, R.; Kothandaraman, G.; Hsu, D.; Aden, A.; Dutta, A.

    2010-06-01

    A techno-economic analysis on the production of cellulosic ethanol by fermentation was conducted to understand the viability of liquid biofuel production processes within the next 5-8 years. Initially, 35 technologies were reviewed, then a two-step down selection was performed to choose scenarios to be evaluated in a more detailed economic analysis. The lignocellulosic ethanol process was selected because it is well studied and portions of the process have been tested at pilot scales. Seven process variations were selected and examined in detail. Process designs were constrained to public data published in 2007 or earlier, without projecting for future process improvements. Economic analysis was performed for an 'nth plant' (mature technology) to obtain total investment and product value (PV). Sensitivity analysis was performed on PV to assess the impact of variations in process and economic parameters. Results show that the modeled dilute acid pretreatment process without any downstream process variation had the lowest PV of $3.40/gal of ethanol ($5.15/gallon of gasoline equivalent) in 2007 dollars. Sensitivity analysis shows that PV is most sensitive to feedstock and enzyme costs.

  4. Attention-deficit hyperactivity disorder in adults: A systematic review and meta-analysis of genetic, pharmacogenetic and biochemical studies

    Science.gov (United States)

    Bonvicini, C; Faraone, S V; Scassellati, C

    2016-01-01

    The adult form of attention-deficit/hyperactivity disorder has a prevalence of up to 5% and is the most severe long-term outcome of this common disorder. Family studies in clinical samples as well as twin studies suggest a familial liability and consequently different genes were investigated in association studies. Pharmacotherapy with methylphenidate (MPH) seems to be the first-line treatment of choice in adults with attention-deficit hyperactive disorder (ADHD) and some studies were conducted on the genes influencing the response to this drug. Finally some peripheral biomarkers were identified in ADHD adult patients. We believe this work is the first systematic review and meta-analysis of candidate gene association studies, pharmacogenetic and biochemical (metabolomics) studies performed in adults with ADHD to identify potential genetic, predictive and peripheral markers linked specifically to ADHD in adults. After screening 5129 records, we selected 87 studies of which 61 were available for candidate gene association studies, 5 for pharmacogenetics and 21 for biochemical studies. Of these, 15 genetic, 2 pharmacogenetic and 6 biochemical studies were included in the meta-analyses. We obtained an association between adult ADHD and the gene BAIAP2 (brain-specific angiogenesis inhibitor 1-associated protein 2), even after Bonferroni correction, with any heterogeneity in effect size and no publication bias. If we did not apply the Bonferroni correction, a trend was found for the carriers allele 9R of dopamine transporter SLC6A3 40 bp variable tandem repeat polymorphism (VNTR) and for 6/6 homozygotes of SLC6A3 30 bp VNTR. Negative results were obtained for the 9-6 haplotype, the dopamine receptor DRD4 48 bp VNTR, and the enzyme COMT SNP rs4680. Concerning pharmacogenetic studies, no association was found for the SLC6A3 40 bp and response to MPH with only two studies selected. For the metabolomics studies, no differences between ADHD adults and controls were

  5. Pin count-aware biochemical application compilation for mVLSI biochips

    DEFF Research Database (Denmark)

    Lander Raagaard, Michael; Pop, Paul

    2015-01-01

    Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. In this paper we are interested in flow-based biochips, in which the fluidic flow manipulated using integrated microvalves, which are cont...... a biochemical application. We focus on the compilation task, where the strategy is to delay operations, without missing their deadlines, such that the sharing of control signals is maximized. The evaluation shows a significant reduction in the number of control pins required....

  6. Effect of nonylphenol on male reproduction: Analysis of rat epididymal biochemical markers and antioxidant defense enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Aly, Hamdy A.A., E-mail: hamdyaali@yahoo.com [Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah (Saudi Arabia); Domènech, Òscar [Department of Physical Chemistry, Faculty of Pharmacy, Barcelona University (Spain); Banjar, Zainy M. [Department of Medical Biology, School of Medicine, King Abdulaziz University, Jeddah (Saudi Arabia)

    2012-06-01

    The mechanism by which nonylphenol (NP) interferes with male reproduction is not fully elucidated. Therefore, the present study was conducted to evaluate the effect of NP on male reproductive organ's weight, sperm characteristics, and to elucidate the nature and mechanism of action of NP on the epididymis. Adult male Wistar rats were gavaged with NP, dissolved in corn oil, at 0, 100, 200 or 300 mg/kg/day for 30 consecutive days. Control rats were gavaged with vehicle (corn oil) alone. Body weight did not show any significant change while, absolute testes and epididymides weights were significantly decreased. Sperm count in cauda and caput/corpus epididymides, and sperm motility was significantly decreased. Daily sperm production was significantly decreased in a dose-related manner. Sperm transit time in cauda epididymis was significantly decreased by 300 mg/kg, while in the caput/corpus epididymis it was significantly decreased by 200 and 300 mg/kg of NP. Plasma LDH was significantly increased while; plasma testosterone was significantly decreased in a dose-related pattern. In the epididymal sperm, NP decreased acrosome integrity, Δψm and 5′-nucleotidase activity. Hydrogen peroxide (H{sub 2}O{sub 2}) production and LPO were significantly increased in a dose-related pattern. The activities of SOD, CAT and GPx were significantly decreased in the epididymal sperm. In conclusion, this study revealed that NP treatment impairs spermatogenesis and has a cytotoxic effect on epididymal sperm. It disrupts the prooxidant and antioxidant balance. This leads oxidative stress in epididymal sperms of rat. Moreover, the reduction in sperm transit time may affect sperm quality and fertility potential. -- Highlights: ► The nature and mechanism of action of NP on rat epididymis were elucidated. ► NP decreased sperm count, motility, daily sperm production and sperm transit time. ► NP decreased sperm acrosome integrity, Δψm and 5′-nucleotidase activity. ► Plasma

  7. Effect of nonylphenol on male reproduction: Analysis of rat epididymal biochemical markers and antioxidant defense enzymes

    International Nuclear Information System (INIS)

    Aly, Hamdy A.A.; Domènech, Òscar; Banjar, Zainy M.

    2012-01-01

    The mechanism by which nonylphenol (NP) interferes with male reproduction is not fully elucidated. Therefore, the present study was conducted to evaluate the effect of NP on male reproductive organ's weight, sperm characteristics, and to elucidate the nature and mechanism of action of NP on the epididymis. Adult male Wistar rats were gavaged with NP, dissolved in corn oil, at 0, 100, 200 or 300 mg/kg/day for 30 consecutive days. Control rats were gavaged with vehicle (corn oil) alone. Body weight did not show any significant change while, absolute testes and epididymides weights were significantly decreased. Sperm count in cauda and caput/corpus epididymides, and sperm motility was significantly decreased. Daily sperm production was significantly decreased in a dose-related manner. Sperm transit time in cauda epididymis was significantly decreased by 300 mg/kg, while in the caput/corpus epididymis it was significantly decreased by 200 and 300 mg/kg of NP. Plasma LDH was significantly increased while; plasma testosterone was significantly decreased in a dose-related pattern. In the epididymal sperm, NP decreased acrosome integrity, Δψm and 5′-nucleotidase activity. Hydrogen peroxide (H 2 O 2 ) production and LPO were significantly increased in a dose-related pattern. The activities of SOD, CAT and GPx were significantly decreased in the epididymal sperm. In conclusion, this study revealed that NP treatment impairs spermatogenesis and has a cytotoxic effect on epididymal sperm. It disrupts the prooxidant and antioxidant balance. This leads oxidative stress in epididymal sperms of rat. Moreover, the reduction in sperm transit time may affect sperm quality and fertility potential. -- Highlights: ► The nature and mechanism of action of NP on rat epididymis were elucidated. ► NP decreased sperm count, motility, daily sperm production and sperm transit time. ► NP decreased sperm acrosome integrity, Δψm and 5′-nucleotidase activity. ► Plasma LDH was

  8. Office of Integrated Assessment and Policy Analysis

    International Nuclear Information System (INIS)

    Parzyck, D.C.

    1980-01-01

    The mission of the Office of Integrated Assessments and Policy Analysis (OIAPA) is to examine current and future policies related to the development and use of energy technologies. The principal ongoing research activity to date has focused on the impacts of several energy sources, including coal, oil shale, solar, and geothermal, from the standpoint of the Resource Conservation and Recovery Act. An additional project has recently been initiated on an evaluation of impacts associated with the implementation of the Toxic Substances Control Act. The impacts of the Resource Conservation and Recovery Act and the Toxic Substances Control Act on energy supply constitute the principal research focus of OIAPA for the near term. From these studies a research approach will be developed to identify certain common elements in the regulatory evaluation cycle as a means of evaluating subsequent environmental, health, and socioeconomic impact. It is planned that an integrated assessment team examine studies completed or underway on the following aspects of major regulations: health, risk assessment, testing protocols, environment control cost/benefits, institutional structures, and facility siting. This examination would assess the methodologies used, determine the general applicability of such studies, and present in a logical form information that appears to have broad general application. A suggested action plan for the State of Tennessee on radioactive and hazardous waste management is outlined

  9. Microfluidic device for continuous single cells analysis via Raman spectroscopy enhanced by integrated plasmonic nanodimers

    KAUST Repository

    Perozziello, Gerardo

    2015-12-11

    In this work a Raman flow cytometer is presented. It consists of a microfluidic device that takes advantages of the basic principles of Raman spectroscopy and flow cytometry. The microfluidic device integrates calibrated microfluidic channels- where the cells can flow one-by-one -, allowing single cell Raman analysis. The microfluidic channel integrates plasmonic nanodimers in a fluidic trapping region. In this way it is possible to perform Enhanced Raman Spectroscopy on single cell. These allow a label-free analysis, providing information about the biochemical content of membrane and cytoplasm of the each cell. Experiments are performed on red blood cells (RBCs), peripheral blood lymphocytes (PBLs) and myelogenous leukemia tumor cells (K562). © 2015 Optical Society of America.

  10. First molecular and biochemical analysis of in vivo affinity maturation in an ectothermic vertebrate.

    Science.gov (United States)

    Dooley, Helen; Stanfield, Robyn L; Brady, Rebecca A; Flajnik, Martin F

    2006-02-07

    The cartilaginous fish are the oldest phylogenetic group in which Igs have been found. Sharks produce a unique Ig isotype, IgNAR, a heavy-chain homodimer that does not associate with light chains. Instead, the variable (V) regions of IgNAR bind antigen as soluble single domains. Our group has shown that IgNAR plays an integral part in the humoral response of nurse sharks (Ginglymostoma cirratum) upon antigen challenge. Here, we generated phage-displayed libraries of IgNAR V regions from an immunized animal and found a family of clones derived from the same rearrangement event but differentially mutated during expansion. Because of the cluster organization of shark Ig genes and the paucicopy nature of IgNAR, we were able to construct the putative ancestor of this family. By studying mutations in the context of clone affinities, we found evidence that affinity maturation occurs for this isotype. Subsequently, we were able to identify mutations important in the affinity improvement of this family. Because the family clones were all obtained after immunization, they provide insight into the in vivo maturation mechanisms, in general, and for single-domain antibody fragments.

  11. Integrating Data Transformation in Principal Components Analysis

    KAUST Repository

    Maadooliat, Mehdi

    2015-01-02

    Principal component analysis (PCA) is a popular dimension reduction method to reduce the complexity and obtain the informative aspects of high-dimensional datasets. When the data distribution is skewed, data transformation is commonly used prior to applying PCA. Such transformation is usually obtained from previous studies, prior knowledge, or trial-and-error. In this work, we develop a model-based method that integrates data transformation in PCA and finds an appropriate data transformation using the maximum profile likelihood. Extensions of the method to handle functional data and missing values are also developed. Several numerical algorithms are provided for efficient computation. The proposed method is illustrated using simulated and real-world data examples.

  12. Biochemical and Computational Analysis of the Substrate Specificities of Cfr and RlmN Methyltransferases

    DEFF Research Database (Denmark)

    Ntokou, Eleni; Hansen, Lykke Haastrup; Kongsted, Jacob

    2015-01-01

    -ray structure of RlmN. We used a trinucleotide as target sequence and assessed its positioning at the active site for methylation. The calculations are in accordance with different poses of the trinucleotide in the two enzymes indicating major evolutionary changes to shift the C2/C8 specificities. To explore......Cfr and RlmN methyltransferases both modify adenine 2503 in 23S rRNA (Escherichia coli numbering). RlmN methylates position C2 of adenine while Cfr methylates position C8, and to a lesser extent C2, conferring antibiotic resistance to peptidyl transferase inhibitors. Cfr and RlmN show high sequence...... interchangeability between Cfr and RlmN we constructed various combinations of their genes. The function of the mixed genes was investigated by RNA primer extension analysis to reveal methylation at 23S rRNA position A2503 and by MIC analysis to reveal antibiotic resistance. The catalytic site is expected...

  13. What can we learn from global sensitivity analysis of biochemical systems?

    Science.gov (United States)

    Kent, Edward; Neumann, Stefan; Kummer, Ursula; Mendes, Pedro

    2013-01-01

    Most biological models of intermediate size, and probably all large models, need to cope with the fact that many of their parameter values are unknown. In addition, it may not be possible to identify these values unambiguously on the basis of experimental data. This poses the question how reliable predictions made using such models are. Sensitivity analysis is commonly used to measure the impact of each model parameter on its variables. However, the results of such analyses can be dependent on an exact set of parameter values due to nonlinearity. To mitigate this problem, global sensitivity analysis techniques are used to calculate parameter sensitivities in a wider parameter space. We applied global sensitivity analysis to a selection of five signalling and metabolic models, several of which incorporate experimentally well-determined parameters. Assuming these models represent physiological reality, we explored how the results could change under increasing amounts of parameter uncertainty. Our results show that parameter sensitivities calculated with the physiological parameter values are not necessarily the most frequently observed under random sampling, even in a small interval around the physiological values. Often multimodal distributions were observed. Unsurprisingly, the range of possible sensitivity coefficient values increased with the level of parameter uncertainty, though the amount of parameter uncertainty at which the pattern of control was able to change differed among the models analysed. We suggest that this level of uncertainty can be used as a global measure of model robustness. Finally a comparison of different global sensitivity analysis techniques shows that, if high-throughput computing resources are available, then random sampling may actually be the most suitable technique.

  14. Recent advances in biochemical and molecular analysis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency

    Directory of Open Access Journals (Sweden)

    Jin-Ho Choi

    2016-03-01

    Full Text Available The term congenital adrenal hyperplasia (CAH covers a group of autosomal recessive disorders caused by defects in one of the steroidogenic enzymes involved in the synthesis of cortisol or aldosterone from cholesterol in the adrenal glands. Approximately 95% of all CAH cases are caused by 21-hydroxylase deficiency encoded by the CYP21A2 gene. The disorder is categorized into classical forms, including the salt-wasting and the simple virilizing types, and nonclassical forms based on the severity of the disease. The severity of the clinical features varies according to the level of residual 21-hydroxylase activity. Newborn screening for CAH is performed in many countries to prevent salt-wasting crises in the neonatal period, to prevent male sex assignment in affected females, and to reduce long-term morbidities, such as short stature, gender confusion, and psychosexual disturbances. 17α-hydroxyprogesterone is a marker for 21-hydroxylase deficiency and is measured using a radioimmunoassay, an enzyme-linked immunosorbent assay, or a fluoroimmunoassay. Recently, liquid chromatography linked with tandem mass spectrometry was developed for rapid, highly specific, and sensitive analysis of multiple analytes. Urinary steroid analysis by gas chromatography mass spectrometry also provides qualitative and quantitative data on the excretion of steroid hormone metabolites. Molecular analysis of CYP21A2 is useful for genetic counseling, confirming diagnosis, and predicting prognoses. In conclusion, early detection using neonatal screening tests and treatment can prevent the worst outcomes of 21-hydroxylase deficiency.

  15. A New Data Analysis System to Quantify Associations between Biochemical Parameters of Chronic Kidney Disease-Mineral Bone Disease.

    Directory of Open Access Journals (Sweden)

    Mariano Rodriguez

    Full Text Available In hemodialysis patients, deviations from KDIGO recommended values of individual parameters, phosphate, calcium or parathyroid hormone (PTH, are associated with increased mortality. However, it is widely accepted that these parameters are not regulated independently of each other and that therapy aimed to correct one parameter often modifies the others. The aim of the present study is to quantify the degree of association between parameters of chronic kidney disease and mineral bone disease (CKD-MBD.Data was extracted from a cohort of 1758 adult HD patients between January 2000 and June 2013 obtaining a total of 46.141 records (10 year follow-up. We used an advanced data analysis system called Random Forest (RF which is based on self-learning procedure with similar axioms to those utilized for the development of artificial intelligence. This new approach is particularly useful when the variables analyzed are closely dependent to each other.The analysis revealed a strong association between PTH and phosphate that was superior to that of PTH and Calcium. The classical linear regression analysis between PTH and phosphate shows a correlation coefficient is 0.27, p<0.001, the possibility to predict PTH changes from phosphate modification is marginal. Alternatively, RF assumes that changes in phosphate will cause modifications in other associated variables (calcium and others that may also affect PTH values. Using RF the correlation coefficient between changes in serum PTH and phosphate is 0.77, p<0.001; thus, the power of prediction is markedly increased. The effect of therapy on biochemical variables was also analyzed using this RF.Our results suggest that the analysis of the complex interactions between mineral metabolism parameters in CKD-MBD may demand a more advanced data analysis system such as RF.

  16. Spermine oxidase (SMO) activity in breast tumor tissues and biochemical analysis of the anticancer spermine analogues BENSpm and CPENSpm

    International Nuclear Information System (INIS)

    Cervelli, Manuela; Grillo, Rosalba; Woster, Patrick M; Casero, Robert A Jr; Mariottini, Paolo; Bellavia, Gabriella; Fratini, Emiliano; Amendola, Roberto; Polticelli, Fabio; Barba, Marco; Federico, Rodolfo; Signore, Fabrizio; Gucciardo, Giacomo

    2010-01-01

    Polyamine metabolism has a critical role in cell death and proliferation representing a potential target for intervention in breast cancer (BC). This study investigates the expression of spermine oxidase (SMO) and its prognostic significance in BC. Biochemical analysis of Spm analogues BENSpm and CPENSpm, utilized in anticancer therapy, was also carried out to test their property in silico and in vitro on the recombinant SMO enzyme. BC tissue samples were analyzed for SMO transcript level and SMO activity. Student's t test was applied to evaluate the significance of the differences in value observed in T and NT samples. The structure modeling analysis of BENSpm and CPENSpm complexes formed with the SMO enzyme and their inhibitory activity, assayed by in vitro experiments, were examined. Both the expression level of SMO mRNA and SMO enzyme activity were significantly lower in BC samples compared to NT samples. The modeling of BENSpm and CPENSpm complexes formed with SMO and their inhibition properties showed that both were good inhibitors. This study shows that underexpression of SMO is a negative marker in BC. The SMO induction is a remarkable chemotherapeutical target. The BENSpm and CPENSpm are efficient SMO inhibitors. The inhibition properties shown by these analogues could explain their poor positive outcomes in Phases I and II of clinical trials

  17. Spermine oxidase (SMO activity in breast tumor tissues and biochemical analysis of the anticancer spermine analogues BENSpm and CPENSpm

    Directory of Open Access Journals (Sweden)

    Gucciardo Giacomo

    2010-10-01

    Full Text Available Abstract Background Polyamine metabolism has a critical role in cell death and proliferation representing a potential target for intervention in breast cancer (BC. This study investigates the expression of spermine oxidase (SMO and its prognostic significance in BC. Biochemical analysis of Spm analogues BENSpm and CPENSpm, utilized in anticancer therapy, was also carried out to test their property in silico and in vitro on the recombinant SMO enzyme. Methods BC tissue samples were analyzed for SMO transcript level and SMO activity. Student's t test was applied to evaluate the significance of the differences in value observed in T and NT samples. The structure modeling analysis of BENSpm and CPENSpm complexes formed with the SMO enzyme and their inhibitory activity, assayed by in vitro experiments, were examined. Results Both the expression level of SMO mRNA and SMO enzyme activity were significantly lower in BC samples compared to NT samples. The modeling of BENSpm and CPENSpm complexes formed with SMO and their inhibition properties showed that both were good inhibitors. Conclusions This study shows that underexpression of SMO is a negative marker in BC. The SMO induction is a remarkable chemotherapeutical target. The BENSpm and CPENSpm are efficient SMO inhibitors. The inhibition properties shown by these analogues could explain their poor positive outcomes in Phases I and II of clinical trials.

  18. Raman Spectroscopic Analysis of Biochemical Changes in Individual Triglyceride-Rich Lipoproteins in the Pre- and Postprandial State

    Energy Technology Data Exchange (ETDEWEB)

    Chan, J; Motton, D; Rutledge, J; Keim, N; Huser, T

    2004-09-13

    Individual triglyceride-rich lipoprotein (TGRL) particles derived from human volunteers are non-destructively analyzed by laser tweezers Raman microspectroscopy and information on their composition and distribution is obtained. The Raman signature of single optically trapped very low-density lipoproteins (VLDL), a subclass of TGRL, which play an important role in cardiovascular disease, exhibits distinct peaks associated with molecular vibrations of fatty acids, proteins, lipids, and structural rearrangements of lipids. Our analysis of pre- and postprandial VLDL exhibits the signature of biochemical changes in individual lipoprotein particles following the consumption of meals. Interaction of VLDL with endothelium leads to the breakdown of complex triacylglycerols and the formation of a highly ordered core of free saturated fatty acids in the particle. A particle distribution analysis reveals trends in the degree to which this process has occurred in particles at different times during the postprandial period. Differences in particle distributions based on the different ratios of polyunsaturated to saturated fats in the consumed meals are also easily discerned. Individual lipoprotein particles hydrolyzed in-vitro through addition of lipoprotein lipase (LpL) exhibit strikingly similar changes in their Raman spectra. These results demonstrate the feasibility of monitoring the dynamics of lipid metabolism of individual TGRL particles as they interact with LpL in the endothelial cell wall using Raman spectroscopy.

  19. Different energy metabolism in two human small cell lung cancer subpopulations examined by 31P magnetic resonance spectroscopy and biochemical analysis in vivo and in vitro

    DEFF Research Database (Denmark)

    Kristjansen, P E; Spang-Thomsen, M; Quistorff, B

    1991-01-01

    Two human small cell lung cancer tumor lines, maintained as solid tumor xenografts on nude mice and as in vitro cell cultures, were studied by in vivo 31P magnetic resonance spectroscopy and by biochemical analysis of extracts of solid tumors and cell cultures. The tumor lines CPH SCCL 54A and CPH...

  20. Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831.

    Science.gov (United States)

    Sánchez-Carrón, Guiomar; García-García, María Inmaculada; Zapata-Pérez, Rubén; Takami, Hideto; García-Carmona, Francisco; Sánchez-Ferrer, Alvaro

    2013-01-01

    Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD(+) salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC). The enzyme was active towards nicotinamide and several analogues, including the prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km  = 43.5 mM(-1)s(-1)) than pyrazinamidase (kcat/Km  = 3.2 mM(-1)s(-1)). Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65) was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales.

  1. Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831.

    Directory of Open Access Journals (Sweden)

    Guiomar Sánchez-Carrón

    Full Text Available Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD(+ salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC. The enzyme was active towards nicotinamide and several analogues, including the prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km  = 43.5 mM(-1s(-1 than pyrazinamidase (kcat/Km  = 3.2 mM(-1s(-1. Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65 was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales.

  2. Neutron-activation analysis for investigation of biochemical manganese in soils cotton soweol zone of Uzbekistan

    International Nuclear Information System (INIS)

    Zhumamuratov, A.; Tillaev, T.; Khatamov, Sh.; Suvanov, M.; Osinskaya, N.S.; Rakhmanova, T.P.

    2004-01-01

    Full text: For many years we neutron activation analysis of soils sampled from different areas of landscape-geochemical regions of Uzbekistan including zone of extreme ecological catastrophe of Aral. Content of manganese and some other elements in the 'soil-cotton' system was investigated. Neutron-activation method of manganese determining with productivity up to 400 samples on shift with detection limit of 1,1 10 -5 % and discrepancies not more than 10%. Was developed extremely uniform distribution of manganese in cotton sowed soils of the Republic (340-1800mg/kg) is determined. Practically all soils of cotton-sowed zone of Republic are with lack of manganese. Distribution of manganese on soil profile of separate organs of cotton (leaves seeds etc.) was studied. Correlation between gross concentration of manganese and its active part extracted by distilled water on the basis of quantity analysis was found. Successive comparison of gross content of manganese in the soil with crop capacity of cotton in different zones of Republic made it possible to find interconnection between these quantities, which proves necessity of using micro-additions of manganese in the soils where its low concentration is detected

  3. Qualitative Analysis of Integration Adapter Modeling

    OpenAIRE

    Ritter, Daniel; Holzleitner, Manuel

    2015-01-01

    Integration Adapters are a fundamental part of an integration system, since they provide (business) applications access to its messaging channel. However, their modeling and configuration remain under-represented. In previous work, the integration control and data flow syntax and semantics have been expressed in the Business Process Model and Notation (BPMN) as a semantic model for message-based integration, while adapter and the related quality of service modeling were left for further studi...

  4. PHIDIAS- Pathogen Host Interaction Data Integration and Analysis

    Indian Academy of Sciences (India)

    PHIDIAS- Pathogen Host Interaction Data Integration and Analysis- allows searching of integrated genome sequences, conserved domains and gene expressions data related to pathogen host interactions in high priority agents for public health and security ...

  5. Using of a combined approach by biochemical and image analysis to develop a new method to estimate seed maturity stage for Bordeaux area grapevine

    Directory of Open Access Journals (Sweden)

    Amélie RABOT

    2017-03-01

    Full Text Available Aim: The importance of phenolic maturity (depending on tannins and anthocyans of the grape is crucial at harvest and determines the final quality of wine. The work presented here aims to characterize the evolution of phenolic maturity of seeds for 3 varieties combining macroscopic analysis and biochemical analyzes of these tannins at phenological stages of interest. Methods and results: Using R software for macroscopic analyzes have been shown that the color varies dramatically (from green to dark brown in the two months between the bunch closure and maturity. Biochemical analysis (HPLC measurement shows that tannins in seeds are increasing from bunch closure to early veraison and decrease after this step until maturity. Conclusion: All together these results have shown that the color variation is correlated to the tannins content in the seeds. Significance of the study: Nowadays, no easy ways of prediction of phenolic maturity are known. The aim of this work is to use these results (usually considered independently to have an knowledge of seed level of phenolic maturity necessary without biochemical analysis to establish a date of great harvest for the most favorable conditions for the extraction of tannins required for the organoleptic quality of a wine .The originality of this work is to use the combined visual seeds and its biochemical composition in tannins (correlation established by CPA. Forward, these results will help to develop a decision support tool based on simply system to acquiring seed image easily usable by winemakers.

  6. Molecular and biochemical analysis of conjugation and adolescence in Tetrahymena thermophila

    International Nuclear Information System (INIS)

    Rogers, M.B.

    1986-01-01

    A previously unrecognized stage in the development of sexual maturity in Tetrahymena thermophila, adolescence, has been described. When the progeny of successfully mated cells are grown logarithmically, they are unable to form mating pairs for about 65 generations. This period is known as immaturity. During the next stage, adolescence, the progeny pair with mature cells but not with other adolescent cells despite the presence of complementary mating types. Adolescence persists for 20-25 generations before the cells attain maturity (the ability to mate with any cell of different mating type). Once paired with mature cells, adolescents successfully complete conjugation was shown genetically. Mating pairs formed between adolescent and mature cells are indistinguishable from those formed between mature cells by the criteria of cytology and two-dimensional gel electrophoresis of proteins extracted from mating pairs pulse-labelled with [ 35 S]methionine. An analysis of proteins induced during the first ten hours of conjugation was carried out using two-dimensional gel electrophoresis. The protein patterns obtained from all controls were similar. The synthesis of numerous large and basic proteins were induced during conjugation. The majority of the proteins were detected during meiosis and none were mating type specific. A library of micronuclear DNA was constructed in the plasmic PUC18. The library was screened by differential colony hybridization using cDNA complementary to polyA + RNA isolated from conjugating and control cells. Eight recombinant clones were isolated which contain sequences transcriptionally induced in conjugating cells

  7. Biochemical characterisation and dietary fibre analysis of sugar beet supplemented cookies

    International Nuclear Information System (INIS)

    Pasha, I.; Jahangir, M.F.; Akhter, S.; Manzoor, M.S.

    2016-01-01

    This study was planned to utilize sugar beet powder as a rich source of dietary fibre in cookies. Purposely, five treatments namely T1, T2, T3, T4 and T5 with 4%, 8%, 12%, 16% and 20% sugar beet powder addition in wheat flour were chosen to estimate fibre, antioxidant profiling and engineering properties of cookies. Results showed an increased content of all above mentioned parameters. With the increment in sugar beet powder addition in treatments, dietary fibre analysis have shown that total dietary fibre (TDF), insoluble dietary fibre (IDF) and soluble dietary fibre (SDF) have depicted increasing trend with maximum for T5 for all dietary fibre types. Significant results were obtained for in vitro antioxidant studies including total phenolic content (TPC) and DPPH that showed increasing trend with T1 0.6 mg GAE/g and maximum values for T5 with 2.0 mg GAE/g for TPC and for DPPH with T5 being maximum value of 1.7% and minimum for T1 with 1.3%. T5 treatment with 20% sugar beet gave best physicochemical results but disturbed sensory properties while T3 with 12% sugar beet powder showed good physicochemical and sensory characteristics. Therefore, T3 with 12% level is considered as the best source of dietary fibre in bakery products and can be considered as the prospective choice to address metabolic syndromes. (author)

  8. Biochemical Stability Analysis of Nano Scaled Contrast Agents Used in Biomolecular Imaging Detection of Tumor Cells

    Science.gov (United States)

    Kim, Jennifer; Kyung, Richard

    Imaging contrast agents are materials used to improve the visibility of internal body structures in the imaging process. Many agents that are used for contrast enhancement are now studied empirically and computationally by researchers. Among various imaging techniques, magnetic resonance imaging (MRI) has become a major diagnostic tool in many clinical specialties due to its non-invasive characteristic and its safeness in regards to ionizing radiation exposure. Recently, researchers have prepared aqueous fullerene nanoparticles using electrochemical methods. In this paper, computational simulations of thermodynamic stabilities of nano scaled contrast agents that can be used in biomolecular imaging detection of tumor cells are presented using nanomaterials such as fluorescent functionalized fullerenes. In addition, the stability and safety of different types of contrast agents composed of metal oxide a, b, and c are tested in the imaging process. Through analysis of the computational simulations, the stabilities of the contrast agents, determined by optimized energies of the conformations, are presented. The resulting numerical data are compared. In addition, Density Functional Theory (DFT) is used in order to model the electron properties of the compound.

  9. Biochemical and structural analysis of the hyperpolarization-activated K(+) channel MVP.

    Science.gov (United States)

    Randich, Amelia M; Cuello, Luis G; Wanderling, Sherry S; Perozo, Eduardo

    2014-03-18

    In contrast to the majority of voltage-gated ion channels, hyperpolarization-activated channels remain closed at depolarizing potentials and are activated at hyperpolarizing potentials. The basis for this reverse polarity is thought to be a result of differences in the way the voltage-sensing domain (VSD) couples to the pore domain. In the absence of structural data, the molecular mechanism of this reverse polarity coupling remains poorly characterized. Here we report the characterization of the structure and local dynamics of the closed activation gate (lower S6 region) of MVP, a hyperpolarization-activated potassium channel from Methanococcus jannaschii, by electron paramagnetic resonance (EPR) spectroscopy. We show that a codon-optimized version of MVP has high expression levels in Escherichia coli, is purified as a stable tetramer, and exhibits expected voltage-dependent activity when reconstituted in liposomes. EPR analysis of the mid to lower S6 region revealed positions exhibiting strong spin-spin coupling, indicating that the activation gate of MVP is closed at 0 mV. A comparison of local environmental parameters along the activation gate for MVP and KcsA indicates that MVP adopts a different closed conformation. These structural details set the stage for future evaluations of reverse electromechanical coupling in MVP.

  10. Biochemical and Structural Analysis of the Hyperpolarization-Activated K+ Channel MVP

    Science.gov (United States)

    2015-01-01

    In contrast to the majority of voltage-gated ion channels, hyperpolarization-activated channels remain closed at depolarizing potentials and are activated at hyperpolarizing potentials. The basis for this reverse polarity is thought to be a result of differences in the way the voltage-sensing domain (VSD) couples to the pore domain. In the absence of structural data, the molecular mechanism of this reverse polarity coupling remains poorly characterized. Here we report the characterization of the structure and local dynamics of the closed activation gate (lower S6 region) of MVP, a hyperpolarization-activated potassium channel from Methanococcus jannaschii, by electron paramagnetic resonance (EPR) spectroscopy. We show that a codon-optimized version of MVP has high expression levels in Escherichia coli, is purified as a stable tetramer, and exhibits expected voltage-dependent activity when reconstituted in liposomes. EPR analysis of the mid to lower S6 region revealed positions exhibiting strong spin–spin coupling, indicating that the activation gate of MVP is closed at 0 mV. A comparison of local environmental parameters along the activation gate for MVP and KcsA indicates that MVP adopts a different closed conformation. These structural details set the stage for future evaluations of reverse electromechanical coupling in MVP. PMID:24490868

  11. Biochemical analysis of respiratory metabolism in the heterofermentative Lactobacillus spicheri and Lactobacillus reuteri.

    Science.gov (United States)

    Ianniello, R G; Zheng, J; Zotta, T; Ricciardi, A; Gänzle, M G

    2015-09-01

    This study evaluated the aerobic and respiratory metabolism in Lactobacillus reuteri and Lactobacillus spicheri, two heterofermentative species used in sourdough fermentation. In silico genome analysis, production of metabolites and gene expression of pyruvate oxidase, pyruvate dehydrogenase and cytochrome oxidase were assessed in anaerobic and aerobic cultures of Lact. reuteri and Lact. spicheri. Respiring homofermentative Lactobacillus casei N87 and Lact. rhamnosus N132 were used for comparison. Aerobiosis and respiration increased the biomass production of heterofermentative strains compared to anaerobic cultivation. Respiration led to acetoin production by Lact. rhamnosus and Lact. casei, but not in heterofermentative strains, in which lactate and acetate were the major end-products. Lactobacillus spicheri LP38 showed the highest oxygen uptake. Pyruvate oxidase, respiratory cytochromes, NADH oxidase and NADH peroxidase were present in the genome of Lact. spicheri LP38. Both Lact. spicheri LP38 and Lact. rhamnosus N132 overexpressed pox in aerobic cultures, while cydA was up-regulated only when haeme was supplied; pdh was repressed during aerobic growth. Aerobic and respiratory growth provided physiological and metabolic advantages also in heterofermentative lactobacilli. The exploitation of oxygen-tolerant phenotypes of Lact. spicheri may be useful for the development of improved starter cultures. © 2015 The Society for Applied Microbiology.

  12. Enzyme and biochemical producing fungi

    DEFF Research Database (Denmark)

    Lübeck, Peter Stephensen; Lübeck, Mette; Nilsson, Lena

    2010-01-01

    factories for sustainable production of important molecules. For developing fungi into efficient cell factories, the project includes identification of important factors that control the flux through the pathways using metabolic flux analysis and metabolic engineering of biochemical pathways....

  13. Structural and chemical analysis of process residue from biochemical conversion of wheat straw (Triticum aestivum L.) to ethanol

    DEFF Research Database (Denmark)

    Hansen, Mads Anders Tengstedt; Jørgensen, Henning; Laursen, Kristian Holst

    2013-01-01

    Biochemical conversion of lignocellulose to fermentable carbohydrates for ethanol production is now being implemented in large-scale industrial production. Applying hydrothermal pretreatment and enzymatic hydrolysis for the conversion process, a residue containing substantial amounts of lignin...

  14. Comparative analysis of whole mount processing and systematic sampling of radical prostatectomy specimens: pathological outcomes and risk of biochemical recurrence.

    Science.gov (United States)

    Salem, Shady; Chang, Sam S; Clark, Peter E; Davis, Rodney; Herrell, S Duke; Kordan, Yakup; Wills, Marcia L; Shappell, Scott B; Baumgartner, Roxelyn; Phillips, Sharon; Smith, Joseph A; Cookson, Michael S; Barocas, Daniel A

    2010-10-01

    Whole mount processing is more resource intensive than routine systematic sampling of radical retropubic prostatectomy specimens. We compared whole mount and systematic sampling for detecting pathological outcomes, and compared the prognostic value of pathological findings across pathological methods. We included men (608 whole mount and 525 systematic sampling samples) with no prior treatment who underwent radical retropubic prostatectomy at Vanderbilt University Medical Center between January 2000 and June 2008. We used univariate and multivariate analysis to compare the pathological outcome detection rate between pathological methods. Kaplan-Meier curves and the log rank test were used to compare the prognostic value of pathological findings across pathological methods. There were no significant differences between the whole mount and the systematic sampling groups in detecting extraprostatic extension (25% vs 30%), positive surgical margins (31% vs 31%), pathological Gleason score less than 7 (49% vs 43%), 7 (39% vs 43%) or greater than 7 (12% vs 13%), seminal vesicle invasion (8% vs 10%) or lymph node involvement (3% vs 5%). Tumor volume was higher in the systematic sampling group and whole mount detected more multiple surgical margins (each p systematic sampling yield similar pathological information. Each method stratifies patients into comparable risk groups for biochemical recurrence. Thus, while whole mount is more resource intensive, it does not appear to result in improved detection of clinically important pathological outcomes or prognostication. Copyright © 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  15. Prediction of phospholipidosis-inducing potential of drugs by in vitro biochemical and physicochemical assays followed by multivariate analysis.

    Science.gov (United States)

    Kuroda, Yukihiro; Saito, Madoka

    2010-03-01

    An in vitro method to predict phospholipidosis-inducing potential of cationic amphiphilic drugs (CADs) was developed using biochemical and physicochemical assays. The following parameters were applied to principal component analysis, as well as physicochemical parameters: pK(a) and clogP; dissociation constant of CADs from phospholipid, inhibition of enzymatic phospholipid degradation, and metabolic stability of CADs. In the score plot, phospholipidosis-inducing drugs (amiodarone, propranolol, imipramine, chloroquine) were plotted locally forming the subspace for positive CADs; while non-inducing drugs (chlorpromazine, chloramphenicol, disopyramide, lidocaine) were placed scattering out of the subspace, allowing a clear discrimination between both classes of CADs. CADs that often produce false results by conventional physicochemical or cell-based assay methods were accurately determined by our method. Basic and lipophilic disopyramide could be accurately predicted as a nonphospholipidogenic drug. Moreover, chlorpromazine, which is often falsely predicted as a phospholipidosis-inducing drug by in vitro methods, could be accurately determined. Because this method uses the pharmacokinetic parameters pK(a), clogP, and metabolic stability, which are usually obtained in the early stages of drug development, the method newly requires only the two parameters, binding to phospholipid, and inhibition of lipid degradation enzyme. Therefore, this method provides a cost-effective approach to predict phospholipidosis-inducing potential of a drug. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  16. Migration in Deltas: An Integrated Analysis

    Science.gov (United States)

    Nicholls, Robert J.; Hutton, Craig W.; Lazar, Attila; Adger, W. Neil; Allan, Andrew; Arto, Inaki; Vincent, Katharine; Rahman, Munsur; Salehin, Mashfiqus; Sugata, Hazra; Ghosh, Tuhin; Codjoe, Sam; Appeaning-Addo, Kwasi

    2017-04-01

    Deltas and low-lying coastal regions have long been perceived as vulnerable to global sea-level rise, with the potential for mass displacement of exposed populations. The assumption of mass displacement of populations in deltas requires a comprehensive reassessment in the light of present and future migration in deltas, including the potential role of adaptation to influence these decisions. At present, deltas are subject to multiple drivers of environmental change and often have high population densities as they are accessible and productive ecosystems. Climate change, catchment management, subsidence and land cover change drive environmental change across all deltas. Populations in deltas are also highly mobile, with significant urbanization trends and the growth of large cities and mega-cities within or adjacent to deltas across Asia and Africa. Such migration is driven primarily by economic opportunity, yet environmental change in general, and climate change in particular, are likely to play an increasing direct and indirect role in future migration trends. The policy challenges centre on the role of migration within regional adaptation strategies to climate change; the protection of vulnerable populations; and the future of urban settlements within deltas. This paper reviews current knowledge on migration and adaptation to environmental change to discern specific issues pertinent to delta regions. It develops a new integrated methodology to assess present and future migration in deltas using the Volta delta in Ghana, Mahanadi delta in India and Ganges-Brahmaputra-Meghna delta across India and Bangladesh. The integrated method focuses on: biophysical changes and spatial distribution of vulnerability; demographic changes and migration decision-making using multiple methods and data; macro-economic trends and scenarios in the deltas; and the policies and governance structures that constrain and enable adaptation. The analysis is facilitated by a range of

  17. The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients.

    Science.gov (United States)

    Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

    2017-10-03

    The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages PHI. In biochemical recurrence prediction PHI, PSA, [-2]proPSA, PHI- and PSA-density were the strongest predictors. In conclusion, due to heterogeneity of time spans to biochemical recurrence, longer follow up periods are crucial. This study with a median follow up of more than 5 years, confirmed a clinical value for PHI as an independent biomarker essential for biochemical recurrence prediction.

  18. Integration of risk analysis, land use planning, and cost analysis

    International Nuclear Information System (INIS)

    Rajen, G.; Sanchez, G.

    1994-01-01

    The Department of Energy (DOE) and the Pueblo of San Ildefonso (Pueblo), which is a sovereign Indian tribe, have often been involved in adversarial situations regarding the Los Alamos National Laboratory (LANL). The Pueblo shares a common boundary with the LANL. This paper describes an on-going project that could alter the DOE and the Pueblo's relationship to one of cooperation; and unite the DOE and the Pueblo in a Pollution Prevention/Waste Minimization, and Integrated Risk Analysis and Land Use Planning effort

  19. IMP: Integrated method for power analysis

    Energy Technology Data Exchange (ETDEWEB)

    1989-03-01

    An integrated, easy to use, economical package of microcomputer programs has been developed which can be used by small hydro developers to evaluate potential sites for small scale hydroelectric plants in British Columbia. The programs enable evaluation of sites located far from the nearest stream gauging station, for which streamflow data are not available. For each of the province's 6 hydrologic regions, a streamflow record for one small watershed is provided in the data base. The program can then be used to generate synthetic streamflow records and to compare results obtained by the modelling procedure with the actual data. The program can also be used to explore the significance of modelling parameters and to develop a detailed appreciation for the accuracy which can be obtained under various circumstances. The components of the program are an atmospheric model of precipitation; a watershed model that will generate a continuous series of streamflow data, based on information from the atmospheric model; a flood frequency analysis system that uses site-specific topographic data plus information from the atmospheric model to generate a flood frequency curve; a hydroelectric power simulation program which determines daily energy output for a run-of-river or reservoir storage site based on selected generation facilities and the time series generated in the watershed model; and a graphic analysis package that provides direct visualization of data and modelling results. This report contains a description of the programs, a user guide, the theory behind the model, the modelling methodology, and results from a workshop that reviewed the program package. 32 refs., 16 figs., 18 tabs.

  20. Histo-chemical and biochemical analysis reveals association of er1 mediated powdery mildew resistance and redox balance in pea.

    Science.gov (United States)

    Mohapatra, Chinmayee; Chand, Ramesh; Navathe, Sudhir; Sharma, Sandeep

    2016-09-01

    Powdery mildew caused by Erysiphe pisi is one of the important diseases responsible for heavy yield losses in pea crop worldwide. The most effective method of controlling the disease is the use of resistant varieties. The resistance to powdery mildew in pea is recessive and governed by a single gene er1. The objective of present study is to investigate if er1 mediated powdery mildew resistance is associated with changes in the redox status of the pea plant. 16 pea genotypes were screened for powdery mildew resistance in field condition for two years and, also, analyzed for the presence/absence of er1 gene. Histochemical analysis with DAB and NBT staining indicates accumulation of reactive oxygen species (ROS) in surrounding area of powdery mildew infection which was higher in susceptible genotypes as compared to resistant genotypes. A biochemical study revealed that the activity of superoxide dismutase (SOD) and catalase, enzymes involved in scavenging ROS, was increased in, both, resistant and susceptible genotypes after powdery mildew infection. However, both enzymes level was always higher in resistant than susceptible genotypes throughout time course of infection. Moreover, irrespective of any treatment, the total phenol (TP) and malondialdehyde (MDA) content was significantly high and low in resistant genotypes, respectively. The powdery mildew infection elevated the MDA content but decreased the total phenol in pea genotypes. Statistical analysis showed a strong positive correlation between AUDPC and MDA; however, a negative correlation was observed between AUDPC and SOD, CAT and TP. Heritability of antioxidant was also high. The study identified few novel genotypes resistant to powdery mildew infection that carried the er1 gene and provided further clue that er1 mediated defense response utilizes antioxidant machinery to confer powdery mildew resistance in pea. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. K West integrated water treatment system subproject safety analysis document

    International Nuclear Information System (INIS)

    SEMMENS, L.S.

    1999-01-01

    This Accident Analysis evaluates unmitigated accident scenarios, and identifies Safety Significant and Safety Class structures, systems, and components for the K West Integrated Water Treatment System

  2. K West integrated water treatment system subproject safety analysis document

    Energy Technology Data Exchange (ETDEWEB)

    SEMMENS, L.S.

    1999-02-24

    This Accident Analysis evaluates unmitigated accident scenarios, and identifies Safety Significant and Safety Class structures, systems, and components for the K West Integrated Water Treatment System.

  3. Integrating health and environmental impact analysis.

    Science.gov (United States)

    Reis, S; Morris, G; Fleming, L E; Beck, S; Taylor, T; White, M; Depledge, M H; Steinle, S; Sabel, C E; Cowie, H; Hurley, F; Dick, J McP; Smith, R I; Austen, M

    2015-10-01

    Scientific investigations have progressively refined our understanding of the influence of the environment on human health, and the many adverse impacts that human activities exert on the environment, from the local to the planetary level. Nonetheless, throughout the modern public health era, health has been pursued as though our lives and lifestyles are disconnected from ecosystems and their component organisms. The inadequacy of the societal and public health response to obesity, health inequities, and especially global environmental and climate change now calls for an ecological approach which addresses human activity in all its social, economic and cultural complexity. The new approach must be integral to, and interactive, with the natural environment. We see the continuing failure to truly integrate human health and environmental impact analysis as deeply damaging, and we propose a new conceptual model, the ecosystems-enriched Drivers, Pressures, State, Exposure, Effects, Actions or 'eDPSEEA' model, to address this shortcoming. The model recognizes convergence between the concept of ecosystems services which provides a human health and well-being slant to the value of ecosystems while equally emphasizing the health of the environment, and the growing calls for 'ecological public health' as a response to global environmental concerns now suffusing the discourse in public health. More revolution than evolution, ecological public health will demand new perspectives regarding the interconnections among society, the economy, the environment and our health and well-being. Success must be built on collaborations between the disparate scientific communities of the environmental sciences and public health as well as interactions with social scientists, economists and the legal profession. It will require outreach to political and other stakeholders including a currently largely disengaged general public. The need for an effective and robust science-policy interface has

  4. Noise analysis of switched integrator preamplifiers

    International Nuclear Information System (INIS)

    Sun Hongbo; Li Yulan; Zhu Weibin

    2004-01-01

    The main noise sources of switched integrator preamplifiers are discussed, and their noise performance are given combined PSpice simulation and experiments on them. Then, some practical methods on how to reduce noise of preamplifiers in two different integrator modes are provided. (authors)

  5. Social Ecological Model Analysis for ICT Integration

    Science.gov (United States)

    Zagami, Jason

    2013-01-01

    ICT integration of teacher preparation programmes was undertaken by the Australian Teaching Teachers for the Future (TTF) project in all 39 Australian teacher education institutions and highlighted the need for guidelines to inform systemic ICT integration approaches. A Social Ecological Model (SEM) was used to positively inform integration…

  6. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

    Science.gov (United States)

    Zhang, Fan; Drabier, Renee

    2012-01-01

    Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpret and distill such large amounts of data. Extensive pathway and network analysis allow for the discovery of highly significant pathways from a set of disease vs. healthy samples in the NGS and GWAS. Knowledge of activation of these processes will lead to elucidation of the complex biological pathways affected by drug treatment, to patient stratification studies of new and existing drug treatments, and to understanding the underlying anti-cancer drug effects. There are approximately 141 biological human pathway resources as of Jan 2012 according to the Pathguide database. However, most currently available resources do not contain disease, drug or organ specificity information such as disease-pathway, drug-pathway, and organ-pathway associations. Systematically integrating pathway, disease, drug and organ specificity together becomes increasingly crucial for understanding the interrelationships between signaling, metabolic and regulatory pathway, drug action, disease susceptibility, and organ specificity from high-throughput omics data (genomics, transcriptomics, proteomics and metabolomics). We designed the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (IPAD, http://bioinfo.hsc.unt.edu/ipad), defining inter-association between pathway, disease, drug and organ specificity, based on six criteria: 1) comprehensive pathway coverage; 2) gene/protein to pathway/disease/drug/organ association; 3) inter-association between pathway, disease, drug, and organ; 4) multiple and quantitative measurement of enrichment and inter-association; 5) assessment of enrichment and inter-association analysis with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources; and 6) cross-linking of

  7. CFD Analysis for Advanced Integrated Head Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Won Ho; Kang, Tae Kyo; Cho, Yeon Ho; Kim, Hyun Min [KEPCO Engineering and Construction Co., Daejeon (Korea, Republic of)

    2016-10-15

    The Integrated Head Assembly (IHA) is permanently installed on the reactor vessel closure head during the normal plant operation and refueling operation. It consists of a number of systems and components such as the head lifting system, seismic support system, Control Element Drive Mechanism (CEDM) cooling system, cable support system, cooling shroud assemblies. With the operating experiences of the IHA, the needs for the design change to the current APR1400 IHA arouse to improve the seismic resistance and to accommodate the convenient maintenance. In this paper, the effects of the design changes were rigorously studied for the various sizes of the inlet openings to assure the proper cooling of the CEDMs. And the system pressure differentials and required flow rate for the CEDM cooling fan were analyzed regarding the various operating conditions for determining the capacity of the fan. As a part of the design process of the AIHA, the number of air inlets and baffle regions are reduced by simplifying the design of the APR1400 IHA. The design change of the baffle regions has been made such that the maximum possible space are occupied inside the IHA cooling shroud shell while avoiding the interference with CEDMs. So, only the air inlet opening was studied for the design change to supply a sufficient cooling air flow for each CEDM. The size and location of the air inlets in middle cooling shroud assembly were determined by the CFD analyses of the AIHA. And the case CFD analyses were performed depending on the ambient air temperature and fan operating conditions. The size of the air inlet openings is increased by comparison with the initial AIHA design, and it is confirmed that the cooling air flow rate for each CEDM meet the design requirement of 800 SCFM ± 10% with the increased air inlets. At the initial analysis, the fan outlet flow rate was assumed as 48.3 lbm/s, but the result revealed that the less outflow rate at the fan is enough to meet the design requirement

  8. Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

    Science.gov (United States)

    Popovsky-Sarid, Sigal; Borovsky, Yelena; Faigenboim, Adi; Parsons, Eugene P; Lohrey, Gregory T; Alkalai-Tuvia, Sharon; Fallik, Elazar; Jenks, Matthew A; Paran, Ilan

    2017-02-01

    Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.

  9. Sensitivity Analysis for Design Optimization Integrated Software Tools, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this proposed project is to provide a new set of sensitivity analysis theory and codes, the Sensitivity Analysis for Design Optimization Integrated...

  10. Game analysis of product-service integration

    Directory of Open Access Journals (Sweden)

    Heping Zhong

    2014-10-01

    Full Text Available Purpose: This paper aims at defining the value creation mechanism and income distribution strategies of product-service integration in order to promote product-service integration of a firm.Design/methodology/approach: This paper conducts researches quantitatively on the coordination mechanism of product-service integration by using game theory, and uses the methods of Shapley value and Equal growth rate to further discuss income distribution strategies of product-service integration.Findings: Product-service integration increases the total income of a firm and the added value of the income decreases as the unit price demand variation coefficient of products and services increases, while decreases as the marginal cost of products increases, decreases as the marginal cost of services increases. Moreover, the findings suggest that both income distribution strategies of product-service integration based on Shapley value method and Equal growth rate method can make the product department and service department of a firm win-win and realize the pareto improvement. The choice of what kind of distribution strategy to coordinate the actions between departments depends on the department playing dominant role in the firm. Generally speaking, for a firm at the center of market, when the product department is the main contributor to firm income, the service department will choose the income distribution strategy of product-service integration based on Shapley value method; when the service department is the main contributor to firm income, the service department will choose the income distribution strategy of product-service integration based on Equal growth rate method.Research limitations/implications: This paper makes some strict assumptions such as complete information, risk neutral, linear cost function and so on and the discussion is limited to the simple relationship between product department and service department.Practical implications: Product

  11. Advanced Concept Architecture Design and Integrated Analysis (ACADIA)

    Science.gov (United States)

    2017-11-03

    1 Advanced Concept Architecture Design and Integrated Analysis (ACADIA) Submitted to the National Institute of Aerospace (NIA) on...Research Report 20161001 - 20161030 Advanced Concept Architecture Design and Integrated Analysis (ACADIA) W911NF-16-2-0229 8504Cedric Justin, Youngjun

  12. Integrating fire management analysis into land management planning

    Science.gov (United States)

    Thomas J. Mills

    1983-01-01

    The analysis of alternative fire management programs should be integrated into the land and resource management planning process, but a single fire management analysis model cannot meet all planning needs. Therefore, a set of simulation models that are analytically separate from integrated land management planning models are required. The design of four levels of fire...

  13. Real analysis measure theory, integration, and Hilbert spaces

    CERN Document Server

    Stein, Elias M

    2005-01-01

    Real Analysis is the third volume in the Princeton Lectures in Analysis, a series of four textbooks that aim to present, in an integrated manner, the core areas of analysis. Here the focus is on the development of measure and integration theory, differentiation and integration, Hilbert spaces, and Hausdorff measure and fractals. This book reflects the objective of the series as a whole: to make plain the organic unity that exists between the various parts of the subject, and to illustrate the wide applicability of ideas of analysis to other fields of mathematics and science. After

  14. Semantic web for integrated network analysis in biomedicine.

    Science.gov (United States)

    Chen, Huajun; Ding, Li; Wu, Zhaohui; Yu, Tong; Dhanapalan, Lavanya; Chen, Jake Y

    2009-03-01

    The Semantic Web technology enables integration of heterogeneous data on the World Wide Web by making the semantics of data explicit through formal ontologies. In this article, we survey the feasibility and state of the art of utilizing the Semantic Web technology to represent, integrate and analyze the knowledge in various biomedical networks. We introduce a new conceptual framework, semantic graph mining, to enable researchers to integrate graph mining with ontology reasoning in network data analysis. Through four case studies, we demonstrate how semantic graph mining can be applied to the analysis of disease-causal genes, Gene Ontology category cross-talks, drug efficacy analysis and herb-drug interactions analysis.

  15. Integrated risk analysis of global climate change

    International Nuclear Information System (INIS)

    Shlyakhter, Alexander; Wilson, Richard; Valverde A, L.J. Jr.

    1995-01-01

    This paper discusses several factors that should be considered in integrated risk analyses of global climate change. We begin by describing how the problem of global climate change can be subdivided into largely independent parts that can be linked together in an analytically tractable fashion. Uncertainty plays a central role in integrated risk analyses of global climate change. Accordingly, we consider various aspects of uncertainty as they relate to the climate change problem. We also consider the impacts of these uncertainties on various risk management issues, such as sequential decision strategies, value of information, and problems of interregional and intergenerational equity. (author)

  16. Integrated watershed analysis: adapting to changing times

    Science.gov (United States)

    Gordon H. Reeves

    2013-01-01

    Resource managers are increasingly required to conduct integrated analyses of aquatic and terrestrial ecosystems before undertaking any activities. Th ere are a number of research studies on the impacts of management actions on these ecosystems, as well as a growing body of knowledge about ecological processes that aff ect them, particularly aquatic ecosystems, which...

  17. Relay Feedback Analysis for Double Integral Plants

    Directory of Open Access Journals (Sweden)

    Zhen Ye

    2011-01-01

    Full Text Available Double integral plants under relay feedback are studied. Complete results on the uniqueness of solutions, existence, and stability of the limit cycles are established using the point transformation method. Analytical expressions are also given for determining the amplitude and period of a limit cycle from the plant parameters.

  18. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Directory of Open Access Journals (Sweden)

    Nancy Martínez-Montiel

    Full Text Available The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization

  19. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Science.gov (United States)

    Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

    2016-01-01

    The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability

  20. Biochemical analysis of the Hormoconis resinae fungal mycelium in the corrosion of aeronautical aluminium alloys

    Directory of Open Access Journals (Sweden)

    Araya, R.

    2007-06-01

    Full Text Available Biochemical analyses of the Hormoconis resinae fungal mycelium would explain behaviour differences of corrosive and non-corrosive strains on Al and its aeronautical alloys. In previous works its aggressiveness had been studied through SEM-EDX surface analysis, electrochemical techniques and immersion testing. In this paper separation of the proteins of the mycelium produced by a non-corrosive strain and its culture along three generations was performed. Cultures were prepared in batch in the presence and absence of pure Al and AA 2024, AA 7005 and AA 7075 alloys. The mycelia grown throughout the three generations increasingly
    recovered usual characteristics at the third replication, included their corrosiveness on Al and its alloys previously shown by all our strains. Amongst the bio-molecule fractions isolated and analysed during this preliminary study only the proteins revealed changes with the generation grown. When this fungal strain was cultured in the presence of alloy metal sheets electrophoresis of the protean fraction was correlative with the distinct mycelia behaviour observed, including corrosiveness on Al and its alloys.

    Las diferencias entre el comportamiento corrosivo y no corrosivo de una cepa del hongo Hormoconis resinae sobre aluminio y sus aleaciones aeronáuticas se explicarían a través de análisis bioquímicos del micelio. En trabajos previos, el comportamiento corrosivo se estudió mediante análisis de superficie SEM-EDX, técnicas electroquímicas y ensayos de inmersión. En este trabajo, se llevó a cabo la separación de proteínas del micelio producido por una cepa que perdió su corrosividad y su cultivo a través de tres generaciones. Cultivos en batch, en presencia y ausencia de aluminio y sus aleaciones AA 2024, AA 7005 y AA 7075, a través de tres generaciones del micelio crecido, fueron recuperando sus características, incluida su habitual corrosividad, en la tercera replicaci

  1. Efficacy of transsphenoidal surgery in achieving biochemical cure of growth hormone-secreting pituitary adenomas among patients with cavernous sinus invasion: a systematic review and meta-analysis.

    Science.gov (United States)

    Briceno, Vanessa; Zaidi, Hasan A; Doucette, Joanne A; Onomichi, Kaho B; Alreshidi, Amer; Mekary, Rania A; Smith, Timothy R

    2017-05-01

    Growth hormone-secreting pituitary adenomas in adults can result in severe craniofacial disfigurement and potentially fatal medical complications. Surgical resection leading to remission of the disease is dependent on complete surgical resection of the tumor. Lesions that invade the cavernous sinus may not be safely accessible via an endonasal transsphenoidal surgery (TSS), and the rates of biochemical remission of patients with residual disease vary widely in the literature. We conducted a meta-analysis to examine the prevalence of biochemical remission after TSS among patients with growth hormone-secreting pituitary adenomas with and without cavernous sinus invasion. Embase, PubMed, and Cochrane Library databases were searched for relevant publications. Fourteen studies with 972 patients with biochemically confirmed growth hormone-secreting pituitary adenomas were included in the meta-analysis. The overall remission prevalence under a fixed-effect model was 47.6% (95% CI = 40.8-54.4%) for patients with invasive macroadenomas (I 2  = 74.6%, p < 0.01); 76.4% (95% CI = 72.2-80.1%) for patients with non-invasive macroadenomas (I 2  = 59.6%, p = 0.03); and 74.2% (95% CI = 66.3-80.7%) for patients with non-invasive microadenomas (I 2  = 36.4, p = 0.10). The significant difference among the three groups resulted from the difference between patients with or without cavernous sinus invasion (p = 0.01) and not from the size of adenomas among those without cavernous sinus invasion (p = 0.66). The prevalence of biochemical remission in patients with cavernous sinus invasion was lower than in patients without cavernous sinus invasion after TSS for acromegaly.

  2. Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

    Science.gov (United States)

    Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

    2015-01-01

    Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.

  3. Integration of video and radiation analysis data

    International Nuclear Information System (INIS)

    Menlove, H.O.; Howell, J.A.; Rodriguez, C.A.; Eccleston, G.W.; Beddingfield, D.; Smith, J.E.; Baumgart, C.W.

    1995-01-01

    For the past several years, the integration of containment and surveillance (C/S) with nondestructive assay (NDA) sensors for monitoring the movement of nuclear material has focused on the hardware and communications protocols in the transmission network. Little progress has been made in methods to utilize the combined C/S and NDA data for safeguards and to reduce the inspector time spent in nuclear facilities. One of the fundamental problems in the integration of the combined data is that the two methods operate in different dimensions. The C/S video data is spatial in nature; whereas, the NDA sensors provide radiation levels versus time data. The authors have introduced a new method to integrate spatial (digital video) with time (radiation monitoring) information. This technology is based on pattern recognition by neural networks, provides significant capability to analyze complex data, and has the ability to learn and adapt to changing situations. This technique has the potential of significantly reducing the frequency of inspection visits to key facilities without a loss of safeguards effectiveness

  4. Fast and Cost-Effective Biochemical Spectrophotometric Analysis of Solution of Insect “Blood” and Body Surface Elution

    Directory of Open Access Journals (Sweden)

    Aleksandra Łoś

    2018-05-01

    Full Text Available Using insect hemolymph (“blood” and insect body surface elutions, researchers can perform rapid and cheap biochemical analyses to determine the insect’s immunology status. The authors of this publication describe a detailed methodology for a quick marking of the concentration of total proteins and evaluation of the proteolytic system activity (acid, neutral, and alkaline proteases and protease inhibitors, as well as a methodology for quick “liver” tests in insects: alanine aminotransferase (ALT, aspartate aminotransferase (AST, alkaline phosphatase (ALP, and urea and glucose concentration analyses. The meaning and examples of an interpretation of the results of the presented methodology for biochemical parameter determination are described for the example of honey bees.

  5. Integration of Design and Control through Model Analysis

    DEFF Research Database (Denmark)

    Russel, Boris Mariboe; Henriksen, Jens Peter; Jørgensen, Sten Bay

    2002-01-01

    A systematic computer aided analysis of the process model is proposed as a pre-solution step for integration of design and control problems. The process model equations are classified in terms of balance equations, constitutive equations and conditional equations. Analysis of the phenomena models...... (structure selection) issues for the integrated problems are considered. (C) 2002 Elsevier Science Ltd. All rights reserved....... representing the constitutive equations identify the relationships between the important process and design variables, which help to understand, define and address some of the issues related to integration of design and control. Furthermore, the analysis is able to identify a set of process (control) variables...

  6. Phytochemical analysis and In-vitro Biochemical Characterization of aqueous and methanolic extract of Triphala, a conventional herbal remedy

    Directory of Open Access Journals (Sweden)

    Romana Parveen

    2018-03-01

    Results revealed the presence of valuable bioactive compounds such as flavonoids, alkaloids, phenols, etc which might be responsible for biochemical activities. Extracts exhibited satisfactory radical-scavenging activity comparable with ascorbic acid. Methanolic extracts demonstrated higher antioxidant activity compared to aqueous extract. Extracts showed promising antibacterial potential against tested strain comparable to ampicillin. Hence, it can be concluded that triphala may be a promising candidate in pharmaceuticals and future medicine.

  7. Fast and Cost-Effective Biochemical Spectrophotometric Analysis of Solution of Insect “Blood” and Body Surface Elution

    OpenAIRE

    Aleksandra Łoś; Aneta Strachecka

    2018-01-01

    Using insect hemolymph (“blood”) and insect body surface elutions, researchers can perform rapid and cheap biochemical analyses to determine the insect’s immunology status. The authors of this publication describe a detailed methodology for a quick marking of the concentration of total proteins and evaluation of the proteolytic system activity (acid, neutral, and alkaline proteases and protease inhibitors), as well as a methodology for quick “liver” tests in insects: alanine aminotransferase ...

  8. High-dose rate brachytherapy in the treatment of prostate cancer: acute toxicity and biochemical behavior analysis

    International Nuclear Information System (INIS)

    Esteves, Sergio Carlos Barros; Oliveira, Antonio Carlos Zuliani de; Cardoso, Herbeni; Tagawa, Eduardo Komai; Castelo, Roberto; D'Imperio, Marcio

    2006-01-01

    Objective: this study focuses on the biochemical response of the following variables: prostate volume, prostate-specific antigen (PSA) value, Gleason scores, staging, the risk of the disease, and hormone therapy. Objective: in the period between February of 1998 and July of 2001, 46 patients with prostate cancer were treated with radiotherapy, in a combination of teletherapy and high-dose rate (HDR) brachytherapy. The age ranged from 51 to 79 years (averaging 66.4 years). T1c stage was the most frequent one: 30 (65%). The Gleason score was below 7 in 78% of the patients. PSA ranged from 3.4 to 33.3, being below 10 in 39% of the cases. The average prostatic volume was 32.3 cc. Twenty-eight percent of the patients received hormone therapy. Teletherapy dose ranged from 45 to 50.4 Gy, associated to four fractions of 4 Gy of HDR brachytherapy. Results: the follow-up period varied from 6 to 43 months. Four patients missed the follow-up and four died (one due to the disease). Out of the 39 patients that were analyzed, 76% presented a less than 1.5 PSA. None of the analyzed variables were found to be of statistical significance (p > 0.05) regarding biochemical control. Conclusion: the use of HDR brachytherapy was found to be effective in the treatment of prostate cancer and, in this study, the variables considered as prognostic factors did not interfere in the biochemical control. (author)

  9. Analysis of Optimal Operation of an Energy Integrated Distillation Plant

    DEFF Research Database (Denmark)

    Li, Hong Wen; Hansen, C.A.; Gani, Rafiqul

    2003-01-01

    The efficiency of manufacturing systems can be significantly increased through diligent application of control based on mathematical models thereby enabling more tight integration of decision making with systems operation. In the present paper analysis of optimal operation of an energy integrated...

  10. Integrated program of using of Probabilistic Safety Analysis in Spain

    International Nuclear Information System (INIS)

    1998-01-01

    Since 25 June 1986, when the CSN (Nuclear Safety Conseil) approve the Integrated Program of Probabilistic Safety Analysis, this program has articulated the main activities of CSN. This document summarize the activities developed during these years and reviews the Integrated programme

  11. A case-control analysis of common variants in GIP with type 2 diabetes and related biochemical parameters in a South Indian population

    Directory of Open Access Journals (Sweden)

    Kumar Harish

    2010-07-01

    Full Text Available Abstract Background Glucose-dependent insulinotropic polypeptide (GIP is one of the incretins, which plays a crucial role in the secretion of insulin upon food stimulus and in the regulation of postprandial glucose level. It also exerts an effect on the synthesis and secretion of lipoprotein lipase, from adipocytes, important for lipid metabolism. The aim of our study was to do a case-control association analysis of common variants in GIP in association with type 2 diabetes and related biochemical parameters. Method A total of 2000 subjects which includes 1000 (584M/416F cases with type 2 diabetes and 1000 (470M/530F normoglycemic control subjects belonging to Dravidian ethnicity from South India were recruited to assess the effect of single nucleotide polymorphisms (SNPs in GIP (rs2291725, rs2291726, rs937301 on type 2 diabetes in a case-control manner. The SNPs were genotyped by using tetra primer amplification refractory mutation system-PCR (ARMS PCR. For statistical analysis, our study population was divided into sub-groups based on gender (male and female. Association analysis was carried out using chi-squared test and the comparison of biochemical parameters among the three genotypes were performed using analysis of covariance (ANCOVA. Result Initial analysis revealed that, out of the total three SNPs selected for the present study, two SNPs namely rs2291726 and rs937301 were in complete linkage disequilibrium (LD with each other. Therefore, only two SNPs, rs2291725 and rs2291726, were genotyped for the association studies. No significant difference in the allele frequency and genotype distribution of any of the SNPs in GIP were observed between cases and controls (P > 0.05. Analysis of biochemical parameters among the three genotypes showed a significant association of total cholesterol (P = 0.042 and low density lipoprotein (LDL with the G allele of the SNP rs2291726 in GIP (P = 0.004, but this was observed only in the case of female

  12. Analysis of integrated video and radiation data

    International Nuclear Information System (INIS)

    Howell, J.A.; Menlove, H.O.; Rodriguez, C.A.; Beddingfield, D.; Vasil, A.

    1995-01-01

    We have developed prototype software for a facility-monitoring application that will detect anomalous activity in a nuclear facility. The software, which forms the basis of a simple model, automatically reviews and analyzes integrated safeguards data from continuous unattended monitoring systems. This technology, based on pattern recognition by neural networks, provides significant capability to analyze complex data and has the ability to learn and adapt to changing situations. It is well suited for large automated facilities, reactors, spent-fuel storage facilities, reprocessing plants, and nuclear material storage vaults

  13. Signal integrity analysis on discontinuous microstrip line

    International Nuclear Information System (INIS)

    Qiao, Qingyang; Dai, Yawen; Chen, Zipeng

    2013-01-01

    In high speed PCB design, microstirp lines were used to control the impedance, however, the discontinuous microstrip line can cause signal integrity problems. In this paper, we use the transmission line theory to study the characteristics of microstrip lines. Research results indicate that the discontinuity such as truncation, gap and size change result in the problems such as radiation, reflection, delay and ground bounce. We change the discontinuities to distributed parameter circuits, analysed the steady-state response and transient response and the phase delay. The transient response cause radiation and voltage jump.

  14. Advantages of Integrative Data Analysis for Developmental Research

    Science.gov (United States)

    Bainter, Sierra A.; Curran, Patrick J.

    2015-01-01

    Amid recent progress in cognitive development research, high-quality data resources are accumulating, and data sharing and secondary data analysis are becoming increasingly valuable tools. Integrative data analysis (IDA) is an exciting analytical framework that can enhance secondary data analysis in powerful ways. IDA pools item-level data across…

  15. Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

    CERN Document Server

    Laurinavichius, K S

    1998-01-01

    Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

  16. Integrated care: a comprehensive bibliometric analysis and literature review

    Directory of Open Access Journals (Sweden)

    Xiaowei Sun

    2014-06-01

    Full Text Available Introduction: Integrated care could not only fix up fragmented health care but also improve the continuity of care and the quality of life. Despite the volume and variety of publications, little is known about how ‘integrated care’ has developed. There is a need for a systematic bibliometric analysis on studying the important features of the integrated care literature.Aim: To investigate the growth pattern, core journals and jurisdictions and identify the key research domains of integrated care.Methods: We searched Medline/PubMed using the search strategy ‘(delivery of health care, integrated [MeSH Terms] OR integrated care [Title/Abstract]’ without time and language limits. Second, we extracted the publishing year, journals, jurisdictions and keywords of the retrieved articles. Finally, descriptive statistical analysis by the Bibliographic Item Co-occurrence Matrix Builder and hierarchical clustering by SPSS were used.Results: As many as 9090 articles were retrieved. Results included: (1 the cumulative numbers of the publications on integrated care rose perpendicularly after 1993; (2 all documents were recorded by 1646 kinds of journals. There were 28 core journals; (3 the USA is the predominant publishing country; and (4 there are six key domains including: the definition/models of integrated care, interdisciplinary patient care team, disease management for chronically ill patients, types of health care organizations and policy, information system integration and legislation/jurisprudence.Discussion and conclusion: Integrated care literature has been most evident in developed countries. International Journal of Integrated Care is highly recommended in this research area. The bibliometric analysis and identification of publication hotspots provides researchers and practitioners with core target journals, as well as an overview of the field for further research in integrated care.

  17. An operator expansion technique for path integral analysis

    International Nuclear Information System (INIS)

    Tsvetkov, I.V.

    1995-01-01

    A new method of path integral analysis in the framework of a power series technique is presented. The method is based on the operator expansion of an exponential. A regular procedure to calculate the correction terms is found. (orig.)

  18. Analysis of Price Variation and Market Integration of Prosopis ...

    African Journals Online (AJOL)

    Analysis of Price Variation and Market Integration of Prosopis Africana (guill. ... select five markets based on the presence of traders selling the commodity in the markets ... T- test result showed that Prosopis africana seed trade is profitable and ...

  19. BISEN: Biochemical simulation environment

    NARCIS (Netherlands)

    Vanlier, J.; Wu, F.; Qi, F.; Vinnakota, K.C.; Han, Y.; Dash, R.K.; Yang, F.; Beard, D.A.

    2009-01-01

    The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for

  20. Integrating Data Transformation in Principal Components Analysis

    KAUST Repository

    Maadooliat, Mehdi; Huang, Jianhua Z.; Hu, Jianhua

    2015-01-01

    Principal component analysis (PCA) is a popular dimension reduction method to reduce the complexity and obtain the informative aspects of high-dimensional datasets. When the data distribution is skewed, data transformation is commonly used prior

  1. Cost benefit analysis of power plant database integration

    International Nuclear Information System (INIS)

    Wilber, B.E.; Cimento, A.; Stuart, R.

    1988-01-01

    A cost benefit analysis of plant wide data integration allows utility management to evaluate integration and automation benefits from an economic perspective. With this evaluation, the utility can determine both the quantitative and qualitative savings that can be expected from data integration. The cost benefit analysis is then a planning tool which helps the utility to develop a focused long term implementation strategy that will yield significant near term benefits. This paper presents a flexible cost benefit analysis methodology which is both simple to use and yields accurate, verifiable results. Included in this paper is a list of parameters to consider, a procedure for performing the cost savings analysis, and samples of this procedure when applied to a utility. A case study is presented involving a specific utility where this procedure was applied. Their uses of the cost-benefit analysis are also described

  2. Development of data analysis tool for combat system integration

    Directory of Open Access Journals (Sweden)

    Seung-Chun Shin

    2013-03-01

    Full Text Available System integration is an important element for the construction of naval combat ships. In particular, because impeccable combat system integration together with the sensors and weapons can ensure the combat capability and survivability of the ship, the integrated performance of the combat system should be verified and validated whether or not it fulfills the requirements of the end user. In order to conduct systematic verification and validation, a data analysis tool is requisite. This paper suggests the Data Extraction, Recording and Analysis Tool (DERAT for the data analysis of the integrated performance of the combat system, including the functional definition, architecture and effectiveness of the DERAT by presenting the test results.

  3. Integrated systems analysis of the PIUS reactor

    Energy Technology Data Exchange (ETDEWEB)

    Fullwood, F.; Kroeger, P.; Higgins, J. [Brookhaven National Lab., Upton, NY (United States)] [and others

    1993-11-01

    Results are presented of a systems failure analysis of the PIUS plant systems that are used during normal reactor operation and postulated accidents. This study was performed to provide the NRC with an understanding of the behavior of the plant. The study applied two diverse failure identification methods, Failure Modes Effects & Criticality Analysis (FMECA) and Hazards & Operability (HAZOP) to the plant systems, supported by several deterministic analyses. Conventional PRA methods were also used along with a scheme for classifying events by initiator frequency and combinations of failures. Principal results of this study are: (a) an extensive listing of potential event sequences, grouped in categories that can be used by the NRC, (b) identification of support systems that are important to safety, and (c) identification of key operator actions.

  4. Integrated systems analysis of the PIUS reactor

    International Nuclear Information System (INIS)

    Fullwood, F.; Kroeger, P.; Higgins, J.

    1993-11-01

    Results are presented of a systems failure analysis of the PIUS plant systems that are used during normal reactor operation and postulated accidents. This study was performed to provide the NRC with an understanding of the behavior of the plant. The study applied two diverse failure identification methods, Failure Modes Effects ampersand Criticality Analysis (FMECA) and Hazards ampersand Operability (HAZOP) to the plant systems, supported by several deterministic analyses. Conventional PRA methods were also used along with a scheme for classifying events by initiator frequency and combinations of failures. Principal results of this study are: (a) an extensive listing of potential event sequences, grouped in categories that can be used by the NRC, (b) identification of support systems that are important to safety, and (c) identification of key operator actions

  5. Integrative data analysis of male reproductive disorders

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel

    of such data in conjunction with data from publicly available repositories. This thesis presents an introduction to disease genetics and molecular systems biology, followed by four studies that each provide detailed clues to the etiology of male reproductive disorders. Finally, a fifth study illustrates......-wide association data with respect to copy number variation and show that the aggregated effect of rare variants can influence the risk for testicular cancer. Paper V provides an example of the application of RNA-Seq for expression analysis of a species with an unsequenced genome. We analysed the plant...... of this thesis is the identification of the molecular basis of male reproductive disorders, with a special focus on testicular cancer. To this end, clinical samples were characterized by microarraybased transcription and genomic variation assays and molecular entities were identified by computational analysis...

  6. Biochemical Analysis Reveals the Multifactorial Mechanism of Histone H3 Clipping by Chicken Liver Histone H3 Protease

    KAUST Repository

    Chauhan, Sakshi

    2016-09-02

    Proteolytic clipping of histone H3 has been identified in many organisms. Despite several studies, the mechanism of clipping, the substrate specificity, and the significance of this poorly understood epigenetic mechanism are not clear. We have previously reported histone H3 specific proteolytic clipping and a protein inhibitor in chicken liver. However, the sites of clipping are still not known very well. In this study, we attempt to identify clipping sites in histone H3 and to determine the mechanism of inhibition by stefin B protein, a cysteine protease inhibitor. By employing site-directed mutagenesis and in vitro biochemical assays, we have identified three distinct clipping sites in recombinant human histone H3 and its variants (H3.1, H3.3, and H3t). However, post-translationally modified histones isolated from chicken liver and Saccharomyces cerevisiae wild-type cells showed different clipping patterns. Clipping of histone H3 N-terminal tail at three sites occurs in a sequential manner. We have further observed that clipping sites are regulated by the structure of the N-terminal tail as well as the globular domain of histone H3. We also have identified the QVVAG region of stefin B protein to be very crucial for inhibition of the protease activity. Altogether, our comprehensive biochemical studies have revealed three distinct clipping sites in histone H3 and their regulation by the structure of histone H3, histone modifications marks, and stefin B.

  7. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Directory of Open Access Journals (Sweden)

    Melody K Morris

    2011-03-01

    Full Text Available Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL, converts a prior knowledge network (obtained from literature or interactome databases into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a generating experimentally testable biological hypotheses concerning pathway crosstalk, (b establishing capability for quantitative prediction of protein activity, and (c prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  8. An integrated platform for biomolecule interaction analysis

    Science.gov (United States)

    Jan, Chia-Ming; Tsai, Pei-I.; Chou, Shin-Ting; Lee, Shu-Sheng; Lee, Chih-Kung

    2013-02-01

    We developed a new metrology platform which can detect real-time changes in both a phase-interrogation mode and intensity mode of a SPR (surface plasmon resonance). We integrated a SPR and ellipsometer to a biosensor chip platform to create a new biomolecular interaction measurement mechanism. We adopted a conductive ITO (indium-tinoxide) film to the bio-sensor platform chip to expand the dynamic range and improve measurement accuracy. The thickness of the conductive film and the suitable voltage constants were found to enhance performance. A circularly polarized ellipsometry configuration was incorporated into the newly developed platform to measure the label-free interactions of recombinant human C-reactive protein (CRP) with immobilized biomolecule target monoclonal human CRP antibody at various concentrations. CRP was chosen as it is a cardiovascular risk biomarker and is an acute phase reactant as well as a specific prognostic indicator for inflammation. We found that the sensitivity of a phaseinterrogation SPR is predominantly dependent on the optimization of the sample incidence angle. The effect of the ITO layer effective index under DC and AC effects as well as an optimal modulation were experimentally performed and discussed. Our experimental results showed that the modulated dynamic range for phase detection was 10E-2 RIU based on a current effect and 10E-4 RIU based on a potential effect of which a 0.55 (°/RIU) measurement was found by angular-interrogation. The performance of our newly developed metrology platform was characterized to have a higher sensitivity and less dynamic range when compared to a traditional full-field measurement system.

  9. An analysis of 3D particle path integration algorithms

    International Nuclear Information System (INIS)

    Darmofal, D.L.; Haimes, R.

    1996-01-01

    Several techniques for the numerical integration of particle paths in steady and unsteady vector (velocity) fields are analyzed. Most of the analysis applies to unsteady vector fields, however, some results apply to steady vector field integration. Multistep, multistage, and some hybrid schemes are considered. It is shown that due to initialization errors, many unsteady particle path integration schemes are limited to third-order accuracy in time. Multistage schemes require at least three times more internal data storage than multistep schemes of equal order. However, for timesteps within the stability bounds, multistage schemes are generally more accurate. A linearized analysis shows that the stability of these integration algorithms are determined by the eigenvalues of the local velocity tensor. Thus, the accuracy and stability of the methods are interpreted with concepts typically used in critical point theory. This paper shows how integration schemes can lead to erroneous classification of critical points when the timestep is finite and fixed. For steady velocity fields, we demonstrate that timesteps outside of the relative stability region can lead to similar integration errors. From this analysis, guidelines for accurate timestep sizing are suggested for both steady and unsteady flows. In particular, using simulation data for the unsteady flow around a tapered cylinder, we show that accurate particle path integration requires timesteps which are at most on the order of the physical timescale of the flow

  10. Integrating human factors into process hazard analysis

    International Nuclear Information System (INIS)

    Kariuki, S.G.; Loewe, K.

    2007-01-01

    A comprehensive process hazard analysis (PHA) needs to address human factors. This paper describes an approach that systematically identifies human error in process design and the human factors that influence its production and propagation. It is deductive in nature and therefore considers human error as a top event. The combinations of different factors that may lead to this top event are analysed. It is qualitative in nature and is used in combination with other PHA methods. The method has an advantage because it does not look at the operator error as the sole contributor to the human failure within a system but a combination of all underlying factors

  11. Integrative Genomic Analysis of Complex traits

    DEFF Research Database (Denmark)

    Ehsani, Ali Reza

    In the last decade rapid development in biotechnologies has made it possible to extract extensive information about practically all levels of biological organization. An ever-increasing number of studies are reporting miltilayered datasets on the entire DNA sequence, transceroption, protein...... expression, and metabolite abundance of more and more populations in a multitude of invironments. However, a solid model for including all of this complex information in one analysis, to disentangle genetic variation and the underlying genetic architecture of complex traits and diseases, has not yet been...

  12. A Dose–Response Analysis of Biochemical Control Outcomes After {sup 125}I Monotherapy for Patients With Favorable-Risk Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Shiraishi, Yutaka, E-mail: shiraishi@rad.med.keio.ac.jp [Department of Radiology, Keio University School of Medicine, Tokyo (Japan); Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Yorozu, Atsunori [Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Ohashi, Toshio [Department of Radiology, Keio University School of Medicine, Tokyo (Japan); Toya, Kazuhito [Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Saito, Shiro; Nishiyama, Toru; Yagi, Yasuto [Department of Urology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Shigematsu, Naoyuki [Department of Radiology, Keio University School of Medicine, Tokyo (Japan)

    2014-12-01

    Purpose: To define the optimal dose for {sup 125}I prostate implants by correlating postimplantation dosimetry findings with biochemical failure and toxicity. Methods and Materials: Between 2003 and 2009, 683 patients with prostate cancer were treated with {sup 125}I prostate brachytherapy without supplemental external beam radiation therapy and were followed up for a median time of 80 months. Implant dose was defined as the D90 (the minimal dose received by 90% of the prostate) on postoperative day 1 and 1 month after implantation. Therefore, 2 dosimetric variables (day 1 D90 and day 30 D90) were analyzed for each patient. We investigated the dose effects on biochemical control and toxicity. Results: The 7-year biochemical failure-free survival (BFFS) rate for the group overall was 96.4% according to the Phoenix definition. A multivariate analysis found day 1 D90 and day 30 D90 to be the most significant factors affecting BFFS. The cutoff points for day 1 D90 and day 30 D90, calculated from ROC curves, were 163 Gy and 175 Gy, respectively. By use of univariate analysis, various dosimetric cutoff points for day 30 D90 were tested. We found that day 30 D90 cutoff points from 130 to 180 Gy appeared to be good for the entire cohort. Greater D90s were associated with an increase in late genitourinary or gastrointestinal toxicity ≥ grade 2, but the increase was not statistically significant. Conclusions: Improvements in BFFS rates were seen with increasing D90 levels. Day 30 D90 doses of 130 to 180 Gy were found to serve as cutoff levels. For low-risk and low-tier intermediate-risk prostate cancer patients, high prostate D90s, even with doses exceeding 180 Gy, achieve better treatment results and are feasible.

  13. PREDICTORS OF BIOCHEMICAL REMISSION AND RECURRENCE AFTER SURGICAL AND RADIATION TREATMENTS OF CUSHING DISEASE: A SYSTEMATIC REVIEW AND META-ANALYSIS.

    Science.gov (United States)

    Abu Dabrh, Abd Moain Abu; Singh Ospina, Naykky M; Al Nofal, Alaa; Farah, Wigdan H; Barrionuevo, Patricia; Sarigianni, Maria; Mohabbat, Arya B; Benkhadra, Khalid; Carranza Leon, Barbara G; Gionfriddo, Michael R; Wang, Zhen; Mohammed, Khaled; Ahmed, Ahmed T; Elraiyah, Tarig A; Haydour, Qusay; Alahdab, Fares; Prokop, Larry J; Murad, Mohammad Hassan

    2016-04-01

    We conducted a systematic review and meta-analysis to synthesize the evidence about predictors that may affect biochemical remission and recurrence after transsphenoidal surgery (TSS), radiosurgery (RS), and radiotherapy (RT) in Cushing disease. We searched multiple databases through December 2014 including original controlled and uncontrolled studies that enrolled patients with Cushing disease who received TSS (first-line), RS, or RT. We extracted data independently, in duplicates. Outcomes of interest were biochemical remission and recurrence. A meta-analysis was conducted using the random-effects model to estimate event rates with 95% confidence intervals (CIs). First-line TSS was associated with high remission (76% [95% CI, 72 to 79%]) and low recurrence rates (10% [95% CI, 6 to 16%]). Remission after TSS was higher in patients with microadenomas or positive-adrenocorticotropic hormone tumor histology. RT was associated with a high remission rate (RS, 68% [95% CI, 61 to 77%]; RT, 66% [95% CI, 58 to 75%]) but also with a high recurrence rate (RS, 32% [95% CI, 16 to 60%]; RT, 26% [95% CI, 14 to 48%]). Remission after RS was higher at short-term follow-up (≤2 years) and with high-dose radiation, while recurrence was higher in women and with lower-dose radiation. Remission was after RT in adults who received TSS prior to RT, and with lower radiation doses. There was heterogeneity (nonstandardization) in the criteria and cutoff points used to define biochemical remission and recurrence. First-line TSS is associated with high remission and low recurrence, while RS and RT are associated with reasonable remission rates but important recurrence rates. The current evidence warrants low confidence due to the noncomparative nature of the studies, high heterogeneity, and imprecision.

  14. Project analysis and integration economic analyses summary

    Science.gov (United States)

    Macomber, H. L.

    1986-01-01

    An economic-analysis summary was presented for the manufacture of crystalline-silicon modules involving silicon ingot/sheet, growth, slicing, cell manufacture, and module assembly. Economic analyses provided: useful quantitative aspects for complex decision-making to the Flat-plate Solar Array (FSA) Project; yardsticks for design and performance to industry; and demonstration of how to evaluate and understand the worth of research and development both to JPL and other government agencies and programs. It was concluded that future research and development funds for photovoltaics must be provided by the Federal Government because the solar industry today does not reap enough profits from its present-day sales of photovoltaic equipment.

  15. Integrative analysis of metabolomics and transcriptomics data

    DEFF Research Database (Denmark)

    Brink-Jensen, Kasper; Bak, Søren; Jørgensen, Kirsten

    2013-01-01

    ) measurements from the same samples, to identify genes controlling the production of metabolites. Due to the high dimensionality of both LC-MS and DNA microarray data, dimension reduction and variable selection are key elements of the analysis. Our proposed approach starts by identifying the basis functions......The abundance of high-dimensional measurements in the form of gene expression and mass spectroscopy calls for models to elucidate the underlying biological system. For widely studied organisms like yeast, it is possible to incorporate prior knowledge from a variety of databases, an approach used...... ("building blocks") that constitute the output from a mass spectrometry experiment. Subsequently, the weights of these basis functions are related to the observations from the corresponding gene expression data in order to identify which genes are associated with specific patterns seen in the metabolite data...

  16. Vertically Integrated Seismological Analysis II : Inference

    Science.gov (United States)

    Arora, N. S.; Russell, S.; Sudderth, E.

    2009-12-01

    Methods for automatically associating detected waveform features with hypothesized seismic events, and localizing those events, are a critical component of efforts to verify the Comprehensive Test Ban Treaty (CTBT). As outlined in our companion abstract, we have developed a hierarchical model which views detection, association, and localization as an integrated probabilistic inference problem. In this abstract, we provide more details on the Markov chain Monte Carlo (MCMC) methods used to solve this inference task. MCMC generates samples from a posterior distribution π(x) over possible worlds x by defining a Markov chain whose states are the worlds x, and whose stationary distribution is π(x). In the Metropolis-Hastings (M-H) method, transitions in the Markov chain are constructed in two steps. First, given the current state x, a candidate next state x‧ is generated from a proposal distribution q(x‧ | x), which may be (more or less) arbitrary. Second, the transition to x‧ is not automatic, but occurs with an acceptance probability—α(x‧ | x) = min(1, π(x‧)q(x | x‧)/π(x)q(x‧ | x)). The seismic event model outlined in our companion abstract is quite similar to those used in multitarget tracking, for which MCMC has proved very effective. In this model, each world x is defined by a collection of events, a list of properties characterizing those events (times, locations, magnitudes, and types), and the association of each event to a set of observed detections. The target distribution π(x) = P(x | y), the posterior distribution over worlds x given the observed waveform data y at all stations. Proposal distributions then implement several types of moves between worlds. For example, birth moves create new events; death moves delete existing events; split moves partition the detections for an event into two new events; merge moves combine event pairs; swap moves modify the properties and assocations for pairs of events. Importantly, the rules for

  17. Development of safety analysis technology for integral reactor

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Suk K.; Song, J. H.; Chung, Y. J. and others

    1999-03-01

    Inherent safety features and safety system characteristics of the SMART integral reactor are investigated in this study. Performance and safety of the SMART conceptual design have been evaluated and confirmed through the performance and safety analyses using safety analysis system codes as well as a preliminary performance and safety analysis methodology. SMART design base events and their acceptance criteria are identified to develop a preliminary PIRT for the SMART integral reactor. Using the preliminary PIRT, a set of experimental program for the thermal hydraulic separate effect tests and the integral effect tests was developed for the thermal hydraulic model development and the system code validation. Safety characteristics as well as the safety issues of the integral reactor has been identified during the study, which will be used to resolve the safety issues and guide the regulatory criteria for the integral reactor. The results of the performance and safety analyses performed during the study were used to feedback for the SMART conceptual design. The performance and safety analysis code systems as well as the preliminary safety analysis methodology developed in this study will be validated as the SMART design evolves. The performance and safety analysis technology developed during the study will be utilized for the SMART basic design development. (author)

  18. Biochemical and Biophysical Methods for Analysis of Poly(ADP-Ribose) Polymerase 1 and Its Interactions with Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Chassé, Maggie H.; Muthurajan, Uma M.; Clark, Nicholas J.; Kramer, Michael A.; Chakravarthy, Srinivas; Irving, Thomas; Luger, Karolin [Children; (IIT); (Colorado); (Amgen)

    2018-01-18

    Poly (ADP-Ribose) Polymerase I (PARP-1) is a first responder to DNA damage and participates in the regulation of gene expression. The interaction of PARP-1 with chromatin and DNA is complex and involves at least two different modes of interaction. In its enzymatically inactive state, PARP-1 binds native chromatin with similar affinity as it binds free DNA ends. Automodification of PARP-1 affects interaction with chromatin and DNA to different extents. Here we describe a series of biochemical and biophysical techniques to quantify and dissect the different binding modes of PARP-1 with its various substrates. The techniques listed here allow for high throughput and quantitative measurements of the interaction of different PARP-1 constructs (inactive and automodified) with chromatin and DNA damage models.

  19. Overcoming barriers to integrating economic analysis into risk assessment.

    Science.gov (United States)

    Hoffmann, Sandra

    2011-09-01

    Regulatory risk analysis is designed to provide decisionmakers with a clearer understanding of how policies are likely to affect risk. The systems that produce risk are biological, physical, and social and economic. As a result, risk analysis is an inherently interdisciplinary task. Yet in practice, risk analysis has been interdisciplinary in only limited ways. Risk analysis could provide more accurate assessments of risk if there were better integration of economics and other social sciences into risk assessment itself. This essay examines how discussions about risk analysis policy have influenced the roles of various disciplines in risk analysis. It explores ways in which integrated bio/physical-economic modeling could contribute to more accurate assessments of risk. It reviews examples of the kind of integrated economics-bio/physical modeling that could be used to enhance risk assessment. The essay ends with a discussion of institutional barriers to greater integration of economic modeling into risk assessment and provides suggestions on how these might be overcome. © 2011 Society for Risk Analysis.

  20. A network analysis of leadership theory : the infancy of integration.

    OpenAIRE

    Meuser, J. D.; Gardner, W. L.; Dinh, J. E.; Hu, J.; Liden, R. C.; Lord, R. G.

    2016-01-01

    We investigated the status of leadership theory integration by reviewing 14 years of published research (2000 through 2013) in 10 top journals (864 articles). The authors of these articles examined 49 leadership approaches/theories, and in 293 articles, 3 or more of these leadership approaches were included in their investigations. Focusing on these articles that reflected relatively extensive integration, we applied an inductive approach and used graphic network analysis as a guide for drawi...

  1. Integrated analysis of oxide nuclear fuel sintering

    International Nuclear Information System (INIS)

    Baranov, V.; Kuzmin, R.; Tenishev, A.; Timoshin, I.; Khlunov, A.; Ivanov, A.; Petrov, I.

    2011-01-01

    Dilatometric and thermal-gravimetric investigations have been carried out for the sintering process of oxide nuclear fuel in gaseous Ar - 8% H 2 atmosphere at temperatures up to 1600 0 C. The pressed compacts were fabricated under real production conditions of the OAO MSZ with application of two different technologies, so called 'dry' and 'wet' technologies. Effects of the grain size growth after the heating to different temperatures were observed. In order to investigate the effects produced by rate of heating on properties of sintered fuel pellets, the heating rates were varied from 1 to 8 0 C per minute. Time of isothermal overexposure at maximal temperature (1600 0 C) was about 8 hours. Real production conditions were imitated. The results showed that the sintering process of the fuel pellets produced by two technologies differs. The samples sintered under different heating rates were studied with application of scanning electronic microscopy analysis for determination of mean grain size. A simulation of heating profile for industrial furnaces was performed to reduce the beam cycles and estimate the effects of variation of the isothermal overexposure temperatures. Based on this data, an optimization of the sintering conditions was performed in operations terms of OAO MSZ. (authors)

  2. Integrated Network Analysis and Effective Tools in Plant Systems Biology

    Directory of Open Access Journals (Sweden)

    Atsushi eFukushima

    2014-11-01

    Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

  3. Momentum integral network method for thermal-hydraulic transient analysis

    International Nuclear Information System (INIS)

    Van Tuyle, G.J.

    1983-01-01

    A new momentum integral network method has been developed, and tested in the MINET computer code. The method was developed in order to facilitate the transient analysis of complex fluid flow and heat transfer networks, such as those found in the balance of plant of power generating facilities. The method employed in the MINET code is a major extension of a momentum integral method reported by Meyer. Meyer integrated the momentum equation over several linked nodes, called a segment, and used a segment average pressure, evaluated from the pressures at both ends. Nodal mass and energy conservation determined nodal flows and enthalpies, accounting for fluid compression and thermal expansion

  4. Study on integrated design and analysis platform of NPP

    International Nuclear Information System (INIS)

    Lu Dongsen; Gao Zuying; Zhou Zhiwei

    2001-01-01

    Many calculation software have been developed to nuclear system's design and safety analysis, such as structure design software, fuel design and manage software, thermal hydraulic analysis software, severe accident simulation software, etc. This study integrates those software to a platform, develops visual modeling tool for Retran, NGFM90. And in this platform, a distribution calculation method is also provided for couple calculation between different software. The study will improve the design and analysis of NPP

  5. Gel-free/label-free proteomic, photosynthetic, and biochemical analysis of cowpea (Vigna unguiculata [L.] Walp.) resistance against Cowpea severe mosaic virus (CPSMV).

    Science.gov (United States)

    Varela, Anna Lidia N; Komatsu, Setsuko; Wang, Xin; Silva, Rodolpho G G; Souza, Pedro Filho N; Lobo, Ana Karla M; Vasconcelos, Ilka M; Silveira, Joaquim A G; Oliveira, Jose T A

    2017-06-23

    Cowpea severe mosaic virus (CPSMV) causes significant losses in cowpea (Vigna unguiculata) production. In this present study biochemical, physiological, and proteomic analysis were done to identify pathways and defense proteins that are altered during the incompatible interaction between the cowpea genotype BRS-Marataoã and CPSMV. The leaf protein extracts from mock- (MI) and CPSMV-inoculated plantlets (V) were evaluated at 2 and 6days post-inoculation (DPI). Data support the assumptions that increases in biochemical (high hydrogen peroxide, antioxidant enzymes, and secondary compounds) and physiological responses (high photosynthesis index and chlorophyll content), confirmed by label-free comparative proteomic approach, in which quantitative changes in proteasome proteins, proteins related to photosynthesis, redox homeostasis, regulation factors/RNA processing proteins were observed may be implicated in the resistance of BRS-Marataoã to CPSMV. This pioneering study provides information for the selection of specific pathways and proteins, altered in this incompatible relationship, which could be chosen as targets for detailed studies to advance our understanding of the molecular, physiological, and biochemistry basis of the resistance mechanism of cowpea and design approachs to engineer plants that are more productive. This is a pioneering study in which an incompatible relationship between a resistant cowpea and Cowpea severe mosaic virus (CPSMV) was conducted to comparatively evaluate proteomic profiles by Gel-free/label-free methodology and some physiological and biochemical parameters to shed light on how a resistant cowpea cultivar deals with the virus attack. Specific proteins and associated pathways were altered in the cowpea plants challenged with CPSMV and will contribute to our knowledge on the biological process tailored by cowpea in response to CPSMV. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Integrated failure probability estimation based on structural integrity analysis and failure data: Natural gas pipeline case

    International Nuclear Information System (INIS)

    Dundulis, Gintautas; Žutautaitė, Inga; Janulionis, Remigijus; Ušpuras, Eugenijus; Rimkevičius, Sigitas; Eid, Mohamed

    2016-01-01

    In this paper, the authors present an approach as an overall framework for the estimation of the failure probability of pipelines based on: the results of the deterministic-probabilistic structural integrity analysis (taking into account loads, material properties, geometry, boundary conditions, crack size, and defected zone thickness), the corrosion rate, the number of defects and failure data (involved into the model via application of Bayesian method). The proposed approach is applied to estimate the failure probability of a selected part of the Lithuanian natural gas transmission network. The presented approach for the estimation of integrated failure probability is a combination of several different analyses allowing us to obtain: the critical crack's length and depth, the failure probability of the defected zone thickness, dependency of the failure probability on the age of the natural gas transmission pipeline. A model's uncertainty analysis and uncertainty propagation analysis are performed, as well. - Highlights: • Degradation mechanisms of natural gas transmission pipelines. • Fracture mechanic analysis of the pipe with crack. • Stress evaluation of the pipe with critical crack. • Deterministic-probabilistic structural integrity analysis of gas pipeline. • Integrated estimation of pipeline failure probability by Bayesian method.

  7. Direct integration multiple collision integral transport analysis method for high energy fusion neutronics

    International Nuclear Information System (INIS)

    Koch, K.R.

    1985-01-01

    A new analysis method specially suited for the inherent difficulties of fusion neutronics was developed to provide detailed studies of the fusion neutron transport physics. These studies should provide a better understanding of the limitations and accuracies of typical fusion neutronics calculations. The new analysis method is based on the direct integration of the integral form of the neutron transport equation and employs a continuous energy formulation with the exact treatment of the energy angle kinematics of the scattering process. In addition, the overall solution is analyzed in terms of uncollided, once-collided, and multi-collided solution components based on a multiple collision treatment. Furthermore, the numerical evaluations of integrals use quadrature schemes that are based on the actual dependencies exhibited in the integrands. The new DITRAN computer code was developed on the Cyber 205 vector supercomputer to implement this direct integration multiple-collision fusion neutronics analysis. Three representative fusion reactor models were devised and the solutions to these problems were studied to provide suitable choices for the numerical quadrature orders as well as the discretized solution grid and to understand the limitations of the new analysis method. As further verification and as a first step in assessing the accuracy of existing fusion-neutronics calculations, solutions obtained using the new analysis method were compared to typical multigroup discrete ordinates calculations

  8. IMG: the integrated microbial genomes database and comparative analysis system

    Science.gov (United States)

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2012-01-01

    The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

  9. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

    Directory of Open Access Journals (Sweden)

    Krebs Olga

    2007-03-01

    Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

  10. An integrated biochemical prediction model of all-cause mortality in patients undergoing lower extremity bypass surgery for advanced peripheral artery disease.

    Science.gov (United States)

    Owens, Christopher D; Kim, Ji Min; Hevelone, Nathanael D; Gasper, Warren J; Belkin, Michael; Creager, Mark A; Conte, Michael S

    2012-09-01

    Patients with advanced peripheral artery disease (PAD) have a high prevalence of cardiovascular (CV) risk factors and shortened life expectancy. However, CV risk factors poorly predict midterm (model was used to assess the main outcome of all-cause mortality. A clinical model was constructed with known CV risk factors, and the incremental value of the addition of clinical chemistry, lipid assessment, and a panel of 11 inflammatory parameters was investigated using the C statistic, the integrated discrimination improvement index, and Akaike information criterion. The study monitored 225 patients for a median of 893 days (interquartile range, 539-1315 days). In this study, 50 patients (22.22%) died during the follow-up period. By life-table analysis (expressed as percent surviving ± standard error), survival at 1, 2, 3, 4, and 5 years, respectively, was 90.5% ± 1.9%, 83.4% ± 2.5%, 77.5% ± 3.1%, 71.0% ± 3.8%, and 65.3% ± 6.5%. Compared with survivors, decedents were older, diabetic, had extant coronary artery disease, and were more likely to present with critical limb ischemia as their indication for bypass surgery (P model and produced a final C statistic of 0.82. A risk prediction model including traditional risk factors and parameters of inflammation, renal function, and nutrition had excellent discriminatory ability in predicting all-cause mortality in patients with clinically advanced PAD undergoing bypass surgery. Copyright © 2012 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

  11. Integrative sparse principal component analysis of gene expression data.

    Science.gov (United States)

    Liu, Mengque; Fan, Xinyan; Fang, Kuangnan; Zhang, Qingzhao; Ma, Shuangge

    2017-12-01

    In the analysis of gene expression data, dimension reduction techniques have been extensively adopted. The most popular one is perhaps the PCA (principal component analysis). To generate more reliable and more interpretable results, the SPCA (sparse PCA) technique has been developed. With the "small sample size, high dimensionality" characteristic of gene expression data, the analysis results generated from a single dataset are often unsatisfactory. Under contexts other than dimension reduction, integrative analysis techniques, which jointly analyze the raw data of multiple independent datasets, have been developed and shown to outperform "classic" meta-analysis and other multidatasets techniques and single-dataset analysis. In this study, we conduct integrative analysis by developing the iSPCA (integrative SPCA) method. iSPCA achieves the selection and estimation of sparse loadings using a group penalty. To take advantage of the similarity across datasets and generate more accurate results, we further impose contrasted penalties. Different penalties are proposed to accommodate different data conditions. Extensive simulations show that iSPCA outperforms the alternatives under a wide spectrum of settings. The analysis of breast cancer and pancreatic cancer data further shows iSPCA's satisfactory performance. © 2017 WILEY PERIODICALS, INC.

  12. Quantitative Raman spectral changes of the differentiation of mesenchymal stem cells into islet-like cells by biochemical component analysis and multiple peak fitting

    Science.gov (United States)

    Su, Xin; Fang, Shaoyin; Zhang, Daosen; Zhang, Qinnan; He, Yingtian; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

    2015-12-01

    Mesenchymal stem cells (MSCs) differentiate into islet-like cells, providing a possible solution for type I diabetes treatment. To search for the precise molecular mechanism of the directional differentiation of MSC-derived islet-like cells, biomolecular composition, and structural conformation information during MSC differentiation, is required. Because islet-like cells lack specific surface markers, the commonly employed immunostaining technique is not suitable for their identification, physical separation, and enrichment. Combining Raman spectroscopic data, a fitting accuracy-improved biochemical component analysis, and multiple peaks fitting approach, we identified the quantitative biochemical and intensity change of Raman peaks that show the differentiation of MSCs into islet-like cells. Along with increases in protein and glycogen content, and decreases in deoxyribonucleic acid and ribonucleic acid content, in islet-like cells relative to MSCs, it was found that a characteristic peak of insulin (665 cm-1) has twice the intensity in islet-like cells relative to MSCs, indicating differentiation of MSCs into islet-like cells was successful. Importantly, these Raman signatures provide useful information on the structural and pathological states during MSC differentiation and help to develop noninvasive and label-free Raman sorting methods for stem cells and their lineages.

  13. Train integrity detection risk analysis based on PRISM

    Science.gov (United States)

    Wen, Yuan

    2018-04-01

    GNSS based Train Integrity Monitoring System (TIMS) is an effective and low-cost detection scheme for train integrity detection. However, as an external auxiliary system of CTCS, GNSS may be influenced by external environments, such as uncertainty of wireless communication channels, which may lead to the failure of communication and positioning. In order to guarantee the reliability and safety of train operation, a risk analysis method of train integrity detection based on PRISM is proposed in this article. First, we analyze the risk factors (in GNSS communication process and the on-board communication process) and model them. Then, we evaluate the performance of the model in PRISM based on the field data. Finally, we discuss how these risk factors influence the train integrity detection process.

  14. Biochemical and functional analysis of two Plasmodium falciparum blood-stage 6-cys proteins: P12 and P41.

    Directory of Open Access Journals (Sweden)

    Tana Taechalertpaisarn

    Full Text Available The genomes of Plasmodium parasites that cause malaria in humans, other primates, birds, and rodents all encode multiple 6-cys proteins. Distinct 6-cys protein family members reside on the surface at each extracellular life cycle stage and those on the surface of liver infective and sexual stages have been shown to play important roles in hepatocyte growth and fertilization respectively. However, 6-cys proteins associated with the blood-stage forms of the parasite have no known function. Here we investigate the biochemical nature and function of two blood-stage 6-cys proteins in Plasmodium falciparum, the most pathogenic species to afflict humans. We show that native P12 and P41 form a stable heterodimer on the infective merozoite surface and are secreted following invasion, but could find no evidence that this complex mediates erythrocyte-receptor binding. That P12 and P41 do not appear to have a major role as adhesins to erythrocyte receptors was supported by the observation that antisera to these proteins did not substantially inhibit erythrocyte invasion. To investigate other functional roles for these proteins their genes were successfully disrupted in P. falciparum, however P12 and P41 knockout parasites grew at normal rates in vitro and displayed no other obvious phenotypic changes. It now appears likely that these blood-stage 6-cys proteins operate as a pair and play redundant roles either in erythrocyte invasion or in host-immune interactions.

  15. Biochemical Analysis of Two Single Mutants that Give Rise to a Polymorphic G6PD A-Double Mutant

    Directory of Open Access Journals (Sweden)

    Edson Jiovany Ramírez-Nava

    2017-10-01

    Full Text Available Glucose-6-phosphate dehydrogenase (G6PD is a key regulatory enzyme that plays a crucial role in the regulation of cellular energy and redox balance. Mutations in the gene encoding G6PD cause the most common enzymopathy that drives hereditary nonspherocytic hemolytic anemia. To gain insights into the effects of mutations in G6PD enzyme efficiency, we have investigated the biochemical, kinetic, and structural changes of three clinical G6PD variants, the single mutations G6PD A+ (Asn126AspD and G6PD Nefza (Leu323Pro, and the double mutant G6PD A− (Asn126Asp + Leu323Pro. The mutants showed lower residual activity (≤50% of WT G6PD and displayed important kinetic changes. Although all Class III mutants were located in different regions of the three-dimensional structure of the enzyme and were not close to the active site, these mutants had a deleterious effect over catalytic activity and structural stability. The results indicated that the G6PD Nefza mutation was mainly responsible for the functional and structural alterations observed in the double mutant G6PD A−. Moreover, our study suggests that the G6PD Nefza and G6PD A− mutations affect enzyme functions in a similar fashion to those reported for Class I mutations.

  16. Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases.

    Science.gov (United States)

    Vardakou, Maria; Salmon, Melissa; Faraldos, Juan A; O'Maille, Paul E

    2014-01-01

    Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.

  17. Argentinean integrated small reactor design and scale economy analysis of integrated reactor

    International Nuclear Information System (INIS)

    Florido, P. C.; Bergallo, J. E.; Ishida, M. V.

    2000-01-01

    This paper describes the design of CAREM, which is Argentinean integrated small reactor project and the scale economy analysis results of integrated reactor. CAREM project consists on the development, design and construction of a small nuclear power plant. CAREM is an advanced reactor conceived with new generation design solutions and standing on the large experience accumulated in the safe operation of Light Water Reactors. The CAREM is an indirect cycle reactor with some distinctive and characteristic features that greatly simplify the reactor and also contribute to a highly level of safety: integrated primary cooling system, self pressurized, primary cooling by natural circulation and safety system relying on passive features. For a fully doupled economic evaluation of integrated reactors done by IREP (Integrated Reactor Evaluation Program) code transferred to IAEA, CAREM have been used as a reference point. The results shows that integrated reactors become competitive with power larger than 200MWe with Argentinean cheapest electricity option. Due to reactor pressure vessel construction limit, low pressure drop steam generator are used to reach power output of 200MWe for natural circulation. For forced circulation, 300MWe can be achieved. (author)

  18. Development of Probabilistic Structural Analysis Integrated with Manufacturing Processes

    Science.gov (United States)

    Pai, Shantaram S.; Nagpal, Vinod K.

    2007-01-01

    An effort has been initiated to integrate manufacturing process simulations with probabilistic structural analyses in order to capture the important impacts of manufacturing uncertainties on component stress levels and life. Two physics-based manufacturing process models (one for powdered metal forging and the other for annular deformation resistance welding) have been linked to the NESSUS structural analysis code. This paper describes the methodology developed to perform this integration including several examples. Although this effort is still underway, particularly for full integration of a probabilistic analysis, the progress to date has been encouraging and a software interface that implements the methodology has been developed. The purpose of this paper is to report this preliminary development.

  19. Integration of rocket turbine design and analysis through computer graphics

    Science.gov (United States)

    Hsu, Wayne; Boynton, Jim

    1988-01-01

    An interactive approach with engineering computer graphics is used to integrate the design and analysis processes of a rocket engine turbine into a progressive and iterative design procedure. The processes are interconnected through pre- and postprocessors. The graphics are used to generate the blade profiles, their stacking, finite element generation, and analysis presentation through color graphics. Steps of the design process discussed include pitch-line design, axisymmetric hub-to-tip meridional design, and quasi-three-dimensional analysis. The viscous two- and three-dimensional analysis codes are executed after acceptable designs are achieved and estimates of initial losses are confirmed.

  20. INS integrated motion analysis for autonomous vehicle navigation

    Science.gov (United States)

    Roberts, Barry; Bazakos, Mike

    1991-01-01

    The use of inertial navigation system (INS) measurements to enhance the quality and robustness of motion analysis techniques used for obstacle detection is discussed with particular reference to autonomous vehicle navigation. The approach to obstacle detection used here employs motion analysis of imagery generated by a passive sensor. Motion analysis of imagery obtained during vehicle travel is used to generate range measurements to points within the field of view of the sensor, which can then be used to provide obstacle detection. Results obtained with an INS integrated motion analysis approach are reviewed.

  1. Integrating computer programs for engineering analysis and design

    Science.gov (United States)

    Wilhite, A. W.; Crisp, V. K.; Johnson, S. C.

    1983-01-01

    The design of a third-generation system for integrating computer programs for engineering and design has been developed for the Aerospace Vehicle Interactive Design (AVID) system. This system consists of an engineering data management system, program interface software, a user interface, and a geometry system. A relational information system (ARIS) was developed specifically for the computer-aided engineering system. It is used for a repository of design data that are communicated between analysis programs, for a dictionary that describes these design data, for a directory that describes the analysis programs, and for other system functions. A method is described for interfacing independent analysis programs into a loosely-coupled design system. This method emphasizes an interactive extension of analysis techniques and manipulation of design data. Also, integrity mechanisms exist to maintain database correctness for multidisciplinary design tasks by an individual or a team of specialists. Finally, a prototype user interface program has been developed to aid in system utilization.

  2. Analysis and Modeling of Integrated Magnetics for LLC resonant Converters

    DEFF Research Database (Denmark)

    Li, Mingxiao; Ouyang, Ziwei; Zhao, Bin

    2017-01-01

    Shunt-inserted transformers are widely used toobtain high leakage inductance. This paper investigates thismethod in depth to make it applicable to integrate resonantinductor for the LLC resonant converters. The analysis andmodel of magnetizing inductance and leakage inductance forshunt...... transformers can provide a significantdifference. The way to obtain the desirable magnetizing andleakage inductance value for LLC resonant converters issimplified by the creation of air gaps together with a magneticshunt. The calculation and relation are validated by finiteelement analysis (FEA) simulations...

  3. Integrated dynamic modeling and management system mission analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, A.K.

    1994-12-28

    This document summarizes the mission analysis performed on the Integrated Dynamic Modeling and Management System (IDMMS). The IDMMS will be developed to provide the modeling and analysis capability required to understand the TWRS system behavior in terms of the identified TWRS performance measures. The IDMMS will be used to demonstrate in a verified and validated manner the satisfactory performance of the TWRS system configuration and assurance that the requirements have been satisfied.

  4. Integrated dynamic modeling and management system mission analysis

    International Nuclear Information System (INIS)

    Lee, A.K.

    1994-01-01

    This document summarizes the mission analysis performed on the Integrated Dynamic Modeling and Management System (IDMMS). The IDMMS will be developed to provide the modeling and analysis capability required to understand the TWRS system behavior in terms of the identified TWRS performance measures. The IDMMS will be used to demonstrate in a verified and validated manner the satisfactory performance of the TWRS system configuration and assurance that the requirements have been satisfied

  5. Heater-Integrated Cantilevers for Nano-Samples Thermogravimetric Analysis

    OpenAIRE

    Toffoli, Valeria; Carrato, Sergio; Lee, Dongkyu; Jeon, Sangmin; Lazzarino, Marco

    2013-01-01

    The design and characteristics of a micro-system for thermogravimetric analysis (TGA) in which heater, temperature sensor and mass sensor are integrated into a single device are presented. The system consists of a suspended cantilever that incorporates a microfabricated resistor, used as both heater and thermometer. A three-dimensional finite element analysis was used to define the structure parameters. TGA sensors were fabricated by standard microlithographic techniques and tested using mill...

  6. On the Integration of Digital Design and Analysis Tools

    DEFF Research Database (Denmark)

    Klitgaard, Jens; Kirkegaard, Poul Henning

    2006-01-01

    The aim of this research is to look into integrated digital design and analysis tools in order to find out if it is suited for use by architects and designers or only by specialists and technicians - and if not, then to look at what can be done to make them more available to architects and design...

  7. Multi-criteria decision analysis integrated with GIS for radio ...

    African Journals Online (AJOL)

    Multi-criteria decision analysis integrated with GIS for radio astronomical observatory site selection in peninsular of Malaysia. R Umar, Z.Z. Abidin, Z.A. Ibrahim, M.K.A. Kamarudin, S.N. Hazmin, A Endut, H Juahir ...

  8. Integrated analysis for genotypic adaptation in rice | Das | African ...

    African Journals Online (AJOL)

    Integrated analysis for genotypic adaptation in rice. S Das, RC Misra, MC Pattnaik, SK Sinha. Abstract. Development of varieties with high yield potential coupled with wide adaptability is an important plant breeding objective. The presence of genotype by environment (GxE) interaction plays a crucial role in determining the ...

  9. Integration of Design and Control Through Model Analysis

    DEFF Research Database (Denmark)

    Russel, Boris Mariboe; Henriksen, Jens Peter; Jørgensen, Sten Bay

    2000-01-01

    of the phenomena models representing the process model identify the relationships between the important process and design variables, which help to understand, define and address some of the issues related to integration of design and control issues. The model analysis is highlighted through examples involving...... processes with mass and/or energy recycle. (C) 2000 Elsevier Science Ltd. All rights reserved....

  10. Enhancing yeast transcription analysis through integration of heterogeneous data

    DEFF Research Database (Denmark)

    Grotkjær, Thomas; Nielsen, Jens

    2004-01-01

    of Saccharomyces cerevisiae whole genome transcription data. A special focus is on the quantitative aspects of normalisation and mathematical modelling approaches, since they are expected to play an increasing role in future DNA microarray analysis studies. Data analysis is exemplified with cluster analysis......DNA microarray technology enables the simultaneous measurement of the transcript level of thousands of genes. Primary analysis can be done with basic statistical tools and cluster analysis, but effective and in depth analysis of the vast amount of transcription data requires integration with data...... from several heterogeneous data Sources, such as upstream promoter sequences, genome-scale metabolic models, annotation databases and other experimental data. In this review, we discuss how experimental design, normalisation, heterogeneous data and mathematical modelling can enhance analysis...

  11. Biochemical and kinetic analysis of the GH3 family beta-xylosidase from Aspergillus awamori X-100.

    Science.gov (United States)

    Eneyskaya, Elena V; Ivanen, Dina R; Bobrov, Kirill S; Isaeva-Ivanova, Lyudmila S; Shabalin, Konstantin A; Savel'ev, Andrew N; Golubev, Alexander M; Kulminskaya, Anna A

    2007-01-15

    The beta-xylosidase from Aspergillus awamori X-100 belonging to the family 3 glycoside hydrolase revealed a distinctive transglycosylating ability to produce xylooligosaccharides with degree of polymerization more than 7. In order to explain this fact, the enzyme has been subjected to the detailed biochemical study. The enzymatic hydrolysis of p-nitrophenyl beta-D-xylopyranoside was found to occur with overall retention of substrate anomeric configuration suggesting cleavage of xylosidic bonds through a double-displacement mechanism. Kinetic study with aryl beta-xylopyranosides substrates, in which leaving group pK(a)s were in the range of 3.96-10.32, revealed monotonic function of log(k(cat)) and no correlation of log(k(cat)/Km) versus pKa values indicating deglycosylation as a rate-limiting step for the enzymatic hydrolysis. The classical bell-shaped pH dependence of k(cat)/Km indicated two ionizable groups in the beta-xylosidase active site with apparent pKa values of 2.2 and 6.4. The kinetic parameters of hydrolysis, Km and k(cat), of p-nitrophenyl beta-D-1,4-xylooligosaccharides were very close to those for hydrolysis of p-nitrophenyl-beta-D-xylopyranoside. Increase of p-nitrophenyl-beta-D-xylopyranoside concentration up to 80 mM led to increasing of the reaction velocity resulting in k(cat)(app)=81 s(-1). Addition of alpha-methyl D-xylopyranoside to the reaction mixture at high concentration of p-nitrophenyl-beta-D-xylopyranoside (50 mM) caused an acceleration of the beta-xylosidase-catalyzed reactions and appearance of a new transglycosylation product, alpha-methyl D-xylopyranosyl-1,4-beta-D-xylopyranoside, that was identified by 1H NMR spectroscopy. The kinetic model suggested for the enzymatic reaction was consistent with the results obtained.

  12. Integration of End-User Cloud Storage for CMS Analysis

    CERN Document Server

    Riahi, Hassen; Álvarez Ayllón, Alejandro; Balcas, Justas; Ciangottini, Diego; Hernández, José M; Keeble, Oliver; Magini, Nicolò; Manzi, Andrea; Mascetti, Luca; Mascheroni, Marco; Tanasijczuk, Andres Jorge; Vaandering, Eric Wayne

    2018-01-01

    End-user Cloud storage is increasing rapidly in popularity in research communities thanks to the collaboration capabilities it offers, namely synchronisation and sharing. CERN IT has implemented a model of such storage named, CERNBox, integrated with the CERN AuthN and AuthZ services. To exploit the use of the end-user Cloud storage for the distributed data analysis activity, the CMS experiment has started the integration of CERNBox as a Grid resource. This will allow CMS users to make use of their own storage in the Cloud for their analysis activities as well as to benefit from synchronisation and sharing capabilities to achieve results faster and more effectively. It will provide an integration model of Cloud storages in the Grid, which is implemented and commissioned over the world’s largest computing Grid infrastructure, Worldwide LHC Computing Grid (WLCG). In this paper, we present the integration strategy and infrastructure changes needed in order to transparently integrate end-user Cloud storage with...

  13. Application of Stochastic Sensitivity Analysis to Integrated Force Method

    Directory of Open Access Journals (Sweden)

    X. F. Wei

    2012-01-01

    Full Text Available As a new formulation in structural analysis, Integrated Force Method has been successfully applied to many structures for civil, mechanical, and aerospace engineering due to the accurate estimate of forces in computation. Right now, it is being further extended to the probabilistic domain. For the assessment of uncertainty effect in system optimization and identification, the probabilistic sensitivity analysis of IFM was further investigated in this study. A set of stochastic sensitivity analysis formulation of Integrated Force Method was developed using the perturbation method. Numerical examples are presented to illustrate its application. Its efficiency and accuracy were also substantiated with direct Monte Carlo simulations and the reliability-based sensitivity method. The numerical algorithm was shown to be readily adaptable to the existing program since the models of stochastic finite element and stochastic design sensitivity are almost identical.

  14. 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.

  15. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  16. Containment integrity analysis with SAMPSON/DCRA module

    International Nuclear Information System (INIS)

    Hosoda, Seigo; Shirakawa, Noriyuki; Naitoh, Masanori

    2006-01-01

    The integrity of PWR containment under a severe accident is analyzed using the debris concrete reaction analysis code. If core fuels melt through the pressure vessel and the debris accumulates on the reactor cavity of a lower part of containment, its temperature continues to rise due to decay heat and the debris ablates the concrete floor. In case that cooling water is issued into the containment cavity and the amount of debris is limited to 30% of core fuels, our analyses showed that the debris could be cooled and frozen so that integrity of containment could hold. (author)

  17. k-OptForce: integrating kinetics with flux balance analysis for strain design.

    Directory of Open Access Journals (Sweden)

    Anupam Chowdhury

    2014-02-01

    Full Text Available Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics and reaction flux changes (for reactions with only stoichiometric information. Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis

  18. Plant-wide integrated equipment monitoring and analysis system

    International Nuclear Information System (INIS)

    Morimoto, C.N.; Hunter, T.A.; Chiang, S.C.

    2004-01-01

    A nuclear power plant equipment monitoring system monitors plant equipment and reports deteriorating equipment conditions. The more advanced equipment monitoring systems can also provide information for understanding the symptoms and diagnosing the root cause of a problem. Maximizing the equipment availability and minimizing or eliminating consequential damages are the ultimate goals of equipment monitoring systems. GE Integrated Equipment Monitoring System (GEIEMS) is designed as an integrated intelligent monitoring and analysis system for plant-wide application for BWR plants. This approach reduces system maintenance efforts and equipment monitoring costs and provides information for integrated planning. This paper describes GEIEMS and how the current system is being upgraded to meet General Electric's vision for plant-wide decision support. (author)

  19. STINGRAY: system for integrated genomic resources and analysis.

    Science.gov (United States)

    Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

    2014-03-07

    The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

  20. An Integrated Solution for Performing Thermo-fluid Conjugate Analysis

    Science.gov (United States)

    Kornberg, Oren

    2009-01-01

    A method has been developed which integrates a fluid flow analyzer and a thermal analyzer to produce both steady state and transient results of 1-D, 2-D, and 3-D analysis models. The Generalized Fluid System Simulation Program (GFSSP) is a one dimensional, general purpose fluid analysis code which computes pressures and flow distributions in complex fluid networks. The MSC Systems Improved Numerical Differencing Analyzer (MSC.SINDA) is a one dimensional general purpose thermal analyzer that solves network representations of thermal systems. Both GFSSP and MSC.SINDA have graphical user interfaces which are used to build the respective model and prepare it for analysis. The SINDA/GFSSP Conjugate Integrator (SGCI) is a formbase graphical integration program used to set input parameters for the conjugate analyses and run the models. The contents of this paper describes SGCI and its thermo-fluids conjugate analysis techniques and capabilities by presenting results from some example models including the cryogenic chill down of a copper pipe, a bar between two walls in a fluid stream, and a solid plate creating a phase change in a flowing fluid.

  1. Analysis of Waste Isolation Pilot Plant Samples: Integrated Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Britt, Phillip F [ORNL

    2015-03-01

    Analysis of Waste Isolation Pilot Plant Samples: Integrated Summary Report. Summaries of conclusions, analytical processes, and analytical results. Analysis of samples taken from the Waste Isolation Pilot Plant (WIPP) near Carlsbad, New Mexico in support of the WIPP Technical Assessment Team (TAT) activities to determine to the extent feasible the mechanisms and chemical reactions that may have resulted in the breach of at least one waste drum and release of waste material in WIPP Panel 7 Room 7 on February 14, 2014. This report integrates and summarizes the results contained in three separate reports, described below, and draws conclusions based on those results. Chemical and Radiochemical Analyses of WIPP Samples R-15 C5 SWB and R16 C-4 Lip; PNNL-24003, Pacific Northwest National Laboratory, December 2014 Analysis of Waste Isolation Pilot Plant (WIPP) Underground and MgO Samples by the Savannah River National Laboratory (SRNL); SRNL-STI-2014-00617; Savannah River National Laboratory, December 2014 Report for WIPP UG Sample #3, R15C5 (9/3/14); LLNL-TR-667015; Lawrence Livermore National Laboratory, January 2015 This report is also contained in the Waste Isolation Pilot Plant Technical Assessment Team Report; SRNL-RP-2015-01198; Savannah River National Laboratory, March 17, 2015, as Appendix C: Analysis Integrated Summary Report.

  2. Metabolomic Analysis of Biochemical Changes in the Plasma of High-Fat Diet and Streptozotocin-Induced Diabetic Rats after Treatment with Isoflavones Extract of Radix Puerariae

    Directory of Open Access Journals (Sweden)

    Yan Zhang

    2016-01-01

    Full Text Available The main purpose of this study was to investigate the protective effects of total isoflavones from Radix Puerariae (PTIF in diabetic rats. Diabetes was induced by a high-fat diet and intraperitoneal injection of low-dose streptozotocin (STZ; 40 mg/kg. At 26 weeks onwards, PTIF 421 mg/kg was administrated to the rats once daily consecutively for 10 weeks. Metabolic profiling changes were analyzed by Ultraperformance Liquid Chromatography-Quadrupole-Exactive Orbitrap-Mass Spectrometry (UPLC-Q-Exactive Orbitrap-MS. The principal component discriminant analysis (PCA-DA, partial least-squares discriminant analysis (PLS-DA, and orthogonal partial least-squares discriminant analysis (OPLS-DA were used for multivariate analysis. Moreover, free amino acids in serum were determined by high-performance liquid chromatography with fluorescence detector (HPLC-FLD. Additionally, oxidative stress and inflammatory cytokines were evaluated. Eleven potential metabolite biomarkers, which are mainly related to the coagulation, lipid metabolism, and amino acid metabolism, have been identified. PCA-DA scores plots indicated that biochemical changes in diabetic rats were gradually restored to normal after administration of PTIF. Furthermore, the levels of BCAAs, glutamate, arginine, and tyrosine were significantly increased in diabetic rats. Treatment with PTIF could regulate the disturbed amino acid metabolism. Consequently, PTIF has great therapeutic potential in the treatment of DM by improving metabolism disorders and inhibiting oxidative damage.

  3. Biochemical analysis of cerebrospinal fluid in the laboratories of deployed medical treatment facilities: are Multistix 10 SG strip and iSTAT useful?

    Science.gov (United States)

    Lefrere, Bertrand; Plantamura, J; Renard, C; Ceppa, F; Delacour, H

    2017-12-01

    During military deployment, the diagnosis and the management of acute bacterial meningitis can be problematic, as deployed Medical Treatment Facilities (MTFs) often have a limited laboratory diagnostic capability. However, French Role 2 and 3 MTFs have point-of-care (POC) testing to perform urinary (Multistix 10 SG strip) and blood (iSTAT handheld analyser) biochemical testing mentioned in AMedP8.5. The purpose of this study was to compare the accuracy of this urine test strip and of the iSTAT CHEM8 and CG4 cartridges with a standard hospital bench top analyser in order to determine if these POC devices have a potential role in the biochemical analysis of cerebrospinal fluid (CSF protein, CSF glucose and CSF lactate, respectively). Agreement between the index methods and the reference methods (suitable kits on the Cobas 6 000 System) was evaluated by parallel testing of 30 CSF samples by both techniques. For CSF protein, agreement between the strip and the reference method was evaluated determining the κ coefficient. For CSF glucose and CSF lactate subgroups, least squares linear regressions were calculated and Bland-Altman analyses were performed. The Multistix 10 SG strip can be used to make a semiquantitative determination of CSF protein. A good agreement between the strip and the reference method was observed (κ coefficient: 0.93 (IC 95 0.82 to 1)). This strip is thus well adapted to demonstrate an elevation of CSF protein level as observed in acute bacterial meningitis. The iSTAT CHEM8 and CG4+ cartridges correlated well with the reference methods for the determination of CSF glucose and CSF lactate, respectively (r 2 >0.98) but exhibited a negative bias (∼ -7% and ∼ -15%, respectively). The combined use of the Multistix 10 SG strip and of the iSTAT system appears to be an attractive solution for the biochemical investigation of CSF in medical treatment facilities with limited laboratory diagnostic capability. Published by the BMJ Publishing Group

  4. Vehicle Integrated Performance Analysis, the VIPA Experience: Reconnecting with Technical Integration

    Science.gov (United States)

    McGhee, David S.

    2005-01-01

    Today's NASA is facing significant challenges and changes. The Exploration initiative indicates a large increase in projects with limited increase in budget. The Columbia report has criticized NASA for its lack of insight and technical integration impacting its ability to provide safety. The Aldridge report is advocating NASA find new ways of doing business. Very early in the Space Launch Initiative (SLI) program a small team of engineers at MSFC were asked to propose a process for performing a system level assessment of a launch vehicle. The request was aimed primarily at providing insight and making NASA a "smart buyer." Out of this effort the VIPA team was created. The difference between the VIPA effort and many integration attempts is that VIPA focuses on using experienced people from various disciplines and a process which focuses them on a technically integrated assessment. Most previous attempts have focused on developing an all encompassing software tool. In addition, VIPA anchored its process formulation in the experience of its members and in early developmental Space Shuttle experience. The primary reference for this is NASA-TP-2001-210092, "Launch Vehicle Design Process: Characterization, Technical Integration, and Lessons Learned," and discussions with its authors. The foundations of VIPA's process are described. The VIPA team also recognized the need to drive detailed analysis earlier in the design process. Analyses and techniques typically done in later design phases, are brought forward using improved computing technology. The intent is to allow the identification of significant sensitivities, trades, and design issues much earlier in the program. This process is driven by the T-model for Technical Integration described in the aforementioned reference. VIPA's approach to performing system level technical integration is discussed in detail. Proposed definitions are offered to clarify this discussion and the general systems integration dialog. VIPA

  5. Slot-waveguide biochemical sensor.

    Science.gov (United States)

    Barrios, Carlos A; Gylfason, Kristinn B; Sánchez, Benito; Griol, Amadeu; Sohlström, H; Holgado, M; Casquel, R

    2007-11-01

    We report an experimental demonstration of an integrated biochemical sensor based on a slot-waveguide microring resonator. The microresonator is fabricated on a Si3N4-SiO2 platform and operates at a wavelength of 1.3 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n=1.33 to 1.42. A linear shift of the resonant wavelength with increasing ambient refractive index of 212 nm/refractive index units (RIU) is observed. The sensor detects a minimal refractive index variation of 2x10(-4) RIU.

  6. INTEGRATION OF FACILITY MODELING CAPABILITIES FOR NUCLEAR NONPROLIFERATION ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Gorensek, M.; Hamm, L.; Garcia, H.; Burr, T.; Coles, G.; Edmunds, T.; Garrett, A.; Krebs, J.; Kress, R.; Lamberti, V.; Schoenwald, D.; Tzanos, C.; Ward, R.

    2011-07-18

    Developing automated methods for data collection and analysis that can facilitate nuclear nonproliferation assessment is an important research area with significant consequences for the effective global deployment of nuclear energy. Facility modeling that can integrate and interpret observations collected from monitored facilities in order to ascertain their functional details will be a critical element of these methods. Although improvements are continually sought, existing facility modeling tools can characterize all aspects of reactor operations and the majority of nuclear fuel cycle processing steps, and include algorithms for data processing and interpretation. Assessing nonproliferation status is challenging because observations can come from many sources, including local and remote sensors that monitor facility operations, as well as open sources that provide specific business information about the monitored facilities, and can be of many different types. Although many current facility models are capable of analyzing large amounts of information, they have not been integrated in an analyst-friendly manner. This paper addresses some of these facility modeling capabilities and illustrates how they could be integrated and utilized for nonproliferation analysis. The inverse problem of inferring facility conditions based on collected observations is described, along with a proposed architecture and computer framework for utilizing facility modeling tools. After considering a representative sampling of key facility modeling capabilities, the proposed integration framework is illustrated with several examples.

  7. Integration of facility modeling capabilities for nuclear nonproliferation analysis

    International Nuclear Information System (INIS)

    Garcia, Humberto; Burr, Tom; Coles, Garill A.; Edmunds, Thomas A.; Garrett, Alfred; Gorensek, Maximilian; Hamm, Luther; Krebs, John; Kress, Reid L.; Lamberti, Vincent; Schoenwald, David; Tzanos, Constantine P.; Ward, Richard C.

    2012-01-01

    Developing automated methods for data collection and analysis that can facilitate nuclear nonproliferation assessment is an important research area with significant consequences for the effective global deployment of nuclear energy. Facility modeling that can integrate and interpret observations collected from monitored facilities in order to ascertain their functional details will be a critical element of these methods. Although improvements are continually sought, existing facility modeling tools can characterize all aspects of reactor operations and the majority of nuclear fuel cycle processing steps, and include algorithms for data processing and interpretation. Assessing nonproliferation status is challenging because observations can come from many sources, including local and remote sensors that monitor facility operations, as well as open sources that provide specific business information about the monitored facilities, and can be of many different types. Although many current facility models are capable of analyzing large amounts of information, they have not been integrated in an analyst-friendly manner. This paper addresses some of these facility modeling capabilities and illustrates how they could be integrated and utilized for nonproliferation analysis. The inverse problem of inferring facility conditions based on collected observations is described, along with a proposed architecture and computer framework for utilizing facility modeling tools. After considering a representative sampling of key facility modeling capabilities, the proposed integration framework is illustrated with several examples.

  8. Integration Of Facility Modeling Capabilities For Nuclear Nonproliferation Analysis

    International Nuclear Information System (INIS)

    Gorensek, M.; Hamm, L.; Garcia, H.; Burr, T.; Coles, G.; Edmunds, T.; Garrett, A.; Krebs, J.; Kress, R.; Lamberti, V.; Schoenwald, D.; Tzanos, C.; Ward, R.

    2011-01-01

    Developing automated methods for data collection and analysis that can facilitate nuclear nonproliferation assessment is an important research area with significant consequences for the effective global deployment of nuclear energy. Facility modeling that can integrate and interpret observations collected from monitored facilities in order to ascertain their functional details will be a critical element of these methods. Although improvements are continually sought, existing facility modeling tools can characterize all aspects of reactor operations and the majority of nuclear fuel cycle processing steps, and include algorithms for data processing and interpretation. Assessing nonproliferation status is challenging because observations can come from many sources, including local and remote sensors that monitor facility operations, as well as open sources that provide specific business information about the monitored facilities, and can be of many different types. Although many current facility models are capable of analyzing large amounts of information, they have not been integrated in an analyst-friendly manner. This paper addresses some of these facility modeling capabilities and illustrates how they could be integrated and utilized for nonproliferation analysis. The inverse problem of inferring facility conditions based on collected observations is described, along with a proposed architecture and computer framework for utilizing facility modeling tools. After considering a representative sampling of key facility modeling capabilities, the proposed integration framework is illustrated with several examples.

  9. Combination and Integration of Qualitative and Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Philipp Mayring

    2001-02-01

    Full Text Available In this paper, I am going to outline ways of combining qualitative and quantitative steps of analysis on five levels. On the technical level, programs for the computer-aided analysis of qualitative data offer various combinations. Where the data are concerned, the employment of categories (for instance by using qualitative content analysis allows for combining qualitative and quantitative forms of data analysis. On the individual level, the creation of types and the inductive generalisation of cases allow for proceeding from individual case material to quantitative generalisations. As for research design, different models can be distinguished (preliminary study, generalisation, elaboration, triangulation which combine qualitative and quantitative steps of analysis. Where the logic of research is concerned, it can be shown that an extended process model which combined qualitative and quantitative research can be appropriate and thus lead to an integration of the two approaches. URN: urn:nbn:de:0114-fqs010162

  10. Inertial navigation sensor integrated motion analysis for autonomous vehicle navigation

    Science.gov (United States)

    Roberts, Barry; Bhanu, Bir

    1992-01-01

    Recent work on INS integrated motion analysis is described. Results were obtained with a maximally passive system of obstacle detection (OD) for ground-based vehicles and rotorcraft. The OD approach involves motion analysis of imagery acquired by a passive sensor in the course of vehicle travel to generate range measurements to world points within the sensor FOV. INS data and scene analysis results are used to enhance interest point selection, the matching of the interest points, and the subsequent motion-based computations, tracking, and OD. The most important lesson learned from the research described here is that the incorporation of inertial data into the motion analysis program greatly improves the analysis and makes the process more robust.

  11. Sparse Group Penalized Integrative Analysis of Multiple Cancer Prognosis Datasets

    Science.gov (United States)

    Liu, Jin; Huang, Jian; Xie, Yang; Ma, Shuangge

    2014-01-01

    SUMMARY In cancer research, high-throughput profiling studies have been extensively conducted, searching for markers associated with prognosis. Because of the “large d, small n” characteristic, results generated from the analysis of a single dataset can be unsatisfactory. Recent studies have shown that integrative analysis, which simultaneously analyzes multiple datasets, can be more effective than single-dataset analysis and classic meta-analysis. In most of existing integrative analysis, the homogeneity model has been assumed, which postulates that different datasets share the same set of markers. Several approaches have been designed to reinforce this assumption. In practice, different datasets may differ in terms of patient selection criteria, profiling techniques, and many other aspects. Such differences may make the homogeneity model too restricted. In this study, we assume the heterogeneity model, under which different datasets are allowed to have different sets of markers. With multiple cancer prognosis datasets, we adopt the AFT (accelerated failure time) model to describe survival. This model may have the lowest computational cost among popular semiparametric survival models. For marker selection, we adopt a sparse group MCP (minimax concave penalty) approach. This approach has an intuitive formulation and can be computed using an effective group coordinate descent algorithm. Simulation study shows that it outperforms the existing approaches under both the homogeneity and heterogeneity models. Data analysis further demonstrates the merit of heterogeneity model and proposed approach. PMID:23938111

  12. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays.

    Science.gov (United States)

    Hou, Sen; Sun, Lili; Wieczorek, Stefan A; Kalwarczyk, Tomasz; Kaminski, Tomasz S; Holyst, Robert

    2014-01-15

    Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3' or 5') end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye. Existing methods are insufficient to measure the percentage of the doubly-labeled dsDNA component in the fluorescent DNA sample and it is even difficult to distinguish the doubly-labeled DNA component from the singly-labeled component. Accurate measurement of the percentage of such doubly labeled dsDNA component is a critical prerequisite for quantitative biochemical measurements, which has puzzled scientists for decades. We established a fluorescence correlation spectroscopy (FCS) system to measure the percentage of doubly labeled dsDNA (PDL) in the total fluorescent dsDNA pool. The method is based on comparative analysis of the given sample and a reference dsDNA sample prepared by adding certain amount of unlabeled ssDNA into the original ssDNA solution. From FCS autocorrelation functions, we obtain the number of fluorescent dsDNA molecules in the focal volume of the confocal microscope and PDL. We also calculate the labeling efficiency of ssDNA. The method requires minimal amount of material. The samples have the concentration of DNA in the nano-molar/L range and the volume of tens of microliters. We verify our method by using restriction enzyme Hind III to cleave the fluorescent dsDNA. The kinetics of the reaction depends strongly on PDL, a critical parameter for quantitative biochemical measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Comparative biochemical analysis during the anaerobic digestion of lignocellulosic biomass from six morphological parts of Williams Cavendish banana (Triploid Musa AAA group) plants.

    Science.gov (United States)

    Kamdem, Irénée; Hiligsmann, Serge; Vanderghem, Caroline; Bilik, Igor; Paquot, Michel; Thonart, Philippe

    2013-12-01

    We studied banana lignocellulosic biomass (BALICEBIOM) that is abandoned after fruit harvesting, and assessed its biochemical methane potential, because of its potential as an energy source. We monitored biogas production from six morphological parts (MPs) of the "Williams Cavendish" banana cultivar using a modified operating procedure (KOP) using KOH. Volatile fatty acid (VFA) production was measured using high performance liquid chromatography. The bulbs, leaf sheaths, petioles-midribs, leaf blades, rachis stems, and floral stalks gave total biogas production of 256, 205, 198, 126, 253, and 221 ml g⁻¹ dry matter, respectively, and total biomethane production of 150, 141, 127, 98, 162, and 144 ml g⁻¹, respectively. The biogas production rates and yields depended on the biochemical composition of the BALICEBIOM and the ability of anaerobic microbes to access fermentable substrates. There were no significant differences between the biogas analysis results produced using KOP and gas chromatography. Acetate was the major VFA in all the MP sample culture media. The bioconversion yields for each MP were below 50 %, showing that these substrates were not fully biodegraded after 188 days. The estimated electricity that could be produced from biogas combustion after fermenting all of the BALICEBIOM produced annually by the Cameroon Development Corporation-Del Monte plantations for 188 days is approximately 10.5 × 10⁶ kW h (which would be worth 0.80-1.58 million euros in the current market). This bioenergy could serve the requirements of about 42,000 people in the region, although CH₄ productivity could be improved.

  14. Simulation analysis of globally integrated logistics and recycling strategies

    Energy Technology Data Exchange (ETDEWEB)

    Song, S.J.; Hiroshi, K. [Hiroshima Inst. of Tech., Graduate School of Mechanical Systems Engineering, Dept. of In formation and Intelligent Systems Engineering, Hiroshima (Japan)

    2004-07-01

    This paper focuses on the optimal analysis of world-wide recycling activities associated with managing the logistics and production activities in global manufacturing whose activities stretch across national boundaries. Globally integrated logistics and recycling strategies consist of the home country and two free trading economic blocs, NAFTA and ASEAN, where significant differences are found in production and disassembly cost, tax rates, local content rules and regulations. Moreover an optimal analysis of globally integrated value-chain was developed by applying simulation optimization technique as a decision-making tool. The simulation model was developed and analyzed by using ProModel packages, and the results help to identify some of the appropriate conditions required to make well-performed logistics and recycling plans in world-wide collaborated manufacturing environment. (orig.)

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

    Science.gov (United States)

    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.

  16. LLIMAS: Revolutionizing integrating modeling and analysis at MIT Lincoln Laboratory

    Science.gov (United States)

    Doyle, Keith B.; Stoeckel, Gerhard P.; Rey, Justin J.; Bury, Mark E.

    2017-08-01

    MIT Lincoln Laboratory's Integrated Modeling and Analysis Software (LLIMAS) enables the development of novel engineering solutions for advanced prototype systems through unique insights into engineering performance and interdisciplinary behavior to meet challenging size, weight, power, environmental, and performance requirements. LLIMAS is a multidisciplinary design optimization tool that wraps numerical optimization algorithms around an integrated framework of structural, thermal, optical, stray light, and computational fluid dynamics analysis capabilities. LLIMAS software is highly extensible and has developed organically across a variety of technologies including laser communications, directed energy, photometric detectors, chemical sensing, laser radar, and imaging systems. The custom software architecture leverages the capabilities of existing industry standard commercial software and supports the incorporation of internally developed tools. Recent advances in LLIMAS's Structural-Thermal-Optical Performance (STOP), aeromechanical, and aero-optical capabilities as applied to Lincoln prototypes are presented.

  17. 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.

  18. Sensitivity Analysis Based on Markovian Integration by Parts Formula

    Directory of Open Access Journals (Sweden)

    Yongsheng Hang

    2017-10-01

    Full Text Available Sensitivity analysis is widely applied in financial risk management and engineering; it describes the variations brought by the changes of parameters. Since the integration by parts technique for Markov chains is well developed in recent years, in this paper we apply it for computation of sensitivity and show the closed-form expressions for two commonly-used time-continuous Markovian models. By comparison, we conclude that our approach outperforms the existing technique of computing sensitivity on Markovian models.

  19. Corporate Disclosure, Materiality, and Integrated Report: An Event Study Analysis

    OpenAIRE

    Maria Cleofe Giorgino; Enrico Supino; Federico Barnabè

    2017-01-01

    Within the extensive literature investigating the impacts of corporate disclosure in supporting the sustainable growth of an organization, few studies have included in the analysis the materiality issue referred to the information being disclosed. This article aims to address this gap, exploring the effect produced on capital markets by the publication of a recent corporate reporting tool, Integrated Report (IR). The features of this tool are that it aims to represent the multidimensional imp...

  20. Process Integration Analysis of an Industrial Hydrogen Production Process

    OpenAIRE

    Stolten, Detlef; Grube, Thomas; Tock, Laurence; Maréchal, François; Metzger, Christian; Arpentinier, Philippe

    2010-01-01

    The energy efficiency of an industrial hydrogen production process using steam methane reforming (SMR) combined with the water gas shift reaction (WGS) is analyzed using process integration techniques based on heat cascade calculation and pinch analysis with the aim of identifying potential measures to enhance the process performance. The challenge is to satisfy the high temperature heat demand of the SMR reaction by minimizing the consumption of natural gas to feed the combustion and to expl...

  1. Building-integrated renewable energy policy analysis in China

    Institute of Scientific and Technical Information of China (English)

    姚春妮; 郝斌

    2009-01-01

    With the dramatic development of renewable energy all over the world,and for purpose of adjusting energy structure,the Ministry of Construction of China plans to promote the large scale application of renewable energy in buildings. In order to ensure the validity of policy-making,this work firstly exerts a method to do cost-benefit analysis for three kinds of technologies such as building-integrated solar hot water (BISHW) system,building-integrated photovoltaic (BIPV) technology and ground water heat pump (GWHP). Through selecting a representative city of every climate region,the analysis comes into different results for different climate regions in China and respectively different suggestion for policy-making. On the analysis basis,the Ministry of Construction (MOC) and the Ministry of Finance of China (MOF) united to start-up Building-integrated Renewable Energy Demonstration Projects (BIREDP) in 2006. In the demonstration projects,renewable energy takes place of traditional energy to supply the domestic hot water,electricity,air-conditioning and heating. Through carrying out the demonstration projects,renewable energy related market has been expanded. More and more relative companies and local governments take the opportunity to promote the large scale application of renewable energy in buildings.

  2. Lectures on functional analysis and the Lebesgue integral

    CERN Document Server

    Komornik, Vilmos

    2016-01-01

    This textbook, based on three series of lectures held by the author at the University of Strasbourg, presents functional analysis in a non-traditional way by generalizing elementary theorems of plane geometry to spaces of arbitrary dimension. This approach leads naturally to the basic notions and theorems. Most results are illustrated by the small ℓp spaces. The Lebesgue integral, meanwhile, is treated via the direct approach of Frigyes Riesz, whose constructive definition of measurable functions leads to optimal, clear-cut versions of the classical theorems of Fubini-Tonelli and Radon-Nikodým. Lectures on Functional Analysis and the Lebesgue Integral presents the most important topics for students, with short, elegant proofs. The exposition style follows the Hungarian mathematical tradition of Paul Erdős and others. The order of the first two parts, functional analysis and the Lebesgue integral, may be reversed. In the third and final part they are combined to study various spaces of continuous and integ...

  3. Heater-Integrated Cantilevers for Nano-Samples Thermogravimetric Analysis

    Directory of Open Access Journals (Sweden)

    Valeria Toffoli

    2013-12-01

    Full Text Available The design and characteristics of a micro-system for thermogravimetric analysis (TGA in which heater, temperature sensor and mass sensor are integrated into a single device are presented. The system consists of a suspended cantilever that incorporates a microfabricated resistor, used as both heater and thermometer. A three-dimensional finite element analysis was used to define the structure parameters. TGA sensors were fabricated by standard microlithographic techniques and tested using milli-Q water and polyurethane microcapsule. The results demonstrated that our approach provides a faster and more sensitive TGA with respect to commercial systems.

  4. Heater-Integrated Cantilevers for Nano-Samples Thermogravimetric Analysis

    Science.gov (United States)

    Toffoli, Valeria; Carrato, Sergio; Lee, Dongkyu; Jeon, Sangmin; Lazzarino, Marco

    2013-01-01

    The design and characteristics of a micro-system for thermogravimetric analysis (TGA) in which heater, temperature sensor and mass sensor are integrated into a single device are presented. The system consists of a suspended cantilever that incorporates a microfabricated resistor, used as both heater and thermometer. A three-dimensional finite element analysis was used to define the structure parameters. TGA sensors were fabricated by standard microlithographic techniques and tested using milli-Q water and polyurethane microcapsule. The results demonstrated that our approach provides a faster and more sensitive TGA with respect to commercial systems.

  5. Contamination assessment of a coastal lagoon (Ria de Aveiro, Portugal) using defence and damage biochemical indicators in gill of Liza aurata - An integrated biomarker approach

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, M. [CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro (Portugal)], E-mail: migueloliveira@ua.pt; Maria, V.L. [CIMA and Faculty of Marine and Environmental Sciences, University of Algarve, Campus Gambelas, 8005-139 Faro (Portugal); Ahmad, I. [CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro (Portugal); Serafim, A.; Bebianno, M.J. [CIMA and Faculty of Marine and Environmental Sciences, University of Algarve, Campus Gambelas, 8005-139 Faro (Portugal); Pacheco, M.; Santos, M.A. [CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro (Portugal)

    2009-03-15

    Fish gill importance in toxicants uptake, bioconcentration and excretion allied to meagre knowledge on branchial damage/protection responses substantiate this study. Five critical sites in Ria de Aveiro (Portugal) were assessed in comparison with a reference site (Torreira), focusing on Liza aurata gill antioxidant defences versus damage (oxidative and genetic). Only in Barra fish displayed damage (lipid peroxidation) though no differences were found in antioxidants. In all other sites, except Rio, antioxidant alterations were found. Thus, fish from Gafanha, Laranjo and Vagos showed higher total glutathione, glutathione peroxidase and catalase. Higher glutathione reductase and glutathione S-transferase activity was also found in the first and the last sites, respectively. In Laranjo, metallothionein levels were higher though lower in Gafanha and Vagos. In general, damage was not accompanied by defences weakening confirming that predicting damage based on antioxidants depletion is not straightforward. The integrated biomarker response index ranked sites as: Gafanha > Barra > Laranjo > Vagos > Rio > Torreira. - The integration of antioxidant defence and damage responses in fish, using gill as a key organ, can improve the aquatic contamination assessment.

  6. Structural integrity analysis of an INPP building under external loading

    International Nuclear Information System (INIS)

    Dundulis, G.; Karalevicius, R.; Uspuras, E.; Kulak, R.F.; Marchertas, A.

    2005-01-01

    After the terrorist attacks in New York and Washington D. C. using civil airplanes, the evaluation of civil airplane crashes into civil and NPP structures has become very important. The interceptions of many terrorists' communications reveal that the use of commandeered commercial aircraft is still a major part of their plans for destruction. Aircraft crash or other flying objects in the territory of the Ignalina Nuclear Power Plant (INPP) represents a concern to the plant. Aircraft traveling at high velocity have a destructive potential. The aircraft crash may damage the roof and walls of buildings, pipelines, electric motors, cases of power supplies, power cables of electricity transmission and other elements and systems, which are important for safety. Therefore, the evaluation of the structural response to an of aircraft crash is important and was selected for analysis. The structural integrity analysis due to the effects of an aircraft crash on an NPP building structure is the subject of this paper. The finite element method was used for the structural analysis of a typical Ignalina NPP building. The structural integrity analysis was performed for a portion of the ALS using the dynamic loading of an aircraft crash impact model. The computer code NEPTUNE was used for this analysis. The local effects caused by impact of the aircraft's engine on the building wall were evaluated independently by using an empirical formula. (authors)

  7. Penalized differential pathway analysis of integrative oncogenomics studies.

    Science.gov (United States)

    van Wieringen, Wessel N; van de Wiel, Mark A

    2014-04-01

    Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving cancer patients. The two molecular levels involved are linked through the central dogma of molecular biology. DNA copy number aberrations abound in the cancer cell. Here we investigate how these aberrations affect gene expression levels within a pathway using observational integrative genomics data of cancer patients. In particular, we aim to identify differential edges between regulatory networks of two groups involving these molecular levels. Motivated by the rate equations, the regulatory mechanism between DNA copy number aberrations and gene expression levels within a pathway is modeled by a simultaneous-equations model, for the one- and two-group case. The latter facilitates the identification of differential interactions between the two groups. Model parameters are estimated by penalized least squares using the lasso (L1) penalty to obtain a sparse pathway topology. Simulations show that the inclusion of DNA copy number data benefits the discovery of gene-gene interactions. In addition, the simulations reveal that cis-effects tend to be over-estimated in a univariate (single gene) analysis. In the application to real data from integrative oncogenomic studies we show that inclusion of prior information on the regulatory network architecture benefits the reproducibility of all edges. Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature.

  8. A universal electronical adaptation of automats for biochemical analysis to a central processing computer by applying CAMAC-signals

    International Nuclear Information System (INIS)

    Schaefer, R.

    1975-01-01

    A universal expansion of a CAMAC-subsystem - BORER 3000 - for adapting analysis instruments in biochemistry to a processing computer is described. The possibility of standardizing input interfaces for lab instruments with such circuits is discussed and the advantages achieved by applying the CAMAC-specifications are described

  9. Analysis of Biochemical Control and Prognostic Factors in Patients Treated With Either Low-Dose Three-Dimensional Conformal Radiation Therapy or High-Dose Intensity-Modulated Radiotherapy for Localized Prostate Cancer

    International Nuclear Information System (INIS)

    Vora, Sujay A.; Wong, William W.; Schild, Steven E.; Ezzell, Gary A.; Halyard, Michele Y.

    2007-01-01

    Purpose: To identify prognostic factors and evaluate biochemical control rates for patients with localized prostate cancer treated with either high-dose intensity-modulated radiotherapy (IMRT) or conventional-dose three-dimensional conformal radiotherapy 3D-CRT. Methods: Four hundred sixteen patients with a minimum follow-up of 3 years (median, 5 years) were included. Two hundred seventy-one patients received 3D-CRT with a median dose of 68.4 Gy (range, 66-71 Gy). The next 145 patients received IMRT with a median dose of 75.6 Gy (range, 70.2-77.4 Gy). Biochemical control rates were calculated according to both American Society for Therapeutic Radiology and Oncology (ASTRO) consensus definitions. Prognostic factors were identified using both univariate and multivariate analyses. Results: The 5-year biochemical control rate was 60.4% for 3D-CRT and 74.1% for IMRT (p < 0.0001, first ASTRO Consensus definition). Using the ASTRO Phoenix definition, the 5-year biochemical control rate was 74.4% and 84.6% with 3D-RT and IMRT, respectively (p = 0.0326). Univariate analyses determined that PSA level, T stage, Gleason score, perineural invasion, and radiation dose were predictive of biochemical control. On multivariate analysis, dose, Gleason score, and perineural invasion remained significant. Conclusion: On the basis of both ASTRO definitions, dose, Gleason score, and perineural invasion were predictive of biochemical control. Intensity-modulated radiotherapy allowed delivery of higher doses of radiation with very low toxicity, resulting in improved biochemical control

  10. Lab-on-Valve Micro Sequential Injection: A Versatile Approach for Implementing Integrated Sample Pre-preparations and Executing (Bio)Chemical Assays

    DEFF Research Database (Denmark)

    Hansen, Elo Harald

    waste generation. Most recently, the socalled third generation of FIA has emerged, that is, the Lab-on-Valve (LOV) approach, the conceptual basis of which is to incorporate all the necessary unit operational manipulations required, and, when possible, even the detection device into a single small...... integrated microconduit, or “laboratory”, placed atop a selection valve. The lecture will detail the evolution of the three generations of FIA, emphasis being placed on the LOV approach. Proven itself as a versatile front end to a variety of detection techniques, its utility will be exemplified by a series...... of the renewable microcolumn concept. Despite their excellent analytical chemical capabilities, ETAAS as well as ICPMS often require that the samples are subjected to suitable pretreatment in order to obtain the necessary sensitivity and selectivity. Either in order to separate the analyte from potentially...

  11. Lab-on-Valve Micro Sequential Injection: A Versatile Approach for Implementing Integrated Sample Pre-preparations and Executing (Bio)Chemical Assays

    DEFF Research Database (Denmark)

    Hansen, Elo Harald

    waste generation. Most recently, the Lab-on-Valve (LOV) approach has emerged. Termed the third generation of FIA, the conceptual basis of the LOV is to incorporate all the necessary unit operational manipulations required in a chemical assay, and, when possible, even the detection device, into a single...... small integrated microconduit, or “laboratory”, placed atop a selection valve. In the lecture emphasis will be placed on the LOV approach. Proven itself as a versatile front end to a variety of detection techniques, its utility will be exemplified by various applications. Particular focus......-phase microcolumn concept utilising hydrophobic as well as hydrophilic bead materials. Although ETAAS and ICPMS both are characterised by excellent analytical chemical capabilities, they nevertheless often require that the samples be subjected to suitable pretreatment in order to obtain the necessary sensitivity...

  12. SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

    Science.gov (United States)

    Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

    2013-01-01

    SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

  13. Integration of facility modeling capabilities for nuclear nonproliferation analysis

    International Nuclear Information System (INIS)

    Burr, Tom; Gorensek, M.B.; Krebs, John; Kress, Reid L.; Lamberti, Vincent; Schoenwald, David; Ward, Richard C.

    2012-01-01

    Developing automated methods for data collection and analysis that can facilitate nuclearnonproliferation assessment is an important research area with significant consequences for the effective global deployment of nuclear energy. Facilitymodeling that can integrate and interpret observations collected from monitored facilities in order to ascertain their functional details will be a critical element of these methods. Although improvements are continually sought, existing facilitymodeling tools can characterize all aspects of reactor operations and the majority of nuclear fuel cycle processing steps, and include algorithms for data processing and interpretation. Assessing nonproliferation status is challenging because observations can come from many sources, including local and remote sensors that monitor facility operations, as well as open sources that provide specific business information about the monitored facilities, and can be of many different types. Although many current facility models are capable of analyzing large amounts of information, they have not been integrated in an analyst-friendly manner. This paper addresses some of these facilitymodelingcapabilities and illustrates how they could be integrated and utilized for nonproliferationanalysis. The inverse problem of inferring facility conditions based on collected observations is described, along with a proposed architecture and computer framework for utilizing facilitymodeling tools. After considering a representative sampling of key facilitymodelingcapabilities, the proposed integration framework is illustrated with several examples.

  14. Ultraviolet transparent silicon oxynitride waveguides for biochemical microsystems

    DEFF Research Database (Denmark)

    Mogensen, Klaus Bo; Friis, Peter; Hübner, Jörg

    2001-01-01

    The UV wavelength region is of great interest in absorption spectroscopy, which is employed for chemical analysis, since many organic compounds absorb in only this region. Germanium-doped silica, which is often preferred as the waveguide core material in optical devices for telecommunication....... The applicability of these waveguides was demonstrated in a biochemical microsystem consisting of multimode buried-channel SiOxNy waveguides that were monolithically integrated with microfluidic channels. Absorption measurements of a beta -blocking agent, propranolol, at 212-215 nm were performed. The detection...

  15. Integrated situational awareness for cyber attack detection, analysis, and mitigation

    Science.gov (United States)

    Cheng, Yi; Sagduyu, Yalin; Deng, Julia; Li, Jason; Liu, Peng

    2012-06-01

    Real-time cyberspace situational awareness is critical for securing and protecting today's enterprise networks from various cyber threats. When a security incident occurs, network administrators and security analysts need to know what exactly has happened in the network, why it happened, and what actions or countermeasures should be taken to quickly mitigate the potential impacts. In this paper, we propose an integrated cyberspace situational awareness system for efficient cyber attack detection, analysis and mitigation in large-scale enterprise networks. Essentially, a cyberspace common operational picture will be developed, which is a multi-layer graphical model and can efficiently capture and represent the statuses, relationships, and interdependencies of various entities and elements within and among different levels of a network. Once shared among authorized users, this cyberspace common operational picture can provide an integrated view of the logical, physical, and cyber domains, and a unique visualization of disparate data sets to support decision makers. In addition, advanced analyses, such as Bayesian Network analysis, will be explored to address the information uncertainty, dynamic and complex cyber attack detection, and optimal impact mitigation issues. All the developed technologies will be further integrated into an automatic software toolkit to achieve near real-time cyberspace situational awareness and impact mitigation in large-scale computer networks.

  16. Measure and integral an introduction to real analysis

    CERN Document Server

    Wheeden, Richard L

    2015-01-01

    Now considered a classic text on the topic, Measure and Integral: An Introduction to Real Analysis provides an introduction to real analysis by first developing the theory of measure and integration in the simple setting of Euclidean space, and then presenting a more general treatment based on abstract notions characterized by axioms and with less geometric content.Published nearly forty years after the first edition, this long-awaited Second Edition also:Studies the Fourier transform of functions in the spaces L1, L2, and Lp, 1 p Shows the Hilbert transform to be a bounded operator on L2, as an application of the L2 theory of the Fourier transform in the one-dimensional caseCovers fractional integration and some topics related to mean oscillation properties of functions, such as the classes of Hölder continuous functions and the space of functions of bounded mean oscillationDerives a subrepresentation formula, which in higher dimensions plays a role roughly similar to the one played by the fundamental theor...

  17. Integrative Analysis of Cancer Diagnosis Studies with Composite Penalization

    Science.gov (United States)

    Liu, Jin; Huang, Jian; Ma, Shuangge

    2013-01-01

    Summary In cancer diagnosis studies, high-throughput gene profiling has been extensively conducted, searching for genes whose expressions may serve as markers. Data generated from such studies have the “large d, small n” feature, with the number of genes profiled much larger than the sample size. Penalization has been extensively adopted for simultaneous estimation and marker selection. Because of small sample sizes, markers identified from the analysis of single datasets can be unsatisfactory. A cost-effective remedy is to conduct integrative analysis of multiple heterogeneous datasets. In this article, we investigate composite penalization methods for estimation and marker selection in integrative analysis. The proposed methods use the minimax concave penalty (MCP) as the outer penalty. Under the homogeneity model, the ridge penalty is adopted as the inner penalty. Under the heterogeneity model, the Lasso penalty and MCP are adopted as the inner penalty. Effective computational algorithms based on coordinate descent are developed. Numerical studies, including simulation and analysis of practical cancer datasets, show satisfactory performance of the proposed methods. PMID:24578589

  18. Comparative binding characteristics of Tc-CPI, Tc-TBI, and Tc-MIBI in cultured heart cells: Correlation with biochemical analysis and animal images

    International Nuclear Information System (INIS)

    Piwnica-Worms, D.; Kronauge, J.F.; Holman, B.L.; Davison, A.; Jones, A.G.

    1987-01-01

    Hexakis (isonitrile)technetium (I) complexes are a new class of cationic, lipophilic myocaridal perfusion imaging agents. To better understand their cellular mechanisms of uptake and washout, chick heart cells grown in culture were used as a model myocardial system. Tc-MIBI showed uptake to a plateau at a rate similar to Tc-CPI (t1/2 = 4.1 +- 0.7 minutes); however, the plateau was 63% greater. Tc-TBI uptake approached a plateau 900% greater than Tc-CPI binding. Heart cell studies showed washout of Tc-CPI>Tc-TBI>Tc-MIBI, which correlated with kinetic analysis of rabbit myocardial images. Biochemical in vitro analysis in human plasma demonstrated 75% enzymatic ester hydrolysis of Tc-CPI by 3 minutes, but no hydrolysis of Tc-TBI and Tc-MIBI. The results suggest that metabolism of the ester function of Tc-CPI following myocardial uptake may in part account for the more rapid cellular washout rates of Tc-CPI compared with Tc-TBI and Tc-MIBI

  19. Methodology for dimensional variation analysis of ITER integrated systems

    International Nuclear Information System (INIS)

    Fuentes, F. Javier; Trouvé, Vincent; Cordier, Jean-Jacques; Reich, Jens

    2016-01-01

    Highlights: • Tokamak dimensional management methodology, based on 3D variation analysis, is presented. • Dimensional Variation Model implementation workflow is described. • Methodology phases are described in detail. The application of this methodology to the tolerance analysis of ITER Vacuum Vessel is presented. • Dimensional studies are a valuable tool for the assessment of Tokamak PCR (Project Change Requests), DR (Deviation Requests) and NCR (Non-Conformance Reports). - Abstract: The ITER machine consists of a large number of complex systems highly integrated, with critical functional requirements and reduced design clearances to minimize the impact in cost and performances. Tolerances and assembly accuracies in critical areas could have a serious impact in the final performances, compromising the machine assembly and plasma operation. The management of tolerances allocated to part manufacture and assembly processes, as well as the control of potential deviations and early mitigation of non-compliances with the technical requirements, is a critical activity on the project life cycle. A 3D tolerance simulation analysis of ITER Tokamak machine has been developed based on 3DCS dedicated software. This integrated dimensional variation model is representative of Tokamak manufacturing functional tolerances and assembly processes, predicting accurate values for the amount of variation on critical areas. This paper describes the detailed methodology to implement and update the Tokamak Dimensional Variation Model. The model is managed at system level. The methodology phases are illustrated by its application to the Vacuum Vessel (VV), considering the status of maturity of VV dimensional variation model. The following topics are described in this paper: • Model description and constraints. • Model implementation workflow. • Management of input and output data. • Statistical analysis and risk assessment. The management of the integration studies based on

  20. Methodology for dimensional variation analysis of ITER integrated systems

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes, F. Javier, E-mail: FranciscoJavier.Fuentes@iter.org [ITER Organization, Route de Vinon-sur-Verdon—CS 90046, 13067 St Paul-lez-Durance (France); Trouvé, Vincent [Assystem Engineering & Operation Services, rue J-M Jacquard CS 60117, 84120 Pertuis (France); Cordier, Jean-Jacques; Reich, Jens [ITER Organization, Route de Vinon-sur-Verdon—CS 90046, 13067 St Paul-lez-Durance (France)

    2016-11-01

    Highlights: • Tokamak dimensional management methodology, based on 3D variation analysis, is presented. • Dimensional Variation Model implementation workflow is described. • Methodology phases are described in detail. The application of this methodology to the tolerance analysis of ITER Vacuum Vessel is presented. • Dimensional studies are a valuable tool for the assessment of Tokamak PCR (Project Change Requests), DR (Deviation Requests) and NCR (Non-Conformance Reports). - Abstract: The ITER machine consists of a large number of complex systems highly integrated, with critical functional requirements and reduced design clearances to minimize the impact in cost and performances. Tolerances and assembly accuracies in critical areas could have a serious impact in the final performances, compromising the machine assembly and plasma operation. The management of tolerances allocated to part manufacture and assembly processes, as well as the control of potential deviations and early mitigation of non-compliances with the technical requirements, is a critical activity on the project life cycle. A 3D tolerance simulation analysis of ITER Tokamak machine has been developed based on 3DCS dedicated software. This integrated dimensional variation model is representative of Tokamak manufacturing functional tolerances and assembly processes, predicting accurate values for the amount of variation on critical areas. This paper describes the detailed methodology to implement and update the Tokamak Dimensional Variation Model. The model is managed at system level. The methodology phases are illustrated by its application to the Vacuum Vessel (VV), considering the status of maturity of VV dimensional variation model. The following topics are described in this paper: • Model description and constraints. • Model implementation workflow. • Management of input and output data. • Statistical analysis and risk assessment. The management of the integration studies based on

  1. Technology integrated teaching in Malaysian schools: GIS, a SWOT analysis

    Directory of Open Access Journals (Sweden)

    Habibah Lateh, vasugiammai muniandy

    2011-08-01

    , articles and proceeding papers. Researches had been continuously done in integrating GIS into Geography syllabus. Thus, this article describes and discusses the barriers and opportunities of implementing GIS in schools with a deep focus of how GIS could enhance the process of teaching and learning geography. The purpose of the study is to determine the effectiveness of GIS in enhancing students’ interest towards the subject. Barriers that might limit the implementation of GIS in schools also briefly discussedin this article. The capabilities of GIS in schools and teaching with GIS is also a part of this article. SWOT analysis is used to find the strength, threaten, opportunities and weakness of GIS to be integrated in Malaysian schools. A content analysis was performed using articles from local and abroad publications regarding technology integration and GIS. Conference proceedings were also analyzed. This content analysis included 35 articles selected from ICT and GIS publication in Malaysia and abroad. The content analysis was done in order to identify the barriers of trying GIS in schools in Malaysia. Thus, this article discusses strengths, weaknesses, opportunities and threatens. The future of GIS in Malaysian Schools has been added into the conclusion.

  2. Analysis on working pressure selection of ACME integral test facility

    International Nuclear Information System (INIS)

    Chen Lian; Chang Huajian; Li Yuquan; Ye Zishen; Qin Benke

    2011-01-01

    An integral effects test facility, advanced core cooling mechanism experiment facility (ACME) was designed to verify the performance of the passive safety system and validate its safety analysis codes of a pressurized water reactor power plant. Three test facilities for AP1000 design were introduced and review was given. The problems resulted from the different working pressures of its test facilities were analyzed. Then a detailed description was presented on the working pressure selection of ACME facility as well as its characteristics. And the approach of establishing desired testing initial condition was discussed. The selected 9.3 MPa working pressure covered almost all important passive safety system enables the ACME to simulate the LOCAs with the same pressure and property similitude as the prototype. It's expected that the ACME design would be an advanced core cooling integral test facility design. (authors)

  3. Application of symplectic integrator to numerical fluid analysis

    International Nuclear Information System (INIS)

    Tanaka, Nobuatsu

    2000-01-01

    This paper focuses on application of the symplectic integrator to numerical fluid analysis. For the purpose, we introduce Hamiltonian particle dynamics to simulate fluid behavior. The method is based on both the Hamiltonian formulation of a system and the particle methods, and is therefore called Hamiltonian Particle Dynamics (HPD). In this paper, an example of HPD applications, namely the behavior of incompressible inviscid fluid, is solved. In order to improve accuracy of HPD with respect to space, CIVA, which is a highly accurate interpolation method, is combined, but the combined method is subject to problems in that the invariants of the system are not conserved in a long-time computation. For solving the problems, symplectic time integrators are introduced and the effectiveness is confirmed by numerical analyses. (author)

  4. Biochemical applications of FT-IR spectroscopy

    NARCIS (Netherlands)

    Pistorius, A.M.A.

    1996-01-01

    This thesis describes the use of (FT-)IR spectroscopy in general biochemical research. In chapter 3, IR spectroscopy is used in the quantitation of residual detergent after reconstitution of an integral membrane protein in a pre-defined lipid matrix. This chapter discusses the choice of the

  5. An audit of the contribution to post-mortem examination diagnosis of individual analyte results obtained from biochemical analysis of the vitreous.

    Science.gov (United States)

    Mitchell, Rebecca; Charlwood, Cheryl; Thomas, Sunethra Devika; Bellis, Maria; Langlois, Neil E I

    2013-12-01

    Biochemical analysis of the vitreous humor from the eye is an accepted accessory test for post-mortem investigation of cause of death. Modern biochemical analyzers allow testing of a range of analytes from a sample. However, it is not clear which analytes should be requested in order to prevent unnecessary testing (and expense). The means and standard deviation of the values obtained from analysis of the vitreous humor for sodium, potassium, chloride, osmolality, glucose, ketones (β-hydroxybutyrate), creatinine, urea, calcium, lactate, and ammonia were calculated from which the contribution of each analyte was reviewed in the context of post-mortem findings and final cause of death. For sodium 32 cases were regarded as high (more than one standard deviation above the mean), from which 9 contributed to post-mortem diagnosis [drowning (4), heat related death (2), diabetic hyperglycemia (2), and dehydration (1)], but 25 low values (greater than one standard deviation below the mean) made no contribution. For chloride 29 high values contributed to 4 cases--3 drowning and 1 heat-related, but these were all previously identified by a high sodium level. There were 29 high and 35 low potassium values, none of which contributed to determining the final cause of death. Of 22 high values of creatinine, 12 contributed to a diagnosis of renal failure. From 32 high values of urea, 18 contributed to 16 cases of renal failure (2 associated with diabetic hyperglycemia), 1 heat-related death, and one case with dehydration. Osmolarity contributed to 12 cases (5 heat-related, 4 diabetes, 2 renal failure, and 1 dehydration) from 36 high values. There was no contribution from 32 high values and 19 low values of calcium and there was no contribution from 4 high and 2 low values of ammonia. There were 11 high values of glucose, which contributed to the diagnosis of 6 cases of diabetic hyperglycemia and 21 high ketone levels contributed to 8 cases: 4 diabetic ketosis, 3 hypothermia, 3

  6. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  7. Integrated information system for analysis of nuclear power plants

    International Nuclear Information System (INIS)

    Galperin, A.

    1994-01-01

    Performing complicated engineering analyses of a nuclear power plant requires storage and manipulation of a large amount of information, both data and knowledge. This information is characterized by its multidisciplinary nature, complexity, and diversity. The problems caused by inefficient and lengthy manual operations involving the data flow management within the frame-work of the safety-related analysis of a power plant can be solved by applying the computer aided engineering principles. These principles are the basis of the design of an integrated information storage system (IRIS). The basic idea is to create a computerized environment, which includes both database and functional capabilities. Consideration and analysis of the data types and required data manipulation capabilities as well as operational requirements, resulted in the choice of an object-oriented data-base management system (OODBMS) as a development platform for solving the software engineering problems. Several advantages of OODBMSs over conventional relations database systems were found of crucial importance, especially providing the necessary flexibility for different data types and extensibility potential. A detailed design of a data model is produced for the plant technical data and for the storage of analysis results. The overall system architecture was designed to assure the feasibility of integrating database capabilities with procedures and functions written in conventional algorithmic programming languages

  8. Vertically integrated analysis of human DNA. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Olson, M.

    1997-10-01

    This project has been oriented toward improving the vertical integration of the sequential steps associated with the large-scale analysis of human DNA. The central focus has been on an approach to the preparation of {open_quotes}sequence-ready{close_quotes} maps, which is referred to as multiple-complete-digest (MCD) mapping, primarily directed at cosmid clones. MCD mapping relies on simple experimental steps, supported by advanced image-analysis and map-assembly software, to produce extremely accurate restriction-site and clone-overlap maps. We believe that MCD mapping is one of the few high-resolution mapping systems that has the potential for high-level automation. Successful automation of this process would be a landmark event in genome analysis. Once other higher organisms, paving the way for cost-effective sequencing of these genomes. Critically, MCD mapping has the potential to provide built-in quality control for sequencing accuracy and to make possible a highly integrated end product even if there are large numbers of discontinuities in the actual sequence.

  9. DESIGN ANALYSIS OF ELECTRICAL MACHINES THROUGH INTEGRATED NUMERICAL APPROACH

    Directory of Open Access Journals (Sweden)

    ARAVIND C.V.

    2016-02-01

    Full Text Available An integrated design platform for the newer type of machines is presented in this work. The machine parameters are evaluated out using developed modelling tool. With the machine parameters, the machine is modelled using computer aided tool. The designed machine is brought to simulation tool to perform electromagnetic and electromechanical analysis. In the simulation, conditions setting are performed to setup the materials, meshes, rotational speed and the excitation circuit. Electromagnetic analysis is carried out to predict the behavior of the machine based on the movement of flux in the machines. Besides, electromechanical analysis is carried out to analyse the speed-torque characteristic, the current-torque characteristic and the phase angle-torque characteristic. After all the results are analysed, the designed machine is used to generate S block function that is compatible with MATLAB/SIMULINK tool for the dynamic operational characteristics. This allows the integration of existing drive system into the new machines designed in the modelling tool. An example of the machine design is presented to validate the usage of such a tool.

  10. Solid waste integrated cost analysis model: 1991 project year report

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    The purpose of the City of Houston's 1991 Solid Waste Integrated Cost Analysis Model (SWICAM) project was to continue the development of a computerized cost analysis model. This model is to provide solid waste managers with tool to evaluate the dollar cost of real or hypothetical solid waste management choices. Those choices have become complicated by the implementation of Subtitle D of the Resources Conservation and Recovery Act (RCRA) and the EPA's Integrated Approach to managing municipal solid waste;. that is, minimize generation, maximize recycling, reduce volume (incinerate), and then bury (landfill) only the remainder. Implementation of an integrated solid waste management system involving all or some of the options of recycling, waste to energy, composting, and landfilling is extremely complicated. Factors such as hauling distances, markets, and prices for recyclable, costs and benefits of transfer stations, and material recovery facilities must all be considered. A jurisdiction must determine the cost impacts of implementing a number of various possibilities for managing, handling, processing, and disposing of waste. SWICAM employs a single Lotus 123 spreadsheet to enable a jurisdiction to predict or assess the costs of its waste management system. It allows the user to select his own process flow for waste material and to manipulate the model to include as few or as many options as he or she chooses. The model will calculate the estimated cost for those choices selected. The user can then change the model to include or exclude waste stream components, until the mix of choices suits the user. Graphs can be produced as a visual communication aid in presenting the results of the cost analysis. SWICAM also allows future cost projections to be made.

  11. Biochemical analysis of murine leukemia viruses isolated from radiation-induced leukemias of strain BALB/c

    International Nuclear Information System (INIS)

    Ellis, R.W.; Hopkins, N.; Fleissner, E.

    1980-01-01

    Murine leukemia viruses isolated from radiation-induced BALB/c leukemias were characterized with respect to viral proteins and RNA. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the viral structural proteins revealed that for p12, p15, p30, and gp70, three to four electrophoretic variants of each could be detected. There was no correlation found between any of these mobilities and N- or B-tropism of the viruses. Proteins of all xenotropic viral isolates were identical in their gel electrophoretic profiles. The similar phenotypes of multiple viral clones from individual leukemias and of isolates grown in different cells suggest that the polymorphism of ecotropic viruses was generated in vivo rather than during in vitro virus growth. By two-dimensional fingerprinting of RNase T1-resistant oligonucleotides from 70S viral RNA, the previously reported association of N- and B-tropism with two distinct oligonucleotides was confirmed. The presence of two other oligonucleotides was correlated with positive and negative phenotypes of the virus-coded G/sub IX/ cell surface antigen. The RNAs of two B-tropic isolates with distinctive p15 and p12 phenotypes differed from the RNA of a prototype N-tropic virus by the absence of three oligonucleotides mapping in the 5' portion (gag region) of the prototype RNA. In addition, one small-plaque B-tropic virus displayed extensive changes in the RNA sequences associated with the env region of the prototype

  12. High-throughput quantitative biochemical characterization of algal biomass by NIR spectroscopy; multiple linear regression and multivariate linear regression analysis.

    Science.gov (United States)

    Laurens, L M L; Wolfrum, E J

    2013-12-18

    One of the challenges associated with microalgal biomass characterization and the comparison of microalgal strains and conversion processes is the rapid determination of the composition of algae. We have developed and applied a high-throughput screening technology based on near-infrared (NIR) spectroscopy for the rapid and accurate determination of algal biomass composition. We show that NIR spectroscopy can accurately predict the full composition using multivariate linear regression analysis of varying lipid, protein, and carbohydrate content of algal biomass samples from three strains. We also demonstrate a high quality of predictions of an independent validation set. A high-throughput 96-well configuration for spectroscopy gives equally good prediction relative to a ring-cup configuration, and thus, spectra can be obtained from as little as 10-20 mg of material. We found that lipids exhibit a dominant, distinct, and unique fingerprint in the NIR spectrum that allows for the use of single and multiple linear regression of respective wavelengths for the prediction of the biomass lipid content. This is not the case for carbohydrate and protein content, and thus, the use of multivariate statistical modeling approaches remains necessary.

  13. Biochemical and Structural Analysis of an Eis Family Aminoglycoside Acetyltransferase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Green, Keith D.; Biswas, Tapan; Chang, Changsoo; Wu, Ruiying; Chen, Wenjing; Janes, Brian K.; Chalupska, Dominika; Gornicki, Piotr; Hanna, Philip C.; Tsodikov, Oleg V.; Joachimiak, Andrzej; Garneau-Tsodikova, Sylvie

    2015-05-26

    Proteins from the enhanced intracellular survival (Eis) family are versatile acetyltransferases that acetylate amines at multiple positions of several aminoglycosides (AGs). Their upregulation confers drug resistance. Homologues of Eis are present in diverse bacteria, including many pathogens. Eis from Mycobacterium tuberculosis (Eis_Mtb) has been well characterized. In this study, we explored the AG specificity and catalytic efficiency of the Eis family protein from Bacillus anthracis (Eis_Ban). Kinetic analysis of specificity and catalytic efficiency of acetylation of six AGs indicates that Eis_Ban displays significant differences from Eis_Mtb in both substrate binding and catalytic efficiency. The number of acetylated amines was also different for several AGs, indicating a distinct regiospecificity of Eis_Ban. Furthermore, most recently identified inhibitors of Eis_Mtb did not inhibit Eis_Ban, underscoring the differences between these two enzymes. To explain these differences, we determined an Eis_Ban crystal structure. The comparison of the crystal structures of Eis_Ban and Eis_Mtb demonstrates that critical residues lining their respective substrate binding pockets differ substantially, explaining their distinct specificities. Our results suggest that acetyltransferases of the Eis family evolved divergently to garner distinct specificities while conserving catalytic efficiency, possibly to counter distinct chemical challenges. The unique specificity features of these enzymes can be utilized as tools for developing AGs with novel modifications and help guide specific AG treatments to avoid Eis-mediated resistance.

  14. Biochemical and structural analysis of a site directed mutant of manganese dependent aminopeptidase P from Streptomyces lavendulae

    Directory of Open Access Journals (Sweden)

    ARYA NANDAN

    2015-08-01

    Full Text Available Aminopeptidase P (APP removes N-terminal amino acids from peptides and proteins when the penultimate residue is proline. To understand the structure-function relationships of aminopeptidase P of Streptomyces lavendulae, a conserved arginine residue was replaced with lysine (R453K by site-directed mutagenesis. The overexpressed wild and mutant enzymes were of nearly 60 kDa and purified by nickel affinity chromatography. Kinetic analysis of R453K variant using Gly-Pro-pNA as the substrate revealed an increase in Km with a decrease in Vmax, leading to overall decrease in the catalytic efficiency, indicating that the guanidinium group of arginine plays an important role in substrate binding in APP. We constructed three dimensional models for the catalytic domains of wild and mutant enzyme and it revealed an interaction in R453 of native enzyme through hydrogen bonding with the adjacent residues making a substrate binding cavity whereas K453 did not participate in any hydrogen bonding. Hence, R453 in APP of S. lavenduale must be playing a critical role in the hydrolysis of the substrate.

  15. An Integrated Analysis of Changes in Water Stress in Europe

    DEFF Research Database (Denmark)

    Henrichs, T.; Lehner, B.; Alcamo, J.

    2002-01-01

    Future changes in water availability with climate change and changes in water use due to socio-economic development are to occur in parallel. In an integrated analysis we bring together these aspects of global change in a consistent manner, and analyse the water stress situation in Europe. We find...... that today high water stress exists in one-fifth of European river basin area. Under a scenario projection, increases in water use throughout Eastern Europe are accompanied by decreases in water availability in most of Southern Europe--combining these trends leads to a marked increase in water stress...

  16. Case for integral core-disruptive accident analysis

    International Nuclear Information System (INIS)

    Luck, L.B.; Bell, C.R.

    1985-01-01

    Integral analysis is an approach used at the Los Alamos National Laboratory to cope with the broad multiplicity of accident paths and complex phenomena that characterize the transition phase of core-disruptive accident progression in a liquid-metal-cooled fast breeder reactor. The approach is based on the combination of a reference calculation, which is intended to represent a band of similar accident paths, and associated system- and separate-effect studies, which are designed to determine the effect of uncertainties. Results are interpreted in the context of a probabilistic framework. The approach was applied successfully in two studies; illustrations from the Clinch River Breeder Reactor licensing assessment are included

  17. Integrated polymer waveguides for absorbance detection in chemical analysis systems

    DEFF Research Database (Denmark)

    Mogensen, Klaus Bo; El-Ali, Jamil; Wolff, Anders

    2003-01-01

    A chemical analysis system for absorbance detection with integrated polymer waveguides is reported for the first time. The fabrication procedure relies on structuring of a single layer of the photoresist SU-8, so both the microfluidic channel network and the optical components, which include planar....... The emphasis of this paper is on the signal-to-noise ratio of the detection and its relation to the sensitivity. Two absorbance cells with an optical path length of 100 μm and 1000 μm were characterized and compared in terms of sensitivity, limit of detection and effective path length for measurements...

  18. Integrated Modeling for the James Webb Space Telescope (JWST) Project: Structural Analysis Activities

    Science.gov (United States)

    Johnston, John; Mosier, Mark; Howard, Joe; Hyde, Tupper; Parrish, Keith; Ha, Kong; Liu, Frank; McGinnis, Mark

    2004-01-01

    This paper presents viewgraphs about structural analysis activities and integrated modeling for the James Webb Space Telescope (JWST). The topics include: 1) JWST Overview; 2) Observatory Structural Models; 3) Integrated Performance Analysis; and 4) Future Work and Challenges.

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

    Science.gov (United States)

    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.

  20. Integrative analysis of the mitochondrial proteome in yeast.

    Directory of Open Access Journals (Sweden)

    Holger Prokisch

    2004-06-01

    Full Text Available In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.

  1. The interpretation of forensic biochemical expert test made in human body fluids: scientific - legal analysis in the research on sexual offenses

    International Nuclear Information System (INIS)

    Chaves Carballo, Diana

    2014-01-01

    The contributions of science and technology have covered the whole of human life, and relationships of coexistence are even found in the various disciplines of knowledge through legal forensics. Therefore, it is increasingly imperative that the law enforcement agents are interdisciplinary professionals, with knowledge beyond the legal knowledge to enable them make the most of the scientific knowledge in judicial proceedings. Among the natural sciences applied to right, forensic biochemistry has contributed an extremely relevant test for the investigation of various sexual offenses, much has been so, that the Organismo de Investigacion Judicial of Costa Rica has in its Departamento de Laboratorios de Ciencias Forenses with specialized sections in this discipline. A diversity of skills are performed of presumptive and confirmatory character for the presence of biological fluids, sexually transmitted diseases and identification of DNA by genetic markers. Updated information is given with respect to the correct interpretation of forensic biochemical expertises achievable for identification of semen, blood and human saliva in the investigation of sexual offenses. A scientific and legal language is used allowing the most of this information in the criminal process. The main objective has been to interpret, legal and scientifically, forensic biochemical expert evidence performed in human body fluids during the investigation of sexual offenses. A legal, doctrinal and scientific review is presented with compilation of related jurisprudence and criminology reports analysis of Seccion de Bioquimica of the Departamento de Laboratorios Forenses of the Organismo de Investigacion Juridica issued during the investigation of sexual offenses. Two types of attainable skills have existed for the identification of biological fluids, each with a different binding. In addition, it has been clear, due to the lexicon employed when making a forensic biochemist opinion, that to make a proper

  2. Mechanical factors and vitamin D deficiency in schoolchildren with low back pain: biochemical and cross-sectional survey analysis

    Directory of Open Access Journals (Sweden)

    Alghadir AH

    2017-04-01

    serum bone-specific alkaline phosphatase compared with moderate and healthy schoolchildren. Stepwise regression analysis revealed that age, gender, demographic parameters, PA, vitamin D levels, Ca, CK, and LDH associated with ~56.8%–86.7% of the incidence of LBP among schoolchildren.Conclusion: In children and adolescents, LBP was shown to be linked with limited sun exposure, inadequate vitamin D diets, adiposity, lower PA, sedentary lifestyles, vitamin 25 (OH D deficiency, and lower levels of Ca, CK, and LDH. Keywords: low back pain, LBP, mechanical factors, 25(OHD concentrations, muscle pain, physical activity

  3. PET/CT with {sup 11}C-choline for evaluation of prostate cancer patients with biochemical recurrence: meta-analysis and critical review of available data

    Energy Technology Data Exchange (ETDEWEB)

    Fanti, Stefano; Castellucci, Paolo [S. Orsola-Malpighi University Hospital, Department of Nuclear Medicine, Bologna (Italy); Minozzi, Silvia [Lazio Regional Health Service, Cochrane Review Group on Drugs and Alcohol, Department of Epidemiology, Rome (Italy); Balduzzi, Sara [University of Modena and Reggio Emilia, Department of Diagnostic Medicine, Clinical and Public Health, Modena (Italy); Herrmann, Ken [David Geffen School of Medicine at UCLA, Department of Molecular and Medical Pharmacology, Los Angeles, CA (United States); University Hospital Wuerzburg, Department of Nuclear Medicine, Wuerzburg (Germany); Krause, Bernd Joachim [Universitaetsmedizin Rostock, Department of Nuclear Medicine, Rostock (Germany); Oyen, Wim [Radboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen (Netherlands); Chiti, Arturo [Humanitas Research Hospital, Nuclear Medicine, Rozzano, Milano (Italy); Humanitas University, Rozzano, Milano (Italy)

    2016-01-15

    For the last decade PET and PET/CT with {sup 11}C-choline have been proposed for the evaluation of prostate cancer (PC), but the diagnostic performance of {sup 11}C-choline PET/CT is still a matter of debate. We performed a comprehensive review of the most important clinical application of {sup 11}C-choline PET, restaging of patients with biochemical relapse, following a rigorous methodological approach and including assessment of the risk of bias. We conducted a systematic review and meta-analysis of the literature assessing {sup 11}C-choline PET/CT for its accuracy in the diagnosis and ability to detect the site of recurrence of PC in the restaging of patients with biochemical recurrence after initial treatment with curative intent. We performed a comprehensive literature search of PubMed and the Cochrane Library to determine the accuracy for the detection of the site of recurrence (prostate bed recurrences, metastatic spread to locoregional pelvic lymph nodes or distant metastases). Only studies with a reference standard (for prostatic bed histopathology, for histopathology or biopsy of distant metastases or a composite reference standard with clinical follow-up of at least 12 months, correlative imaging and clinical data) were included. Overall 425 studies were retrieved, of which 43 were judged as potentially relevant and 29 with 2,686 participants were finally included. Of these 29 studies, 18 reported results for any relapse, All 18 studies, with a total of 2,126 participants, reported detection rates. The pooled rate was 62 % (95 % CI 53 - 71 %). Of the 18 studies, 12 with 1,270 participants reported useful data to derive sensitivity and specificity. The pooled sensitivity was 89 % (95 % CI 83 - 93 %) and the pooled specificity was 89 % (95 % CI 73 - 96 %). Of 11 studies reporting results for local relapse, 9 with 993 participants reported detection rates. The pooled rate was 27 % (95 % CI 16 - 38 %). Six studies with 491 participants reported sensitivity

  4. Raman spectroscopic biochemical mapping of tissues

    Science.gov (United States)

    Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

    2006-02-01

    Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

  5. Integrated intelligent instruments using supercritical fluid technology for soil analysis

    International Nuclear Information System (INIS)

    Liebman, S.A.; Phillips, C.; Fitzgerald, W.; Levy, E.J.

    1994-01-01

    Contaminated soils pose a significant challenge for characterization and remediation programs that require rapid, accurate and comprehensive data in the field or laboratory. Environmental analyzers based on supercritical fluid (SF) technology have been designed and developed for meeting these global needs. The analyzers are designated the CHAMP Systems (Chemical Hazards Automated Multimedia Processors). The prototype instrumentation features SF extraction (SFE) and on-line capillary gas chromatographic (GC) analysis with chromatographic and/or spectral identification detectors, such as ultra-violet, Fourier transform infrared and mass spectrometers. Illustrations are given for a highly automated SFE-capillary GC/flame ionization (FID) configuration to provide validated screening analysis for total extractable hydrocarbons within ca. 5--10 min, as well as a full qualitative/quantitative analysis in 25--30 min. Data analysis using optional expert system and neural networks software is demonstrated for test gasoline and diesel oil mixtures in this integrated intelligent instrument approach to trace organic analysis of soils and sediments

  6. Integrative Analysis of Prognosis Data on Multiple Cancer Subtypes

    Science.gov (United States)

    Liu, Jin; Huang, Jian; Zhang, Yawei; Lan, Qing; Rothman, Nathaniel; Zheng, Tongzhang; Ma, Shuangge

    2014-01-01

    Summary In cancer research, profiling studies have been extensively conducted, searching for genes/SNPs associated with prognosis. Cancer is diverse. Examining the similarity and difference in the genetic basis of multiple subtypes of the same cancer can lead to a better understanding of their connections and distinctions. Classic meta-analysis methods analyze each subtype separately and then compare analysis results across subtypes. Integrative analysis methods, in contrast, analyze the raw data on multiple subtypes simultaneously and can outperform meta-analysis methods. In this study, prognosis data on multiple subtypes of the same cancer are analyzed. An AFT (accelerated failure time) model is adopted to describe survival. The genetic basis of multiple subtypes is described using the heterogeneity model, which allows a gene/SNP to be associated with prognosis of some subtypes but not others. A compound penalization method is developed to identify genes that contain important SNPs associated with prognosis. The proposed method has an intuitive formulation and is realized using an iterative algorithm. Asymptotic properties are rigorously established. Simulation shows that the proposed method has satisfactory performance and outperforms a penalization-based meta-analysis method and a regularized thresholding method. An NHL (non-Hodgkin lymphoma) prognosis study with SNP measurements is analyzed. Genes associated with the three major subtypes, namely DLBCL, FL, and CLL/SLL, are identified. The proposed method identifies genes that are different from alternatives and have important implications and satisfactory prediction performance. PMID:24766212

  7. Elucidating the Molecular Basis and Regulation of Chromium(VI) Reduction by Shewanella oneidensis MR-1 and Resistance to Metal Toxicity Using Integrated Biochemical, Genomic and Proteomic Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Dorothea K. Thompson; Robert Hettich

    2007-02-06

    Shewanella oneidensis MR-1 is a model environmental organism that possesses diverse respiratory capacities, including the ability to reduce soluble Cr(VI) to sparingly soluble, less toxic Cr(III). Chromate is a serious anthropogenic pollutant found in subsurface sediment and groundwater environments due to its widespread use in defense and industrial applications. Effective bioremediation of chromate-contaminated sites requires knowledge of the molecular mechanisms and regulation of heavy metal resistance and biotransformation by dissimilatory metal-reducing bacteria. Towards this goal, our ERSP-funded work was focused on the identification and functional analysis of genes/proteins comprising the response pathways for chromate detoxification and/or reduction. Our work utilized temporal transcriptomic profiling and whole-cell proteomic analyses to characterize the dynamic molecular response of MR-1 to an acute chromate shock (up to 90 min) as well as to a 24-h, low-dose exposure. In addition, we have examined the transcriptome of MR-1 cells actively engaged in chromate reduction. These studies implicated the involvement of a functionally undefined DNA-binding response regulator (SO2426) and a putative azoreductase (SO3585) in the chromate stress response of MR-1.

  8. Integrated Data Analysis (IDCA) Program - PETN Class 4 Standard

    Energy Technology Data Exchange (ETDEWEB)

    Sandstrom, Mary M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Brown, Geoffrey W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Daniel N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Pollard, Colin J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Warner, Kirstin F. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Sorensen, Daniel N. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Remmers, Daniel L. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Shelley, Timothy J. [Air Force Research Lab. (AFRL), Tyndall AFB, FL (United States); Reyes, Jose A. [Applied Research Associates, Tyndall AFB, FL (United States); Phillips, Jason J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hsu, Peter C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Reynolds, John G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-08-01

    The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of PETN Class 4. The PETN was found to have: 1) an impact sensitivity (DH50) range of 6 to 12 cm, 2) a BAM friction sensitivity (F50) range 7 to 11 kg, TIL (0/10) of 3.7 to 7.2 kg, 3) a ABL friction sensitivity threshold of 5 or less psig at 8 fps, 4) an ABL ESD sensitivity threshold of 0.031 to 0.326 j/g, and 5) a thermal sensitivity of an endothermic feature with Tmin = ~ 141 °C, and a exothermic feature with a Tmax = ~205°C.

  9. Integrated Data Collection Analysis (IDCA) Program — Ammonium Nitrate

    Energy Technology Data Exchange (ETDEWEB)

    Sandstrom, Mary M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Brown, Geoffrey W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Daniel N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Pollard, Colin J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Warner, Kirstin F. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Sorensen, Daniel N. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Remmers, Daniel L. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Phillips, Jason J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Shelley, Timothy J. [Bureau of Alcohol, Tobacco and Firearms, Redstone Arsenal, AL (United States); Reyes, Jose A. [Applied Research Associates, Tyndall AFB, FL (United States); Hsu, Peter C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Reynolds, John G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-05-17

    The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of ammonium nitrate (AN). AN was tested, in most cases, as both received from manufacturer and dried/sieved. The participants found the AN to be: 1) insensitive in Type 12A impact testing (although with a wide range of values), 2) completely insensitive in BAM friction testing, 3) less sensitive than the RDX standard in ABL friction testing, 4) less sensitive than RDX in ABL ESD testing, and 5) less sensitive than RDX and PETN in DSC thermal analyses.

  10. An integrated economic and distributional analysis of energy policies

    International Nuclear Information System (INIS)

    Labandeira, Xavier; Labeaga, Jose M.; Rodriguez, Miguel

    2009-01-01

    Most public policies, particularly those in the energy sphere, have not only efficiency but also distributional effects. However, there is a trade-off between modelling approaches suitable for calculating those impacts on the economy. For the former most of the studies have been conducted with general equilibrium models, whereas partial equilibrium models represent the main approach for distributional analysis. This paper proposes a methodology to simultaneously carry out an analysis of the distributional and efficiency consequences of changes in energy taxation. In order to do so, we have integrated a microeconomic household demand model and a computable general equilibrium model for the Spanish economy. We illustrate the advantages of this approach by simulating a revenue-neutral reform in Spanish indirect taxation, with a large increase of energy taxes that serve an environmental purpose. The results show that the reforms bring about significant efficiency and distributional effects, in some cases counterintuitive, and demonstrate the academic and social utility of this approximation. (author)

  11. An integrated economic and distributional analysis of energy policies

    Energy Technology Data Exchange (ETDEWEB)

    Labandeira, Xavier [Facultade de CC. Economicas, University of Vigo, 36310 Vigo (Spain); Labeaga, Jose M. [Instituto de Estudios Fiscales, Avda. Cardenal Herrera Oria 378, 28035 Madrid (Spain); Rodriguez, Miguel [Facultade de CC. Empresariais e Turismo, University of Vigo, 32004 Ourense (Spain)

    2009-12-15

    Most public policies, particularly those in the energy sphere, have not only efficiency but also distributional effects. However, there is a trade-off between modelling approaches suitable for calculating those impacts on the economy. For the former most of the studies have been conducted with general equilibrium models, whereas partial equilibrium models represent the main approach for distributional analysis. This paper proposes a methodology to simultaneously carry out an analysis of the distributional and efficiency consequences of changes in energy taxation. In order to do so, we have integrated a microeconomic household demand model and a computable general equilibrium model for the Spanish economy. We illustrate the advantages of this approach by simulating a revenue-neutral reform in Spanish indirect taxation, with a large increase of energy taxes that serve an environmental purpose. The results show that the reforms bring about significant efficiency and distributional effects, in some cases counterintuitive, and demonstrate the academic and social utility of this approximation. (author)

  12. Simulation analysis for integrated evaluation of technical and commercial risk

    International Nuclear Information System (INIS)

    Gutleber, D.S.; Heiberger, E.M.; Morris, T.D.

    1995-01-01

    Decisions to invest in oil- and gasfield acquisitions or participating interests often are based on the perceived ability to enhance the economic value of the underlying asset. A multidisciplinary approach integrating reservoir engineering, operations and drilling, and deal structuring with Monte Carlo simulation modeling can overcome weaknesses of deterministic analysis and significantly enhance investment decisions. This paper discusses the use of spreadsheets and Monte Carlo simulation to generate probabilistic outcomes for key technical and economic parameters for ultimate identification of the economic volatility and value of potential deal concepts for a significant opportunity. The approach differs from a simple risk analysis for an individual well by incorporating detailed, full-field simulations that vary the reservoir parameters, capital and operating cost assumptions, and schedules on timing in the framework of various deal structures

  13. Integrating Pavement Crack Detection and Analysis Using Autonomous Unmanned Aerial Vehicle Imagery

    Science.gov (United States)

    2015-03-27

    INTEGRATING PAVEMENT CRACK DETECTION AND ANALYSIS USING AUTONOMOUS UNMANNED AERIAL VEHICLE...protection in the United States. AFIT-ENV-MS-15-M-195 INTEGRATING PAVEMENT CRACK DETECTION AND ANALYSIS USING AUTONOMOUS UNMANNED AERIAL...APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. AFIT-ENV-MS-15-M-195 INTEGRATING PAVEMENT CRACK DETECTION AND ANALYSIS USING AUTONOMOUS

  14. Sensitivity Analysis of the Integrated Medical Model for ISS Programs

    Science.gov (United States)

    Goodenow, D. A.; Myers, J. G.; Arellano, J.; Boley, L.; Garcia, Y.; Saile, L.; Walton, M.; Kerstman, E.; Reyes, D.; Young, M.

    2016-01-01

    Sensitivity analysis estimates the relative contribution of the uncertainty in input values to the uncertainty of model outputs. Partial Rank Correlation Coefficient (PRCC) and Standardized Rank Regression Coefficient (SRRC) are methods of conducting sensitivity analysis on nonlinear simulation models like the Integrated Medical Model (IMM). The PRCC method estimates the sensitivity using partial correlation of the ranks of the generated input values to each generated output value. The partial part is so named because adjustments are made for the linear effects of all the other input values in the calculation of correlation between a particular input and each output. In SRRC, standardized regression-based coefficients measure the sensitivity of each input, adjusted for all the other inputs, on each output. Because the relative ranking of each of the inputs and outputs is used, as opposed to the values themselves, both methods accommodate the nonlinear relationship of the underlying model. As part of the IMM v4.0 validation study, simulations are available that predict 33 person-missions on ISS and 111 person-missions on STS. These simulated data predictions feed the sensitivity analysis procedures. The inputs to the sensitivity procedures include the number occurrences of each of the one hundred IMM medical conditions generated over the simulations and the associated IMM outputs: total quality time lost (QTL), number of evacuations (EVAC), and number of loss of crew lives (LOCL). The IMM team will report the results of using PRCC and SRRC on IMM v4.0 predictions of the ISS and STS missions created as part of the external validation study. Tornado plots will assist in the visualization of the condition-related input sensitivities to each of the main outcomes. The outcomes of this sensitivity analysis will drive review focus by identifying conditions where changes in uncertainty could drive changes in overall model output uncertainty. These efforts are an integral

  15. Multi - band Persistent Scatterer Interferometry data integration for landslide analysis

    Science.gov (United States)

    Bianchini, Silvia; Mateos, Rosa; Mora, Oscar; García, Inma; Sánchez, Ciscu; Sanabria, Margarita; López, Maite; Mulas, Joaquin; Hernández, Mario; Herrera, Gerardo

    2013-04-01

    We present a methodology to perform a geomorphological assessment of ground movements over wide areas, by improving Persistent Scatterer Interferometry (PSI) analysis for landslide studies. The procedure relies on the integrated use of multi-band EO data acquired by different satellite sensors in different time intervals, to provide a detailed investigation of ground displacements. The methodology, throughout the cross-comparison and integration of PS data in different microwave bands (ALOS in L-band, ERS1/2 and ENVISAT in C-band, COSMOSKY-MED in X-band), is applied on the Tramontana Range in the northwestern part of Mallorca island (Spain), extensively affected by mass movements across time, especially during the last years. We increase the confidence degree of the available interferometric data and we homogenize all PS targets by implementing and classifying them through common criteria. Therefore, PSI results are combined with geo-thematic data and pre-existing landslide inventories of the study area, in order to improve the landslide database, providing additional information on the detected ground displacements. The results of this methodology are used to elaborate landslide activity maps, permitting to jointly exploit heterogeneous PS data for analyzing landslides at regional scale. Moreover, from a geomorphological perspective, the proposed approach exploits the implemented PS data to achieve a reliable spatial analysis of movement rates, whatever referred to certain landslide phenomena or to other natural processes, in order to perform ground motion activity maps within a wide area.

  16. Integrated severe accident containment analysis with the CONTAIN computer code

    International Nuclear Information System (INIS)

    Bergeron, K.D.; Williams, D.C.; Rexroth, P.E.; Tills, J.L.

    1985-12-01

    Analysis of physical and radiological conditions iunside the containment building during a severe (core-melt) nuclear reactor accident requires quantitative evaluation of numerous highly disparate yet coupled phenomenologies. These include two-phase thermodynamics and thermal-hydraulics, aerosol physics, fission product phenomena, core-concrete interactions, the formation and combustion of flammable gases, and performance of engineered safety features. In the past, this complexity has meant that a complete containment analysis would require application of suites of separate computer codes each of which would treat only a narrower subset of these phenomena, e.g., a thermal-hydraulics code, an aerosol code, a core-concrete interaction code, etc. In this paper, we describe the development and some recent applications of the CONTAIN code, which offers an integrated treatment of the dominant containment phenomena and the interactions among them. We describe the results of a series of containment phenomenology studies, based upon realistic accident sequence analyses in actual plants. These calculations highlight various phenomenological effects that have potentially important implications for source term and/or containment loading issues, and which are difficult or impossible to treat using a less integrated code suite

  17. Integrative analysis to select cancer candidate biomarkers to targeted validation

    Science.gov (United States)

    Heberle, Henry; Domingues, Romênia R.; Granato, Daniela C.; Yokoo, Sami; Canevarolo, Rafael R.; Winck, Flavia V.; Ribeiro, Ana Carolina P.; Brandão, Thaís Bianca; Filgueiras, Paulo R.; Cruz, Karen S. P.; Barbuto, José Alexandre; Poppi, Ronei J.; Minghim, Rosane; Telles, Guilherme P.; Fonseca, Felipe Paiva; Fox, Jay W.; Santos-Silva, Alan R.; Coletta, Ricardo D.; Sherman, Nicholas E.; Paes Leme, Adriana F.

    2015-01-01

    Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS. PMID:26540631

  18. Integrated modeling and analysis methodology for precision pointing applications

    Science.gov (United States)

    Gutierrez, Homero L.

    2002-07-01

    Space-based optical systems that perform tasks such as laser communications, Earth imaging, and astronomical observations require precise line-of-sight (LOS) pointing. A general approach is described for integrated modeling and analysis of these types of systems within the MATLAB/Simulink environment. The approach can be applied during all stages of program development, from early conceptual design studies to hardware implementation phases. The main objective is to predict the dynamic pointing performance subject to anticipated disturbances and noise sources. Secondary objectives include assessing the control stability, levying subsystem requirements, supporting pointing error budgets, and performing trade studies. The integrated model resides in Simulink, and several MATLAB graphical user interfaces (GUI"s) allow the user to configure the model, select analysis options, run analyses, and process the results. A convenient parameter naming and storage scheme, as well as model conditioning and reduction tools and run-time enhancements, are incorporated into the framework. This enables the proposed architecture to accommodate models of realistic complexity.

  19. Integrated dynamic landscape analysis and modeling system (IDLAMS) : installation manual.

    Energy Technology Data Exchange (ETDEWEB)

    Li, Z.; Majerus, K. A.; Sundell, R. C.; Sydelko, P. J.; Vogt, M. C.

    1999-02-24

    The Integrated Dynamic Landscape Analysis and Modeling System (IDLAMS) is a prototype, integrated land management technology developed through a joint effort between Argonne National Laboratory (ANL) and the US Army Corps of Engineers Construction Engineering Research Laboratories (USACERL). Dr. Ronald C. Sundell, Ms. Pamela J. Sydelko, and Ms. Kimberly A. Majerus were the principal investigators (PIs) for this project. Dr. Zhian Li was the primary software developer. Dr. Jeffrey M. Keisler, Mr. Christopher M. Klaus, and Mr. Michael C. Vogt developed the decision analysis component of this project. It was developed with funding support from the Strategic Environmental Research and Development Program (SERDP), a land/environmental stewardship research program with participation from the US Department of Defense (DoD), the US Department of Energy (DOE), and the US Environmental Protection Agency (EPA). IDLAMS predicts land conditions (e.g., vegetation, wildlife habitats, and erosion status) by simulating changes in military land ecosystems for given training intensities and land management practices. It can be used by military land managers to help predict the future ecological condition for a given land use based on land management scenarios of various levels of training intensity. It also can be used as a tool to help land managers compare different land management practices and further determine a set of land management activities and prescriptions that best suit the needs of a specific military installation.

  20. The practical implementation of integrated safety management for nuclear safety analysis and fire hazards analysis documentation

    International Nuclear Information System (INIS)

    COLLOPY, M.T.

    1999-01-01

    In 1995 Mr. Joseph DiNunno of the Defense Nuclear Facilities Safety Board issued an approach to describe the concept of an integrated safety management program which incorporates hazard and safety analysis to address a multitude of hazards affecting the public, worker, property, and the environment. Since then the U S . Department of Energy (DOE) has adopted a policy to systematically integrate safety into management and work practices at all levels so that missions can be completed while protecting the public, worker, and the environment. While the DOE and its contractors possessed a variety of processes for analyzing fire hazards at a facility, activity, and job; the outcome and assumptions of these processes have not always been consistent for similar types of hazards within the safety analysis and the fire hazard analysis. Although the safety analysis and the fire hazard analysis are driven by different DOE Orders and requirements, these analyses should not be entirely independent and their preparation should be integrated to ensure consistency of assumptions, consequences, design considerations, and other controls. Under the DOE policy to implement an integrated safety management system, identification of hazards must be evaluated and agreed upon to ensure that the public. the workers. and the environment are protected from adverse consequences. The DOE program and contractor management need a uniform, up-to-date reference with which to plan. budget, and manage nuclear programs. It is crucial that DOE understand the hazards and risks necessarily to authorize the work needed to be performed. If integrated safety management is not incorporated into the preparation of the safety analysis and the fire hazard analysis, inconsistencies between assumptions, consequences, design considerations, and controls may occur that affect safety. Furthermore, confusion created by inconsistencies may occur in the DOE process to grant authorization of the work. In accordance with

  1. Measures of Biochemical Sociology

    Science.gov (United States)

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  2. The role of overall treatment time in the outcome of radiotherapy of prostate cancer: An analysis of biochemical failure in 4839 men treated between 1987 and 1995

    International Nuclear Information System (INIS)

    Thames, Howard D.; Kuban, Deborah; Levy, Larry B.; Horwitz, Eric M.; Kupelian, Patrick; Martinez, Alvaro; Michalski, Jeffrey; Pisansky, Thomas; Sandler, Howard; Shipley, William; Zelefsky, Michael; Zietman, Anthony

    2010-01-01

    Purpose: Assess the importance of overall time (OT) and dose for biochemical failure (BF) after external-beam radiotherapy of prostate cancer in a retrospective analysis of a nine-institution database with 4839 patients. Patients and methods: Relevant baseline factors (T stage, Gleason score, initial PSA) were available for 4338 men. Cox models were used to estimate the effects of dose and OT corrected for baseline factors, treatment year, institution and interactions, and differences in post-treatment PSA-measurement intervals. After exclusion of very short and long intervals, patient numbers were 1445 events/3426 at risk (endpoint all BFs), and 1177 events/3354 at risk (endpoint exclusion of BFs that were likely distant failures). Separate analyses were carried out by risk group for men who received <70 Gy and ≥70 Gy. Results: Neither dose nor OT was significant when the analysis was restricted to doses <70 Gy, while for patients treated to 70 Gy or higher there were significant influences of both dose and OT on outcome in low- and intermediate-risk patients. These effects were quantified as a relative increase after 5 years followup of 6% in BFs for a 1-week increase in OT, a relative decrease of 15% in BFs for a 6-Gy increase in dose, and a dose equivalent of proliferation of 0.24 Gy/day. As the dose per fraction was nearly constant, the data contain no information on the α/β ratio. Conclusion: The results show that OT and dose are significant determinants of outcome of radiotherapy in low- and intermediate-risk patients treated to 70 Gy or higher, and suggest that meaningful improvements in outcome may be targeted by modest increases in total dose and decreases in OT.

  3. Molecular cloning, biochemical characterization, and expression analysis of two glutathione S-transferase paralogs from the big-belly seahorse (Hippocampus abdominalis).

    Science.gov (United States)

    Tharuka, M D Neranjan; Bathige, S D N K; Lee, Jehee

    2017-12-01

    Glutathione S-transferases (GSTs, EC 2.5.1.18) are important Phase II detoxifying enzymes that catalyze hydrophobic, electrophilic xenobiotic substance with the conjugation of reduced glutathione (GSH). In this study, GSTμ and GSTρ paralogs of GST in the big belly seahorse (Hippocampus abdominalis; HaGSTρ, HaGSTμ) were biochemically, molecularly, functionally characterized to determine their detoxification range and protective capacities upon different pathogenic stresses. HaGSTρ and HaGSTμ are composed of coding sequences of 681bp and 654bp, which encode proteins 225 and 217 amino acids, with predicted molecular masses of 26.06kDa and 25.74kDa respectively. Sequence analysis revealed that both HaGSTs comprise the characteristic GSH-binding site in the thioredoxin-like N-terminal domain and substrate binding site in the C-terminal domain. The recombinant HaGSTρ and HaGSTμ proteins catalyzed the model GST substrate 1-chloro-2, 4-dinitrobenzene (CDNB). Enzyme kinetic analysis revealed different K m and V max values for each rHaGST, suggesting that they have different conjugation rates. The optimum conditions (pH, temperature) and inhibitory assays of each protein demonstrated different optimal ranges. However, HaGSTμ was highly expressed in the ovary and gill, whereas HaGSTρ was highly expressed in the gill and pouch. mRNA expression of HaGSTρ and HaGSTμ was significantly elevated upon lipopolysaccharide, Poly (I:C), and Edwardsiella tarda challenges in liver and in blood cells as well as with Streptococcus iniae challenge in blood cells. From these collective experimental results, we propose that HaGSTρ and HaGSTμ are effective in detoxifying xenobiotic toxic agents, and importantly, their mRNA expression could be stimulated by immunological stress signals in the aquatic environment. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. A broad-spectrum analysis of the effects of teflubenzuron exposure on the biochemical activities and microbial community structure of soil.

    Science.gov (United States)

    Cycoń, Mariusz; Wójcik, Marcin; Borymski, Sławomir; Piotrowska-Seget, Zofia

    2012-10-15

    We evaluated the response of soil bacteria to applications of the insecticide teflubenzuron at the field rate dosage (FR; 0.15 mg/kg of soil) and at a higher dosage (10*FR; 1.5 mg/kg of soil). When applied at the FR dosage, teflubenzuron had no effect on several biochemical parameters of the soil, including substrate-induced respiration (SIR), dehydrogenase (DHA) and phosphatase activities (PHOS), and N-NO(3)(-) and N-NH(4)(+) concentrations. Additionally, no differences were observed in the culturable fraction of the soil bacteria (the number of heterotrophic, nitrifying, denitrifying and N(2)-fixing bacteria; the growth strategy; the ecophysiological and colony development indices; and the physiological state). In contrast, treatment with the 10*FR dosage of the insecticide significantly increased SIR, DHA, PHOS and N-NH(4)(+) levels and the number of heterotrophic and denitrifying bacteria. Decreases in urease activity (URE) and the number of nitrifying and N(2)-fixing bacteria were also observed. A phospholipid fatty acid (PLFA) method-based analysis of the entire soil microorganism population revealed that teflubenzuron treatment affected the total fatty acid level as well as those considered to be of Gram-positive bacteria, Gram-negative bacteria and fungi. This effect was observed on days 1 and 14 post-treatment. A principal component analysis (PCA) of the PLFAs showed that teflubenzuron treatment significantly shifted the microbial community structure; however, all of the observed effects were transient. Studies on the degradation of teflubenzuron revealed that this process is characterised by a short lag phase and a rate constant (k) of 0.020/day. This degradation rate follows first-order kinetics, and the DT50 was 33.5 days. This is the first study that thoroughly examines the functional and structural status of both the culturable and non-culturable fractions of the soil microbial community after teflubenzuron application. Copyright © 2012 Elsevier Ltd

  5. Integrated Software Environment for Pressurized Thermal Shock Analysis

    Directory of Open Access Journals (Sweden)

    Dino Araneo

    2011-01-01

    Full Text Available The present paper describes the main features and an application to a real Nuclear Power Plant (NPP of an Integrated Software Environment (in the following referred to as “platform” developed at University of Pisa (UNIPI to perform Pressurized Thermal Shock (PTS analysis. The platform is written in Java for the portability and it implements all the steps foreseen in the methodology developed at UNIPI for the deterministic analysis of PTS scenarios. The methodology starts with the thermal hydraulic analysis of the NPP with a system code (such as Relap5-3D and Cathare2, during a selected transient scenario. The results so obtained are then processed to provide boundary conditions for the next step, that is, a CFD calculation. Once the system pressure and the RPV wall temperature are known, the stresses inside the RPV wall can be calculated by mean a Finite Element (FE code. The last step of the methodology is the Fracture Mechanics (FM analysis, using weight functions, aimed at evaluating the stress intensity factor (KI at crack tip to be compared with the critical stress intensity factor KIc. The platform automates all these steps foreseen in the methodology once the user specifies a number of boundary conditions at the beginning of the simulation.

  6. SEURAT: visual analytics for the integrated analysis of microarray data.

    Science.gov (United States)

    Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

    2010-06-03

    In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

  7. SEURAT: Visual analytics for the integrated analysis of microarray data

    Directory of Open Access Journals (Sweden)

    Bullinger Lars

    2010-06-01

    Full Text Available Abstract Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

  8. Transient flow analysis of integrated valve opening process

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xinming; Qin, Benke; Bo, Hanliang, E-mail: bohl@tsinghua.edu.cn; Xu, Xingxing

    2017-03-15

    Highlights: • The control rod hydraulic driving system (CRHDS) is a new type of built-in control rod drive technology and the integrated valve (IV) is the key control component. • The transient flow experiment induced by IV is conducted and the test results are analyzed to get its working mechanism. • The theoretical model of IV opening process is established and applied to get the changing rule of the transient flow characteristic parameters. - Abstract: The control rod hydraulic driving system (CRHDS) is a new type of built-in control rod drive technology and the IV is the key control component. The working principle of integrated valve (IV) is analyzed and the IV hydraulic experiment is conducted. There is transient flow phenomenon in the valve opening process. The theoretical model of IV opening process is established by the loop system control equations and boundary conditions. The valve opening boundary condition equation is established based on the IV three dimensional flow field analysis results and the dynamic analysis of the valve core movement. The model calculation results are in good agreement with the experimental results. On this basis, the model is used to analyze the transient flow under high temperature condition. The peak pressure head is consistent with the one under room temperature and the pressure fluctuation period is longer than the one under room temperature. Furthermore, the changing rule of pressure transients with the fluid and loop structure parameters is analyzed. The peak pressure increases with the flow rate and the peak pressure decreases with the increase of the valve opening time. The pressure fluctuation period increases with the loop pipe length and the fluctuation amplitude remains largely unchanged under different equilibrium pressure conditions. The research results lay the base for the vibration reduction analysis of the CRHDS.

  9. Stochastic analysis of biochemical systems

    CERN Document Server

    Anderson, David F

    2015-01-01

    This book focuses on counting processes and continuous-time Markov chains motivated by examples and applications drawn from chemical networks in systems biology.  The book should serve well as a supplement for courses in probability and stochastic processes.  While the material is presented in a manner most suitable for students who have studied stochastic processes up to and including martingales in continuous time, much of the necessary background material is summarized in the Appendix. Students and Researchers with a solid understanding of calculus, differential equations, and elementary probability and who are well-motivated by the applications will find this book of interest.    David F. Anderson is Associate Professor in the Department of Mathematics at the University of Wisconsin and Thomas G. Kurtz is Emeritus Professor in the Departments of Mathematics and Statistics at that university. Their research is focused on probability and stochastic processes with applications in biology and other ar...

  10. Performance Analysis of a Photovoltaic-Thermal Integrated System

    International Nuclear Information System (INIS)

    Radziemska, E.

    2009-01-01

    The present commercial photovoltaic solar cells (PV) converts solar energy into electricity with a relatively low efficiency, less than 20%. More than 80% of the absorbed solar energy is dumped to the surroundings again after photovoltaic conversion. Hybrid PV/T systems consist of PV modules coupled with the heat extraction devices. The PV/T collectors generate electric power and heat simultaneously. Stabilizing temperature of photovoltaic modules at low level is highly desirable to obtain efficiency increase. The total efficiency of 60-80% can be achieved with the whole PV/T system provided that the T system is operated near ambient temperature. The value of the low-T heat energy is typically much smaller than the value of the PV electricity. The PV/T systems can exist in many designs, but the most common models are with the use of water or air as a working fuid. Efficiency is the most valuable parameter for the economic analysis. It has substantial meaning in the case of installations with great nominal power, as air-cooled Building Integrated Photovoltaic Systems (BIPV). In this paper the performance analysis of a hybrid PV/T system is presented: an energetic analysis as well as an exergetic analysis. Exergy is always destroyed when a process involves a temperature change. This destruction is proportional to the entropy increase of the system together with its surroundings the destroyed exergy has been called energy. Exergy analysis identifies the location, the magnitude, and the sources of thermodynamic inefficiencies in a system. This information, which cannot be provided by other means (e.g., an energy analysis), is very useful for the improvement and cost-effectiveness of the system. Calculations were carried out for the tested water-cooled ASE-100-DGL-SM Solar watt module.

  11. Performance Analysis of a Photovoltaic-Thermal Integrated System

    Directory of Open Access Journals (Sweden)

    Ewa Radziemska

    2009-01-01

    Full Text Available The present commercial photovoltaic solar cells (PV converts solar energy into electricity with a relatively low efficiency, less than 20%. More than 80% of the absorbed solar energy is dumped to the surroundings again after photovoltaic conversion. Hybrid PV/T systems consist of PV modules coupled with the heat extraction devices. The PV/T collectors generate electric power and heat simultaneously. Stabilizing temperature of photovoltaic modules at low level is higly desirable to obtain efficiency increase. The total efficiency of 60–80% can be achieved with the whole PV/T system provided that the T system is operated near ambient temperature. The value of the low-T heat energy is typically much smaller than the value of the PV electricity. The PV/T systems can exist in many designs, but the most common models are with the use of water or air as a working fuid. Efficiency is the most valuable parameter for the economic analysis. It has substantial meaning in the case of installations with great nominal power, as air-cooled Building Integrated Photovoltaic Systems (BIPV. In this paper the performance analysis of a hybrid PV/T system is presented: an energetic analysis as well as an exergetic analysis. Exergy is always destroyed when a process involves a temperature change. This destruction is proportional to the entropy increase of the system together with its surroundings—the destroyed exergy has been called anergy. Exergy analysis identifies the location, the magnitude, and the sources of thermodynamic inefficiences in a system. This information, which cannot be provided by other means (e.g., an energy analysis, is very useful for the improvement and cost-effictiveness of the system. Calculations were carried out for the tested water-cooled ASE-100-DGL-SM Solarwatt module.

  12. PEA: an integrated R toolkit for plant epitranscriptome analysis.

    Science.gov (United States)

    Zhai, Jingjing; Song, Jie; Cheng, Qian; Tang, Yunjia; Ma, Chuang

    2018-05-29

    The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by the absence of computational tools for the systematic analysis of epitranscriptome sequencing data. In addition, no tools have yet been designed for accurate prediction of CMRs in plants, or to extend epitranscriptome analysis from a fraction of the transcriptome to its entirety. Here, we introduce PEA, an integrated R toolkit to facilitate the analysis of plant epitranscriptome data. The PEA toolkit contains a comprehensive collection of functions required for read mapping, CMR calling, motif scanning and discovery, and gene functional enrichment analysis. PEA also takes advantage of machine learning technologies for transcriptome-scale CMR prediction, with high prediction accuracy, using the Positive Samples Only Learning algorithm, which addresses the two-class classification problem by using only positive samples (CMRs), in the absence of negative samples (non-CMRs). Hence PEA is a versatile epitranscriptome analysis pipeline covering CMR calling, prediction, and annotation, and we describe its application to predict N6-methyladenosine (m6A) modifications in Arabidopsis thaliana. Experimental results demonstrate that the toolkit achieved 71.6% sensitivity and 73.7% specificity, which is superior to existing m6A predictors. PEA is potentially broadly applicable to the in-depth study of epitranscriptomics. PEA Docker image is available at https://hub.docker.com/r/malab/pea, source codes and user manual are available at https://github.com/cma2015/PEA. chuangma2006@gmail.com. Supplementary data are available at Bioinformatics online.

  13. Climate-dependent evolution of Antarctic ectotherms: An integrative analysis

    Science.gov (United States)

    Pörtner, Hans O.

    2006-04-01

    The paper explores the climate-dependent evolution of marine Antarctic fauna and tries to identify key mechanisms involved as well as the driving forces that have caused the physiological and life history characteristics observed today. In an integrative approach it uses the recent concept of oxygen and capacity limited thermal tolerance to identify potential links between molecular, cellular, whole-organism, and ecological characteristics of marine animal life in the Antarctic. As a generalized pattern, minimization of baseline energy costs, for the sake of maximized growth in the cold, appears as one over-arching principle shaping the evolution and functioning of Antarctic marine ectotherms. This conclusion is supported by recent comparisons with (sub-) Arctic ectotherms, where elevated levels of energy turnover result at unstable, including cold temperatures, and are related to wide windows of thermal tolerance and associated metabolic features. At biochemical levels, metabolic regulation at low temperatures in general, is supported by the cold compensation of enzyme kinetic parameters like substrate affinities and turnover numbers, through minute structural modifications of the enzyme molecule. These involve a shift in protein folding, sometimes supported by the replacement of individual amino acids. The hypothesis is developed that efficient metabolic regulation at low rates in Antarctic marine stenotherms occurs through high mitochondrial densities at low capacities and possibly enhanced levels of Arrhenius activation energies or activation enthalpies. This contrasts the more costly patterns of metabolic regulation at elevated rates in cold-adapted eurytherms. Energy savings in Antarctic ectotherms, largely exemplified in fish, typically involve low-cost, diffusive oxygen distribution due to high density of lipid membranes, loss of haemoglobin, myoglobin and the heat shock response, reduced anaerobic capacity, large myocytes with low ion exchange activities

  14. HTGR-INTEGRATED COAL TO LIQUIDS PRODUCTION ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Anastasia M Gandrik; Rick A Wood

    2010-10-01

    As part of the DOE’s Idaho National Laboratory (INL) nuclear energy development mission, the INL is leading a program to develop and design a high temperature gas-cooled reactor (HTGR), which has been selected as the base design for the Next Generation Nuclear Plant. Because an HTGR operates at a higher temperature, it can provide higher temperature process heat, more closely matched to chemical process temperatures, than a conventional light water reactor. Integrating HTGRs into conventional industrial processes would increase U.S. energy security and potentially reduce greenhouse gas emissions (GHG), particularly CO2. This paper focuses on the integration of HTGRs into a coal to liquids (CTL) process, for the production of synthetic diesel fuel, naphtha, and liquefied petroleum gas (LPG). The plant models for the CTL processes were developed using Aspen Plus. The models were constructed with plant production capacity set at 50,000 barrels per day of liquid products. Analysis of the conventional CTL case indicated a potential need for hydrogen supplementation from high temperature steam electrolysis (HTSE), with heat and power supplied by the HTGR. By supplementing the process with an external hydrogen source, the need to “shift” the syngas using conventional water-gas shift reactors was eliminated. HTGR electrical power generation efficiency was set at 40%, a reactor size of 600 MWth was specified, and it was assumed that heat in the form of hot helium could be delivered at a maximum temperature of 700°C to the processes. Results from the Aspen Plus model were used to perform a preliminary economic analysis and a life cycle emissions assessment. The following conclusions were drawn when evaluating the nuclear assisted CTL process against the conventional process: • 11 HTGRs (600 MWth each) are required to support production of a 50,000 barrel per day CTL facility. When compared to conventional CTL production, nuclear integration decreases coal

  15. HTGR-Integrated Coal To Liquids Production Analysis

    International Nuclear Information System (INIS)

    Gandrik, Anastasia M.; Wood, Rick A.

    2010-01-01

    As part of the DOE's Idaho National Laboratory (INL) nuclear energy development mission, the INL is leading a program to develop and design a high temperature gas-cooled reactor (HTGR), which has been selected as the base design for the Next Generation Nuclear Plant. Because an HTGR operates at a higher temperature, it can provide higher temperature process heat, more closely matched to chemical process temperatures, than a conventional light water reactor. Integrating HTGRs into conventional industrial processes would increase U.S. energy security and potentially reduce greenhouse gas emissions (GHG), particularly CO2. This paper focuses on the integration of HTGRs into a coal to liquids (CTL) process, for the production of synthetic diesel fuel, naphtha, and liquefied petroleum gas (LPG). The plant models for the CTL processes were developed using Aspen Plus. The models were constructed with plant production capacity set at 50,000 barrels per day of liquid products. Analysis of the conventional CTL case indicated a potential need for hydrogen supplementation from high temperature steam electrolysis (HTSE), with heat and power supplied by the HTGR. By supplementing the process with an external hydrogen source, the need to 'shift' the syngas using conventional water-gas shift reactors was eliminated. HTGR electrical power generation efficiency was set at 40%, a reactor size of 600 MWth was specified, and it was assumed that heat in the form of hot helium could be delivered at a maximum temperature of 700 C to the processes. Results from the Aspen Plus model were used to perform a preliminary economic analysis and a life cycle emissions assessment. The following conclusions were drawn when evaluating the nuclear assisted CTL process against the conventional process: (1) 11 HTGRs (600 MWth each) are required to support production of a 50,000 barrel per day CTL facility. When compared to conventional CTL production, nuclear integration decreases coal consumption by 66

  16. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  17. RADIA: RNA and DNA integrated analysis for somatic mutation detection.

    Directory of Open Access Journals (Sweden)

    Amie J Radenbaugh

    Full Text Available The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis, a novel computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating an individual's DNA and RNA, we are able to detect mutations that would otherwise be missed by traditional algorithms that examine only the DNA. We demonstrate high sensitivity (84% and very high precision (98% and 99% for RADIA in patient data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to patient data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back mutations at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA.

  18. Integrity analysis of an upper guide structure flange

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ki Hyoung; Kang, Sung Sik; Jhung, Myung Jo [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2015-10-15

    The integrity assessment of reactor vessel internals should be conducted in the design process to secure the safety of nuclear power plants. Various loads such as self-weight, seismic load, flow-induced load, and preload are applied to the internals. Therefore, the American Society of Mechanical Engineers (ASME) Code, Section III, defines the stress limit for reactor vessel internals. The present study focused on structural response analyses of the upper guide structure upper flange. The distributions of the stress intensity in the flange body were analyzed under various design load cases during normal operation. The allowable stress intensities along the expected sections of stress concentration were derived from the results of the finite element analysis for evaluating the structural integrity of the flange design. Furthermore, seismic analyses of the upper flange were performed to identify dynamic behavior with respect to the seismic and impact input. The mode superposition and full transient methods were used to perform time–history analyses, and the displacement at the lower end of the flange was obtained. The effect of the damping ratio on the response of the flange was also evaluated, and the acceleration was obtained. The results of elastic and seismic analyses in this study will be used as basic information to judge whether a flange design meets the acceptance criteria.

  19. Development of safety analysis technology for integral reactor

    International Nuclear Information System (INIS)

    Kim, Hee Cheol; Kim, K. K.; Kim, S. H.

    2002-04-01

    The state-of-the-arts for the integral reactor was performed to investigate the safety features. The safety and performance of SMART were assessed using the technologies developed during the study. For this purpose, the computer code system and the analysis methodology were developed and the safety and performance analyses on SMART basic design were carried out for the design basis event and accident. The experimental facilities were designed for the core flow distribution test and the self-pressurizing pressurizer performance test. The tests on the 2-phase critical flow with non-condensable gas were completed and the results were used to assess the critical flow model. Probabilistic Safety Assessment(PSA) was carried out to evaluate the safety level and to optimize the design by identifying and remedying any weakness in the design. A joint study with KINS was carried out to promote licensing environment. The generic safety issues of integral reactors were identified and the solutions were formulated. The economic evaluation of the SMART desalination plant and the activities related to the process control were carried out in the scope of the study

  20. Visual Data Analysis as an Integral Part of Environmental Management

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, Joerg; Bethel, E. Wes; Horsman, Jennifer L.; Hubbard, Susan S.; Krishnan, Harinarayan; Romosan,, Alexandru; Keating, Elizabeth H.; Monroe, Laura; Strelitz, Richard; Moore, Phil; Taylor, Glenn; Torkian, Ben; Johnson, Timothy C.; Gorton, Ian

    2012-10-01

    The U.S. Department of Energy's (DOE) Office of Environmental Management (DOE/EM) currently supports an effort to understand and predict the fate of nuclear contaminants and their transport in natural and engineered systems. Geologists, hydrologists, physicists and computer scientists are working together to create models of existing nuclear waste sites, to simulate their behavior and to extrapolate it into the future. We use visualization as an integral part in each step of this process. In the first step, visualization is used to verify model setup and to estimate critical parameters. High-performance computing simulations of contaminant transport produces massive amounts of data, which is then analyzed using visualization software specifically designed for parallel processing of large amounts of structured and unstructured data. Finally, simulation results are validated by comparing simulation results to measured current and historical field data. We describe in this article how visual analysis is used as an integral part of the decision-making process in the planning of ongoing and future treatment options for the contaminated nuclear waste sites. Lessons learned from visually analyzing our large-scale simulation runs will also have an impact on deciding on treatment measures for other contaminated sites.

  1. Self-organizing ontology of biochemically relevant small molecules.

    Science.gov (United States)

    Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel

    2012-01-06

    The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. We conclude that the proposed methodology can ease the burden of chemical data annotators and

  2. Self-organizing ontology of biochemically relevant small molecules

    Science.gov (United States)

    2012-01-01

    Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

  3. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  4. Integral finite element analysis of turntable bearing with flexible rings

    Science.gov (United States)

    Deng, Biao; Liu, Yunfei; Guo, Yuan; Tang, Shengjin; Su, Wenbin; Lei, Zhufeng; Wang, Pengcheng

    2018-03-01

    This paper suggests a method to calculate the internal load distribution and contact stress of the thrust angular contact ball turntable bearing by FEA. The influence of the stiffness of the bearing structure and the plastic deformation of contact area on the internal load distribution and contact stress of the bearing is considered. In this method, the load-deformation relationship of the rolling elements is determined by the finite element contact analysis of a single rolling element and the raceway. Based on this, the nonlinear contact between the rolling elements and the inner and outer ring raceways is same as a nonlinear compression spring and bearing integral finite element analysis model including support structure was established. The effects of structural deformation and plastic deformation on the built-in stress distribution of slewing bearing are investigated on basis of comparing the consequences of load distribution, inner and outer ring stress, contact stress and other finite element analysis results with the traditional bearing theory, which has guiding function for improving the design of slewing bearing.

  5. Development and assessment of best estimate integrated safety analysis code

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Bub Dong; Lee, Young Jin; Hwang, Moon Kyu (and others)

    2007-03-15

    Improvement of the integrated safety analysis code MARS3.0 has been carried out and a multi-D safety analysis application system has been established. Iterative matrix solver and parallel processing algorithm have been introduced, and a LINUX version has been generated to enable MARS to run in cluster PCs. MARS variables and sub-routines have been reformed and modularised to simplify code maintenance. Model uncertainty analyses have been performed for THTF, FLECHT, NEPTUN, and LOFT experiments as well as APR1400 plant. Participations in international cooperation research projects such as OECD BEMUSE, SETH, PKL, BFBT, and TMI-2 have been actively pursued as part of code assessment efforts. The assessment, evaluation and experimental data obtained through international cooperation projects have been registered and maintained in the T/H Databank. Multi-D analyses of APR1400 LBLOCA, DVI Break, SLB, and SGTR have been carried out as a part of application efforts in multi-D safety analysis. GUI based 3D input generator has been developed for user convenience. Operation of the MARS Users Group (MUG) was continued and through MUG, the technology has been transferred to 24 organisations. A set of 4 volumes of user manuals has been compiled and the correction reports for the code errors reported during MARS development have been published.

  6. Development and assessment of best estimate integrated safety analysis code

    International Nuclear Information System (INIS)

    Chung, Bub Dong; Lee, Young Jin; Hwang, Moon Kyu

    2007-03-01

    Improvement of the integrated safety analysis code MARS3.0 has been carried out and a multi-D safety analysis application system has been established. Iterative matrix solver and parallel processing algorithm have been introduced, and a LINUX version has been generated to enable MARS to run in cluster PCs. MARS variables and sub-routines have been reformed and modularised to simplify code maintenance. Model uncertainty analyses have been performed for THTF, FLECHT, NEPTUN, and LOFT experiments as well as APR1400 plant. Participations in international cooperation research projects such as OECD BEMUSE, SETH, PKL, BFBT, and TMI-2 have been actively pursued as part of code assessment efforts. The assessment, evaluation and experimental data obtained through international cooperation projects have been registered and maintained in the T/H Databank. Multi-D analyses of APR1400 LBLOCA, DVI Break, SLB, and SGTR have been carried out as a part of application efforts in multi-D safety analysis. GUI based 3D input generator has been developed for user convenience. Operation of the MARS Users Group (MUG) was continued and through MUG, the technology has been transferred to 24 organisations. A set of 4 volumes of user manuals has been compiled and the correction reports for the code errors reported during MARS development have been published

  7. Integrating Process Mining and Cognitive Analysis to Study EHR Workflow.

    Science.gov (United States)

    Furniss, Stephanie K; Burton, Matthew M; Grando, Adela; Larson, David W; Kaufman, David R

    2016-01-01

    There are numerous methods to study workflow. However, few produce the kinds of in-depth analyses needed to understand EHR-mediated workflow. Here we investigated variations in clinicians' EHR workflow by integrating quantitative analysis of patterns of users' EHR-interactions with in-depth qualitative analysis of user performance. We characterized 6 clinicians' patterns of information-gathering using a sequential process-mining approach. The analysis revealed 519 different screen transition patterns performed across 1569 patient cases. No one pattern was followed for more than 10% of patient cases, the 15 most frequent patterns accounted for over half ofpatient cases (53%), and 27% of cases exhibited unique patterns. By triangulating quantitative and qualitative analyses, we found that participants' EHR-interactive behavior was associated with their routine processes, patient case complexity, and EHR default settings. The proposed approach has significant potential to inform resource allocation for observation and training. In-depth observations helped us to explain variation across users.

  8. Bayesian tomography and integrated data analysis in fusion diagnostics

    Science.gov (United States)

    Li, Dong; Dong, Y. B.; Deng, Wei; Shi, Z. B.; Fu, B. Z.; Gao, J. M.; Wang, T. B.; Zhou, Yan; Liu, Yi; Yang, Q. W.; Duan, X. R.

    2016-11-01

    In this article, a Bayesian tomography method using non-stationary Gaussian process for a prior has been introduced. The Bayesian formalism allows quantities which bear uncertainty to be expressed in the probabilistic form so that the uncertainty of a final solution can be fully resolved from the confidence interval of a posterior probability. Moreover, a consistency check of that solution can be performed by checking whether the misfits between predicted and measured data are reasonably within an assumed data error. In particular, the accuracy of reconstructions is significantly improved by using the non-stationary Gaussian process that can adapt to the varying smoothness of emission distribution. The implementation of this method to a soft X-ray diagnostics on HL-2A has been used to explore relevant physics in equilibrium and MHD instability modes. This project is carried out within a large size inference framework, aiming at an integrated analysis of heterogeneous diagnostics.

  9. System integration and control strategy analysis of PEMFC car

    International Nuclear Information System (INIS)

    Sun, L.; Chen, Y.; Liu, Y.; Shi, P.

    2004-01-01

    A new fuel car was designed according to the prototype LN2000 hydrogen-oxygen fuel cell car. The new prototype consists of a compact fuel cell engine with separated fuel cell stack, nickel metal hydride battery, a motor with power of 30Kw/100Kw and an inverter with high efficiency. With in the powertrain, a two-shift Planet gear transmission was employed. The power performance was greatly improved. New battery with EMS, new self-developed fuel cell engine, the motor propulsion system and electronic controlled transmission make it feasible to control the whole fuel car automatically and efficiently with optimization. The presents the system integration and the control strategy analysis of the fuel cell car prototype. The paper can be used for reference for engineers in the field of fuel cell vehicle. (author)

  10. Urban Integrated Industrial Cogeneration Systems Analysis. Phase II final report

    Energy Technology Data Exchange (ETDEWEB)

    1984-01-01

    Through the Urban Integrated Industrial Cogeneration Systems Analysis (UIICSA), the City of Chicago embarked upon an ambitious effort to identify the measure the overall industrial cogeneration market in the city and to evaluate in detail the most promising market opportunities. This report discusses the background of the work completed during Phase II of the UIICSA and presents the results of economic feasibility studies conducted for three potential cogeneration sites in Chicago. Phase II focused on the feasibility of cogeneration at the three most promising sites: the Stockyards and Calumet industrial areas, and the Ford City commercial/industrial complex. Each feasibility case study considered the energy load requirements of the existing facilities at the site and the potential for attracting and serving new growth in the area. Alternative fuels and technologies, and ownership and financing options were also incorporated into the case studies. Finally, site specific considerations such as development incentives, zoning and building code restrictions and environmental requirements were investigated.

  11. Neutronics analysis for integration of ITER diagnostics port EP10

    Energy Technology Data Exchange (ETDEWEB)

    Colling, Bethany, E-mail: bethany.colling@ccfe.ac.uk [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Department of Engineering, Lancaster University, Lancashire LA1 4YR (United Kingdom); Eade, Tim [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Joyce, Malcolm J. [Department of Engineering, Lancaster University, Lancashire LA1 4YR (United Kingdom); Pampin, Raul; Seyvet, Fabien [Fusion for Energy, Josep Pla 2, Torres Diagonal Litoral B3, 08019 Barcelona (Spain); Turner, Andrew [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Udintsev, Victor [ITER Organization, Route de Vinon-sur-Verdon, CS 90 046, 13067 St. Paul Lez Durance Cedex (France)

    2016-11-01

    Shutdown dose rate calculations have been performed on an integrated ITER C-lite neutronics model with equatorial port 10. A ‘fully shielded’ configuration, optimised for a given set of diagnostic designs (i.e. shielding in all available space within the port plug drawers), results in a shutdown dose rate in the port interspace, from the activation of materials comprising equatorial port 10, in excess of 2000 μSv/h. Achieving dose rates of 100 μSv/h or less, as required in areas where hands-on maintenance can be performed, in the port interspace region will be challenging. A combination of methods will need to be implemented, such as reducing mass and/or the use of reduced activation steel in the port interspace, optimisation of the diagnostic designs and shielding of the port interspace floor. Further analysis is required to test these options and the ongoing design optimisation of the EP10 diagnostic systems.

  12. Advanced data analysis in neuroscience integrating statistical and computational models

    CERN Document Server

    Durstewitz, Daniel

    2017-01-01

    This book is intended for use in advanced graduate courses in statistics / machine learning, as well as for all experimental neuroscientists seeking to understand statistical methods at a deeper level, and theoretical neuroscientists with a limited background in statistics. It reviews almost all areas of applied statistics, from basic statistical estimation and test theory, linear and nonlinear approaches for regression and classification, to model selection and methods for dimensionality reduction, density estimation and unsupervised clustering.  Its focus, however, is linear and nonlinear time series analysis from a dynamical systems perspective, based on which it aims to convey an understanding also of the dynamical mechanisms that could have generated observed time series. Further, it integrates computational modeling of behavioral and neural dynamics with statistical estimation and hypothesis testing. This way computational models in neuroscience are not only explanat ory frameworks, but become powerfu...

  13. Life-cycle analysis of product integrated polymer solar cells

    DEFF Research Database (Denmark)

    Espinosa Martinez, Nieves; García-Valverde, Rafael; Krebs, Frederik C

    2011-01-01

    A life cycle analysis (LCA) on a product integrated polymer solar module is carried out in this study. These assessments are well-known to be useful in developmental stages of a product in order to identify the bottlenecks for the up-scaling in its production phase for several aspects spanning from...... economics through design to functionality. An LCA study was performed to quantify the energy use and greenhouse gas (GHG) emissions from electricity use in the manufacture of a light-weight lamp based on a plastic foil, a lithium-polymer battery, a polymer solar cell, printed circuitry, blocking diode......, switch and a white light emitting semiconductor diode. The polymer solar cell employed in this prototype presents a power conversion efficiency in the range of 2 to 3% yielding energy payback times (EPBT) in the range of 1.3–2 years. Based on this it is worthwhile to undertake a life-cycle study...

  14. Integrated aerosol and thermalhydraulics modelling for CANDU safety analysis

    International Nuclear Information System (INIS)

    McDonald, B.H.; Hanna, B.N.

    1990-08-01

    Analysis of postulated accidents in CANDU reactors that could result in severe fuel damage requires the ability to model the formation of aerosols containing fission product materials and the transport of these aerosols from the fuel, through containment, to any leak to the atmosphere. Best-estimate calculations require intimate coupling and simultaneous solution of all the equations describing the entire range of physical and chemical phenomena involved. The prototype CATHENA/PACE-3D has been developed for integrated calculation of thermalhydraulic and aerosol events in a CANDU reactor during postulated accidents. Examples demonstrate the ability of CATHENA/PACE-3D to produce realistic flow and circulation patterns and reasonable accuracy in solution of two simple fluid-flow test cases for which analytical solutions exist

  15. 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.

  16. The IMBA suite: integrated modules for bioassay analysis

    Energy Technology Data Exchange (ETDEWEB)

    Birchall, A.; Jarvis, N.S.; Peace, M.S.; Riddell, A.E.; Battersby, W.P

    1998-07-01

    The increasing complexity of models representing the biokinetic behaviour of radionuclides in the body following intake poses problems for people who are required to implement these models. The problem is exacerbated by the current paucity of suitable software. In order to remedy this situation, a collaboration between British Nuclear Fuels, Westlakes Research Institute and the National Radiological Protection Board has started with the aim of producing a suite of modules for estimating intakes and doses from bioassay measurements using the new ICRP models. Each module will have a single purpose (e.g. to calculate respiratory tract deposition) and will interface with other software using data files. The elements to be implemented initially are plutonium, uranium, caesium, iodine and tritium. It is intended to make the software available to other parties under terms yet to be decided. This paper describes the proposed suite of integrated modules for bioassay analysis, IMBA. (author)

  17. ANALYSIS OF ENVIRONMENTAL FRAGILITY USING MULTI-CRITERIA ANALYSIS (MCE FOR INTEGRATED LANDSCAPE ASSESSMENT

    Directory of Open Access Journals (Sweden)

    Abimael Cereda Junior

    2014-01-01

    Full Text Available The Geographic Information Systems brought greater possibilitie s to the representation and interpretation of the landscap e as well as the integrated a nalysis. However, this approach does not dispense technical and methodological substan tiation for achieving the computational universe. This work is grounded in ecodynamic s and empirical analysis of natural and anthr opogenic environmental Fragility a nd aims to propose and present an integrated paradigm of Multi-criteria Analysis and F uzzy Logic Model of Environmental Fragility, taking as a case study of the Basin of Monjolinho Stream in São Carlos-SP. The use of this methodology allowed for a reduct ion in the subjectivism influences of decision criteria, which factors might have its cartographic expression, respecting the complex integrated landscape.

  18. Functional Module Analysis for Gene Coexpression Networks with Network Integration.

    Science.gov (United States)

    Zhang, Shuqin; Zhao, Hongyu; Ng, Michael K

    2015-01-01

    Network has been a general tool for studying the complex interactions between different genes, proteins, and other small molecules. Module as a fundamental property of many biological networks has been widely studied and many computational methods have been proposed to identify the modules in an individual network. However, in many cases, a single network is insufficient for module analysis due to the noise in the data or the tuning of parameters when building the biological network. The availability of a large amount of biological networks makes network integration study possible. By integrating such networks, more informative modules for some specific disease can be derived from the networks constructed from different tissues, and consistent factors for different diseases can be inferred. In this paper, we have developed an effective method for module identification from multiple networks under different conditions. The problem is formulated as an optimization model, which combines the module identification in each individual network and alignment of the modules from different networks together. An approximation algorithm based on eigenvector computation is proposed. Our method outperforms the existing methods, especially when the underlying modules in multiple networks are different in simulation studies. We also applied our method to two groups of gene coexpression networks for humans, which include one for three different cancers, and one for three tissues from the morbidly obese patients. We identified 13 modules with three complete subgraphs, and 11 modules with two complete subgraphs, respectively. The modules were validated through Gene Ontology enrichment and KEGG pathway enrichment analysis. We also showed that the main functions of most modules for the corresponding disease have been addressed by other researchers, which may provide the theoretical basis for further studying the modules experimentally.

  19. Brachytherapy Improves Biochemical Failure–Free Survival in Low- and Intermediate-Risk Prostate Cancer Compared With Conventionally Fractionated External Beam Radiation Therapy: A Propensity Score Matched Analysis

    International Nuclear Information System (INIS)

    Smith, Graham D.; Pickles, Tom; Crook, Juanita; Martin, Andre-Guy; Vigneault, Eric; Cury, Fabio L.; Morris, Jim; Catton, Charles; Lukka, Himu; Warner, Andrew; Yang, Ying; Rodrigues, George

    2015-01-01

    Purpose: To compare, in a retrospective study, biochemical failure-free survival (bFFS) and overall survival (OS) in low-risk and intermediate-risk prostate cancer patients who received brachytherapy (BT) (either low-dose-rate brachytherapy [LDR-BT] or high-dose-rate brachytherapy with external beam radiation therapy [HDR-BT+EBRT]) versus external beam radiation therapy (EBRT) alone. Methods and Materials: Patient data were obtained from the ProCaRS database, which contains 7974 prostate cancer patients treated with primary radiation therapy at four Canadian cancer institutions from 1994 to 2010. Propensity score matching was used to obtain the following 3 matched cohorts with balanced baseline prognostic factors: (1) low-risk LDR-BT versus EBRT; (2) intermediate-risk LDR-BT versus EBRT; and (3) intermediate-risk HDR-BT+EBRT versus EBRT. Kaplan-Meier survival analysis was performed to compare differences in bFFS (primary endpoint) and OS in the 3 matched groups. Results: Propensity score matching created acceptable balance in the baseline prognostic factors in all matches. Final matches included 2 1:1 matches in the intermediate-risk cohorts, LDR-BT versus EBRT (total n=254) and HDR-BT+EBRT versus EBRT (total n=388), and one 4:1 match in the low-risk cohort (LDR-BT:EBRT, total n=400). Median follow-up ranged from 2.7 to 7.3 years for the 3 matched cohorts. Kaplan-Meier survival analysis showed that all BT treatment options were associated with statistically significant improvements in bFFS when compared with EBRT in all cohorts (intermediate-risk EBRT vs LDR-BT hazard ratio [HR] 4.58, P=.001; intermediate-risk EBRT vs HDR-BT+EBRT HR 2.08, P=.007; low-risk EBRT vs LDR-BT HR 2.90, P=.004). No significant difference in OS was found in all comparisons (intermediate-risk EBRT vs LDR-BT HR 1.27, P=.687; intermediate-risk EBRT vs HDR-BT+EBRT HR 1.55, P=.470; low-risk LDR-BT vs EBRT HR 1.41, P=.500). Conclusions: Propensity score matched analysis showed that BT options led

  20. The Holistic Integrity Test (HIT - quantified resilience analysis

    Directory of Open Access Journals (Sweden)

    Dobson Mike

    2016-01-01

    Full Text Available The Holistic Integrity Test (HIT - Quantified Resilience Analysis. Rising sea levels and wider climate change mean we face an increasing risk from flooding and other natural hazards. Tough economic times make it difficult to economically justify or afford the desired level of engineered risk reduction. Add to this significant uncertainty from a range of future predictions, constantly updated with new science. We therefore need to understand not just how to reduce the risk, but what could happen should above design standard events occur. In flood terms this includes not only the direct impacts (damage and loss of life, but the wider cascade impacts to infrastructure systems and the longer term impacts on the economy and society. However, understanding the “what if” is only the first part of the equation; a range of improvement measures to mitigate such effects need to be identified and implemented. These measures should consider reducing the risk, lessening the consequences, aiding the response, and speeding up the recovery. However, they need to be objectively assessed through quantitative analysis, which underpins them technically and economically. Without such analysis, it cannot be predicted how measures will perform if the extreme events occur. It is also vital to consider all possible hazards as measures for one hazard may hinder the response to another. The Holistic Integrity Test (HIT, uses quantitative system analysis and “HITs” the site, its infrastructure, contained dangers and wider regional system to determine how it copes with a range of severe shock events, Before, During and After the event, whilst also accounting for uncertainty (as illustrated in figure 1. First explained at the TINCE 2014 Nuclear Conference in Paris, it was explained in terms of a Nuclear Facility needing to analyse the site in response to post Fukushima needs; the hit is however universally applicable. The HIT has three key risk reduction goals: The

  1. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  2. Practical use of the integrated reporting framework – an analysis of the content of integrated reports of selected companies

    Directory of Open Access Journals (Sweden)

    Monika Raulinajtys-Grzybek

    2017-09-01

    Full Text Available Practical use of the integrated reporting framework – an analysis of the content of integrated reports of selected companies The purpose of the article is to provide a research tool for an initial assessment of whether a company’s integrated reports meet the objectives set out in the IIRC Integrated Reporting Framework and its empirical verification. In particular, the research addresses whether the reports meet the goal of improving the quality of information available and covering all factors that influence the organization’s ability to create value. The article uses the theoretical output on the principles of preparing integrated reports and analyzes the content of selected integrated reports. Based on the source analysis, a research tool has been developed for an initial assessment of whether an integrated report fulfills its objectives. It consists of 42 questions that verify the coverage of the defined elements and the implementation of the guiding principles set by the IIRC. For empirical verification of the tool, a comparative analysis was carried out for reports prepared by selected companies operating in the utilities sector. Answering questions from the research tool allows a researcher to formulate conclusions about the implementation of the guiding principles and the completeness of the presentation of the content elements. As a result of the analysis of selected integrated reports, it was stated that various elements of the report are presented with different levels of accuracy in different reports. Reports provide the most complete information on performance and strategy. The information about business model and prospective data is in some cases presented without making a link to other parts of the report – e.g. risks and opportunities, financial data or capitals. The absence of such links limits the ability to claim that an integrated report meets its objectives, since a set of individual reports, each presenting

  3. Integrating PROOF Analysis in Cloud and Batch Clusters

    International Nuclear Information System (INIS)

    Rodríguez-Marrero, Ana Y; Fernández-del-Castillo, Enol; López García, Álvaro; Marco de Lucas, Jesús; Matorras Weinig, Francisco; González Caballero, Isidro; Cuesta Noriega, Alberto

    2012-01-01

    High Energy Physics (HEP) analysis are becoming more complex and demanding due to the large amount of data collected by the current experiments. The Parallel ROOT Facility (PROOF) provides researchers with an interactive tool to speed up the analysis of huge volumes of data by exploiting parallel processing on both multicore machines and computing clusters. The typical PROOF deployment scenario is a permanent set of cores configured to run the PROOF daemons. However, this approach is incapable of adapting to the dynamic nature of interactive usage. Several initiatives seek to improve the use of computing resources by integrating PROOF with a batch system, such as Proof on Demand (PoD) or PROOF Cluster. These solutions are currently in production at Universidad de Oviedo and IFCA and are positively evaluated by users. Although they are able to adapt to the computing needs of users, they must comply with the specific configuration, OS and software installed at the batch nodes. Furthermore, they share the machines with other workloads, which may cause disruptions in the interactive service for users. These limitations make PROOF a typical use-case for cloud computing. In this work we take profit from Cloud Infrastructure at IFCA in order to provide a dynamic PROOF environment where users can control the software configuration of the machines. The Proof Analysis Framework (PAF) facilitates the development of new analysis and offers a transparent access to PROOF resources. Several performance measurements are presented for the different scenarios (PoD, SGE and Cloud), showing a speed improvement closely correlated with the number of cores used.

  4. Marketing Mix Formulation for Higher Education: An Integrated Analysis Employing Analytic Hierarchy Process, Cluster Analysis and Correspondence Analysis

    Science.gov (United States)

    Ho, Hsuan-Fu; Hung, Chia-Chi

    2008-01-01

    Purpose: The purpose of this paper is to examine how a graduate institute at National Chiayi University (NCYU), by using a model that integrates analytic hierarchy process, cluster analysis and correspondence analysis, can develop effective marketing strategies. Design/methodology/approach: This is primarily a quantitative study aimed at…

  5. Behavior and analysis of an integral abutment bridge.

    Science.gov (United States)

    2013-08-01

    As a result of abutment spalling on the integral abutment bridge over 400 South Street in Salt Lake City, Utah, the Utah Department of Transportation (UDOT) instigated research measures to better understand the behavior of integral abutment bridges. ...

  6. Reverse Engineering Integrated Circuits Using Finite State Machine Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Oler, Kiri J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Miller, Carl H. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-04-12

    In this paper, we present a methodology for reverse engineering integrated circuits, including a mathematical verification of a scalable algorithm used to generate minimal finite state machine representations of integrated circuits.

  7. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  8. Process integration and pinch analysis in sugarcane industry

    Energy Technology Data Exchange (ETDEWEB)

    Prado, Adelk de Carvalho; Pinheiro, Ricardo Brant [UFMG, Departamento de Engenharia Nuclear, Programa de Pos-Graduacao em Ciencias e Tecnicas Nucleares, Belo Horizonte, MG (Brazil)], E-mail: rbp@nuclear.ufmg.br

    2010-07-01

    Process integration techniques were applied, particularly through the Pinch Analysis method, to sugarcane industry. Research was performed upon harvest data from an agroindustrial complex which processes sugarcane plant in excess of 3.5 million metric tons per year, producing motor fuel grade ethanol, standard quality sugar, and delivering excess electric power to the grid. Pinch Analysis was used in assessing internal heat recovery as well as external utility demand targets, while keeping the lowest but economically achievable targets for entropy increase. Efficiency on the use of energy was evaluated for the plant as it was found (the base case) as well as for five selected process and/or plant design modifications, always with guidance of the method. The first alternative design (case 2) was proposed to evaluate equipment mean idle time in the base case, to support subsequent comparisons. Cases 3 and 4 were used to estimate the upper limits of combined heat and power generation while raw material supply of the base case is kept; both the cases did not prove worth implementing. Cases 5 and 6 were devised to deal with the bottleneck of the plant, namely boiler capacity, in order to allow for some production increment. Inexpensive, minor modifications considered in case 5 were found unable to produce reasonable outcome gain. Nevertheless, proper changes in cane juice evaporation section (case 6) could allow sugar and ethanol combined production to rise up to 9.1% relative to the base case, without dropping cogenerated power. (author)

  9. Integrated Data Collection Analysis (IDCA) Program - SSST Testing Methods

    Energy Technology Data Exchange (ETDEWEB)

    Sandstrom, Mary M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Brown, Geoffrey W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Daniel N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Pollard, Colin J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Warner, Kirstin F. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Remmers, Daniel L. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Sorensen, Daniel N. [Naval Surface Warfare Center (NSWC), Indian Head, MD (United States). Indian Head Division; Whinnery, LeRoy L. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Phillips, Jason J. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Shelley, Timothy J. [Bureau of Alcohol, Tobacco and Firearms (ATF), Huntsville, AL (United States); Reyes, Jose A. [Applied Research Associates, Tyndall AFB, FL (United States); Hsu, Peter C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Reynolds, John G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-03-25

    The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the methods used for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis during the IDCA program. These methods changed throughout the Proficiency Test and the reasons for these changes are documented in this report. The most significant modifications in standard testing methods are: 1) including one specified sandpaper in impact testing among all the participants, 2) diversifying liquid test methods for selected participants, and 3) including sealed sample holders for thermal testing by at least one participant. This effort, funded by the Department of Homeland Security (DHS), is putting the issues of safe handling of these materials in perspective with standard military explosives. The study is adding SSST testing results for a broad suite of different HMEs to the literature. Ultimately the study will suggest new guidelines and methods and possibly establish the SSST testing accuracies needed to develop safe handling practices for HMEs. Each participating testing laboratory uses identical test materials and preparation methods wherever possible. The testing performers involved are Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), Indian Head Division, Naval Surface Warfare Center, (NSWC IHD), Sandia National Laboratories (SNL), and Air Force Research Laboratory (AFRL/RXQL). These tests are conducted as a proficiency study in order to establish some consistency in test protocols, procedures, and experiments and to compare results when these testing variables cannot be made consistent.

  10. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

    Directory of Open Access Journals (Sweden)

    Zhongqi Ge

    2018-04-01

    Full Text Available Summary: Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies. : Ge et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to provide a comprehensive characterization of the ubiquitin pathway. They detect somatic driver candidates in the ubiquitin pathway and identify a cluster of patients with poor survival, highlighting the importance of this pathway in cancer development. Keywords: ubiquitin pathway, pan-cancer analysis, The Cancer Genome Atlas, tumor subtype, cancer prognosis, therapeutic targets, biomarker, FBXW7

  11. Penalized differential pathway analysis of integrative oncogenomics studies

    NARCIS (Netherlands)

    van Wieringen, W.N.; van de Wiel, M.A.

    2014-01-01

    Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving

  12. Integrated metabonomics analysis of the size-response relationship of silica nanoparticles-induced toxicity in mice

    Science.gov (United States)

    Lu, Xiaoyan; Tian, Yu; Zhao, Qinqin; Jin, Tingting; Xiao, Shun; Fan, Xiaohui

    2011-02-01

    Understanding the underlying properties-dependent interactions of nanostructures with biological systems is essential to nanotoxicological research. This study investigates the relationship between particle size and toxicity, and further reveals the mechanism of injury, using silica particles (SP) with diameters of 30, 70, and 300 nm (SP30, SP70, and SP300) as model materials. The biochemical compositions of liver tissues and serum of mice treated with SP30, SP70, and SP300 were analyzed by integrated metabonomics analysis based on gas chromatography-mass spectrometry (GC-MS) and in combination with pattern recognition approaches. Histopathological examinations and serum biochemical analysis were simultaneously performed. The toxicity induced by three different sizes of SP mainly involved hepatocytic necrosis, increased serum aminotransferase, and inflammatory cytokines. Moreover, the toxic effects of SP were dose-dependent for each particle size. The doses of SP30, SP70, and SP300 that were toxic to the liver were 10, 40, and 200 mg kg - 1, respectively. In this study, surface area has a greater effect than particle number on the toxicity of SP30, SP70, and SP300 in the liver. The disturbances in energy metabolism, amino acid metabolism, lipid metabolism, and nucleotide metabolism may be attributable to the hepatotoxicity induced by SP. In addition, no major differences were found in the response of biological systems caused by the different SP sizes among the metabolite profiles. The results suggest that not only nano-sized but also submicro-sized SP can cause similar extents of liver injury, which is dependent on the exposure dose, and the mechanism of toxicity may be almost the same.

  13. Integrated metabonomics analysis of the size-response relationship of silica nanoparticles-induced toxicity in mice

    International Nuclear Information System (INIS)

    Lu Xiaoyan; Tian Yu; Zhao Qinqin; Jin Tingting; Xiao Shun; Fan Xiaohui

    2011-01-01

    Understanding the underlying properties-dependent interactions of nanostructures with biological systems is essential to nanotoxicological research. This study investigates the relationship between particle size and toxicity, and further reveals the mechanism of injury, using silica particles (SP) with diameters of 30, 70, and 300 nm (SP30, SP70, and SP300) as model materials. The biochemical compositions of liver tissues and serum of mice treated with SP30, SP70, and SP300 were analyzed by integrated metabonomics analysis based on gas chromatography-mass spectrometry (GC-MS) and in combination with pattern recognition approaches. Histopathological examinations and serum biochemical analysis were simultaneously performed. The toxicity induced by three different sizes of SP mainly involved hepatocytic necrosis, increased serum aminotransferase, and inflammatory cytokines. Moreover, the toxic effects of SP were dose-dependent for each particle size. The doses of SP30, SP70, and SP300 that were toxic to the liver were 10, 40, and 200 mg kg -1 , respectively. In this study, surface area has a greater effect than particle number on the toxicity of SP30, SP70, and SP300 in the liver. The disturbances in energy metabolism, amino acid metabolism, lipid metabolism, and nucleotide metabolism may be attributable to the hepatotoxicity induced by SP. In addition, no major differences were found in the response of biological systems caused by the different SP sizes among the metabolite profiles. The results suggest that not only nano-sized but also submicro-sized SP can cause similar extents of liver injury, which is dependent on the exposure dose, and the mechanism of toxicity may be almost the same.

  14. Integrated metabonomics analysis of the size-response relationship of silica nanoparticles-induced toxicity in mice

    Energy Technology Data Exchange (ETDEWEB)

    Lu Xiaoyan; Tian Yu; Zhao Qinqin; Jin Tingting; Xiao Shun; Fan Xiaohui, E-mail: fanxh@zju.edu.cn [Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China)

    2011-02-04

    Understanding the underlying properties-dependent interactions of nanostructures with biological systems is essential to nanotoxicological research. This study investigates the relationship between particle size and toxicity, and further reveals the mechanism of injury, using silica particles (SP) with diameters of 30, 70, and 300 nm (SP30, SP70, and SP300) as model materials. The biochemical compositions of liver tissues and serum of mice treated with SP30, SP70, and SP300 were analyzed by integrated metabonomics analysis based on gas chromatography-mass spectrometry (GC-MS) and in combination with pattern recognition approaches. Histopathological examinations and serum biochemical analysis were simultaneously performed. The toxicity induced by three different sizes of SP mainly involved hepatocytic necrosis, increased serum aminotransferase, and inflammatory cytokines. Moreover, the toxic effects of SP were dose-dependent for each particle size. The doses of SP30, SP70, and SP300 that were toxic to the liver were 10, 40, and 200 mg kg{sup -1}, respectively. In this study, surface area has a greater effect than particle number on the toxicity of SP30, SP70, and SP300 in the liver. The disturbances in energy metabolism, amino acid metabolism, lipid metabolism, and nucleotide metabolism may be attributable to the hepatotoxicity induced by SP. In addition, no major differences were found in the response of biological systems caused by the different SP sizes among the metabolite profiles. The results suggest that not only nano-sized but also submicro-sized SP can cause similar extents of liver injury, which is dependent on the exposure dose, and the mechanism of toxicity may be almost the same.

  15. An integrated internal flow analysis for ramjet propulsion system

    Science.gov (United States)

    Hsieh, Shih-Yang

    An integrated numerical analysis has been conducted to study the ramjet internal flowfield. Emphasis is placed on the establishment of a unified numerical scheme and accurate representation of the internal flow development. The theoretical model is based on the complete conservation equations of mass, momentum, energy, and species concentration, with consideration of finite-rate chemical reactions and variable properties. Turbulence closure is achieved using a low-Reynolds number k-epsilon two-equation model. A new computation procedure capable of treating time-accurate, chemically reacting flows over a wide range of Mach number was developed. This numerical scheme allows for a unified treatment of the entire flowfield in a ramjet engine, including both the supersonic inlet and the combustion chamber. The algorithm is based on scaling the pressure terms in the momentum equations and preconditioning the conservation equations to circumvent numerical difficulties at low Mach numbers. The resulting equations are solved using the lower-upper (LU) factorization method in a fully-coupled manner, with the incorporation of a flux-differencing upwind TVD scheme to achieve high-order spatial accuracy. The transient behavior of the modeled system is preserved through implementation of the dual time-stepping integration technique. Calculations have been carried out for the flowfield in a typical ramjet engine consisting of an axisymmetric mixed-compression supersonic inlet and a coaxial dump combustor. Distinguished shock structures in the forward section of the inlet were clearly captured. The boundary layer thickening and flow separation behind the terminal shock due to shock/boundary-layer interactions and inlet configuration were observed. The mutual coupling between the inlet and combustor was carefully examined. In particular, strong vortices arising from the inlet shock/acoustic and shock/boundary-layer interactions may convect downstream and affect the combustion

  16. Packaged integrated opto-fluidic solution for harmful fluid analysis

    Science.gov (United States)

    Allenet, T.; Bucci, D.; Geoffray, F.; Canto, F.; Couston, L.; Jardinier, E.; Broquin, J.-E.

    2016-02-01

    Advances in nuclear fuel reprocessing have led to a surging need for novel chemical analysis tools. In this paper, we present a packaged lab-on-chip approach with co-integration of optical and micro-fluidic functions on a glass substrate as a solution. A chip was built and packaged to obtain light/fluid interaction in order for the entire device to make spectral measurements using the photo spectroscopy absorption principle. The interaction between the analyte solution and light takes place at the boundary between a waveguide and a fluid micro-channel thanks to the evanescent part of the waveguide's guided mode that propagates into the fluid. The waveguide was obtained via ion exchange on a glass wafer. The input and the output of the waveguides were pigtailed with standard single mode optical fibers. The micro-scale fluid channel was elaborated with a lithography procedure and hydrofluoric acid wet etching resulting in a 150+/-8 μm deep channel. The channel was designed with fluidic accesses, in order for the chip to be compatible with commercial fluidic interfaces/chip mounts. This allows for analyte fluid in external capillaries to be pumped into the device through micro-pipes, hence resulting in a fully packaged chip. In order to produce this co-integrated structure, two substrates were bonded. A study of direct glass wafer-to-wafer molecular bonding was carried-out to improve detector sturdiness and durability and put forward a bonding protocol with a bonding surface energy of γ>2.0 J.m-2. Detector viability was shown by obtaining optical mode measurements and detecting traces of 1.2 M neodymium (Nd) solute in 12+/-1 μL of 0.01 M and pH 2 nitric acid (HNO3) solvent by obtaining an absorption peak specific to neodymium at 795 nm.

  17. Optical Slot-Waveguide Based Biochemical Sensors

    Directory of Open Access Journals (Sweden)

    Carlos Angulo Barrios

    2009-06-01

    Full Text Available Slot-waveguides allow light to be guided and strongly confined inside a nanometer-scale region of low refractive index. Thus stronger light-analyte interaction can be obtained as compared to that achievable by a conventional waveguide, in which the propagating beam is confined to the high-refractive-index core of the waveguide. In addition, slot-waveguides can be fabricated by employing CMOS compatible materials and technology, enabling miniaturization, integration with electronic, photonic and fluidic components in a chip, and mass production. These advantages have made the use of slot-waveguides for highly sensitive biochemical optical integrated sensors an emerging field. In this paper, recent achievements in slot-waveguide based biochemical sensing will be reviewed. These include slot-waveguide ring resonator based refractometric label-free biosensors, label-based optical sensing, and nano-opto-mechanical sensors.

  18. Harmonic analysis in integrated energy system based on compressed sensing

    International Nuclear Information System (INIS)

    Yang, Ting; Pen, Haibo; Wang, Dan; Wang, Zhaoxia

    2016-01-01

    Highlights: • We propose a harmonic/inter-harmonic analysis scheme with compressed sensing theory. • Property of sparseness of harmonic signal in electrical power system is proved. • The ratio formula of fundamental and harmonic components sparsity is presented. • Spectral Projected Gradient-Fundamental Filter reconstruction algorithm is proposed. • SPG-FF enhances the precision of harmonic detection and signal reconstruction. - Abstract: The advent of Integrated Energy Systems enabled various distributed energy to access the system through different power electronic devices. The development of this has made the harmonic environment more complex. It needs low complexity and high precision of harmonic detection and analysis methods to improve power quality. To solve the shortages of large data storage capacities and high complexity of compression in sampling under the Nyquist sampling framework, this research paper presents a harmonic analysis scheme based on compressed sensing theory. The proposed scheme enables the performance of the functions of compressive sampling, signal reconstruction and harmonic detection simultaneously. In the proposed scheme, the sparsity of the harmonic signals in the base of the Discrete Fourier Transform (DFT) is numerically calculated first. This is followed by providing a proof of the matching satisfaction of the necessary conditions for compressed sensing. The binary sparse measurement is then leveraged to reduce the storage space in the sampling unit in the proposed scheme. In the recovery process, the scheme proposed a novel reconstruction algorithm called the Spectral Projected Gradient with Fundamental Filter (SPG-FF) algorithm to enhance the reconstruction precision. One of the actual microgrid systems is used as simulation example. The results of the experiment shows that the proposed scheme effectively enhances the precision of harmonic and inter-harmonic detection with low computing complexity, and has good

  19. [Integrity].

    Science.gov (United States)

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  20. From organizational integration to clinical integration: analysis of the path between one level of integration to another using official documents

    Science.gov (United States)

    Mandza, Matey; Gagnon, Dominique; Carrier, Sébastien; Belzile, Louise; Demers, Louis

    2010-01-01

    Purpose Services’ integration comprises organizational, normative, economic, informational and clinical dimensions. Since 2004, the province of Quebec has devoted significant efforts to unify the governance of the main health and social care organizations of its various territories. Notwithstanding the uniformity of the national plan’s prescription, the territorial integration modalities greatly vary across the province. Theory This research is based upon a conceptual model of integration that comprises six components: inter-organizational partnership, case management, standardized assessment, a single entry point, a standardized service planning tool and a shared clinical file. Methods We conducted an embedded case study in six contrasted sites in terms of their level of integration. All documents prescribing the implementation of integration were retrieved and analyzed. Results and conclusions The analyzed documents demonstrate a growing local appropriation of the current integrative reform. Interestingly however, no link seems to exist between the quality of local prescriptions and the level of integration achieved in each site. This finding leads us to hypothesize that the variable quality of the operational accompaniment offered to implement these prescriptions is a variable in play.

  1. Proceedings of a NEA workshop on probabilistic structure integrity analysis and its relationship to deterministic analysis

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-07-01

    This workshop was hosted jointly by the Swedish Nuclear Power Inspectorate (SKi) and the Swedish Royal Institute of Technology (KTH). It was sponsored by the Principal Working Group 3 (PWG-3) of the NEA CSNI. PWG-3 deals with the integrity of structures and components, and has three sub-groups, dealing with the integrity of metal components and structures, ageing of concrete structures, and the seismic behaviour of structures. The sub-group dealing with metal components has three mains areas of activity: non-destructive examination; fracture mechanics; and material degradation. The topic of this workshop is primarily probabilistic fracture mechanics, but probabilistic integrity analysis includes NDE and materials degradation also. Session 1 (5 papers) was devoted to the development of probabilistic models; Session 2 (5 papers) to the random modelling of defects and material properties; Session 3 (8 papers) to the applications of probabilistic modelling to nuclear components; Sessions 4 is a concluding panel discussion

  2. Proceedings of a NEA workshop on probabilistic structure integrity analysis and its relationship to deterministic analysis

    International Nuclear Information System (INIS)

    1996-01-01

    This workshop was hosted jointly by the Swedish Nuclear Power Inspectorate (SKi) and the Swedish Royal Institute of Technology (KTH). It was sponsored by the Principal Working Group 3 (PWG-3) of the NEA CSNI. PWG-3 deals with the integrity of structures and components, and has three sub-groups, dealing with the integrity of metal components and structures, ageing of concrete structures, and the seismic behaviour of structures. The sub-group dealing with metal components has three mains areas of activity: non-destructive examination; fracture mechanics; and material degradation. The topic of this workshop is primarily probabilistic fracture mechanics, but probabilistic integrity analysis includes NDE and materials degradation also. Session 1 (5 papers) was devoted to the development of probabilistic models; Session 2 (5 papers) to the random modelling of defects and material properties; Session 3 (8 papers) to the applications of probabilistic modelling to nuclear components; Sessions 4 is a concluding panel discussion

  3. Canonical integration and analysis of periodic maps using non-standard analysis and life methods

    Energy Technology Data Exchange (ETDEWEB)

    Forest, E.; Berz, M.

    1988-06-01

    We describe a method and a way of thinking which is ideally suited for the study of systems represented by canonical integrators. Starting with the continuous description provided by the Hamiltonians, we replace it by a succession of preferably canonical maps. The power series representation of these maps can be extracted with a computer implementation of the tools of Non-Standard Analysis and analyzed by the same tools. For a nearly integrable system, we can define a Floquet ring in a way consistent with our needs. Using the finite time maps, the Floquet ring is defined only at the locations s/sub i/ where one perturbs or observes the phase space. At most the total number of locations is equal to the total number of steps of our integrator. We can also produce pseudo-Hamiltonians which describe the motion induced by these maps. 15 refs., 1 fig.

  4. An analysis of clinical and treatment related prognostic factors on outcome using biochemical control as an end-point in patients with prostate cancer treated with external beam irradiation

    International Nuclear Information System (INIS)

    Horwitz, Eric M.; Vicini, Frank A.; Ziaja, Ellen L.; Dmuchowski, Carl F.; Stromberg, Jannifer S.; Gustafson, Gary S.; Martinez, Alvaro A.

    1997-01-01

    Purpose: We reviewed our institution's experience in treating patients with clinically localized prostate cancer with external beam irradiation (RT) to determine if previously analyzed clinical and treatment related prognostic factors affected outcome when biochemical control was used as an end-point to evaluate results. Materials and methods: Between 1 January 1987 and 31 December 1991, 470 patients with clinically localized prostate cancer were treated with external beam RT using localized prostate fields at William Beaumont Hospital. Biochemical control was defined as PSA nadir ≤1.5 ng/ml within 1 year of treatment. After achieving nadir, if two consecutive increases of PSA were noted, the patient was scored a failure at the time of the first increase. Prognostic factors, including the total number of days in treatment, the method of diagnosis, a history of any pretreatment transurethral resection of the prostate (TURP) and the type of boost were analyzed. Results: Median follow-up was 48 months. No statistically significant difference in rates of biochemical control were noted for treatment time, overall time (date of biopsy to completion of RT), history of any pretreatment TURP, history of diagnosis by TURP, or boost techniques. Patients diagnosed by TURP had a significant improvement in the overall rate of biochemical control (P < 0.03) compared to transrectal/transperineal biopsy. The 5-year actuarial rates were 58 versus 39%, respectively. This improvement was not evident when pretreatment PSA, T stage, or Gleason score were controlled for. On multivariate analysis, no variable was associated with outcome. When analysis was limited to a more favorable group of patients (T1/T2 tumors, pretreatment PSA ≤20 ng/ml and Gleason score <7), none of these variables were significantly predictive of biochemical control when controlling for pretreatment PSA, T stage and Gleason score. Conclusions: No significant effect of treatment time, overall time, pretreatment

  5. Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer's disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids.

    Science.gov (United States)

    Bautista-Aguilera, Oscar M; Esteban, Gerard; Chioua, Mourad; Nikolic, Katarina; Agbaba, Danica; Moraleda, Ignacio; Iriepa, Isabel; Soriano, Elena; Samadi, Abdelouahid; Unzeta, Mercedes; Marco-Contelles, José

    2014-01-01

    The design, synthesis, and biochemical evaluation of donepezil-pyridyl hybrids (DPHs) as multipotent cholinesterase (ChE) and monoamine oxidase (MAO) inhibitors for the potential treatment of Alzheimer's disease (AD) is reported. The 3D-quantitative structure-activity relationship study was used to define 3D-pharmacophores for inhibition of MAO A/B, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes and to design DPHs as novel multi-target drug candidates with potential impact in the therapy of AD. DPH14 (Electrophorus electricus AChE [EeAChE]: half maximal inhibitory concentration [IC50] =1.1±0.3 nM; equine butyrylcholinesterase [eqBuChE]: IC50 =600±80 nM) was 318-fold more potent for the inhibition of AChE, and 1.3-fold less potent for the inhibition of BuChE than the reference compound ASS234. DPH14 is a potent human recombinant BuChE (hBuChE) inhibitor, in the same range as DPH12 or DPH16, but 13.1-fold less potent than DPH15 for the inhibition of human recombinant AChE (hAChE). Compared with donepezil, DPH14 is almost equipotent for the inhibition of hAChE, and 8.8-fold more potent for hBuChE. Concerning human monoamine oxidase (hMAO) A inhibition, only DPH9 and 5 proved active, compound DPH9 being the most potent (IC50 [MAO A] =5,700±2,100 nM). For hMAO B, only DPHs 13 and 14 were moderate inhibitors, and compound DPH14 was the most potent (IC50 [MAO B] =3,950±940 nM). Molecular modeling of inhibitor DPH14 within EeAChE showed a binding mode with an extended conformation, interacting simultaneously with both catalytic and peripheral sites of EeAChE thanks to a linker of appropriate length. Absortion, distribution, metabolism, excretion and toxicity analysis showed that structures lacking phenyl-substituent show better druglikeness profiles; in particular, DPHs13-15 showed the most suitable absortion, distribution, metabolism, excretion and toxicity properties. Novel donepezil-pyridyl hybrid DPH14 is a potent, moderately selective h

  6. Microblogging for Class: An Analysis of Affective, Cognitive, Personal Integrative, and Social Integrative Gratifications

    Science.gov (United States)

    Gant, Camilla; Hadley, Patrick D.

    2014-01-01

    This study shows that undergraduate students can gratify cognitive, affective, social integrative, and personal integrative needs microblogging via a learning management system discussion tool. Moreover, the researchers find that microblogging about news regarding mass media events and issues via Blackboard heightened engagement, expanded…

  7. An example of system integration for RCRA policy analysis

    International Nuclear Information System (INIS)

    Tonn, B.; Goeltz, R.; Schmidt, K.

    1991-01-01

    This paper describes the synthesis of various computer technologies and software systems used on a project to estimate the costs of remediating Solid Waste Management Units (SWMUs) that fall under the corrective action provisions of the Resource Conservation and Recovery Act (RCRA). The project used two databases collected by Research Triangle Institute (RTI) that contain information on SWMUs and a PC-based software system called CORA that develops cost estimates for remediating SWMUs. The project team developed rules to categorize every SWMU in the databases by the kinds of technologies required to clean them up. These results were input into CORA, which estimated costs associated with the technologies. Early on, several computing challenges presented themselves. First, the databases have several hundred thousand records each. Second, the categorization rules could not be written to cover all combinations of variables. Third, CORA is run interactively and the analysis plan called for running CORA tens of thousands of times. Fourth, large data transfers needed to take place between RTI and Oak Ridge National Laboratory. Solutions to these problems required systems integration. SWMU categorization was streamlined by using INTERNET as was the data transfer. SAS was used to create files used by a program called SuperKey that was used to run CORA. Because the analysis plan required the generation of hundreds of thousands of cost estimates, memory management software was needed to allow the portable IBM P70 to do the job. During the course of the project, several other software packages were used, including: SAS System for Personal Computers (SAS/PC), DBase III, LOTUS 1-2-3, PIZAZZ PLUS, LOTUS Freelance Plus, and Word Perfect. Only the comprehensive use of all available hardware and software resources allowed this project to be completed within the time and budget constraints. 5 refs., 3 figs., 3 tabs

  8. The Venetian Ghetto: Semantic Modelling for an Integrated Analysis

    Directory of Open Access Journals (Sweden)

    Alessandra Ferrighi

    2017-12-01

    Full Text Available In the digital era, historians are embracing information technology as a research tool. New technologies offer investigation and interpretation, synthesis and communication tools that are more effective than the more traditional study methods, as they guarantee a multidisciplinary approach and analyses integration. Among the available technologies the best suited for the study or urban phenomena are databases (DB, the Geographic Information System (GIS, the Building Information Modelling (BIM and the multimedia tools (Video, APP for the dissemination of results. The case study described here concerns the analysis of part of Venice that changed its appearance from 1516 onwards, with the creation of the Jewish Ghetto. This was an event that would have repercussions throughout Europe, changing the course of history. Our research confirms that the exclusive use of one of the systems mentioned above (DB, GIS, BIM makes it possible to manage the complexity of the subject matter only partially. Consequently, it became necessary to analyse the possible interactions between such tools, so as to create a link between an alphanumeric DB and a geographical DB. The use of only GIS and BIM that provide for a 4D time management of objects turned out to be able to manage information and geometry in an effective and scalable way, providing a starting point for the mapping in depth of the historical analysis. Software products for digital modelling have changed in nature over time, going from simple viewing tools to simulation tools. The reconstruction of the time phases of the three Ghettos (Nuovo, Vecchio, and Nuovissimo and their visualisation through digital narratives of the history of that specific area of the city, for instance through videos, is making it possible for an increasing number of scholars and the general public to access the results of the study.

  9. IRRAS, Integrated Reliability and Risk Analysis System for PC

    International Nuclear Information System (INIS)

    Russell, K.D.

    1995-01-01

    1 - Description of program or function: IRRAS4.16 is a program developed for the purpose of performing those functions necessary to create and analyze a complete Probabilistic Risk Assessment (PRA). This program includes functions to allow the user to create event trees and fault trees, to define accident sequences and basic event failure data, to solve system and accident sequence fault trees, to quantify cut sets, and to perform uncertainty analysis on the results. Also included in this program are features to allow the analyst to generate reports and displays that can be used to document the results of an analysis. Since this software is a very detailed technical tool, the user of this program should be familiar with PRA concepts and the methods used to perform these analyses. 2 - Method of solution: IRRAS4.16 is written entirely in MODULA-2 and uses an integrated commercial graphics package to interactively construct and edit fault trees. The fault tree solving methods used are industry recognized top down algorithms. For quantification, the program uses standard methods to propagate the failure information through the generated cut sets. 3 - Restrictions on the complexity of the problem: Due to the complexity of and the variety of ways a fault tree can be defined it is difficult to define limits on the complexity of the problem solved by this software. It is, however, capable of solving a substantial fault tree due to efficient methods. At this time, the software can efficiently solve problems as large as other software currently used on mainframe computers. Does not include source code

  10. Corporate Disclosure, Materiality, and Integrated Report: An Event Study Analysis

    Directory of Open Access Journals (Sweden)

    Maria Cleofe Giorgino

    2017-11-01

    Full Text Available Within the extensive literature investigating the impacts of corporate disclosure in supporting the sustainable growth of an organization, few studies have included in the analysis the materiality issue referred to the information being disclosed. This article aims to address this gap, exploring the effect produced on capital markets by the publication of a recent corporate reporting tool, Integrated Report (IR. The features of this tool are that it aims to represent the multidimensional impact of the organization’s activity and assumes materiality as a guiding principle of the report drafting. Adopting the event study methodology associated with a statistical significance test for categorical data, our results verify that an organization’s release of IR is able to produce a statistically significant impact on the related share prices. Moreover, the term “integrated” assigned to the reports plays a significant role in the impact on capital markets. Our findings have beneficial implications for both researchers and practitioners, adding new evidence for the IR usefulness as a corporate disclosure tool and the effect of an organization’s decision to disclose material information.

  11. Linking Ayurveda and Western medicine by integrative analysis

    Directory of Open Access Journals (Sweden)

    Fazlin Mohd Fauzi

    2013-01-01

    Full Text Available In this article, we discuss our recent work in elucidating the mode-of-action of compounds used in traditional medicine including Ayurvedic medicine. Using computational (′in silico′ approach, we predict potential targets for Ayurvedic anti-cancer compounds, obtained from the Indian Plant Anticancer Database given its chemical structure. In our analysis, we observed that: (i the targets predicted can be connected to cancer pathogenesis i.e. steroid-5-alpha reductase 1 and 2 and estrogen receptor-β, and (ii predominantly hormone-dependent cancer targets were predicted for the anti-cancer compounds. Through the use of our in silico target prediction, we conclude that understanding how traditional medicine such as Ayurveda work through linking with the ′western′ understanding of chemistry and protein targets can be a fruitful avenue in addition to bridging the gap between the two different schools of thinking. Given that compounds used in Ayurveda have been tested and used for thousands of years (although not in the same approach as Western medicine, they can potentially be developed into potential new drugs. Hence, to further advance the case of Ayurvedic medicine, we put forward some suggestions namely: (a employing and integrating novel analytical methods given the advancements of ′omics′ and (b sharing experimental data and clinical results on studies done on Ayurvedic compounds in an easy and accessible way.

  12. Extreme Wave Analysis by Integrating Model and Wave Buoy Data

    Directory of Open Access Journals (Sweden)

    Fabio Dentale

    2018-03-01

    Full Text Available Estimating the extreme values of significant wave height (HS, generally described by the HS return period TR function HS(TR and by its confidence intervals, is a necessity in many branches of coastal science and engineering. The availability of indirect wave data generated by global and regional wind and wave model chains have brought radical changes to the estimation procedures of such probability distribution—weather and wave modeling systems are routinely run all over the world, and HS time series for each grid point are produced and published after assimilation (analysis of the ground truth. However, while the sources of such indirect data are numerous, and generally of good quality, many aspects of their procedures are hidden to the users, who cannot evaluate the reliability and the limits of the HS(TR deriving from such data. In order to provide a simple engineering tool to evaluate the probability of extreme sea-states as well as the quality of such estimates, we propose here a procedure based on integrating HS time series generated by model chains with those recorded by wave buoys in the same area.

  13. MEASURE: An integrated data-analysis and model identification facility

    Science.gov (United States)

    Singh, Jaidip; Iyer, Ravi K.

    1990-01-01

    The first phase of the development of MEASURE, an integrated data analysis and model identification facility is described. The facility takes system activity data as input and produces as output representative behavioral models of the system in near real time. In addition a wide range of statistical characteristics of the measured system are also available. The usage of the system is illustrated on data collected via software instrumentation of a network of SUN workstations at the University of Illinois. Initially, statistical clustering is used to identify high density regions of resource-usage in a given environment. The identified regions form the states for building a state-transition model to evaluate system and program performance in real time. The model is then solved to obtain useful parameters such as the response-time distribution and the mean waiting time in each state. A graphical interface which displays the identified models and their characteristics (with real time updates) was also developed. The results provide an understanding of the resource-usage in the system under various workload conditions. This work is targeted for a testbed of UNIX workstations with the initial phase ported to SUN workstations on the NASA, Ames Research Center Advanced Automation Testbed.

  14. Signal Integrity Analysis in Single and Bundled Carbon Nanotube Interconnects

    International Nuclear Information System (INIS)

    Majumder, M.K.; Pandya, N.D.; Kaushik, B.K.; Manhas, S.K.

    2013-01-01

    Carbon nanotube (CN T) can be considered as an emerging interconnect material in current nano scale regime. They are more promising than other interconnect materials such as Al or Cu because of their robustness to electromigration. This research paper aims to address the crosstalk-related issues (signal integrity) in interconnect lines. Different analytical models of single- (SWCNT), double- (DWCNT), and multiwalled CNTs (MWCNT) are studied to analyze the crosstalk delay at global interconnect lengths. A capacitively coupled three-line bus architecture employing CMOS driver is used for accurate estimation of crosstalk delay. Each line in bus architecture is represented with the equivalent RLC models of single and bundled SWCNT, DWCNT, and MWCNT interconnects. Crosstalk delay is observed at middle line (victim) when it switches in opposite direction with respect to the other two lines (aggressors). Using the data predicted by ITRS 2012, a comparative analysis on the basis of crosstalk delay is performed for bundled SWCNT/DWCNT and single MWCNT interconnects. It is observed that the overall crosstalk delay is improved by 40.92% and 21.37% for single MWCNT in comparison to bundled SWCNT and bundled DWCNT interconnects, respectively.

  15. Functional analysis in the study of differential and integral equations

    International Nuclear Information System (INIS)

    Sell, G.R.

    1976-01-01

    This paper illustrates the use of functional analysis in the study of differential equations. Our particular starting point, the theory of flows or dynamical systems, originated with the work of H. Poincare, who is the founder of the qualitative theory of ordinary differential equations. In the qualitative theory one tries to describe the behaviour of a solution, or a collection of solutions, without ''solving'' the differential equation. As a starting point one assumes the existence, and sometimes the uniqueness, of solutions and then one tries to describe the asymptotic behaviour, as time t→+infinity, of these solutions. We compare the notion of a flow with that of a C 0 -group of bounded linear operators on a Banach space. We shall show how the concept C 0 -group, or more generally a C 0 -semigroup, can be used to study the behaviour of solutions of certain differential and integral equations. Our main objective is to show how the concept of a C 0 -group and especially the notion of weak-compactness can be used to prove the existence of an invariant measure for a flow on a compact Hausdorff space. Applications to the theory of ordinary differential equations are included. (author)

  16. iDASH: integrating data for analysis, anonymization, and sharing

    Science.gov (United States)

    Bafna, Vineet; Boxwala, Aziz A; Chapman, Brian E; Chapman, Wendy W; Chaudhuri, Kamalika; Day, Michele E; Farcas, Claudiu; Heintzman, Nathaniel D; Jiang, Xiaoqian; Kim, Hyeoneui; Kim, Jihoon; Matheny, Michael E; Resnic, Frederic S; Vinterbo, Staal A

    2011-01-01

    iDASH (integrating data for analysis, anonymization, and sharing) is the newest National Center for Biomedical Computing funded by the NIH. It focuses on algorithms and tools for sharing data in a privacy-preserving manner. Foundational privacy technology research performed within iDASH is coupled with innovative engineering for collaborative tool development and data-sharing capabilities in a private Health Insurance Portability and Accountability Act (HIPAA)-certified cloud. Driving Biological Projects, which span different biological levels (from molecules to individuals to populations) and focus on various health conditions, help guide research and development within this Center. Furthermore, training and dissemination efforts connect the Center with its stakeholders and educate data owners and data consumers on how to share and use clinical and biological data. Through these various mechanisms, iDASH implements its goal of providing biomedical and behavioral researchers with access to data, software, and a high-performance computing environment, thus enabling them to generate and test new hypotheses. PMID:22081224

  17. Linking Ayurveda and Western medicine by integrative analysis.

    Science.gov (United States)

    Fauzi, Fazlin Mohd; Koutsoukas, Alexios; Lowe, Robert; Joshi, Kalpana; Fan, Tai-Ping; Glen, Robert C; Bender, Andreas

    2013-04-01

    In this article, we discuss our recent work in elucidating the mode-of-action of compounds used in traditional medicine including Ayurvedic medicine. Using computational ('in silico') approach, we predict potential targets for Ayurvedic anti-cancer compounds, obtained from the Indian Plant Anticancer Database given its chemical structure. In our analysis, we observed that: (i) the targets predicted can be connected to cancer pathogenesis i.e. steroid-5-alpha reductase 1 and 2 and estrogen receptor-β, and (ii) predominantly hormone-dependent cancer targets were predicted for the anti-cancer compounds. Through the use of our in silico target prediction, we conclude that understanding how traditional medicine such as Ayurveda work through linking with the 'western' understanding of chemistry and protein targets can be a fruitful avenue in addition to bridging the gap between the two different schools of thinking. Given that compounds used in Ayurveda have been tested and used for thousands of years (although not in the same approach as Western medicine), they can potentially be developed into potential new drugs. Hence, to further advance the case of Ayurvedic medicine, we put forward some suggestions namely: (a) employing and integrating novel analytical methods given the advancements of 'omics' and (b) sharing experimental data and clinical results on studies done on Ayurvedic compounds in an easy and accessible way.

  18. Thermally-induced voltage alteration for integrated circuit analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cole, E.I. Jr.

    2000-06-20

    A thermally-induced voltage alteration (TIVA) apparatus and method are disclosed for analyzing an integrated circuit (IC) either from a device side of the IC or through the IC substrate to locate any open-circuit or short-circuit defects therein. The TIVA apparatus uses constant-current biasing of the IC while scanning a focused laser beam over electrical conductors (i.e. a patterned metallization) in the IC to produce localized heating of the conductors. This localized heating produces a thermoelectric potential due to the Seebeck effect in any conductors with open-circuit defects and a resistance change in any conductors with short-circuit defects, both of which alter the power demand by the IC and thereby change the voltage of a source or power supply providing the constant-current biasing. By measuring the change in the supply voltage and the position of the focused and scanned laser beam over time, any open-circuit or short-circuit defects in the IC can be located and imaged. The TIVA apparatus can be formed in part from a scanning optical microscope, and has applications for qualification testing or failure analysis of ICs.

  19. Bayesian Integrated Data Analysis of Fast-Ion Measurements by Velocity-Space Tomography

    DEFF Research Database (Denmark)

    Salewski, M.; Nocente, M.; Jacobsen, A.S.

    2018-01-01

    Bayesian integrated data analysis combines measurements from different diagnostics to jointly measure plasma parameters of interest such as temperatures, densities, and drift velocities. Integrated data analysis of fast-ion measurements has long been hampered by the complexity of the strongly non...... framework. The implementation for different types of diagnostics as well as the uncertainties are discussed, and we highlight the importance of integrated data analysis of all available detectors....

  20. Control Synthesis for the Flow-Based Microfluidic Large-Scale Integration Biochips

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2013-01-01

    In this paper we are interested in flow-based microfluidic biochips, which are able to integrate the necessary functions for biochemical analysis on-chip. In these chips, the flow of liquid is manipulated using integrated microvalves. By combining severalmicrovalves, more complex units, such asmi......In this paper we are interested in flow-based microfluidic biochips, which are able to integrate the necessary functions for biochemical analysis on-chip. In these chips, the flow of liquid is manipulated using integrated microvalves. By combining severalmicrovalves, more complex units...

  1. An Empirical Analysis of Post-Merger Organizational Integration

    DEFF Research Database (Denmark)

    Smeets, Valerie Anne Rolande; Ierulli, Kathryn; Gibbs, Michael

    2016-01-01

    existing establishments. Worker turnover is high after merger, but new hiring yields stable total employment. Target employees have higher turnover and reassignment, particularly if the target firm is small relative to the acquiring firm. These findings may suggest integration is costly, but can......We study post-merger organizational integration using linked employer-employee data. Integration is implemented by reassigning a small number of high skilled workers, especially in R&D and management. Workforce mixing is concentrated to establishments set up after merger rather than to previously...... be achieved by focusing on key employees. Alternatively, reassigning a few key employees is sufficient for achieving integration....

  2. Strategic Mobility 21: Integrated Tracking System Analysis and Concept Design

    National Research Council Canada - National Science Library

    Mallon, Lawrence G; Savacool, Edwin

    2007-01-01

    ... (ITS). This ITS design document identifies the technical and functional requirements for developing, procuring, and integrating components of an ITS capable of supporting an inland regional port, multi...

  3. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

    Full Text Available Introduction: Animations of biochemical processes and virtual laboratory environments lead to true molecular simulations. The use of interactive software’s in education can improve cognitive capacity, better learning and, mainly, it makes information acquisition easier. Material and Methods: This work presents the development of a biochemical hypermedia to understanding of the galactose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of galactose conversion to glucose-1-phosphate (to glycogen synthesis, glucose-6-phosphate (glycolysis intermediary, UDP-galactose (substrate to mucopolysaccharides synthesis and collagen’s glycosylation. There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of galactose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion: This hypermedia was presented for undergraduate students (UFSC who revealed that it was extremely effective in promoting the understanding of the theme.

  4. Analysis of the Variability of Epstein-Barr Virus Genes in Infectious Mononucleosis: Investigation of the Potential Correlation with Biochemical Parameters of Hepatic Involvement

    Directory of Open Access Journals (Sweden)

    Banko Ana

    2016-09-01

    Full Text Available Background: Primary Epstein-Barr virus (EBV infection is usually asymptomatic, although at times it results in the benign lymphoproliferative disease, infectious mononucleosis (IM, during which almost half of patients develop hepatitis. The aims of the present study are to evaluate polymorphisms of EBV genes circulating in IM isolates from this geographic region and to investigate the correlation of viral sequence patterns with the available IM biochemical parameters.

  5. Living PRAs [probabilistic risk analysis] made easier with IRRAS [Integrated Reliability and Risk Analysis System

    International Nuclear Information System (INIS)

    Russell, K.D.; Sattison, M.B.; Rasmuson, D.M.

    1989-01-01

    The Integrated Reliability and Risk Analysis System (IRRAS) is an integrated PRA software tool that gives the user the ability to create and analyze fault trees and accident sequences using an IBM-compatible microcomputer. This program provides functions that range from graphical fault tree and event tree construction to cut set generation and quantification. IRRAS contains all the capabilities and functions required to create, modify, reduce, and analyze event tree and fault tree models used in the analysis of complex systems and processes. IRRAS uses advanced graphic and analytical techniques to achieve the greatest possible realization of the potential of the microcomputer. When the needs of the user exceed this potential, IRRAS can call upon the power of the mainframe computer. The role of the Idaho National Engineering Laboratory if the IRRAS program is that of software developer and interface to the user community. Version 1.0 of the IRRAS program was released in February 1987 to prove the concept of performing this kind of analysis on microcomputers. This version contained many of the basic features needed for fault tree analysis and was received very well by the PRA community. Since the release of Version 1.0, many user comments and enhancements have been incorporated into the program providing a much more powerful and user-friendly system. This version is designated ''IRRAS 2.0''. Version 3.0 will contain all of the features required for efficient event tree and fault tree construction and analysis. 5 refs., 26 figs

  6. Short circuit analysis of distribution system with integration of DG

    DEFF Research Database (Denmark)

    Su, Chi; Liu, Zhou; Chen, Zhe

    2014-01-01

    and as a result bring challenges to the network protection system. This problem has been frequently discussed in the literature, but mostly considering only the balanced fault situation. This paper presents an investigation on the influence of full converter based wind turbine (WT) integration on fault currents......Integration of distributed generation (DG) such as wind turbines into distribution system is increasing all around the world, because of the flexible and environmentally friendly characteristics. However, DG integration may change the pattern of the fault currents in the distribution system...... during both balanced and unbalanced faults. Major factors such as external grid short circuit power capacity, WT integration location, connection type of WT integration transformer are taken into account. In turn, the challenges brought to the protection system in the distribution network are presented...

  7. Effect of the combination of metformin hydrochloride and melatonin on oxidative stress before and during pregnancy, and biochemical and histopathological analysis of the livers of rats after treatment for polycystic ovary syndrome

    International Nuclear Information System (INIS)

    Lemos, Ana Janaina Jeanine M.; Peixoto, Christina A.; Teixeira, Álvaro Aguiar C.; Luna, Rayana Leal A.; Rocha, Sura Wanessa S.; Santos, Hilda Michelly P.; Silva, Amanda Karolina S.; Nunes, Ana Karolina S.; Wanderley-Teixeira, Valéria

    2014-01-01

    The aim of the present study was to analyze the effect of a combination of metformin hydrochloride and melatonin on oxidative stress together with a biochemical and histopathological analysis of the livers of Wistar rats induced with PCOS. The results indicated that a combination of the drugs was more effective in the reduction of plasmatic levels of liver enzyme alanine aminotransferase, nitric oxide and total glutathione, and decreased the inflammatory response and histopathological damage, producing results that were significantly similar to animals from the control group. A mixture of the drugs produced more effective results against liver toxicity caused by PCOS, encouraging the normalization of biochemical parameters. During pregnancy, there was reduced oxidative stress compared to monotherapeutic use of these drugs. Interestingly, the combination of the drugs caused a physiological reaction similar to responses identified in healthy rats without induction of the PCOS control group. However, the clinical and physiological effectiveness of the combination should be further explored, especially with respect to the possible side effects on offspring. - Highlights: • Studies have documented increased oxidative stress in patients with PCOS. • It has been noted that women with PCOS have a high prevalence of liver alterations. • Liver disease in pregnancy may be pre-existing increasing the newborn mortality. • Metformin/melatonin associated reduced oxidative stress in liver in pregnant rats. • Association of metformin/melatonin normalizes hepatic biochemical parameters

  8. Effect of the combination of metformin hydrochloride and melatonin on oxidative stress before and during pregnancy, and biochemical and histopathological analysis of the livers of rats after treatment for polycystic ovary syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Lemos, Ana Janaina Jeanine M. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Unit of Medical and Health Sciences, Universidade Federal de Campina Grande (Brazil); Peixoto, Christina A. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Teixeira, Álvaro Aguiar C. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Luna, Rayana Leal A.; Rocha, Sura Wanessa S. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Santos, Hilda Michelly P. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Silva, Amanda Karolina S.; Nunes, Ana Karolina S. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Wanderley-Teixeira, Valéria, E-mail: valeria@dmfa.ufrpe.br [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil)

    2014-10-01

    The aim of the present study was to analyze the effect of a combination of metformin hydrochloride and melatonin on oxidative stress together with a biochemical and histopathological analysis of the livers of Wistar rats induced with PCOS. The results indicated that a combination of the drugs was more effective in the reduction of plasmatic levels of liver enzyme alanine aminotransferase, nitric oxide and total glutathione, and decreased the inflammatory response and histopathological damage, producing results that were significantly similar to animals from the control group. A mixture of the drugs produced more effective results against liver toxicity caused by PCOS, encouraging the normalization of biochemical parameters. During pregnancy, there was reduced oxidative stress compared to monotherapeutic use of these drugs. Interestingly, the combination of the drugs caused a physiological reaction similar to responses identified in healthy rats without induction of the PCOS control group. However, the clinical and physiological effectiveness of the combination should be further explored, especially with respect to the possible side effects on offspring. - Highlights: • Studies have documented increased oxidative stress in patients with PCOS. • It has been noted that women with PCOS have a high prevalence of liver alterations. • Liver disease in pregnancy may be pre-existing increasing the newborn mortality. • Metformin/melatonin associated reduced oxidative stress in liver in pregnant rats. • Association of metformin/melatonin normalizes hepatic biochemical parameters.

  9. AnalyzeHOLE: An Integrated Wellbore Flow Analysis Tool

    Energy Technology Data Exchange (ETDEWEB)

    Keith J. Halford

    2009-10-01

    Conventional interpretation of flow logs assumes that hydraulic conductivity is directly proportional to flow change with depth. However, well construction can significantly alter the expected relation between changes in fluid velocity and hydraulic conductivity. Strong hydraulic conductivity contrasts between lithologic intervals can be masked in continuously screened wells. Alternating intervals of screen and blank casing also can greatly complicate the relation between flow and hydraulic properties. More permeable units are not necessarily associated with rapid fluid-velocity increases. Thin, highly permeable units can be misinterpreted as thick and less permeable intervals or not identified at all. These conditions compromise standard flow-log interpretation because vertical flow fields are induced near the wellbore. AnalyzeHOLE, an integrated wellbore analysis tool for simulating flow and transport in wells and aquifer systems, provides a better alternative for simulating and evaluating complex well-aquifer system interaction. A pumping well and adjacent aquifer system are simulated with an axisymmetric, radial geometry in a two-dimensional MODFLOW model. Hydraulic conductivities are distributed by depth and estimated with PEST by minimizing squared differences between simulated and measured flows and drawdowns. Hydraulic conductivity can vary within a lithology but variance is limited with regularization. Transmissivity of the simulated system also can be constrained to estimates from single-well, pumping tests. Water-quality changes in the pumping well are simulated with simple mixing models between zones of differing water quality. These zones are differentiated by backtracking thousands of particles from the well screens with MODPATH. An Excel spreadsheet is used to interface the various components of AnalyzeHOLE by (1) creating model input files, (2) executing MODFLOW, MODPATH, PEST, and supporting FORTRAN routines, and (3) importing and graphically

  10. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C

    2006-07-01

    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  11. Graphical User Interface for Simulink Integrated Performance Analysis Model

    Science.gov (United States)

    Durham, R. Caitlyn

    2009-01-01

    The J-2X Engine (built by Pratt & Whitney Rocketdyne,) in the Upper Stage of the Ares I Crew Launch Vehicle, will only start within a certain range of temperature and pressure for Liquid Hydrogen and Liquid Oxygen propellants. The purpose of the Simulink Integrated Performance Analysis Model is to verify that in all reasonable conditions the temperature and pressure of the propellants are within the required J-2X engine start boxes. In order to run the simulation, test variables must be entered at all reasonable values of parameters such as heat leak and mass flow rate. To make this testing process as efficient as possible in order to save the maximum amount of time and money, and to show that the J-2X engine will start when it is required to do so, a graphical user interface (GUI) was created to allow the input of values to be used as parameters in the Simulink Model, without opening or altering the contents of the model. The GUI must allow for test data to come from Microsoft Excel files, allow those values to be edited before testing, place those values into the Simulink Model, and get the output from the Simulink Model. The GUI was built using MATLAB, and will run the Simulink simulation when the Simulate option is activated. After running the simulation, the GUI will construct a new Microsoft Excel file, as well as a MATLAB matrix file, using the output values for each test of the simulation so that they may graphed and compared to other values.

  12. A multilayered integrated sensor for three-dimensional, micro total analysis systems

    International Nuclear Information System (INIS)

    Xiao, Jing; Song, Fuchuan; Seo, Sang-Woo

    2013-01-01

    This paper presents a layer-by-layer integration approach of different functional devices and demonstrates a heterogeneously integrated optical sensor featuring a micro-ring resonator and a high-speed thin-film InGaAs-based photodetector co-integrated with a microfluidic droplet generation device. A thin optical device structure allows a seamless integration with other polymer-based devices on a silicon platform. The integrated sensor successfully demonstrates its transient measurement capability of two-phase liquid flow in a microfluidic droplet generation device. The proposed approach represents an important step toward fully integrated micro total analysis systems. (paper)

  13. Integrated safety analysis to operate while constructing Urenco USA

    International Nuclear Information System (INIS)

    Kohrt, Rick; Su, Shiaw-Der; Lehman, Richard

    2013-01-01

    The URENCO USA (UUSA) site in Lea County, New Mexico, USA is authorized by the U.S. Nuclear Regulatory Commission (NRC) for construction and operation of a uranium enrichment facility under 10 CFR 70 (Ref 1). The facility employs the gas centrifuge process to separate natural uranium hexafluoride (UF 6 ) feed material into a product stream enriched up to 5% U-235 and a depleted UF 6 stream containing approximately 0.2 to 0.34% U-235. Initial plant operations, with a limited number of cascades on line, commenced in the second half of 2010. Construction activities continue as each subsequent cascade is commissioned and placed into service. UUSA performed an Integrated Safety Analysis (ISA) to allow the facility to operate while constructing the remainder of the facility. The ISA Team selected the What-If/Checklist method based on guidance in NUREG-1513 (Ref 2) and AIChE Guidelines (Ref 3). Of the three methods recommended for high risk events HAZOP, What-If/Checklist, or Failure Modes and Effects Analysis (FMEA), the What-If/Checklist lends itself best to construction activities. It combines the structure of a checklist with an unstructured 'brainstorming' approach to create a list of specific accident events that could produce an undesirable consequence. The What-If/Checklist for Operate While Constructing divides the UUSA site into seven areas and creates what-if questions for sixteen different construction activities, such as site preparation, external construction cranes, and internal construction lifts. The result is a total of 112 nodes, for which the Operate While Constructing ISA Team created hundreds of what-if questions. For each what-if question the team determined the likelihood, consequences, safeguards, and acceptability of risk. What-if questions with unacceptable risk are the accident sequences and their selected safeguards are the Items Relied on For Safety (IROFS). The final ISA identified four (4) new accident sequences that, unless

  14. A comparison of integrated safety analysis and probabilistic risk assessment

    International Nuclear Information System (INIS)

    Damon, Dennis R.; Mattern, Kevin S.

    2013-01-01

    The U.S. Nuclear Regulatory Commission conducted a comparison of two standard tools for risk informing the regulatory process, namely, the Probabilistic Risk Assessment (PRA) and the Integrated Safety Analysis (ISA). PRA is a calculation of risk metrics, such as Large Early Release Frequency (LERF), and has been used to assess the safety of all commercial power reactors. ISA is an analysis required for fuel cycle facilities (FCFs) licensed to possess potentially critical quantities of special nuclear material. A PRA is usually more detailed and uses more refined models and data than an ISA, in order to obtain reasonable quantitative estimates of risk. PRA is considered fully quantitative, while most ISAs are typically only partially quantitative. The extension of PRA methodology to augment or supplant ISAs in FCFs has long been considered. However, fuel cycle facilities have a wide variety of possible accident consequences, rather than a few surrogates like LERF or core damage as used for reactors. It has been noted that a fuel cycle PRA could be used to better focus attention on the most risk-significant structures, systems, components, and operator actions. ISA and PRA both identify accident sequences; however, their treatment is quite different. ISA's identify accidents that lead to high or intermediate consequences, as defined in 10 Code of Federal Regulations (CFR) 70, and develop a set of Items Relied on For Safety (IROFS) to assure adherence to performance criteria. PRAs identify potential accident scenarios and estimate their frequency and consequences to obtain risk metrics. It is acceptable for ISAs to provide bounding evaluations of accident consequences and likelihoods in order to establish acceptable safety; but PRA applications usually require a reasonable quantitative estimate, and often obtain metrics of uncertainty. This paper provides the background, features, and methodology associated with the PRA and ISA. The differences between the

  15. Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

    Science.gov (United States)

    Me´ndez, Eduardo; Cerda´, María F.

    2016-01-01

    Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

  16. Building-integrated PV -- Analysis and US market potential

    International Nuclear Information System (INIS)

    Frantzis, L.; Hill, S.; Teagan, P.; Friedman, D.

    1994-01-01

    Arthur D Little, Inc., in conjunction with Solar Design Associates, conducted a study for the US Department of Energy (DOE), Office of Building Technologies (OBT) to determine the market potential for building-integrated photovoltaics (BIPV). This study defines BIPV as two types of applications: (1) where the PV modules are an integral part of the building, often serving as the exterior weathering skin, and (2) the PV modules are mounted on the existing building exterior. Both of these systems are fully integrated with the energy usage of the building and have potential for significant market penetration in the US

  17. Implantable biochemical fuel cell

    Energy Technology Data Exchange (ETDEWEB)

    Richter, G; Rao, J R

    1978-01-05

    Implantable biochemical fuel cells for the operation of heart pacemakers or artificial hearts convert oxidisable body substances such as glucose on the anode side and reduce the oxygen contained in body fluids at the cathode. The anode and cathode are separated by membranes which are impermeable to albumen and blood corpuscles in body fluids. A chemical shortcircuit cannot occur in practice if, according to the invention, one or more selective oxygen electrodes with carbon as catalyst are arranged so that the mixture which diffuses into the cell from body fluids during operation reaches the fuel cell electrode through the porous oxygen electrode. The membranes used must be permeable to water. Cellulose, polymerised polyvinyl alcohol or an ion exchanger with a buffering capacity between pH5 and 8 act as permeable materials.

  18. Improvements to Integrated Tradespace Analysis of Communications Architectures (ITACA) Network Loading Analysis Tool

    Science.gov (United States)

    Lee, Nathaniel; Welch, Bryan W.

    2018-01-01

    NASA's SCENIC project aims to simplify and reduce the cost of space mission planning by replicating the analysis capabilities of commercially licensed software which are integrated with relevant analysis parameters specific to SCaN assets and SCaN supported user missions. SCENIC differs from current tools that perform similar analyses in that it 1) does not require any licensing fees, 2) will provide an all-in-one package for various analysis capabilities that normally requires add-ons or multiple tools to complete. As part of SCENIC's capabilities, the ITACA network loading analysis tool will be responsible for assessing the loading on a given network architecture and generating a network service schedule. ITACA will allow users to evaluate the quality of service of a given network architecture and determine whether or not the architecture will satisfy the mission's requirements. ITACA is currently under development, and the following improvements were made during the fall of 2017: optimization of runtime, augmentation of network asset pre-service configuration time, augmentation of Brent's method of root finding, augmentation of network asset FOV restrictions, augmentation of mission lifetimes, and the integration of a SCaN link budget calculation tool. The improvements resulted in (a) 25% reduction in runtime, (b) more accurate contact window predictions when compared to STK(Registered Trademark) contact window predictions, and (c) increased fidelity through the use of specific SCaN asset parameters.

  19. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2017-06-01

    Full Text Available Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other

  20. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism.

    Science.gov (United States)

    Wang, Lei; Sun, Xiaoliang; Weiszmann, Jakob; Weckwerth, Wolfram

    2017-01-01

    Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed

  1. Development and analysis of a new integrated power and cooling ...

    Indian Academy of Sciences (India)

    It consists of characteristics of Rankine cycle and vapour .... Solar thermal integrated plant material flow details with respect to figure 1 at Tsep .... Design features of parabolic trough collector with vacuum tube at the focal line have been col-.

  2. Integrated proteomic and genomic analysis of colorectal cancer

    Science.gov (United States)

    Investigators who analyzed 95 human colorectal tumor samples have determined how gene alterations identified in previous analyses of the same samples are expressed at the protein level. The integration of proteomic and genomic data, or proteogenomics, pro

  3. Integrated policy analysis of sustainable urban and transportation development

    NARCIS (Netherlands)

    Zhang, J.; Feng, T.; Fujiwara, A.; Fujiwara, A.; Zhang, Junyi

    2013-01-01

    Sustainable urban and transportation development needs to balance economic sustainability, environmental sustainability, and social equity. This study conducts integrated policy analyses by explicitly incorporating these sustainability goals and optimizing the performance of transportation networks.

  4. Strategic Mobility 21: Integrated Tracking System Analysis and Concept Design

    National Research Council Canada - National Science Library

    Mallon, Lawrence G; Savacool, Edwin

    2007-01-01

    .... This design document supports the SM21 efforts in developing a dual-use multi-modal node at the Southern California Logistics Airport in Victorville, CA that will be supported by an Integrated Tracking System...

  5. Economic analysis of the structure, Integration and Performance of ...

    African Journals Online (AJOL)

    The data for the study were collected with the aid of a questionnaire. Statistical tools such as simple descriptive statistics, Gini coefficient, Shepherd-Futrel functional ... Key words: Rice; Market structure; Market integration and Performance.

  6. Critical Analysis of Methods for Integrating Economic and Environmental Indicators

    NARCIS (Netherlands)

    Huguet Ferran, Pau; Heijungs, Reinout; Vogtländer, Joost G.

    2018-01-01

    The application of environmental strategies requires scoring and evaluation methods that provide an integrated vision of the economic and environmental performance of systems. The vector optimisation, ratio and weighted addition of indicators are the three most prevalent techniques for addressing

  7. Wellbore integrity analysis of a natural CO2 producer

    KAUST Repository

    Crow, Walter; Carey, J. William; Gasda, Sarah; Brian Williams, D.; Celia, Michael

    2010-01-01

    integrity, defined as the maintenance of isolation between subsurface intervals. In this report, we investigate a 30-year-old well from a natural CO2 production reservoir using a suite of downhole and laboratory tests to characterize isolation performance

  8. Integral abutment bridges under thermal loading : field monitoring and analysis.

    Science.gov (United States)

    2017-08-01

    Integral abutment bridges (IABs) have gained popularity throughout the United States due to their low construction and maintenance costs. Previous research on IABs has been heavily focused on substructure performance, leaving a need for better unders...

  9. An Empirical Analysis of Post-Merger Organizational Integration

    OpenAIRE

    Smeets, Valerie Anne Rolande; Gibbs, Michael; Ierulli, Kathryn

    2015-01-01

    We study post-merger organizational integration using linked employer-employee data. Integration is implemented by reassigning a small number of high skilled workers, especially in R&D and management. Workforce mixing is concentrated to establishments set up after merger rather than to previously existing establishments. Worker turnover is high after merger, but new hiring yields stable total employment. Target employees have higher turnover and reassignment, particularly if the target fi...

  10. Energy efficiency analysis of styrene production by adiabatic ethylbenzene dehydrogenation using exergy analysis and heat integration

    Directory of Open Access Journals (Sweden)

    Ali Emad

    2018-03-01

    Full Text Available Styrene is a valuable commodity for polymer industries. The main route for producing styrene by dehydrogenation of ethylbenzene consumes a substantial amount of energy because of the use of high-temperature steam. In this work, the process energy requirements and recovery are studied using Exergy analysis and Heat Integration (HI based on Pinch design method. The amount of steam plays a key role in the trade-off between Styrene yield and energy savings. Therefore, optimizing the operating conditions for energy reduction is infeasible. Heat integration indicated an insignificant reduction in the net energy demand and exergy losses, but 24% and 34% saving in external heating and cooling duties, respectively. When the required steam is generated by recovering the heat of the hot reactor effluent, a considerable saving in the net energy demand, as well as the heating and cooling utilities, can be achieved. Moreover, around 68% reduction in the exergy destruction is observed.

  11. Heat integration and analysis of decarbonised IGCC sites

    Energy Technology Data Exchange (ETDEWEB)

    Ng, K.S.; Lopez, Y.; Campbell, G.M.; Sadhukhan, J. [University of Manchester, Manchester (United Kingdom). School of Chemical Engineering & Analytical Science

    2010-02-15

    Integrated gasification combined cycle (IGCC) power generation systems have become of interest due to their high combined heat and power (CHP) generation efficiency and flexibility to include carbon capture and storage (CCS) in order to reduce CO{sub 2} emissions. However, IGCC's biggest challenge is its high cost of energy production. In this study, decarbonised coal IGCC sites integrated with CCS have been investigated for heat integration and economic value analyses. It is envisaged that the high energy production cost of an IGCC site can be offset by maximising site-wide heat recovery and thereby improving the cost of electricity (COE) of CHP generation. Strategies for designing high efficiency CHP networks have been proposed based on thermodynamic heuristics and pinch theory. Additionally, a comprehensive methodology to determine the COE from a process site has been developed. In this work, we have established thermodynamic and economic comparisons between IGCC sites with and without CCS and a trade-off between the degree of decarbonisation and the COE from the heat integrated IGCC sites. The results show that the COE from the heat integrated decarbonised IGCC sites is significantly lower compared to IGCC sites without heat integration making application of CCS in IGCC sites economically competitive.

  12. Analysis of an integrated carbon cylce for storage of renewables

    Science.gov (United States)

    Streibel, Martin; Nakaten, Natalie; Kempka, Thomas; Kühn, Michael

    2013-04-01

    In order to mitigate the consequences of climate change the energy concept of the Government of Germany foresees the reduction of CO2 emissions by 80 % in 2050 compared to the status in 1990. Different routes are followed to achieve this goal. Most advanced is the construction of renewable energy sources in order to replace fossil fuel driven parts of the electricity generation. The increasing share of renewable energy sources in power production introduces the problem of high fluctuation of energy generated by windmills and photovoltaic. On top the production is not driven by demand but by availability of wind and sun. In this context, the "Power to Gas" concept has been developed. Main idea is the storage of excess renewable energy in form of hydrogen produced by electrolysis. If in a second step H2 reacts with CO2 to form CH4 the current natural gas infrastructure can be used. In times of energy production by renewables below the actual electricity demand CH4 is combusted to produce electricity. The emissions can be further reduced if CO2 is captured in the power plant and buffered in a dynamic geological storage (CCS). Subsequently the CO2 is back produced when excess energy is available to synthesise CH4. Storing CH4 locally also reduces energy for transport. Hence an integrated almost closed carbon cycle is implemented. In the present study this extended "Power to Gas" concept is elaborated on a regional-scale for the State of Brandenburg and the control area of 50 hertz. Focus of the analysis is the energetic balance of the concept for the integration of a geological CH4 and CO2 storage. Therefore, the energy conversion efficiency for the "Power to Gas" concept has been calculated using available data from literature. According to our calculations approximately 33 % of the wind energy used can be regained by combusting the synthesised CH4 in a combined cycle plant. In order to fuel a peaking power plant with a power of 120 MW for 2,500 hours a year

  13. Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline.

    Science.gov (United States)

    Pappas, Derek J; Marin, Wesley; Hollenbach, Jill A; Mack, Steven J

    2016-03-01

    Bridging ImmunoGenomic Data-Analysis Workflow Gaps (BIGDAWG) is an integrated data-analysis pipeline designed for the standardized analysis of highly-polymorphic genetic data, specifically for the HLA and KIR genetic systems. Most modern genetic analysis programs are designed for the analysis of single nucleotide polymorphisms, but the highly polymorphic nature of HLA and KIR data require specialized methods of data analysis. BIGDAWG performs case-control data analyses of highly polymorphic genotype data characteristic of the HLA and KIR loci. BIGDAWG performs tests for Hardy-Weinberg equilibrium, calculates allele frequencies and bins low-frequency alleles for k×2 and 2×2 chi-squared tests, and calculates odds ratios, confidence intervals and p-values for each allele. When multi-locus genotype data are available, BIGDAWG estimates user-specified haplotypes and performs the same binning and statistical calculations for each haplotype. For the HLA loci, BIGDAWG performs the same analyses at the individual amino-acid level. Finally, BIGDAWG generates figures and tables for each of these comparisons. BIGDAWG obviates the error-prone reformatting needed to traffic data between multiple programs, and streamlines and standardizes the data-analysis process for case-control studies of highly polymorphic data. BIGDAWG has been implemented as the bigdawg R package and as a free web application at bigdawg.immunogenomics.org. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  14. Integration of Formal Job Hazard Analysis and ALARA Work Practice

    International Nuclear Information System (INIS)

    NELSEN, D.P.

    2002-01-01

    ALARA work practices have traditionally centered on reducing radiological exposure and controlling contamination. As such, ALARA policies and procedures are not well suited to a wide range of chemical and human health issues. Assessing relative risk, identifying appropriate engineering/administrative controls and selecting proper Personal Protective Equipment (PPE) for non nuclear work activities extends beyond the limitations of traditional ALARA programs. Forging a comprehensive safety management program in today's (2002) work environment requires a disciplined dialog between health and safety professionals (e.g. safety, engineering, environmental, quality assurance, industrial hygiene, ALARA, etc.) and personnel working in the field. Integrating organizational priorities, maintaining effective pre-planning of work and supporting a team-based approach to safety management represents today's hallmark of safety excellence. Relying on the mandates of any single safety program does not provide industrial hygiene with the tools necessary to implement an integrated safety program. The establishment of tools and processes capable of sustaining a comprehensive safety program represents a key responsibility of industrial hygiene. Fluor Hanford has built integrated safety management around three programmatic attributes: (1) Integration of radiological, chemical and ergonomic issues under a single program. (2) Continuous improvement in routine communications among work planning/scheduling, job execution and management. (3) Rapid response to changing work conditions, formalized work planning and integrated worker involvement

  15. Analysis on the integration of ERP and e-commerce

    Science.gov (United States)

    Wang, Yongqing; Shi, Yuliana

    2017-08-01

    With the continuous development of China's modern economic construction, a variety of information technology are emerging. The new economic development characterized by e-commerce has accelerated the globalization of the economy. In face of increasingly fierce market competition, for enterprises, the constructions of ERP and e-commerce are necessary ways to enhance the core competitiveness of enterprises. At present, most of the internal ERP systems and external e-commerce systems are in relatively independent state. However, with the increasing fierce market competition, a single mode of operation has been unable to meet the requirements of enterprise development. Accordingly, the effective integration of ERP and e-commerce in the new era has become one of the most important topics for enterprise development. This paper firstly analyzes the relationship between ERP and e-commerce, and then analyzes the necessity and feasibility of integration, and finally discusses the integration strategies and technologies.

  16. A New Riemann Type Hydrodynamical Hierarchy and its Integrability Analysis

    International Nuclear Information System (INIS)

    Golenia, Jolanta Jolanta; Bogolubov, Nikolai N. Jr.; Popowicz, Ziemowit; Pavlov, Maxim V.; Prykarpat