WorldWideScience

Sample records for genetic code tracing

  1. Particle tracing code for multispecies gas

    International Nuclear Information System (INIS)

    Eaton, R.R.; Fox, R.L.; Vandevender, W.H.

    1979-06-01

    Details are presented for the development of a computer code designed to calculate the flow of a multispecies gas mixture using particle tracing techniques. The current technique eliminates the need for a full simulation by utilizing local time averaged velocity distribution functions to obtain the dynamic properties for probable collision partners. The development of this concept reduces statistical scatter experienced in conventional Monte Carlo simulations. The technique is applicable to flow problems involving gas mixtures with disparate masses and trace constituents in the Knudsen number, Kn, range from 1.0 to less than 0.01. The resulting code has previously been used to analyze several aerodynamic isotope enrichment devices

  2. The Alba ray tracing code: ART

    Science.gov (United States)

    Nicolas, Josep; Barla, Alessandro; Juanhuix, Jordi

    2013-09-01

    The Alba ray tracing code (ART) is a suite of Matlab functions and tools for the ray tracing simulation of x-ray beamlines. The code is structured in different layers, which allow its usage as part of optimization routines as well as an easy control from a graphical user interface. Additional tools for slope error handling and for grating efficiency calculations are also included. Generic characteristics of ART include the accumulation of rays to improve statistics without memory limitations, and still providing normalized values of flux and resolution in physically meaningful units.

  3. Papa, a Particle Tracing Code in Pascal

    NARCIS (Netherlands)

    Haselhoff, E.H.; Haselhoff, Eltjo H.; Ernst, G.J.

    1990-01-01

    During the design of a 10 ¿m high-gain FEL oscillator (TEUFEL Project) we developed a new particle-tracing code to perform simulations of thermionic- and photo-cathode electron injectors/accelerators. The program allows predictions of current, energy and beam emittance in a user-specified linac

  4. What Froze the Genetic Code?

    Directory of Open Access Journals (Sweden)

    Lluís Ribas de Pouplana

    2017-04-01

    Full Text Available The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

  5. What Froze the Genetic Code?

    Science.gov (United States)

    Ribas de Pouplana, Lluís; Torres, Adrian Gabriel; Rafels-Ybern, Àlbert

    2017-04-05

    The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

  6. Assessment of TRACE code against CHF experiments

    International Nuclear Information System (INIS)

    Audrius Jasiulevicius; Rafael Macian-Juan; Paul Coddington

    2005-01-01

    Full text of publication follows: This paper reports on the validation of the USNRC 'consolidate' code TRACE with data obtained during Critical Heat Flux (CHF) experiments in single channels and round and annular tubes. CHF is one of the key reactor safety parameters, because it determines the conditions for the onset of transition boiling in the core rod bundles, leading to the low heat transfer rates characteristics of the post-CHF heat transfer regime. In the context of the participation of PSI in the the International Programme for uncertainty analysis BEMUSE, we have carried out extensive work for the validation of some important TRACE models. The present work is aimed at assessing the range of validity for the CHF correlations and post-CHF heat transfer models currently included in TRACE. The heat transfer experiments selected for the assessment were performed at the Royal Institute of Technology (RIT) in Stockholm, Sweden and at the Atomic Energy Establishment in Winfrith, UK. The experimental investigations of the CHF and post-CHF heat transfer at RIT for flow of water in vertical tubes and annulus were performed at pressures ranging from 1 to 20 MPa and coolant mass fluxes from 500 to 3000 kg/m 2 s. The liquid was subcooled by 10 deg. C and 40 deg. C at the inlet of the test section. The experiments were performed on two different types of test sections. Experiments with uniformly heated single 7.0 m long tubes were carried out with three different inner tube diameters of 10, 14.9 and 24.7 mm. A series of experiments with non-uniform axial power distribution were also conducted in order to study the effect of the axial heat flux distribution on the CHF conditions in both 7.0 m long single tubes and 3.65 long annulus. Several different axial power profiles were employed with bottom, middle and top power peaks as well as the double-humped axial power profiles. In total more than 100 experiments with uniform axial heat flux distribution and several hundreds

  7. Genetic coding and gene expression - new Quadruplet genetic coding model

    Science.gov (United States)

    Shankar Singh, Rama

    2012-07-01

    Successful demonstration of human genome project has opened the door not only for developing personalized medicine and cure for genetic diseases, but it may also answer the complex and difficult question of the origin of life. It may lead to making 21st century, a century of Biological Sciences as well. Based on the central dogma of Biology, genetic codons in conjunction with tRNA play a key role in translating the RNA bases forming sequence of amino acids leading to a synthesized protein. This is the most critical step in synthesizing the right protein needed for personalized medicine and curing genetic diseases. So far, only triplet codons involving three bases of RNA, transcribed from DNA bases, have been used. Since this approach has several inconsistencies and limitations, even the promise of personalized medicine has not been realized. The new Quadruplet genetic coding model proposed and developed here involves all four RNA bases which in conjunction with tRNA will synthesize the right protein. The transcription and translation process used will be the same, but the Quadruplet codons will help overcome most of the inconsistencies and limitations of the triplet codes. Details of this new Quadruplet genetic coding model and its subsequent potential applications including relevance to the origin of life will be presented.

  8. Computation of the Genetic Code

    Science.gov (United States)

    Kozlov, Nicolay N.; Kozlova, Olga N.

    2018-03-01

    One of the problems in the development of mathematical theory of the genetic code (summary is presented in [1], the detailed -to [2]) is the problem of the calculation of the genetic code. Similar problems in the world is unknown and could be delivered only in the 21st century. One approach to solving this problem is devoted to this work. For the first time provides a detailed description of the method of calculation of the genetic code, the idea of which was first published earlier [3]), and the choice of one of the most important sets for the calculation was based on an article [4]. Such a set of amino acid corresponds to a complete set of representations of the plurality of overlapping triple gene belonging to the same DNA strand. A separate issue was the initial point, triggering an iterative search process all codes submitted by the initial data. Mathematical analysis has shown that the said set contains some ambiguities, which have been founded because of our proposed compressed representation of the set. As a result, the developed method of calculation was limited to the two main stages of research, where the first stage only the of the area were used in the calculations. The proposed approach will significantly reduce the amount of computations at each step in this complex discrete structure.

  9. Perspective on the audit calculation for SFR using TRACE code

    Energy Technology Data Exchange (ETDEWEB)

    Shin, An Dong; Choi, Yong Won; Bang, Young Suk; Bae, Moo Hoon; Huh, Byung Gil; Seol, Kwang One [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2012-10-15

    Korean Sodium Cooled Fast Reactor (SFR) is being developed by KAERI. The Prototype SFR will be a first SFR applied for licensing. KINS started research programs for preparing new concept design licensing recently. Safety analysis for the certain reactor is based on the computational estimation with conservatism and/or uncertainty of modeling. For the audit calculation for sodium cooled fast reactor (SFR), TRACE code is considered as one of analytical tool for SFR since TRACE code have already sodium related properties and models in it and have experience in the liquid metal coolant system area in abroad. Applicability of TRACE code for SFR is prechecked before real audit calculation. In this study, Demonstration Fast Reactor (DFR) 600 steady state conditions is simulated for identification of area of modeling improvements of TRACE code.

  10. Evaluation of ATLAS 100% DVI Line Break Using TRACE Code

    International Nuclear Information System (INIS)

    Huh, Byung Gil; Bang, Young Seok; Cheong, Ae Ju; Woo, Sweng Woong

    2011-01-01

    ATLAS (Advanced Thermal-Hydraulic Test Loop for Accident Simulation) is an integral effect test facility in KAERI. It had installed completely to simulate the accident for the OPR1000 and the APR1400 in 2005. After then, several tests for LBLOCA, DVI line break have been performed successfully to resolve the safety issues of the APR1400. Especially, a DVI line break is considered as another spectrum among the SBLOCAs in APR1400 because the DVI line is directly connected to the reactor vessel and the thermal hydraulic behaviors are expected to be different from those for the cold leg injection. However, there are not enough experimental data for the DVI line break. Therefore, integral effect data for the DVI line break of ATLAS is very useful and available for an improvement and validation of safety codes. For the DVI line break in ATLAS, several analyses using MARS and RELAP codes were performed in the ATLAS DSP (Domestic Standard Problem) meetings. However, TRACE code has still not used to simulate a DVI line break. TRACE code has developed as the unified code for the reactor thermal hydraulic analyses in USNRC. In this study, the 100% DVI line break in ATLAS was evaluated by TRACE code. The objectives of this study are to identify the prediction capability of TRACE code for the major thermal hydraulic phenomena of a DVI line break in ATLAS

  11. Evolutionary implications of genetic code deviations

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1986-07-01

    By extending the standard genetic code into a temperature dependent regime, we propose a train of molecular events leading to alternative coding. The first few examples of these deviations have already been reported in some ciliated protozoans and Gram positive bacteria. A possible range of further alternative coding, still within the context of universality, is pointed out. (author)

  12. Simulation of the turbine discharge transient with the code Trace

    International Nuclear Information System (INIS)

    Mejia S, D. M.; Filio L, C.

    2014-10-01

    In this paper the results of the simulation of the turbine discharge transient are shown, occurred in Unit 1 of nuclear power plant of Laguna Verde (NPP-L V), carried out with the model of this unit for the best estimate code Trace. The results obtained by the code Trace are compared with those obtained from the Process Information Integral System (PIIS) of the NPP-L V. The reactor pressure, level behavior in the down-comer, steam flow and flow rate through the recirculation circuits are compared. The results of the simulation for the operation power of 2027 MWt, show concordance with the system PIIS. (Author)

  13. Documentation for TRACE: an interactive beam-transport code

    International Nuclear Information System (INIS)

    Crandall, K.R.; Rusthoi, D.P.

    1985-01-01

    TRACE is an interactive, first-order, beam-dynamics computer program. TRACE includes space-charge forces and mathematical models for a number of beamline elements not commonly found in beam-transport codes, such as permanent-magnet quadrupoles, rf quadrupoles, rf gaps, accelerator columns, and accelerator tanks. TRACE provides an immediate graphic display of calculative results, has a powerful and easy-to-use command procedure, includes eight different types of beam-matching or -fitting capabilities, and contains its own internal HELP package. This report describes the models and equations used for each of the transport elements, the fitting procedures, and the space-charge/emittance calculations, and provides detailed instruction for using the code

  14. Analysis of an XADS Target with the System Code TRACE

    International Nuclear Information System (INIS)

    Jaeger, Wadim; Sanchez Espinoza, Victor H.; Feng, Bo

    2008-01-01

    Accelerator-driven systems (ADS) present an option to reduce the radioactive waste of the nuclear industry. The experimental Accelerator-Driven System (XADS) has been designed to investigate the feasibility of using ADS on an industrial scale to burn minor actinides. The target section lies in the middle of the subcritical core and is bombarded by a proton beam to produce spallation neutrons. The thermal energy produced from this reaction requires a heat removal system for the target section. The target is cooled by liquid lead-bismuth-eutectics (LBE) in the primary system which in turn transfers the heat via a heat exchanger (HX) to the secondary coolant, Diphyl THT (DTHT), a synthetic diathermic fluid. Since this design is still in development, a detailed investigation of the system is necessary to evaluate the behavior during normal and transient operations. Due to the lack of experimental facilities and data for ADS, the analyses are mostly done using thermal hydraulic codes. In addition to evaluating the thermal hydraulics of the XADS, this paper also benchmarks a new code developed by the NRC, TRACE, against other established codes. The events used in this study are beam power switch-on/off transients and a loss of heat sink accident. The obtained results from TRACE were in good agreement with the results of various other codes. (authors)

  15. SolTrace: A Ray-Tracing Code for Complex Solar Optical Systems

    Energy Technology Data Exchange (ETDEWEB)

    Wendelin, Tim [National Renewable Energy Lab. (NREL), Golden, CO (United States); Dobos, Aron [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lewandowski, Allan [Allan Lewandowski Solar Consulting LLC, Evergreen, CO (United States)

    2013-10-01

    SolTrace is an optical simulation tool designed to model optical systems used in concentrating solar power (CSP) applications. The code was first written in early 2003, but has seen significant modifications and changes since its inception, including conversion from a Pascal-based software development platform to C++. SolTrace is unique in that it can model virtually any optical system utilizingthe sun as the source. It has been made available for free and as such is in use worldwide by industry, universities, and research laboratories. The fundamental design of the code is discussed, including enhancements and improvements over the earlier version. Comparisons are made with other optical modeling tools, both non-commercial and commercial in nature. Finally, modeled results are shownfor some typical CSP systems and, in one case, compared to measured optical data.

  16. The Genetic Code: Yesterday, Today and Tomorrow

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 17; Issue 12. The Genetic Code: Yesterday, Today and Tomorrow. Jiqiang Ling Dieter Söll. General Article Volume 17 Issue 12 December 2012 pp 1136-1142. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

    Science.gov (United States)

    Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

    2018-01-01

    The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

  18. Representation mutations from standard genetic codes

    Science.gov (United States)

    Aisah, I.; Suyudi, M.; Carnia, E.; Suhendi; Supriatna, A. K.

    2018-03-01

    Graph is widely used in everyday life especially to describe model problem and describe it concretely and clearly. In addition graph is also used to facilitate solve various kinds of problems that are difficult to be solved by calculation. In Biology, graph can be used to describe the process of protein synthesis in DNA. Protein has an important role for DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). Proteins are composed of amino acids. In this study, amino acids are related to genetics, especially the genetic code. The genetic code is also known as the triplet or codon code which is a three-letter arrangement of DNA nitrogen base. The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). While on RNA thymine (T) is replaced with Urasil (U). The set of all Nitrogen bases in RNA is denoted by N = {C U, A, G}. This codon works at the time of protein synthesis inside the cell. This codon also encodes the stop signal as a sign of the stop of protein synthesis process. This paper will examine the process of protein synthesis through mathematical studies and present it in three-dimensional space or graph. The study begins by analysing the set of all codons denoted by NNN such that to obtain geometric representations. At this stage there is a matching between the sets of all nitrogen bases N with Z 2 × Z 2; C=(\\overline{0},\\overline{0}),{{U}}=(\\overline{0},\\overline{1}),{{A}}=(\\overline{1},\\overline{0}),{{G}}=(\\overline{1},\\overline{1}). By matching the algebraic structure will be obtained such as group, group Klein-4,Quotien group etc. With the help of Geogebra software, the set of all codons denoted by NNN can be presented in a three-dimensional space as a multicube NNN and also can be represented as a graph, so that can easily see relationship between the codon.

  19. HOW TO REPRESENT THE GENETIC CODE?

    Directory of Open Access Journals (Sweden)

    N.S. Santos-Magalhães

    2004-05-01

    Full Text Available The advent of molecular genetic comprises a true revolution of far-reaching consequences for human-kind, which evolved into a specialized branch of the modern-day Biochemistry. The analysis of specicgenomic information are gaining wide-ranging interest because of their signicance to the early diag-nosis of disease, and the discovery of modern drugs. In order to take advantage of a wide assortmentof signal processing (SP algorithms, the primary step of modern genomic SP involves convertingsymbolic-DNA sequences into complex-valued signals. How to represent the genetic code? Despitebeing extensively known, the DNA mapping into proteins is one of the relevant discoveries of genetics.The genetic code (GC is revisited in this work, addressing other descriptions for it, which can beworthy for genomic SP. Three original representations are discussed. The inner-to-outer map buildson the unbalanced role of nucleotides of a codon. A two-dimensional-Gray genetic representationis oered as a structured map that can help interpreting DNA spectrograms or scalograms. Theseare among the powerful visual tools for genome analysis, which depends on the choice of the geneticmapping. Finally, the world-chart for the GC is investigated. Evoking the cyclic structure of thegenetic mapping, it can be folded joining the left-right borders, and the top-bottom frontiers. As aresult, the GC can be drawn on the surface of a sphere resembling a world-map. Eight parallels oflatitude are required (four in each hemisphere as well as four meridians of longitude associated tofour corresponding anti-meridians. The tropic circles have 11.25o, 33.75o, 56.25o, and 78.5o (Northand South. Starting from an arbitrary Greenwich meridian, the meridians of longitude can be plottedat 22.5o, 67.5o, 112.5o, and 157.5o (East and West. Each triplet is assigned to a single point on thesurface that we named Nirenberg-Kohamas Earth. Despite being valuable, usual representations forthe GC can be

  20. A Realistic Model under which the Genetic Code is Optimal

    NARCIS (Netherlands)

    Buhrman, H.; van der Gulik, P.T.S.; Klau, G.W.; Schaffner, C.; Speijer, D.; Stougie, L.

    2013-01-01

    The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the mean square measure as a function quantifying error robustness, a value can be obtained for a genetic code which reflects the error robustness of that code. By

  1. Flexibility of the genetic code with respect to DNA structure

    DEFF Research Database (Denmark)

    Baisnée, P. F.; Baldi, Pierre; Brunak, Søren

    2001-01-01

    Motivation. The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA...... structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding...... sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure? Results. We develop an index for code flexibility with respect to DNA structure. Using five different di- or tri-nucleotide models of sequence-dependent DNA structure, we show...

  2. Simulation of the turbine discharge transient with the code Trace; Simulacion del transitorio disparo de turbina con el codigo TRACE

    Energy Technology Data Exchange (ETDEWEB)

    Mejia S, D. M.; Filio L, C., E-mail: dulcemaria.mejia@cnsns.gob.mx [Comision Nacional de Seguridad Nuclear y Salvaguardias, Dr. Jose Ma. Barragan No. 779, Col. Narvarte, 03020 Mexico D. F. (Mexico)

    2014-10-15

    In this paper the results of the simulation of the turbine discharge transient are shown, occurred in Unit 1 of nuclear power plant of Laguna Verde (NPP-L V), carried out with the model of this unit for the best estimate code Trace. The results obtained by the code Trace are compared with those obtained from the Process Information Integral System (PIIS) of the NPP-L V. The reactor pressure, level behavior in the down-comer, steam flow and flow rate through the recirculation circuits are compared. The results of the simulation for the operation power of 2027 MWt, show concordance with the system PIIS. (Author)

  3. A multiobjective approach to the genetic code adaptability problem.

    Science.gov (United States)

    de Oliveira, Lariza Laura; de Oliveira, Paulo S L; Tinós, Renato

    2015-02-19

    The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why exactly the canonical code was selected among this huge number of possible genetic codes. Many researchers argue that the organization of the canonical code is a product of natural selection and that the code's robustness against mutations would support this hypothesis. In order to investigate the natural selection hypothesis, some researches employ optimization algorithms to identify regions of the genetic code space where best codes, according to a given evaluation function, can be found (engineering approach). The optimization process uses only one objective to evaluate the codes, generally based on the robustness for an amino acid property. Only one objective is also employed in the statistical approach for the comparison of the canonical code with random codes. We propose a multiobjective approach where two or more objectives are considered simultaneously to evaluate the genetic codes. In order to test our hypothesis that the multiobjective approach is useful for the analysis of the genetic code adaptability, we implemented a multiobjective optimization algorithm where two objectives are simultaneously optimized. Using as objectives the robustness against mutation with the amino acids properties polar requirement (objective 1) and robustness with respect to hydropathy index or molecular volume (objective 2), we found solutions closer to the canonical genetic code in terms of robustness, when compared with the results using only one objective reported by other authors. Using more objectives, more optimal solutions are obtained and, as a consequence, more information can be used to investigate the adaptability of the genetic code. The multiobjective approach

  4. National Society of Genetic Counselors Code of Ethics.

    Science.gov (United States)

    2018-02-01

    This document is the revised Code of Ethics of the National Society of Genetic Counselors (NSGC) that was adopted in April 2017 after majority vote of the full membership of the NSGC. The explication of the revisions is published in this volume of the Journal of Genetic Counseling. This is the fourth revision to the Code of Ethics since its original adoption in 1992.

  5. Divided multimodal attention sensory trace and context coding strategies in spatially congruent auditory and visual presentation.

    Science.gov (United States)

    Kristjánsson, Tómas; Thorvaldsson, Tómas Páll; Kristjánsson, Arni

    2014-01-01

    Previous research involving both unimodal and multimodal studies suggests that single-response change detection is a capacity-free process while a discriminatory up or down identification is capacity-limited. The trace/context model assumes that this reflects different memory strategies rather than inherent differences between identification and detection. To perform such tasks, one of two strategies is used, a sensory trace or a context coding strategy, and if one is blocked, people will automatically use the other. A drawback to most preceding studies is that stimuli are presented at separate locations, creating the possibility of a spatial confound, which invites alternative interpretations of the results. We describe a series of experiments, investigating divided multimodal attention, without the spatial confound. The results challenge the trace/context model. Our critical experiment involved a gap before a change in volume and brightness, which according to the trace/context model blocks the sensory trace strategy, simultaneously with a roaming pedestal, which should block the context coding strategy. The results clearly show that people can use strategies other than sensory trace and context coding in the tasks and conditions of these experiments, necessitating changes to the trace/context model.

  6. A search for symmetries in the genetic code

    International Nuclear Information System (INIS)

    Hornos, J.E.M.; Hornos, Y.M.M.

    1991-01-01

    A search for symmetries based on the classification theorem of Cartan for the compact simple Lie algebras is performed to verify to what extent the genetic code is a manifestation of some underlying symmetry. An exact continuous symmetry group cannot be found to reproduce the present, universal code. However a unique approximate symmetry group is compatible with codon assignment for the fundamental amino acids and the termination codon. In order to obtain the actual genetic code, the symmetry must be slightly broken. (author). 27 refs, 3 figs, 6 tabs

  7. The evolution of the mitochondrial genetic code in arthropods revisited.

    Science.gov (United States)

    Abascal, Federico; Posada, David; Zardoya, Rafael

    2012-04-01

    A variant of the invertebrate mitochondrial genetic code was previously identified in arthropods (Abascal et al. 2006a, PLoS Biol 4:e127) in which, instead of translating the AGG codon as serine, as in other invertebrates, some arthropods translate AGG as lysine. Here, we revisit the evolution of the genetic code in arthropods taking into account that (1) the number of arthropod mitochondrial genomes sequenced has triplicated since the original findings were published; (2) the phylogeny of arthropods has been recently resolved with confidence for many groups; and (3) sophisticated probabilistic methods can be applied to analyze the evolution of the genetic code in arthropod mitochondria. According to our analyses, evolutionary shifts in the genetic code have been more common than previously inferred, with many taxonomic groups displaying two alternative codes. Ancestral character-state reconstruction using probabilistic methods confirmed that the arthropod ancestor most likely translated AGG as lysine. Point mutations at tRNA-Lys and tRNA-Ser correlated with the meaning of the AGG codon. In addition, we identified three variables (GC content, number of AGG codons, and taxonomic information) that best explain the use of each of the two alternative genetic codes.

  8. Mathematical fundamentals for the noise immunity of the genetic code.

    Science.gov (United States)

    Fimmel, Elena; Strüngmann, Lutz

    2018-02-01

    Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept. The genetic code can be seen as a key to biological self-organisation. All living organisms have the same molecular bases - an alphabet consisting of four letters (nitrogenous bases): adenine, cytosine, guanine, and thymine. Linearly ordered sequences of these bases contain the genetic information for synthesis of proteins in all forms of life. Thus, one of the most fascinating riddles of nature is to explain why the genetic code is as it is. Genetic coding possesses noise immunity which is the fundamental feature that allows to pass on the genetic information from parents to their descendants. Hence, since the time of the discovery of the genetic code, scientists have tried to explain the noise immunity of the genetic information. In this chapter we will discuss recent results in mathematical modelling of the genetic code with respect to noise immunity, in particular error-detection and error-correction. We will focus on two central properties: Degeneracy and frameshift correction. Different amino acids are encoded by different quantities of codons and a connection between this degeneracy and the noise immunity of genetic information is a long standing hypothesis. Biological implications of the degeneracy have been intensively studied and whether the natural code is a frozen accident or a highly optimised product of evolution is still controversially discussed. Symmetries in the structure of

  9. Unnatural reactive amino acid genetic code additions

    Energy Technology Data Exchange (ETDEWEB)

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, Christopher J.; Schultz, Peter G.

    2017-10-25

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  10. Quantum algorithms and the genetic code

    Indian Academy of Sciences (India)

    the process of replication. One generation of organisms produces the next generation, which is essentially a copy of itself. The self-similarity is maintained by the hereditary information—the genetic code—that is passed on from one generation to the next. The long chains of DNA molecules residing in the nuclei of the cells ...

  11. High fidelity analysis of BWR fuel assembly with COBRA-TF/PARCS and trace codes

    International Nuclear Information System (INIS)

    Abarca, A.; Miro, R.; Barrachina, T.; Verdu, G.; Soler, A.

    2013-01-01

    The growing importance of detailed reactor core and fuel assembly description for light water reactors (LWRs) as well as the sub-channel safety analysis requires high fidelity models and coupled neutronic/thermalhydraulic codes. Hand in hand with advances in the computer technology, the nuclear safety analysis is beginning to use a more detailed thermal hydraulics and neutronics. Previously, a PWR core and a 16 by 16 fuel assembly models were developed to test and validate our COBRA-TF/PARCS v2.7 (CTF/PARCS) coupled code. In this work, a comparison of the modeling and simulation advantages and disadvantages of modern 10 by 10 BWR fuel assembly with CTF/PARCS and TRACE codes has been done. The objective of the comparison is making known the main advantages of using the sub-channel codes to perform high resolution nuclear safety analysis. The sub-channel codes, like CTF, permits obtain accurate predictions, in two flow regime, of the thermalhydraulic parameters important to safety with high local resolution. The modeled BWR fuel assembly has 91 fuel rods (81 full length and 10 partial length fuel rods) and a big square central water rod. This assembly has been modeled with high level of detail with CTF code and using the BWR modeling parameters provided by TRACE. The same neutronic PARCS's model has been used for the simulation with both codes. To compare the codes a coupled steady state has be performed. (author)

  12. Deciphering the genetic regulatory code using an inverse error control coding framework.

    Energy Technology Data Exchange (ETDEWEB)

    Rintoul, Mark Daniel; May, Elebeoba Eni; Brown, William Michael; Johnston, Anna Marie; Watson, Jean-Paul

    2005-03-01

    We have found that developing a computational framework for reconstructing error control codes for engineered data and ultimately for deciphering genetic regulatory coding sequences is a challenging and uncharted area that will require advances in computational technology for exact solutions. Although exact solutions are desired, computational approaches that yield plausible solutions would be considered sufficient as a proof of concept to the feasibility of reverse engineering error control codes and the possibility of developing a quantitative model for understanding and engineering genetic regulation. Such evidence would help move the idea of reconstructing error control codes for engineered and biological systems from the high risk high payoff realm into the highly probable high payoff domain. Additionally this work will impact biological sensor development and the ability to model and ultimately develop defense mechanisms against bioagents that can be engineered to cause catastrophic damage. Understanding how biological organisms are able to communicate their genetic message efficiently in the presence of noise can improve our current communication protocols, a continuing research interest. Towards this end, project goals include: (1) Develop parameter estimation methods for n for block codes and for n, k, and m for convolutional codes. Use methods to determine error control (EC) code parameters for gene regulatory sequence. (2) Develop an evolutionary computing computational framework for near-optimal solutions to the algebraic code reconstruction problem. Method will be tested on engineered and biological sequences.

  13. Simulation of the KAERI PASCAL Test with MARS-KS and TRACE Codes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kyung Won; Cheong, Aeju; Shin, Andong; Cho, Min Ki [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2016-10-15

    In order to validate the operational performance of the PAFS, KAERI has performed the experimental investigation using the PASCAL (PAFS Condensing heat removal Assessment Loop) facility. In this study, we simulated the KAERI PASCAL SS-540-P1 test with MARS-KS V1.4 and TRACE V5.0 p4 codes to assess the code predictability for the condensation heat transfer inside the passive auxiliary feedwater system. We simulated the KAERI PASCAL SS-540-P1 test with MARS-KS V1.4 and TRACE V5.0 p4 codes to assess the code predictability for the condensation heat transfer inside the passive auxiliary feedwater system. The calculated results of heat flux, inner wall surface temperature of the condensing tube, fluid temperature, and steam mass flow rate are compared with the experimental data. The result shows that the MARS-KS generally under-predict the heat fluxes. The TRACE over-predicts the heat flux at tube inlet region and under-predicts it at tube outlet region. The TRACE prediction shows larger amount of steam condensation by about 3% than the MARS-KS prediction.

  14. Real coded genetic algorithm for fuzzy time series prediction

    Science.gov (United States)

    Jain, Shilpa; Bisht, Dinesh C. S.; Singh, Phool; Mathpal, Prakash C.

    2017-10-01

    Genetic Algorithm (GA) forms a subset of evolutionary computing, rapidly growing area of Artificial Intelligence (A.I.). Some variants of GA are binary GA, real GA, messy GA, micro GA, saw tooth GA, differential evolution GA. This research article presents a real coded GA for predicting enrollments of University of Alabama. Data of Alabama University is a fuzzy time series. Here, fuzzy logic is used to predict enrollments of Alabama University and genetic algorithm optimizes fuzzy intervals. Results are compared to other eminent author works and found satisfactory, and states that real coded GA are fast and accurate.

  15. On the Organizational Dynamics of the Genetic Code

    KAUST Repository

    Zhang, Zhang

    2011-06-07

    The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

  16. On the Organizational Dynamics of the Genetic Code

    KAUST Repository

    Zhang, Zhang; Yu, Jun

    2011-01-01

    The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

  17. Tracing the origin of 'blue Weimaraner' dogs by molecular genetics.

    Science.gov (United States)

    Gerding, W M; Schreiber, S; Dekomien, G; Epplen, J T

    2011-04-01

    Weimaraner dogs are defined by light brown coat colour termed grey including several shadings ranging from silver and deer to mouse grey. In contrast, the so-called blue Weimaraners (BW) with lightened black-pigmented coat have been proposed to represent spontaneous revertants in the Weimaraner breed. In order to investigate the genetic determinants of the characteristic grey coat colour versus those of BW, known variation in coat colour genes including TYRP1 and MLPH were analysed in a number of grey and blue dogs. Variations at the B locus cause grey coat colour in Weimaraners via two non-functional TYRP1 copies (bb) including the b(s), b(d) and b(c) alleles. In all BW, at least one functional TYRP1 allele (Bb or BB genotype) was identified. Defined microsatellite alleles in TYRP1 intron 4 are linked to this functional B allele in BW. These alleles were also detected in various other dog breeds, but not in grey Weimaraners. The combination of a dominant trait for blue versus grey together with a specific TYRP1 haplotype in BW suggests that blue coat colour is not the result of spontaneous (back-) mutation in grey Weimaraners. This inference is even emphasized by the presence of a unique Y-chomosomal haplotype in a male offspring of the supposed ancestor of the BW population which - according to pedigree information - carries a copy of the original Y chromosome. Thus, molecular genetic analyses of coat colours combined with Y-chromosomal haplotypes allow tracing the origin of atypical dogs in respective canine populations. © 2010 Blackwell Verlag GmbH.

  18. Origins of gene, genetic code, protein and life

    Indian Academy of Sciences (India)

    Unknown

    have concluded that newly-born genes are products of nonstop frames (NSF) ... research to determine tertiary structures of proteins such ... the present earth, is favourable for new genes to arise, if ..... NGG) in the universal genetic code table, cannot satisfy ..... which has been proposed to explain the development of life on.

  19. The Search for Symmetries in the Genetic Code:

    Science.gov (United States)

    Antoneli, Fernando; Forger, Michael; Hornos, José Eduardo M.

    We give a full classification of the possible schemes for obtaining the distribution of multiplets observed in the standard genetic code by symmetry breaking in the context of finite groups, based on an extended notion of partial symmetry breaking that incorporates the intuitive idea of "freezing" first proposed by Francis Crick, which is given a precise mathematical meaning.

  20. CMCpy: Genetic Code-Message Coevolution Models in Python

    Science.gov (United States)

    Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

    2013-01-01

    Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

  1. TRACE/VALKIN: a neutronics-thermohydraulics coupled code to analyze strong 3D transients

    Energy Technology Data Exchange (ETDEWEB)

    Rafael Miro; Gumersindo Verdu; Ana Maria Sanchez [Chemical and Nuclear Engineering Department. Polytechnic University of Valencia. Cami de Vera s/n. 46022 Valencia (Spain); Damian Ginestar [Applied Mathematics Department. Polytechnic University of Valencia. Cami de Vera s/n. 46022 Valencia (Spain)

    2005-07-01

    Full text of publication follows: A nuclear reactor simulator consists mainly of two different blocks, which solve the models used for the basic physical phenomena taking place in the reactor. In this way, there is a neutronic module which simulates the neutron balance in the reactor core, and a thermal-hydraulics module, which simulates the heat transfer in the fuel, the heat transfer from the fuel to the water, and the different condensation and evaporation processes taking place in the reactor core and in the condenser systems. TRACE is a two-phase, two-fluid thermal-hydraulic reactor systems analysis code. The TRACE acronym stands for TRAC/RELAP Advanced Computational Engine, reflecting its ability to run both RELAP5 and TRAC legacy input models. It includes a three-dimensional kinetics module called PARCS for performing advanced analysis of coupled core thermal-hydraulic/kinetics problems. TRACE-VALKIN code is a new time domain analysis code to study transients in LWR reactors. This code uses the best estimate code TRACE to give account of the heat transfer and thermal-hydraulic processes, and a 3D neutronics module. This module has two options, the MODKIN option that makes use of a modal method based on the assumption that the neutronic flux can be approximately expanded in terms of the dominant lambda modes associated with a static configuration of the reactor core, and the NOKIN option that uses a one-step backward discretization of the neutron diffusion equation. The lambda modes are obtained using the Implicit Restarted Arnoldi approach or the Jacob-Davidson algorithm. To check the performance of the coupled code TRACE-VALKIN against complex 3D neutronic transients, using the cross-sections tables generated with the translator SIMTAB from SIMULATE to TRACE/VALKIN, the Cofrentes NPP SCRAM-61 transient is simulated. Cofrentes NPP is a General Electric BWR-6 design located in Valencia-land (Spain). It is in operation since 1985 and currently in its fifteenth

  2. Assessment of GOTHIC and TRACE codes against selected PANDA experiments on a Passive Containment Condenser

    Energy Technology Data Exchange (ETDEWEB)

    Papini, Davide, E-mail: davide.papini@psi.ch; Adamsson, Carl; Andreani, Michele; Prasser, Horst-Michael

    2014-10-15

    Highlights: • Code comparison on the performance of a Passive Containment Condenser. • Simulation of separate effect tests with pure steam and non-condensable gases. • Role of the secondary side and accuracy of pool boiling models are discussed. • GOTHIC and TRACE predict the experimental performance with slight underestimation. • Recirculatory flow pattern with injection of light non-condensable gas is inferred. - Abstract: Typical passive safety systems for ALWRs (Advanced Light Water Reactors) rely on the condensation of steam to remove the decay heat from the core or the containment. In the present paper the three-dimensional containment code GOTHIC and the one-dimensional system code TRACE are compared on the calculation of a variety of phenomena characterizing the response of a passive condenser submerged in a boiling pool. The investigation addresses the conditions of interest for the Passive Containment Cooling System (PCCS) proposed for the ESBWR (Economic Simplified Boiling Water Reactor). The analysis of selected separate effect tests carried out on a PCC (Passive Containment Condenser) unit in the PANDA large-scale thermal-hydraulic facility is presented to assess the code predictions. Both pure steam conditions (operating pressure of 3 bar, 6 bar and 9 bar) and the effect on the condensation heat transfer of non-condensable gases heavier than steam (air) and lighter than steam (helium) are considered. The role of the secondary side (pool side) heat transfer on the condenser performance is examined too. In general, this study shows that both the GOTHIC and TRACE codes are able to reasonably predict the heat transfer capability of the PCC as well as the influence of non-condensable gas on the system. A slight underestimation of the condenser performance is obtained with both codes. For those tests where the experimental and simulated efficiencies agree better the possibility of compensating errors among different parts of the heat transfer

  3. Adaptation and implementation of the TRACE code for transient analysis in designs lead cooled fast reactors

    International Nuclear Information System (INIS)

    Lazaro, A.; Ammirabile, L.; Martorell, S.

    2015-01-01

    Lead-Cooled Fast Reactor (LFR) has been identified as one of promising future reactor concepts in the technology road map of the Generation IVC International Forum (GIF)as well as in the Deployment Strategy of the European Sustainable Nuclear Industrial Initiative (ESNII), both aiming at improved sustainability, enhanced safety, economic competitiveness, and proliferation resistance. This new nuclear reactor concept requires the development of computational tools to be applied in design and safety assessments to confirm improved inherent and passive safety features of this design. One approach to this issue is to modify the current computational codes developed for the simulation of Light Water Reactors towards their applicability for the new designs. This paper reports on the performed modifications of the TRACE system code to make it applicable to LFR safety assessments. The capabilities of the modified code are demonstrated on series of benchmark exercises performed versus other safety analysis codes. (Author)

  4. Digitized forensics: retaining a link between physical and digital crime scene traces using QR-codes

    Science.gov (United States)

    Hildebrandt, Mario; Kiltz, Stefan; Dittmann, Jana

    2013-03-01

    The digitization of physical traces from crime scenes in forensic investigations in effect creates a digital chain-of-custody and entrains the challenge of creating a link between the two or more representations of the same trace. In order to be forensically sound, especially the two security aspects of integrity and authenticity need to be maintained at all times. Especially the adherence to the authenticity using technical means proves to be a challenge at the boundary between the physical object and its digital representations. In this article we propose a new method of linking physical objects with its digital counterparts using two-dimensional bar codes and additional meta-data accompanying the acquired data for integration in the conventional documentation of collection of items of evidence (bagging and tagging process). Using the exemplary chosen QR-code as particular implementation of a bar code and a model of the forensic process, we also supply a means to integrate our suggested approach into forensically sound proceedings as described by Holder et al.1 We use the example of the digital dactyloscopy as a forensic discipline, where currently progress is being made by digitizing some of the processing steps. We show an exemplary demonstrator of the suggested approach using a smartphone as a mobile device for the verification of the physical trace to extend the chain-of-custody from the physical to the digital domain. Our evaluation of the demonstrator is performed towards the readability and the verification of its contents. We can read the bar code despite its limited size of 42 x 42 mm and rather large amount of embedded data using various devices. Furthermore, the QR-code's error correction features help to recover contents of damaged codes. Subsequently, our appended digital signature allows for detecting malicious manipulations of the embedded data.

  5. Two-phase wall friction model for the trace computer code

    International Nuclear Information System (INIS)

    Wang Weidong

    2005-01-01

    The wall drag model in the TRAC/RELAP5 Advanced Computational Engine computer code (TRACE) has certain known deficiencies. For example, in an annular flow regime, the code predicts an unphysical high liquid velocity compared to the experimental data. To address those deficiencies, a new wall frictional drag package has been developed and implemented in the TRACE code to model the wall drag for two-phase flow system code. The modeled flow regimes are (1) annular/mist, (2) bubbly/slug, and (3) bubbly/slug with wall nucleation. The new models use void fraction (instead of flow quality) as the correlating variable to minimize the calculation oscillation. In addition, the models allow for transitions between the three regimes. The annular/mist regime is subdivided into three separate regimes for pure annular flow, annular flow with entrainment, and film breakdown. For adiabatic two-phase bubbly/slug flows, the vapor phase primarily exists outside of the boundary layer, and the wall shear uses single-phase liquid velocity for friction calculation. The vapor phase wall friction drag is set to zero for bubbly/slug flows. For bubbly/slug flows with wall nucleation, the bubbles are presented within the hydrodynamic boundary layer, and the two-phase wall friction drag is significantly higher with a pronounced mass flux effect. An empirical correlation has been studied and applied to account for nucleate boiling. Verification and validation tests have been performed, and the test results showed a significant code improvement. (authors)

  6. Programming peptidomimetic syntheses by translating genetic codes designed de novo.

    Science.gov (United States)

    Forster, Anthony C; Tan, Zhongping; Nalam, Madhavi N L; Lin, Hening; Qu, Hui; Cornish, Virginia W; Blacklow, Stephen C

    2003-05-27

    Although the universal genetic code exhibits only minor variations in nature, Francis Crick proposed in 1955 that "the adaptor hypothesis allows one to construct, in theory, codes of bewildering variety." The existing code has been expanded to enable incorporation of a variety of unnatural amino acids at one or two nonadjacent sites within a protein by using nonsense or frameshift suppressor aminoacyl-tRNAs (aa-tRNAs) as adaptors. However, the suppressor strategy is inherently limited by compatibility with only a small subset of codons, by the ways such codons can be combined, and by variation in the efficiency of incorporation. Here, by preventing competing reactions with aa-tRNA synthetases, aa-tRNAs, and release factors during translation and by using nonsuppressor aa-tRNA substrates, we realize a potentially generalizable approach for template-encoded polymer synthesis that unmasks the substantially broader versatility of the core translation apparatus as a catalyst. We show that several adjacent, arbitrarily chosen sense codons can be completely reassigned to various unnatural amino acids according to de novo genetic codes by translating mRNAs into specific peptide analog polymers (peptidomimetics). Unnatural aa-tRNA substrates do not uniformly function as well as natural substrates, revealing important recognition elements for the translation apparatus. Genetic programming of peptidomimetic synthesis should facilitate mechanistic studies of translation and may ultimately enable the directed evolution of small molecules with desirable catalytic or pharmacological properties.

  7. On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

    Directory of Open Access Journals (Sweden)

    Wang Tao

    2011-09-01

    Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

  8. The genetic code as a periodic table: algebraic aspects.

    Science.gov (United States)

    Bashford, J D; Jarvis, P D

    2000-01-01

    The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

  9. A versatile ray-tracing code for studying rf wave propagation in toroidal magnetized plasmas

    International Nuclear Information System (INIS)

    Peysson, Y; Decker, J; Morini, L

    2012-01-01

    A new ray-tracing code named C3PO has been developed to study the propagation of arbitrary electromagnetic radio-frequency (rf) waves in magnetized toroidal plasmas. Its structure is designed for maximum flexibility regarding the choice of coordinate system and dielectric model. The versatility of this code makes it particularly suitable for integrated modeling systems. Using a coordinate system that reflects the nested structure of magnetic flux surfaces in tokamaks, fast and accurate calculations inside the plasma separatrix can be performed using analytical derivatives of a spline-Fourier interpolation of the axisymmetric toroidal MHD equilibrium. Applications to reverse field pinch magnetic configuration are also included. The effects of 3D perturbations of the axisymmetric toroidal MHD equilibrium, due to the discreteness of the magnetic coil system or plasma fluctuations in an original quasi-optical approach, are also studied. Using a Runge–Kutta–Fehlberg method for solving the set of ordinary differential equations, the ray-tracing code is extensively benchmarked against analytical models and other codes for lower hybrid and electron cyclotron waves. (paper)

  10. The "Wow! signal" of the terrestrial genetic code

    Science.gov (United States)

    shCherbak, Vladimir I.; Makukov, Maxim A.

    2013-05-01

    It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like "signal" in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of

  11. Comparative study of boron transport models in NRC Thermal-Hydraulic Code Trace

    Energy Technology Data Exchange (ETDEWEB)

    Olmo-Juan, Nicolás; Barrachina, Teresa; Miró, Rafael; Verdú, Gumersindo; Pereira, Claubia, E-mail: nioljua@iqn.upv.es, E-mail: tbarrachina@iqn.upv.es, E-mail: rmiro@iqn.upv.es, E-mail: gverdu@iqn.upv.es, E-mail: claubia@nuclear.ufmg.br [Institute for Industrial, Radiophysical and Environmental Safety (ISIRYM). Universitat Politècnica de València (Spain); Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Nuclear

    2017-07-01

    Recently, the interest in the study of various types of transients involving changes in the boron concentration inside the reactor, has led to an increase in the interest of developing and studying new models and tools that allow a correct study of boron transport. Therefore, a significant variety of different boron transport models and spatial difference schemes are available in the thermal-hydraulic codes, as TRACE. According to this interest, in this work it will be compared the results obtained using the different boron transport models implemented in the NRC thermal-hydraulic code TRACE. To do this, a set of models have been created using the different options and configurations that could have influence in boron transport. These models allow to reproduce a simple event of filling or emptying the boron concentration in a long pipe. Moreover, with the aim to compare the differences obtained when one-dimensional or three-dimensional components are chosen, it has modeled many different cases using only pipe components or a mix of pipe and vessel components. In addition, the influence of the void fraction in the boron transport has been studied and compared under close conditions to BWR commercial model. A final collection of the different cases and boron transport models are compared between them and those corresponding to the analytical solution provided by the Burgers equation. From this comparison, important conclusions are drawn that will be the basis of modeling the boron transport in TRACE adequately. (author)

  12. Neutronic / thermal-hydraulic coupling with the code system Trace / Parcs

    International Nuclear Information System (INIS)

    Mejia S, D. M.; Del Valle G, E.

    2015-09-01

    The developed models for Parcs and Trace codes corresponding for the cycle 15 of the Unit 1 of the Laguna Verde nuclear power plant are described. The first focused to the neutronic simulation and the second to thermal hydraulics. The model developed for Parcs consists of a core of 444 fuel assemblies wrapped in a radial reflective layer and two layers, a superior and another inferior, of axial reflector. The core consists of 27 total axial planes. The model for Trace includes the vessel and its internal components as well as various safety systems. The coupling between the two codes is through two maps that allow its intercommunication. Both codes are used in coupled form performing a dynamic simulation that allows obtaining acceptably a stable state from which is carried out the closure of all the main steam isolation valves (MSIVs) followed by the performance of safety relief valves (SRVs) and ECCS. The results for the power and reactivities introduced by the moderator density, the fuel temperature and total temperature are shown. Data are also provided like: the behavior of the pressure in the steam dome, the water level in the downcomer, the flow through the MSIVs and SRVs. The results are explained for the power, the pressure in the steam dome and the water level in the downcomer which show agreement with the actions of the MSIVs, SRVs and ECCS. (Author)

  13. Related research with thermo hydraulics safety by means of Trace code; Investigaciones relacionadas con seguridad termohidraulica con el codigo TRACE

    Energy Technology Data Exchange (ETDEWEB)

    Chaparro V, F. J.; Del Valle G, E. [IPN, Escuela Superior de Fisica y Matematicas, UP - Adolfo Lopez Mateos, Edif. 9, 07738 Mexico D. F. (Mexico); Rodriguez H, A.; Gomez T, A. M. [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico); Sanchez E, V. H.; Jager, W., E-mail: evalle@esfm.ipn.mx [Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz I, D-76344 Eggenstein - Leopoldshafen (Germany)

    2014-10-15

    In this article the results of the design of a pressure vessel of a BWR/5 similar to the type of Laguna Verde NPP are presented, using the Trace code. A thermo hydraulics Vessel component capable of simulating the behavior of fluids and heat transfer that occurs within the reactor vessel was created. The Vessel component consists of a three-dimensional cylinder divided into 19 axial sections, 4 azimuthal sections and two concentric radial rings. The inner ring is used to contain the core and the central part of the reactor, while the outer ring is used as a down comer. Axial an azimuthal divisions were made with the intention that the dimensions of the internal components, heights and orientation of the external connections match the reference values of a reactor BWR/5 type. In the model internal components as, fuel assemblies, steam separators, jet pumps, guide tubes, etc. are included and main external connections as, steam lines, feed-water or penetrations of the recirculation system. The model presents significant simplifications because the object is to keep symmetry between each azimuthal section of the vessel. In most internal components lack a detailed description of the geometry and initial values of temperature, pressure, fluid velocity, etc. given that it only considered the most representative data, however with these simulations are obtained acceptable results in important parameters such as the total flow through the core, the pressure in the vessel, percentage of vacuums fraction, pressure drop in the core and the steam separators. (Author)

  14. A symbiotic liaison between the genetic and epigenetic code

    Directory of Open Access Journals (Sweden)

    Holger eHeyn

    2014-05-01

    Full Text Available With rapid advances in sequencing technologies, we are undergoing a paradigm shift from hypothesis- to data-driven research. Genome-wide profiling efforts gave informative insights into biological processes; however, considering the wealth of variation, the major challenge remains their meaningful interpretation. In particular sequence variation in non-coding contexts is often challenging to interpret. Here, data integration approaches for the identification of functional genetic variability represent a likely solution. Exemplary, functional linkage analysis integrating genotype and expression data determined regulatory quantitative trait loci (QTL and proposed causal relationships. In addition to gene expression, epigenetic regulation and specifically DNA methylation was established as highly valuable surrogate mark for functional variance of the genetic code. Epigenetic modification served as powerful mediator trait to elucidate mechanisms forming phenotypes in health and disease. Particularly, integrative studies of genetic and DNA methylation data yet guided interpretation strategies of risk genotypes, but also proved their value for physiological traits, such as natural human variation and aging. This Perspective seeks to illustrate the power of data integration in the genomic era exemplified by DNA methylation quantitative trait loci (meQTLs. However, the model is further extendable to virtually all traceable molecular traits.

  15. Developments in the ray-tracing code Zgoubi for 6-D multiturn tracking in FFAG rings

    International Nuclear Information System (INIS)

    Lemuet, F.; Meot, F.

    2005-01-01

    A geometrical method for 3-D modeling of the magnetic field in scaling and non-scaling FFAG magnets has been installed in the ray-tracing code Zgoubi. The method in particular allows a good simulation of transverse non-linearities, of field fall-offs and possible merging fields in configurations of neighboring magnets, while using realistic models of magnetic fields. That yields an efficient tool for FFAG lattice design and optimizations, and for 6-D tracking studies. It is applied for illustration to the simulation of an acceleration cycle in a 150 MeV radial sector proton FFAG

  16. On Francis Crick, the genetic code, and a clever kid.

    Science.gov (United States)

    Goldstein, Bob

    2018-04-02

    A few years ago, Francis Crick's son told me a story that I can't get out of my mind. I had contacted Michael Crick by email while digging through the background of the researchers who had cracked the genetic code in the 1960s. Francis had died in 2004, and I was contacting some of the people who knew him when he was struggling to decipher the code. Francis didn't appear to struggle often - he is known mostly for his successes - and, as it turns out, this one well-known struggle may have had a clue sitting just barely out of sight. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Quantum control using genetic algorithms in quantum communication: superdense coding

    International Nuclear Information System (INIS)

    Domínguez-Serna, Francisco; Rojas, Fernando

    2015-01-01

    We present a physical example model of how Quantum Control with genetic algorithms is applied to implement the quantum superdense code protocol. We studied a model consisting of two quantum dots with an electron with spin, including spin-orbit interaction. The electron and the spin get hybridized with the site acquiring two degrees of freedom, spin and charge. The system has tunneling and site energies as time dependent control parameters that are optimized by means of genetic algorithms to prepare a hybrid Bell-like state used as a transmission channel. This state is transformed to obtain any state of the four Bell basis as required by superdense protocol to transmit two bits of classical information. The control process protocol is equivalent to implement one of the quantum gates in the charge subsystem. Fidelities larger than 99.5% are achieved for the hybrid entangled state preparation and the superdense operations. (paper)

  18. GRay: A MASSIVELY PARALLEL GPU-BASED CODE FOR RAY TRACING IN RELATIVISTIC SPACETIMES

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Chi-kwan; Psaltis, Dimitrios; Özel, Feryal [Department of Astronomy, University of Arizona, 933 N. Cherry Ave., Tucson, AZ 85721 (United States)

    2013-11-01

    We introduce GRay, a massively parallel integrator designed to trace the trajectories of billions of photons in a curved spacetime. This graphics-processing-unit (GPU)-based integrator employs the stream processing paradigm, is implemented in CUDA C/C++, and runs on nVidia graphics cards. The peak performance of GRay using single-precision floating-point arithmetic on a single GPU exceeds 300 GFLOP (or 1 ns per photon per time step). For a realistic problem, where the peak performance cannot be reached, GRay is two orders of magnitude faster than existing central-processing-unit-based ray-tracing codes. This performance enhancement allows more effective searches of large parameter spaces when comparing theoretical predictions of images, spectra, and light curves from the vicinities of compact objects to observations. GRay can also perform on-the-fly ray tracing within general relativistic magnetohydrodynamic algorithms that simulate accretion flows around compact objects. Making use of this algorithm, we calculate the properties of the shadows of Kerr black holes and the photon rings that surround them. We also provide accurate fitting formulae of their dependencies on black hole spin and observer inclination, which can be used to interpret upcoming observations of the black holes at the center of the Milky Way, as well as M87, with the Event Horizon Telescope.

  19. Mise en Scene: Conversion of Scenarios to CSP Traces for the Requirements-to-Design-to-Code Project

    Science.gov (United States)

    Carter. John D.; Gardner, William B.; Rash, James L.; Hinchey, Michael G.

    2007-01-01

    The "Requirements-to-Design-to-Code" (R2D2C) project at NASA's Goddard Space Flight Center is based on deriving a formal specification expressed in Communicating Sequential Processes (CSP) notation from system requirements supplied in the form of CSP traces. The traces, in turn, are to be extracted from scenarios, a user-friendly medium often used to describe the required behavior of computer systems under development. This work, called Mise en Scene, defines a new scenario medium (Scenario Notation Language, SNL) suitable for control-dominated systems, coupled with a two-stage process for automatic translation of scenarios to a new trace medium (Trace Notation Language, TNL) that encompasses CSP traces. Mise en Scene is offered as an initial solution to the problem of the scenarios-to-traces "D2" phase of R2D2C. A survey of the "scenario" concept and some case studies are also provided.

  20. Amino acid fermentation at the origin of the genetic code

    Directory of Open Access Journals (Sweden)

    de Vladar Harold P

    2012-02-01

    Full Text Available Abstract There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can

  1. Amino acid fermentation at the origin of the genetic code.

    Science.gov (United States)

    de Vladar, Harold P

    2012-02-10

    There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments

  2. Amino acid fermentation at the origin of the genetic code

    Science.gov (United States)

    2012-01-01

    There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments

  3. Decoding the non-coding genome: elucidating genetic risk outside the coding genome.

    Science.gov (United States)

    Barr, C L; Misener, V L

    2016-01-01

    Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  4. Feasibility Study of Coupling the CASMO-4/TABLES-3/SIMULATE-3 Code System to TRACE/PARCS

    International Nuclear Information System (INIS)

    Demaziere, Christophe; Staalek, Mathias

    2004-12-01

    This report investigates the feasibility of coupling the Studsvik Scandpower CASMO-4/TABLES-3/SIMULATE-3 codes to the US NRC TRACE/PARCS codes. The data required by TRACE/PARCS are actually the ones necessary to run its neutronic module PARCS. Such data are the macroscopic nuclear cross-sections, some microscopic nuclear cross-sections important for the Xenon and Samarium poisoning effects, the Assembly Discontinuity Factors, and the kinetic parameters. All these data can be retrieved from the Studsvik Scandpower codes. The data functionalization is explained in detail for both systems of codes and the possibility of coupling each of these codes to TRACE/PARCS is discussed. Due to confidentiality restrictions in the use of the CASMO-4 files and to an improper format of the TABLES-3 output files, it is demonstrated that TRACE/PARCS can only be coupled to SIMULATE-3. Specifically-dedicated SIMULATE-3 input decks allow easily editing the neutronic data at specific operating statepoints. Although the data functionalization is different between both systems of codes, such a procedure permits reconstructing a set of data directly compatible with PARCS

  5. Radiation heat transfer model in a spent fuel pool by TRACE code

    International Nuclear Information System (INIS)

    Sanchez-Saez, F.; Carlos, S.; Villanueva, J.F.; Martorell, S.

    2014-01-01

    Nuclear policies have experienced an important change since Fukushima Daiichi nuclear plant accident and the safety of spent fuels has been in the spot issue among all the safety concerns. The work presented consists of the thermohydraulic simulation of spent fuel pool behavior after a loss of coolant throughout transfer channel with loss of cooling transient is produced. The simulation is done with the TRACE code. One of the most important variables that define the behavior of the pool is cladding temperature, which evolution depends on the heat emission. In this work convection and radiation heat transfer is considered. When both heat transfer models are considered, a clear delay in achieving the maximum peak cladding temperature (1477 K) is observed compared with the simulation in which only convection heat transfer is considered. (authors)

  6. Adaptation and implementation of the TRACE code for transient analysis on designs of cooled lead fast reactors

    International Nuclear Information System (INIS)

    Lazaro, A.; Ammirabile, L.; Martorell, S.

    2014-01-01

    The article describes the changes implemented in the TRACE code to include thermodynamic tables of liquid lead drawn from experimental results. He then explains the process for developing a thermohydraulic model for the prototype ALFRED and analysis of a selection of representative transient conducted within the framework of international research projects. The study demonstrates the applicability of TRACE code to simulate designs of cooled lead fast reactors and exposes the high safety margins are there in this technology to accommodate the most severe transients identified in their security study. (Author)

  7. Arbitrariness is not enough: towards a functional approach to the genetic code.

    Science.gov (United States)

    Lacková, Ľudmila; Matlach, Vladimír; Faltýnek, Dan

    2017-12-01

    Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about "code" in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign's object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

  8. Analyses of SBO sequence of VVER1000 reactor using TRACE and MELCOR codes

    International Nuclear Information System (INIS)

    Mazzini, Guido; Kyncl, Milos; Miglierini, Bruno; Kopecek, Vit

    2015-01-01

    In response to the Fukushima accident, the European Commission ordered to perform stress tests to all European Nuclear Power Plants (NPPs). Due to shortage of time a number of conclusions in national stress tests reports were based on engineering judgment only. In the Czech Republic, as a follow up, a consortium of Research Organizations and Universities has decided to simulate selected stress tests scenarios, in particular station Black-Out (SBO) and Loss of Ultimate Sink (LoUS), with the aim to verify conclusions made in the national stress report and to analyse time response of respective source term releases. These activities are carried out in the frame of the project 'Prevention, preparedness and mitigation of consequences of Severe Accident (SA) at Czech NPPs in relation to lessons learned from stress tests after Fukushima' financed by the Ministry of Interior. The Research Centre Rez has been working on the preparation of a MELCOR model for VVER1000 NPP starting with a plant systems nodalization. The basic idea of this paper is to benchmark the MELCOR model with the validated TRACE model, first comparing the steady state and continuing in a long term SBO plus another event until the beginning of the severe accident. The presented work focuses mainly on the preliminary comparison of the thermo-hydraulics of the two models created in MELCOR and TRACE codes. After that, preliminary general results of the SA progression showing the hydrogen production and the relocation phenomena will be shortly discussed. This scenario is considered closed after some seconds to the break of the lower head. (author)

  9. Simulated evolution applied to study the genetic code optimality using a model of codon reassignments.

    Science.gov (United States)

    Santos, José; Monteagudo, Angel

    2011-02-21

    As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the fact that the best possible codes show the patterns of the

  10. Simulated evolution applied to study the genetic code optimality using a model of codon reassignments

    Directory of Open Access Journals (Sweden)

    Monteagudo Ángel

    2011-02-01

    Full Text Available Abstract Background As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Results Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Conclusions Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the

  11. A model of polarized-beam AGS in the ray-tracing code Zgoubi

    Energy Technology Data Exchange (ETDEWEB)

    Meot, F. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ahrens, L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Brown, K. [Brookhaven National Lab. (BNL), Upton, NY (United States); Dutheil, Y. [Brookhaven National Lab. (BNL), Upton, NY (United States); Glenn, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Huang, H. [Brookhaven National Lab. (BNL), Upton, NY (United States); Roser, T. [Brookhaven National Lab. (BNL), Upton, NY (United States); Shoefer, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tsoupas, N. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-07-12

    A model of the Alternating Gradient Synchrotron, based on the AGS snapramps, has been developed in the stepwise ray-tracing code Zgoubi. It has been used over the past 5 years in a number of accelerator studies aimed at enhancing RHIC proton beam polarization. It is also used to study and optimize proton and Helion beam polarization in view of future RHIC and eRHIC programs. The AGS model in Zgoubi is operational on-line via three different applications, ’ZgoubiFromSnaprampCmd’, ’AgsZgoubiModel’ and ’AgsModelViewer’, with the latter two essentially interfaces to the former which is the actual model ’engine’. All three commands are available from the controls system application launcher in the AGS ’StartUp’ menu, or from eponymous commands on shell terminals. Main aspects of the model and of its operation are presented in this technical note, brief excerpts from various studies performed so far are given for illustration, means and methods entering in ZgoubiFromSnaprampCmd are developed further in appendix.

  12. Related research with thermo hydraulics safety by means of Trace code

    International Nuclear Information System (INIS)

    Chaparro V, F. J.; Del Valle G, E.; Rodriguez H, A.; Gomez T, A. M.; Sanchez E, V. H.; Jager, W.

    2014-10-01

    In this article the results of the design of a pressure vessel of a BWR/5 similar to the type of Laguna Verde NPP are presented, using the Trace code. A thermo hydraulics Vessel component capable of simulating the behavior of fluids and heat transfer that occurs within the reactor vessel was created. The Vessel component consists of a three-dimensional cylinder divided into 19 axial sections, 4 azimuthal sections and two concentric radial rings. The inner ring is used to contain the core and the central part of the reactor, while the outer ring is used as a down comer. Axial an azimuthal divisions were made with the intention that the dimensions of the internal components, heights and orientation of the external connections match the reference values of a reactor BWR/5 type. In the model internal components as, fuel assemblies, steam separators, jet pumps, guide tubes, etc. are included and main external connections as, steam lines, feed-water or penetrations of the recirculation system. The model presents significant simplifications because the object is to keep symmetry between each azimuthal section of the vessel. In most internal components lack a detailed description of the geometry and initial values of temperature, pressure, fluid velocity, etc. given that it only considered the most representative data, however with these simulations are obtained acceptable results in important parameters such as the total flow through the core, the pressure in the vessel, percentage of vacuums fraction, pressure drop in the core and the steam separators. (Author)

  13. Neutronic / thermal-hydraulic coupling with the code system Trace / Parcs; Acoplamiento neutronico / termohidraulico con el sistema de codigos TRACE / PARCS

    Energy Technology Data Exchange (ETDEWEB)

    Mejia S, D. M. [Comision Nacional de Seguridad Nuclear y Salvaguardias, Dr. Barragan 779, Col. Narvarte, 03020 Ciudad de Mexico (Mexico); Del Valle G, E., E-mail: dulcemaria.mejia@cnsns.gob.mx [IPN, Escuela Superior de Fisica y Matematicas, Av. IPN s/n, Col. Lindavista, 07738 Ciudad de Mexico (Mexico)

    2015-09-15

    The developed models for Parcs and Trace codes corresponding for the cycle 15 of the Unit 1 of the Laguna Verde nuclear power plant are described. The first focused to the neutronic simulation and the second to thermal hydraulics. The model developed for Parcs consists of a core of 444 fuel assemblies wrapped in a radial reflective layer and two layers, a superior and another inferior, of axial reflector. The core consists of 27 total axial planes. The model for Trace includes the vessel and its internal components as well as various safety systems. The coupling between the two codes is through two maps that allow its intercommunication. Both codes are used in coupled form performing a dynamic simulation that allows obtaining acceptably a stable state from which is carried out the closure of all the main steam isolation valves (MSIVs) followed by the performance of safety relief valves (SRVs) and ECCS. The results for the power and reactivities introduced by the moderator density, the fuel temperature and total temperature are shown. Data are also provided like: the behavior of the pressure in the steam dome, the water level in the downcomer, the flow through the MSIVs and SRVs. The results are explained for the power, the pressure in the steam dome and the water level in the downcomer which show agreement with the actions of the MSIVs, SRVs and ECCS. (Author)

  14. Probable relationship between partitions of the set of codons and the origin of the genetic code.

    Science.gov (United States)

    Salinas, Dino G; Gallardo, Mauricio O; Osorio, Manuel I

    2014-03-01

    Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Safety related investigations of the VVER-1000 reactor type by the coupled code system TRACE/PARCS

    International Nuclear Information System (INIS)

    Jaeger, Wadim; Lischke, Wolfgang; Sanchez Espinoza, Victor Hugo

    2007-01-01

    This study was performed at the Institute of Reactor Safety at the Research Center Karlsruhe. It is embedded in the ongoing investigations of the international code application and maintenance program (CAMP) for qualification and validation of system codes like TRACE [1] and PARCS [2]. The predestinated reactor type for the validation of these two codes was the Russian designed VVER-1000 because the OECD/NEA VVER-1000 Coolant Transient Benchmark Phase 2 [3] includes detailed information of the Bulgarian nuclear power plant (NPP) Kozloduy unit 6. The posttest-investigations of a coolant mixing experiment have shown that the predicted parameters (coolant temperature, pressure drop, etc.) are in good agreement to the measured data. The coolant mixing pattern especially in the downcomer has been also reproduced quiet well by TRACE. The coupled code system TRACE/PARCS which was applied on a postulated main steam line break (MSLB) provides good results compared to reference values and the ones of other participants of the benchmark. It can be pointed out that the developed three-dimensional nodalisation of the reactor pressure vessel (RPV) is appropriate for the description of transients where the thermal-hydraulics and the neutronics are strongly linked. (author)

  16. A genetic code alteration is a phenotype diversity generator in the human pathogen Candida albicans.

    Directory of Open Access Journals (Sweden)

    Isabel Miranda

    Full Text Available BACKGROUND: The discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments. It is now clear that codon identity alterations involve sense and non-sense codons and can occur in organisms with complex genomes and proteomes. However, the biological functions, the molecular mechanisms of evolution and the diversity of genetic code alterations remain largely unknown. In various species of the genus Candida, the leucine CUG codon is decoded as serine by a unique serine tRNA that contains a leucine 5'-CAG-3'anticodon (tRNA(CAG(Ser. We are using this codon identity redefinition as a model system to elucidate the evolution of genetic code alterations. METHODOLOGY/PRINCIPAL FINDINGS: We have reconstructed the early stages of the Candida genetic code alteration by engineering tRNAs that partially reverted the identity of serine CUG codons back to their standard leucine meaning. Such genetic code manipulation had profound cellular consequences as it exposed important morphological variation, altered gene expression, re-arranged the karyotype, increased cell-cell adhesion and secretion of hydrolytic enzymes. CONCLUSION/SIGNIFICANCE: Our study provides the first experimental evidence for an important role of genetic code alterations as generators of phenotypic diversity of high selective potential and supports the hypothesis that they speed up evolution of new phenotypes.

  17. Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal

    Science.gov (United States)

    Zamudio, Gabriel S.; José, Marco V.

    2018-03-01

    In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.

  18. Critical review of conservation equations for two-phase flow in the U.S. NRC TRACE code

    International Nuclear Information System (INIS)

    Wulff, Wolfgang

    2011-01-01

    Research highlights: → Field equations as implemented in TRACE are incorrect. → Boundary conditions needed for cooling of nuclear fuel elements are wrong. → The two-fluid model in TRACE is not closed. → Three-dimensional flow modeling in TRACE has no basis. - Abstract: The field equations for two-phase flow in the computer code TRAC/RELAP Advanced Computational Engine or TRACE are examined to determine their validity, their capabilities and limitations in resolving nuclear reactor safety issues. TRACE was developed for the NRC to predict thermohydraulic phenomena in nuclear power plants during operational transients and postulated accidents. TRACE is based on the rigorously derived and well-established two-fluid field equations for 1-D and 3-D two-phase flow. It is shown that: (1)The two-fluid field equations for mass conservation as implemented in TRACE are wrong because local mass balances in TRACE are in conflict with mass conservation for the whole reactor system, as shown in Section . (2)Wrong equations of motion are used in TRACE in place of momentum balances, compromising at branch points the prediction of momentum transfer between, and the coupling of, loops in hydraulic networks by impedance (form loss and wall shear) and by inertia and thereby the simulation of reactor component interactions. (3)Most seriously, TRACE calculation of heat transfer from fuel elements is incorrect for single and two-phase flows, because Eq. of the TRACE Manual is wrong (see Section ). (4)Boundary conditions for momentum and energy balances in TRACE are restricted to flow regimes with single-phase wall contact because TRACE lacks constitutive relations for solid-fluid exchange of momentum and heat in prevailing flow regimes. Without a quantified assessment of consequences from (3) to (4), predictions of phasic fluid velocities, fuel temperatures and important safety parameters, e.g., peak clad temperature, are questionable. Moreover, TRACE cannot predict 3-D single- or

  19. An analysis of options available for developing a common laser ray tracing package for Ares and Kull code frameworks

    Energy Technology Data Exchange (ETDEWEB)

    Weeratunga, S K

    2008-11-06

    Ares and Kull are mature code frameworks that support ALE hydrodynamics for a variety of HEDP applications at LLNL, using two widely different meshing approaches. While Ares is based on a 2-D/3-D block-structured mesh data base, Kull is designed to support unstructured, arbitrary polygonal/polyhedral meshes. In addition, both frameworks are capable of running applications on large, distributed-memory parallel machines. Currently, both these frameworks separately support assorted collections of physics packages related to HEDP, including one for the energy deposition by laser/ion-beam ray tracing. This study analyzes the options available for developing a common laser/ion-beam ray tracing package that can be easily shared between these two code frameworks and concludes with a set of recommendations for its development.

  20. Validation and application of the system code TRACE for safety related investigations of innovative nuclear energy systems

    Energy Technology Data Exchange (ETDEWEB)

    Jaeger, Wadim

    2011-12-19

    The system code TRACE is the latest development of the U.S. Nuclear Regulatory Commission (US NRC). TRACE, developed for the analysis of operational conditions, transients and accidents of light water reactors (LWR), is a best-estimate code with two fluid, six equation models for mass, energy, and momentum conservation, and related closure models. Since TRACE is mainly applied to LWR specific issues, the validation process related to innovative nuclear systems (liquid metal cooled systems, systems operated with supercritical water, etc.) is very limited, almost not existing. In this work, essential contribution to the validation of TRACE related to lead and lead alloy cooled systems as well as systems operated with supercritical water is provided in a consistent and corporate way. In a first step, model discrepancies of the TRACE source code were removed. This inconsistencies caused the wrong prediction of the thermo physical properties of supercritical water and lead bismuth eutectic, and hence the incorrect prediction of heat transfer relevant characteristic numbers like Reynolds or Prandtl number. In addition to the correction of the models to predict these quantities, models describing the thermo physical properties of lead and Diphyl THT (synthetic heat transfer medium) were implemented. Several experiments and numerical benchmarks were used to validate the modified TRACE version. These experiments, mainly focused on wall-to-fluid heat transfer, revealed that not only the thermo physical properties are afflicted with inconsistencies but also the heat transfer models. The models for the heat transfer to liquid metals were enhanced in a way that the code can now distinguish between pipe and bundle flow by using the right correlation. The heat transfer to supercritical water was not existing in TRACE up to now. Completely new routines were implemented to overcome that issue. The comparison of the calculations to the experiments showed, on one hand, the necessity

  1. The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

    Science.gov (United States)

    Komar, Anton A

    2016-01-01

    Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

  2. The coevolution of genes and genetic codes: Crick's frozen accident revisited.

    Science.gov (United States)

    Sella, Guy; Ardell, David H

    2006-09-01

    The standard genetic code is the nearly universal system for the translation of genes into proteins. The code exhibits two salient structural characteristics: it possesses a distinct organization that makes it extremely robust to errors in replication and translation, and it is highly redundant. The origin of these properties has intrigued researchers since the code was first discovered. One suggestion, which is the subject of this review, is that the code's organization is the outcome of the coevolution of genes and genetic codes. In 1968, Francis Crick explored the possible implications of coevolution at different stages of code evolution. Although he argues that coevolution was likely to influence the evolution of the code, he concludes that it falls short of explaining the organization of the code we see today. The recent application of mathematical modeling to study the effects of errors on the course of coevolution, suggests a different conclusion. It shows that coevolution readily generates genetic codes that are highly redundant and similar in their error-correcting organization to the standard code. We review this recent work and suggest that further affirmation of the role of coevolution can be attained by investigating the extent to which the outcome of coevolution is robust to other influences that were present during the evolution of the code.

  3. Codon size reduction as the origin of the triplet genetic code.

    Directory of Open Access Journals (Sweden)

    Pavel V Baranov

    Full Text Available The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon

  4. Critical roles for a genetic code alteration in the evolution of the genus Candida.

    Science.gov (United States)

    Silva, Raquel M; Paredes, João A; Moura, Gabriela R; Manadas, Bruno; Lima-Costa, Tatiana; Rocha, Rita; Miranda, Isabel; Gomes, Ana C; Koerkamp, Marian J G; Perrot, Michel; Holstege, Frank C P; Boucherie, Hélian; Santos, Manuel A S

    2007-10-31

    During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.

  5. Genetic hotels for the standard genetic code: evolutionary analysis based upon novel three-dimensional algebraic models.

    Science.gov (United States)

    José, Marco V; Morgado, Eberto R; Govezensky, Tzipe

    2011-07-01

    Herein, we rigorously develop novel 3-dimensional algebraic models called Genetic Hotels of the Standard Genetic Code (SGC). We start by considering the primeval RNA genetic code which consists of the 16 codons of type RNY (purine-any base-pyrimidine). Using simple algebraic operations, we show how the RNA code could have evolved toward the current SGC via two different intermediate evolutionary stages called Extended RNA code type I and II. By rotations or translations of the subset RNY, we arrive at the SGC via the former (type I) or via the latter (type II), respectively. Biologically, the Extended RNA code type I, consists of all codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The Extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. Since the dimensions of remarkable subsets of the Genetic Hotels are not necessarily integer numbers, we also introduce the concept of algebraic fractal dimension. A general decoding function which maps each codon to its corresponding amino acid or the stop signals is also derived. The Phenotypic Hotel of amino acids is also illustrated. The proposed evolutionary paths are discussed in terms of the existing theories of the evolution of the SGC. The adoption of 3-dimensional models of the Genetic and Phenotypic Hotels will facilitate the understanding of the biological properties of the SGC.

  6. How American Nurses Association Code of Ethics informs genetic/genomic nursing.

    Science.gov (United States)

    Tluczek, Audrey; Twal, Marie E; Beamer, Laura Curr; Burton, Candace W; Darmofal, Leslie; Kracun, Mary; Zanni, Karen L; Turner, Martha

    2018-01-01

    Members of the Ethics and Public Policy Committee of the International Society of Nurses in Genetics prepared this article to assist nurses in interpreting the American Nurses Association (2015) Code of Ethics for Nurses with Interpretive Statements (Code) within the context of genetics/genomics. The Code explicates the nursing profession's norms and responsibilities in managing ethical issues. The nearly ubiquitous application of genetic/genomic technologies in healthcare poses unique ethical challenges for nursing. Therefore, authors conducted literature searches that drew from various professional resources to elucidate implications of the code in genetic/genomic nursing practice, education, research, and public policy. We contend that the revised Code coupled with the application of genomic technologies to healthcare creates moral obligations for nurses to continually refresh their knowledge and capacities to translate genetic/genomic research into evidence-based practice, assure the ethical conduct of scientific inquiry, and continually develop or revise national/international guidelines that protect the rights of individuals and populations within the context of genetics/genomics. Thus, nurses have an ethical responsibility to remain knowledgeable about advances in genetics/genomics and incorporate emergent evidence into their work.

  7. Junk DNA and the long non-coding RNA twist in cancer genetics

    NARCIS (Netherlands)

    H. Ling (Hui); K. Vincent; M. Pichler; R. Fodde (Riccardo); I. Berindan-Neagoe (Ioana); F.J. Slack (Frank); G.A. Calin (George)

    2015-01-01

    textabstractThe central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs

  8. National Society of Genetic Counselors Code of Ethics: Explication of 2017 Revisions.

    Science.gov (United States)

    Senter, Leigha; Bennett, Robin L; Madeo, Anne C; Noblin, Sarah; Ormond, Kelly E; Schneider, Kami Wolfe; Swan, Kelli; Virani, Alice

    2018-02-01

    The Code of Ethics (COE) of the National Society of Genetic Counselors (NSGC) was adopted in 1992 and was later revised and adopted in 2006. In 2016, the NSGC Code of Ethics Review Task Force (COERTF) was convened to review the COE. The COERTF reviewed ethical codes written by other professional organizations and suggested changes that would better reflect the current and evolving nature of the genetic counseling profession. The COERTF received input from the society's legal counsel, Board of Directors, and members-at-large. A revised COE was proposed to the membership and approved and adopted in April 2017. The revisions and rationale for each are presented.

  9. Efficient Dual Domain Decoding of Linear Block Codes Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Ahmed Azouaoui

    2012-01-01

    Full Text Available A computationally efficient algorithm for decoding block codes is developed using a genetic algorithm (GA. The proposed algorithm uses the dual code in contrast to the existing genetic decoders in the literature that use the code itself. Hence, this new approach reduces the complexity of decoding the codes of high rates. We simulated our algorithm in various transmission channels. The performance of this algorithm is investigated and compared with competitor decoding algorithms including Maini and Shakeel ones. The results show that the proposed algorithm gives large gains over the Chase-2 decoding algorithm and reach the performance of the OSD-3 for some quadratic residue (QR codes. Further, we define a new crossover operator that exploits the domain specific information and compare it with uniform and two point crossover. The complexity of this algorithm is also discussed and compared to other algorithms.

  10. Translation of the model plant of the CN code TRAC-BF1 Cofrentes of a SNAP-TRACE

    International Nuclear Information System (INIS)

    Escriva, A.; Munuz-Cobo, J. L.; Concejal, A.; Melara, J.; Albendea, M.

    2012-01-01

    It aims to develop a three-dimensional model of the CN Cofrentes whose consistent results Compared with those in current use programs (TRAC-BFl, RETRAN) validated with data of the plant. This comparison should be done globally and that you can not carry a compensation of errors. To check the correct translation of the results obtained have been compared with TRACE and the programs currently in use and the relevant adjustments have been made, taking into account that both the correlations and models are different codes. During the completion of this work we have detected several errors that must be corrected in future versions of these tools.

  11. Open Genetic Code: on open source in the life sciences

    OpenAIRE

    Deibel, Eric

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first ...

  12. Symmetries in Genetic Systems and the Concept of Geno-Logical Coding

    Directory of Open Access Journals (Sweden)

    Sergey V. Petoukhov

    2016-12-01

    Full Text Available The genetic code of amino acid sequences in proteins does not allow understanding and modeling of inherited processes such as inborn coordinated motions of living bodies, innate principles of sensory information processing, quasi-holographic properties, etc. To be able to model these phenomena, the concept of geno-logical coding, which is connected with logical functions and Boolean algebra, is put forward. The article describes basic pieces of evidence in favor of the existence of the geno-logical code, which exists in p­arallel with the known genetic code of amino acid sequences but which serves for transferring inherited processes along chains of generations. These pieces of evidence have been received due to the analysis of symmetries in structures of molecular-genetic systems. The analysis has revealed a close connection of the genetic system with dyadic groups of binary numbers and with other mathematical objects, which are related with dyadic groups: Walsh functions (which are algebraic characters of dyadic groups, bit-reversal permutations, logical holography, etc. These results provide a new approach for mathematical modeling of genetic structures, which uses known mathematical formalisms from technological fields of noise-immunity coding of information, binary analysis, logical holography, and digital devices of artificial intellect. Some opportunities for a development of algebraic-logical biology are opened.

  13. The Graph, Geometry and Symmetries of the Genetic Code with Hamming Metric

    Directory of Open Access Journals (Sweden)

    Reijer Lenstra

    2015-07-01

    Full Text Available The similarity patterns of the genetic code result from similar codons encoding similar messages. We develop a new mathematical model to analyze these patterns. The physicochemical characteristics of amino acids objectively quantify their differences and similarities; the Hamming metric does the same for the 64 codons of the codon set. (Hamming distances equal the number of different codon positions: AAA and AAC are at 1-distance; codons are maximally at 3-distance. The CodonPolytope, a 9-dimensional geometric object, is spanned by 64 vertices that represent the codons and the Euclidian distances between these vertices correspond one-to-one with intercodon Hamming distances. The CodonGraph represents the vertices and edges of the polytope; each edge equals a Hamming 1-distance. The mirror reflection symmetry group of the polytope is isomorphic to the largest permutation symmetry group of the codon set that preserves Hamming distances. These groups contain 82,944 symmetries. Many polytope symmetries coincide with the degeneracy and similarity patterns of the genetic code. These code symmetries are strongly related with the face structure of the polytope with smaller faces displaying stronger code symmetries. Splitting the polytope stepwise into smaller faces models an early evolution of the code that generates this hierarchy of code symmetries. The canonical code represents a class of 41,472 codes with equivalent symmetries; a single class among an astronomical number of symmetry classes comprising all possible codes.

  14. Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

    Science.gov (United States)

    Kubyshkin, Vladimir; Budisa, Nediljko

    2017-08-01

    The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Statistical safety evaluation of BWR turbine trip scenario using coupled neutron kinetics and thermal hydraulics analysis code SKETCH-INS/TRACE5.0

    International Nuclear Information System (INIS)

    Ichikawa, Ryoko; Masuhara, Yasuhiro; Kasahara, Fumio

    2012-01-01

    The Best Estimate Plus Uncertainty (BEPU) method has been prepared for the regulatory cross-check analysis at Japan Nuclear Energy Safety Organization (JNES) on base of the three-dimensional neutron-kinetics/thermal-hydraulics coupled code SKETCH-INS/TRACE5.0. In the preparation, TRACE5.0 is verified against the large-scale thermal-hydraulic tests carried out with NUPEC facility. These tests were focused on the pressure drop of steam-liquid two phase flow and void fraction distribution. From the comparison of the experimental data with other codes (RELAP5/MOD3.3 and TRAC-BF1), TRACE5.0 was judged better than other codes. It was confirmed that TRACE5.0 has high reliability for thermal hydraulics behavior and are used as a best-estimate code for the statistical safety evaluation. Next, the coupled code SKETCH-INS/TRACE5.0 was applied to turbine trip tests performed at the Peach Bottom-2 BWR4 Plant. The turbine trip event shows the rapid power peak due to the voids collapse with the pressure increase. The analyzed peak value of core power is better simulated than the previous version SKETCH-INS/TRAC-BF1. And the statistical safety evaluation using SKETCH-INS/TRACE5.0 was applied to the loss of load transient for examining the influence of the choice of sampling method. (author)

  16. Model with Peach Bottom Turbine trip and thermal-Hydraulic code TRACE V5P3

    International Nuclear Information System (INIS)

    Mesado, C.; Miro, R.; Barrachina, T.; Verdu, G.

    2014-01-01

    This work is the continuation of the work presented previously in the thirty-ninth meeting annual of the Spanish Nuclear society. The semi-automatic translation of the Thermo-hydraulic model TRAC-BF1 Peach Bottom Turbine Trip to TRACE was presented in such work. This article is intended to validate the model obtained in TRACE, why compare the model results result from the translation with the Benchmark results: NEA/OECD BWR Peach Bottom Turbine Trip (PBTT), in particular is of the extreme scenario 2 of exercise 3, in which there is SCRAM in the reactor. Among other data present in the (transitional) Benchmark , are: total power, axial profile of power, pressure Dome, total reactivity and its components. (Author)

  17. Analysis of an ADS spurious opening event at a BWR/6 by means of the TRACE code

    International Nuclear Information System (INIS)

    Nikitin, Konstantin; Manera, Annalisa

    2011-01-01

    Highlights: → The spurious opening of 8 relief valves of the ADS system in a BWR/6 has been simulated. → The valves opening results in a fast depressurization and significant loads on the RPV internals. → This event has been modeled by means of the TRACE and TRAC-BF1 codes. The results are in good agreement with the available plant data. - Abstract: The paper presents the results of a post-event analysis of a spurious opening of 8 relief valves of the automatic depressurization system (ADS) occurred in a BWR/6. The opening of the relief valves results in a fast depressurization (pressure blow down) of the primary system which might lead to significant dynamic loads on the RPV and associated internals. In addition, the RPV level swelling caused by the fast depressurization might lead to undesired water carry-over into the steam line and through the safety relief valves (SRVs). Therefore, the transient needs to be characterized in terms of evolution of pressure, temperature and fluid distribution in the system. This event has been modeled by means of the TRACE and TRAC-BF1 codes. The results are in good agreement with the plant data.

  18. The Impact of Diagnostic Code Misclassification on Optimizing the Experimental Design of Genetic Association Studies

    Directory of Open Access Journals (Sweden)

    Steven J. Schrodi

    2017-01-01

    Full Text Available Diagnostic codes within electronic health record systems can vary widely in accuracy. It has been noted that the number of instances of a particular diagnostic code monotonically increases with the accuracy of disease phenotype classification. As a growing number of health system databases become linked with genomic data, it is critically important to understand the effect of this misclassification on the power of genetic association studies. Here, I investigate the impact of this diagnostic code misclassification on the power of genetic association studies with the aim to better inform experimental designs using health informatics data. The trade-off between (i reduced misclassification rates from utilizing additional instances of a diagnostic code per individual and (ii the resulting smaller sample size is explored, and general rules are presented to improve experimental designs.

  19. A Novel Real-coded Quantum-inspired Genetic Algorithm and Its Application in Data Reconciliation

    Directory of Open Access Journals (Sweden)

    Gao Lin

    2012-06-01

    Full Text Available Traditional quantum-inspired genetic algorithm (QGA has drawbacks such as premature convergence, heavy computational cost, complicated coding and decoding process etc. In this paper, a novel real-coded quantum-inspired genetic algorithm is proposed based on interval division thinking. Detailed comparisons with some similar approaches for some standard benchmark functions test validity of the proposed algorithm. Besides, the proposed algorithm is used in two typical nonlinear data reconciliation problems (distilling process and extraction process and simulation results show its efficiency in nonlinear data reconciliation problems.

  20. The trace ion module for the Monte Carlo code Eirene, a unified approach to plasma chemistry in the ITER divertor

    International Nuclear Information System (INIS)

    Seebacher, J.; Reiter, D.; Borner, P.

    2007-01-01

    Modelling of kinetic transport effects in magnetic fusion devices is of great importance for understanding the physical processes in both the core and and the scrape off layer (SOL) plasma. For SOL simulation the EIRENE code is a well established tool for modelling of neutral, impurities and radiation transport. Recently a new trace ion transport module (tim), has been developed and incorporated into EIRENE. The tim essentially consists of two parts: 1) A trajectory integrator tracing the deterministic motion of a guiding centre particle in general 3D electric and magnetic fields. 2) A stochastic representation of the Fokker Planck collision operator in suitable guiding centre coordinates treating Coulomb collisions with the plasma background species. The TIM enables integrated SOL simulation packages such as B2-EIRENE, EDGE2D-EIRENE (2D) or EMC3-EIRENE (3D) to treat the physical and chemical processes near the divertor targets and in the bulk of the SOL in greater detail than before, and in particular on a kinetic rather than a fluid level. One of the physics applications is the formation and transport of hydrocarbon molecules and ions in the divertor in tokamaks, where the tritium co deposition via hydrocarbons remains a serious issue for next generation fusion devices like ITER. Real tokamak modelling scenarios will be discussed with the code packages B2-EIRENE (2D) and EMC3-EIRENE (3D). A brief overview of the theoretical basis of the tim will be given including code verification studies of the basic physics properties. Applications to hydrocarbon transport studies in TEXTOR and ITER, comparing present (fluid) approximations in edge modelling with the new extended kinetic model, will be presented. (Author)

  1. Open Genetic Code: on open source in the life sciences.

    Science.gov (United States)

    Deibel, Eric

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

  2. Study of the source term of radiation of the CDTN GE-PET trace 8 cyclotron with the MCNPX code

    Energy Technology Data Exchange (ETDEWEB)

    Benavente C, J. A.; Lacerda, M. A. S.; Fonseca, T. C. F.; Da Silva, T. A. [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Av. Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais (Brazil); Vega C, H. R., E-mail: jhonnybenavente@gmail.com [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas, Zac. (Mexico)

    2015-10-15

    Full text: The knowledge of the neutron spectra in a PET cyclotron is important for the optimization of radiation protection of the workers and individuals of the public. The main objective of this work is to study the source term of radiation of the GE-PET trace 8 cyclotron of the Development Center of Nuclear Technology (CDTN/CNEN) using computer simulation by the Monte Carlo method. The MCNPX version 2.7 code was used to calculate the flux of neutrons produced from the interaction of the primary proton beam with the target body and other cyclotron components, during 18F production. The estimate of the source term and the corresponding radiation field was performed from the bombardment of a H{sub 2}{sup 18}O target with protons of 75 μA current and 16.5 MeV of energy. The values of the simulated fluxes were compared with those reported by the accelerator manufacturer (GE Health care Company). Results showed that the fluxes estimated with the MCNPX codes were about 70% lower than the reported by the manufacturer. The mean energies of the neutrons were also different of that reported by GE Health Care. It is recommended to investigate other cross sections data and the use of physical models of the code itself for a complete characterization of the source term of radiation. (Author)

  3. Ray-tracing 3D dust radiative transfer with DART-Ray: code upgrade and public release

    Science.gov (United States)

    Natale, Giovanni; Popescu, Cristina C.; Tuffs, Richard J.; Clarke, Adam J.; Debattista, Victor P.; Fischera, Jörg; Pasetto, Stefano; Rushton, Mark; Thirlwall, Jordan J.

    2017-11-01

    We present an extensively updated version of the purely ray-tracing 3D dust radiation transfer code DART-Ray. The new version includes five major upgrades: 1) a series of optimizations for the ray-angular density and the scattered radiation source function; 2) the implementation of several data and task parallelizations using hybrid MPI+OpenMP schemes; 3) the inclusion of dust self-heating; 4) the ability to produce surface brightness maps for observers within the models in HEALPix format; 5) the possibility to set the expected numerical accuracy already at the start of the calculation. We tested the updated code with benchmark models where the dust self-heating is not negligible. Furthermore, we performed a study of the extent of the source influence volumes, using galaxy models, which are critical in determining the efficiency of the DART-Ray algorithm. The new code is publicly available, documented for both users and developers, and accompanied by several programmes to create input grids for different model geometries and to import the results of N-body and SPH simulations. These programmes can be easily adapted to different input geometries, and for different dust models or stellar emission libraries.

  4. Adaptation and implementation of the TRACE code for transient analysis on designs of cooled lead fast reactors; Adaptacion y aplicacion del codigo TRACE para el analisis de transitorios en disenos de reactores rapidos refrigerados por plomo

    Energy Technology Data Exchange (ETDEWEB)

    Lazaro, A.; Ammirabile, L.; Martorell, S.

    2014-07-01

    The article describes the changes implemented in the TRACE code to include thermodynamic tables of liquid lead drawn from experimental results. He then explains the process for developing a thermohydraulic model for the prototype ALFRED and analysis of a selection of representative transient conducted within the framework of international research projects. The study demonstrates the applicability of TRACE code to simulate designs of cooled lead fast reactors and exposes the high safety margins are there in this technology to accommodate the most severe transients identified in their security study. (Author)

  5. Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code.

    Science.gov (United States)

    Koonin, Eugene V

    2017-05-23

    Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code. The subsequent 49 years of code studies have elucidated notable features of the standard code, such as high robustness to errors, but failed to develop a compelling explanation for codon assignments. In particular, stereochemical affinity between amino acids and the cognate codons or anticodons does not seem to account for the origin and evolution of the code. Here, I expand Crick's hypothesis on RNA-only translation system by presenting evidence that this early translation already attained high fidelity that allowed protein evolution. I outline an experimentally testable scenario for the evolution of the code that combines a distinct version of the stereochemical hypothesis, in which amino acids are recognized via unique sites in the tertiary structure of proto-tRNAs, rather than by anticodons, expansion of the code via proto-tRNA duplication, and the frozen accident.

  6. [Direct genetic manipulation and criminal code in Venezuela: absolute criminal law void?].

    Science.gov (United States)

    Cermeño Zambrano, Fernando G De J

    2002-01-01

    The judicial regulation of genetic biotechnology applied to the human genome is of big relevance currently in Venezuela due to the drafting of an innovative bioethical law in the country's parliament. This article will highlight the constitutional normative of Venezuela's 1999 Constitution regarding this subject, as it establishes the framework from which this matter will be legally regulated. The approach this article makes towards the genetic biotechnology applied to the human genome is made taking into account the Venezuelan penal law and by highlighting the violent genetic manipulations that have criminal relevance. The genetic biotechnology applied to the human genome has another important relevance as a consequence of the reformulation of the Venezuelan Penal Code discussed by the country's National Assembly. Therefore, a concise study of the country's penal code will be made in this article to better understand what judicial-penal properties have been protected by the Venezuelan penal legislation. This last step will enable us to identify the penal tools Venezuela counts on to face direct genetic manipulations. We will equally indicate the existing punitive loophole and that should be covered by the penal legislator. In conclusion, this essay concerns criminal policy, referred to the direct genetic manipulations on the human genome that haven't been typified in Venezuelan law, thus discovering a genetic biotechnology paradise.

  7. Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

    NARCIS (Netherlands)

    P.T.S. van der Gulik (Peter); W.D. Hoff (Wouter)

    2011-01-01

    htmlabstractThe origin of the genetic code is a central open problem regarding the early evolution of life. Here, we consider two undeveloped but important aspects of possible scenarios for the evolutionary pathway of the translation machinery: the role of unassigned codons in early stages

  8. Real-Coded Quantum-Inspired Genetic Algorithm-Based BP Neural Network Algorithm

    Directory of Open Access Journals (Sweden)

    Jianyong Liu

    2015-01-01

    Full Text Available The method that the real-coded quantum-inspired genetic algorithm (RQGA used to optimize the weights and threshold of BP neural network is proposed to overcome the defect that the gradient descent method makes the algorithm easily fall into local optimal value in the learning process. Quantum genetic algorithm (QGA is with good directional global optimization ability, but the conventional QGA is based on binary coding; the speed of calculation is reduced by the coding and decoding processes. So, RQGA is introduced to explore the search space, and the improved varied learning rate is adopted to train the BP neural network. Simulation test shows that the proposed algorithm is effective to rapidly converge to the solution conformed to constraint conditions.

  9. Towards A Genetic Business Code For Growth in the South African Transport Industry

    Directory of Open Access Journals (Sweden)

    J.H. Vermeulen

    2003-11-01

    Full Text Available As with each living organism, it is proposed that an organisation possesses a genetic code. In the fast-changing business environment it would be invaluable to know what constitutes organisational growth and success in terms of such a code. To identify this genetic code a quantitative methodological framework, supplemented by a qualitative approach, was used and the views of top management in the Transport Industry were solicited. The Repertory Grid was used as the primary data-collection method. Through a phased data-analysis process an integrated profile of first- and second-order constructs, and opposite poles, was compiled. By utilising deductive and inductive strategies three strands of a Genetic Business Growth Code were identified, namely a Leadership Strand, Organisational Architecture Strand and Internal Orientation Strand. The study confirmed the value of a Genetic Business Code for growth in the Transport Industry. Opsomming Daar word voorgestel dat ’n organisasie, soos elke lewende organisme, oor ’n genetiese kode beskik. In die snelveranderende sake-omgewing sal dit onskatbaar wees om te weet wat organisasiegroei en –sukses veroorsaak. ’n Kwantitatiewe metodologie-raamwerk, aangevul deur ’n kwalitatiewe benadering is gebruik om hierdie genetiese kode te identifiseer, en die menings van topbestuur in die Vervoerbedryf is ingewin met behulp van die “Repertory Grid" as die vernaamste metode van data-insameling. ’n Geïntegreerde profiel van eerste- en tweedeordekonstrukte, met hulle teenoorgestelde pole, is opgestel. Drie stringe van ’n Genetiese Sakegroeikode, nl. ’n Leierskapstring, die Organisasieargitektuur-string en die Innerlike-ingesteldheidstring is geïdentifiseer deur deduktiewe en induktiewe strategieë te gebruik. Die studie bevestig die waarde van ’n Genetiese Sakekode vir groei in die Vervoerbedryf.

  10. Tracing Technological Development Trajectories: A Genetic Knowledge Persistence-Based Main Path Approach.

    Directory of Open Access Journals (Sweden)

    Hyunseok Park

    Full Text Available The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological trajectories but nonetheless have some limitations. They have high potential to miss some dominant patents from the identified main paths; nonetheless, the high network complexity of their main paths makes qualitative tracing of trajectories problematic. The proposed method searches backward and forward paths from the high-persistence patents which are identified based on a standard genetic knowledge persistence algorithm. We tested the new method by applying it to the desalination and the solar photovoltaic domains and compared the results to output from the same domains using a prior method. The empirical results show that the proposed method can dramatically reduce network complexity without missing any dominantly important patents. The main paths identified by our approach for two test cases are almost 10x less complex than the main paths identified by the existing approach. The proposed approach identifies all dominantly important patents on the main paths, but the main paths identified by the existing approach miss about 20% of dominantly important patents.

  11. Automation of RELAP5 input calibration and code validation using genetic algorithm

    International Nuclear Information System (INIS)

    Phung, Viet-Anh; Kööp, Kaspar; Grishchenko, Dmitry; Vorobyev, Yury; Kudinov, Pavel

    2016-01-01

    Highlights: • Automated input calibration and code validation using genetic algorithm is presented. • Predictions generally overlap experiments for individual system response quantities (SRQs). • It was not possible to predict simultaneously experimental maximum flow rate and oscillation period. • Simultaneous consideration of multiple SRQs is important for code validation. - Abstract: Validation of system thermal-hydraulic codes is an important step in application of the codes to reactor safety analysis. The goal of the validation process is to determine how well a code can represent physical reality. This is achieved by comparing predicted and experimental system response quantities (SRQs) taking into account experimental and modelling uncertainties. Parameters which are required for the code input but not measured directly in the experiment can become an important source of uncertainty in the code validation process. Quantification of such parameters is often called input calibration. Calibration and uncertainty quantification may become challenging tasks when the number of calibrated input parameters and SRQs is large and dependencies between them are complex. If only engineering judgment is employed in the process, the outcome can be prone to so called “user effects”. The goal of this work is to develop an automated approach to input calibration and RELAP5 code validation against data on two-phase natural circulation flow instability. Multiple SRQs are used in both calibration and validation. In the input calibration, we used genetic algorithm (GA), a heuristic global optimization method, in order to minimize the discrepancy between experimental and simulation data by identifying optimal combinations of uncertain input parameters in the calibration process. We demonstrate the importance of the proper selection of SRQs and respective normalization and weighting factors in the fitness function. In the code validation, we used maximum flow rate as the

  12. Automation of RELAP5 input calibration and code validation using genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Phung, Viet-Anh, E-mail: vaphung@kth.se [Division of Nuclear Power Safety, Royal Institute of Technology, Roslagstullsbacken 21, 10691 Stockholm (Sweden); Kööp, Kaspar, E-mail: kaspar@safety.sci.kth.se [Division of Nuclear Power Safety, Royal Institute of Technology, Roslagstullsbacken 21, 10691 Stockholm (Sweden); Grishchenko, Dmitry, E-mail: dmitry@safety.sci.kth.se [Division of Nuclear Power Safety, Royal Institute of Technology, Roslagstullsbacken 21, 10691 Stockholm (Sweden); Vorobyev, Yury, E-mail: yura3510@gmail.com [National Research Center “Kurchatov Institute”, Kurchatov square 1, Moscow 123182 (Russian Federation); Kudinov, Pavel, E-mail: pavel@safety.sci.kth.se [Division of Nuclear Power Safety, Royal Institute of Technology, Roslagstullsbacken 21, 10691 Stockholm (Sweden)

    2016-04-15

    Highlights: • Automated input calibration and code validation using genetic algorithm is presented. • Predictions generally overlap experiments for individual system response quantities (SRQs). • It was not possible to predict simultaneously experimental maximum flow rate and oscillation period. • Simultaneous consideration of multiple SRQs is important for code validation. - Abstract: Validation of system thermal-hydraulic codes is an important step in application of the codes to reactor safety analysis. The goal of the validation process is to determine how well a code can represent physical reality. This is achieved by comparing predicted and experimental system response quantities (SRQs) taking into account experimental and modelling uncertainties. Parameters which are required for the code input but not measured directly in the experiment can become an important source of uncertainty in the code validation process. Quantification of such parameters is often called input calibration. Calibration and uncertainty quantification may become challenging tasks when the number of calibrated input parameters and SRQs is large and dependencies between them are complex. If only engineering judgment is employed in the process, the outcome can be prone to so called “user effects”. The goal of this work is to develop an automated approach to input calibration and RELAP5 code validation against data on two-phase natural circulation flow instability. Multiple SRQs are used in both calibration and validation. In the input calibration, we used genetic algorithm (GA), a heuristic global optimization method, in order to minimize the discrepancy between experimental and simulation data by identifying optimal combinations of uncertain input parameters in the calibration process. We demonstrate the importance of the proper selection of SRQs and respective normalization and weighting factors in the fitness function. In the code validation, we used maximum flow rate as the

  13. Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding

    Science.gov (United States)

    Carter, Charles W; Wills, Peter R

    2018-01-01

    Abstract Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. The resulting inversion symmetries in aaRS structural biology would have stabilized the initial and subsequent differentiation of coding specificities, rapidly promoting diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexive, nanoenvironmental sensing in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: 1) aaRS enzymes must be interdependent; 2) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; 3) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; and 4) the Central Dogma’s emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene–replicase–translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today. PMID:29077934

  14. Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.

    Directory of Open Access Journals (Sweden)

    Kiyofumi Hamashima

    Full Text Available The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs. However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNA(Gly (CCC and nev-tRNA(Ile (UAU, which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG codon and isoleucine (AUA codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3' end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.

  15. ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

    Science.gov (United States)

    Engqvist, Martin K M; Nielsen, Jens

    2015-08-21

    The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

  16. Validation of the U.S. NRC coupled code system TRITON/TRACE/PARCS with the special power excursion reactor test III (SPERT III)

    Energy Technology Data Exchange (ETDEWEB)

    Wang, R. C.; Xu, Y.; Downar, T. [Dept. of Nuclear Engineering and Radiological Sciences, Univ. of Michigan, Ann Arbor, MI 48104 (United States); Hudson, N. [RES Div., U.S. NRC, Rockville, MD (United States)

    2012-07-01

    The Special Power Excursion Reactor Test III (SPERT III) was a series of reactivity insertion experiments conducted in the 1950's. This paper describes the validation of the U.S. NRC Coupled Code system TRITON/PARCS/TRACE to simulate reactivity insertion accidents (RIA) by using several of the SPERT III tests. The work here used the SPERT III E-core configuration tests in which the RIA was initiated by ejecting a control rod. The resulting super-prompt reactivity excursion and negative reactivity feedback produced the familiar bell shaped power increase and decrease. The energy deposition during such a power peak has important safety consequences and provides validation basis for core coupled multi-physics codes. The transients of five separate tests are used to benchmark the PARCS/TRACE coupled code. The models were thoroughly validated using the original experiment documentation. (authors)

  17. Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

    Science.gov (United States)

    Santos, José; Monteagudo, Ángel

    2017-03-27

    The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

  18. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

    Science.gov (United States)

    Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

    2016-07-01

    The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. © 2016 Mühlhausen et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Adaptation and implementation of the TRACE code for transient analysis in designs lead cooled fast reactors; Adaptacion y aplicacion del codigo TRACE para el analisis de transitorios en disenos de reactores rapidos refrigerados por plomo

    Energy Technology Data Exchange (ETDEWEB)

    Lazaro, A.; Ammirabile, L.; Martorell, S.

    2015-07-01

    Lead-Cooled Fast Reactor (LFR) has been identified as one of promising future reactor concepts in the technology road map of the Generation IVC International Forum (GIF)as well as in the Deployment Strategy of the European Sustainable Nuclear Industrial Initiative (ESNII), both aiming at improved sustainability, enhanced safety, economic competitiveness, and proliferation resistance. This new nuclear reactor concept requires the development of computational tools to be applied in design and safety assessments to confirm improved inherent and passive safety features of this design. One approach to this issue is to modify the current computational codes developed for the simulation of Light Water Reactors towards their applicability for the new designs. This paper reports on the performed modifications of the TRACE system code to make it applicable to LFR safety assessments. The capabilities of the modified code are demonstrated on series of benchmark exercises performed versus other safety analysis codes. (Author)

  20. Uncertainty Methods Framework Development for the TRACE Thermal-Hydraulics Code by the U.S.NRC

    International Nuclear Information System (INIS)

    Bajorek, Stephen M.; Gingrich, Chester

    2013-01-01

    The Code of Federal Regulations, Title 10, Part 50.46 requires that the Emergency Core Cooling System (ECCS) performance be evaluated for a number of postulated Loss-Of-Coolant-Accidents (LOCAs). The rule allows two methods for calculation of the acceptance criteria; using a realistic model in the so-called 'Best Estimate' approach, or the more prescriptive following Appendix K to Part 50. Because of the conservatism of Appendix K, recent Evaluation Model submittals to the NRC used the realistic approach. With this approach, the Evaluation Model must demonstrate that the Peak Cladding Temperature (PCT), the Maximum Local Oxidation (MLO) and Core-Wide Oxidation (CWO) remain below their regulatory limits with a 'high probability'. Guidance for Best Estimate calculations following 50.46(a)(1) was provided by Regulatory Guide 1.157. This Guide identified a 95% probability level as being acceptable for comparisons of best-estimate predictions to the applicable regulatory limits, but was vague with respect to acceptable methods in which to determine the code uncertainty. Nor, did it specify if a confidence level should be determined. As a result, vendors have developed Evaluation Models utilizing several different methods to combine uncertainty parameters and determine the PCT and other variables to a high probability. In order to quantify the accuracy of TRACE calculations for a wide variety of applications and to audit Best Estimate calculations made by industry, the NRC is developing its own independent methodology to determine the peak cladding temperature and other parameters of regulatory interest to a high probability. Because several methods are in use, and each vendor's methodology ranges different parameters, the NRC method must be flexible and sufficiently general. Not only must the method apply to LOCA analysis for conventional light-water reactors, it must also be extendable to new reactor designs and type of analyses where the acceptance criteria are less

  1. Advanced Design of Dumbbell-shaped Genetic Minimal Vectors Improves Non-coding and Coding RNA Expression.

    Science.gov (United States)

    Jiang, Xiaoou; Yu, Han; Teo, Cui Rong; Tan, Genim Siu Xian; Goh, Sok Chin; Patel, Parasvi; Chua, Yiqiang Kevin; Hameed, Nasirah Banu Sahul; Bertoletti, Antonio; Patzel, Volker

    2016-09-01

    Dumbbell-shaped DNA minimal vectors lacking nontherapeutic genes and bacterial sequences are considered a stable, safe alternative to viral, nonviral, and naked plasmid-based gene-transfer systems. We investigated novel molecular features of dumbbell vectors aiming to reduce vector size and to improve the expression of noncoding or coding RNA. We minimized small hairpin RNA (shRNA) or microRNA (miRNA) expressing dumbbell vectors in size down to 130 bp generating the smallest genetic expression vectors reported. This was achieved by using a minimal H1 promoter with integrated transcriptional terminator transcribing the RNA hairpin structure around the dumbbell loop. Such vectors were generated with high conversion yields using a novel protocol. Minimized shRNA-expressing dumbbells showed accelerated kinetics of delivery and transcription leading to enhanced gene silencing in human tissue culture cells. In primary human T cells, minimized miRNA-expressing dumbbells revealed higher stability and triggered stronger target gene suppression as compared with plasmids and miRNA mimics. Dumbbell-driven gene expression was enhanced up to 56- or 160-fold by implementation of an intron and the SV40 enhancer compared with control dumbbells or plasmids. Advanced dumbbell vectors may represent one option to close the gap between durable expression that is achievable with integrating viral vectors and short-term effects triggered by naked RNA.

  2. An automatic scaling method for obtaining the trace and parameters from oblique ionogram based on hybrid genetic algorithm

    Science.gov (United States)

    Song, Huan; Hu, Yaogai; Jiang, Chunhua; Zhou, Chen; Zhao, Zhengyu; Zou, Xianjian

    2016-12-01

    Scaling oblique ionogram plays an important role in obtaining ionospheric structure at the midpoint of oblique sounding path. The paper proposed an automatic scaling method to extract the trace and parameters of oblique ionogram based on hybrid genetic algorithm (HGA). The extracted 10 parameters come from F2 layer and Es layer, such as maximum observation frequency, critical frequency, and virtual height. The method adopts quasi-parabolic (QP) model to describe F2 layer's electron density profile that is used to synthesize trace. And it utilizes secant theorem, Martyn's equivalent path theorem, image processing technology, and echoes' characteristics to determine seven parameters' best fit values, and three parameter's initial values in QP model to set up their searching spaces which are the needed input data of HGA. Then HGA searches the three parameters' best fit values from their searching spaces based on the fitness between the synthesized trace and the real trace. In order to verify the performance of the method, 240 oblique ionograms are scaled and their results are compared with manual scaling results and the inversion results of the corresponding vertical ionograms. The comparison results show that the scaling results are accurate or at least adequate 60-90% of the time.

  3. An Order Coding Genetic Algorithm to Optimize Fuel Reloads in a Nuclear Boiling Water Reactor

    International Nuclear Information System (INIS)

    Ortiz, Juan Jose; Requena, Ignacio

    2004-01-01

    A genetic algorithm is used to optimize the nuclear fuel reload for a boiling water reactor, and an order coding is proposed for the chromosomes and appropriate crossover and mutation operators. The fitness function was designed so that the genetic algorithm creates fuel reloads that, on one hand, satisfy the constrictions for the radial power peaking factor, the minimum critical power ratio, and the maximum linear heat generation rate while optimizing the effective multiplication factor at the beginning and end of the cycle. To find the values of these variables, a neural network trained with the behavior of a reactor simulator was used to predict them. The computation time is therefore greatly decreased in the search process. We validated this method with data from five cycles of the Laguna Verde Nuclear Power Plant in Mexico

  4. The standard genetic code and its relation to mutational pressure: robustness and equilibrium criteria

    International Nuclear Information System (INIS)

    Hernandez Caceres, Jose Luis; Hong, Rolando; Martinez Ortiz, Carlos; Sautie Castellanos, Miguel; Valdes, Kiria; Guevara Erra, Ramon

    2004-10-01

    Under the assumption of even point mutation pressure on the DNA strand, rates for transitions from one amino acid into another were assessed. Nearly 25% of all mutations were silent. About 48% of the mutations from a given amino acid stream either into the same amino acid or into an amino acid of the same class. These results suggest a great stability of the Standard Genetic Code respect to mutation load. Concepts from chemical equilibrium theory are applicable into this case provided that mutation rate constants are given. It was obtained that unequal synonymic codon usage may lead to changes in the equilibrium concentrations. Data from real biological species showed that several amino acids are close to the respective equilibrium concentration. However in all the cases the concentration of leucine nearly doubled its equilibrium concentration, whereas for the stop command (Term) it was about 10 times lower. The overall distance from equilibrium for a set of species suggests that eukaryotes are closer to equilibrium than prokaryotes, and the HIV virus was closest to equilibrium among 15 species. We obtained that contemporary species are closer to the equilibrium than the Last Universal Common Ancestor (LUCA) was. Similarly, nonpreserved regions in proteins are closer to equilibrium than the preserved ones. We suggest that this approach can be useful for exploring some aspects of biological evolution in the framework of Standard Genetic Code properties. (author)

  5. Mapping the Plasticity of the E. coli Genetic Code with Orthogonal Pair Directed Sense Codon Reassignment.

    Science.gov (United States)

    Schmitt, Margaret A; Biddle, Wil; Fisk, John Domenic

    2018-04-18

    The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in E. coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8% to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively-characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.

  6. A nuclear reload optimization approach using a real coded genetic algorithm with random keys

    International Nuclear Information System (INIS)

    Lima, Alan M.M. de; Schirru, Roberto; Medeiros, Jose A.C.C.

    2009-01-01

    The fuel reload of a Pressurized Water Reactor is made whenever the burn up of the fuel assemblies in the nucleus of the reactor reaches a certain value such that it is not more possible to maintain a critical reactor producing energy at nominal power. The problem of fuel reload optimization consists on determining the positioning of the fuel assemblies within the nucleus of the reactor in an optimized way to minimize the cost benefit relationship of fuel assemblies cost per maximum burn up, and also satisfying symmetry and safety restrictions. The fuel reload optimization problem difficulty grows exponentially with the number of fuel assemblies in the nucleus of the reactor. During decades the fuel reload optimization problem was solved manually by experts that used their knowledge and experience to build configurations of the reactor nucleus, and testing them to verify if safety restrictions of the plant are satisfied. To reduce this burden, several optimization techniques have been used, included the binary code genetic algorithm. In this work we show the use of a real valued coded approach of the genetic algorithm, with different recombination methods, together with a transformation mechanism called random keys, to transform the real values of the genes of each chromosome in a combination of discrete fuel assemblies for evaluation of the reload optimization. Four different recombination methods were tested: discrete recombination, intermediate recombination, linear recombination and extended linear recombination. For each of the 4 recombination methods 10 different tests using different seeds for the random number generator were conducted 10 generating, totaling 40 tests. The results of the application of the genetic algorithm are shown with formulation of real numbers for the problem of the nuclear reload of the plant Angra 1 type PWR. Since the best results in the literature for this problem were found by the parallel PSO we will it use for comparison

  7. About the use of the Monte-Carlo code based tracing algorithm and the volume fraction method for S n full core calculations

    Energy Technology Data Exchange (ETDEWEB)

    Gurevich, M. I.; Oleynik, D. S. [RRC Kurchatov Inst., Kurchatov Sq., 1, 123182, Moscow (Russian Federation); Russkov, A. A.; Voloschenko, A. M. [Keldysh Inst. of Applied Mathematics, Miusskaya Sq., 4, 125047, Moscow (Russian Federation)

    2006-07-01

    The tracing algorithm that is implemented in the geometrical module of Monte-Carlo transport code MCU is applied to calculate the volume fractions of original materials by spatial cells of the mesh that overlays problem geometry. In this way the 3D combinatorial geometry presentation of the problem geometry, used by MCU code, is transformed to the user defined 2D or 3D bit-mapped ones. Next, these data are used in the volume fraction (VF) method to approximate problem geometry by introducing additional mixtures for spatial cells, where a few original materials are included. We have found that in solving realistic 2D and 3D core problems a sufficiently fast convergence of the VF method takes place if the spatial mesh is refined. Virtually, the proposed variant of implementation of the VF method seems as a suitable geometry interface between Monte-Carlo and S{sub n} transport codes. (authors)

  8. A sensitive method to extract DNA from biological traces present on ammunition for the purpose of genetic profiling.

    Science.gov (United States)

    Dieltjes, Patrick; Mieremet, René; Zuniga, Sofia; Kraaijenbrink, Thirsa; Pijpe, Jeroen; de Knijff, Peter

    2011-07-01

    Exploring technological limits is a common practice in forensic DNA research. Reliable genetic profiling based on only a few cells isolated from trace material retrieved from a crime scene is nowadays more and more the rule rather than the exception. On many crime scenes, cartridges, bullets, and casings (jointly abbreviated as CBCs) are regularly found, and even after firing, these potentially carry trace amounts of biological material. Since 2003, the Forensic Laboratory for DNA Research is routinely involved in the forensic investigation of CBCs in the Netherlands. Reliable DNA profiles were frequently obtained from CBCs and used to match suspects, victims, or other crime scene-related DNA traces. In this paper, we describe the sensitive method developed by us to extract DNA from CBCs. Using PCR-based genotyping of autosomal short tandem repeats, we were able to obtain reliable and reproducible DNA profiles in 163 out of 616 criminal cases (26.5%) and in 283 out of 4,085 individual CBC items (6.9%) during the period January 2003-December 2009. We discuss practical aspects of the method and the sometimes unexpected effects of using cell lysis buffer on the subsequent investigation of striation patterns on CBCs.

  9. Genetic coding and united-hypercomplex systems in the models of algebraic biology.

    Science.gov (United States)

    Petoukhov, Sergey V

    2017-08-01

    Structured alphabets of DNA and RNA in their matrix form of representations are connected with Walsh functions and a new type of systems of multidimensional numbers. This type generalizes systems of complex numbers and hypercomplex numbers, which serve as the basis of mathematical natural sciences and many technologies. The new systems of multi-dimensional numbers have interesting mathematical properties and are called in a general case as "systems of united-hypercomplex numbers" (or briefly "U-hypercomplex numbers"). They can be widely used in models of multi-parametrical systems in the field of algebraic biology, artificial life, devices of biological inspired artificial intelligence, etc. In particular, an application of U-hypercomplex numbers reveals hidden properties of genetic alphabets under cyclic permutations in their doublets and triplets. A special attention is devoted to the author's hypothesis about a multi-linguistic in DNA-sequences in a relation with an ensemble of U-numerical sub-alphabets. Genetic multi-linguistic is considered as an important factor to provide noise-immunity properties of the multi-channel genetic coding. Our results attest to the conformity of the algebraic properties of the U-numerical systems with phenomenological properties of the DNA-alphabets and with the complementary device of the double DNA-helix. It seems that in the modeling field of algebraic biology the genetic-informational organization of living bodies can be considered as a set of united-hypercomplex numbers in some association with the famous slogan of Pythagoras "the numbers rule the world". Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Translation of the model plant of the CN code TRAC-BF1 Cofrentes of a SNAP-TRACE; Traduccion del modelo de planta de CN Cofrentes del codigo TRAC-BF1 a SNAP-TRACE

    Energy Technology Data Exchange (ETDEWEB)

    Escriva, A.; Munuz-Cobo, J. L.; Concejal, A.; Melara, J.; Albendea, M.

    2012-07-01

    It aims to develop a three-dimensional model of the CN Cofrentes whose consistent results Compared with those in current use programs (TRAC-BFl, RETRAN) validated with data of the plant. This comparison should be done globally and that you can not carry a compensation of errors. To check the correct translation of the results obtained have been compared with TRACE and the programs currently in use and the relevant adjustments have been made, taking into account that both the correlations and models are different codes. During the completion of this work we have detected several errors that must be corrected in future versions of these tools.

  11. Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code.

    Science.gov (United States)

    Hauf, Matthias; Richter, Florian; Schneider, Tobias; Faidt, Thomas; Martins, Berta M; Baumann, Tobias; Durkin, Patrick; Dobbek, Holger; Jacobs, Karin; Möglich, Andreas; Budisa, Nediljko

    2017-09-19

    Marine mussels exhibit potent underwater adhesion abilities under hostile conditions by employing 3,4-dihydroxyphenylalanine (DOPA)-rich mussel adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Herein, a novel strategy based on genetic code expansion has been developed by engineering efficient aminoacyl-transfer RNA synthetases (aaRSs) for the photocaged noncanonical amino acid ortho-nitrobenzyl DOPA (ONB-DOPA). The engineered ONB-DOPARS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-DOPA to yield photocaged, spatiotemporally controlled underwater adhesives. Upon exposure to UV light, these proteins feature elevated wet adhesion properties. This concept offers new perspectives for the production of recombinant bioadhesives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Tracing the evolution of male lineages in bears using genetic markers on the Y chromosome

    OpenAIRE

    Bidon, Tobias

    2015-01-01

    The mammalian family of bears (Ursidae) comprises eight extant species, occurring on four different continents. Among them are the iconic and well-known brown and polar bears, both widely distributed across the Northern hemisphere. Their intraspecific genetic structuring has been extensively investigated, albeit with a focus on genetic markers from maternally inherited parts of their genomes (mitochondrial DNA). The evolutionary relationship and divergence time between brown and polar bears h...

  13. Genetic Tracing of Jatropha curcas L. from Its Mesoamerican Origin to the World

    Science.gov (United States)

    Li, Haiyan; Tsuchimoto, Suguru; Harada, Kyuya; Yamasaki, Masanori; Sakai, Hiroe; Wada, Naoki; Alipour, Atefeh; Sasai, Tomohiro; Tsunekawa, Atsushi; Tsujimoto, Hisashi; Ando, Takayuki; Tomemori, Hisashi; Sato, Shusei; Hirakawa, Hideki; Quintero, Victor P.; Zamarripa, Alfredo; Santos, Primitivo; Hegazy, Adel; Ali, Abdalla M.; Fukui, Kiichi

    2017-01-01

    Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change. PMID:28936216

  14. Genetic Tracing of Jatropha curcas L. from Its Mesoamerican Origin to the World

    Directory of Open Access Journals (Sweden)

    Haiyan Li

    2017-09-01

    Full Text Available Jatropha curcas L. (Jatropha, a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change.

  15. Genetic Tracing of Jatropha curcas L. from Its Mesoamerican Origin to the World.

    Science.gov (United States)

    Li, Haiyan; Tsuchimoto, Suguru; Harada, Kyuya; Yamasaki, Masanori; Sakai, Hiroe; Wada, Naoki; Alipour, Atefeh; Sasai, Tomohiro; Tsunekawa, Atsushi; Tsujimoto, Hisashi; Ando, Takayuki; Tomemori, Hisashi; Sato, Shusei; Hirakawa, Hideki; Quintero, Victor P; Zamarripa, Alfredo; Santos, Primitivo; Hegazy, Adel; Ali, Abdalla M; Fukui, Kiichi

    2017-01-01

    Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change.

  16. Analysis of PWR control rod ejection accident with the coupled code system SKETCH-INS/TRACE by incorporating pin power reconstruction model

    International Nuclear Information System (INIS)

    Nakajima, T.; Sakai, T.

    2010-01-01

    The pin power reconstruction model was incorporated in the 3-D nodal kinetics code SKETCH-INS in order to produce accurate calculation of three-dimensional pin power distributions throughout the reactor core. In order to verify the employed pin power reconstruction model, the PWR MOX/UO_2 core transient benchmark problem was analyzed with the coupled code system SKETCH-INS/TRACE by incorporating the model and the influence of pin power reconstruction model was studied. SKETCH-INS pin power distributions for 3 benchmark problems were compared with the PARCS solutions which were provided by the host organisation of the benchmark. SKETCH-INS results were in good agreement with the PARCS results. The capability of employed pin power reconstruction model was confirmed through the analysis of benchmark problems. A PWR control rod ejection benchmark problem was analyzed with the coupled code system SKETCH-INS/ TRACE by incorporating the pin power reconstruction model. The influence of pin power reconstruction model was studied by comparing with the result of conventional node averaged flux model. The results indicate that the pin power reconstruction model has significant effect on the pin powers during transient and hence on the fuel enthalpy

  17. From chemical metabolism to life: the origin of the genetic coding process

    Directory of Open Access Journals (Sweden)

    Antoine Danchin

    2017-06-01

    Full Text Available Looking for origins is so much rooted in ideology that most studies reflect opinions that fail to explore the first realistic scenarios. To be sure, trying to understand the origins of life should be based on what we know of current chemistry in the solar system and beyond. There, amino acids and very small compounds such as carbon dioxide, dihydrogen or dinitrogen and their immediate derivatives are ubiquitous. Surface-based chemical metabolism using these basic chemicals is the most likely beginning in which amino acids, coenzymes and phosphate-based small carbon molecules were built up. Nucleotides, and of course RNAs, must have come to being much later. As a consequence, the key question to account for life is to understand how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to carry over the basic metabolic pathways that drive the pursuit of life.

  18. Chromatin remodeling: the interface between extrinsic cues and the genetic code?

    Science.gov (United States)

    Ezzat, Shereen

    2008-10-01

    The successful completion of the human genome project ushered a new era of hope and skepticism. However, the promise of finding the fundamental basis of human traits and diseases appears less than fulfilled. The original premise was that the DNA sequence of every gene would allow precise characterization of critical differences responsible for altered cellular functions. The characterization of intragenic mutations in cancers paved the way for early screening and the design of targeted therapies. However, it has also become evident that unmasking genetic codes alone cannot explain the diversity of disease phenotypes within a population. Further, classic genetics has not been able to explain the differences that have been observed among identical twins or even cloned animals. This new reality has re-ignited interest in the field of epigenetics. While traditionally defined as heritable changes that can alter gene expression without affecting the corresponding DNA sequence, this definition has come into question. The extent to which epigenetic change can also be acquired in response to chemical stimuli represents an exciting dimension in the "nature vs nurture" debate. In this review I will describe a series of studies in my laboratory that illustrate the significance of epigenetics and its potential clinical implications.

  19. Conventional and genetic talent identification in sports: will recent developments trace talent?

    Science.gov (United States)

    Breitbach, Sarah; Tug, Suzan; Simon, Perikles

    2014-11-01

    The purpose of talent identification (TI) is the earliest possible selection of auspicious athletes with the goal of systematically maximizing their potential. The literature proposes excellent reviews on various facets of talent research on different scientific issues such as sports sciences or genetics. However, the approaches of conventional and genetic testing have only been discussed separately by and for the respective groups of interest. In this article, we combine the discoveries of these disciplines into a single review to provide a comprehensive overview and elucidate the prevailing limitations. Fundamental problems in TI reside in the difficulties of defining the construct ‘talent’ or groups of different performance levels that represent the target variable of testing. Conventional and genetic testing reveal a number of methodological and technical limitations, and parallels are summarised in terms of the test designs, the point in time of testing, psychological skills or traits and unknown interactions between different variables. In conclusion, many deficiencies in the current talent research have gained attention. Alternative solutions include the talent development approach, while genetic testing is re-emphasised as a tool for risk stratification in sport participation. Future research needs to clearly define the group of interest and comprehensively implement all methodological improvement suggestions.

  20. ARDISC (Argonne Dispersion Code): computer programs to calculate the distribution of trace element migration in partially equilibrating media

    International Nuclear Information System (INIS)

    Strickert, R.; Friedman, A.M.; Fried, S.

    1979-04-01

    A computer program (ARDISC, the Argonne Dispersion Code) is described which simulates the migration of nuclides in porous media and includes first order kinetic effects on the retention constants. The code allows for different absorption and desorption rates and solves the coupled migration equations by arithmetic reiterations. Input data needed are the absorption and desorption rates, equilibrium surface absorption coefficients, flow rates and volumes, and media porosities

  1. Nanoparticle based bio-bar code technology for trace analysis of aflatoxin B1 in Chinese herbs

    Directory of Open Access Journals (Sweden)

    Yu-yan Yu

    2018-04-01

    Full Text Available A novel and sensitive assay for aflatoxin B1 (AFB1 detection has been developed by using bio-bar code assay (BCA. The method that relies on polyclonal antibodies encoded with DNA modified gold nanoparticle (NP and monoclonal antibodies modified magnetic microparticle (MMP, and subsequent detection of amplified target in the form of bio-bar code using a fluorescent quantitative polymerase chain reaction (FQ-PCR detection method. First, NP probes encoded with DNA that was unique to AFB1, MMP probes with monoclonal antibodies that bind AFB1 specifically were prepared. Then, the MMP-AFB1-NP sandwich compounds were acquired, dehybridization of the oligonucleotides on the nanoparticle surface allows the determination of the presence of AFB1 by identifying the oligonucleotide sequence released from the NP through FQ-PCR detection. The bio-bar code techniques system for detecting AFB1 was established, and the sensitivity limit was about 10−8 ng/mL, comparable ELISA assays for detecting the same target, it showed that we can detect AFB1 at low attomolar levels with the bio-bar-code amplification approach. This is also the first demonstration of a bio-bar code type assay for the detection of AFB1 in Chinese herbs. Keywords: Aflatoxin B1, Bio-bar code assay, Chinese herbs, Magnetic microparticle probes, Nanoparticle probes

  2. FishPopTrace: a new genetic technique for fisheries monitoring and the identification of IUU

    DEFF Research Database (Denmark)

    Helyar, Sarah; Limborg, Morten; Bekkevold, Dorte

    2012-01-01

    nucleotide polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. In addition, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability....../authenticity of products throughout the food supply chain, allowing effective enforcement of fisheries regulations, and the identification of IUU. Here we demonstrate the utility of SNP panels developed in a European Commission‐funded consortium, FishPopTrace, to scenarios that are relevant for the identification......The importance of marine organisms for both economic and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilization and conservation of exploited fish stocks. However, in most cases our understanding of these spatial patterns...

  3. Sparse genetic tracing reveals regionally specific functional organization of mammalian nociceptors.

    Science.gov (United States)

    Olson, William; Abdus-Saboor, Ishmail; Cui, Lian; Burdge, Justin; Raabe, Tobias; Ma, Minghong; Luo, Wenqin

    2017-10-12

    The human distal limbs have a high spatial acuity for noxious stimuli but a low density of pain-sensing neurites. To elucidate mechanisms underlying regional differences in processing nociception, we sparsely traced non-peptidergic nociceptors across the body using a newly generated Mrgprd CreERT2 mouse line. We found that mouse plantar paw skin is also innervated by a low density of Mrgprd + nociceptors, while individual arbors in different locations are comparable in size. Surprisingly, the central arbors of plantar paw and trunk innervating nociceptors have distinct morphologies in the spinal cord. This regional difference is well correlated with a heightened signal transmission for plantar paw circuits, as revealed by both spinal cord slice recordings and behavior assays. Taken together, our results elucidate a novel somatotopic functional organization of the mammalian pain system and suggest that regional central arbor structure could facilitate the "enlarged representation" of plantar paw regions in the CNS.

  4. Assessing flow paths in a karst aquifer based on multiple dye tracing tests using stochastic simulation and the MODFLOW-CFP code

    Science.gov (United States)

    Assari, Amin; Mohammadi, Zargham

    2017-09-01

    Karst systems show high spatial variability of hydraulic parameters over small distances and this makes their modeling a difficult task with several uncertainties. Interconnections of fractures have a major role on the transport of groundwater, but many of the stochastic methods in use do not have the capability to reproduce these complex structures. A methodology is presented for the quantification of tortuosity using the single normal equation simulation (SNESIM) algorithm and a groundwater flow model. A training image was produced based on the statistical parameters of fractures and then used in the simulation process. The SNESIM algorithm was used to generate 75 realizations of the four classes of fractures in a karst aquifer in Iran. The results from six dye tracing tests were used to assign hydraulic conductivity values to each class of fractures. In the next step, the MODFLOW-CFP and MODPATH codes were consecutively implemented to compute the groundwater flow paths. The 9,000 flow paths obtained from the MODPATH code were further analyzed to calculate the tortuosity factor. Finally, the hydraulic conductivity values calculated from the dye tracing experiments were refined using the actual flow paths of groundwater. The key outcomes of this research are: (1) a methodology for the quantification of tortuosity; (2) hydraulic conductivities, that are incorrectly estimated (biased low) with empirical equations that assume Darcian (laminar) flow with parallel rather than tortuous streamlines; and (3) an understanding of the scale-dependence and non-normal distributions of tortuosity.

  5. Use of fluorescent proteins and color-coded imaging to visualize cancer cells with different genetic properties.

    Science.gov (United States)

    Hoffman, Robert M

    2016-03-01

    Fluorescent proteins are very bright and available in spectrally-distinct colors, enable the imaging of color-coded cancer cells growing in vivo and therefore the distinction of cancer cells with different genetic properties. Non-invasive and intravital imaging of cancer cells with fluorescent proteins allows the visualization of distinct genetic variants of cancer cells down to the cellular level in vivo. Cancer cells with increased or decreased ability to metastasize can be distinguished in vivo. Gene exchange in vivo which enables low metastatic cancer cells to convert to high metastatic can be color-coded imaged in vivo. Cancer stem-like and non-stem cells can be distinguished in vivo by color-coded imaging. These properties also demonstrate the vast superiority of imaging cancer cells in vivo with fluorescent proteins over photon counting of luciferase-labeled cancer cells.

  6. Nanoparticle based bio-bar code technology for trace analysis of aflatoxin B1 in Chinese herbs.

    Science.gov (United States)

    Yu, Yu-Yan; Chen, Yuan-Yuan; Gao, Xuan; Liu, Yuan-Yuan; Zhang, Hong-Yan; Wang, Tong-Ying

    2018-04-01

    A novel and sensitive assay for aflatoxin B1 (AFB1) detection has been developed by using bio-bar code assay (BCA). The method that relies on polyclonal antibodies encoded with DNA modified gold nanoparticle (NP) and monoclonal antibodies modified magnetic microparticle (MMP), and subsequent detection of amplified target in the form of bio-bar code using a fluorescent quantitative polymerase chain reaction (FQ-PCR) detection method. First, NP probes encoded with DNA that was unique to AFB1, MMP probes with monoclonal antibodies that bind AFB1 specifically were prepared. Then, the MMP-AFB1-NP sandwich compounds were acquired, dehybridization of the oligonucleotides on the nanoparticle surface allows the determination of the presence of AFB1 by identifying the oligonucleotide sequence released from the NP through FQ-PCR detection. The bio-bar code techniques system for detecting AFB1 was established, and the sensitivity limit was about 10 -8  ng/mL, comparable ELISA assays for detecting the same target, it showed that we can detect AFB1 at low attomolar levels with the bio-bar-code amplification approach. This is also the first demonstration of a bio-bar code type assay for the detection of AFB1 in Chinese herbs. Copyright © 2017. Published by Elsevier B.V.

  7. Maximization Network Throughput Based on Improved Genetic Algorithm and Network Coding for Optical Multicast Networks

    Science.gov (United States)

    Wei, Chengying; Xiong, Cuilian; Liu, Huanlin

    2017-12-01

    Maximal multicast stream algorithm based on network coding (NC) can improve the network's throughput for wavelength-division multiplexing (WDM) networks, which however is far less than the network's maximal throughput in terms of theory. And the existing multicast stream algorithms do not give the information distribution pattern and routing in the meantime. In the paper, an improved genetic algorithm is brought forward to maximize the optical multicast throughput by NC and to determine the multicast stream distribution by hybrid chromosomes construction for multicast with single source and multiple destinations. The proposed hybrid chromosomes are constructed by the binary chromosomes and integer chromosomes, while the binary chromosomes represent optical multicast routing and the integer chromosomes indicate the multicast stream distribution. A fitness function is designed to guarantee that each destination can receive the maximum number of decoding multicast streams. The simulation results showed that the proposed method is far superior over the typical maximal multicast stream algorithms based on NC in terms of network throughput in WDM networks.

  8. Physicochemical basis for the origin of the genetic code - Lecture 3

    International Nuclear Information System (INIS)

    Ponnamperuma, C.

    1992-01-01

    A study of the association of homocodonic amino acids and selected heterocodonic amino acids with selected nucleotides in aqueous solution was undertaken to examine a possible physical basis for the origin of codon assignments. These interactions were studied using 1H nuclear magnetic resonance spectroscopy (NMR). Association constants for the various interactions were determined by fitting the changes in the chemical shifts of the anomeric and ring protons of the nucleoside moieties as a function of amino acid concentration to an isotherm which described the binding interaction. The strongest association of all homocodonic amino acids were with their respective anticodonic nucleotide sequences. The strength of association was seen to increase with increase in the chain length of the anticodonic nucleotide. The association of these amino acids with different phosphate esters of nucleotides suggests that a definite isomeric structure is required for association with a specified amino acid; the 5'-mononucleotides and (3'-5')-linked dinucleotides are the favored geometries for strong associations. Use of heterocodonic amino acids and nonprotein amino acids supports these findings. We conclude that there is at least a physicochemical, anticodonic contribution to the origin of the genetic code. (author)

  9. Enhancement of combined heat and power economic dispatch using self adaptive real-coded genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Subbaraj, P. [Kalasalingam University, Srivilliputhur, Tamilnadu 626 190 (India); Rengaraj, R. [Electrical and Electronics Engineering, S.S.N. College of Engineering, Old Mahabalipuram Road, Thirupporur (T.K), Kalavakkam, Kancheepuram (Dist.) 603 110, Tamilnadu (India); Salivahanan, S. [S.S.N. College of Engineering, Old Mahabalipuram Road, Thirupporur (T.K), Kalavakkam, Kancheepuram (Dist.) 603 110, Tamilnadu (India)

    2009-06-15

    In this paper, a self adaptive real-coded genetic algorithm (SARGA) is implemented to solve the combined heat and power economic dispatch (CHPED) problem. The self adaptation is achieved by means of tournament selection along with simulated binary crossover (SBX). The selection process has a powerful exploration capability by creating tournaments between two solutions. The better solution is chosen and placed in the mating pool leading to better convergence and reduced computational burden. The SARGA integrates penalty parameterless constraint handling strategy and simultaneously handles equality and inequality constraints. The population diversity is introduced by making use of distribution index in SBX operator to create a better offspring. This leads to a high diversity in population which can increase the probability towards the global optimum and prevent premature convergence. The SARGA is applied to solve CHPED problem with bounded feasible operating region which has large number of local minima. The numerical results demonstrate that the proposed method can find a solution towards the global optimum and compares favourably with other recent methods in terms of solution quality, handling constraints and computation time. (author)

  10. A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Adi Oron-Gottesman

    2016-11-01

    Full Text Available Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM, composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF-like element in ribosomal protein bS1 (bacterial S1, apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA.

  11. The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization.

    Science.gov (United States)

    Błażej, Paweł; Wnȩtrzak, Małgorzata; Mackiewicz, Paweł

    2016-12-01

    One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure

  12. Feral Cat Globetrotters: genetic traces of historical human-mediated dispersal.

    Science.gov (United States)

    Koch, Katrin; Algar, Dave; Schwenk, Klaus

    2016-08-01

    Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA (ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human-mediated global dispersal patterns of feral cats.

  13. On the Impact of Zero-padding in Network Coding Efficiency with Internet Traffic and Video Traces

    DEFF Research Database (Denmark)

    Taghouti, Maroua; Roetter, Daniel Enrique Lucani; Pedersen, Morten Videbæk

    2016-01-01

    Random Linear Network Coding (RLNC) theoretical results typically assume that packets have equal sizes while in reality, data traffic presents a random packet size distribution. Conventional wisdom considers zero-padding of original packets as a viable alternative, but its effect can reduce the e...

  14. Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

    Science.gov (United States)

    Gussow, Ayal B; Copeland, Brett R; Dhindsa, Ryan S; Wang, Quanli; Petrovski, Slavé; Majoros, William H; Allen, Andrew S; Goldstein, David B

    2017-01-01

    There is broad agreement that genetic mutations occurring outside of the protein-coding regions play a key role in human disease. Despite this consensus, we are not yet capable of discerning which portions of non-coding sequence are important in the context of human disease. Here, we present Orion, an approach that detects regions of the non-coding genome that are depleted of variation, suggesting that the regions are intolerant of mutations and subject to purifying selection in the human lineage. We show that Orion is highly correlated with known intolerant regions as well as regions that harbor putatively pathogenic variation. This approach provides a mechanism to identify pathogenic variation in the human non-coding genome and will have immediate utility in the diagnostic interpretation of patient genomes and in large case control studies using whole-genome sequences.

  15. Quantum Genetics in terms of Quantum Reversible Automata and Quantum Computation of Genetic Codes and Reverse Transcription

    CERN Document Server

    Baianu,I C

    2004-01-01

    The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In previous publications (Baianu,1971a, b) the formal concept of quantum automaton and quantum computation, respectively, were introduced and their possible implications for genetic processes and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b; 1977; 1987; 2004; Baianu et al, 2004). The notions of topological semigroup, quantum automaton, or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebra...

  16. The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

    Science.gov (United States)

    Di Giulio, Massimo

    2017-11-07

    The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal

  17. Genetic traces of east-to-west human expansion waves in Eurasia.

    Science.gov (United States)

    Chaix, Raphaëlle; Austerlitz, Frédéric; Hegay, Tatyana; Quintana-Murci, Lluís; Heyer, Evelyne

    2008-07-01

    In this study, we describe the landscape of human demographic expansions in Eurasia using a large continental Y chromosome and mitochondrial DNA dataset. Variation at these two uniparentally-inherited genetic systems retraces expansions that occurred in the past 60 ky, and shows a clear decrease of expansion ages from east to west Eurasia. To investigate the demographic events at the origin of this westward decrease of expansion ages, the estimated divergence ages between Eurasian populations are compared with the estimated expansion ages within each population. Both markers suggest that the demographic expansion diffused from east to west in Eurasia in a demic way, i.e., through migrations of individuals (and not just through diffusion of new technologies), highlighting the prominent role of eastern regions within Eurasia during Palaeolithic times. (c) 2008 Wiley-Liss, Inc.

  18. A binary mixed integer coded genetic algorithm for multi-objective optimization of nuclear research reactor fuel reloading

    International Nuclear Information System (INIS)

    Binh, Do Quang; Huy, Ngo Quang; Hai, Nguyen Hoang

    2014-01-01

    This paper presents a new approach based on a binary mixed integer coded genetic algorithm in conjunction with the weighted sum method for multi-objective optimization of fuel loading patterns for nuclear research reactors. The proposed genetic algorithm works with two types of chromosomes: binary and integer chromosomes, and consists of two types of genetic operators: one working on binary chromosomes and the other working on integer chromosomes. The algorithm automatically searches for the most suitable weighting factors of the weighting function and the optimal fuel loading patterns in the search process. Illustrative calculations are implemented for a research reactor type TRIGA MARK II loaded with the Russian VVR-M2 fuels. Results show that the proposed genetic algorithm can successfully search for both the best weighting factors and a set of approximate optimal loading patterns that maximize the effective multiplication factor and minimize the power peaking factor while satisfying operational and safety constraints for the research reactor.

  19. A binary mixed integer coded genetic algorithm for multi-objective optimization of nuclear research reactor fuel reloading

    Energy Technology Data Exchange (ETDEWEB)

    Binh, Do Quang [University of Technical Education Ho Chi Minh City (Viet Nam); Huy, Ngo Quang [University of Industry Ho Chi Minh City (Viet Nam); Hai, Nguyen Hoang [Centre for Research and Development of Radiation Technology, Ho Chi Minh City (Viet Nam)

    2014-12-15

    This paper presents a new approach based on a binary mixed integer coded genetic algorithm in conjunction with the weighted sum method for multi-objective optimization of fuel loading patterns for nuclear research reactors. The proposed genetic algorithm works with two types of chromosomes: binary and integer chromosomes, and consists of two types of genetic operators: one working on binary chromosomes and the other working on integer chromosomes. The algorithm automatically searches for the most suitable weighting factors of the weighting function and the optimal fuel loading patterns in the search process. Illustrative calculations are implemented for a research reactor type TRIGA MARK II loaded with the Russian VVR-M2 fuels. Results show that the proposed genetic algorithm can successfully search for both the best weighting factors and a set of approximate optimal loading patterns that maximize the effective multiplication factor and minimize the power peaking factor while satisfying operational and safety constraints for the research reactor.

  20. FitSKIRT: genetic algorithms to automatically fit dusty galaxies with a Monte Carlo radiative transfer code

    Science.gov (United States)

    De Geyter, G.; Baes, M.; Fritz, J.; Camps, P.

    2013-02-01

    We present FitSKIRT, a method to efficiently fit radiative transfer models to UV/optical images of dusty galaxies. These images have the advantage that they have better spatial resolution compared to FIR/submm data. FitSKIRT uses the GAlib genetic algorithm library to optimize the output of the SKIRT Monte Carlo radiative transfer code. Genetic algorithms prove to be a valuable tool in handling the multi- dimensional search space as well as the noise induced by the random nature of the Monte Carlo radiative transfer code. FitSKIRT is tested on artificial images of a simulated edge-on spiral galaxy, where we gradually increase the number of fitted parameters. We find that we can recover all model parameters, even if all 11 model parameters are left unconstrained. Finally, we apply the FitSKIRT code to a V-band image of the edge-on spiral galaxy NGC 4013. This galaxy has been modeled previously by other authors using different combinations of radiative transfer codes and optimization methods. Given the different models and techniques and the complexity and degeneracies in the parameter space, we find reasonable agreement between the different models. We conclude that the FitSKIRT method allows comparison between different models and geometries in a quantitative manner and minimizes the need of human intervention and biasing. The high level of automation makes it an ideal tool to use on larger sets of observed data.

  1. Validation of the TRACE code for the system dynamic simulations of the molten salt reactor experiment and the preliminary study on the dual fluid molten salt reactor

    International Nuclear Information System (INIS)

    He, Xun

    2016-01-01

    MSR concept using the mathematic tools. In particular, the aim of the first part is to demonstrate the suitability of the TRACE code for the similar MSR designs by using a modified version of the TRACE code to implement the simulations for the steady-state, transient and accidental conditions. The basic approach of this part is to couple the thermal-hydraulic model and the modified point-kinetic model. The equivalent thermal-hydraulic model of the MSRE was built in 1D with three loops including all the critical main components. The point-kinetic model was improved through considering the precursor drift in order to produce more practical results in terms of the delayed neutron behavior. Additionally, new working fluids, namely the molten salts, were embedded into the source code of TRACE. Most results of the simulations show good agreements with the ORNL's reports and with another recent study and the errors were predictable and in an acceptable range. Therefore, the necessary code modification of TRACE appears to be successful and the model will be refined and its functions will be extended further in order to investigate new MSR design. Another part of this thesis is to implement a preliminary study on a new concept of molten salt reactor, namely the Dual Fluid Reactor (DFR). The DFR belongs to the group of the molten salt fast reactors (MSFR) and it is recently considered to be an option of minimum-waste and inherently safe operation of the nuclear reactors in the future. The DFR is using two separately circulating fluids in the reactor core. One is the fuel salt based on the mixture of tri-chlorides of uranium and plutonium (UCl_3-PuCl_3), while another is the coolant composed of the pure lead (Pb). The current work focuses on the basic dynamic behavior of a scaled-down DFR with 500 MW thermal output (DFR-500) instead of its reference design with 3000 MW thermal output (DFR-3000). For this purpose 10 parallel single fuel channels, as the representative samples

  2. Validation of the TRACE code for the system dynamic simulations of the molten salt reactor experiment and the preliminary study on the dual fluid molten salt reactor

    Energy Technology Data Exchange (ETDEWEB)

    He, Xun

    2016-06-14

    one is about the demonstration of a new MSR concept using the mathematic tools. In particular, the aim of the first part is to demonstrate the suitability of the TRACE code for the similar MSR designs by using a modified version of the TRACE code to implement the simulations for the steady-state, transient and accidental conditions. The basic approach of this part is to couple the thermal-hydraulic model and the modified point-kinetic model. The equivalent thermal-hydraulic model of the MSRE was built in 1D with three loops including all the critical main components. The point-kinetic model was improved through considering the precursor drift in order to produce more practical results in terms of the delayed neutron behavior. Additionally, new working fluids, namely the molten salts, were embedded into the source code of TRACE. Most results of the simulations show good agreements with the ORNL's reports and with another recent study and the errors were predictable and in an acceptable range. Therefore, the necessary code modification of TRACE appears to be successful and the model will be refined and its functions will be extended further in order to investigate new MSR design. Another part of this thesis is to implement a preliminary study on a new concept of molten salt reactor, namely the Dual Fluid Reactor (DFR). The DFR belongs to the group of the molten salt fast reactors (MSFR) and it is recently considered to be an option of minimum-waste and inherently safe operation of the nuclear reactors in the future. The DFR is using two separately circulating fluids in the reactor core. One is the fuel salt based on the mixture of tri-chlorides of uranium and plutonium (UCl{sub 3}-PuCl{sub 3}), while another is the coolant composed of the pure lead (Pb). The current work focuses on the basic dynamic behavior of a scaled-down DFR with 500 MW thermal output (DFR-500) instead of its reference design with 3000 MW thermal output (DFR-3000). For this purpose 10 parallel

  3. PCR-free quantitative detection of genetically modified organism from raw materials. An electrochemiluminescence-based bio bar code method.

    Science.gov (United States)

    Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R

    2008-05-15

    A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.

  4. Breaking the code: Statistical methods and methodological issues in psychiatric genetics

    NARCIS (Netherlands)

    Stringer, S.

    2015-01-01

    The genome-wide association (GWA) era has confirmed the heritability of many psychiatric disorders, most notably schizophrenia. Thousands of genetic variants with individually small effect sizes cumulatively constitute a large contribution to the heritability of psychiatric disorders. This thesis

  5. [Assisted reproduction and artificial insemination and genetic manipulation in the Criminal Code of the Federal District, Mexico].

    Science.gov (United States)

    Brena Sesma, Ingrid

    2004-01-01

    The article that one presents has for purpose outline and comment on the recent modifications to the Penal Code for the Federal District of México which establish, for the first time, crimes related to the artificial procreation and to the genetic manipulation. Also one refers to the interaction of the new legal texts with the sanitary legislation of the country. Since it will be stated in some cases they present confrontations between the penal and the sanitary reglamentation and some points related to the legality or unlawfulness of a conduct that stayed without the enough development. These lacks will complicate the application of the new rules of the Penal Code of the Federal District.

  6. Genetic variants in long non-coding RNA MIAT contribute to risk of paranoid schizophrenia in a Chinese Han population.

    Science.gov (United States)

    Rao, Shu-Quan; Hu, Hui-Ling; Ye, Ning; Shen, Yan; Xu, Qi

    2015-08-01

    The heritability of schizophrenia has been reported to be as high as ~80%, but the contribution of genetic variants identified to this heritability remains to be estimated. Long non-coding RNAs (LncRNAs) are involved in multiple processes critical to normal cellular function and dysfunction of lncRNA MIAT may contribute to the pathophysiology of schizophrenia. However, the genetic evidence of lncRNAs involved in schizophrenia has not been documented. Here, we conducted a two-stage association analysis on 8 tag SNPs that cover the whole MIAT locus in two independent Han Chinese schizophrenia case-control cohorts (discovery sample from Shanxi Province: 1093 patients with paranoid schizophrenia and 1180 control subjects; replication cohort from Jilin Province: 1255 cases and 1209 healthy controls). In discovery stage, significant genetic association with paranoid schizophrenia was observed for rs1894720 (χ(2)=74.20, P=7.1E-18), of which minor allele (T) had an OR of 1.70 (95% CI=1.50-1.91). This association was confirmed in the replication cohort (χ(2)=22.66, P=1.9E-06, OR=1.32, 95%CI 1.18-1.49). Besides, a weak genotypic association was detected for rs4274 (χ(2)=4.96, df=2, P=0.03); the AA carriers showed increased disease risk (OR=1.30, 95%CI=1.03-1.64). No significant association was found between any haplotype and paranoid schizophrenia. The present studies showed that lncRNA MIAT was a novel susceptibility gene for paranoid schizophrenia in the Chinese Han population. Considering that most lncRNAs locate in non-coding regions, our result may explain why most susceptibility loci for schizophrenia identified by genome wide association studies were out of coding regions. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. An enhancement of selection and crossover operations in real-coded genetic algorithm for large-dimensionality optimization

    Energy Technology Data Exchange (ETDEWEB)

    Kwak, Noh Sung; Lee, Jongsoo [Yonsei University, Seoul (Korea, Republic of)

    2016-01-15

    The present study aims to implement a new selection method and a novel crossover operation in a real-coded genetic algorithm. The proposed selection method facilitates the establishment of a successively evolved population by combining several subpopulations: an elitist subpopulation, an off-spring subpopulation and a mutated subpopulation. A probabilistic crossover is performed based on the measure of probabilistic distance between the individuals. The concept of ‘allowance’ is suggested to describe the level of variance in the crossover operation. A number of nonlinear/non-convex functions and engineering optimization problems are explored to verify the capacities of the proposed strategies. The results are compared with those obtained from other genetic and nature-inspired algorithms.

  8. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    Science.gov (United States)

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  9. Remediating Viking Origins: Genetic Code as Archival Memory of the Remote Past.

    Science.gov (United States)

    Scully, Marc; King, Turi; Brown, Steven D

    2013-10-01

    This article introduces some early data from the Leverhulme Trust-funded research programme, 'The Impact of the Diasporas on the Making of Britain: evidence, memories, inventions'. One of the interdisciplinary foci of the programme, which incorporates insights from genetics, history, archaeology, linguistics and social psychology, is to investigate how genetic evidence of ancestry is incorporated into identity narratives. In particular, we investigate how 'applied genetic history' shapes individual and familial narratives, which are then situated within macro-narratives of the nation and collective memories of immigration and indigenism. It is argued that the construction of genetic evidence as a 'gold standard' about 'where you really come from' involves a remediation of cultural and archival memory, in the construction of a 'usable past'. This article is based on initial questionnaire data from a preliminary study of those attending DNA collection sessions in northern England. It presents some early indicators of the perceived importance of being of Viking descent among participants, notes some emerging patterns and considers the implications for contemporary debates on migration, belonging and local and national identity.

  10. Innovation of genetic algorithm code GenA for WWER fuel loading optimization

    International Nuclear Information System (INIS)

    Sustek, J.

    2005-01-01

    One of the stochastic search techniques - genetic algorithms - was recently used for optimization of arrangement of fuel assemblies (FA) in core of reactors WWER-440 and WWER-1000. Basic algorithm was modified by incorporation of SPEA scheme. Both were enhanced and some results are presented (Authors)

  11. Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval

    DEFF Research Database (Denmark)

    Lin, Honghuang; van Setten, Jessica; Smith, Albert V

    2018-01-01

    BACKGROUND: Electrical conduction from the cardiac sinoatrial node to the ventricles is critical for normal heart function. Genome-wide association studies have identified more than a dozen common genetic loci that are associated with PR interval. However, it is unclear whether rare and low-frequ...

  12. Efficacy of a web-based intelligent tutoring system for communicating genetic risk of breast cancer: a fuzzy-trace theory approach.

    Science.gov (United States)

    Wolfe, Christopher R; Reyna, Valerie F; Widmer, Colin L; Cedillos, Elizabeth M; Fisher, Christopher R; Brust-Renck, Priscila G; Weil, Audrey M

    2015-01-01

    . Many healthy women consider genetic testing for breast cancer risk, yet BRCA testing issues are complex. . To determine whether an intelligent tutor, BRCA Gist, grounded in fuzzy-trace theory (FTT), increases gist comprehension and knowledge about genetic testing for breast cancer risk, improving decision making. . In 2 experiments, 410 healthy undergraduate women were randomly assigned to 1 of 3 groups: an online module using a Web-based tutoring system (BRCA Gist) that uses artificial intelligence technology, a second group read highly similar content from the National Cancer Institute (NCI) Web site, and a third that completed an unrelated tutorial. . BRCA Gist applied FTT and was designed to help participants develop gist comprehension of topics relevant to decisions about BRCA genetic testing, including how breast cancer spreads, inherited genetic mutations, and base rates. . We measured content knowledge, gist comprehension of decision-relevant information, interest in testing, and genetic risk and testing judgments. . Control knowledge scores ranged from 54% to 56%, NCI improved significantly to 65% and 70%, and BRCA Gist improved significantly more to 75% and 77%, P tutors, such as BRCA Gist, are scalable, cost-effective ways of helping people understand complex issues, improving decision making. © The Author(s) 2014.

  13. PIXE-based quantification of health-proactive trace elements in genetically transformed roots of a multi-medicinal plant, Sida acuta Burm.f

    International Nuclear Information System (INIS)

    Somanatha Jena; Lopamudra Sahu; Chand, P.K.; Ray, D.K.; Mishra, S.K.

    2015-01-01

    Inorganic element composition of genetically transformed hairy root cultures (HRCs) of a medicinal plant, Sida acuta was determined using PIXE technique. HRCs had a higher accumulation of pro-health trace elements compared to natural roots. It was estimated that < 160 g d.wt. of a selected rhizoclone could suffice to provide nearly all tested essential elements catering to per diem requirement of the human body. The ideal multi-elemental profile ushers a new possibility of integrating hairy root extracts in modern therapeutics ('rhizotherapy') as complementary medicine or a dietary nutraceutical supplement. (author)

  14. Dynamics of genetic variation at gliadin-coding loci in bread wheat cultivars developed in small grains research center (Kragujevac during last 35 years

    Directory of Open Access Journals (Sweden)

    Novosljska-Dragovič Aleksandra

    2005-01-01

    Full Text Available Multiple alleles of gliadin-coding loci are well-known genetic markers of common wheat genotypes. Based on analysis of gliadin patterns in common wheat cultivars developed at the Small Grains Research Center in Kragujevac dynamics of genetic variability at gliadin-coding loci has been surveyed for the period of 35 years. It was shown that long-term breeding of the wheat cultivars involved gradual replacement of ancient alleles for those widely spread in some regions in the world, which belong to well-known cultivars-donor of some important traits. Developing cultivars whose pedigree involved much new foreign genetic material has increased genetic diversity as well as has changed frequency of alleles of gliadin-coding loci. So we can conclude that the genetic profile of modern Serbian cultivars has changed considerably. Genetic formula of gliadin was made for each the cultivar studied. The most frequent alleles of gliadin-coding loci among modern cultivars should be of great interest of breeders because these alleles are probably linked with genes that confer advantage to their carriers at present.

  15. Insight on trace element detoxification in the Black-tailed Godwit (Limosa limosa) through genetic, enzymatic and metallothionein analyses

    International Nuclear Information System (INIS)

    Lucia, Magali; Bocher, Pierrick; Cosson, Richard P.; Churlaud, Carine; Robin, Frédéric; Bustamante, Paco

    2012-01-01

    Trace element concentrations (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, Zn) were investigated in the liver, kidneys, muscle and feathers of 31 black-tailed godwits (Limosa limosa) accidentally killed during catches by mist net in the Pertuis Charentais, Atlantic coast of France. Analyses of carbon and nitrogen stable isotope ratios were carried out in liver, muscle and feathers in order to elucidate dietary patterns and to determine whether differences in diet explained the variation in elemental uptake. This study also aimed to have a preliminary assessment of sub-lethal effects triggered by trace elements through the investigation of gene expressions by quantitative real-time PCR, antioxidant enzyme activities (catalase, superoxide dismutase, glutathione peroxidase), and metallothionein (MT) levels. The results showed that Cr and Ni concentrations in tissues of adults were lower than in juveniles in part because adults may have eliminated these trace elements through moulting. Except for Cd and Ni, trace element concentrations were negatively correlated to the body mass of godwits. Ag, As, Hg and Se concentrations were positively linked with the trophic position of birds. The diet could be considered as a fundamental route of exposure for these elements demonstrating therefore the qualitative linkage between dietary habits of godwits and their contaminant concentrations. Our results strongly suggest that even though trace element concentrations were mostly below toxicity threshold level, the elevated concentrations of As, Ag, Cd, Cu, Fe and Se may however trigger sub-lethal effects. Trace elements appear to enhance expression of genes involved in oxidative stress defence, which indicates the production of reactive oxygen species. Moreover, birds with the highest concentrations appeared to have an increased mitochondrial metabolism suggesting that the fight against trace element toxicity requires additional energetic needs notably to produce detoxification

  16. Insight on trace element detoxification in the Black-tailed Godwit (Limosa limosa) through genetic, enzymatic and metallothionein analyses

    Energy Technology Data Exchange (ETDEWEB)

    Lucia, Magali, E-mail: m.lucia33@laposte.net [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France); Bocher, Pierrick [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France); Cosson, Richard P. [Mer Molecules Sante (MMS), Universite de Nantes, EA 2663, 2 rue de la Houssiniere, BP 92208, 44322 Nantes Cedex 3 (France); Churlaud, Carine; Robin, Frederic; Bustamante, Paco [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France)

    2012-04-15

    Trace element concentrations (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, Zn) were investigated in the liver, kidneys, muscle and feathers of 31 black-tailed godwits (Limosa limosa) accidentally killed during catches by mist net in the Pertuis Charentais, Atlantic coast of France. Analyses of carbon and nitrogen stable isotope ratios were carried out in liver, muscle and feathers in order to elucidate dietary patterns and to determine whether differences in diet explained the variation in elemental uptake. This study also aimed to have a preliminary assessment of sub-lethal effects triggered by trace elements through the investigation of gene expressions by quantitative real-time PCR, antioxidant enzyme activities (catalase, superoxide dismutase, glutathione peroxidase), and metallothionein (MT) levels. The results showed that Cr and Ni concentrations in tissues of adults were lower than in juveniles in part because adults may have eliminated these trace elements through moulting. Except for Cd and Ni, trace element concentrations were negatively correlated to the body mass of godwits. Ag, As, Hg and Se concentrations were positively linked with the trophic position of birds. The diet could be considered as a fundamental route of exposure for these elements demonstrating therefore the qualitative linkage between dietary habits of godwits and their contaminant concentrations. Our results strongly suggest that even though trace element concentrations were mostly below toxicity threshold level, the elevated concentrations of As, Ag, Cd, Cu, Fe and Se may however trigger sub-lethal effects. Trace elements appear to enhance expression of genes involved in oxidative stress defence, which indicates the production of reactive oxygen species. Moreover, birds with the highest concentrations appeared to have an increased mitochondrial metabolism suggesting that the fight against trace element toxicity requires additional energetic needs notably to produce detoxification

  17. Discovery of coding genetic variants influencing diabetes-related serum biomarkers and their impact on risk of type 2 diabetes

    DEFF Research Database (Denmark)

    Ahluwalia, Tarun Veer Singh; Allin, Kristine Højgaard; Sandholt, Camilla Helene

    2015-01-01

    CONTEXT: Type 2 diabetes (T2D) prevalence is spiraling globally, and knowledge of its pathophysiological signatures is crucial for a better understanding and treatment of the disease. OBJECTIVE: We aimed to discover underlying coding genetic variants influencing fasting serum levels of nine......-nucleotide polymorphisms and were tested for association with each biomarker. Identified loci were tested for association with T2D through a large-scale meta-analysis involving up to 17 024 T2D cases and up to 64 186 controls. RESULTS: We discovered 11 associations between single-nucleotide polymorphisms and five distinct......, of which the association with the CELSR2 locus has not been shown previously. CONCLUSION: The identified loci influence processes related to insulin signaling, cell communication, immune function, apoptosis, DNA repair, and oxidative stress, all of which could provide a rationale for novel diabetes...

  18. Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

    Science.gov (United States)

    Wohlin, Åsa

    2015-03-21

    The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

  19. Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

    Science.gov (United States)

    Rubini, Marina; Lepthien, Sandra; Golbik, Ralph; Budisa, Nediljko

    2006-07-01

    The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

  20. Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont.

    Directory of Open Access Journals (Sweden)

    John P McCutcheon

    2009-07-01

    Full Text Available The genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. Recoding of UGA from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. Small genomes typically exhibit low guanine plus cytosine (GC content, and this bias in base composition has been proposed to drive UGA Stop to Tryptophan (Stop-->Trp recoding. Using a combination of genome sequencing and high-throughput proteomics, we show that an alpha-Proteobacterial symbiont of cicadas has the unprecedented combination of an extremely small genome (144 kb, a GC-biased base composition (58.4%, and a coding reassignment of UGA Stop-->Trp. Although it is not clear why this tiny genome lacks the low GC content typical of other small bacterial genomes, these observations support a role of genome reduction rather than base composition as a driver of codon reassignment.

  1. Tracing the Trans-Pacific Evolutionary History of a Domesticated Seaweed (Gracilaria chilensis) with Archaeological and Genetic Data

    Science.gov (United States)

    Guillemin, Marie-Laure; Valero, Myriam; Faugeron, Sylvain; Nelson, Wendy; Destombe, Christophe

    2014-01-01

    The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile. PMID:25501717

  2. “AquaTrace” The development of tools for tracing and evaluating the genetic impact of fish from aquaculture

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Bekkevold, Dorte; Svåsand, Terje

    2012-01-01

    Aquaculture represents a key solution to meet the escalating demand for fish. Accordingly, development of appropriate legislation within the European Union aquaculture sector underpinned by cutting‐edge research and technology is required. This necessitates implementation of breeding programmes...... to identify of the genetic origin of both wild and farmed fish (assignment and genetic traceability), as well as for the detection of interbreeding genetic introgression between farmed and wild stocks. This work will be carried out on three marine fish of economic significance: the European sea bass...... (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and turbot (Scophthalmus maximus). To address quantitative effects of farm introgression, the rationale is to examine links between key fitness and life‐history traits and specific functional genetic variation between wild and farmed fish, using...

  3. Stochastic optimization of GeantV code by use of genetic algorithms

    Science.gov (United States)

    Amadio, G.; Apostolakis, J.; Bandieramonte, M.; Behera, S. P.; Brun, R.; Canal, P.; Carminati, F.; Cosmo, G.; Duhem, L.; Elvira, D.; Folger, G.; Gheata, A.; Gheata, M.; Goulas, I.; Hariri, F.; Jun, S. Y.; Konstantinov, D.; Kumawat, H.; Ivantchenko, V.; Lima, G.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.

    2017-10-01

    GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) and handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. The goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.

  4. Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

    Directory of Open Access Journals (Sweden)

    Brunner Sylvia

    2008-05-01

    Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

  5. Human growth hormone-related latrogenic Creutzfeldt-Jakob disease: Search for a genetic susceptibility by analysis of the PRNP coding region

    Energy Technology Data Exchange (ETDEWEB)

    Jaegly, A.; Boussin, F.; Deslys, J.P. [CEA/CRSSA/DSV/DPTE, Fontenay-aux-Roses (France)] [and others

    1995-05-20

    The human PRNP gene encoding PrP is located on chromosome 20 and consists of two exons and a single intron. The open reading frame is entirely fitted into the second exon. Genetic studies indicate that all of the familial and several sporadic forms of TSSEs are associated with mutations in the PRNP 759-bp coding region. Moreover, homozygosity at codon 129, a locus harboring a polymorphism among the general population, was proposed as a genetic susceptibility marker for both sporadic and iatrogenic CJD. To assess whether additional genetic predisposition markers exist in the PRNP gene, the authors sequenced the PRNP coding region of 17 of the 32 French patients who developed a hGH-related CJD.

  6. Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

    Science.gov (United States)

    Mitchison, A

    1997-01-01

    In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

  7. Role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Woese, Carl R.; Goldenfeld, Nigel; Luthey-Schulten, Zaida

    2011-03-31

    Our main goal is to develop the conceptual and computational tools necessary to understand the evolution of the universal processes of translation and replication and to identify events of horizontal gene transfer that occurred within the components. We will attempt to uncover the major evolutionary transitions that accompanied the development of protein synthesis by the ribosome and associated components of the translation apparatus. Our project goes beyond standard genomic approaches to explore homologs that are represented at both the structure and sequence level. Accordingly, use of structural phylogenetic analysis allows us to probe further back into deep evolutionary time than competing approaches, permitting greater resolution of primitive folds and structures. Specifically, our work focuses on the elements of translation, ranging from the emergence of the canonical genetic code to the evolution of specific protein folds, mediated by the predominance of horizontal gene transfer in early life. A unique element of this study is the explicit accounting for the impact of phenotype selection on translation, through a coevolutionary control mechanism. Our work contributes to DOE mission objectives through: (1) sophisticated computer simulation of protein dynamics and evolution, and the further refinement of techniques for structural phylogeny, which complement sequence information, leading to improved annotation of genomic databases; (2) development of evolutionary approaches to exploring cellular function and machinery in an integrated way; and (3) documentation of the phenotype interaction with translation over evolutionary time, reflecting the system response to changing selection pressures through horizontal gene transfer.

  8. Genetic Recombination Between Stromal and Cancer Cells Results in Highly Malignant Cells Identified by Color-Coded Imaging in a Mouse Lymphoma Model.

    Science.gov (United States)

    Nakamura, Miki; Suetsugu, Atsushi; Hasegawa, Kousuke; Matsumoto, Takuro; Aoki, Hitomi; Kunisada, Takahiro; Shimizu, Masahito; Saji, Shigetoyo; Moriwaki, Hisataka; Hoffman, Robert M

    2017-12-01

    The tumor microenvironment (TME) promotes tumor growth and metastasis. We previously established the color-coded EL4 lymphoma TME model with red fluorescent protein (RFP) expressing EL4 implanted in transgenic C57BL/6 green fluorescent protein (GFP) mice. Color-coded imaging of the lymphoma TME suggested an important role of stromal cells in lymphoma progression and metastasis. In the present study, we used color-coded imaging of RFP-lymphoma cells and GFP stromal cells to identify yellow-fluorescent genetically recombinant cells appearing only during metastasis. The EL4-RFP lymphoma cells were injected subcutaneously in C57BL/6-GFP transgenic mice and formed subcutaneous tumors 14 days after cell transplantation. The subcutaneous tumors were harvested and transplanted to the abdominal cavity of nude mice. Metastases to the liver, perigastric lymph node, ascites, bone marrow, and primary tumor were imaged. In addition to EL4-RFP cells and GFP-host cells, genetically recombinant yellow-fluorescent cells, were observed only in the ascites and bone marrow. These results indicate genetic exchange between the stromal and cancer cells. Possible mechanisms of genetic exchange are discussed as well as its ramifications for metastasis. J. Cell. Biochem. 118: 4216-4221, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code.

    Science.gov (United States)

    Yinda, Claude Kwe; Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Vanhulle, Emiel; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle

    2018-01-01

    Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.

  10. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  11. Software trace cache

    OpenAIRE

    Ramírez Bellido, Alejandro; Larriba Pey, Josep; Valero Cortés, Mateo

    2005-01-01

    We explore the use of compiler optimizations, which optimize the layout of instructions in memory. The target is to enable the code to make better use of the underlying hardware resources regardless of the specific details of the processor/architecture in order to increase fetch performance. The Software Trace Cache (STC) is a code layout algorithm with a broader target than previous layout optimizations. We target not only an improvement in the instruction cache hit rate, but also an increas...

  12. TORBEAM 2.0, a paraxial beam tracing code for electron-cyclotron beams in fusion plasmas for extended physics applications

    Science.gov (United States)

    Poli, E.; Bock, A.; Lochbrunner, M.; Maj, O.; Reich, M.; Snicker, A.; Stegmeir, A.; Volpe, F.; Bertelli, N.; Bilato, R.; Conway, G. D.; Farina, D.; Felici, F.; Figini, L.; Fischer, R.; Galperti, C.; Happel, T.; Lin-Liu, Y. R.; Marushchenko, N. B.; Mszanowski, U.; Poli, F. M.; Stober, J.; Westerhof, E.; Zille, R.; Peeters, A. G.; Pereverzev, G. V.

    2018-04-01

    The paraxial WKB code TORBEAM (Poli, 2001) is widely used for the description of electron-cyclotron waves in fusion plasmas, retaining diffraction effects through the solution of a set of ordinary differential equations. With respect to its original form, the code has undergone significant transformations and extensions, in terms of both the physical model and the spectrum of applications. The code has been rewritten in Fortran 90 and transformed into a library, which can be called from within different (not necessarily Fortran-based) workflows. The models for both absorption and current drive have been extended, including e.g. fully-relativistic calculation of the absorption coefficient, momentum conservation in electron-electron collisions and the contribution of more than one harmonic to current drive. The code can be run also for reflectometry applications, with relativistic corrections for the electron mass. Formulas that provide the coupling between the reflected beam and the receiver have been developed. Accelerated versions of the code are available, with the reduced physics goal of inferring the location of maximum absorption (including or not the total driven current) for a given setting of the launcher mirrors. Optionally, plasma volumes within given flux surfaces and corresponding values of minimum and maximum magnetic field can be provided externally to speed up the calculation of full driven-current profiles. These can be employed in real-time control algorithms or for fast data analysis.

  13. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

    Science.gov (United States)

    Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-03-01

    Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  14. The materiality of Code

    DEFF Research Database (Denmark)

    Soon, Winnie

    2014-01-01

    This essay studies the source code of an artwork from a software studies perspective. By examining code that come close to the approach of critical code studies (Marino, 2006), I trace the network artwork, Pupufu (Lin, 2009) to understand various real-time approaches to social media platforms (MSN......, Twitter and Facebook). The focus is not to investigate the functionalities and efficiencies of the code, but to study and interpret the program level of code in order to trace the use of various technological methods such as third-party libraries and platforms’ interfaces. These are important...... to understand the socio-technical side of a changing network environment. Through the study of code, including but not limited to source code, technical specifications and other materials in relation to the artwork production, I would like to explore the materiality of code that goes beyond technical...

  15. Instance-based Policy Learning by Real-coded Genetic Algorithms and Its Application to Control of Nonholonomic Systems

    Science.gov (United States)

    Miyamae, Atsushi; Sakuma, Jun; Ono, Isao; Kobayashi, Shigenobu

    The stabilization control of nonholonomic systems have been extensively studied because it is essential for nonholonomic robot control problems. The difficulty in this problem is that the theoretical derivation of control policy is not necessarily guaranteed achievable. In this paper, we present a reinforcement learning (RL) method with instance-based policy (IBP) representation, in which control policies for this class are optimized with respect to user-defined cost functions. Direct policy search (DPS) is an approach for RL; the policy is represented by parametric models and the model parameters are directly searched by optimization techniques including genetic algorithms (GAs). In IBP representation an instance consists of a state and an action pair; a policy consists of a set of instances. Several DPSs with IBP have been previously proposed. In these methods, sometimes fail to obtain optimal control policies when state-action variables are continuous. In this paper, we present a real-coded GA for DPSs with IBP. Our method is specifically designed for continuous domains. Optimization of IBP has three difficulties; high-dimensionality, epistasis, and multi-modality. Our solution is designed for overcoming these difficulties. The policy search with IBP representation appears to be high-dimensional optimization; however, instances which can improve the fitness are often limited to active instances (instances used for the evaluation). In fact, the number of active instances is small. Therefore, we treat the search problem as a low dimensional problem by restricting search variables only to active instances. It has been commonly known that functions with epistasis can be efficiently optimized with crossovers which satisfy the inheritance of statistics. For efficient search of IBP, we propose extended crossover-like mutation (extended XLM) which generates a new instance around an instance with satisfying the inheritance of statistics. For overcoming multi-modality, we

  16. The Future of Genetics in Psychology and Psychiatry: Microarrays, Genome-Wide Association, and Non-Coding RNA

    Science.gov (United States)

    Plomin, Robert; Davis, Oliver S. P.

    2009-01-01

    Background: Much of what we thought we knew about genetics needs to be modified in light of recent discoveries. What are the implications of these advances for identifying genes responsible for the high heritability of many behavioural disorders and dimensions in childhood? Methods: Although quantitative genetics such as twin studies will continue…

  17. Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

    Directory of Open Access Journals (Sweden)

    Singh Nagendra

    2009-03-01

    Full Text Available Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS markers for the rice (Oryza sativa L. genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS. Primers were designed for 17,966 (92% GNMS repeats, including 4,288 (94% hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3% followed by markers in the promoter region (53.3% and least in the CDS (26.6%. The robust polymerase chain reaction (PCR amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya compared to short

  18. TraceContract

    Science.gov (United States)

    Kavelund, Klaus; Barringer, Howard

    2012-01-01

    TraceContract is an API (Application Programming Interface) for trace analysis. A trace is a sequence of events, and can, for example, be generated by a running program, instrumented appropriately to generate events. An event can be any data object. An example of a trace is a log file containing events that a programmer has found important to record during a program execution. Trace - Contract takes as input such a trace together with a specification formulated using the API and reports on any violations of the specification, potentially calling code (reactions) to be executed when violations are detected. The software is developed as an internal DSL (Domain Specific Language) in the Scala programming language. Scala is a relatively new programming language that is specifically convenient for defining such internal DSLs due to a number of language characteristics. This includes Scala s elegant combination of object-oriented and functional programming, a succinct notation, and an advanced type system. The DSL offers a combination of data-parameterized state machines and temporal logic, which is novel. As an extension of Scala, it is a very expressive and convenient log file analysis framework.

  19. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  20. Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

    Directory of Open Access Journals (Sweden)

    Shima Fayaz

    2012-01-01

    Full Text Available Homologous recombination (HR is the major pathway for repairing double strand breaks (DSBs in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC we used high resolution melting (HRM analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536 was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432-4.969; p = 0.38 compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion.

  1. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  2. Trace analysis

    International Nuclear Information System (INIS)

    Warner, M.

    1987-01-01

    What is the current state of quantitative trace analytical chemistry? What are today's research efforts? And what challenges does the future hold? These are some of the questions addressed at a recent four-day symposium sponsored by the National Bureau of Standards (NBS) entitled Accuracy in Trace Analysis - Accomplishments, Goals, Challenges. The two plenary sessions held on the first day of the symposium reviewed the history of quantitative trace analysis, discussed the present situation from academic and industrial perspectives, and summarized future needs. The remaining three days of the symposium consisted of parallel sessions dealing with the measurement process; quantitation in materials; environmental, clinical, and nutrient analysis; and advances in analytical techniques

  3. Use of PRIM code to analyze potential radiation-induced genetic and somatic effects to man from Jackpile-Paguate mines

    International Nuclear Information System (INIS)

    Momeni, M.H.

    1983-01-01

    Potential radiation-induced effects from inhalation and ingestion of land external exposure to radioactive materials at the Jackpile-Paguate uranium mine complex near Paguate, New Mexico, were analyzed. The Uranium Dispersion and Dosimetry (UDAD) computer code developed at Argonne National Laboratory was used to calculate the dose rates and the time-integrated doses to tissues at risk as a function of age and time for the population within 80 km of the mines. The ANL computer code Potential Radiation-Induced Biological Effects on Man (PRIM) then was used to calculate the potential radiation-induced somatic and genetic effects among the same population on the basis of absolute and relative risk models as a function of duration of exposure and age at time of exposure. The analyses were based on the recommendations in BEIR II and WASH-1400 and the lifetable method. The death rates were calculated for radiation exposure from the mines and for naturally induced effects for 19 age cohorts, 20 time intervals, and for each sex. The results indicated that under present conditions of the radiation environment at the mines, the number of potential fatal radiation-induced neoplasms that could occur among the regional population over the next 85 years would be 95 using the absolute risk model, and 243 using the relative risk model. Over the same period, there would be less than two radiation-induced genetic effects (dominant and multifactorials). After decommissioning f the mine site, these risks would decrease to less than 1 and less than 3 potential radiation-induced deaths under the relative and absolute risk models, respectively, and 0.001 genetic disorders. Because of various sources of error, the uncertainty in these predicted risks could be a factor of five

  4. The Poitiers School of Mathematical and Theoretical Biology: Besson-Gavaudan-Schützenberger's Conjectures on Genetic Code and RNA Structures.

    Science.gov (United States)

    Demongeot, J; Hazgui, H

    2016-12-01

    The French school of theoretical biology has been mainly initiated in Poitiers during the sixties by scientists like J. Besson, G. Bouligand, P. Gavaudan, M. P. Schützenberger and R. Thom, launching many new research domains on the fractal dimension, the combinatorial properties of the genetic code and related amino-acids as well as on the genetic regulation of the biological processes. Presently, the biological science knows that RNA molecules are often involved in the regulation of complex genetic networks as effectors, e.g., activators (small RNAs as transcription factors), inhibitors (micro-RNAs) or hybrids (circular RNAs). Examples of such networks will be given showing that (1) there exist RNA "relics" that have played an important role during evolution and have survived in many genomes, whose probability distribution of their sub-sequences is quantified by the Shannon entropy, and (2) the robustness of the dynamics of the networks they regulate can be characterized by the Kolmogorov-Sinaï dynamic entropy and attractor entropy.

  5. Social Welfare Improvement by TCSC using Real Code Based Genetic Algorithm in Double-Sided Auction Market

    Directory of Open Access Journals (Sweden)

    MASOUM, M. A. S.

    2011-05-01

    Full Text Available This paper presents a genetic algorithm (GA to maximize total system social welfare and alleviate congestion by best placement and sizing of TCSC device, in a double-sided auction market. To introduce more accurate modeling, the valve loading effects is incorporated to the conventional quadratic smooth generator cost curves. By adding the valve point effect, the model presents nondifferentiable and nonconvex regions that challenge most gradient-based optimization algorithms. In addition, quadratic consumer benefit functions integrated in the objective function to guarantee that locational marginal prices charged at the demand buses is less than or equal to DisCos benefit, earned by selling that power to retail customers. The proposed approach makes use of the genetic algorithm to optimal schedule GenCos, DisCos and TCSC location and size, while the Newton-Raphson algorithm minimizes the mismatch of the power flow equations. Simulation results on the modified IEEE 14-bus and 30-bus test systems (with/without line flow constraints, before and after the compensation are used to examine the impact of TCSC on the total system social welfare improvement. Several cases are considered to test and validate the consistency of detecting best solutions. Simulation results are compared to solutions obtained by sequential quadratic programming (SQP approaches.

  6. A method to optimize the shield compact and lightweight combining the structure with components together by genetic algorithm and MCNP code.

    Science.gov (United States)

    Cai, Yao; Hu, Huasi; Pan, Ziheng; Hu, Guang; Zhang, Tao

    2018-05-17

    To optimize the shield for neutrons and gamma rays compact and lightweight, a method combining the structure and components together was established employing genetic algorithms and MCNP code. As a typical case, the fission energy spectrum of 235 U which mixed neutrons and gamma rays was adopted in this study. Six types of materials were presented and optimized by the method. Spherical geometry was adopted in the optimization after checking the geometry effect. Simulations have made to verify the reliability of the optimization method and the efficiency of the optimized materials. To compare the materials visually and conveniently, the volume and weight needed to build a shield are employed. The results showed that, the composite multilayer material has the best performance. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Trace conditioning in insects-keep the trace!

    Science.gov (United States)

    Dylla, Kristina V; Galili, Dana S; Szyszka, Paul; Lüdke, Alja

    2013-01-01

    Trace conditioning is a form of associative learning that can be induced by presenting a conditioned stimulus (CS) and an unconditioned stimulus (US) following each other, but separated by a temporal gap. This gap distinguishes trace conditioning from classical delay conditioning, where the CS and US overlap. To bridge the temporal gap between both stimuli and to form an association between CS and US in trace conditioning, the brain must keep a neural representation of the CS after its termination-a stimulus trace. Behavioral and physiological studies on trace and delay conditioning revealed similarities between the two forms of learning, like similar memory decay and similar odor identity perception in invertebrates. On the other hand differences were reported also, like the requirement of distinct brain structures in vertebrates or disparities in molecular mechanisms in both vertebrates and invertebrates. For example, in commonly used vertebrate conditioning paradigms the hippocampus is necessary for trace but not for delay conditioning, and Drosophila delay conditioning requires the Rutabaga adenylyl cyclase (Rut-AC), which is dispensable in trace conditioning. It is still unknown how the brain encodes CS traces and how they are associated with a US in trace conditioning. Insects serve as powerful models to address the mechanisms underlying trace conditioning, due to their simple brain anatomy, behavioral accessibility and established methods of genetic interference. In this review we summarize the recent progress in insect trace conditioning on the behavioral and physiological level and emphasize similarities and differences compared to delay conditioning. Moreover, we examine proposed molecular and computational models and reassess different experimental approaches used for trace conditioning.

  8. Trace conditioning in insects – Keep the trace!

    Directory of Open Access Journals (Sweden)

    Kristina V Dylla

    2013-08-01

    Full Text Available Trace conditioning is a form of associative learning that can be induced by presenting a conditioned stimulus (CS and an unconditioned stimulus (US following each other, but separated by a temporal gap. This gap distinguishes trace conditioning from classical delay conditioning, where the CS and US overlap. To bridge the temporal gap between both stimuli and to form an association between CS and US in trace conditioning, the brain must keep a neural representation of the CS after its termination – a stimulus trace. Behavioral and physiological studies on trace and delay conditioning revealed similarities between the two forms of learning, like similar memory decay and similar odor identity perception in invertebrates. On the other hand differences were reported also, like the requirement of distinct brain structures in vertebrates or disparities in molecular mechanisms in both vertebrates and invertebrates. For example, in commonly used vertebrate conditioning paradigms the hippocampus is necessary for trace but not for delay conditioning, and Drosophila delay conditioning requires the Rutabaga adenylyl cyclase, which is dispensable in trace conditioning. It is still unknown how the brain encodes CS traces and how they are associated with a US in trace conditioning. Insects serve as powerful models to address the mechanisms underlying trace conditioning, due to their simple brain anatomy, behavioral accessibility and established methods of genetic interference. In this review we summarize the recent progress in insect trace conditioning on the behavioral and physiological level and emphasize similarities and differences compared to delay conditioning. Moreover, we examine proposed molecular and computational models and reassess different experimental approaches used for trace conditioning.

  9. An RNA Phage Lab: MS2 in Walter Fiers' laboratory of molecular biology in Ghent, from genetic code to gene and genome, 1963-1976.

    Science.gov (United States)

    Pierrel, Jérôme

    2012-01-01

    The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück's phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers' laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his 'RNA phage lab' with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.

  10. An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy.

    Science.gov (United States)

    Völler, Jan-Stefan; Biava, Hernan; Hildebrandt, Peter; Budisa, Nediljko

    2017-11-01

    To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. A Real-Coded Genetic Algorithm with System Reduction and Restoration for Rapid and Reliable Power Flow Solution of Power Systems

    Directory of Open Access Journals (Sweden)

    Hassan Abdullah Kubba

    2015-05-01

    Full Text Available The paper presents a highly accurate power flow solution, reducing the possibility of ending at local minima, by using Real-Coded Genetic Algorithm (RCGA with system reduction and restoration. The proposed method (RCGA is modified to reduce the total computing time by reducing the system in size to that of the generator buses, which, for any realistic system, will be smaller in number, and the load buses are eliminated. Then solving the power flow problem for the generator buses only by real-coded GA to calculate the voltage phase angles, whereas the voltage magnitudes are specified resulted in reduced computation time for the solution. Then the system is restored by calculating the voltages of the load buses in terms of the calculated voltages of the generator buses, after a derivation of equations for calculating the voltages of the load busbars. The proposed method was demonstrated on 14-bus IEEE test systems and the practical system 362-busbar IRAQI NATIONAL GRID (ING. The proposed method has reliable convergence, a highly accurate solution and less computing time for on-line applications. The method can conveniently be applied for on-line analysis and planning studies of large power systems.

  12. Genetic Predictions of Prion Disease Susceptibility in Carnivore Species Based on Variability of the Prion Gene Coding Region

    Science.gov (United States)

    Stewart, Paula; Campbell, Lauren; Skogtvedt, Susan; Griffin, Karen A.; Arnemo, Jon M.; Tryland, Morten; Girling, Simon; Miller, Michael W.; Tranulis, Michael A.; Goldmann, Wilfred

    2012-01-01

    Mammalian species vary widely in their apparent susceptibility to prion diseases. For example, several felid species developed prion disease (feline spongiform encephalopathy or FSE) during the bovine spongiform encephalopathy (BSE) epidemic in the United Kingdom, whereas no canine BSE cases were detected. Whether either of these or other groups of carnivore species can contract other prion diseases (e.g. chronic wasting disease or CWD) remains an open question. Variation in the host-encoded prion protein (PrPC) largely explains observed disease susceptibility patterns within ruminant species, and may explain interspecies differences in susceptibility as well. We sequenced and compared the open reading frame of the PRNP gene encoding PrPC protein from 609 animal samples comprising 29 species from 22 genera of the Order Carnivora; amongst these samples were 15 FSE cases. Our analysis revealed that FSE cases did not encode an identifiable disease-associated PrP polymorphism. However, all canid PrPs contained aspartic acid or glutamic acid at codon 163 which we propose provides a genetic basis for observed susceptibility differences between canids and felids. Among other carnivores studied, wolverine (Gulo gulo) and pine marten (Martes martes) were the only non-canid species to also express PrP-Asp163, which may impact on their prion diseases susceptibility. Populations of black bear (Ursus americanus) and mountain lion (Puma concolor) from Colorado showed little genetic variation in the PrP protein and no variants likely to be highly resistant to prions in general, suggesting that strain differences between BSE and CWD prions also may contribute to the limited apparent host range of the latter. PMID:23236380

  13. Genetic predictions of prion disease susceptibility in carnivore species based on variability of the prion gene coding region.

    Directory of Open Access Journals (Sweden)

    Paula Stewart

    Full Text Available Mammalian species vary widely in their apparent susceptibility to prion diseases. For example, several felid species developed prion disease (feline spongiform encephalopathy or FSE during the bovine spongiform encephalopathy (BSE epidemic in the United Kingdom, whereas no canine BSE cases were detected. Whether either of these or other groups of carnivore species can contract other prion diseases (e.g. chronic wasting disease or CWD remains an open question. Variation in the host-encoded prion protein (PrP(C largely explains observed disease susceptibility patterns within ruminant species, and may explain interspecies differences in susceptibility as well. We sequenced and compared the open reading frame of the PRNP gene encoding PrP(C protein from 609 animal samples comprising 29 species from 22 genera of the Order Carnivora; amongst these samples were 15 FSE cases. Our analysis revealed that FSE cases did not encode an identifiable disease-associated PrP polymorphism. However, all canid PrPs contained aspartic acid or glutamic acid at codon 163 which we propose provides a genetic basis for observed susceptibility differences between canids and felids. Among other carnivores studied, wolverine (Gulo gulo and pine marten (Martes martes were the only non-canid species to also express PrP-Asp163, which may impact on their prion diseases susceptibility. Populations of black bear (Ursus americanus and mountain lion (Puma concolor from Colorado showed little genetic variation in the PrP protein and no variants likely to be highly resistant to prions in general, suggesting that strain differences between BSE and CWD prions also may contribute to the limited apparent host range of the latter.

  14. MouSensor: A Versatile Genetic Platform to Create Super Sniffer Mice for Studying Human Odor Coding

    Directory of Open Access Journals (Sweden)

    Charlotte D’Hulst

    2016-07-01

    Full Text Available Typically, ∼0.1% of the total number of olfactory sensory neurons (OSNs in the main olfactory epithelium express the same odorant receptor (OR in a singular fashion and their axons coalesce into homotypic glomeruli in the olfactory bulb. Here, we have dramatically increased the total number of OSNs expressing specific cloned OR coding sequences by multimerizing a 21-bp sequence encompassing the predicted homeodomain binding site sequence, TAATGA, known to be essential in OR gene choice. Singular gene choice is maintained in these “MouSensors.” In vivo synaptopHluorin imaging of odor-induced responses by known M71 ligands shows functional glomerular activation in an M71 MouSensor. Moreover, a behavioral avoidance task demonstrates that specific odor detection thresholds are significantly decreased in multiple transgenic lines, expressing mouse or human ORs. We have developed a versatile platform to study gene choice and axon identity, to create biosensors with great translational potential, and to finally decode human olfaction.

  15. MouSensor: A Versatile Genetic Platform to Create Super Sniffer Mice for Studying Human Odor Coding.

    Science.gov (United States)

    D'Hulst, Charlotte; Mina, Raena B; Gershon, Zachary; Jamet, Sophie; Cerullo, Antonio; Tomoiaga, Delia; Bai, Li; Belluscio, Leonardo; Rogers, Matthew E; Sirotin, Yevgeniy; Feinstein, Paul

    2016-07-26

    Typically, ∼0.1% of the total number of olfactory sensory neurons (OSNs) in the main olfactory epithelium express the same odorant receptor (OR) in a singular fashion and their axons coalesce into homotypic glomeruli in the olfactory bulb. Here, we have dramatically increased the total number of OSNs expressing specific cloned OR coding sequences by multimerizing a 21-bp sequence encompassing the predicted homeodomain binding site sequence, TAATGA, known to be essential in OR gene choice. Singular gene choice is maintained in these "MouSensors." In vivo synaptopHluorin imaging of odor-induced responses by known M71 ligands shows functional glomerular activation in an M71 MouSensor. Moreover, a behavioral avoidance task demonstrates that specific odor detection thresholds are significantly decreased in multiple transgenic lines, expressing mouse or human ORs. We have developed a versatile platform to study gene choice and axon identity, to create biosensors with great translational potential, and to finally decode human olfaction. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Trace element partitioning in rock forming minerals of co-genetic, subduction-related alkaline and tholeiitic mafic rocks in the Ural Mountains, Russia

    Science.gov (United States)

    Krause, J.; Brügmann, G. E.; Pushkarev, E. V.

    2009-04-01

    The partitioning of trace elements between rock forming minerals in igneous rocks is largely controlled by physical and chemical parameters e.g. temperature, pressure and chemical composition of the minerals and the coexisting melt. In the present study partition coefficients for REE between hornblende, orthopyroxene, feldspars, apatite and clinopyroxene in a suite of co-genetic alkaline and tholeiitic mafic rocks from the Ural Mountains (Russia) were calculated. The results give insights to the influence of the chemical composition of the parental melt on the partitioning behaviour of the REE. Nepheline-bearing, alkaline melanogabbros (tilaites) are assumed to represent the most fractionated products of the melt that formed the ultramafic cumulates in zoned mafic-ultramafic complexes in the Ural Mountains. Co-genetic with the latter is a suite of olivine gabbros, gabbronorites and hornblende gabbros formed from a tholeiitic parental melt. Negative anomalies for the HFSE along with low Nb and Ta contents and a positive Sr anomaly indicate a subduction related origin of all parental melts. The nepheline gabbros consist predominantly of coarse-grained clinopyroxene phenocrysts in a matrix of fine grained clinopyroxene, olivine, plagioclase, K-feldspar and nepheline with accessory apatite. The tholeiitic gabbros have equigranular to porphyric textures with phenocrysts of olivine, pyroxene and hornblende in a plagioclase rich matrix with olivine hornblende, pyroxene and accessory apatite. Element concentrations of adjacent matrix grains and rims of phenochrysts were measured with LA-ICPMS. The distribution of REE between hornblende and clinopyroxene in the tholeiitic rocks is similar for most of the elements (DHbl•Cpx(La-Tm) = 2.7-2.8, decreasing to 2.6 and 2.4 for Yb and Lu, respectively). These values are about two times higher than published data (e.g. Ionov et al. 1997). Partition coefficients for orthopyroxene/clinopyroxene systematically decrease from the HREE

  17. Linac particle tracing simulations

    International Nuclear Information System (INIS)

    Lysenko, W.P.

    1979-01-01

    A particle tracing code was developed to study space--charge effects in proton or heavy-ion linear accelerators. The purpose is to study space--charge phenomena as directly as possible without the complications of many accelerator details. Thus, the accelerator is represented simply by harmonic oscillator or impulse restoring forces. Variable parameters as well as mismatched phase--space distributions were studied. This study represents the initial search for those features of the accelerator or of the phase--space distribution that lead to emittance growth

  18. Osteoporosis and trace elements

    DEFF Research Database (Denmark)

    Aaseth, J.; Boivin, G.; Andersen, Ole

    2012-01-01

    More than 200 million people are affected by osteoporosis worldwide, as estimated by 2 million annual hip fractures and other debilitating bone fractures (vertebrae compression and Colles' fractures). Osteoporosis is a multi-factorial disease with potential contributions from genetic, endocrine...... in new bone and results in a net gain in bone mass, but may be associated with a tissue of poor quality. Aluminum induces impairment of bone formation. Gallium and cadmium suppresses bone turnover. However, exact involvements of the trace elements in osteoporosis have not yet been fully clarified...

  19. Code Cactus; Code Cactus

    Energy Technology Data Exchange (ETDEWEB)

    Fajeau, M; Nguyen, L T; Saunier, J [Commissariat a l' Energie Atomique, Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)

    1966-09-01

    This code handles the following problems: -1) Analysis of thermal experiments on a water loop at high or low pressure; steady state or transient behavior; -2) Analysis of thermal and hydrodynamic behavior of water-cooled and moderated reactors, at either high or low pressure, with boiling permitted; fuel elements are assumed to be flat plates: - Flowrate in parallel channels coupled or not by conduction across plates, with conditions of pressure drops or flowrate, variable or not with respect to time is given; the power can be coupled to reactor kinetics calculation or supplied by the code user. The code, containing a schematic representation of safety rod behavior, is a one dimensional, multi-channel code, and has as its complement (FLID), a one-channel, two-dimensional code. (authors) [French] Ce code permet de traiter les problemes ci-dessous: 1. Depouillement d'essais thermiques sur boucle a eau, haute ou basse pression, en regime permanent ou transitoire; 2. Etudes thermiques et hydrauliques de reacteurs a eau, a plaques, a haute ou basse pression, ebullition permise: - repartition entre canaux paralleles, couples on non par conduction a travers plaques, pour des conditions de debit ou de pertes de charge imposees, variables ou non dans le temps; - la puissance peut etre couplee a la neutronique et une representation schematique des actions de securite est prevue. Ce code (Cactus) a une dimension d'espace et plusieurs canaux, a pour complement Flid qui traite l'etude d'un seul canal a deux dimensions. (auteurs)

  20. All about Genetics (For Parents)

    Science.gov (United States)

    ... Videos for Educators Search English Español All About Genetics KidsHealth / For Parents / All About Genetics What's in ... the way they pick up special laboratory dyes. Genetic Problems Errors in the genetic code or "gene ...

  1. Improved Transient Performance of a Fuzzy Modified Model Reference Adaptive Controller for an Interacting Coupled Tank System Using Real-Coded Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Asan Mohideen Khansadurai

    2014-01-01

    Full Text Available The main objective of the paper is to design a model reference adaptive controller (MRAC with improved transient performance. A modification to the standard direct MRAC called fuzzy modified MRAC (FMRAC is used in the paper. The FMRAC uses a proportional control based Mamdani-type fuzzy logic controller (MFLC to improve the transient performance of a direct MRAC. The paper proposes the application of real-coded genetic algorithm (RGA to tune the membership function parameters of the proposed FMRAC offline so that the transient performance of the FMRAC is improved further. In this study, a GA based modified MRAC (GAMMRAC, an FMRAC, and a GA based FMRAC (GAFMRAC are designed for a coupled tank setup in a hybrid tank process and their transient performances are compared. The results show that the proposed GAFMRAC gives a better transient performance than the GAMMRAC or the FMRAC. It is concluded that the proposed controller can be used to obtain very good transient performance for the control of nonlinear processes.

  2. A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia.

    Science.gov (United States)

    Barry, Elizabeth G; Witherspoon, David J; Lampe, David J

    2004-02-01

    Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences.

  3. Tracing Clues

    DEFF Research Database (Denmark)

    Feldt, Liv Egholm

    The past is all messiness and blurred relations. However, we tend to sort the messiness out through rigorous analytical studies leaving the messiness behind. Carlo Ginzburgs´ article Clues. Roots of an Evidential Paradigm from 1986 invigorates methodological elements of (historical) research, which...... central methodological elements will be further elaborated and discussed through a historical case study that traces how networks of philanthropic concepts and practices influenced the Danish welfare state in the period from the Danish constitution of 1849 until today. The overall aim of this paper...

  4. A symmetry model for genetic coding via a wallpaper group composed of the traditional four bases and an imaginary base E: towards category theory-like systematization of molecular/genetic biology.

    Science.gov (United States)

    Sawamura, Jitsuki; Morishita, Shigeru; Ishigooka, Jun

    2014-05-07

    methodology, there is fertile ground to consider a symmetry model for genetic coding based on our specific wallpaper group. A more integrated formulation containing "central dogma" for future molecular/genetic biology remains to be explored.

  5. The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory.

    Science.gov (United States)

    Di Giulio, Massimo

    2016-06-21

    I analyze the mechanism on which are based the majority of theories that put to the center of the origin of the genetic code the physico-chemical properties of amino acids. As this mechanism is based on excessive mutational steps, I conclude that it could not have been operative or if operative it would not have allowed a full realization of predictions of these theories, because this mechanism contained, evidently, a high indeterminacy. I make that disapproving the four-column theory of the origin of the genetic code (Higgs, 2009) and reply to the criticism that was directed towards the coevolution theory of the origin of the genetic code. In this context, I suggest a new hypothesis that clarifies the mechanism by which the domains of codons of the precursor amino acids would have evolved, as predicted by the coevolution theory. This mechanism would have used particular elongation factors that would have constrained the evolution of all amino acids belonging to a given biosynthetic family to the progenitor pre-tRNA, that for first recognized, the first codons that evolved in a certain codon domain of a determined precursor amino acid. This happened because the elongation factors recognized two characteristics of the progenitor pre-tRNAs of precursor amino acids, which prevented the elongation factors from recognizing the pre-tRNAs belonging to biosynthetic families of different precursor amino acids. Finally, I analyze by means of Fisher's exact test, the distribution, within the genetic code, of the biosynthetic classes of amino acids and the ones of polarity values of amino acids. This analysis would seem to support the biosynthetic classes of amino acids over the ones of polarity values, as the main factor that led to the structuring of the genetic code, with the physico-chemical properties of amino acids playing only a subsidiary role in this evolution. As a whole, the full analysis brings to the conclusion that the coevolution theory of the origin of the

  6. Trace spaces

    DEFF Research Database (Denmark)

    Fajstrup, Lisbeth; Goubault, Eric; Haucourt, Emmanuel

    2012-01-01

    in the interleaving semantics of a concurrent program, but rather some equivalence classes. The purpose of this paper is to describe a new algorithm to compute such equivalence classes, and a representative per class, which is based on ideas originating in algebraic topology. We introduce a geometric semantics...... of concurrent languages, where programs are interpreted as directed topological spaces, and study its properties in order to devise an algorithm for computing dihomotopy classes of execution paths. In particular, our algorithm is able to compute a control-flow graph for concurrent programs, possibly containing...... loops, which is “as reduced as possible” in the sense that it generates traces modulo equivalence. A preliminary implementation was achieved, showing promising results towards efficient methods to analyze concurrent programs, with very promising results compared to partial-order reduction techniques....

  7. The ‘Morbid Anatomy’ of the Human Genome: Tracing the Observational and Representational Approaches of Postwar Genetics and Biomedicine The William Bynum Prize Essay

    Science.gov (United States)

    Hogan, Andrew J.

    2014-01-01

    This paper explores evolving conceptions and depictions of the human genome among human and medical geneticists during the postwar period. Historians of science and medicine have shown significant interest in the use of informational approaches in postwar genetics, which treat the genome as an expansive digital data set composed of three billion DNA nucleotides. Since the 1950s, however, geneticists have largely interacted with the human genome at the microscopically visible level of chromosomes. Mindful of this, I examine the observational and representational approaches of postwar human and medical genetics. During the 1970s and 1980s, the genome increasingly came to be understood as, at once, a discrete part of the human anatomy and a standardised scientific object. This paper explores the role of influential medical geneticists in recasting the human genome as being a visible, tangible, and legible entity, which was highly relevant to traditional medical thinking and practice. I demonstrate how the human genome was established as an object amenable to laboratory and clinical research, and argue that the observational and representational approaches of postwar medical genetics reflect, more broadly, the interdisciplinary efforts underlying the development of contemporary biomedicine. PMID:25045177

  8. The 'morbid anatomy' of the human genome: tracing the observational and representational approaches of postwar genetics and biomedicine the William Bynum Prize Essay.

    Science.gov (United States)

    Hogan, Andrew J

    2014-07-01

    This paper explores evolving conceptions and depictions of the human genome among human and medical geneticists during the postwar period. Historians of science and medicine have shown significant interest in the use of informational approaches in postwar genetics, which treat the genome as an expansive digital data set composed of three billion DNA nucleotides. Since the 1950s, however, geneticists have largely interacted with the human genome at the microscopically visible level of chromosomes. Mindful of this, I examine the observational and representational approaches of postwar human and medical genetics. During the 1970s and 1980s, the genome increasingly came to be understood as, at once, a discrete part of the human anatomy and a standardised scientific object. This paper explores the role of influential medical geneticists in recasting the human genome as being a visible, tangible, and legible entity, which was highly relevant to traditional medical thinking and practice. I demonstrate how the human genome was established as an object amenable to laboratory and clinical research, and argue that the observational and representational approaches of postwar medical genetics reflect, more broadly, the interdisciplinary efforts underlying the development of contemporary biomedicine.

  9. A genetic polymorphism in the coding region of the gastric intrinsic factor gene (GIF) is associated with congenital intrinsic factor deficiency.

    Science.gov (United States)

    Gordon, Marilyn M; Brada, Nancy; Remacha, Angel; Badell, Isabel; del Río, Elisabeth; Baiget, Montserrat; Santer, René; Quadros, Edward V; Rothenberg, Sheldon P; Alpers, David H

    2004-01-01

    Congenital intrinsic factor (IF) deficiency is a disorder characterized by megaloblastic anemia due to the absence of gastric IF (GIF, GenBank NM_005142) and GIF antibodies, with probable autosomal recessive inheritance. Most of the reported patients are isolated cases without genetic studies of the parents or siblings. Complete exonic sequences were determined from the PCR products generated from genomic DNA of five affected individuals. All probands had the identical variant (g.68A>G) in the second position of the fifth codon in the coding sequence of the gene that introduces a restriction enzyme site for Msp I and predicts a change in the mature protein from glutamine(5) (CAG) to arginine(5) (CGG). Three subjects were homozygous for this base exchange and two subjects were heterozygous, one of which was apparently a compound heterozygote at positions 1 and 2 of the fifth codon ([g.67C>G] + [g.68A>G]). The other patient, heterozygous for position 2, had one heterozygous unaffected parent. Most parents were heterozygous for this base exchange, confirming the pattern of autosomal recessive inheritance for congenital IF deficiency. cDNA encoding GIF was mutated at base pair g.68 (A>G) and expressed in COS-7 cells. The apparent size, secretion rate, and sensitivity to pepsin hydrolysis of the expressed IF were similar to native IF. The allelic frequency of g.68A>G was 0.067 and 0.038 in two control populations. This sequence aberration is not the cause of the phenotype, but is associated with the genotype of congenital IF deficiency and could serve as a marker for inheritance of this disorder. Copyright 2003 Wiley-Liss, Inc.

  10. ED-XRF spectrometry-based trace element composition of genetically engineered rhizoclones vis-a-vis natural roots of a multi-medicinal plant, butterfly pea (Clitoria ternatea L.)

    International Nuclear Information System (INIS)

    Swain, S.S.; Chand, P.K.

    2012-01-01

    The energy dispersive X-ray fluorescence set-up incorporating a molybdenum secondary exciter was used for quantitative determination of major and minor elements in genetically transformed root somaclones (rhizoclones) of butterfly pea (Clitoria ternatea L.) which had been established via explant co-cultivation with Agrobacterium rhizogenes. The multi-elemental composition of these transformed rhizoclones was compared with that of the naturally grown in vivo donor plant. Trace elements namely Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Rb, Sr and Pb in addition to two macro-elements K and Ca were identified and quantified in root tissues of both sources. The elemental content of transformed root cultures was found to be at par with that of the natural roots of in vivo grown plants of the same species. These findings are implicated on the context of utilization of such Agrobacterium-mediated genetically transformed root cultures as a viable alternative to natural roots, the former being a fast-proliferating renewable resource of medicinally useful minerals essential for designing of effective drugs, besides providing an ex situ means for plant conservation. (author)

  11. Ray Trace

    International Nuclear Information System (INIS)

    Kowalski, S.

    1981-01-01

    During the past decade, a very general RAYTRACE code has been developed at MIT for following the trajectories of charged particles through ion-optical systems. The motion of a particle carrying charge Q is governed by the Lorentz equation, F = Q[E + V x B], where E is the electric field and B is the magnetic field. In a rectangular (x,y,z) coordinate system the equations of motion along each of the axes may be written as mx = Q(E/sub x/ + V/sub Y/B/sub z/ - v/sub z/B/sub Y/), my = Q(E/sub Y/ + v/sub z/B/sub x/ - v/sub x/B/sub z/, mz = Q(E/sub z/ + v/sub x/B/sub Y/ - v/sub Y/B/sub x/). These three particle differential equations of motion are solved by means of a step-by-step numerical integration with time as the independent variable. Accuracy is limited only by the uncertainties in our knowledge of the electric and magnetic fields. Current versions of the code may be used to calculate trajectories through an arbitrary arrangement of elements including dipoles, quadrupoles, general multipoles, solenoids, velocity selectors, drifts and thin lenses

  12. Eco-logo-genetical characteristic of seed progeny of the Taraxacum officinale S.L. from the zone of east-ural radioactive trace

    International Nuclear Information System (INIS)

    Pozolotina, V.; Ulyanova, E.

    2004-01-01

    Levels of soil contamination with 90 Sr and 137 Cs radionuclides within the zone of Eastern-Ural radioactive trace, at the plots differently distant from the place of Kyshtym accident of 1957, exceed values of the global level 4-40 times. It was shown that the same coeno-population from EURT in the different years revealed the whole variety of previously described low-level irradiation effects. They are: stimulating one (vitality indexes in seed progeny exceed significantly those registered in the background samples); the depressing one, marked for high mortality level; and an indifferent effect showing neither significant differences from the background plants. Variation scope exceeding the normal one in regard to plants growth and development rates, as well as high frequencies of chromosome and morphological aberrations indicate to the plant genome non-stability caused by chronic low-level irradiation loads. Seed progeny also demonstrated the similar ambiguous response to additional irradiation, which is confirmed by allozyme analysis results. Standard electrophoretic methods are applicable to the dandelion studies. Some enzyme systems (Got, Dia) seem to be more suitable for seedlings, whereas the others provided satisfactory results being used for the seed material. In plant coeno-populations situated in radionuclides-polluted zone, genomic recombination processes show higher intensity. High enzymatic variability provides the material for natural selection and increase the adaptive potential of coeno-populations. (author)

  13. Theory of epigenetic coding.

    Science.gov (United States)

    Elder, D

    1984-06-07

    The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.

  14. Traces et espaces de consommation

    Directory of Open Access Journals (Sweden)

    Franck Cochoy

    2016-10-01

    Full Text Available L’avènement des technologies numériques mobiles contribue à une évolution des modalités de distribution et de consommation. Le présent article porte sur l’usage des QR-codes, ces codes-barres bidimensionnels qui offrent à tout usager équipé d’un smartphone l’accès à des contenus commerciaux en ligne. Ils participent à l’Internet des objets et donc au couplage entre espace physique et univers numérique. Ils permettent aussi la collecte de traces numériques porteuses de sens pour les professionnels mais aussi pour les sciences sociales. Grâce à ces traces, on peut comprendre les nouveaux liens marchands tissés entre l’espace physique et le développement de flux informationnels continus. À partir de l’analyse des traces enregistrées à l’occasion de la visite des QR-codes apposés sur trois produits alimentaires (une boîte de sel, une barre chocolatée, une bouteille d’eau, notre enquête s’attache à expliciter les enjeux théoriques, méthodologiques et analytiques du processus de numérisation de l’espace de mobilité physique marchand.

  15. A novel pseudoderivative-based mutation operator for real-coded adaptive genetic algorithms [v2; ref status: indexed, http://f1000r.es/1td

    OpenAIRE

    Maxinder S Kanwal; Avinash S Ramesh; Lauren A Huang

    2013-01-01

    Recent development of large databases, especially those in genetics and proteomics, is pushing the development of novel computational algorithms that implement rapid and accurate search strategies. One successful approach has been to use artificial intelligence and methods, including pattern recognition (e.g. neural networks) and optimization techniques (e.g. genetic algorithms). The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate that ...

  16. Trace determination of safranin O dye using ultrasound assisted dispersive solid-phase micro extraction: Artificial neural network-genetic algorithm and response surface methodology.

    Science.gov (United States)

    Dil, Ebrahim Alipanahpour; Ghaedi, Mehrorang; Asfaram, Arash; Mehrabi, Fatemeh; Bazrafshan, Ali Akbar; Ghaedi, Abdol Mohammad

    2016-11-01

    In this study, ultrasound assisted dispersive solid-phase micro extraction combined with spectrophotometry (USA-DSPME-UV) method based on activated carbon modified with Fe2O3 nanoparticles (Fe2O3-NPs-AC) was developed for pre-concentration and determination of safranin O (SO). It is known that the efficiency of USA-DSPME-UV method may be affected by pH, amount of adsorbent, ultrasound time and eluent volume and the extent and magnitude of their contribution on response (in term of main and interaction part) was studied by using central composite design (CCD) and artificial neural network-genetic algorithms (ANN-GA). Accordingly by adjustment of experimental conditions suggested by ANN-GA at pH 6.5, 1.1mg of adsorbent, 10min ultrasound and 150μL of eluent volume led to achievement of best operation performance like low LOD (6.3ngmL(-1)) and LOQ (17.5ngmL(-1)) in the range of 25-3500ngmL(-1). In following stage, the SO content in real water and wastewater samples with recoveries between 93.27-99.41% with RSD lower than 3% was successfully determined. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Following the traces of spectral music: genetic analysis of compositional models in Périodes, by Gérard Grisey

    Directory of Open Access Journals (Sweden)

    François-Xavier Féron

    2015-09-01

    Full Text Available First developed in the mid-1970s, spectral music represents one of the main genres of contemporary French music. In Périodes (1974 for 7 instruments, Gérard Grisey (1946-1998 sets the foundation of this new approach to music composition, which explores both the acoustical properties of sound and specific features of the auditory system. Gérard Grisey’s archives at the Paul Sacher Foundation in Basel contain, among other things, musical manuscripts (drafts, autograph notes, drawings, etc. of each of the composer’s works, as well as manuscripts of his writings, lesson notes, and books from his library. An examination of these documents, in addition to information gained from interviews with some of the composer’s close friends, allow us to understand better how Grisey imagined, developed, and brought to fruition his spectral approach to composition. In this paper, we begin by describing the composer’s education and explore his particular investigation of musical acoustics between 1972 and 1974 by studying the work of Émile Leipp and Fritz Winckel. We then look closely at two models (the respiratory cycle and the harmonic spectrum built on an E1 fundamental that lie at the heart of the piece and underscore both their structural and auditory influence. Finally, after conducting a detailed analysis of the last section of the piece where Grisey uses instruments to recreate a sound spectrum, we question the existence of a trombone’s spectrogram that the composer himself claims to have used as a model. Through this genetic study of Périodes, we seek, in general, to document the construction of the cycle entitled Les espaces acoustiques (1974-1985 considered emblematic of the spectral aesthetic.

  18. Epidemic contact tracing via communication traces.

    Directory of Open Access Journals (Sweden)

    Katayoun Farrahi

    Full Text Available Traditional contact tracing relies on knowledge of the interpersonal network of physical interactions, where contagious outbreaks propagate. However, due to privacy constraints and noisy data assimilation, this network is generally difficult to reconstruct accurately. Communication traces obtained by mobile phones are known to be good proxies for the physical interaction network, and they may provide a valuable tool for contact tracing. Motivated by this assumption, we propose a model for contact tracing, where an infection is spreading in the physical interpersonal network, which can never be fully recovered; and contact tracing is occurring in a communication network which acts as a proxy for the first. We apply this dual model to a dataset covering 72 students over a 9 month period, for which both the physical interactions as well as the mobile communication traces are known. Our results suggest that a wide range of contact tracing strategies may significantly reduce the final size of the epidemic, by mainly affecting its peak of incidence. However, we find that for low overlap between the face-to-face and communication interaction network, contact tracing is only efficient at the beginning of the outbreak, due to rapidly increasing costs as the epidemic evolves. Overall, contact tracing via mobile phone communication traces may be a viable option to arrest contagious outbreaks.

  19. Epidemic contact tracing via communication traces.

    Science.gov (United States)

    Farrahi, Katayoun; Emonet, Rémi; Cebrian, Manuel

    2014-01-01

    Traditional contact tracing relies on knowledge of the interpersonal network of physical interactions, where contagious outbreaks propagate. However, due to privacy constraints and noisy data assimilation, this network is generally difficult to reconstruct accurately. Communication traces obtained by mobile phones are known to be good proxies for the physical interaction network, and they may provide a valuable tool for contact tracing. Motivated by this assumption, we propose a model for contact tracing, where an infection is spreading in the physical interpersonal network, which can never be fully recovered; and contact tracing is occurring in a communication network which acts as a proxy for the first. We apply this dual model to a dataset covering 72 students over a 9 month period, for which both the physical interactions as well as the mobile communication traces are known. Our results suggest that a wide range of contact tracing strategies may significantly reduce the final size of the epidemic, by mainly affecting its peak of incidence. However, we find that for low overlap between the face-to-face and communication interaction network, contact tracing is only efficient at the beginning of the outbreak, due to rapidly increasing costs as the epidemic evolves. Overall, contact tracing via mobile phone communication traces may be a viable option to arrest contagious outbreaks.

  20. Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora.

    Science.gov (United States)

    Qiu, Ying-Xiong; Fu, Cheng-Xing; Comes, Hans Peter

    2011-04-01

    The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-)temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences

  1. Predictive coding of music--brain responses to rhythmic incongruity.

    Science.gov (United States)

    Vuust, Peter; Ostergaard, Leif; Pallesen, Karen Johanne; Bailey, Christopher; Roepstorff, Andreas

    2009-01-01

    During the last decades, models of music processing in the brain have mainly discussed the specificity of brain modules involved in processing different musical components. We argue that predictive coding offers an explanatory framework for functional integration in musical processing. Further, we provide empirical evidence for such a network in the analysis of event-related MEG-components to rhythmic incongruence in the context of strong metric anticipation. This is seen in a mismatch negativity (MMNm) and a subsequent P3am component, which have the properties of an error term and a subsequent evaluation in a predictive coding framework. There were both quantitative and qualitative differences in the evoked responses in expert jazz musicians compared with rhythmically unskilled non-musicians. We propose that these differences trace a functional adaptation and/or a genetic pre-disposition in experts which allows for a more precise rhythmic prediction.

  2. LUCID - an optical design and raytrace code

    International Nuclear Information System (INIS)

    Nicholas, D.J.; Duffey, K.P.

    1980-11-01

    A 2D optical design and ray trace code is described. The code can operate either as a geometric optics propagation code or provide a scalar diffraction treatment. There are numerous non-standard options within the code including design and systems optimisation procedures. A number of illustrative problems relating to the design of optical components in the field of high power lasers is included. (author)

  3. Geochemical computer codes. A review

    International Nuclear Information System (INIS)

    Andersson, K.

    1987-01-01

    In this report a review of available codes is performed and some code intercomparisons are also discussed. The number of codes treating natural waters (groundwater, lake water, sea water) is large. Most geochemical computer codes treat equilibrium conditions, although some codes with kinetic capability are available. A geochemical equilibrium model consists of a computer code, solving a set of equations by some numerical method and a data base, consisting of thermodynamic data required for the calculations. There are some codes which treat coupled geochemical and transport modeling. Some of these codes solve the equilibrium and transport equations simultaneously while other solve the equations separately from each other. The coupled codes require a large computer capacity and have thus as yet limited use. Three code intercomparisons have been found in literature. It may be concluded that there are many codes available for geochemical calculations but most of them require a user that us quite familiar with the code. The user also has to know the geochemical system in order to judge the reliability of the results. A high quality data base is necessary to obtain a reliable result. The best results may be expected for the major species of natural waters. For more complicated problems, including trace elements, precipitation/dissolution, adsorption, etc., the results seem to be less reliable. (With 44 refs.) (author)

  4. Coding Partitions

    Directory of Open Access Journals (Sweden)

    Fabio Burderi

    2007-05-01

    Full Text Available Motivated by the study of decipherability conditions for codes weaker than Unique Decipherability (UD, we introduce the notion of coding partition. Such a notion generalizes that of UD code and, for codes that are not UD, allows to recover the ``unique decipherability" at the level of the classes of the partition. By tacking into account the natural order between the partitions, we define the characteristic partition of a code X as the finest coding partition of X. This leads to introduce the canonical decomposition of a code in at most one unambiguouscomponent and other (if any totally ambiguouscomponents. In the case the code is finite, we give an algorithm for computing its canonical partition. This, in particular, allows to decide whether a given partition of a finite code X is a coding partition. This last problem is then approached in the case the code is a rational set. We prove its decidability under the hypothesis that the partition contains a finite number of classes and each class is a rational set. Moreover we conjecture that the canonical partition satisfies such a hypothesis. Finally we consider also some relationships between coding partitions and varieties of codes.

  5. A novel pseudoderivative-based mutation operator for real-coded adaptive genetic algorithms [v2; ref status: indexed, http://f1000r.es/1td

    Directory of Open Access Journals (Sweden)

    Maxinder S Kanwal

    2013-11-01

    Full Text Available Recent development of large databases, especially those in genetics and proteomics, is pushing the development of novel computational algorithms that implement rapid and accurate search strategies. One successful approach has been to use artificial intelligence and methods, including pattern recognition (e.g. neural networks and optimization techniques (e.g. genetic algorithms. The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate that is derived from comparing the fitness values of successive generations. We propose a novel pseudoderivative-based mutation rate operator designed to allow a genetic algorithm to escape local optima and successfully continue to the global optimum. Once proven successful, this algorithm can be implemented to solve real problems in neurology and bioinformatics. As a first step towards this goal, we tested our algorithm on two 3-dimensional surfaces with multiple local optima, but only one global optimum, as well as on the N-queens problem, an applied problem in which the function that maps the curve is implicit. For all tests, the adaptive mutation rate allowed the genetic algorithm to find the global optimal solution, performing significantly better than other search methods, including genetic algorithms that implement fixed mutation rates.

  6. An approach based on genetic algorithms with coding in real for the solution of a DC OPF to hydrothermal systems; Uma abordagem baseada em algoritmos geneticos com codificacao em real para a solucao de um FPO DC para sistemas hidrotermicos

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Diego R.; Silva, Alessandro L. da; Luciano, Edson Jose Rezende; Nepomuceno, Leonardo [Universidade Estadual Paulista (UNESP), Bauru, SP (Brazil). Dept. de Engenharia Eletrica], Emails: diego_eng.eletricista@hotmail.com, alessandrolopessilva@uol.com.br, edson.joserl@uol.com.br, leo@feb.unesp.br

    2009-07-01

    Problems of DC Optimal Power Flow (OPF) have been solved by various conventional optimization methods. When the modeling of DC OPF involves discontinuous functions or not differentiable, the use of solution methods based on conventional optimization is often not possible because of the difficulty in calculating the gradient vectors at points of discontinuity/non-differentiability of these functions. This paper proposes a method for solving the DC OPF based on Genetic Algorithms (GA) with real coding. The proposed GA has specific genetic operators to improve the quality and viability of the solution. The results are analyzed for an IEEE test system, and its solutions are compared, when possible, with those obtained by a method of interior point primal-dual logarithmic barrier. The results highlight the robustness of the method and feasibility of obtaining the solution to real systems.

  7. Using genetic algorithms to calibrate the user-defined parameters of IIST model for SBLOCA analysis

    International Nuclear Information System (INIS)

    Tsai, Chiung-Wen; Shih, Chunkuan; Wang, Jong-Rong

    2014-01-01

    Highlights: • The genetic algorithm is proposed to search the user-defined parameters of important correlations. • The TRACE IIST model was employed as a case study to demonstrate the capability of GAs. • The multi-objective optimization strategy was incorporated to evaluate multi objective functions simultaneously. - Abstract: The thermal–hydraulic system codes, i.e., TRACE, have been designed to predict, investigate, and simulate nuclear reactor transients and accidents. Implementing relevant correlations, these codes are able to represent important phenomena such as two-phase flow, critical flow, and countercurrent flow. Furthermore, the thermal–hydraulic system codes permit users to modify the coefficients corresponding to the correlations, providing a certain degree of freedom to calibrate the numerical results, i.e., peak cladding temperature. These coefficients are known as user-defined parameters (UDPs). Practically, defining a series of UDPs is complex, highly relied on expert opinions and engineering experiences. This study proposes another approach – the genetic algorithms (GAs), providing rigorous procedures and mitigating human judgments and mistakes, to calibrate the UDPs of important correlations for a 2% small break loss of coolant accident (SBLOCA). The TRACE IIST model was employed as a case study to demonstrate the capability of GAs. The UDPs were evolved by GAs to reduce the deviations between TRACE results and IIST experimental data

  8. Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection.

    Science.gov (United States)

    Mendes-Junior, C T; Castelli, E C; Meyer, D; Simões, A L; Donadi, E A

    2013-12-01

    HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.

  9. Genetic variants in promoters and coding regions of the muscle glycogen synthase and the insulin-responsive GLUT4 genes in NIDDM

    DEFF Research Database (Denmark)

    Bjørbaek, C; Echwald, Søren Morgenthaler; Hubricht, P

    1994-01-01

    To examine the hypothesis that variants in the regulatory or coding regions of the glycogen synthase (GS) and insulin-responsive glucose transporter (GLUT4) genes contribute to insulin-resistant glucose processing of muscle from non-insulin-dependent diabetes mellitus (NIDDM) patients, promoter...... volunteers. By applying inverse polymerase chain reaction and direct DNA sequencing, 532 base pairs (bp) of the GS promoter were identified and the transcriptional start site determined by primer extension. SSCP scanning of the promoter region detected five single nucleotide substitutions, positioned at 42......'-untranslated region, and the coding region of the GLUT4 gene showed four polymorphisms, all single nucleotide substitutions, positioned at -581, 1, 30, and 582. None of the three changes in the regulatory region of the gene had any major influence on expression of the GLUT4 gene in muscle. The variant at 582...

  10. Speaking Code

    DEFF Research Database (Denmark)

    Cox, Geoff

    Speaking Code begins by invoking the “Hello World” convention used by programmers when learning a new language, helping to establish the interplay of text and code that runs through the book. Interweaving the voice of critical writing from the humanities with the tradition of computing and software...

  11. Re-Os, Sm-Nd, U-Pb, and stepwise lead leaching isotope systematics in shear-zone hosted gold mineralization: genetic tracing and age constraints of crustal hydrothermal activity

    Science.gov (United States)

    Frei, R.; Nägler, Th. F.; Schönberg, R.; Kramers, J. D.

    1998-06-01

    A combined Re-Os, Sm-Nd, U-Pb, and stepwise Pb leaching (PbSL) isotope study of hydrothermal (Mo-W)-bearing minerals and base metal sulfides from two adjacent shear zone hosted gold deposits (RAN, Kimberley) in the Harare-Shamva greenstone belt (Zimbabwe) constrain the timing of the mineralizing events to two periods. During an initial Late Archean event (2.60 Ga) a first molybdenite-scheelite bearing paragenesis was deposited in both shear zone systems, followed by a local reactivation of the shear systems during an Early Proterozoic (1.96 Ga) tectono-thermal overprint, during which base metal sulfides and most of the gold was (re-)deposited. While PbSL has revealed an open-system behavior of the U-Pb systematics in molybdenite and wolframite from the RAN mine, initial Archean Re-Os ages are still preserved implying that this system in these minerals was more resistant to the overprint. A similar retentivity could be shown for the Sm-Nd system in scheelite and powellite associated with the above ore minerals. Re-Os isotopic data from the Proterozoic mineralization in the Kimberley mine point to a recent gain of Re, most pronouncedly affecting Fe-rich sulfides such as pyrrhotite. A significant Re-loss in powellitic scheelite (an alteration phase of molybdenite-bearing scheelite), coupled with a marked loss of U in W-Mo ore minerals, complements the observation of a major Re uptake in Fe-sulfides during oxidizing conditions in a weathering environment. Pyrrhotite under these conditions behaves as an efficient Re-sink. Lead isotope signatures from PbSL residues of molybdenite, powellite, and quartz indicate a continental crustal source and/or contamination for the mineralizing fluid by interaction of the fluids with older sedimentary material as represented by the direct host country rocks. Our investigation reveals the potential of the Re-Os isotopic system applied to crustal hydrothermal ore minerals for genetic tracing and dating purposes. The simplified chemical

  12. Radiobiological and genetic effects of Bromus inermis seed progeny from populations of the East-Ural Radioactive Trace (Russia, Kyshtym accident) - Radiobiological and genetic effects for Bromus inermis Leyss. Populations at the East-Ural radioactive trace (Russia, Kyshtym accident in 1957)

    Energy Technology Data Exchange (ETDEWEB)

    Antonova, Elena V.; Pozolotna, Vera N. [Institute of Plant and Animal Ecology UB RAS, 8 Marta str. 202, 620144, Ekaterinburg (Russian Federation); Karimullina, Elina M. [Institute of Plant and Animal Ecology UB RAS, 8 Marta str. 202, 620144, Ekaterinburg (Russian Federation); Department of Developmental and Cell Biology, University of California, 2011 Biological Sciences III, Irvine, CA 92697-2300 (United States); Roeder, Marion S. [Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466, Gatersleben (Germany)

    2014-07-01

    This investigation dedicates the problem of remote consequences of radiation impact on plant populations. This is a part of a complex research, which includes the classic triad of radioecology (Timofeev-Ressovsky 1963): 'accumulation and migration of radionuclides in different components of ecosystems - assessment of radiation dose - investigation of radiobiological effects'. We used the populations of smooth brome (Bromus inermis Leyss.) as a model system for the investigation of radiobiological and genetic effects. It is radiosensitive plant (Preobrazhenskaya 1971). These species may be used as objects for bio-indication at the radioactive contaminated areas, and as well as large-scale radioecological studies, because the adaptation processes are faster for radiosensitive species (Shevchenko et al., 1992; Pozolotina et al. 2005). We calculated external and internal whole-body dose rates by ERICA Tool (Karimullina et al., 2013). The total dose rate for brome was under 100 mGy h{sup -1} at the most polluted site but 43-110 times (Tier 3) exceeded the background along the pollution gradient. Therefore it can be concluded that herbaceous plant populations currently exist under low level chronic exposure at the EURT area. During seven years we have studied variability of viability, mutability and radioresistance of brome seed progeny. The combined effects of radiation exposure and weather conductions at the EURT area were absent. It may be connect with wide variability of inter-population test parameters. At the same time the weather conductions had an influence on the quality of seed progeny at the background area. We analyzed also correlation between original viability and radioresistance of seed progeny from the all plots. This dependence was positive. It was shown negative dependence between original viability of seed progeny and low weight molecular antioxidants content too. Ionizing radiation is a mutagenic factor and, accordingly, elevated mutation

  13. Coding Labour

    Directory of Open Access Journals (Sweden)

    Anthony McCosker

    2014-03-01

    Full Text Available As well as introducing the Coding Labour section, the authors explore the diffusion of code across the material contexts of everyday life, through the objects and tools of mediation, the systems and practices of cultural production and organisational management, and in the material conditions of labour. Taking code beyond computation and software, their specific focus is on the increasingly familiar connections between code and labour with a focus on the codification and modulation of affect through technologies and practices of management within the contemporary work organisation. In the grey literature of spreadsheets, minutes, workload models, email and the like they identify a violence of forms through which workplace affect, in its constant flux of crisis and ‘prodromal’ modes, is regulated and governed.

  14. Interactive Stable Ray Tracing

    DEFF Research Database (Denmark)

    Dal Corso, Alessandro; Salvi, Marco; Kolb, Craig

    2017-01-01

    Interactive ray tracing applications running on commodity hardware can suffer from objectionable temporal artifacts due to a low sample count. We introduce stable ray tracing, a technique that improves temporal stability without the over-blurring and ghosting artifacts typical of temporal post-pr...

  15. Decoding the codes: A content analysis of the news coverage of genetic cloning by three online news sites and three national daily newspapers, 1996 through 1998

    Science.gov (United States)

    Hyde, Jon E.

    This study compared news coverage of genetic cloning research in three online news sites (CNN.com, ABC.com, and MSNBC.com) and three national daily newspapers (The New York Times, The Washington Post, and USA Today). The study involved the analysis of 230 online and print news articles concerning genetic cloning published from 1996 through 1998. Articles were examined with respect to formats, sources, focus, tone, and assessments about the impact of cloning research. Findings indicated that while print news formats remained relatively constant for the duration of this study, online news formats changed significantly with respect to the kinds of media used to represent the news, the layouts used to represent cloning news, and the emphasis placed on audio-visual content. Online stories were as much as 20 to 70% shorter than print stories. More than 50% of the articles appearing online were composed by outside sources (wire services, guest columnists, etc.). By comparison, nearly 90% of the articles published by print newspapers were written "in-house" by science reporters. Online news sites cited fewer sources and cited a smaller variety of sources than the newspapers examined here. In both news outlets, however, the sources most frequently cited were those with vested interests in furthering cloning research. Both online and print news coverage of cloning tends to focus principally on the technical procedures and on the future benefits of cloning. More than 60% of the articles focused on the techniques and technologies of cloning. Less than 25% of the articles focused on social, ethical, or legal issues associated with cloning. Similarly, articles from all six sources (75%) tended to be both positive and future-oriented. Less than 5% of the total articles examined here had a strongly negative or critical tone. Moreover, both online and print news sources increasingly conveyed a strong sense of acceptance about the possibility of human cloning. Data from this study

  16. SIMULATE-3 K coupled code applications

    Energy Technology Data Exchange (ETDEWEB)

    Joensson, Christian [Studsvik Scandpower AB, Vaesteraas (Sweden); Grandi, Gerardo; Judd, Jerry [Studsvik Scandpower Inc., Idaho Falls, ID (United States)

    2017-07-15

    This paper describes the coupled code system TRACE/SIMULATE-3 K/VIPRE and the application of this code system to the OECD PWR Main Steam Line Break. A short description is given for the application of the coupled system to analyze DNBR and the flexibility the system creates for the user. This includes the possibility to compare and evaluate the result with the TRACE/SIMULATE-3K (S3K) coupled code, the S3K standalone code (core calculation) as well as performing single-channel calculations with S3K and VIPRE. This is the typical separate-effect-analyses required for advanced calculations in order to develop methodologies to be used for safety analyses in general. The models and methods of the code systems are presented. The outline represents the analysis approach starting with the coupled code system, reactor and core model calculation (TRACE/S3K). This is followed by a more detailed core evaluation (S3K standalone) and finally a very detailed thermal-hydraulic investigation of the hot pin condition (VIPRE).

  17. Speech coding

    Energy Technology Data Exchange (ETDEWEB)

    Ravishankar, C., Hughes Network Systems, Germantown, MD

    1998-05-08

    Speech is the predominant means of communication between human beings and since the invention of the telephone by Alexander Graham Bell in 1876, speech services have remained to be the core service in almost all telecommunication systems. Original analog methods of telephony had the disadvantage of speech signal getting corrupted by noise, cross-talk and distortion Long haul transmissions which use repeaters to compensate for the loss in signal strength on transmission links also increase the associated noise and distortion. On the other hand digital transmission is relatively immune to noise, cross-talk and distortion primarily because of the capability to faithfully regenerate digital signal at each repeater purely based on a binary decision. Hence end-to-end performance of the digital link essentially becomes independent of the length and operating frequency bands of the link Hence from a transmission point of view digital transmission has been the preferred approach due to its higher immunity to noise. The need to carry digital speech became extremely important from a service provision point of view as well. Modem requirements have introduced the need for robust, flexible and secure services that can carry a multitude of signal types (such as voice, data and video) without a fundamental change in infrastructure. Such a requirement could not have been easily met without the advent of digital transmission systems, thereby requiring speech to be coded digitally. The term Speech Coding is often referred to techniques that represent or code speech signals either directly as a waveform or as a set of parameters by analyzing the speech signal. In either case, the codes are transmitted to the distant end where speech is reconstructed or synthesized using the received set of codes. A more generic term that is applicable to these techniques that is often interchangeably used with speech coding is the term voice coding. This term is more generic in the sense that the

  18. Optimal codes as Tanner codes with cyclic component codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Pinero, Fernando; Zeng, Peng

    2014-01-01

    In this article we study a class of graph codes with cyclic code component codes as affine variety codes. Within this class of Tanner codes we find some optimal binary codes. We use a particular subgraph of the point-line incidence plane of A(2,q) as the Tanner graph, and we are able to describe ...

  19. Genetic classes and genetic categories : Protecting genetic groups through data protection law

    NARCIS (Netherlands)

    Hallinan, Dara; de Hert, Paul; Taylor, L.; Floridi, L.; van der Sloot, B.

    2017-01-01

    Each person shares genetic code with others. Thus, one individual’s genome can reveal information about other individuals. When multiple individuals share aspects of genetic architecture, they form a ‘genetic group’. From a social and legal perspective, two types of genetic group exist: Those which

  20. A two warehouse deterministic inventory model for deteriorating items with a linear trend in time dependent demand over finite time horizon by Elitist Real-Coded Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    A.K. Bhunia

    2013-04-01

    Full Text Available This paper deals with a deterministic inventory model developed for deteriorating items having two separate storage facilities (owned and rented warehouses due to limited capacity of the existing storage (owned warehouse with linear time dependent demand (increasing over a fixed finite time horizon. The model is formulated with infinite replenishment and the successive replenishment cycle lengths are in arithmetic progression. Partially backlogged shortages are allowed. The stocks of rented warehouse (RW are transported to the owned warehouse (OW in continuous release pattern. For this purpose, the model is formulated as a constrained non-linear mixed integer programming problem. For solving the problem, an advanced genetic algorithm (GA has been developed. This advanced GA is based on ranking selection, elitism, whole arithmetic crossover and non-uniform mutation dependent on the age of the population. Our objective is to determine the optimal replenishment number, lot-size of two-warehouses (OW and RW by maximizing the profit function. The model is illustrated with four numerical examples and sensitivity analyses of the optimal solution are performed with respect to different parameters.

  1. Nuclear traces in glass

    International Nuclear Information System (INIS)

    Segovia A, M. de N.

    1978-01-01

    The charged particles produce, in dielectric materials, physical and chemical effects which make evident the damaged zone along the trajectory of the particle. This damaged zone is known as the latent trace. The latent traces can be enlarged by an etching of the detector material. This treatment attacks preferently the zones of the material where the charged particles have penetrated, producing concavities which can be observed through a low magnification optical microscope. These concavities are known as developed traces. In this work we describe the glass characteristics as a detector of the fission fragments traces. In the first chapter we present a summary of the existing basic theories to explain the formation of traces in solids. In the second chapter we describe the etching method used for the traces development. In the following chapters we determine some chatacteristics of the traces formed on the glass, such as: the development optimum time; the diameter variation of the traces and their density according to the temperature variation of the detector; the glass response to a radiation more penetrating than that of the fission fragments; the distribution of the developed traces and the existing relation between this ditribution and the fission fragments of 252 Cf energies. The method which has been used is simple and cheap and can be utilized in laboratories whose resources are limited. The commercial glass which has been employed allows the registration of the fission fragments and subsequently the realization of experiments which involve the counting of the traces as well as the identification of particles. (author)

  2. Aztheca Code

    International Nuclear Information System (INIS)

    Quezada G, S.; Espinosa P, G.; Centeno P, J.; Sanchez M, H.

    2017-09-01

    This paper presents the Aztheca code, which is formed by the mathematical models of neutron kinetics, power generation, heat transfer, core thermo-hydraulics, recirculation systems, dynamic pressure and level models and control system. The Aztheca code is validated with plant data, as well as with predictions from the manufacturer when the reactor operates in a stationary state. On the other hand, to demonstrate that the model is applicable during a transient, an event occurred in a nuclear power plant with a BWR reactor is selected. The plant data are compared with the results obtained with RELAP-5 and the Aztheca model. The results show that both RELAP-5 and the Aztheca code have the ability to adequately predict the behavior of the reactor. (Author)

  3. A Computer Library for Ray Tracing in Analytical Media

    International Nuclear Information System (INIS)

    Miqueles, Eduardo; Coimbra, Tiago A; Figueiredo, J J S de

    2013-01-01

    Ray tracing technique is an important tool not only for forward but also for inverse problems in Geophysics, which most of the seismic processing steps depends on. However, implementing ray tracing codes can be very time consuming. This article presents a computer library to trace rays in 2.5D media composed by stack of layers. The velocity profile inside each layer is such that the eikonal equation can be analitically solved. Therefore, the ray tracing within such profile is made fast and accurately. The great advantage of an analytical ray tracing library is the numerical precision of the quantities computed and the fast execution of the implemented codes. Although ray tracing programs already exist for a long time, for example the seis package by Cervený, with a numerical approach to compute the ray. Regardless of the fact that numerical methods can solve more general problems, the analytical ones could be part of a more sofisticated simulation process, where the ray tracing time is completely relevant. We demonstrate the feasibility of our codes using numerical examples.

  4. Vocable Code

    DEFF Research Database (Denmark)

    Soon, Winnie; Cox, Geoff

    2018-01-01

    a computational and poetic composition for two screens: on one of these, texts and voices are repeated and disrupted by mathematical chaos, together exploring the performativity of code and language; on the other, is a mix of a computer programming syntax and human language. In this sense queer code can...... be understood as both an object and subject of study that intervenes in the world’s ‘becoming' and how material bodies are produced via human and nonhuman practices. Through mixing the natural and computer language, this article presents a script in six parts from a performative lecture for two persons...

  5. NSURE code

    International Nuclear Information System (INIS)

    Rattan, D.S.

    1993-11-01

    NSURE stands for Near-Surface Repository code. NSURE is a performance assessment code. developed for the safety assessment of near-surface disposal facilities for low-level radioactive waste (LLRW). Part one of this report documents the NSURE model, governing equations and formulation of the mathematical models, and their implementation under the SYVAC3 executive. The NSURE model simulates the release of nuclides from an engineered vault, their subsequent transport via the groundwater and surface water pathways tot he biosphere, and predicts the resulting dose rate to a critical individual. Part two of this report consists of a User's manual, describing simulation procedures, input data preparation, output and example test cases

  6. The Aster code; Code Aster

    Energy Technology Data Exchange (ETDEWEB)

    Delbecq, J.M

    1999-07-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  7. Coding Class

    DEFF Research Database (Denmark)

    Ejsing-Duun, Stine; Hansbøl, Mikala

    Denne rapport rummer evaluering og dokumentation af Coding Class projektet1. Coding Class projektet blev igangsat i skoleåret 2016/2017 af IT-Branchen i samarbejde med en række medlemsvirksomheder, Københavns kommune, Vejle Kommune, Styrelsen for IT- og Læring (STIL) og den frivillige forening...... Coding Pirates2. Rapporten er forfattet af Docent i digitale læringsressourcer og forskningskoordinator for forsknings- og udviklingsmiljøet Digitalisering i Skolen (DiS), Mikala Hansbøl, fra Institut for Skole og Læring ved Professionshøjskolen Metropol; og Lektor i læringsteknologi, interaktionsdesign......, design tænkning og design-pædagogik, Stine Ejsing-Duun fra Forskningslab: It og Læringsdesign (ILD-LAB) ved Institut for kommunikation og psykologi, Aalborg Universitet i København. Vi har fulgt og gennemført evaluering og dokumentation af Coding Class projektet i perioden november 2016 til maj 2017...

  8. Uplink Coding

    Science.gov (United States)

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the objectives, meeting goals and overall NASA goals for the NASA Data Standards Working Group. The presentation includes information on the technical progress surrounding the objective, short LDPC codes, and the general results on the Pu-Pw tradeoff.

  9. ANIMAL code

    International Nuclear Information System (INIS)

    Lindemuth, I.R.

    1979-01-01

    This report describes ANIMAL, a two-dimensional Eulerian magnetohydrodynamic computer code. ANIMAL's physical model also appears. Formulated are temporal and spatial finite-difference equations in a manner that facilitates implementation of the algorithm. Outlined are the functions of the algorithm's FORTRAN subroutines and variables

  10. Network Coding

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Network Coding. K V Rashmi Nihar B Shah P Vijay Kumar. General Article Volume 15 Issue 7 July 2010 pp 604-621. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/015/07/0604-0621 ...

  11. MCNP code

    International Nuclear Information System (INIS)

    Cramer, S.N.

    1984-01-01

    The MCNP code is the major Monte Carlo coupled neutron-photon transport research tool at the Los Alamos National Laboratory, and it represents the most extensive Monte Carlo development program in the United States which is available in the public domain. The present code is the direct descendent of the original Monte Carlo work of Fermi, von Neumaum, and Ulam at Los Alamos in the 1940s. Development has continued uninterrupted since that time, and the current version of MCNP (or its predecessors) has always included state-of-the-art methods in the Monte Carlo simulation of radiation transport, basic cross section data, geometry capability, variance reduction, and estimation procedures. The authors of the present code have oriented its development toward general user application. The documentation, though extensive, is presented in a clear and simple manner with many examples, illustrations, and sample problems. In addition to providing the desired results, the output listings give a a wealth of detailed information (some optional) concerning each state of the calculation. The code system is continually updated to take advantage of advances in computer hardware and software, including interactive modes of operation, diagnostic interrupts and restarts, and a variety of graphical and video aids

  12. Expander Codes

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 1. Expander Codes - The Sipser–Spielman Construction. Priti Shankar. General Article Volume 10 ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science Bangalore 560 012, India.

  13. Computer ray tracing speeds.

    Science.gov (United States)

    Robb, P; Pawlowski, B

    1990-05-01

    The results of measuring the ray trace speed and compilation speed of thirty-nine computers in fifty-seven configurations, ranging from personal computers to super computers, are described. A correlation of ray trace speed has been made with the LINPACK benchmark which allows the ray trace speed to be estimated using LINPACK performance data. The results indicate that the latest generation of workstations, using CPUs based on RISC (Reduced Instruction Set Computer) technology, are as fast or faster than mainframe computers in compute-bound situations.

  14. Self-complementary circular codes in coding theory.

    Science.gov (United States)

    Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

    2018-04-01

    Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

  15. Traces of Drosophila Memory

    Science.gov (United States)

    Davis, Ronald L.

    2012-01-01

    Summary Studies using functional cellullar imaging of living flies have identified six memory traces that form in the olfactory nervous system after conditioning with odors. These traces occur in distinct nodes of the olfactory nervous system, form and disappear across different windows of time, and are detected in the imaged neurons as increased calcium influx or synaptic release in response to the conditioned odor. Three traces form at, or near acquisition and co-exist with short-term behavioral memory. One trace forms with a delay after learning and co-exists with intermediate-term behavioral memory. Two traces form many hours after acquisition and co-exist with long-term behavioral memory. The transient memory traces may support behavior across the time-windows of their existence. The experimental approaches for dissecting memory formation in the fly, ranging from the molecular to the systems, make it an ideal system for dissecting the logic by which the nervous system organizes and stores different temporal forms of memory. PMID:21482352

  16. Panda code

    International Nuclear Information System (INIS)

    Altomare, S.; Minton, G.

    1975-02-01

    PANDA is a new two-group one-dimensional (slab/cylinder) neutron diffusion code designed to replace and extend the FAB series. PANDA allows for the nonlinear effects of xenon, enthalpy and Doppler. Fuel depletion is allowed. PANDA has a completely general search facility which will seek criticality, maximize reactivity, or minimize peaking. Any single parameter may be varied in a search. PANDA is written in FORTRAN IV, and as such is nearly machine independent. However, PANDA has been written with the present limitations of the Westinghouse CDC-6600 system in mind. Most computation loops are very short, and the code is less than half the useful 6600 memory size so that two jobs can reside in the core at once. (auth)

  17. CANAL code

    International Nuclear Information System (INIS)

    Gara, P.; Martin, E.

    1983-01-01

    The CANAL code presented here optimizes a realistic iron free extraction channel which has to provide a given transversal magnetic field law in the median plane: the current bars may be curved, have finite lengths and cooling ducts and move in a restricted transversal area; terminal connectors may be added, images of the bars in pole pieces may be included. A special option optimizes a real set of circular coils [fr

  18. Automated addition of Chelex solution to tubes containing trace items

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Hansen, Thomas Møller; Hansen, Anders Johannes

    2011-01-01

    Extraction of DNA from trace items for forensic genetic DNA typing using a manual Chelex based extraction protocol requires addition of Chelex solution to sample tubes containing trace items. Automated of addition of Chelex solution may be hampered by high viscosity of the solution and fast...... sedimentation rate of the Chelex beads. Here, we present a simple method that can be used on an Eppendorf epMotion liquid handler resolving these issues...

  19. From concatenated codes to graph codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom

    2004-01-01

    We consider codes based on simple bipartite expander graphs. These codes may be seen as the first step leading from product type concatenated codes to more complex graph codes. We emphasize constructions of specific codes of realistic lengths, and study the details of decoding by message passing...

  20. Intraoral gothic arch tracing.

    Science.gov (United States)

    Rubel, Barry; Hill, Edward E

    2011-01-01

    In order to create optimum esthetics, function and phonetics in complete denture fabrication, it is necessary to record accurate maxillo-mandibular determinants of occlusion. This requires clinical skill to establish an accurate, verifiable and reproducible vertical dimension of occlusion (VDO) and centric relation (CR). Correct vertical relation depends upon a consideration of several factors, including muscle tone, inter-dental arch space and parallelism of the ridges. Any errors made while taking maxillo-mandibular jaw relation records will result in dentures that are uncomfortable and, possibly, unwearable. The application of a tracing mechanism such as the Gothic arch tracer (a central bearing device) is a demonstrable method of determining centric relation. Intraoral Gothic arch tracers provide the advantage of capturing VDO and CR in an easy-to-use technique for practitioners. Intraoral tracing (Gothic arch tracing) is a preferred method of obtaining consistent positions of the mandible in motion (retrusive, protrusive and lateral) at a comfortable VDO.

  1. Atom trap trace analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Z.-T.; Bailey, K.; Chen, C.-Y.; Du, X.; Li, Y.-M.; O' Connor, T. P.; Young, L.

    2000-05-25

    A new method of ultrasensitive trace-isotope analysis has been developed based upon the technique of laser manipulation of neutral atoms. It has been used to count individual {sup 85}Kr and {sup 81}Kr atoms present in a natural krypton sample with isotopic abundances in the range of 10{sup {minus}11} and 10{sup {minus}13}, respectively. The atom counts are free of contamination from other isotopes, elements,or molecules. The method is applicable to other trace-isotopes that can be efficiently captured with a magneto-optical trap, and has a broad range of potential applications.

  2. Atom trap trace analysis

    International Nuclear Information System (INIS)

    Lu, Z.-T.; Bailey, K.; Chen, C.-Y.; Du, X.; Li, Y.-M.; O'Connor, T. P.; Young, L.

    2000-01-01

    A new method of ultrasensitive trace-isotope analysis has been developed based upon the technique of laser manipulation of neutral atoms. It has been used to count individual 85 Kr and 81 Kr atoms present in a natural krypton sample with isotopic abundances in the range of 10 -11 and 10 -13 , respectively. The atom counts are free of contamination from other isotopes, elements,or molecules. The method is applicable to other trace-isotopes that can be efficiently captured with a magneto-optical trap, and has a broad range of potential applications

  3. Oscilloscope trace photograph digitizing system (TRACE)

    International Nuclear Information System (INIS)

    Richards, M.; Dabbs, R.D.

    1977-10-01

    The digitizing system allows digitization of photographs or sketches of waveforms and then the computer is used to reduce and analyze the data. The software allows for alignment, calibration, removal of baselines, removal of unwanted points and addition of new points which makes for a fairly versatile system as far as data reduction and manipulation are concerned. System considerations are introduced first to orient the potential user to the process of digitizing information. The start up and actual commands for TRACE are discussed. Detailed descriptions of each subroutine and program section are also provided. Three general examples of typical photographs are included. A partial listing of FAWTEK is made available. Once suitable arrays that contain the data are arranged, ''GO FA'' (active FAWTEK) and many mathematical operations to further analyze the data may be performed

  4. Quantum algorithms and the genetic code

    Indian Academy of Sciences (India)

    Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever!) explanation of why living organisms have 4 nucleotide bases and 20 amino acids. It is amazing that these numbers arise as ...

  5. George Gamow and the Genetic Code

    Indian Academy of Sciences (India)

    cause they were held together by hydrogen bonds formed be- tween adenine and ... To return to our story, on the 8th of July Gamow addressed a letter to Watson and ... "For example, the animal will be a cat if Adenine is always followed by ...

  6. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  7. Queer Tracings of Genre

    DEFF Research Database (Denmark)

    Balle, Søren Hattesen

    as (re)tracings of genres that appear somehow residual or defunct in a post-modernist poetic context. On the other, they are made to "encode new [and queer, shb] meanings" (Anne Ferry) inasmuch as Ashbery, for instance, doubles and literalizes Dante's false etymology of the word ‘eclogue' (aig- and logos...

  8. The Trace of Superusers

    DEFF Research Database (Denmark)

    Samson, Kristine; Abasolo, José

    2013-01-01

    The city and its public spaces can be seen as a fragmented whole carrying meanings and traces of culture, use and politics with it. Whereas architects impose new stories and meanings on the urban fabric, the city itself is layered and assembled, a collective of social flows and routines a result ...

  9. Third order trace formula

    Indian Academy of Sciences (India)

    N. Centre for Advanced Scientific Research, Bangalore 560 064, India. 2Indian Institute of ... for rational functions φ with poles off R. In [5,16], Koplienko's trace formula was derived ... be a sequence of complex numbers such that ..... Again if we set the sum of the second and fourth term inside the integral in (2.3) to be. I2 ≡.

  10. Automatic coding method of the ACR Code

    International Nuclear Information System (INIS)

    Park, Kwi Ae; Ihm, Jong Sool; Ahn, Woo Hyun; Baik, Seung Kook; Choi, Han Yong; Kim, Bong Gi

    1993-01-01

    The authors developed a computer program for automatic coding of ACR(American College of Radiology) code. The automatic coding of the ACR code is essential for computerization of the data in the department of radiology. This program was written in foxbase language and has been used for automatic coding of diagnosis in the Department of Radiology, Wallace Memorial Baptist since May 1992. The ACR dictionary files consisted of 11 files, one for the organ code and the others for the pathology code. The organ code was obtained by typing organ name or code number itself among the upper and lower level codes of the selected one that were simultaneous displayed on the screen. According to the first number of the selected organ code, the corresponding pathology code file was chosen automatically. By the similar fashion of organ code selection, the proper pathologic dode was obtained. An example of obtained ACR code is '131.3661'. This procedure was reproducible regardless of the number of fields of data. Because this program was written in 'User's Defined Function' from, decoding of the stored ACR code was achieved by this same program and incorporation of this program into program in to another data processing was possible. This program had merits of simple operation, accurate and detail coding, and easy adjustment for another program. Therefore, this program can be used for automation of routine work in the department of radiology

  11. Error-correction coding

    Science.gov (United States)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

    This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

  12. Analysis of Uncertainty and Sensitivity with TRACE-SUSA and TRACE-DAKOTA. Application to NUPEC BFTB; Analisis de Incertidumbre y Sensibilidad con TRACE-SUSA y TRACE-DAKOTA. Aplicacion a NUPEC BFTB

    Energy Technology Data Exchange (ETDEWEB)

    Montero-Mayorga, J.; Wadim, J.; Sanchez, V. H.

    2012-07-01

    The aim of this work is to test the capabilities of the new tool of uncertainty incorporated into SNAP by simulating experiments with TRACE code and compare these with the results obtained by the same simulations with uncertainty calculation performed with the tool SUSA.

  13. Dynamic Shannon Coding

    OpenAIRE

    Gagie, Travis

    2005-01-01

    We present a new algorithm for dynamic prefix-free coding, based on Shannon coding. We give a simple analysis and prove a better upper bound on the length of the encoding produced than the corresponding bound for dynamic Huffman coding. We show how our algorithm can be modified for efficient length-restricted coding, alphabetic coding and coding with unequal letter costs.

  14. Fundamentals of convolutional coding

    CERN Document Server

    Johannesson, Rolf

    2015-01-01

    Fundamentals of Convolutional Coding, Second Edition, regarded as a bible of convolutional coding brings you a clear and comprehensive discussion of the basic principles of this field * Two new chapters on low-density parity-check (LDPC) convolutional codes and iterative coding * Viterbi, BCJR, BEAST, list, and sequential decoding of convolutional codes * Distance properties of convolutional codes * Includes a downloadable solutions manual

  15. Codes Over Hyperfields

    Directory of Open Access Journals (Sweden)

    Atamewoue Surdive

    2017-12-01

    Full Text Available In this paper, we define linear codes and cyclic codes over a finite Krasner hyperfield and we characterize these codes by their generator matrices and parity check matrices. We also demonstrate that codes over finite Krasner hyperfields are more interesting for code theory than codes over classical finite fields.

  16. Foundations of genetic algorithms 1991

    CERN Document Server

    1991-01-01

    Foundations of Genetic Algorithms 1991 (FOGA 1) discusses the theoretical foundations of genetic algorithms (GA) and classifier systems.This book compiles research papers on selection and convergence, coding and representation, problem hardness, deception, classifier system design, variation and recombination, parallelization, and population divergence. Other topics include the non-uniform Walsh-schema transform; spurious correlations and premature convergence in genetic algorithms; and variable default hierarchy separation in a classifier system. The grammar-based genetic algorithm; condition

  17. On Trace Zero Matrices

    Indian Academy of Sciences (India)

    In this note, we shall try to present an elemen- tary proof of a couple of closely related results which have both proved quite useful, and al~ indicate possible generalisations. The results we have in mind are the following facts: (a) A complex n x n matrix A has trace 0 if and only if it is expressible in the form A = PQ - Q P.

  18. Preconcentration of trace elements

    International Nuclear Information System (INIS)

    Zolotov, Yu. A.; Kuz'min, N.M.

    1990-01-01

    This monograph deals with the theory and practical applications of trace metals preconcentration. It gives general characteristics of the process and describes in detail the methods of preconcentration: solvent extraction, sorption, co-precipitation, volatilization, and others. Special attention is given to preconcentration in combination with subsequent determination methods. The use of preconcentration in analysis of environmental and biological samples, mineral raw materials, high purity substances, and various industrial materials is also considered

  19. A manual to the MAXRAY program library for reflective and dispersive ray tracing

    International Nuclear Information System (INIS)

    Svensson, S.; Nyholm, R.

    1985-07-01

    A general ray tracing program package for reflective and dispersive X-ray optics is described. The package consists of a number of subroutines written in FORTRAN 77 code giving the necessary tools for ray tracing. The program package is available on request from the authors. (authors)

  20. Anisotropic ray trace

    Science.gov (United States)

    Lam, Wai Sze Tiffany

    Optical components made of anisotropic materials, such as crystal polarizers and crystal waveplates, are widely used in many complex optical system, such as display systems, microlithography, biomedical imaging and many other optical systems, and induce more complex aberrations than optical components made of isotropic materials. The goal of this dissertation is to accurately simulate the performance of optical systems with anisotropic materials using polarization ray trace. This work extends the polarization ray tracing calculus to incorporate ray tracing through anisotropic materials, including uniaxial, biaxial and optically active materials. The 3D polarization ray tracing calculus is an invaluable tool for analyzing polarization properties of an optical system. The 3x3 polarization ray tracing P matrix developed for anisotropic ray trace assists tracking the 3D polarization transformations along a ray path with series of surfaces in an optical system. To better represent the anisotropic light-matter interactions, the definition of the P matrix is generalized to incorporate not only the polarization change at a refraction/reflection interface, but also the induced optical phase accumulation as light propagates through the anisotropic medium. This enables realistic modeling of crystalline polarization elements, such as crystal waveplates and crystal polarizers. The wavefront and polarization aberrations of these anisotropic components are more complex than those of isotropic optical components and can be evaluated from the resultant P matrix for each eigen-wavefront as well as for the overall image. One incident ray refracting or reflecting into an anisotropic medium produces two eigenpolarizations or eigenmodes propagating in different directions. The associated ray parameters of these modes necessary for the anisotropic ray trace are described in Chapter 2. The algorithms to calculate the P matrix from these ray parameters are described in Chapter 3 for

  1. Tracers and tracing methods

    International Nuclear Information System (INIS)

    Leclerc, J.P.

    2001-01-01

    The first international congress on 'Tracers and tracing methods' took place in Nancy in May 2001. The objective of this second congress was to present the current status and trends on tracing methods and their applications. It has given the opportunity to people from different fields to exchange scientific information and knowledge about tracer methodologies and applications. The target participants were the researchers, engineers and technologists of various industrial and research sectors: chemical engineering, environment, food engineering, bio-engineering, geology, hydrology, civil engineering, iron and steel production... Two sessions have been planned to cover both fundamental and industrial aspects: 1)fundamental development (tomography, tracer camera visualization and particles tracking; validation of computational fluid dynamics simulations by tracer experiments and numerical residence time distribution; new tracers and detectors or improvement and development of existing tracing methods; data treatments and modeling; reactive tracer experiments and interpretation) 2)industrial applications (geology, hydrogeology and oil field applications; civil engineering, mineral engineering and metallurgy applications; chemical engineering; environment; food engineering and bio-engineering). The program included 5 plenary lectures, 23 oral communications and around 50 posters. Only 9 presentations are interested for the INIS database

  2. Goya - an MHD equilibrium code for toroidal plasmas

    International Nuclear Information System (INIS)

    Scheffel, J.

    1984-09-01

    A description of the GOYA free-boundary equilibrium code is given. The non-linear Grad-Shafranov equation of ideal MHD is solved in a toroidal geometry for plasmas with purely poloidal magnetic fields. The code is based on a field line-tracing procedure, making storage of a large amount of information on a grid unnecessary. Usage of the code is demonstrated by computations of equi/libria for the EXTRAP-T1 device. (Author)

  3. Development Status of TRACE model for PGSFR Safety Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Andong; Choi, Yong Won; Kim, Jihun; Bae, Moohoon [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2014-05-15

    For the preparation of the review of licensing application for PGSFR, TRACE model for the PGSFR is being developed considering the sodium related properties and model in the code. For the use of licensing purpose, it is identified and need to be improved that model uncertainty in the code and conservative conditions for accident analysis is needs to be defined and validated. And current simulations are applicable only to assembly-averaged assessment. So it is also need to be defined for pin-wise assessment within hot assembly. On the basis on the developed model, PGSFR design change will be applied and improved for independent audit calculation for incoming licensing review. Prototype Generation IV Sodium cooled Fast Reactor (PGSFR) of 150MWe is under developing targeting licensing application by 2017. KINS is preparing review of its licensing application, especially the audit calculation tool for transient and accident analysis is being prepared for review. Since 2012, TRACE code applicability study has been doing for the Sodium-cooled Fast Reactor. At first, Sodium properties and the related heat transfer model in the code were reviewed. Demonstration Sodium cooled Fast Reactor (DSFR-600) were model and representing DBAs were assessed until the PGSFR design is fixed. EBR-II Shutdown Heat Removal Test (SHRT) experiment is also being analyzed in terms of IAEA Cooperated Research Program. In this paper, PGSFR TRACE code modeling status and considerations for SFR DBA assessment is introduced.

  4. Mobile code security

    Science.gov (United States)

    Ramalingam, Srikumar

    2001-11-01

    A highly secure mobile agent system is very important for a mobile computing environment. The security issues in mobile agent system comprise protecting mobile hosts from malicious agents, protecting agents from other malicious agents, protecting hosts from other malicious hosts and protecting agents from malicious hosts. Using traditional security mechanisms the first three security problems can be solved. Apart from using trusted hardware, very few approaches exist to protect mobile code from malicious hosts. Some of the approaches to solve this problem are the use of trusted computing, computing with encrypted function, steganography, cryptographic traces, Seal Calculas, etc. This paper focuses on the simulation of some of these existing techniques in the designed mobile language. Some new approaches to solve malicious network problem and agent tampering problem are developed using public key encryption system and steganographic concepts. The approaches are based on encrypting and hiding the partial solutions of the mobile agents. The partial results are stored and the address of the storage is destroyed as the agent moves from one host to another host. This allows only the originator to make use of the partial results. Through these approaches some of the existing problems are solved.

  5. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call...

  6. Vector Network Coding Algorithms

    OpenAIRE

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L x L coding matrices that play a similar role as coding c in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector coding, our algori...

  7. Homological stabilizer codes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  8. Hypothesis of Lithocoding: Origin of the Genetic Code as a "Double Jigsaw Puzzle" of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules.

    Science.gov (United States)

    Skoblikow, Nikolai E; Zimin, Andrei A

    2016-05-01

    The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named "lithocodon") partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named "lithocoding"). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named "lithotranslation") preventing the shift of coding. A table of the presumed "LithoCode" (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed "volcanic scenario".

  9. Diagnostic Coding for Epilepsy.

    Science.gov (United States)

    Williams, Korwyn; Nuwer, Marc R; Buchhalter, Jeffrey R

    2016-02-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  10. Coding of Neuroinfectious Diseases.

    Science.gov (United States)

    Barkley, Gregory L

    2015-12-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  11. BETHSY 9.1b Test Calculation with TRACE Using 3D Vessel Component

    International Nuclear Information System (INIS)

    Berar, O.; Prosek, A.

    2012-01-01

    Recently, several advanced multidimensional computational tools for simulating reactor system behaviour during real and hypothetical transient scenarios were developed. One of such advanced, best-estimate reactor systems codes is TRAC/RELAP Advanced Computational Engine (TRACE), developed by the U.S. Nuclear Regulatory Commission. The advanced TRACE comes with a graphical user interface called SNAP (Symbolic Nuclear Analysis Package). It is intended for pre- and post-processing, running codes, RELAP5 to TRACE input deck conversion, input deck database generation etc. The TRACE code is still not fully development and it will have all the capabilities of RELAP5. The purpose of the present study was therefore to assess the 3D capability of the TRACE on BETHSY 9.1b test. The TRACE input deck was semi-converted (using SNAP and manual corrections) from the RELAP5 input deck. The 3D fluid dynamics within reactor vessel was modelled and compared to 1D fluid dynamics. The 3D calculation was compared both to TRACE 1D calculation and RELAP5 calculation. Namely, the geometry used in TRACE is basically the same, what gives very good basis for the comparison of the codes. The only exception is 3D reactor vessel model in case of TRACE 3D calculation. The TRACE V5.0 Patch 1 and RELAP5/MOD3.3 Patch 4 were used for calculations. The BETHSY 9.1b test (International Standard Problem no. 27 or ISP-27) was 5.08 cm equivalent diameter cold leg break without high pressure safety injection and with delayed ultimate procedure. BETHSY facility was a 3-loop replica of a 900 MWe FRAMATOME pressurized water reactor. For better presentation of the calculated physical phenomena and processes, an animation model using SNAP was developed. In general, the TRACE 3D code calculation is in good agreement with the BETHSY 9.1b test. The TRACE 3D calculation results are as good as or better than the RELAP5 calculated results. Also, the TRACE 3D calculation is not significantly different from TRACE 1D

  12. Piezoelectric trace vapor calibrator

    International Nuclear Information System (INIS)

    Verkouteren, R. Michael; Gillen, Greg; Taylor, David W.

    2006-01-01

    The design and performance of a vapor generator for calibration and testing of trace chemical sensors are described. The device utilizes piezoelectric ink-jet nozzles to dispense and vaporize precisely known amounts of analyte solutions as monodisperse droplets onto a hot ceramic surface, where the generated vapors are mixed with air before exiting the device. Injected droplets are monitored by microscope with strobed illumination, and the reproducibility of droplet volumes is optimized by adjustment of piezoelectric wave form parameters. Complete vaporization of the droplets occurs only across a 10 deg. C window within the transition boiling regime of the solvent, and the minimum and maximum rates of trace analyte that may be injected and evaporated are determined by thermodynamic principles and empirical observations of droplet formation and stability. By varying solution concentrations, droplet injection rates, air flow, and the number of active nozzles, the system is designed to deliver--on demand--continuous vapor concentrations across more than six orders of magnitude (nominally 290 fg/l to 1.05 μg/l). Vapor pulses containing femtogram to microgram quantities of analyte may also be generated. Calibrated ranges of three explosive vapors at ng/l levels were generated by the device and directly measured by ion mobility spectrometry (IMS). These data demonstrate expected linear trends within the limited working range of the IMS detector and also exhibit subtle nonlinear behavior from the IMS measurement process

  13. Coding of Stimuli by Animals: Retrospection, Prospection, Episodic Memory and Future Planning

    Science.gov (United States)

    Zentall, Thomas R.

    2010-01-01

    When animals code stimuli for later retrieval they can either code them in terms of the stimulus presented (as a retrospective memory) or in terms of the response or outcome anticipated (as a prospective memory). Although retrospective memory is typically assumed (as in the form of a memory trace), evidence of prospective coding has been found…

  14. Vector Network Coding

    OpenAIRE

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L X L coding matrices that play a similar role as coding coefficients in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector co...

  15. Entropy Coding in HEVC

    OpenAIRE

    Sze, Vivienne; Marpe, Detlev

    2014-01-01

    Context-Based Adaptive Binary Arithmetic Coding (CABAC) is a method of entropy coding first introduced in H.264/AVC and now used in the latest High Efficiency Video Coding (HEVC) standard. While it provides high coding efficiency, the data dependencies in H.264/AVC CABAC make it challenging to parallelize and thus limit its throughput. Accordingly, during the standardization of entropy coding for HEVC, both aspects of coding efficiency and throughput were considered. This chapter describes th...

  16. Generalized concatenated quantum codes

    International Nuclear Information System (INIS)

    Grassl, Markus; Shor, Peter; Smith, Graeme; Smolin, John; Zeng Bei

    2009-01-01

    We discuss the concept of generalized concatenated quantum codes. This generalized concatenation method provides a systematical way for constructing good quantum codes, both stabilizer codes and nonadditive codes. Using this method, we construct families of single-error-correcting nonadditive quantum codes, in both binary and nonbinary cases, which not only outperform any stabilizer codes for finite block length but also asymptotically meet the quantum Hamming bound for large block length.

  17. Rateless feedback codes

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Koike-Akino, Toshiaki; Orlik, Philip

    2012-01-01

    This paper proposes a concept called rateless feedback coding. We redesign the existing LT and Raptor codes, by introducing new degree distributions for the case when a few feedback opportunities are available. We show that incorporating feedback to LT codes can significantly decrease both...... the coding overhead and the encoding/decoding complexity. Moreover, we show that, at the price of a slight increase in the coding overhead, linear complexity is achieved with Raptor feedback coding....

  18. Traces generating what was there

    CERN Document Server

    2017-01-01

    Traces keep time contained and make visible what was there. Going back to the art of trace-reading, they continue to be a fundamental resource for scientific knowledge production. The contributions study, from the biology laboratory to the large colliders of particle physics, techniques involved in the production of material traces. Following their changes over two centuries, this collection shows the continuities they have in the digital age.

  19. Advanced video coding systems

    CERN Document Server

    Gao, Wen

    2015-01-01

    This comprehensive and accessible text/reference presents an overview of the state of the art in video coding technology. Specifically, the book introduces the tools of the AVS2 standard, describing how AVS2 can help to achieve a significant improvement in coding efficiency for future video networks and applications by incorporating smarter coding tools such as scene video coding. Topics and features: introduces the basic concepts in video coding, and presents a short history of video coding technology and standards; reviews the coding framework, main coding tools, and syntax structure of AV

  20. Coding for dummies

    CERN Document Server

    Abraham, Nikhil

    2015-01-01

    Hands-on exercises help you learn to code like a pro No coding experience is required for Coding For Dummies,your one-stop guide to building a foundation of knowledge inwriting computer code for web, application, and softwaredevelopment. It doesn't matter if you've dabbled in coding or neverwritten a line of code, this book guides you through the basics.Using foundational web development languages like HTML, CSS, andJavaScript, it explains in plain English how coding works and whyit's needed. Online exercises developed by Codecademy, a leading online codetraining site, help hone coding skill

  1. Trace Mineral Losses in Sweat

    National Research Council Canada - National Science Library

    Chinevere, Troy D; McClung, James P; Cheuvront, Samuel N

    2007-01-01

    Copper, iron and zinc are nutritionally essential trace minerals that confer vital biological roles including the maintenance of cell structure and integrity, regulation of metabolism, immune function...

  2. Trace analysis of semiconductor materials

    CERN Document Server

    Cali, J Paul; Gordon, L

    1964-01-01

    Trace Analysis of Semiconductor Materials is a guidebook concerned with procedures of ultra-trace analysis. This book discusses six distinct techniques of trace analysis. These techniques are the most common and can be applied to various problems compared to other methods. Each of the four chapters basically includes an introduction to the principles and general statements. The theoretical basis for the technique involved is then briefly discussed. Practical applications of the techniques and the different instrumentations are explained. Then, the applications to trace analysis as pertaining

  3. Tracing the breeding farm of domesticated pig using feature selection (

    Directory of Open Access Journals (Sweden)

    Taehyung Kwon

    2017-11-01

    Full Text Available Objective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP markers strictly selected through least absolute shrinkage and selection operator (LASSO feature selection. Methods We performed farm tracing of domesticated pig (Sus scrofa from SNP markers and selected the most relevant features for accurate prediction. Considering multi-breed composition of our data, we performed feature selection using LASSO penalization on 4,002 SNPs that are shared between breeds, which also includes 179 SNPs with small between-breed difference. The 100 highest-scored features were extracted from iterative simulations and then evaluated using machine-leaning based classifiers. Results We selected 1,341 SNPs from over 45,000 SNPs through iterative LASSO feature selection, to minimize between-breed differences. We subsequently selected 100 highest-scored SNPs from iterative scoring, and observed high statistical measures in classification of breeding farms by cross-validation only using these SNPs. Conclusion The study represents a successful application of LASSO feature selection on multi-breed pig SNP data to trace the farm information, which provides a valuable method and possibility for further researches on genetic traceability.

  4. Trace impurity analyzer

    International Nuclear Information System (INIS)

    Schneider, W.J.; Edwards, D. Jr.

    1979-01-01

    The desirability for long-term reliability of large scale helium refrigerator systems used on superconducting accelerator magnets has necessitated detection of impurities to levels of a few ppM. An analyzer that measures trace impurity levels of condensable contaminants in concentrations of less than a ppM in 15 atm of He is described. The instrument makes use of the desorption temperature at an indicated pressure of the various impurities to determine the type of contaminant. The pressure rise at that temperature yields a measure of the contaminant level of the impurity. A LN 2 cryogenic charcoal trap is also employed to measure air impurities (nitrogen and oxygen) to obtain the full range of contaminant possibilities. The results of this detector which will be in use on the research and development helium refrigerator of the ISABELLE First-Cell is described

  5. Discussion on LDPC Codes and Uplink Coding

    Science.gov (United States)

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

  6. Locally orderless registration code

    DEFF Research Database (Denmark)

    2012-01-01

    This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows.......This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows....

  7. Decoding Codes on Graphs

    Indian Academy of Sciences (India)

    Shannon limit of the channel. Among the earliest discovered codes that approach the. Shannon limit were the low density parity check (LDPC) codes. The term low density arises from the property of the parity check matrix defining the code. We will now define this matrix and the role that it plays in decoding. 2. Linear Codes.

  8. Manually operated coded switch

    International Nuclear Information System (INIS)

    Barnette, J.H.

    1978-01-01

    The disclosure related to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made

  9. Preimplantation genetic screening.

    Science.gov (United States)

    Harper, Joyce C

    2018-03-01

    Preimplantation genetic diagnosis was first successfully performed in 1989 as an alternative to prenatal diagnosis for couples at risk of transmitting a genetic or chromosomal abnormality, such as cystic fibrosis, to their child. From embryos generated in vitro, biopsied cells are genetically tested. From the mid-1990s, this technology has been employed as an embryo selection tool for patients undergoing in vitro fertilisation, screening as many chromosomes as possible, in the hope that selecting chromosomally normal embryos will lead to higher implantation and decreased miscarriage rates. This procedure, preimplantation genetic screening, was initially performed using fluorescent in situ hybridisation, but 11 randomised controlled trials of screening using this technique showed no improvement in in vitro fertilisation delivery rates. Progress in genetic testing has led to the introduction of array comparative genomic hybridisation, quantitative polymerase chain reaction, and next generation sequencing for preimplantation genetic screening, and three small randomised controlled trials of preimplantation genetic screening using these new techniques indicate a modest benefit. Other trials are still in progress but, regardless of their results, preimplantation genetic screening is now being offered globally. In the near future, it is likely that sequencing will be used to screen the full genetic code of the embryo.

  10. Olfactory memory traces in Drosophila.

    Science.gov (United States)

    Berry, Jacob; Krause, William C; Davis, Ronald L

    2008-01-01

    In Drosophila, the fruit fly, coincident exposure to an odor and an aversive electric shock can produce robust behavioral memory. This behavioral memory is thought to be regulated by cellular memory traces within the central nervous system of the fly. These molecular, physiological, or structural changes in neurons, induced by pairing odor and shock, regulate behavior by altering the neurons' response to the learned environment. Recently, novel in vivo functional imaging techniques have allowed researchers to observe cellular memory traces in intact animals. These investigations have revealed interesting temporal and spatial dynamics of cellular memory traces. First, a short-term cellular memory trace was discovered that exists in the antennal lobe, an early site of olfactory processing. This trace represents the recruitment of new synaptic activity into the odor representation and forms for only a short period of time just after training. Second, an intermediate-term cellular memory trace was found in the dorsal paired medial neuron, a neuron thought to play a role in stabilizing olfactory memories. Finally, a long-term protein synthesis-dependent cellular memory trace was discovered in the mushroom bodies, a structure long implicated in olfactory learning and memory. Therefore, it appears that aversive olfactory associations are encoded by multiple cellular memory traces that occur in different regions of the brain with different temporal domains.

  11. Coding in Muscle Disease.

    Science.gov (United States)

    Jones, Lyell K; Ney, John P

    2016-12-01

    Accurate coding is critically important for clinical practice and research. Ongoing changes to diagnostic and billing codes require the clinician to stay abreast of coding updates. Payment for health care services, data sets for health services research, and reporting for medical quality improvement all require accurate administrative coding. This article provides an overview of administrative coding for patients with muscle disease and includes a case-based review of diagnostic and Evaluation and Management (E/M) coding principles in patients with myopathy. Procedural coding for electrodiagnostic studies and neuromuscular ultrasound is also reviewed.

  12. TRACE/PARCS modelling of rips trip transients for Lungmen ABWR

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C. Y. [Inst. of Nuclear Engineering and Science, National Tsing-Hua Univ., No.101, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Lin, H. T.; Wang, J. R. [Inst. of Nuclear Energy Research, No. 1000, Wenhua Rd., Longtan Township, Taoyuan County 32546, Taiwan (China); Shih, C. [Inst. of Nuclear Engineering and Science, Dept. of Engineering and System Science, National Tsing-Hua Univ., No.101, Kuang-Fu Road, Hsinchu 30013, Taiwan (China)

    2012-07-01

    The objectives of this study are to examine the performances of the steady-state results calculated by the Lungmen TRACE/PARCS model compared to SIMULATE-3 code, as well as to use the analytical results of the final safety analysis report (FSAR) to benchmark the Lungmen TRACE/PARCS model. In this study, three power generation methods in TRACE were utilized to analyze the three reactor internal pumps (RIPs) trip transient for the purpose of validating the TRACE/PARCS model. In general, the comparisons show that the transient responses of key system parameters agree well with the FSAR results, including core power, core inlet flow, reactivity, etc. Further studies will be performed in the future using Lungmen TRACE/PARCS model. After the commercial operation of Lungmen nuclear power plant, TRACE/PARCS model will be verified. (authors)

  13. QR Codes 101

    Science.gov (United States)

    Crompton, Helen; LaFrance, Jason; van 't Hooft, Mark

    2012-01-01

    A QR (quick-response) code is a two-dimensional scannable code, similar in function to a traditional bar code that one might find on a product at the supermarket. The main difference between the two is that, while a traditional bar code can hold a maximum of only 20 digits, a QR code can hold up to 7,089 characters, so it can contain much more…

  14. Tracing Geothermal Fluids

    Energy Technology Data Exchange (ETDEWEB)

    Michael C. Adams; Greg Nash

    2004-03-01

    Geothermal water must be injected back into the reservoir after it has been used for power production. Injection is critical in maximizing the power production and lifetime of the reservoir. To use injectate effectively the direction and velocity of the injected water must be known or inferred. This information can be obtained by using chemical tracers to track the subsurface flow paths of the injected fluid. Tracers are chemical compounds that are added to the water as it is injected back into the reservoir. The hot production water is monitored for the presence of this tracer using the most sensitive analytic methods that are economically feasible. The amount and concentration pattern of the tracer revealed by this monitoring can be used to evaluate how effective the injection strategy is. However, the tracers must have properties that suite the environment that they will be used in. This requires careful consideration and testing of the tracer properties. In previous and parallel investigations we have developed tracers that are suitable from tracing liquid water. In this investigation, we developed tracers that can be used for steam and mixed water/steam environments. This work will improve the efficiency of injection management in geothermal fields, lowering the cost of energy production and increasing the power output of these systems.

  15. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hoffmann, Robert D; Palmgren, Michael

    2016-06-13

    Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3' untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

  16. Codes and curves

    CERN Document Server

    Walker, Judy L

    2000-01-01

    When information is transmitted, errors are likely to occur. Coding theory examines efficient ways of packaging data so that these errors can be detected, or even corrected. The traditional tools of coding theory have come from combinatorics and group theory. Lately, however, coding theorists have added techniques from algebraic geometry to their toolboxes. In particular, by re-interpreting the Reed-Solomon codes, one can see how to define new codes based on divisors on algebraic curves. For instance, using modular curves over finite fields, Tsfasman, Vladut, and Zink showed that one can define a sequence of codes with asymptotically better parameters than any previously known codes. This monograph is based on a series of lectures the author gave as part of the IAS/PCMI program on arithmetic algebraic geometry. Here, the reader is introduced to the exciting field of algebraic geometric coding theory. Presenting the material in the same conversational tone of the lectures, the author covers linear codes, inclu...

  17. Suspension of the NAB Code and Its Effect on Regulation of Advertising.

    Science.gov (United States)

    Maddox, Lynda M.; Zanot, Eric J.

    1984-01-01

    Traces events leading to the suspension of the Television Code of the National Association of Broadcasters in 1982 and looks at changes that have occurred in the informal and formal regulation of advertising as a result of that suspension. (FL)

  18. A Denotational Semantics for Communicating Unstructured Code

    Directory of Open Access Journals (Sweden)

    Nils Jähnig

    2015-03-01

    Full Text Available An important property of programming language semantics is that they should be compositional. However, unstructured low-level code contains goto-like commands making it hard to define a semantics that is compositional. In this paper, we follow the ideas of Saabas and Uustalu to structure low-level code. This gives us the possibility to define a compositional denotational semantics based on least fixed points to allow for the use of inductive verification methods. We capture the semantics of communication using finite traces similar to the denotations of CSP. In addition, we examine properties of this semantics and give an example that demonstrates reasoning about communication and jumps. With this semantics, we lay the foundations for a proof calculus that captures both, the semantics of unstructured low-level code and communication.

  19. Computer program for optical systems ray tracing

    Science.gov (United States)

    Ferguson, T. J.; Konn, H.

    1967-01-01

    Program traces rays of light through optical systems consisting of up to 65 different optical surfaces and computes the aberrations. For design purposes, paraxial tracings with astigmation and third order tracings are provided.

  20. Trace formulae for arithmetical systems

    International Nuclear Information System (INIS)

    Bogomolny, E.B.; Georgeot, B.; Giannoni, M.J.; Schmit, C.

    1992-09-01

    For quantum problems on the pseudo-sphere generated by arithmetic groups there exist special trace formulae, called trace formulae for Hecke operators, which permit the reconstruction of wave functions from the knowledge of periodic orbits. After a short discussion of this subject, the Hecke operators trace formulae are presented for the Dirichlet problem on the modular billiard, which is a prototype of arithmetical systems. The results of numerical computations for these semiclassical type relations are in good agreement with the directly computed eigenfunctions. (author) 23 refs.; 2 figs

  1. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  2. Unveiling Exception Handling Bug Hazards in Android Based on GitHub and Google Code Issues

    NARCIS (Netherlands)

    Coelho, R.; Almeida, L.; Gousios, G.; Van Deursen, A.

    2015-01-01

    This paper reports on a study mining the exception stack traces included in 159,048 issues reported on Android projects hosted in GitHub (482 projects) and Google Code (157 projects). The goal of this study is to investigate whether stack trace information can reveal bug hazards related to exception

  3. Coding for optical channels

    CERN Document Server

    Djordjevic, Ivan; Vasic, Bane

    2010-01-01

    This unique book provides a coherent and comprehensive introduction to the fundamentals of optical communications, signal processing and coding for optical channels. It is the first to integrate the fundamentals of coding theory and optical communication.

  4. SEVERO code - user's manual

    International Nuclear Information System (INIS)

    Sacramento, A.M. do.

    1989-01-01

    This user's manual contains all the necessary information concerning the use of SEVERO code. This computer code is related to the statistics of extremes = extreme winds, extreme precipitation and flooding hazard risk analysis. (A.C.A.S.)

  5. Genetic Mapping

    Science.gov (United States)

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  6. A Message Without a Code?

    Directory of Open Access Journals (Sweden)

    Tom Conley

    1981-01-01

    Full Text Available The photographic paradox is said to be that of a message without a code, a communication lacking a relay or gap essential to the process of communication. Tracing the recurrence of Barthes's definition in the essays included in Image/Music/Text and in La Chambre claire , this paper argues that Barthes's definition is platonic in its will to dematerialize the troubling — graphic — immediacy of the photograph. He writes of the image in order to flee its signature. As a function of media, his categories are written in order to be insufficient and inadequate; to maintain an ineluctable difference between language heard and letters seen; to protect an idiom of loss which the photograph disallows. The article studies the strategies of his definition in «The Photographic Paradox» as instrument of abstraction, opposes the notion of code, in an aural sense, to audio-visual markers of closed relay in advertising, and critiques the layout and order of La Chambre claire in respect to Barthes's ideology of absence.

  7. Synthesizing Certified Code

    OpenAIRE

    Whalen, Michael; Schumann, Johann; Fischer, Bernd

    2002-01-01

    Code certification is a lightweight approach for formally demonstrating software quality. Its basic idea is to require code producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates that can be checked independently. Since code certification uses the same underlying technology as program verification, it requires detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding annotations to th...

  8. FERRET data analysis code

    International Nuclear Information System (INIS)

    Schmittroth, F.

    1979-09-01

    A documentation of the FERRET data analysis code is given. The code provides a way to combine related measurements and calculations in a consistent evaluation. Basically a very general least-squares code, it is oriented towards problems frequently encountered in nuclear data and reactor physics. A strong emphasis is on the proper treatment of uncertainties and correlations and in providing quantitative uncertainty estimates. Documentation includes a review of the method, structure of the code, input formats, and examples

  9. Stylize Aesthetic QR Code

    OpenAIRE

    Xu, Mingliang; Su, Hao; Li, Yafei; Li, Xi; Liao, Jing; Niu, Jianwei; Lv, Pei; Zhou, Bing

    2018-01-01

    With the continued proliferation of smart mobile devices, Quick Response (QR) code has become one of the most-used types of two-dimensional code in the world. Aiming at beautifying the appearance of QR codes, existing works have developed a series of techniques to make the QR code more visual-pleasant. However, these works still leave much to be desired, such as visual diversity, aesthetic quality, flexibility, universal property, and robustness. To address these issues, in this paper, we pro...

  10. Enhancing QR Code Security

    OpenAIRE

    Zhang, Linfan; Zheng, Shuang

    2015-01-01

    Quick Response code opens possibility to convey data in a unique way yet insufficient prevention and protection might lead into QR code being exploited on behalf of attackers. This thesis starts by presenting a general introduction of background and stating two problems regarding QR code security, which followed by a comprehensive research on both QR code itself and related issues. From the research a solution taking advantages of cloud and cryptography together with an implementation come af...

  11. Opening up codings?

    DEFF Research Database (Denmark)

    Steensig, Jakob; Heinemann, Trine

    2015-01-01

    doing formal coding and when doing more “traditional” conversation analysis research based on collections. We are more wary, however, of the implication that coding-based research is the end result of a process that starts with qualitative investigations and ends with categories that can be coded...

  12. Gauge color codes

    DEFF Research Database (Denmark)

    Bombin Palomo, Hector

    2015-01-01

    Color codes are topological stabilizer codes with unusual transversality properties. Here I show that their group of transversal gates is optimal and only depends on the spatial dimension, not the local geometry. I also introduce a generalized, subsystem version of color codes. In 3D they allow...

  13. Refactoring test code

    NARCIS (Netherlands)

    A. van Deursen (Arie); L.M.F. Moonen (Leon); A. van den Bergh; G. Kok

    2001-01-01

    textabstractTwo key aspects of extreme programming (XP) are unit testing and merciless refactoring. Given the fact that the ideal test code / production code ratio approaches 1:1, it is not surprising that unit tests are being refactored. We found that refactoring test code is different from

  14. Genetic privacy.

    Science.gov (United States)

    Sankar, Pamela

    2003-01-01

    During the past 10 years, the number of genetic tests performed more than tripled, and public concern about genetic privacy emerged. The majority of states and the U.S. government have passed regulations protecting genetic information. However, research has shown that concerns about genetic privacy are disproportionate to known instances of information misuse. Beliefs in genetic determinacy explain some of the heightened concern about genetic privacy. Discussion of the debate over genetic testing within families illustrates the most recent response to genetic privacy concerns.

  15. Coalgebraic structure of genetic inheritance.

    Science.gov (United States)

    Tian, Jianjun; Li, Bai-Lian

    2004-09-01

    Although in the broadly defined genetic algebra, multiplication suggests a forward direction of from parents to progeny, when looking from the reverse direction, it also suggests to us a new algebraic structure-coalge- braic structure, which we call genetic coalgebras. It is not the dual coalgebraic structure and can be used in the construction of phylogenetic trees. Math- ematically, to construct phylogenetic trees means we need to solve equations x([n]) = a, or x([n]) = b. It is generally impossible to solve these equations inalgebras. However, we can solve them in coalgebras in the sense of tracing back for their ancestors. A thorough exploration of coalgebraic structure in genetics is apparently necessary. Here, we develop a theoretical framework of the coalgebraic structure of genetics. From biological viewpoint, we defined various fundamental concepts and examined their elementary properties that contain genetic significance. Mathematically, by genetic coalgebra, we mean any coalgebra that occurs in genetics. They are generally noncoassociative and without counit; and in the case of non-sex-linked inheritance, they are cocommutative. Each coalgebra with genetic realization has a baric property. We have also discussed the methods to construct new genetic coalgebras, including cocommutative duplication, the tensor product, linear combinations and the skew linear map, which allow us to describe complex genetic traits. We also put forward certain theorems that state the relationship between gametic coalgebra and gametic algebra. By Brower's theorem in topology, we prove the existence of equilibrium state for the in-evolution operator.

  16. Software Certification - Coding, Code, and Coders

    Science.gov (United States)

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

    We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

  17. Wood construction codes issues in the United States

    Science.gov (United States)

    Douglas R. Rammer

    2006-01-01

    The current wood construction codes find their origin in the 1935 Wood Handbook: Wood as an Engineering Material published by the USDA Forest Service. Many of the current design recommendations can be traced back to statements from this book. Since this time a series of development both historical and recent has led to a multi-layered system for use of wood products in...

  18. The elimination of ray tracing in Monte Carlo shielding programs

    International Nuclear Information System (INIS)

    Bendall, D.E.

    1988-01-01

    The MONK6 code has clearly demonstrated the advantages of hole tracking, which was devised by Woodcock et at. for use in criticality codes from earlier work by Von Neumann. Hole tracking eliminates ray tracing by introducing, for all materials present in the problem, a pseudo scattering reaction that forward scatters without energy loss. The cross section for this reaction is chosen so that the total cross sections for all the materials are equal at a given energy. By this means, tracking takes place with a constant total cross section everywhere, so there is now no need to ray trace. The present work extends hole tracking to shielding codes, where it functions in tandem with Russian roulette and splitting. An algorithm has been evolved and its performance is compared with the ray-tracking code McBEND. A disadvantage with hole tracking occurs when there is a wide variation in total cross section for materials present. As the tracking uses the total cross section of the material that has the maximum cross section, there can be a large number of pseudo collisions in the materials with low total cross sections. In extreme cases, the advantages of hole tracking can be lost by the by the extra time taken in servicing these pseudo collisions; however, techniques for eliminating this problem are under consideration

  19. The network code

    International Nuclear Information System (INIS)

    1997-01-01

    The Network Code defines the rights and responsibilities of all users of the natural gas transportation system in the liberalised gas industry in the United Kingdom. This report describes the operation of the Code, what it means, how it works and its implications for the various participants in the industry. The topics covered are: development of the competitive gas market in the UK; key points in the Code; gas transportation charging; impact of the Code on producers upstream; impact on shippers; gas storage; supply point administration; impact of the Code on end users; the future. (20 tables; 33 figures) (UK)

  20. Coding for Electronic Mail

    Science.gov (United States)

    Rice, R. F.; Lee, J. J.

    1986-01-01

    Scheme for coding facsimile messages promises to reduce data transmission requirements to one-tenth current level. Coding scheme paves way for true electronic mail in which handwritten, typed, or printed messages or diagrams sent virtually instantaneously - between buildings or between continents. Scheme, called Universal System for Efficient Electronic Mail (USEEM), uses unsupervised character recognition and adaptive noiseless coding of text. Image quality of resulting delivered messages improved over messages transmitted by conventional coding. Coding scheme compatible with direct-entry electronic mail as well as facsimile reproduction. Text transmitted in this scheme automatically translated to word-processor form.

  1. NAGRADATA. Code key. Geology

    International Nuclear Information System (INIS)

    Mueller, W.H.; Schneider, B.; Staeuble, J.

    1984-01-01

    This reference manual provides users of the NAGRADATA system with comprehensive keys to the coding/decoding of geological and technical information to be stored in or retreaved from the databank. Emphasis has been placed on input data coding. When data is retreaved the translation into plain language of stored coded information is done automatically by computer. Three keys each, list the complete set of currently defined codes for the NAGRADATA system, namely codes with appropriate definitions, arranged: 1. according to subject matter (thematically) 2. the codes listed alphabetically and 3. the definitions listed alphabetically. Additional explanation is provided for the proper application of the codes and the logic behind the creation of new codes to be used within the NAGRADATA system. NAGRADATA makes use of codes instead of plain language for data storage; this offers the following advantages: speed of data processing, mainly data retrieval, economies of storage memory requirements, the standardisation of terminology. The nature of this thesaurian type 'key to codes' makes it impossible to either establish a final form or to cover the entire spectrum of requirements. Therefore, this first issue of codes to NAGRADATA must be considered to represent the current state of progress of a living system and future editions will be issued in a loose leave ringbook system which can be updated by an organised (updating) service. (author)

  2. XSOR codes users manual

    International Nuclear Information System (INIS)

    Jow, Hong-Nian; Murfin, W.B.; Johnson, J.D.

    1993-11-01

    This report describes the source term estimation codes, XSORs. The codes are written for three pressurized water reactors (Surry, Sequoyah, and Zion) and two boiling water reactors (Peach Bottom and Grand Gulf). The ensemble of codes has been named ''XSOR''. The purpose of XSOR codes is to estimate the source terms which would be released to the atmosphere in severe accidents. A source term includes the release fractions of several radionuclide groups, the timing and duration of releases, the rates of energy release, and the elevation of releases. The codes have been developed by Sandia National Laboratories for the US Nuclear Regulatory Commission (NRC) in support of the NUREG-1150 program. The XSOR codes are fast running parametric codes and are used as surrogates for detailed mechanistic codes. The XSOR codes also provide the capability to explore the phenomena and their uncertainty which are not currently modeled by the mechanistic codes. The uncertainty distributions of input parameters may be used by an. XSOR code to estimate the uncertainty of source terms

  3. Reactor lattice codes

    International Nuclear Information System (INIS)

    Kulikowska, T.

    1999-01-01

    The present lecture has a main goal to show how the transport lattice calculations are realised in a standard computer code. This is illustrated on the example of the WIMSD code, belonging to the most popular tools for reactor calculations. Most of the approaches discussed here can be easily modified to any other lattice code. The description of the code assumes the basic knowledge of reactor lattice, on the level given in the lecture on 'Reactor lattice transport calculations'. For more advanced explanation of the WIMSD code the reader is directed to the detailed descriptions of the code cited in References. The discussion of the methods and models included in the code is followed by the generally used homogenisation procedure and several numerical examples of discrepancies in calculated multiplication factors based on different sources of library data. (author)

  4. DLLExternalCode

    Energy Technology Data Exchange (ETDEWEB)

    2014-05-14

    DLLExternalCode is the a general dynamic-link library (DLL) interface for linking GoldSim (www.goldsim.com) with external codes. The overall concept is to use GoldSim as top level modeling software with interfaces to external codes for specific calculations. The DLLExternalCode DLL that performs the linking function is designed to take a list of code inputs from GoldSim, create an input file for the external application, run the external code, and return a list of outputs, read from files created by the external application, back to GoldSim. Instructions for creating the input file, running the external code, and reading the output are contained in an instructions file that is read and interpreted by the DLL.

  5. Improvement of MARS code reflood model

    International Nuclear Information System (INIS)

    Hwang, Moonkyu; Chung, Bub-Dong

    2011-01-01

    A specifically designed heat transfer model for the reflood process which normally occurs at low flow and low pressure was originally incorporated in the MARS code. The model is essentially identical to that of the RELAP5/MOD3.3 code. The model, however, is known to have under-estimated the peak cladding temperature (PCT) with earlier turn-over. In this study, the original MARS code reflood model is improved. Based on the extensive sensitivity studies for both hydraulic and wall heat transfer models, it is found that the dispersed flow film boiling (DFFB) wall heat transfer is the most influential process determining the PCT, whereas the interfacial drag model most affects the quenching time through the liquid carryover phenomenon. The model proposed by Bajorek and Young is incorporated for the DFFB wall heat transfer. Both space grid and droplet enhancement models are incorporated. Inverted annular film boiling (IAFB) is modeled by using the original PSI model of the code. The flow transition between the DFFB and IABF, is modeled using the TRACE code interpolation. A gas velocity threshold is also added to limit the top-down quenching effect. Assessment calculations are performed for the original and modified MARS codes for the Flecht-Seaset test and RBHT test. Improvements are observed in terms of the PCT and quenching time predictions in the Flecht-Seaset assessment. In case of the RBHT assessment, the improvement over the original MARS code is found marginal. A space grid effect, however, is clearly seen from the modified version of the MARS code. (author)

  6. Numerical modeling of flow boiling instabilities using TRACE

    International Nuclear Information System (INIS)

    Kommer, Eric M.

    2015-01-01

    Highlights: • TRACE was used to realistically model boiling instabilities in single and parallel channel configurations. • Model parameters were chosen to exactly mimic other author’s work in order to provide for direct comparison of results. • Flow stability maps generated by the model show unstable flow at operating points similar to other authors. • The method of adjudicating when a flow is “unstable” is critical in this type of numerical study. - Abstract: Dynamic flow instabilities in two-phase systems are a vitally important area of study due to their effects on a great number of industrial applications, including heat exchangers in nuclear power plants. Several next generation nuclear reactor designs incorporate once through steam generators which will exhibit boiling flow instabilities if not properly designed or when operated outside design limits. A number of numerical thermal hydraulic codes attempt to model instabilities for initial design and for use in accident analysis. TRACE, the Nuclear Regulatory Commission’s newest thermal hydraulic code is used in this study to investigate flow instabilities in both single and dual parallel channel configurations. The model parameters are selected as to replicate other investigators’ experimental and numerical work in order to provide easy comparison. Particular attention is paid to the similarities between analysis using TRACE Version 5.0 and RELAP5/MOD3.3. Comparison of results is accomplished via flow stability maps non-dimensionalized via the phase change and subcooling numbers. Results of this study show that TRACE does indeed model two phase flow instabilities, with the transient response closely mimicking that seen in experimental studies. When compared to flow stability maps generated using RELAP, TRACE shows similar results with differences likely due to the somewhat qualitative criteria used by various authors to determine when the flow is truly unstable

  7. TraceContract: A Scala DSL for Trace Analysis

    Science.gov (United States)

    Barringer, Howard; Havelund, Klaus

    2011-01-01

    In this paper we describe TRACECONTRACT, an API for trace analysis, implemented in the SCALA programming language. We argue that for certain forms of trace analysis the best weapon is a high level programming language augmented with constructs for temporal reasoning. A trace is a sequence of events, which may for example be generated by a running program, instrumented appropriately to generate events. The API supports writing properties in a notation that combines an advanced form of data parameterized state machines with temporal logic. The implementation utilizes SCALA's support for defining internal Domain Specific Languages (DSLs). Furthermore SCALA's combination of object oriented and functional programming features, including partial functions and pattern matching, makes it an ideal host language for such an API.

  8. Measurement of Selected Organic Trace Gases During TRACE-P

    Science.gov (United States)

    Atlas, Elliot

    2004-01-01

    Major goals of the TRACE-P mission were: 1) to investigate the chemical composition of radiatively important gases, aerosols, and their precursors in the Asian outflow over the western Pacific, and 2) to describe and understand the chemical evolution of the Asian outflow as it is transported and mixed into the global troposphere. The research performed as part of this proposal addressed these major goals with a study of the organic chemical composition of gases in the TRACE-P region. This work was a close collaboration with the Blake/Rowland research group at UC-Irvine, and they have provided a separate report for their funded effort.

  9. A Theory of Network Tracing

    Science.gov (United States)

    Acharya, Hrishikesh B.; Gouda, Mohamed G.

    Traceroute is a widely used program for computing the topology of any network in the Internet. Using Traceroute, one starts from a node and chooses any other node in the network. Traceroute obtains the sequence of nodes that occur between these two nodes, as specified by the routing tables in these nodes. Each use of Traceroute in a network produces a trace of nodes that constitute a simple path in this network. In every trace that is produced by Traceroute, each node occurs either by its unique identifier, or by the anonymous identifier"*". In this paper, we introduce the first theory aimed at answering the following important question. Is there an algorithm to compute the topology of a network N from a trace set T that is produced by using Traceroute in network N, assuming that each edge in N occurs in at least one trace in T, and that each node in N occurs by its unique identifier in at least one trace in T? We prove that the answer to this question is "No" if N is an even ring or a general network. However, it is "Yes" if N is a tree or an odd ring. The answer is also "No" if N is mostly-regular, but "Yes" if N is a mostly-regular even ring.

  10. Toric Varieties and Codes, Error-correcting Codes, Quantum Codes, Secret Sharing and Decoding

    DEFF Research Database (Denmark)

    Hansen, Johan Peder

    We present toric varieties and associated toric codes and their decoding. Toric codes are applied to construct Linear Secret Sharing Schemes (LSSS) with strong multiplication by the Massey construction. Asymmetric Quantum Codes are obtained from toric codes by the A.R. Calderbank P.W. Shor and A.......M. Steane construction of stabilizer codes (CSS) from linear codes containing their dual codes....

  11. Common Gene Variants Account for Most Genetic Risk for Autism

    Science.gov (United States)

    ... gene variants account for most genetic risk for autism Roles of heritability, mutations, environment estimated – NIH-funded study. The bulk of risk, or liability, for autism spectrum disorders (ASD) was traced to inherited variations ...

  12. An Optimal Linear Coding for Index Coding Problem

    OpenAIRE

    Pezeshkpour, Pouya

    2015-01-01

    An optimal linear coding solution for index coding problem is established. Instead of network coding approach by focus on graph theoric and algebraic methods a linear coding program for solving both unicast and groupcast index coding problem is presented. The coding is proved to be the optimal solution from the linear perspective and can be easily utilize for any number of messages. The importance of this work is lying mostly on the usage of the presented coding in the groupcast index coding ...

  13. [Trace elements of bone tumors].

    Science.gov (United States)

    Kalashnikov, V M; Zaĭchik, V E; Bizer, V A

    1983-01-01

    Due to activation analysis involving the use of neutrons from a nuclear reactor, the concentrations of 11 trace elements: scandium, iron, cobalt, mercury, rubidium, selenium, silver, antimony, chrome, zinc and terbium in intact bone and skeletal tumors were measured. 76 specimens of bioptates and resected material of operations for bone tumors and 10 specimens of normal bone tissue obtained in autopsies of cases of sudden death were examined. The concentrations of trace elements and their dispersion patterns in tumor tissue were found to be significantly higher than those in normal bone tissue. Also, the concentrations of some trace elements in tumor differed significantly from those in normal tissue; moreover, they were found to depend on the type and histogenesis of the neoplasm.

  14. Trace elements in human milk

    Energy Technology Data Exchange (ETDEWEB)

    Parr, R M [International Atomic Energy Agency, Vienna (Austria). Div. of Life Sciences

    1983-06-01

    Trace elements are those elements having a concentration lower than 10 ppm in body fluids or tissues. A total of 24 elements, both trace and minor elements, present in human milk have been analysed in this study, employing neutron activation analysis and absorption spectroscopy. The analyses have been carried out collaboratively by several different laboratories and the Agency which has also served as a coordinating centre. Although the evaluation of the results, altogether 8500 separate values, is still in progress, enough evidence is already available, however, to show some very interesting differences between different study areas and, in some cases, between different socio-economic groups within a single country. The main value of these data will probably be to throw new light on the nutritional requirements of young babies for trace elements.

  15. The Aesthetics of Coding

    DEFF Research Database (Denmark)

    Andersen, Christian Ulrik

    2007-01-01

    Computer art is often associated with computer-generated expressions (digitally manipulated audio/images in music, video, stage design, media facades, etc.). In recent computer art, however, the code-text itself – not the generated output – has become the artwork (Perl Poetry, ASCII Art, obfuscated...... code, etc.). The presentation relates this artistic fascination of code to a media critique expressed by Florian Cramer, claiming that the graphical interface represents a media separation (of text/code and image) causing alienation to the computer’s materiality. Cramer is thus the voice of a new ‘code...... avant-garde’. In line with Cramer, the artists Alex McLean and Adrian Ward (aka Slub) declare: “art-oriented programming needs to acknowledge the conditions of its own making – its poesis.” By analysing the Live Coding performances of Slub (where they program computer music live), the presentation...

  16. Majorana fermion codes

    International Nuclear Information System (INIS)

    Bravyi, Sergey; Terhal, Barbara M; Leemhuis, Bernhard

    2010-01-01

    We initiate the study of Majorana fermion codes (MFCs). These codes can be viewed as extensions of Kitaev's one-dimensional (1D) model of unpaired Majorana fermions in quantum wires to higher spatial dimensions and interacting fermions. The purpose of MFCs is to protect quantum information against low-weight fermionic errors, that is, operators acting on sufficiently small subsets of fermionic modes. We examine to what extent MFCs can surpass qubit stabilizer codes in terms of their stability properties. A general construction of 2D MFCs is proposed that combines topological protection based on a macroscopic code distance with protection based on fermionic parity conservation. Finally, we use MFCs to show how to transform any qubit stabilizer code to a weakly self-dual CSS code.

  17. DISP1 code

    International Nuclear Information System (INIS)

    Vokac, P.

    1999-12-01

    DISP1 code is a simple tool for assessment of the dispersion of the fission product cloud escaping from a nuclear power plant after an accident. The code makes it possible to tentatively check the feasibility of calculations by more complex PSA3 codes and/or codes for real-time dispersion calculations. The number of input parameters is reasonably low and the user interface is simple enough to allow a rapid processing of sensitivity analyses. All input data entered through the user interface are stored in the text format. Implementation of dispersion model corrections taken from the ARCON96 code enables the DISP1 code to be employed for assessment of the radiation hazard within the NPP area, in the control room for instance. (P.A.)

  18. Phonological coding during reading.

    Science.gov (United States)

    Leinenger, Mallorie

    2014-11-01

    The exact role that phonological coding (the recoding of written, orthographic information into a sound based code) plays during silent reading has been extensively studied for more than a century. Despite the large body of research surrounding the topic, varying theories as to the time course and function of this recoding still exist. The present review synthesizes this body of research, addressing the topics of time course and function in tandem. The varying theories surrounding the function of phonological coding (e.g., that phonological codes aid lexical access, that phonological codes aid comprehension and bolster short-term memory, or that phonological codes are largely epiphenomenal in skilled readers) are first outlined, and the time courses that each maps onto (e.g., that phonological codes come online early [prelexical] or that phonological codes come online late [postlexical]) are discussed. Next the research relevant to each of these proposed functions is reviewed, discussing the varying methodologies that have been used to investigate phonological coding (e.g., response time methods, reading while eye-tracking or recording EEG and MEG, concurrent articulation) and highlighting the advantages and limitations of each with respect to the study of phonological coding. In response to the view that phonological coding is largely epiphenomenal in skilled readers, research on the use of phonological codes in prelingually, profoundly deaf readers is reviewed. Finally, implications for current models of word identification (activation-verification model, Van Orden, 1987; dual-route model, e.g., M. Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001; parallel distributed processing model, Seidenberg & McClelland, 1989) are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  19. The aeroelastic code FLEXLAST

    Energy Technology Data Exchange (ETDEWEB)

    Visser, B. [Stork Product Eng., Amsterdam (Netherlands)

    1996-09-01

    To support the discussion on aeroelastic codes, a description of the code FLEXLAST was given and experiences within benchmarks and measurement programmes were summarized. The code FLEXLAST has been developed since 1982 at Stork Product Engineering (SPE). Since 1992 FLEXLAST has been used by Dutch industries for wind turbine and rotor design. Based on the comparison with measurements, it can be concluded that the main shortcomings of wind turbine modelling lie in the field of aerodynamics, wind field and wake modelling. (au)

  20. Manual tracing versus smartphone application (app) tracing: a comparative study.

    Science.gov (United States)

    Sayar, Gülşilay; Kilinc, Delal Dara

    2017-11-01

    This study aimed to compare the results of conventional manual cephalometric tracing with those acquired with smartphone application cephalometric tracing. The cephalometric radiographs of 55 patients (25 females and 30 males) were traced via the manual and app methods and were subsequently examined with Steiner's analysis. Five skeletal measurements, five dental measurements and two soft tissue measurements were managed based on 21 landmarks. The durations of the performances of the two methods were also compared. SNA (Sella, Nasion, A point angle) and SNB (Sella, Nasion, B point angle) values for the manual method were statistically lower (p < .001) than those for the app method. The ANB value for the manual method was statistically lower than that of app method. L1-NB (°) and upper lip protrusion values for the manual method were statistically higher than those for the app method. Go-GN/SN, U1-NA (°) and U1-NA (mm) values for manual method were statistically lower than those for the app method. No differences between the two methods were found in the L1-NB (mm), occlusal plane to SN, interincisal angle or lower lip protrusion values. Although statistically significant differences were found between the two methods, the cephalometric tracing proceeded faster with the app method than with the manual method.

  1. Tracing a planar algebraic curve

    International Nuclear Information System (INIS)

    Chen Falai; Kozak, J.

    1994-09-01

    In this paper, an algorithm that determines a real algebraic curve is outlined. Its basic step is to divide the plane into subdomains that include only simple branches of the algebraic curve without singular points. Each of the branches is then stably and efficiently traced in the particular subdomain. Except for the tracing, the algorithm requires only a couple of simple operations on polynomials that can be carried out exactly if the coefficients are rational, and the determination of zeros of several polynomials of one variable. (author). 5 refs, 4 figs

  2. Improving performance of single-path code through a time-predictable memory hierarchy

    DEFF Research Database (Denmark)

    Cilku, Bekim; Puffitsch, Wolfgang; Prokesch, Daniel

    2017-01-01

    -predictable memory hierarchy with a prefetcher that exploits the predictability of execution traces in single-path code to speed up code execution. The new memory hierarchy reduces both the cache-miss penalty time and the cache-miss rate on the instruction cache. The benefit of the approach is demonstrated through...

  3. MORSE Monte Carlo code

    International Nuclear Information System (INIS)

    Cramer, S.N.

    1984-01-01

    The MORSE code is a large general-use multigroup Monte Carlo code system. Although no claims can be made regarding its superiority in either theoretical details or Monte Carlo techniques, MORSE has been, since its inception at ORNL in the late 1960s, the most widely used Monte Carlo radiation transport code. The principal reason for this popularity is that MORSE is relatively easy to use, independent of any installation or distribution center, and it can be easily customized to fit almost any specific need. Features of the MORSE code are described

  4. QR codes for dummies

    CERN Document Server

    Waters, Joe

    2012-01-01

    Find out how to effectively create, use, and track QR codes QR (Quick Response) codes are popping up everywhere, and businesses are reaping the rewards. Get in on the action with the no-nonsense advice in this streamlined, portable guide. You'll find out how to get started, plan your strategy, and actually create the codes. Then you'll learn to link codes to mobile-friendly content, track your results, and develop ways to give your customers value that will keep them coming back. It's all presented in the straightforward style you've come to know and love, with a dash of humor thrown

  5. Tokamak Systems Code

    International Nuclear Information System (INIS)

    Reid, R.L.; Barrett, R.J.; Brown, T.G.

    1985-03-01

    The FEDC Tokamak Systems Code calculates tokamak performance, cost, and configuration as a function of plasma engineering parameters. This version of the code models experimental tokamaks. It does not currently consider tokamak configurations that generate electrical power or incorporate breeding blankets. The code has a modular (or subroutine) structure to allow independent modeling for each major tokamak component or system. A primary benefit of modularization is that a component module may be updated without disturbing the remainder of the systems code as long as the imput to or output from the module remains unchanged

  6. Solar Proton Transport Within an ICRU Sphere Surrounded by a Complex Shield: Ray-trace Geometry

    Science.gov (United States)

    Slaba, Tony C.; Wilson, John W.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

    2015-01-01

    A computationally efficient 3DHZETRN code with enhanced neutron and light ion (Z is less than or equal to 2) propagation was recently developed for complex, inhomogeneous shield geometry described by combinatorial objects. Comparisons were made between 3DHZETRN results and Monte Carlo (MC) simulations at locations within the combinatorial geometry, and it was shown that 3DHZETRN agrees with the MC codes to the extent they agree with each other. In the present report, the 3DHZETRN code is extended to enable analysis in ray-trace geometry. This latest extension enables the code to be used within current engineering design practices utilizing fully detailed vehicle and habitat geometries. Through convergence testing, it is shown that fidelity in an actual shield geometry can be maintained in the discrete ray-trace description by systematically increasing the number of discrete rays used. It is also shown that this fidelity is carried into transport procedures and resulting exposure quantities without sacrificing computational efficiency.

  7. Efficient Coding of Information: Huffman Coding -RE ...

    Indian Academy of Sciences (India)

    to a stream of equally-likely symbols so as to recover the original stream in the event of errors. The for- ... The source-coding problem is one of finding a mapping from U to a ... probability that the random variable X takes the value x written as ...

  8. NR-code: Nonlinear reconstruction code

    Science.gov (United States)

    Yu, Yu; Pen, Ue-Li; Zhu, Hong-Ming

    2018-04-01

    NR-code applies nonlinear reconstruction to the dark matter density field in redshift space and solves for the nonlinear mapping from the initial Lagrangian positions to the final redshift space positions; this reverses the large-scale bulk flows and improves the precision measurement of the baryon acoustic oscillations (BAO) scale.

  9. Crucial steps to life: From chemical reactions to code using agents.

    Science.gov (United States)

    Witzany, Guenther

    2016-02-01

    The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the "central dogma," "one gene one protein" and "non-coding DNA is junk" were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning non-random genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not fit with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  10. Trace elements in brazilian soils

    International Nuclear Information System (INIS)

    Rocha, Geraldo Cesar

    1995-01-01

    A literature revision on trace elements (Zn, B, Mn, Mo, Cu, Fe, and Cl) in Brazilian soils was prepared, with special attention to the chemical form and range in the soil, extraction methods and correlation of the amount in soils with soil properties

  11. Digital Traces of Information Systems

    DEFF Research Database (Denmark)

    Hedman, Jonas; Srinivasan, Nikhil; Lindgren, Rikard

    2013-01-01

    . This disconcerting result suggests that IS researchers must pay more attention to the changing landscape of data sources. To motivate and guide fellow colleagues to establish the credibility and reliability of digital traces, we develop a future research agenda that covers both opportunities in theory generation...

  12. Synthesizing Certified Code

    Science.gov (United States)

    Whalen, Michael; Schumann, Johann; Fischer, Bernd

    2002-01-01

    Code certification is a lightweight approach to demonstrate software quality on a formal level. Its basic idea is to require producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates which can be checked independently. Since code certification uses the same underlying technology as program verification, it also requires many detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding theses annotations to the code is time-consuming and error-prone. We address this problem by combining code certification with automatic program synthesis. We propose an approach to generate simultaneously, from a high-level specification, code and all annotations required to certify generated code. Here, we describe a certification extension of AUTOBAYES, a synthesis tool which automatically generates complex data analysis programs from compact specifications. AUTOBAYES contains sufficient high-level domain knowledge to generate detailed annotations. This allows us to use a general-purpose verification condition generator to produce a set of proof obligations in first-order logic. The obligations are then discharged using the automated theorem E-SETHEO. We demonstrate our approach by certifying operator safety for a generated iterative data classification program without manual annotation of the code.

  13. Code of Ethics

    Science.gov (United States)

    Division for Early Childhood, Council for Exceptional Children, 2009

    2009-01-01

    The Code of Ethics of the Division for Early Childhood (DEC) of the Council for Exceptional Children is a public statement of principles and practice guidelines supported by the mission of DEC. The foundation of this Code is based on sound ethical reasoning related to professional practice with young children with disabilities and their families…

  14. Interleaved Product LDPC Codes

    OpenAIRE

    Baldi, Marco; Cancellieri, Giovanni; Chiaraluce, Franco

    2011-01-01

    Product LDPC codes take advantage of LDPC decoding algorithms and the high minimum distance of product codes. We propose to add suitable interleavers to improve the waterfall performance of LDPC decoding. Interleaving also reduces the number of low weight codewords, that gives a further advantage in the error floor region.

  15. Insurance billing and coding.

    Science.gov (United States)

    Napier, Rebecca H; Bruelheide, Lori S; Demann, Eric T K; Haug, Richard H

    2008-07-01

    The purpose of this article is to highlight the importance of understanding various numeric and alpha-numeric codes for accurately billing dental and medically related services to private pay or third-party insurance carriers. In the United States, common dental terminology (CDT) codes are most commonly used by dentists to submit claims, whereas current procedural terminology (CPT) and International Classification of Diseases, Ninth Revision, Clinical Modification (ICD.9.CM) codes are more commonly used by physicians to bill for their services. The CPT and ICD.9.CM coding systems complement each other in that CPT codes provide the procedure and service information and ICD.9.CM codes provide the reason or rationale for a particular procedure or service. These codes are more commonly used for "medical necessity" determinations, and general dentists and specialists who routinely perform care, including trauma-related care, biopsies, and dental treatment as a result of or in anticipation of a cancer-related treatment, are likely to use these codes. Claim submissions for care provided can be completed electronically or by means of paper forms.

  16. Error Correcting Codes

    Indian Academy of Sciences (India)

    Science and Automation at ... the Reed-Solomon code contained 223 bytes of data, (a byte ... then you have a data storage system with error correction, that ..... practical codes, storing such a table is infeasible, as it is generally too large.

  17. Scrum Code Camps

    DEFF Research Database (Denmark)

    Pries-Heje, Lene; Pries-Heje, Jan; Dalgaard, Bente

    2013-01-01

    is required. In this paper we present the design of such a new approach, the Scrum Code Camp, which can be used to assess agile team capability in a transparent and consistent way. A design science research approach is used to analyze properties of two instances of the Scrum Code Camp where seven agile teams...

  18. RFQ simulation code

    International Nuclear Information System (INIS)

    Lysenko, W.P.

    1984-04-01

    We have developed the RFQLIB simulation system to provide a means to systematically generate the new versions of radio-frequency quadrupole (RFQ) linac simulation codes that are required by the constantly changing needs of a research environment. This integrated system simplifies keeping track of the various versions of the simulation code and makes it practical to maintain complete and up-to-date documentation. In this scheme, there is a certain standard version of the simulation code that forms a library upon which new versions are built. To generate a new version of the simulation code, the routines to be modified or added are appended to a standard command file, which contains the commands to compile the new routines and link them to the routines in the library. The library itself is rarely changed. Whenever the library is modified, however, this modification is seen by all versions of the simulation code, which actually exist as different versions of the command file. All code is written according to the rules of structured programming. Modularity is enforced by not using COMMON statements, simplifying the relation of the data flow to a hierarchy diagram. Simulation results are similar to those of the PARMTEQ code, as expected, because of the similar physical model. Different capabilities, such as those for generating beams matched in detail to the structure, are available in the new code for help in testing new ideas in designing RFQ linacs

  19. Error Correcting Codes

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 3. Error Correcting Codes - Reed Solomon Codes. Priti Shankar. Series Article Volume 2 Issue 3 March ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560 012, India ...

  20. 78 FR 18321 - International Code Council: The Update Process for the International Codes and Standards

    Science.gov (United States)

    2013-03-26

    ... Energy Conservation Code. International Existing Building Code. International Fire Code. International... Code. International Property Maintenance Code. International Residential Code. International Swimming Pool and Spa Code International Wildland-Urban Interface Code. International Zoning Code. ICC Standards...

  1. Genetically modified foods and allergy.

    Science.gov (United States)

    Lee, T H; Ho, H K; Leung, T F

    2017-06-01

    2015 marked the 25th anniversary of the commercial use and availability of genetically modified crops. The area of planted biotech crops cultivated globally occupies a cumulative two billion hectares, equivalent to twice the land size of China or the United States. Foods derived from genetically modified plants are widely consumed in many countries and genetically modified soybean protein is extensively used in processed foods throughout the industrialised countries. Genetically modified food technology offers a possible solution to meet current and future challenges in food and medicine. Yet there is a strong undercurrent of anxiety that genetically modified foods are unsafe for human consumption, sometimes fuelled by criticisms based on little or no firm evidence. This has resulted in some countries turning away food destined for famine relief because of the perceived health risks of genetically modified foods. The major concerns include their possible allergenicity and toxicity despite the vigorous testing of genetically modified foods prior to marketing approval. It is imperative that scientists engage the public in a constructive evidence-based dialogue to address these concerns. At the same time, improved validated ways to test the safety of new foods should be developed. A post-launch strategy should be established routinely to allay concerns. Mandatory labelling of genetically modified ingredients should be adopted for the sake of transparency. Such ingredient listing and information facilitate tracing and recall if required.

  2. Validation of thermalhydraulic codes

    International Nuclear Information System (INIS)

    Wilkie, D.

    1992-01-01

    Thermalhydraulic codes require to be validated against experimental data collected over a wide range of situations if they are to be relied upon. A good example is provided by the nuclear industry where codes are used for safety studies and for determining operating conditions. Errors in the codes could lead to financial penalties, to the incorrect estimation of the consequences of accidents and even to the accidents themselves. Comparison between prediction and experiment is often described qualitatively or in approximate terms, e.g. ''agreement is within 10%''. A quantitative method is preferable, especially when several competing codes are available. The codes can then be ranked in order of merit. Such a method is described. (Author)

  3. Fracture flow code

    International Nuclear Information System (INIS)

    Dershowitz, W; Herbert, A.; Long, J.

    1989-03-01

    The hydrology of the SCV site will be modelled utilizing discrete fracture flow models. These models are complex, and can not be fully cerified by comparison to analytical solutions. The best approach for verification of these codes is therefore cross-verification between different codes. This is complicated by the variation in assumptions and solution techniques utilized in different codes. Cross-verification procedures are defined which allow comparison of the codes developed by Harwell Laboratory, Lawrence Berkeley Laboratory, and Golder Associates Inc. Six cross-verification datasets are defined for deterministic and stochastic verification of geometric and flow features of the codes. Additional datasets for verification of transport features will be documented in a future report. (13 figs., 7 tabs., 10 refs.) (authors)

  4. Genetic modification and genetic determinism

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-01-01

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions. PMID:16800884

  5. Huffman coding in advanced audio coding standard

    Science.gov (United States)

    Brzuchalski, Grzegorz

    2012-05-01

    This article presents several hardware architectures of Advanced Audio Coding (AAC) Huffman noiseless encoder, its optimisations and working implementation. Much attention has been paid to optimise the demand of hardware resources especially memory size. The aim of design was to get as short binary stream as possible in this standard. The Huffman encoder with whole audio-video system has been implemented in FPGA devices.

  6. TRACK The New Beam Dynamics Code

    CERN Document Server

    Mustapha, Brahim; Ostroumov, Peter; Schnirman-Lessner, Eliane

    2005-01-01

    The new ray-tracing code TRACK was developed* to fulfill the special requirements of the RIA accelerator systems. The RIA lattice includes an ECR ion source, a LEBT containing a MHB and a RFQ followed by three SC linac sections separated by two stripping stations with appropriate magnetic transport systems. No available beam dynamics code meet all the necessary requirements for an end-to-end simulation of the RIA driver linac. The latest version of TRACK was used for end-to-end simulations of the RIA driver including errors and beam loss analysis.** In addition to the standard capabilities, the code includes the following new features: i) multiple charge states ii) realistic stripper model; ii) static and dynamic errors iii) automatic steering to correct for misalignments iv) detailed beam-loss analysis; v) parallel computing to perform large scale simulations. Although primarily developed for simulations of the RIA machine, TRACK is a general beam dynamics code. Currently it is being used for the design and ...

  7. Advanced Presentation of BETHSY 6.2TC Test Results Calculated by RELAP5 and TRACE

    Directory of Open Access Journals (Sweden)

    Andrej Prošek

    2012-01-01

    Full Text Available Today most software applications come with a graphical user interface, including U.S. Nuclear Regulatory Commission TRAC/RELAP Advanced Computational Engine (TRACE best-estimate reactor system code. The graphical user interface is called Symbolic Nuclear Analysis Package (SNAP. The purpose of the present study was to assess the TRACE computer code and to assess the SNAP capabilities for input deck preparation and advanced presentation of the results. BETHSY 6.2 TC test was selected, which is 15.24 cm equivalent diameter horizontal cold leg break. For calculations the TRACE V5.0 Patch 1 and RELAP5/MOD3.3 Patch 4 were used. The RELAP5 legacy input deck was converted to TRACE input deck using SNAP. The RELAP5 and TRACE comparison to experimental data showed that TRACE results are as good as or better than the RELAP5 calculated results. The developed animation masks were of great help in comparison of results and investigating the calculated physical phenomena and processes.

  8. Report number codes

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, R.N. (ed.)

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.

  9. Report number codes

    International Nuclear Information System (INIS)

    Nelson, R.N.

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name

  10. From Genetics to Genetic Algorithms

    Indian Academy of Sciences (India)

    Genetic algorithms (GAs) are computational optimisation schemes with an ... The algorithms solve optimisation problems ..... Genetic Algorithms in Search, Optimisation and Machine. Learning, Addison-Wesley Publishing Company, Inc. 1989.

  11. From Genetics to Genetic Algorithms

    Indian Academy of Sciences (India)

    artificial genetic system) string feature or ... called the genotype whereas it is called a structure in artificial genetic ... assigned a fitness value based on the cost function. Better ..... way it has produced complex, intelligent living organisms capable of ...

  12. Image Tracing: An Analysis of Its Effectiveness in Children's Pictorial Discrimination Learning

    Science.gov (United States)

    Levin, Joel R.; And Others

    1977-01-01

    A total of 45 fifth grade students were the subjects of an experiment offering support for a component of learning strategy (memory imagery). Various theoretical explanations of the image-tracing phenomenon are considered, including depth of processing, dual coding and frequency. (MS)

  13. Generalised tally-based decoders for traitor tracing and group testing

    NARCIS (Netherlands)

    Skoric, B.; de Groot, W.

    2015-01-01

    We propose a new type of score function for Tardos traitor tracing codes. It is related to the recently introduced tally-based score function, but it utilizes more of the information available to the decoder. It does this by keeping track of sequences of symbols in the distributed codewords instead

  14. Trace Metals Bioaccumulation Potentials of Three Indigenous ...

    African Journals Online (AJOL)

    User

    grasses as bioaccumulators of trace metals from polluted soils. Seeds of ... transfer factor (TF) showed that Zn was the most bioaccumulated trace metals by all the grasses followed by. Pb, Mn ... was used to de-contaminate copper (Cu) and.

  15. Cryptography cracking codes

    CERN Document Server

    2014-01-01

    While cracking a code might seem like something few of us would encounter in our daily lives, it is actually far more prevalent than we may realize. Anyone who has had personal information taken because of a hacked email account can understand the need for cryptography and the importance of encryption-essentially the need to code information to keep it safe. This detailed volume examines the logic and science behind various ciphers, their real world uses, how codes can be broken, and the use of technology in this oft-overlooked field.

  16. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

  17. Transport theory and codes

    International Nuclear Information System (INIS)

    Clancy, B.E.

    1986-01-01

    This chapter begins with a neutron transport equation which includes the one dimensional plane geometry problems, the one dimensional spherical geometry problems, and numerical solutions. The section on the ANISN code and its look-alikes covers problems which can be solved; eigenvalue problems; outer iteration loop; inner iteration loop; and finite difference solution procedures. The input and output data for ANISN is also discussed. Two dimensional problems such as the DOT code are given. Finally, an overview of the Monte-Carlo methods and codes are elaborated on

  18. Gravity inversion code

    International Nuclear Information System (INIS)

    Burkhard, N.R.

    1979-01-01

    The gravity inversion code applies stabilized linear inverse theory to determine the topography of a subsurface density anomaly from Bouguer gravity data. The gravity inversion program consists of four source codes: SEARCH, TREND, INVERT, and AVERAGE. TREND and INVERT are used iteratively to converge on a solution. SEARCH forms the input gravity data files for Nevada Test Site data. AVERAGE performs a covariance analysis on the solution. This document describes the necessary input files and the proper operation of the code. 2 figures, 2 tables

  19. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics. Amit Katiyar. Articles written in Journal of Genetics. Volume 92 Issue 3 December 2013 pp 363-368 Research Article. Expression profile of genes coding for carotenoid biosynthetic pathway during ripening and their association with accumulation of lycopene in tomato fruits.

  20. Distributed trace using central performance counter memory

    Science.gov (United States)

    Satterfield, David L.; Sexton, James C.

    2013-01-22

    A plurality of processing cores, are central storage unit having at least memory connected in a daisy chain manner, forming a daisy chain ring layout on an integrated chip. At least one of the plurality of processing cores places trace data on the daisy chain connection for transmitting the trace data to the central storage unit, and the central storage unit detects the trace data and stores the trace data in the memory co-located in with the central storage unit.

  1. About Genetic Counselors

    Science.gov (United States)

    ... clinical care in many areas of medicine. Assisted Reproductive Technology/Infertility Genetics Cancer Genetics Cardiovascular Genetics Cystic Fibrosis Genetics Fetal Intervention and Therapy Genetics Hematology Genetics Metabolic Genetics ...

  2. TRACE Assessment for BWR ATWS Analysis

    International Nuclear Information System (INIS)

    Cheng, L.Y.; Diamond, D.; Cuadra, Arantxa; Raitses, Gilad; Aronson, Arnold

    2010-01-01

    A TRACE/PARCS input model has been developed in order to be able to analyze anticipated transients without scram (ATWS) in a boiling water reactor. The model is based on one developed previously for the Browns Ferry reactor for doing loss-of-coolant accident analysis. This model was updated by adding the control systems needed for ATWS and a core model using PARCS. The control systems were based on models previously developed for the TRAC-B code. The PARCS model is based on information (e.g., exposure and moderator density (void) history distributions) obtained from General Electric Hitachi and cross sections for GE14 fuel obtained from an independent source. The model is able to calculate an ATWS, initiated by the closure of main steam isolation valves, with recirculation pump trip, water level control, injection of borated water from the standby liquid control system and actuation of the automatic depressurization system. The model is not considered complete and recommendations are made on how it should be improved.

  3. Semiclassical structure of trace formulas

    International Nuclear Information System (INIS)

    Littlejohn, R.G.

    1990-01-01

    Trace formulas provide the only general relations known connecting quantum mechanics with classical mechanics in the case that the classical motion is chaotic. In particular, they connect quantal objects such as the density of states with classical periodic orbits. In this paper, several trace formulas, including those of Gutzwiller, Balian and Bloch, Tabor, and Berry, are examined from a geometrical standpoint. New forms of the amplitude determinant in asymptotic theory are developed as tools for this examination. The meaning of caustics in these formulas is revealed in terms of intersections of Lagrangian manifolds in phase space. The periodic orbits themselves appear as caustics of an unstable kind, lying on the intersection of two Lagrangian manifolds in the appropriate phase space. New insight is obtained into the Weyl correspondence and the Wigner function, especially their caustic structures

  4. Measuring Trace Hydrocarbons in Silanes

    Science.gov (United States)

    Lesser, L. A.

    1984-01-01

    Technique rapid and uses standard analytical equipment. Silane gas containing traces of hydrocarbons injected into carrier gas of moist nitrogen having about 0.2 percent water vapor. Carrier, water and silane pass through short column packed with powdered sodium hydroxide which combines moisture and silane to form nonvolatile sodium silicate. Carrier gas free of silane but containing nonreactive hydrocarbons, pass to silica-gel column where chromatographic separation takes place. Hydrocarbons measured by FID.

  5. Olfactory memory traces in Drosophila

    OpenAIRE

    Berry, Jacob; Krause, William C.; Davis, Ronald L.

    2008-01-01

    In Drosophila the fruit fly, coincident exposure to an odor and an aversive electric shock can produce robust behavioral memory. This behavioral memory is thought to be regulated by cellular memory traces within the central nervous system of the fly. These molecular, physiological or structural changes in neurons, induced by pairing odor and shock, regulate behavior by altering the neurons’ response to the learned environment. Recently, novel in vivo functional imaging techniques have allowed...

  6. On fuzzy semantic similarity measure for DNA coding.

    Science.gov (United States)

    Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin

    2016-02-01

    A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Trace element emissions from coal

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-09-15

    Trace elements are emitted during coal combustion. The quantity, in general, depends on the physical and chemical properties of the element itself, the concentration of the element in the coal, the combustion conditions and the type of particulate control device used, and its collection efficiency as a function of particle size. Some trace elements become concentrated in certain particle streams following combustion such as bottom ash, fly ash, and flue gas particulate matter, while others do not. Various classification schemes have been developed to describe this partitioning behaviour. These classification schemes generally distinguish between: Class 1: elements that are approximately equally concentrated in the fly ash and bottom ash, or show little or no fine particle enrichment, examples include Mn, Be, Co and Cr; Class 2: elements that are enriched in the fly ash relative to bottom ash, or show increasing enrichment with decreasing particle size, examples include As, Cd, Pb and Sb; Class 3: elements which are emitted in the gas phase (primarily Hg (not discussed in this review), and in some cases, Se). Control of class 1 trace elements is directly related to control of total particulate matter emissions, while control of the class 2 elements depends on collection of fine particulates. Due to the variability in particulate control device efficiencies, emission rates of these elements can vary substantially. The volatility of class 3 elements means that particulate controls have only a limited impact on the emissions of these elements.

  8. Trace explosives sensor testbed (TESTbed)

    Science.gov (United States)

    Collins, Greg E.; Malito, Michael P.; Tamanaha, Cy R.; Hammond, Mark H.; Giordano, Braden C.; Lubrano, Adam L.; Field, Christopher R.; Rogers, Duane A.; Jeffries, Russell A.; Colton, Richard J.; Rose-Pehrsson, Susan L.

    2017-03-01

    A novel vapor delivery testbed, referred to as the Trace Explosives Sensor Testbed, or TESTbed, is demonstrated that is amenable to both high- and low-volatility explosives vapors including nitromethane, nitroglycerine, ethylene glycol dinitrate, triacetone triperoxide, 2,4,6-trinitrotoluene, pentaerythritol tetranitrate, and hexahydro-1,3,5-trinitro-1,3,5-triazine. The TESTbed incorporates a six-port dual-line manifold system allowing for rapid actuation between a dedicated clean air source and a trace explosives vapor source. Explosives and explosives-related vapors can be sourced through a number of means including gas cylinders, permeation tube ovens, dynamic headspace chambers, and a Pneumatically Modulated Liquid Delivery System coupled to a perfluoroalkoxy total-consumption microflow nebulizer. Key features of the TESTbed include continuous and pulseless control of trace vapor concentrations with wide dynamic range of concentration generation, six sampling ports with reproducible vapor profile outputs, limited low-volatility explosives adsorption to the manifold surface, temperature and humidity control of the vapor stream, and a graphical user interface for system operation and testing protocol implementation.

  9. Verification of CTF/PARCSv3.2 coupled code in a Turbine Trip scenario

    International Nuclear Information System (INIS)

    Abarca, A.; Hidalga, P.; Miro, R.; Verdu, G.; Sekhri, A.

    2017-01-01

    Multiphysics codes had revealed as a best-estimate approach to simulate core behavior in LWR. Coupled neutronics and thermal-hydraulics codes are being used and improved to achieve reliable results for reactor safety transient analysis. The implementation of the feedback procedure between the coupled codes at each time step allows a more accurate simulation and a better prediction of the safety limits of analyzed scenarios. With the objective of testing the recently developed CTF/PARCSv3.2 coupled code, a code-to-code verification against TRACE has been developed in a BWR Turbine Trip scenario. CTF is a thermal-hydraulic subchannel code that features two-fluid, three-field representation of the two-phase flow, while PARCS code solves the neutronic diffusion equation in a 3D nodal distribution. PARCS features allow as well the use of extended sets of cross section libraries for a more precise neutronic performance in different formats like PMAX or NEMTAB. Using this option the neutronic core composition of KKL will be made taking advantage of the core follow database. The results of the simulation will be verified against TRACE results. TRACE will be used as a reference code for the validation process since it has been a recommended code by the USNRC. The model used for TRACE includes a full core plus relevant components such as the steam lines and the valves affecting and controlling the turbine trip evolution. The coupled code performance has been evaluated using the Turbine Trip event that took place in Kern Kraftwerk Leibstadt (KKL), at the fuel cycle 18. KKL is a Nuclear Power Plant (NPP) located in Leibstadt, Switzerland. This NPP operates with a BWR developing 3600 MWt in fuel cycles of one year. The Turbine Trip is a fast transient developing a pressure peak in the reactor followed by a power decreasing due to the selected control rod insertion. This kind of transient is very useful to check the feedback performance between both coupled codes due to the fast

  10. Fulcrum Network Codes

    DEFF Research Database (Denmark)

    2015-01-01

    Fulcrum network codes, which are a network coding framework, achieve three objectives: (i) to reduce the overhead per coded packet to almost 1 bit per source packet; (ii) to operate the network using only low field size operations at intermediate nodes, dramatically reducing complexity...... in the network; and (iii) to deliver an end-to-end performance that is close to that of a high field size network coding system for high-end receivers while simultaneously catering to low-end ones that can only decode in a lower field size. Sources may encode using a high field size expansion to increase...... the number of dimensions seen by the network using a linear mapping. Receivers can tradeoff computational effort with network delay, decoding in the high field size, the low field size, or a combination thereof....

  11. Supervised Convolutional Sparse Coding

    KAUST Repository

    Affara, Lama Ahmed; Ghanem, Bernard; Wonka, Peter

    2018-01-01

    coding, which aims at learning discriminative dictionaries instead of purely reconstructive ones. We incorporate a supervised regularization term into the traditional unsupervised CSC objective to encourage the final dictionary elements

  12. SASSYS LMFBR systems code

    International Nuclear Information System (INIS)

    Dunn, F.E.; Prohammer, F.G.; Weber, D.P.

    1983-01-01

    The SASSYS LMFBR systems analysis code is being developed mainly to analyze the behavior of the shut-down heat-removal system and the consequences of failures in the system, although it is also capable of analyzing a wide range of transients, from mild operational transients through more severe transients leading to sodium boiling in the core and possible melting of clad and fuel. The code includes a detailed SAS4A multi-channel core treatment plus a general thermal-hydraulic treatment of the primary and intermediate heat-transport loops and the steam generators. The code can handle any LMFBR design, loop or pool, with an arbitrary arrangement of components. The code is fast running: usually faster than real time

  13. OCA Code Enforcement

    Data.gov (United States)

    Montgomery County of Maryland — The Office of the County Attorney (OCA) processes Code Violation Citations issued by County agencies. The citations can be viewed by issued department, issued date...

  14. The fast code

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, L.N.; Wilson, R.E. [Oregon State Univ., Dept. of Mechanical Engineering, Corvallis, OR (United States)

    1996-09-01

    The FAST Code which is capable of determining structural loads on a flexible, teetering, horizontal axis wind turbine is described and comparisons of calculated loads with test data are given at two wind speeds for the ESI-80. The FAST Code models a two-bladed HAWT with degrees of freedom for blade bending, teeter, drive train flexibility, yaw, and windwise and crosswind tower motion. The code allows blade dimensions, stiffnesses, and weights to differ and models tower shadow, wind shear, and turbulence. Additionally, dynamic stall is included as are delta-3 and an underslung rotor. Load comparisons are made with ESI-80 test data in the form of power spectral density, rainflow counting, occurrence histograms, and azimuth averaged bin plots. It is concluded that agreement between the FAST Code and test results is good. (au)

  15. Code Disentanglement: Initial Plan

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbier, John Greaton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kelley, Timothy M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockefeller, Gabriel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Calef, Matthew Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-27

    The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

  16. Induction technology optimization code

    International Nuclear Information System (INIS)

    Caporaso, G.J.; Brooks, A.L.; Kirbie, H.C.

    1992-01-01

    A code has been developed to evaluate relative costs of induction accelerator driver systems for relativistic klystrons. The code incorporates beam generation, transport and pulsed power system constraints to provide an integrated design tool. The code generates an injector/accelerator combination which satisfies the top level requirements and all system constraints once a small number of design choices have been specified (rise time of the injector voltage and aspect ratio of the ferrite induction cores, for example). The code calculates dimensions of accelerator mechanical assemblies and values of all electrical components. Cost factors for machined parts, raw materials and components are applied to yield a total system cost. These costs are then plotted as a function of the two design choices to enable selection of an optimum design based on various criteria. (Author) 11 refs., 3 figs

  17. VT ZIP Code Areas

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) A ZIP Code Tabulation Area (ZCTA) is a statistical geographic entity that approximates the delivery area for a U.S. Postal Service five-digit...

  18. Bandwidth efficient coding

    CERN Document Server

    Anderson, John B

    2017-01-01

    Bandwidth Efficient Coding addresses the major challenge in communication engineering today: how to communicate more bits of information in the same radio spectrum. Energy and bandwidth are needed to transmit bits, and bandwidth affects capacity the most. Methods have been developed that are ten times as energy efficient at a given bandwidth consumption as simple methods. These employ signals with very complex patterns and are called "coding" solutions. The book begins with classical theory before introducing new techniques that combine older methods of error correction coding and radio transmission in order to create narrowband methods that are as efficient in both spectrum and energy as nature allows. Other topics covered include modulation techniques such as CPM, coded QAM and pulse design.

  19. Reactor lattice codes

    International Nuclear Information System (INIS)

    Kulikowska, T.

    2001-01-01

    The description of reactor lattice codes is carried out on the example of the WIMSD-5B code. The WIMS code in its various version is the most recognised lattice code. It is used in all parts of the world for calculations of research and power reactors. The version WIMSD-5B is distributed free of charge by NEA Data Bank. The description of its main features given in the present lecture follows the aspects defined previously for lattice calculations in the lecture on Reactor Lattice Transport Calculations. The spatial models are described, and the approach to the energy treatment is given. Finally the specific algorithm applied in fuel depletion calculations is outlined. (author)

  20. Critical Care Coding for Neurologists.

    Science.gov (United States)

    Nuwer, Marc R; Vespa, Paul M

    2015-10-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  1. Lattice Index Coding

    OpenAIRE

    Natarajan, Lakshmi; Hong, Yi; Viterbo, Emanuele

    2014-01-01

    The index coding problem involves a sender with K messages to be transmitted across a broadcast channel, and a set of receivers each of which demands a subset of the K messages while having prior knowledge of a different subset as side information. We consider the specific case of noisy index coding where the broadcast channel is Gaussian and every receiver demands all the messages from the source. Instances of this communication problem arise in wireless relay networks, sensor networks, and ...

  2. Towards advanced code simulators

    International Nuclear Information System (INIS)

    Scriven, A.H.

    1990-01-01

    The Central Electricity Generating Board (CEGB) uses advanced thermohydraulic codes extensively to support PWR safety analyses. A system has been developed to allow fully interactive execution of any code with graphical simulation of the operator desk and mimic display. The system operates in a virtual machine environment, with the thermohydraulic code executing in one virtual machine, communicating via interrupts with any number of other virtual machines each running other programs and graphics drivers. The driver code itself does not have to be modified from its normal batch form. Shortly following the release of RELAP5 MOD1 in IBM compatible form in 1983, this code was used as the driver for this system. When RELAP5 MOD2 became available, it was adopted with no changes needed in the basic system. Overall the system has been used for some 5 years for the analysis of LOBI tests, full scale plant studies and for simple what-if studies. For gaining rapid understanding of system dependencies it has proved invaluable. The graphical mimic system, being independent of the driver code, has also been used with other codes to study core rewetting, to replay results obtained from batch jobs on a CRAY2 computer system and to display suitably processed experimental results from the LOBI facility to aid interpretation. For the above work real-time execution was not necessary. Current work now centers on implementing the RELAP 5 code on a true parallel architecture machine. Marconi Simulation have been contracted to investigate the feasibility of using upwards of 100 processors, each capable of a peak of 30 MIPS to run a highly detailed RELAP5 model in real time, complete with specially written 3D core neutronics and balance of plant models. This paper describes the experience of using RELAP5 as an analyzer/simulator, and outlines the proposed methods and problems associated with parallel execution of RELAP5

  3. Cracking the Gender Codes

    DEFF Research Database (Denmark)

    Rennison, Betina Wolfgang

    2016-01-01

    extensive work to raise the proportion of women. This has helped slightly, but women remain underrepresented at the corporate top. Why is this so? What can be done to solve it? This article presents five different types of answers relating to five discursive codes: nature, talent, business, exclusion...... in leadership management, we must become more aware and take advantage of this complexity. We must crack the codes in order to crack the curve....

  4. PEAR code review

    International Nuclear Information System (INIS)

    De Wit, R.; Jamieson, T.; Lord, M.; Lafortune, J.F.

    1997-07-01

    As a necessary component in the continuous improvement and refinement of methodologies employed in the nuclear industry, regulatory agencies need to periodically evaluate these processes to improve confidence in results and ensure appropriate levels of safety are being achieved. The independent and objective review of industry-standard computer codes forms an essential part of this program. To this end, this work undertakes an in-depth review of the computer code PEAR (Public Exposures from Accidental Releases), developed by Atomic Energy of Canada Limited (AECL) to assess accidental releases from CANDU reactors. PEAR is based largely on the models contained in the Canadian Standards Association (CSA) N288.2-M91. This report presents the results of a detailed technical review of the PEAR code to identify any variations from the CSA standard and other supporting documentation, verify the source code, assess the quality of numerical models and results, and identify general strengths and weaknesses of the code. The version of the code employed in this review is the one which AECL intends to use for CANDU 9 safety analyses. (author)

  5. KENO-V code

    International Nuclear Information System (INIS)

    Cramer, S.N.

    1984-01-01

    The KENO-V code is the current release of the Oak Ridge multigroup Monte Carlo criticality code development. The original KENO, with 16 group Hansen-Roach cross sections and P 1 scattering, was one ot the first multigroup Monte Carlo codes and it and its successors have always been a much-used research tool for criticality studies. KENO-V is able to accept large neutron cross section libraries (a 218 group set is distributed with the code) and has a general P/sub N/ scattering capability. A supergroup feature allows execution of large problems on small computers, but at the expense of increased calculation time and system input/output operations. This supergroup feature is activated automatically by the code in a manner which utilizes as much computer memory as is available. The primary purpose of KENO-V is to calculate the system k/sub eff/, from small bare critical assemblies to large reflected arrays of differing fissile and moderator elements. In this respect KENO-V neither has nor requires the many options and sophisticated biasing techniques of general Monte Carlo codes

  6. Code, standard and specifications

    International Nuclear Information System (INIS)

    Abdul Nassir Ibrahim; Azali Muhammad; Ab. Razak Hamzah; Abd. Aziz Mohamed; Mohamad Pauzi Ismail

    2008-01-01

    Radiography also same as the other technique, it need standard. This standard was used widely and method of used it also regular. With that, radiography testing only practical based on regulations as mentioned and documented. These regulation or guideline documented in code, standard and specifications. In Malaysia, level one and basic radiographer can do radiography work based on instruction give by level two or three radiographer. This instruction was produced based on guideline that mention in document. Level two must follow the specifications mentioned in standard when write the instruction. From this scenario, it makes clearly that this radiography work is a type of work that everything must follow the rule. For the code, the radiography follow the code of American Society for Mechanical Engineer (ASME) and the only code that have in Malaysia for this time is rule that published by Atomic Energy Licensing Board (AELB) known as Practical code for radiation Protection in Industrial radiography. With the existence of this code, all the radiography must follow the rule or standard regulated automatically.

  7. Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding

    OpenAIRE

    Gao, Yuan; Liu, Pengyu; Wu, Yueying; Jia, Kebin; Gao, Guandong

    2016-01-01

    In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content ...

  8. Contour tracing for segmentation of mammographic masses

    International Nuclear Information System (INIS)

    Elter, Matthias; Held, Christian; Wittenberg, Thomas

    2010-01-01

    CADx systems have the potential to support radiologists in the difficult task of discriminating benign and malignant mammographic lesions. The segmentation of mammographic masses from the background tissue is an important module of CADx systems designed for the characterization of mass lesions. In this work, a novel approach to this task is presented. The segmentation is performed by automatically tracing the mass' contour in-between manually provided landmark points defined on the mass' margin. The performance of the proposed approach is compared to the performance of implementations of three state-of-the-art approaches based on region growing and dynamic programming. For an unbiased comparison of the different segmentation approaches, optimal parameters are selected for each approach by means of tenfold cross-validation and a genetic algorithm. Furthermore, segmentation performance is evaluated on a dataset of ROI and ground-truth pairs. The proposed method outperforms the three state-of-the-art methods. The benchmark dataset will be made available with publication of this paper and will be the first publicly available benchmark dataset for mass segmentation.

  9. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Right from the beginning, genetics has been an international venture, with international networks involving the collaboration of scientists across continents. Janaki Ammal's career illustrates this. This paper traces her scientific path by situating it in the context of her relationships with J. B. S. Haldane and C. D. Darlington.

  10. Trace metal speciation: Finally, correctly addressing trace metal issues

    International Nuclear Information System (INIS)

    Donard, O.F.X.

    2001-01-01

    The history of the development of trace metal speciation was discussed and the reasons behind the relatively slow widespread acceptance of its importance were presented. Partially, this was due to the lack of availability of commercial instrumentation and partly to the drive towards improving sensitivity in analytical chemistry which had focused attention on total concentration determinations. The sophistication and control of analytical instrumentation is now such that the spotlight must be turned onto the chemical species of an element present in a sample since this is what governs its behaviour in the biosphere. Indeed, several companies are currently considering the introduction of instrumentation specifically designed for metal species determination

  11. Adaption of the PARCS Code for Core Design Audit Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyong Chol; Lee, Young Jin; Uhm, Jae Beop; Kim, Hyunjik [Nuclear Safety Evaluation, Daejeon (Korea, Republic of); Jeong, Hun Young; Ahn, Seunghoon; Woo, Swengwoong [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2013-05-15

    The eigenvalue calculation also includes quasi-static core depletion analyses. PARCS has implemented variety of features and has been qualified as a regulatory audit code in conjunction with other NRC thermal-hydraulic codes such as TRACE or RELAP5. In this study, as an adaptation effort for audit applications, PARCS is applied for an audit analysis of a reload core design. The lattice physics code HELIOS is used for cross section generation. PARCS-HELIOS code system has been established as a core analysis tool. Calculation results have been compared on a wide spectrum of calculations such as power distribution, critical soluble boron concentration, and rod worth. A reasonable agreement between the audit calculation and the reference results has been found.

  12. Development and Verification of Behavior of Tritium Analytic Code (BOTANIC)

    International Nuclear Information System (INIS)

    Park, Min Young; Kim, Eung Soo

    2014-01-01

    VHTR, one of the Generation IV reactor concepts, has a relatively high operation temperature and is usually suggested as a heat source for many industrial processes, including hydrogen production process. Thus, it is vital to trace tritium behavior in the VHTR system and the potential permeation rate to the industrial process. In other words, tritium is a crucial issue in terms of safety in the fission reactor system. Therefore, it is necessary to understand the behavior of tritium and the development of the tool to enable this is vital.. In this study, a Behavior of Tritium Analytic Code (BOTANIC) an analytic tool which is capable of analyzing tritium behavior is developed using a chemical process code called gPROMS. BOTANIC was then further verified using the analytic solutions and benchmark codes such as Tritium Permeation Analysis Code (TPAC) and COMSOL. In this study, the Behavior of Tritium Analytic Code, BOTANIC, has been developed using a chemical process code called gPROMS. The code has several distinctive features including non-diluted assumption, flexible applications and adoption of distributed permeation model. Due to these features, BOTANIC has the capability to analyze a wide range of tritium level systems and has a higher accuracy as it has the capacity to solve distributed models. BOTANIC was successfully developed and verified using analytical solution and the benchmark code calculation result. The results showed very good agreement with the analytical solutions and the calculation results of TPAC and COMSOL. Future work will be focused on the total system verification

  13. Single-phase mixing studies by means of a directly coupled CFD/system-code tool

    International Nuclear Information System (INIS)

    Bertolotto, Davide; Chawla, Rakesh; Manera, Annalisa; Smith, Brian; Prasser, Horst-Michael

    2008-01-01

    The present paper describes the coupling of the 3D computational fluid dynamics (CFD) code CFX with the best estimate thermal-hydraulic code TRACE. Two different coupling schemes, i.e. an explicit and a semi-implicit one, have been tested. Verification of the coupled CFX/TRACE code has first been carried out on the basis of a simple test case consisting of a straight pipe filled with liquid subject to a sudden acceleration. As a second validation step, measurements using advanced instrumentation (wire-mesh sensors) have been performed in a simple, specially constructed test facility consisting of two loops connected by a double T-junction. Comparisons of the measurements are made with calculation results obtained using the coupled codes, as well as the individual codes in stand-alone mode, thereby clearly bringing out the effectiveness of the achieved coupling for simulating situations in which three-dimensional mixing phenomena are important. (authors)

  14. SPECTRAL AMPLITUDE CODING OCDMA SYSTEMS USING ENHANCED DOUBLE WEIGHT CODE

    Directory of Open Access Journals (Sweden)

    F.N. HASOON

    2006-12-01

    Full Text Available A new code structure for spectral amplitude coding optical code division multiple access systems based on double weight (DW code families is proposed. The DW has a fixed weight of two. Enhanced double-weight (EDW code is another variation of a DW code family that can has a variable weight greater than one. The EDW code possesses ideal cross-correlation properties and exists for every natural number n. A much better performance can be provided by using the EDW code compared to the existing code such as Hadamard and Modified Frequency-Hopping (MFH codes. It has been observed that theoretical analysis and simulation for EDW is much better performance compared to Hadamard and Modified Frequency-Hopping (MFH codes.

  15. Nuclear code abstracts (1975 edition)

    International Nuclear Information System (INIS)

    Akanuma, Makoto; Hirakawa, Takashi

    1976-02-01

    Nuclear Code Abstracts is compiled in the Nuclear Code Committee to exchange information of the nuclear code developments among members of the committee. Enlarging the collection, the present one includes nuclear code abstracts obtained in 1975 through liaison officers of the organizations in Japan participating in the Nuclear Energy Agency's Computer Program Library at Ispra, Italy. The classification of nuclear codes and the format of code abstracts are the same as those in the library. (auth.)

  16. Some new ternary linear codes

    Directory of Open Access Journals (Sweden)

    Rumen Daskalov

    2017-07-01

    Full Text Available Let an $[n,k,d]_q$ code be a linear code of length $n$, dimension $k$ and minimum Hamming distance $d$ over $GF(q$. One of the most important problems in coding theory is to construct codes with optimal minimum distances. In this paper 22 new ternary linear codes are presented. Two of them are optimal. All new codes improve the respective lower bounds in [11].

  17. ACE - Manufacturer Identification Code (MID)

    Data.gov (United States)

    Department of Homeland Security — The ACE Manufacturer Identification Code (MID) application is used to track and control identifications codes for manufacturers. A manufacturer is identified on an...

  18. Algebraic and stochastic coding theory

    CERN Document Server

    Kythe, Dave K

    2012-01-01

    Using a simple yet rigorous approach, Algebraic and Stochastic Coding Theory makes the subject of coding theory easy to understand for readers with a thorough knowledge of digital arithmetic, Boolean and modern algebra, and probability theory. It explains the underlying principles of coding theory and offers a clear, detailed description of each code. More advanced readers will appreciate its coverage of recent developments in coding theory and stochastic processes. After a brief review of coding history and Boolean algebra, the book introduces linear codes, including Hamming and Golay codes.

  19. Optical coding theory with Prime

    CERN Document Server

    Kwong, Wing C

    2013-01-01

    Although several books cover the coding theory of wireless communications and the hardware technologies and coding techniques of optical CDMA, no book has been specifically dedicated to optical coding theory-until now. Written by renowned authorities in the field, Optical Coding Theory with Prime gathers together in one volume the fundamentals and developments of optical coding theory, with a focus on families of prime codes, supplemented with several families of non-prime codes. The book also explores potential applications to coding-based optical systems and networks. Learn How to Construct

  20. The Aster code

    International Nuclear Information System (INIS)

    Delbecq, J.M.

    1999-01-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  1. Adaptive distributed source coding.

    Science.gov (United States)

    Varodayan, David; Lin, Yao-Chung; Girod, Bernd

    2012-05-01

    We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

  2. Evolving a Dynamic Predictive Coding Mechanism for Novelty Detection

    OpenAIRE

    Haggett, Simon J.; Chu, Dominique; Marshall, Ian W.

    2007-01-01

    Novelty detection is a machine learning technique which identifies new or unknown information in data sets. We present our current work on the construction of a new novelty detector based on a dynamical version of predictive coding. We compare three evolutionary algorithms, a simple genetic algorithm, NEAT and FS-NEAT, for the task of optimising the structure of an illustrative dynamic predictive coding neural network to improve its performance over stimuli from a number of artificially gener...

  3. Salmon tracing: Genotyping to trace back escapees from salmon aquaculture

    NARCIS (Netherlands)

    Blonk, R.J.W.

    2014-01-01

    The overall objective of the project is to assign an escaped salmon back to the farm responsible for the escape with near 100% accuracy. In this report, the potential of a set of genetic markers to assign an escaped salmon was determined for a set of 12 polymorphic microsatellite markers, provided

  4. Speech coding code- excited linear prediction

    CERN Document Server

    Bäckström, Tom

    2017-01-01

    This book provides scientific understanding of the most central techniques used in speech coding both for advanced students as well as professionals with a background in speech audio and or digital signal processing. It provides a clear connection between the whys hows and whats thus enabling a clear view of the necessity purpose and solutions provided by various tools as well as their strengths and weaknesses in each respect Equivalently this book sheds light on the following perspectives for each technology presented Objective What do we want to achieve and especially why is this goal important Resource Information What information is available and how can it be useful and Resource Platform What kind of platforms are we working with and what are their capabilities restrictions This includes computational memory and acoustic properties and the transmission capacity of devices used. The book goes on to address Solutions Which solutions have been proposed and how can they be used to reach the stated goals and ...

  5. Trace emissions from gaseous combustion

    Energy Technology Data Exchange (ETDEWEB)

    Seebold, J.G. [Chevron Research and Technology Co., Richmond, CA (United States)

    2000-07-01

    The U.S. Clean Air Act (CAA) was amended in 1990 to include the development of maximum achievable control technology (MACT) emission standards for hazardous air pollutants (HAPs) for certain stationary sources by November 2000. MACT emissions standards would affect process heaters and industrial boilers since combustion processes are a potential source for many air toxins. The author noted that one of the problems with MACT is the lack of a clear solid scientific footing which is needed to develop environmentally responsible regulations. In order to amend some of these deficiencies, a 4-year, $7 million research project on the origin and fate of trace emissions in the external combustion of gaseous hydrocarbons was undertaken in a collaborative effort between government, universities and industry. This collaborative project entitled the Petroleum Environmental Research Forum (PERF) Project 92-19 produced basic information and phenomenological understanding in two important areas, one basic and one applied. The specific objectives of the project were to measure emissions while operating different full-scale burners under various operating conditions and then to analyze the emission data to identify which operating conditions lead to low air toxic emissions. Another objective was to develop new chemical kinetic mechanisms and predictive models for the formation of air toxic species which would explain the origin and fate of these species in process heaters and industrial boilers. It was determined that a flame is a very effective reactor and that trace emissions from a typical gas-fired industry burner are very small. An unexpected finding was that trace emissions are not affected by hydrocarbon gaseous fuel composition, nor by the use of ultra low nitrous oxide burners. 2 refs., 8 figs.

  6. Tracing Utopia in 'Utopia Station'

    DEFF Research Database (Denmark)

    Schwarzbart, Judith

    This paper will discuss how avant-garde rhetoric and working methods are used to rethink exhibition-making in the wake of the ‘relational aesthetics’ and visual art of the 90s. With Utopia Station curated by Molly Nesbit, Hans Ulrich Obrist, and Rirkrit Tiravanija as key example, we will look...... at the many layers of discourse, ‘thinking-in-process’ and collaboration. These processes led to particular presentational formats (display) and architectural frameworks for activities, and gave way to a variety of other material and situated performative modes of audience encounters. Here, we can trace avant...

  7. Trace elements in human pituitary

    International Nuclear Information System (INIS)

    Kanabrocki, E.L.; Greco, J.; Graham, L.A.; Kaplan, E.; Rubnitz, M.E.; Oester, Y.T.; Brar, S.; Gustafson, P.S.; Nelson, D.M.; Molinari, F.; Moore, C.E.; Kanabrocki, J.A.

    1976-01-01

    Neutron activation analysis was used to determine several trace elements in human pituitaries from adult subjects aged 42 to 83 years who had died of ischemic heart disease, carcinoma and cirrhosis of the liver. None of these subjects suffered from mental disease. The concentrations of Fe, Zn, Rb, Se, Br, Cr, Hg, Cs and Co in dried tissue showed no correlation with the diseases, and the results may therefore be representative of the general population. These elements may play a very fundamental role in pituitary function. (U.K.)

  8. Discovery of Proteomic Code with mRNA Assisted Protein Folding

    Directory of Open Access Journals (Sweden)

    Jan C. Biro

    2008-12-01

    Full Text Available The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.

  9. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  10. Spatially coded backscatter radiography

    International Nuclear Information System (INIS)

    Thangavelu, S.; Hussein, E.M.A.

    2007-01-01

    Conventional radiography requires access to two opposite sides of an object, which makes it unsuitable for the inspection of extended and/or thick structures (airframes, bridges, floors etc.). Backscatter imaging can overcome this problem, but the indications obtained are difficult to interpret. This paper applies the coded aperture technique to gamma-ray backscatter-radiography in order to enhance the detectability of flaws. This spatial coding method involves the positioning of a mask with closed and open holes to selectively permit or block the passage of radiation. The obtained coded-aperture indications are then mathematically decoded to detect the presence of anomalies. Indications obtained from Monte Carlo calculations were utilized in this work to simulate radiation scattering measurements. These simulated measurements were used to investigate the applicability of this technique to the detection of flaws by backscatter radiography

  11. Aztheca Code; Codigo Aztheca

    Energy Technology Data Exchange (ETDEWEB)

    Quezada G, S.; Espinosa P, G. [Universidad Autonoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, 09340 Ciudad de Mexico (Mexico); Centeno P, J.; Sanchez M, H., E-mail: sequga@gmail.com [UNAM, Facultad de Ingenieria, Ciudad Universitaria, Circuito Exterior s/n, 04510 Ciudad de Mexico (Mexico)

    2017-09-15

    This paper presents the Aztheca code, which is formed by the mathematical models of neutron kinetics, power generation, heat transfer, core thermo-hydraulics, recirculation systems, dynamic pressure and level models and control system. The Aztheca code is validated with plant data, as well as with predictions from the manufacturer when the reactor operates in a stationary state. On the other hand, to demonstrate that the model is applicable during a transient, an event occurred in a nuclear power plant with a BWR reactor is selected. The plant data are compared with the results obtained with RELAP-5 and the Aztheca model. The results show that both RELAP-5 and the Aztheca code have the ability to adequately predict the behavior of the reactor. (Author)

  12. The Coding Question.

    Science.gov (United States)

    Gallistel, C R

    2017-07-01

    Recent electrophysiological results imply that the duration of the stimulus onset asynchrony in eyeblink conditioning is encoded by a mechanism intrinsic to the cerebellar Purkinje cell. This raises the general question - how is quantitative information (durations, distances, rates, probabilities, amounts, etc.) transmitted by spike trains and encoded into engrams? The usual assumption is that information is transmitted by firing rates. However, rate codes are energetically inefficient and computationally awkward. A combinatorial code is more plausible. If the engram consists of altered synaptic conductances (the usual assumption), then we must ask how numbers may be written to synapses. It is much easier to formulate a coding hypothesis if the engram is realized by a cell-intrinsic molecular mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Revised SRAC code system

    International Nuclear Information System (INIS)

    Tsuchihashi, Keichiro; Ishiguro, Yukio; Kaneko, Kunio; Ido, Masaru.

    1986-09-01

    Since the publication of JAERI-1285 in 1983 for the preliminary version of the SRAC code system, a number of additions and modifications to the functions have been made to establish an overall neutronics code system. Major points are (1) addition of JENDL-2 version of data library, (2) a direct treatment of doubly heterogeneous effect on resonance absorption, (3) a generalized Dancoff factor, (4) a cell calculation based on the fixed boundary source problem, (5) the corresponding edit required for experimental analysis and reactor design, (6) a perturbation theory calculation for reactivity change, (7) an auxiliary code for core burnup and fuel management, etc. This report is a revision of the users manual which consists of the general description, input data requirements and their explanation, detailed information on usage, mathematics, contents of libraries and sample I/O. (author)

  14. Code query by example

    Science.gov (United States)

    Vaucouleur, Sebastien

    2011-02-01

    We introduce code query by example for customisation of evolvable software products in general and of enterprise resource planning systems (ERPs) in particular. The concept is based on an initial empirical study on practices around ERP systems. We motivate our design choices based on those empirical results, and we show how the proposed solution helps with respect to the infamous upgrade problem: the conflict between the need for customisation and the need for upgrade of ERP systems. We further show how code query by example can be used as a form of lightweight static analysis, to detect automatically potential defects in large software products. Code query by example as a form of lightweight static analysis is particularly interesting in the context of ERP systems: it is often the case that programmers working in this field are not computer science specialists but more of domain experts. Hence, they require a simple language to express custom rules.

  15. The correspondence between projective codes and 2-weight codes

    NARCIS (Netherlands)

    Brouwer, A.E.; Eupen, van M.J.M.; Tilborg, van H.C.A.; Willems, F.M.J.

    1994-01-01

    The hyperplanes intersecting a 2-weight code in the same number of points obviously form the point set of a projective code. On the other hand, if we have a projective code C, then we can make a 2-weight code by taking the multiset of points E PC with multiplicity "Y(w), where W is the weight of

  16. Visualizing code and coverage changes for code review

    NARCIS (Netherlands)

    Oosterwaal, Sebastiaan; van Deursen, A.; De Souza Coelho, R.; Sawant, A.A.; Bacchelli, A.

    2016-01-01

    One of the tasks of reviewers is to verify that code modifications are well tested. However, current tools offer little support in understanding precisely how changes to the code relate to changes to the tests. In particular, it is hard to see whether (modified) test code covers the changed code.

  17. Turbo-Gallager Codes: The Emergence of an Intelligent Coding ...

    African Journals Online (AJOL)

    Today, both turbo codes and low-density parity-check codes are largely superior to other code families and are being used in an increasing number of modern communication systems including 3G standards, satellite and deep space communications. However, the two codes have certain distinctive characteristics that ...

  18. Code of Medical Ethics

    Directory of Open Access Journals (Sweden)

    . SZD-SZZ

    2017-03-01

    Full Text Available Te Code was approved on December 12, 1992, at the 3rd regular meeting of the General Assembly of the Medical Chamber of Slovenia and revised on April 24, 1997, at the 27th regular meeting of the General Assembly of the Medical Chamber of Slovenia. The Code was updated and harmonized with the Medical Association of Slovenia and approved on October 6, 2016, at the regular meeting of the General Assembly of the Medical Chamber of Slovenia.

  19. Supervised Convolutional Sparse Coding

    KAUST Repository

    Affara, Lama Ahmed

    2018-04-08

    Convolutional Sparse Coding (CSC) is a well-established image representation model especially suited for image restoration tasks. In this work, we extend the applicability of this model by proposing a supervised approach to convolutional sparse coding, which aims at learning discriminative dictionaries instead of purely reconstructive ones. We incorporate a supervised regularization term into the traditional unsupervised CSC objective to encourage the final dictionary elements to be discriminative. Experimental results show that using supervised convolutional learning results in two key advantages. First, we learn more semantically relevant filters in the dictionary and second, we achieve improved image reconstruction on unseen data.

  20. CONCEPT computer code

    International Nuclear Information System (INIS)

    Delene, J.

    1984-01-01

    CONCEPT is a computer code that will provide conceptual capital investment cost estimates for nuclear and coal-fired power plants. The code can develop an estimate for construction at any point in time. Any unit size within the range of about 400 to 1300 MW electric may be selected. Any of 23 reference site locations across the United States and Canada may be selected. PWR, BWR, and coal-fired plants burning high-sulfur and low-sulfur coal can be estimated. Multiple-unit plants can be estimated. Costs due to escalation/inflation and interest during construction are calculated

  1. Principles of speech coding

    CERN Document Server

    Ogunfunmi, Tokunbo

    2010-01-01

    It is becoming increasingly apparent that all forms of communication-including voice-will be transmitted through packet-switched networks based on the Internet Protocol (IP). Therefore, the design of modern devices that rely on speech interfaces, such as cell phones and PDAs, requires a complete and up-to-date understanding of the basics of speech coding. Outlines key signal processing algorithms used to mitigate impairments to speech quality in VoIP networksOffering a detailed yet easily accessible introduction to the field, Principles of Speech Coding provides an in-depth examination of the

  2. Model of heat transfer by radiation in a pool of spent fuel by TRACE; Modelo de transmision de calor por radiacion en una piscina de combustible gastado mediante TRACE

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Saez, F.; Carlos Alberola, S.; Martorell Alsina, J. J.; Villanueva Lopez, J. F.

    2013-07-01

    The work involves the simulation thermal-hydraulic of a spent fuel pool to cause a transient loss of coolant with coolant loss through the transfer channel. The simulation performed with the Best Estimate TRACE code. To follow the evolution of behavior of the pool, a variable is important to follow the sheath temperature, whose evolution depends on the heat that gets broadcast. In this simulation was considered the transfer by convection and has been compared with the evolution of Variable considering convection plus radiation. The proposed radiation pattern RADGEN obtains code data for use in TRACE. With this model, obtains an evolution of the temperature in the transient pod less conservative.

  3. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  4. Genetic Romanticism

    DEFF Research Database (Denmark)

    Tupasela, Aaro

    2016-01-01

    inheritance as a way to unify populations within politically and geographically bounded areas. Thus, new genetics have contributed to the development of genetic romanticisms, whereby populations (human, plant, and animal) can be delineated and mobilized through scientific and medical practices to represent...

  5. Evaluation Codes from an Affine Veriety Code Perspective

    DEFF Research Database (Denmark)

    Geil, Hans Olav

    2008-01-01

    Evaluation codes (also called order domain codes) are traditionally introduced as generalized one-point geometric Goppa codes. In the present paper we will give a new point of view on evaluation codes by introducing them instead as particular nice examples of affine variety codes. Our study...... includes a reformulation of the usual methods to estimate the minimum distances of evaluation codes into the setting of affine variety codes. Finally we describe the connection to the theory of one-pointgeometric Goppa codes. Contents 4.1 Introduction...... . . . . . . . . . . . . . . . . . . . . . . . 171 4.9 Codes form order domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 4.10 One-point geometric Goppa codes . . . . . . . . . . . . . . . . . . . . . . . . 176 4.11 Bibliographical Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 References...

  6. Trace Elements in Cardiovascular Diseases

    Energy Technology Data Exchange (ETDEWEB)

    Masironi, R. [Cardiovascular Diseases Unit, World Health Organization, Geneva (Switzerland)

    1970-07-01

    Cardiovascular diseases are the leading cause of death in industrialized countries. Their incidence increases, apparently, as a, function of technological progress so that in the future they may become a major public health problem in developing countries too. Early diagnosis and prevention are the tools best suited to curb such an alarming trend, but our knowledge of these topics is unsatisfactory, Valuable information would be obtained through a systematic investigation of trace elements in relation to cardiovascular function and to various types of cardiovascular diseases. Such studies would provide clues to the following questions: 1. Why does the incidence and type of cardiovascular disease differ from one country to another? May this be related to differences in tissue mineral concentrations among various population groups? 2. Which trace elements if any are beneficial to cardiovascular health, and which are harmful ones that may act as aetiological agents for some cardiovascular diseases? 3. Is it possible to utilize measurements of mineral element concentration for diagnostic purposes in cardiovascular disease? (author)

  7. Brain trace elements and aging

    International Nuclear Information System (INIS)

    Hebbrecht, Geert; Maenhaut, Willy; Reuck, Jacques de

    1999-01-01

    Degenerative mechanisms involved in the aging process of the brain are to a certain extent counteracted by repair mechanisms. In both degenerative and recovery processes, trace elements are involved. The present study focused on the role of two minor (i.e., K and Ca) and six trace elements (i.e., Mn, Fe, Cu, Zn, Se and Rb) in the aging process. The elements were determined by PIXE in cerebral cortex and white matter, basal ganglia, brainstem and cerebellar cortex of 18 postmortem human brains, from persons without a history of neurologic or psychiatric disease who deceased between the age of 7 and 79. This age range allowed us to study the relationship between elemental concentrations and age. The most prominent findings were a concentration decrease for K and Rb and a concentration increase for the elements Ca, Fe, Zn and Se. The study supports recent findings that Ca and Fe are involved in brain degenerative processes initiated by oxygen free radicals, whereas Zn and Se are involved in immunological reactions counteracting the aging process

  8. The Hmong Diaspora: preserved South-East Asian genetic ancestry in French Guianese Asians.

    Science.gov (United States)

    Brucato, Nicolas; Mazières, Stéphane; Guitard, Evelyne; Giscard, Pierre-Henri; Bois, Etienne; Larrouy, Georges; Dugoujon, Jean-Michel

    2012-01-01

    The Hmong Diaspora is one of the widest modern human migrations. Mainly localised in South-East Asia, the United States of America, and metropolitan France, a small community has also settled the Amazonian forest of French Guiana. We have biologically analysed 62 individuals of this unique Guianese population through three complementary genetic markers: mitochondrial DNA (HVS-I/II and coding region SNPs), Y-chromosome (SNPs and STRs), and the Gm allotypic system. All genetic systems showed a high conservation of the Asian gene pool (Asian ancestry: mtDNA=100.0%; NRY=99.1%; Gm=96.6%), without a trace of founder effect. When compared across various Asian populations, the highest correlations were observed with Hmong-Mien groups still living in South-East Asia (Fst<0.05; P-value<0.05). Despite a long history punctuated by exodus, the French Guianese Hmong have maintained their original genetic diversity. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  9. Dealing with an Unconventional Genetic Code in  Mitochondria: The Biogenesis and Pathogenic  Defects of the 5‐Formylcytosine Modification in  Mitochondrial tRNAMet

    Directory of Open Access Journals (Sweden)

    Lindsey Van Haute

    2017-03-01

    Full Text Available Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt‐tRNAMet also recognises AUA during translation initiation and elongation. Post‐transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5‐formylcytosine (f5C modification of position 34 in mt‐tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease.

  10. Tracing the origin of glomerular extracapillary lesions from parietal epithelial cells.

    Science.gov (United States)

    Smeets, Bart; Uhlig, Sandra; Fuss, Astrid; Mooren, Fieke; Wetzels, Jack F M; Floege, Jürgen; Moeller, Marcus J

    2009-12-01

    Cellular lesions form in Bowman's space in both crescentic glomerulonephritis and collapsing glomerulopathy. The pathomechanism and origin of the proliferating cells in these lesions are unknown. In this study, we examined proliferating cells by lineage tracing of either podocytes or parietal epithelial cells (PECs) in the nephrotoxic nephritis model of inflammatory crescentic glomerulonephritis. In addition, we traced the fate of genetically labeled PECs in the Thy-1.1 transgenic mouse model of collapsing glomerulopathy. In both models, cellular bridges composed of PECs were observed between Bowman's capsule and the glomerular tuft. Genetically labeled PECs also populated larger, more advanced cellular lesions. In these lesions, we detected de novo expression of CD44 in activated PECs. In contrast, we rarely identified genetically labeled podocytes within the cellular lesions of crescentic glomerulonephritis. In conclusion, PECs constitute the majority of cells that compose early extracapillary proliferative lesions in both crescentic glomerulonephritis and collapsing glomerulopathy, suggesting similar pathomechanisms in both diseases.

  11. Dual Coding in Children.

    Science.gov (United States)

    Burton, John K.; Wildman, Terry M.

    The purpose of this study was to test the applicability of the dual coding hypothesis to children's recall performance. The hypothesis predicts that visual interference will have a small effect on the recall of visually presented words or pictures, but that acoustic interference will cause a decline in recall of visually presented words and…

  12. Physical layer network coding

    DEFF Research Database (Denmark)

    Fukui, Hironori; Popovski, Petar; Yomo, Hiroyuki

    2014-01-01

    Physical layer network coding (PLNC) has been proposed to improve throughput of the two-way relay channel, where two nodes communicate with each other, being assisted by a relay node. Most of the works related to PLNC are focused on a simple three-node model and they do not take into account...

  13. Radioactive action code

    International Nuclear Information System (INIS)

    Anon.

    1988-01-01

    A new coding system, 'Hazrad', for buildings and transportation containers for alerting emergency services personnel to the presence of radioactive materials has been developed in the United Kingdom. The hazards of materials in the buildings or transport container, together with the recommended emergency action, are represented by a number of codes which are marked on the building or container and interpreted from a chart carried as a pocket-size guide. Buildings would be marked with the familiar yellow 'radioactive' trefoil, the written information 'Radioactive materials' and a list of isotopes. Under this the 'Hazrad' code would be written - three symbols to denote the relative radioactive risk (low, medium or high), the biological risk (also low, medium or high) and the third showing the type of radiation emitted, alpha, beta or gamma. The response cards indicate appropriate measures to take, eg for a high biological risk, Bio3, the wearing of a gas-tight protection suit is advised. The code and its uses are explained. (U.K.)

  14. Building Codes and Regulations.

    Science.gov (United States)

    Fisher, John L.

    The hazard of fire is of great concern to libraries due to combustible books and new plastics used in construction and interiors. Building codes and standards can offer architects and planners guidelines to follow but these standards should be closely monitored, updated, and researched for fire prevention. (DS)

  15. Physics of codes

    International Nuclear Information System (INIS)

    Cooper, R.K.; Jones, M.E.

    1989-01-01

    The title given this paper is a bit presumptuous, since one can hardly expect to cover the physics incorporated into all the codes already written and currently being written. The authors focus on those codes which have been found to be particularly useful in the analysis and design of linacs. At that the authors will be a bit parochial and discuss primarily those codes used for the design of radio-frequency (rf) linacs, although the discussions of TRANSPORT and MARYLIE have little to do with the time structures of the beams being analyzed. The plan of this paper is first to describe rather simply the concepts of emittance and brightness, then to describe rather briefly each of the codes TRANSPORT, PARMTEQ, TBCI, MARYLIE, and ISIS, indicating what physics is and is not included in each of them. It is expected that the vast majority of what is covered will apply equally well to protons and electrons (and other particles). This material is intended to be tutorial in nature and can in no way be expected to be exhaustive. 31 references, 4 figures

  16. Reliability and code level

    NARCIS (Netherlands)

    Kasperski, M.; Geurts, C.P.W.

    2005-01-01

    The paper describes the work of the IAWE Working Group WBG - Reliability and Code Level, one of the International Codification Working Groups set up at ICWE10 in Copenhagen. The following topics are covered: sources of uncertainties in the design wind load, appropriate design target values for the

  17. Ready, steady… Code!

    CERN Multimedia

    Anaïs Schaeffer

    2013-01-01

    This summer, CERN took part in the Google Summer of Code programme for the third year in succession. Open to students from all over the world, this programme leads to very successful collaborations for open source software projects.   Image: GSoC 2013. Google Summer of Code (GSoC) is a global programme that offers student developers grants to write code for open-source software projects. Since its creation in 2005, the programme has brought together some 6,000 students from over 100 countries worldwide. The students selected by Google are paired with a mentor from one of the participating projects, which can be led by institutes, organisations, companies, etc. This year, CERN PH Department’s SFT (Software Development for Experiments) Group took part in the GSoC programme for the third time, submitting 15 open-source projects. “Once published on the Google Summer for Code website (in April), the projects are open to applications,” says Jakob Blomer, one of the o...

  18. CERN Code of Conduct

    CERN Document Server

    Department, HR

    2010-01-01

    The Code is intended as a guide in helping us, as CERN contributors, to understand how to conduct ourselves, treat others and expect to be treated. It is based around the five core values of the Organization. We should all become familiar with it and try to incorporate it into our daily life at CERN.

  19. Nuclear safety code study

    Energy Technology Data Exchange (ETDEWEB)

    Hu, H.H.; Ford, D.; Le, H.; Park, S.; Cooke, K.L.; Bleakney, T.; Spanier, J.; Wilburn, N.P.; O' Reilly, B.; Carmichael, B.

    1981-01-01

    The objective is to analyze an overpower accident in an LMFBR. A simplified model of the primary coolant loop was developed in order to understand the instabilities encountered with the MELT III and SAS codes. The computer programs were translated for switching to the IBM 4331. Numerical methods were investigated for solving the neutron kinetics equations; the Adams and Gear methods were compared. (DLC)

  20. Revised C++ coding conventions

    CERN Document Server

    Callot, O

    2001-01-01

    This document replaces the note LHCb 98-049 by Pavel Binko. After a few years of practice, some simplification and clarification of the rules was needed. As many more people have now some experience in writing C++ code, their opinion was also taken into account to get a commonly agreed set of conventions