WorldWideScience

Sample records for alternative genetic code

  1. 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)

  2. 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.

  3. 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.

  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. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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:

  11. Alternative Fuels Data Center: Codes and Standards Resources

    Science.gov (United States)

    resources linked below help project developers and code officials prepare and review code-compliant projects , storage, and infrastructure. The following charts show the SDOs responsible for these alternative fuel codes and standards. Biodiesel Vehicle and Infrastructure Codes and Standards Chart Electric Vehicle and

  12. 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/

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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...

  19. Acceptability of genetically modified cheese presented as real product alternative

    DEFF Research Database (Denmark)

    Lähteenmäki, Liisa; Grunert, Klaus G.; Ueland, Øydis

    2002-01-01

    alternatives. Consumers in Denmark, Finland, Norway and Sweden (n=738) assessed two cheeses: one was labelled as genetically modified (preferred in an earlier product test) and the other as conventional (neutral in an ealier product test). A smaller control group received two cheeses with blind codes....... Labelling decreased consumers' intentions to buy the originally preferred gm-labelled cheese, but still the intentions were at the same level with the conventionally labelled buy gm cheese could best be explained by respondents' attitudes towards gene technology and perceived taste benefits. General health...... interest was also a reinforcer of intentions for gm cheese with reduced fat content....

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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 ...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Coding potential of the products of alternative splicing in human.

    KAUST Repository

    Leoni, Guido

    2011-01-20

    BACKGROUND: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. RESULTS: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. CONCLUSIONS: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity.

  15. Coding potential of the products of alternative splicing in human.

    KAUST Repository

    Leoni, Guido; Le Pera, Loredana; Ferrè , Fabrizio; Raimondo, Domenico; Tramontano, Anna

    2011-01-01

    BACKGROUND: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. RESULTS: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. CONCLUSIONS: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity.

  16. 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 ...

  17. 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.

  18. 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

  19. Alternative Watson-Crick Synthetic Genetic Systems.

    Science.gov (United States)

    Benner, Steven A; Karalkar, Nilesh B; Hoshika, Shuichi; Laos, Roberto; Shaw, Ryan W; Matsuura, Mariko; Fajardo, Diego; Moussatche, Patricia

    2016-11-01

    In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  20. 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.

  1. 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.

  2. Linguistic Alternants and Code Selection in Baba Malay.

    Science.gov (United States)

    Pakir, Anne

    1989-01-01

    Provides a brief account and explanation of the phenomenon of language use among the Baba community, which uses Hokkien, Malay, and English in the process of code selection and code mixing/switching. Data are drawn from recordings of conversation of the Babas and Nyonyas. (Author/OD)

  3. 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.

  4. 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.

  5. 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)

  6. AMD and the alternative complement pathway: genetics and functional implications.

    Science.gov (United States)

    Tan, Perciliz L; Bowes Rickman, Catherine; Katsanis, Nicholas

    2016-06-21

    Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses. Here, we review the genetic architecture of AMD, considering the contribution of both common and rare alleles to susceptibility, and we explore the possible mechanistic links between photoreceptor degeneration and the alternative complement pathway, a cascade that has emerged as the most potent genetic driver of this disorder.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. GOTHIC code evaluation of alternative passive containment cooling features

    International Nuclear Information System (INIS)

    Gavrilas, M.; Todreas, E.N.; Driscoll, M.J.

    1996-01-01

    Reliance on passive cooling has become an important objective in containment design. Several reactor concepts have been set forth, which are equipped with entirely passively cooled containments. However, the problems that have to be overcome in rejecting the entire heat generated by a severe accident in a high-rating reactor (i.e. one with a rating greater than 1200 MW e ) have been found to be substantial and without obvious solutions. The GOTHIC code was verified and modified for containment cooling applications; optimal mesh sizes, computational time steps and applicable heat transfer correlations were examined. The effect of the break location on circulation patterns that develop inside the containment was also evaluated. The GOTHIC code was then employed to assess the effectiveness of several original heat rejection features that make it possible to cool high-rating containments. Two containment concepts were evaluated: one for a 1200 MW e new pressure tube light-water reactor, and one for a 1300 MW e pressurized-water reactor. The effectiveness of various containment configurations that include specific pressure-limiting features has been predicted. The best-performance configurations-worst-case-accident scenarios that were examined yielded peak pressures of less than 0.30 MPa for the 1200 MW e pressure tube light-water reactor, and less than 0.45 MPa for the 1300 MW e pressurized-water reactor. (orig.)

  13. An alternative covariance estimator to investigate genetic heterogeneity in populations.

    Science.gov (United States)

    Heslot, Nicolas; Jannink, Jean-Luc

    2015-11-26

    For genomic prediction and genome-wide association studies (GWAS) using mixed models, covariance between individuals is estimated using molecular markers. Based on the properties of mixed models, using available molecular data for prediction is optimal if this covariance is known. Under this assumption, adding individuals to the analysis should never be detrimental. However, some empirical studies showed that increasing training population size decreased prediction accuracy. Recently, results from theoretical models indicated that even if marker density is high and the genetic architecture of traits is controlled by many loci with small additive effects, the covariance between individuals, which depends on relationships at causal loci, is not always well estimated by the whole-genome kinship. We propose an alternative covariance estimator named K-kernel, to account for potential genetic heterogeneity between populations that is characterized by a lack of genetic correlation, and to limit the information flow between a priori unknown populations in a trait-specific manner. This is similar to a multi-trait model and parameters are estimated by REML and, in extreme cases, it can allow for an independent genetic architecture between populations. As such, K-kernel is useful to study the problem of the design of training populations. K-kernel was compared to other covariance estimators or kernels to examine its fit to the data, cross-validated accuracy and suitability for GWAS on several datasets. It provides a significantly better fit to the data than the genomic best linear unbiased prediction model and, in some cases it performs better than other kernels such as the Gaussian kernel, as shown by an empirical null distribution. In GWAS simulations, alternative kernels control type I errors as well as or better than the classical whole-genome kinship and increase statistical power. No or small gains were observed in cross-validated prediction accuracy. This alternative

  14. Fast rate of evolution in alternatively spliced coding regions of mammalian genes

    Directory of Open Access Journals (Sweden)

    Nurtdinov Ramil N

    2006-04-01

    Full Text Available Abstract Background At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways. Results A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (dN, the rate of synonymous substitutions (dS, and their ratio (ω = dN/dS appear to be significantly higher in alternatively spliced coding regions compared to constitutive regions. When N-terminal, internal and C-terminal alternatives are analysed separately, C-terminal alternatives appear to make the main contribution to the observed difference. The effects become even more pronounced in a subset of fast evolving genes. Conclusion These results provide evidence of weaker purifying selection and/or stronger positive selection in alternative regions and thus one more confirmation of accelerated evolution in alternative regions. This study corroborates the theory that alternative splicing serves as a testing ground for molecular evolution.

  15. GOTHIC code evaluation of alternative passive containment cooling features

    International Nuclear Information System (INIS)

    Gavrilas, M.; Hejzlar, P.; Todreas, N.E.; Driscoll, M.J.

    1994-01-01

    The GOTHIC code was employed to assess the effectiveness of several original heat rejection features that make it possible to cool large rating containments. The code was first verified and modified for specific containment cooling applications; optimal mesh sizes, computational time steps, and applicable heat transfer correlations were examined. The effect of the break location on circulation patterns that develop inside the containment was also evaluated. GOTHIC was then used to obtain performance predictions for two containment concepts: a 1200 MW e new pressure tube light water reactor, and a 1300 MW e pressurized water reactor. The effectiveness of various containment configurations that include specific pressure-limiting features have been predicted. For the 1200 MW e pressure tube light water reactor, the evaluated pressure-limiting features are: a large water pool connected to the calandria, large containment free volume and an air-convection annulus. For the 1300 MW e pressurized water reactor, an external moat, an internal water pool, and an air-convection annulus were evaluated. The performance of the proposed containment configurations is dependent on the extent of thermal stratification inside the containment. The best-performance configurations/worst-case-accident scenarios that were examined yielded peak pressures of less than 0.30 MPa for the 1200 MW e pressure tube light water reactor, and less than 0.45 MPa for the 1300 MW e pressurized water reactor. The low peak pressure predicted for the 1200 MW e pressure tube light water reactor can be in part attributed to its relatively large free volume, while the relatively high peak pressure predicted for the 1300 MW e pressurized water reactor can be attributed to its relatively small free volume (i.e., the size used was that of a pressurized water reactor containment designed with active heat removal features). (author)

  16. Alternate symbol inversion for improved symbol synchronization in convolutionally coded systems

    Science.gov (United States)

    Simon, M. K.; Smith, J. G.

    1980-01-01

    Inverting alternate symbols of the encoder output of a convolutionally coded system provides sufficient density of symbol transitions to guarantee adequate symbol synchronizer performance, a guarantee otherwise lacking. Although alternate symbol inversion may increase or decrease the average transition density, depending on the data source model, it produces a maximum number of contiguous symbols without transition for a particular class of convolutional codes, independent of the data source model. Further, this maximum is sufficiently small to guarantee acceptable symbol synchronizer performance for typical applications. Subsequent inversion of alternate detected symbols permits proper decoding.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Genetics of alternative splicing evolution during sunflower domestication.

    Science.gov (United States)

    Smith, Chris C R; Tittes, Silas; Mendieta, J Paul; Collier-Zans, Erin; Rowe, Heather C; Rieseberg, Loren H; Kane, Nolan C

    2018-06-11

    Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarily trans -acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wild Helianthus annuus and gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from other Helianthus species. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.

  2. 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.

  3. Alternatives and challenges in optimizing industrial safety using genetic algorithms

    International Nuclear Information System (INIS)

    Martorell, Sebastian; Sanchez, Ana; Carlos, Sofia; Serradell, Vicente

    2004-01-01

    Safety (S) improvement of industrial installations leans on the optimal allocation of designs that use more reliable equipment and testing and maintenance activities to assure a high level of reliability, availability and maintainability (RAM) for their safety-related systems. However, this also requires assigning a certain amount of resources (C) that are usually limited. Therefore, the decision-maker in this context faces in general a multiple-objective optimization problem (MOP) based on RAMS+C criteria where the parameters of design, testing and maintenance act as decision variables. Solutions to the MOP can be obtained by solving the problem directly, or by transforming it into several single-objective problems. A general framework for such MOP based on RAMS+C criteria is proposed in this paper. Then, problem formulation and fundamentals of two major groups of resolution alternatives are presented. Next, both alternatives are implemented in this paper using genetic algorithms (GAs), named single-objective GA and multi-objective GA, respectively, which are then used in the case of application to solve the problem of testing and maintenance optimization based on unavailability and cost criteria. The results show the capabilities and limitations of both approaches. Based on them, future challenges are identified in this field and guidelines provided for further research

  4. A Critique of Schema Theory in Reading and a Dual Coding Alternative (Commentary).

    Science.gov (United States)

    Sadoski, Mark; And Others

    1991-01-01

    Evaluates schema theory and presents dual coding theory as a theoretical alternative. Argues that schema theory is encumbered by lack of a consistent definition, its roots in idealist epistemology, and mixed empirical support. Argues that results of many empirical studies used to demonstrate the existence of schemata are more consistently…

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Open Genetic Code : On open source in the life sciences

    NARCIS (Netherlands)

    Deibel, E.

    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

  10. 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

  11. 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.

  12. 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

  13. TEACHERS’ AND STUDENTS’ ATTITUDE TOWARD CODE ALTERNATION IN PAKISTANI ENGLISH CLASSROOMS

    Directory of Open Access Journals (Sweden)

    Aqsa Tahir

    2016-11-01

    Full Text Available This research is an attempt to explore students‟ and teachers‟ attitude towards code alternation within English classrooms in Pakistan. In a country like Pakistan where official language is English, the national language is Urdu, and every province has its own language, most of the people are bilinguals or multilingual. Therefore, the aim of this study was to find out when and why teachers code switch in L2 English classrooms. It has also explored student‟s preferences of language during learning second language. It has also looked into teachers‟ code-switching patterns and the students‟ priorities. Ten teachers responded to an open ended questioner and 100 students responded to a close ended questioner. Results of teacher‟s responses indicated that they mostly code switch when student‟s response in relation to the comprehensibility is negative and they do not grasp the concepts easily in L2. They never encourage students to speak Urdu. Student‟s results showed that they mostly prefer code-switching into their L1 for better understanding and participation in class. Analysis revealed that students only favored English while getting instructions of test, receiving results, and learning grammatical concepts. In most of the cases, students showed flexibility in language usage. Majority of students (68% agreed upon that they learn better when their teachers code switch in to L1.

  14. 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.

  15. QR Code, Face Recognition, and Google Location as Alternative Solution for Employee's Attendance in Small Companies

    OpenAIRE

    Wongso, Oscar

    2016-01-01

    RFID and biometric time attendance have been used to taking employee's attendances in attendances. But they have disadvantage which is cost a lot in terms of prices when need to be used in several places at the same time. An alternative solution was given by using android application which utilizing QR-Code, Face Recognition, and Google Map Location technologies implemented in smartphone to taking employee's attendances. A test for this system was conduct on one of private colouring studios i...

  16. Alternative conceptual models and codes for unsaturated flow in fractured tuff: Preliminary assessments for GWTT-95

    International Nuclear Information System (INIS)

    Ho, C.K.; Altman, S.J.; Arnold, B.W.

    1995-09-01

    Groundwater travel time (GWTT) calculations will play an important role in addressing site-suitability criteria for the potential high-level nuclear waste repository at Yucca Mountain,Nevada. In support of these calculations, Preliminary assessments of the candidate codes and models are presented in this report. A series of benchmark studies have been designed to address important aspects of modeling flow through fractured media representative of flow at Yucca Mountain. Three codes (DUAL, FEHMN, and TOUGH 2) are compared in these benchmark studies. DUAL is a single-phase, isothermal, two-dimensional flow simulator based on the dual mixed finite element method. FEHMN is a nonisothermal, multiphase, multidimensional simulator based primarily on the finite element method. TOUGH2 is anon isothermal, multiphase, multidimensional simulator based on the integral finite difference method. Alternative conceptual models of fracture flow consisting of the equivalent continuum model (ECM) and the dual permeability (DK) model are used in the different codes

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Alternative Line Coding Scheme with Fixed Dimming for Visible Light Communication

    Science.gov (United States)

    Niaz, M. T.; Imdad, F.; Kim, H. S.

    2017-01-01

    An alternative line coding scheme called fixed-dimming on/off keying (FD-OOK) is proposed for visible-light communication (VLC). FD-OOK reduces the flickering caused by a VLC transmitter and can maintain a 50% dimming level. Simple encoder and decoder are proposed which generates codes where the number of bits representing one is same as the number of bits representing zero. By keeping the number of ones and zeros equal the change in the brightness of lighting may be minimized and kept constant at 50%, thereby reducing the flickering in VLC. The performance of FD-OOK is analysed with two parameters: the spectral efficiency and power requirement.

  3. 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.

  4. 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.

  5. [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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Molecular analysis of human argininosuccinate lyase: Mutant characterization and alternative splicing of the coding region

    International Nuclear Information System (INIS)

    Walker, D.C.; McCloskey, D.A.; Simard, L.R.; McInnes, R.R.

    1990-01-01

    Argininosuccinic acid lyase (ASAL) deficiency is a clinically heterogeneous autosomal recessive urea cycle disorder. The authors previously established by complementation analysis that 29 ASAL-deficient patients have heterogeneous mutations in a single gene. To prove that the ASAL structural gene is the affected locus, they sequenced polymerase chain reaction-amplified ASAL cDNA of a representative mutant from the single complementation group. Fibroblast strain 944 from a late-onset patient who was the product of a consanguineous mating, had only a single base-pair change in the coding region, a C-283→ T transition at a CpG dinucleotide in exon 3. This substitution converts Arg-95 to Cys (R95C), occurs in a stretch of 13 residues that is identical in yeast and human ASAL, and was present in both of the patient's alleles but not in 14 other mutant or 10 normal alleles. They observed that amplified cDNA from mutant 944 and normal cells (liver, keratinocytes, lymphoblasts, and fibroblasts) contained, in addition to the expected 5' 513-base-pair band, a prominent 318-base-pair ASAL band formed by the splicing of exon 2 from the transcript. The short transcript maintains the ASAL reading frame but removes Lys-51, a residue that may be essential for catalysis, since it binds the argininosuccinate substrate. They conclude (i) that the identification of the R95C mutation in strain 944 demonstrates that virtually all ASAL deficiency results from defects in the ASAL structural gene and (ii) that minor alternative splicing of the coding region occurs at the ASAL locus

  14. Language choice, language alternation and code-switching in the Mercator-Hondius Atlas

    Directory of Open Access Journals (Sweden)

    Aleksi Mäkilähde

    2016-05-01

    Full Text Available The atlas of Gerardus Mercator (Gerard de Cremer, or the Atlas sive cosmographicae meditationes de fabrica mundi et fabricati figura, is one of first modern atlases and one of the most famous of those compiled in the Netherlands. The first (unfinished edition was published in 1595, but the copperplates were later acquired by Jodocus Hondius (Joost de Hondt and his business associates. The revised Mercator-Hondius Atlas was published for the first time in 1606 with added maps and texts. The texts printed on verso of the maps were written by Petrus Montanus (Pieter van den Berg, who was a brother-in-law of Hondius and a Latin teacher. Many subsequent editions of the atlas were produced in the years that followed. The first editions were in Latin, but versions in European vernaculars such as French, German and Italian were produced later as well. The present article focuses on the multilingual nature of the Mercator-Hondius Atlas (1613, editio quarta by discussing language choice, language alternation and code-switching patterns in different parts of the atlas. The dominant language of the descriptive texts is Latin, but there are also switches into many other languages, including Greek (written in Greek script and several vernaculars. Furthermore, the map pages tend to indicate the names of different types of area (e.g. cities, seas, and oceans in different languages. The aim of the present article is to provide a preliminary exploration of the possibilities of approaching the atlas with the aid of concepts and ideas derived from modern code-switching studies. I demonstrate how these concepts can be used to describe the language choice patterns in the text and discuss some of the challenges the data poses for a linguistic approach.

  15. 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.

  16. 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.

  17. Alternative Somatic Cell Count Traits as Mastitis Indicators for Genetic Selection

    NARCIS (Netherlands)

    Haas, de Y.; Ouweltjes, W.; Napel, ten J.; Windig, J.J.; Jong, de G.

    2008-01-01

    The aim of this study was to define alternative traits of somatic cell count (SCC) that can be used to decrease genetic susceptibility to clinical and subclinical mastitis (CM and SCM, respectively). Three kinds of SCC traits were evaluated: 1) lactation-averages of SCC, 2) traits derived from the

  18. 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

  19. A long-term, integrated impact assessment of alternative building energy code scenarios in China

    International Nuclear Information System (INIS)

    Yu, Sha; Eom, Jiyong; Evans, Meredydd; Clarke, Leon

    2014-01-01

    China is the second largest building energy user in the world, ranking first and third in residential and commercial energy consumption. Beginning in the early 1980s, the Chinese government has developed a variety of building energy codes to improve building energy efficiency and reduce total energy demand. This paper studies the impact of building energy codes on energy use and CO 2 emissions by using a detailed building energy model that represents four distinct climate zones each with three building types, nested in a long-term integrated assessment framework GCAM. An advanced building stock module, coupled with the building energy model, is developed to reflect the characteristics of future building stock and its interaction with the development of building energy codes in China. This paper also evaluates the impacts of building codes on building energy demand in the presence of economy-wide carbon policy. We find that building energy codes would reduce Chinese building energy use by 13–22% depending on building code scenarios, with a similar effect preserved even under the carbon policy. The impact of building energy codes shows regional and sectoral variation due to regionally differentiated responses of heating and cooling services to shell efficiency improvement. - Highlights: • We assessed long-term impacts of building codes and climate policy using GCAM. • Building energy codes would reduce Chinese building energy use by 13–22%. • The impacts of codes on building energy use vary by climate region and sub-sector

  20. 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)

  1. A Test of Two Alternative Cognitive Processing Models: Learning Styles and Dual Coding

    Science.gov (United States)

    Cuevas, Joshua; Dawson, Bryan L.

    2018-01-01

    This study tested two cognitive models, learning styles and dual coding, which make contradictory predictions about how learners process and retain visual and auditory information. Learning styles-based instructional practices are common in educational environments despite a questionable research base, while the use of dual coding is less…

  2. 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.

  3. 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

  4. Genetic variation in threshold reaction norms for alternative reproductive tactics in male Atlantic salmon, Salmo salar.

    Science.gov (United States)

    Piché, Jacinthe; Hutchings, Jeffrey A; Blanchard, Wade

    2008-07-07

    Alternative reproductive tactics may be a product of adaptive phenotypic plasticity, such that discontinuous variation in life history depends on both the genotype and the environment. Phenotypes that fall below a genetically determined threshold adopt one tactic, while those exceeding the threshold adopt the alternative tactic. We report evidence of genetic variability in maturation thresholds for male Atlantic salmon (Salmo salar) that mature either as large (more than 1 kg) anadromous males or as small (10-150 g) parr. Using a common-garden experimental protocol, we find that the growth rate at which the sneaker parr phenotype is expressed differs among pure- and mixed-population crosses. Maturation thresholds of hybrids were intermediate to those of pure crosses, consistent with the hypothesis that the life-history switch points are heritable. Our work provides evidence, for a vertebrate, that thresholds for alternative reproductive tactics differ genetically among populations and can be modelled as discontinuous reaction norms for age and size at maturity.

  5. 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.

  6. Alternate service delivery models in cancer genetic counseling: a mini-review

    Directory of Open Access Journals (Sweden)

    Adam Hudson Buchanan

    2016-05-01

    Full Text Available Demand for cancer genetic counseling has grown rapidly in recent years as germline genomic information has become increasingly incorporated into cancer care and the field has entered the public consciousness through high-profile celebrity publications. Increased demand and existing variability in the availability of trained cancer genetics clinicians place a priority on developing and evaluating alternate service delivery models for genetic counseling. This mini-review summarizes the state of science regarding service delivery models such as telephone counseling, telegenetics and group counseling. Research on comparative effectiveness of these models in traditional individual, in-person genetic counseling has been promising for improving access to care in a manner acceptable to patients. Yet, it has not fully evaluated the short- and long-term patient- and system-level outcomes that will help answer the question of whether these models achieve the same beneficial psychosocial and behavioral outcomes as traditional cancer genetic counseling. We propose a research agenda focused on comparative effectiveness of available service delivery models and how to match models to patients and practice settings. Only through this rigorous research can clinicians and systems find the optimal balance of clinical quality, ready and secure access to care, and financial sustainability. Such research will be integral to achieving the promise of genomic medicine in oncology.

  7. Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males.

    Science.gov (United States)

    Páez, David James; Bernatchez, Louis; Dodson, Julian J

    2011-07-22

    Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon (Salmo salar L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance.

  8. 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.

  9. MARAS - a computer code for semi-Markov reliability analysis of alternating systems

    International Nuclear Information System (INIS)

    Lee, Kwang Nam; Cho, Nam Zin

    1989-01-01

    It is now recognized that current testing and maintenance requirements invoke too many inadvertent reactor trips and that operating staff must devote significant amount of time and effort to comply with the requirements. With this recognition, the value and the impact of the proposed changes in the allowed outage time (AOT) and surveillance test interval(STI) are evaluated for the alternating system. Because of the testing and AOT requirements, the alternating system exhibits semi-Markovian characteristics which change states in accordance with a Markov chain but take a nonexponentially distributed amount of time between changes. It is observed from the results that there is an optimal point that gives lowest core damage probability and that the optimal point depends on input parameters. With these results, we can conclude that the methodology developed in this study can be applied to the existing alternating systems to evaluate accurately the various alternatives in the technical specifications

  10. An alternative technique for simulating volumetric cylindrical sources in the Morse code utilization

    International Nuclear Information System (INIS)

    Vieira, W.J.; Mendonca, A.G.

    1985-01-01

    In the solution of deep-penetration problems using the Monte Carlo method, calculation techniques and strategies are used in order to increase the particle population in the regions of interest. A common procedure is the coupling of bidimensional calculations, with (r,z) discrete ordinates transformed into source data, and tridimensional Monte Carlo calculations. An alternative technique for this procedure is presented. This alternative proved effective when applied to a sample problem. (F.E.) [pt

  11. 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.

  12. High prevalence of complementary and alternative medicine use in patients with genetically proven mitochondrial disorders.

    Science.gov (United States)

    Franik, Sebastian; Huidekoper, Hidde H; Visser, Gepke; de Vries, Maaike; de Boer, Lonneke; Hermans-Peters, Marion; Rodenburg, Richard; Verhaak, Chris; Vlieger, Arine M; Smeitink, Jan A M; Janssen, Mirian C H; Wortmann, Saskia B

    2015-05-01

    Despite major advances in understanding the pathophysiology of mitochondrial diseases, clinical management of these conditions remains largely supportive, and no effective treatment is available. We therefore assumed that the burden of disease combined with the lack of adequate treatment leaves open a big market for complementary and alternative medicine use. The objective of this study was to evaluate the use and perceived effectiveness of complementary and alternative medicine in children and adults with genetically proven mitochondrial disease. The reported use was surprisingly high, with 88% of children and 91% of adults having used some kind of complementary and alternative medicine in the last 2 years. Also, the mean cost of these treatments was impressive, being 489/year for children and 359/year for adult patients. Over-the-counter remedies (e.g., food supplements, homeopathy) and self-help techniques (e.g., Reiki, yoga) were the most frequently used complementary and alternative therapies in our cohort: 54% of children and 60% of adults reported the various complementary and alternative medicine therapies to be effective. Given the fact that currently no effective treatment exists, further research toward the different therapies is needed, as our study clearly demonstrates that such therapies are highly sought after by affected patients.

  13. 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.

  14. Channel coding/decoding alternatives for compressed TV data on advanced planetary missions.

    Science.gov (United States)

    Rice, R. F.

    1972-01-01

    The compatibility of channel coding/decoding schemes with a specific TV compressor developed for advanced planetary missions is considered. Under certain conditions, it is shown that compressed data can be transmitted at approximately the same rate as uncompressed data without any loss in quality. Thus, the full gains of data compression can be achieved in real-time transmission.

  15. 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.

  16. Caenorhabditis elegans as a powerful alternative model organism to promote research in genetic toxicology and biomedicine.

    Science.gov (United States)

    Honnen, Sebastian

    2017-05-01

    In view of increased life expectancy the risk for disturbed integrity of genetic information increases. This inevitably holds the implication for higher incidence of age-related diseases leading to considerable cost increase in health care systems. To develop preventive strategies it is crucial to evaluate external and internal noxae as possible threats to our DNA. Especially the interplay of DNA damage response (DDR) and DNA repair (DR) mechanisms needs further deciphering. Moreover, there is a distinct need for alternative in vivo test systems for basic research and also risk assessment in toxicology. Especially the evaluation of combinational toxicity of environmentally present genotoxins and adverse effects of clinically used DNA damaging anticancer drugs is a major challenge for modern toxicology. This review focuses on the applicability of Caenorhabditis elegans as a model organism to unravel and tackle scientific questions related to the biological consequences of genotoxin exposure and highlights methods for studying DDR and DR. In this regard large-scale in vivo screens of mixtures of chemicals and extensive parallel sequencing are highlighted as unique advantages of C. elegans. In addition, concise information regarding evolutionary conserved molecular mechanisms of the DDR and DR as well as currently available data obtained from the use of prototypical genotoxins and preferential read-outs of genotoxin testing are discussed. The use of established protocols, which are already available in the community, is encouraged to facilitate and further improve the implementation of C. elegans as a powerful genetic model system in genetic toxicology and biomedicine.

  17. 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.

  18. 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)

  19. 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)

  20. 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.

  1. 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.

  2. 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...

  3. 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

  4. 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.

  5. 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.

  6. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.

    2017-01-01

    conditions and different adaptation strategies depending on the substrates being switched between; in some environments, a persistent "generalist" strain developed, while in another, two "specialist" subpopulations arose that alternated dominance. Diauxic lag phenotype varied across the generalists...... maintain simple, static culturing environments so as to reduce selection pressure complexity. In this study, we investigated the adaptive strategies underlying evolution to fluctuating environments by evolving Escherichia coli to conditions of frequently switching growth substrate. Characterization...... of evolved strains via a number of different data types revealed the various genetic and phenotypic changes implemented in pursuit of growth optimality and how these differed across the different growth substrates and switching protocols. This work not only helps to establish general principles of adaptation...

  7. 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.

  8. 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.

  9. MuSiC: a Multibunch and multiparticle Simulation Code with an alternative approach to wakefield effects

    CERN Document Server

    Migliorati, M

    2015-01-01

    The simulation of beam dynamics in presence of collective effects requires a strong computational effort to take into account, in a self consistent way, the wakefield acting on a given charge and produced by all the others. Generally this is done by means of a convolution integral or sum. Moreover, if the electromagnetic fields consist of resonant modes with high quality factors, responsible, for example, of coupled bunch instabilities, a charge is also affected by itself in previous turns, and a very long record of wakefield must be properly taken into account. In this paper we present a new simulation code for the longitudinal beam dynamics in a circular accelerator, which exploits an alternative approach to the currently used convolution sum, reducing the computing time and avoiding the issues related to the length of wakefield for coupled bunch instabilities. With this approach it is possible to simulate, without the need of a large computing power, simultaneously, the single and multi-bunch beam dynamics...

  10. 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

  11. [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.

  12. 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.

  13. 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.

  14. Fine-scale variation and genetic determinants of alternative splicing across individuals.

    Directory of Open Access Journals (Sweden)

    Jasmin Coulombe-Huntington

    2009-12-01

    Full Text Available Recently, thanks to the increasing throughput of new technologies, we have begun to explore the full extent of alternative pre-mRNA splicing (AS in the human transcriptome. This is unveiling a vast layer of complexity in isoform-level expression differences between individuals. We used previously published splicing sensitive microarray data from lymphoblastoid cell lines to conduct an in-depth analysis on splicing efficiency of known and predicted exons. By combining publicly available AS annotation with a novel algorithm designed to search for AS, we show that many real AS events can be detected within the usually unexploited, speculative majority of the array and at significance levels much below standard multiple-testing thresholds, demonstrating that the extent of cis-regulated differential splicing between individuals is potentially far greater than previously reported. Specifically, many genes show subtle but significant genetically controlled differences in splice-site usage. PCR validation shows that 42 out of 58 (72% candidate gene regions undergo detectable AS, amounting to the largest scale validation of isoform eQTLs to date. Targeted sequencing revealed a likely causative SNP in most validated cases. In all 17 incidences where a SNP affected a splice-site region, in silico splice-site strength modeling correctly predicted the direction of the micro-array and PCR results. In 13 other cases, we identified likely causative SNPs disrupting predicted splicing enhancers. Using Fst and REHH analysis, we uncovered significant evidence that 2 putative causative SNPs have undergone recent positive selection. We verified the effect of five SNPs using in vivo minigene assays. This study shows that splicing differences between individuals, including quantitative differences in isoform ratios, are frequent in human populations and that causative SNPs can be identified using in silico predictions. Several cases affected disease-relevant genes and

  15. 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.

  16. 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.

  17. 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)

  18. 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...

  19. 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.

  20. Alternative Dispute Resolution ( ADR / ODR and Mitigation of Litigation in the Context of the New Code of Civil Procedure: A Shorter Path to Fair Legal System?

    Directory of Open Access Journals (Sweden)

    Leandro André Francisco Lima

    2016-06-01

    Full Text Available This study addresses the use of Alternative Dispute Resolution (ADR’s methods, owing to the new Civil Law Procedure Code, having as it’s theoretical framework the concept of access to justice as a Right to a fair Law system. It’s asked about the possibilities of using the alternative Online Dispute Resolution (ODR's tools by jurisdiction, provided by the information technology, in order to maximize the effects relating to that Right. The pertinence of this question is glimpsed in view of the broad society accession to the virtual life. It is used the hypothetical-deductive method. The research is theoretical, bibliographical and documentary.

  1. Design and simulations of a spectral efficient optical code division multiple access scheme using alternated energy differentiation and single-user soft-decision demodulation

    Science.gov (United States)

    A. Garba, Aminata

    2017-01-01

    This paper presents a new approach to optical Code Division Multiple Access (CDMA) network transmission scheme using alternated amplitude sequences and energy differentiation at the transmitters to allow concurrent and secure transmission of several signals. The proposed system uses error control encoding and soft-decision demodulation to reduce the multi-user interference at the receivers. The design of the proposed alternated amplitude sequences, the OCDMA energy modulators and the soft decision, single-user demodulators are also presented. Simulation results show that the proposed scheme allows achieving spectral efficiencies higher than several reported results for optical CDMA and much higher than the Gaussian CDMA capacity limit.

  2. arXiv AlterBBN v2: A public code for calculating Big-Bang nucleosynthesis constraints in alternative cosmologies

    CERN Document Server

    Arbey, A.; Hickerson, K.P.; Jenssen, E.S.

    We present the version 2 of AlterBBN, an open public code for the calculation of the abundance of the elements from Big-Bang nucleosynthesis. It does not rely on any closed external library or program, aims at being user-friendly and allowing easy modifications, and provides a fast and reliable calculation of the Big-Bang nucleosynthesis constraints in the standard and alternative cosmologies.

  3. On the Representation of Aquifer Compressibility in General Subsurface Flow Codes: How an Alternate Definition of Aquifer Compressibility Matches Results from the Groundwater Flow Equation

    Science.gov (United States)

    Birdsell, D.; Karra, S.; Rajaram, H.

    2017-12-01

    The governing equations for subsurface flow codes in deformable porous media are derived from the fluid mass balance equation. One class of these codes, which we call general subsurface flow (GSF) codes, does not explicitly track the motion of the solid porous media but does accept general constitutive relations for porosity, density, and fluid flux. Examples of GSF codes include PFLOTRAN, FEHM, STOMP, and TOUGH2. Meanwhile, analytical and numerical solutions based on the groundwater flow equation have assumed forms for porosity, density, and fluid flux. We review the derivation of the groundwater flow equation, which uses the form of Darcy's equation that accounts for the velocity of fluids with respect to solids and defines the soil matrix compressibility accordingly. We then show how GSF codes have a different governing equation if they use the form of Darcy's equation that is written only in terms of fluid velocity. The difference is seen in the porosity change, which is part of the specific storage term in the groundwater flow equation. We propose an alternative definition of soil matrix compressibility to correct for the untracked solid velocity. Simulation results show significantly less error for our new compressibility definition than the traditional compressibility when compared to analytical solutions from the groundwater literature. For example, the error in one calculation for a pumped sandstone aquifer goes from 940 to <70 Pa when the new compressibility is used. Code users and developers need to be aware of assumptions in the governing equations and constitutive relations in subsurface flow codes, and our newly-proposed compressibility function should be incorporated into GSF codes.

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. The uses of alternative dispute resolution to resolve genetic disputes. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Stein, Robert E.

    2003-01-01

    The report sets out lessons learned while carrying out the study. It concludes that genetic disputes will increase in number and that ADR processes including mediation, arbitration, the use of independent experts and court-appointed masters can be helpful in resolving them. It suggests additional effort on bioremediation, and workplace disputes and training for ADR neutrals.

  9. Genetics perspective of UV rays and new alternatives for sun protection

    International Nuclear Information System (INIS)

    Vallejo, E.O.; Vargas, N.; Martínez, L.M.; Agudelo, C.A.; Ortiz, I.C.

    2013-01-01

    Ultraviolet (UV), has three different wavelengths: UVA (315-400 nm), UVB (280-315 nm) and UVC (100-280 nm), which impact in different ways on the skin of human beings, and may be responsible of skin aging, burns and cancers. Currently we have multiple sunscreen alternatives, ranging from conventional physical methods to complex molecular mechanisms and inducers of cell repair as Polypodium leucotomos. The purpose of this review is to show the implications of ultraviolet rays on human beings exposed to sunlight and the protection alternatives that are available and show what is to come in photo protection towards the future. (authors) [es

  10. Insects feeding on cadavers as an alternative source of human genetic material

    Directory of Open Access Journals (Sweden)

    Rafał Skowronek

    2015-03-01

    Full Text Available In some criminal cases, the use of classical sources of human genetic material is difficult or even impossible. One solution may be the use of insects, especially blowfly larvae which feed on corpses. A recent review of case reports and experimental studies available in biomedical databases has shown that insects can be a valuable source of human mitochondrial and genomic deoxyribonucleic acid (DNA, allowing for an effective analysis of hypervariable region (HVR sequences and short tandem repeat (STR profiles, respectively. The optimal source of human DNA is the crop (a part of the gut of active third-instar blowfly larvae. Pupae and insect faeces can be also used in forensic genetic practice instead of the contents of the alimentary tract.

  11. 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.

  12. Genetic variations and alternative splicing. The Glioma associated oncogene 1, GLI1.

    Directory of Open Access Journals (Sweden)

    Peter eZaphiropoulos

    2012-07-01

    Full Text Available Alternative splicing is a post-transcriptional regulatory process that is attaining stronger recognition as a modulator of gene expression. Alternative splicing occurs when the primary RNA transcript is differentially processed into more than one mature RNAs. This is the result of a variable definition/inclusion of the exons, the sequences that are excised from the primary RNA to form the mature RNAs. Consequently, RNA expression can generate a collection of differentially spliced RNAs, which may distinctly influence subsequent biological events, such as protein synthesis or other biomolecular interactions. Still the mechanisms that control exon definition and exon inclusion are not fully clarified. This mini-review highlights advances in this field as well as the impact of single nucleotide polymorphisms in affecting splicing decisions. The Glioma associated oncogene 1, GLI1, is taken as an example in addressing the role of nucleotide substitutions for splicing regulation.

  13. The Conciliation in the State Demands as an Alternative for the Economy in the Process in New Civil Procedure Code

    Directory of Open Access Journals (Sweden)

    Eduardo Augusto Salomão Camb

    2016-12-01

    Full Text Available The present study deals with the possibility of conciliation in the demands that involve the Public Power, having as main objective the procedural economy, both as regards the faster process, as to reduction of expenses with the structure of the Judiciary. Despite of the unavailability of the public interest, seeks out the adequacy of this principle with the principles in the New Civil Procedure Code, which encourages conciliation as a means of settling disputes.

  14. 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

    Previously, we suggested prototypal models that describe some clinical states based on group postulates. Here, we demonstrate a group/category theory-like model for molecular/genetic biology as an alternative application of our previous model. Specifically, we focus on deoxyribonucleic acid (DNA) base sequences. We construct a wallpaper pattern based on a five-letter cruciform motif with letters C, A, T, G, and E. Whereas the first four letters represent the standard DNA bases, the fifth is introduced for ease in formulating group operations that reproduce insertions and deletions of DNA base sequences. A basic group Z5 = {r, u, d, l, n} of operations is defined for the wallpaper pattern, with which a sequence of points can be generated corresponding to changes of a base in a DNA sequence by following the orbit of a point of the pattern under operations in group Z5. Other manipulations of DNA sequence can be treated using a vector-like notation 'Dj' corresponding to a DNA sequence but based on the five-letter base set; also, 'Dj's are expressed graphically. Insertions and deletions of a series of letters 'E' are admitted to assist in describing DNA recombination. Likewise, a vector-like notation Rj can be constructed for sequences of ribonucleic acid (RNA). The wallpaper group B = {Z5×∞, ●} (an ∞-fold Cartesian product of Z5) acts on Dj (or Rj) yielding changes to Dj (or Rj) denoted by 'Dj◦B(j→k) = Dk' (or 'Rj◦B(j→k) = Rk'). Based on the operations of this group, two types of groups-a modulo 5 linear group and a rotational group over the Gaussian plane, acting on the five bases-are linked as parts of the wallpaper group for broader applications. As a result, changes, insertions/deletions and DNA (RNA) recombination (partial/total conversion) are described. As an exploratory study, a notation for the canonical "central dogma" via a category theory-like way is presented for future developments. Despite the large incompleteness of our

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Transcranial Alternating Current Stimulation: A potential risk for genetic generalized epilepsy patients (Study Case

    Directory of Open Access Journals (Sweden)

    Daniel San Juan Orta

    2016-11-01

    Full Text Available Transcranial alternating current stimulation (tACS is a re-emergent neuromodulation technique that consists in the external application of oscillating electrical currents that induces changes in cortical excitability. We present the case of a 16-year-old female with pharmaco-resistant juvenile myoclonic epilepsy to three antiepileptic’s drugs characterized by four myoclonic and 20 absence seizures monthly. She received tACS at 1mA@3Hz pulse train during 60 minutes over Fp1-Fp2 (10-20 EEG international system position during 4 consecutive days using an Endeavor™ IOM Systems device® (Natus Medical Incorporated, Middleton, WI, USA. At the one-month follow-up, she reported a 75% increase in seizures frequency (only myoclonic and tonic-clonic events and developed a 24h myoclonic status epilepticus that resolved with oral clonazepam and intravenous valproate. At the two-month follow-up, the patient reported a 15-day seizure-free period.

  20. Transcranial Alternating Current Stimulation: A Potential Risk for Genetic Generalized Epilepsy Patients (Study Case)

    Science.gov (United States)

    San-Juan, Daniel; Sarmiento, Carlos Ignacio; Hernandez-Ruiz, Axel; Elizondo-Zepeda, Ernesto; Santos-Vázquez, Gabriel; Reyes-Acevedo, Gerardo; Zúñiga-Gazcón, Héctor; Zamora-Jarquín, Carol Marina

    2016-01-01

    Transcranial alternating current stimulation (tACS) is a re-emergent neuromodulation technique that consists in the external application of oscillating electrical currents that induces changes in cortical excitability. We present the case of a 16-year-old female with pharmaco-resistant juvenile myoclonic epilepsy to 3 antiepileptic’s drugs characterized by 4 myoclonic and 20 absence seizures monthly. She received tACS at 1 mA at 3 Hz pulse train during 60 min over Fp1–Fp2 (10–20 EEG international system position) during 4 consecutive days using an Endeavor™ IOM Systems device® (Natus Medical Incorporated, Middleton, WI, USA). At the 1-month follow-up, she reported a 75% increase in seizures frequency (only myoclonic and tonic–clonic events) and developed a 24-h myoclonic status epilepticus that resolved with oral clonazepam and intravenous valproate. At the 2-month follow-up, the patient reported a 15-day seizure-free period. PMID:27965623

  1. Neutron flux investigation on certain alternative fluids in a hybrid system by using MCNPX Monte Carlo transport code

    Energy Technology Data Exchange (ETDEWEB)

    Guenay, Mehtap [Inoenue Univ., Malatya (Turkey). Physics Dept.

    2014-04-15

    In this study, the molten salt-heavy metal mixtures 93-85 % Li{sub 20}Sn{sub 80} + 5 % SFG-PuO{sub 2} and 2-10 % UO{sub 2}, 93-85 % Li{sub 20}Sn{sub 80} + 5 % SFG-PuO{sub 2} and 2-10 % NpO{sub 2}, 93-85 % Li{sub 20}Sn{sub 80} + 5 % SFG-PuO{sub 2} and 2-10 % UCO were used as fluids. The fluids were used in the liquid first wall, blanket and shield zones of the designed hybrid reactor system. Four centimeter thick 9Cr2WVTa ferritic steel was used as the structural material. In this study, the effect of mixture components on the neutron flux was investigated in a designed fusion-fission hybrid reactor system. The neutron flux was investigated according to the mixture components, radial flux distribution and energy spectrum in the designed system. Three-dimensional analyses were performed using the most recent MCNPX-2.7.0 Monte Carlo radiation transport code and the ENDF/B-VII.0 nuclear data library. (orig.)

  2. Performance Prediction of Centrifugal Compressor for Drop-In Testing Using Low Global Warming Potential Alternative Refrigerants and Performance Test Codes

    Directory of Open Access Journals (Sweden)

    Joo Hoon Park

    2017-12-01

    Full Text Available As environmental regulations to stall global warming are strengthened around the world, studies using newly developed low global warming potential (GWP alternative refrigerants are increasing. In this study, substitute refrigerants, R-1234ze (E and R-1233zd (E, were used in the centrifugal compressor of an R-134a 2-stage centrifugal chiller with a fixed rotational speed. Performance predictions and thermodynamic analyses of the centrifugal compressor for drop-in testing were performed. A performance prediction method based on the existing ASME PTC-10 performance test code was proposed. The proposed method yielded the expected operating area and operating point of the centrifugal compressor with alternative refrigerants. The thermodynamic performance of the first and second stages of the centrifugal compressor was calculated as the polytropic state. To verify the suitability of the proposed method, the drop-in test results of the two alternative refrigerants were compared. The predicted operating range based on the permissible deviation of ASME PTC-10 confirmed that the temperature difference was very small at the same efficiency. Because the drop-in test of R-1234ze (E was performed within the expected operating range, the centrifugal compressor using R-1234ze (E is considered well predicted. However, the predictions of the operating point and operating range of R-1233zd (E were lower than those of the drop-in test. The proposed performance prediction method will assist in understanding thermodynamic performance at the expected operating point and operating area of a centrifugal compressor using alternative gases based on limited design and structure information.

  3. Hebbian learning in a model with dynamic rate-coded neurons: an alternative to the generative model approach for learning receptive fields from natural scenes.

    Science.gov (United States)

    Hamker, Fred H; Wiltschut, Jan

    2007-09-01

    Most computational models of coding are based on a generative model according to which the feedback signal aims to reconstruct the visual scene as close as possible. We here explore an alternative model of feedback. It is derived from studies of attention and thus, probably more flexible with respect to attentive processing in higher brain areas. According to this model, feedback implements a gain increase of the feedforward signal. We use a dynamic model with presynaptic inhibition and Hebbian learning to simultaneously learn feedforward and feedback weights. The weights converge to localized, oriented, and bandpass filters similar as the ones found in V1. Due to presynaptic inhibition the model predicts the organization of receptive fields within the feedforward pathway, whereas feedback primarily serves to tune early visual processing according to the needs of the task.

  4. 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.

  5. Effects of ovarian fluid and genetic differences on sperm performance and fertilization success of alternative reproductive tactics in Chinook salmon.

    Science.gov (United States)

    Lehnert, S J; Butts, I A E; Flannery, E W; Peters, K M; Heath, D D; Pitcher, T E

    2017-06-01

    In many species, sperm velocity affects variation in the outcome of male competitive fertilization success. In fishes, ovarian fluid (OF) released with the eggs can increase male sperm velocity and potentially facilitate cryptic female choice for males of specific phenotypes and/or genotypes. Therefore, to investigate the effect of OF on fertilization success, we measured sperm velocity and conducted in vitro competitive fertilizations with paired Chinook salmon (Oncorhynchus tshawytscha) males representing two alternative reproductive tactics, jacks (small sneaker males) and hooknoses (large guarding males), in the presence of river water alone and OF mixed with river water. To determine the effect of genetic differences on fertilization success, we genotyped fish at neutral (microsatellites) and functional [major histocompatibility complex (MHC) II ß1] markers. We found that when sperm were competed in river water, jacks sired significantly more offspring than hooknoses; however, in OF, there was no difference in paternity between the tactics. Sperm velocity was significantly correlated with paternity success in river water, but not in ovarian fluid. Paternity success in OF, but not in river water alone, was correlated with genetic relatedness between male and female, where males that were less related to the female attained greater paternity. We found no relationship between MHC II ß1 divergence between mates and paternity success in water or OF. Our results indicate that OF can influence the outcome of sperm competition in Chinook salmon, where OF provides both male tactics with fertilization opportunities, which may in part explain what maintains both tactics in nature. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  6. 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

  7. Preimplantation genetic screening as an alternative to prenatal testing for Down syndrome : preferences of women undergoing in vitro fertilization/intracytoplasmic sperm injection treatment

    NARCIS (Netherlands)

    Twisk, Moniek; Haadsma, Maaike L.; van der Veen, Fulco; Repping, Sjoerd; Mastenbroek, Sebastiaan; Heineman, Maas-Jan; Bossuyt, Patrick M. M.; Korevaar, Johanna C.

    2007-01-01

    Objective: Although the primary goal of preimplantation genetic screening (PGS) is to increase pregnancy rates in women undergoing IVF/intracytoplasmic sperm injection treatment, it has been suggested that it may also be used as an alternative to prenatal testing for Down syndrome. Design: Trade-off

  8. Preimplantation genetic screening as an alternative to prenatal testing for Down syndrome: preferences of women undergoing in vitro fertilization/intracytoplasmic sperm injection treatment

    NARCIS (Netherlands)

    Twisk, Moniek; Haadsma, Maaike L.; van der Veen, Fulco; Repping, Sjoerd; Mastenbroek, Sebastiaan; Heineman, Maas-Jan; Bossuyt, Patrick M. M.; Korevaar, Johanna C.

    2007-01-01

    Objective: Although the primary goal of preimplantation genetic screening (PGS) is to increase pregnancy rates in women undergoing IVF/intracytoplasmic sperm injection treatment, it has been suggested that it may also be used as an alternative to prenatal testing for Down syndrome. Design: Trade-off

  9. Genetically Engineered Islets and Alternative Sources of Insulin-Producing Cells for Treating Autoimmune Diabetes: Quo Vadis?

    Directory of Open Access Journals (Sweden)

    Feng-Cheng Chou

    2012-01-01

    Full Text Available Islet transplantation is a promising therapy for patients with type 1 diabetes that can provide moment-to-moment metabolic control of glucose and allow them to achieve insulin independence. However, two major problems need to be overcome: (1 detrimental immune responses, including inflammation induced by the islet isolation/transplantation procedure, recurrence autoimmunity, and allorejection, can cause graft loss and (2 inadequate numbers of organ donors. Several gene therapy approaches and pharmaceutical treatments have been demonstrated to prolong the survival of pancreatic islet grafts in animal models; however, the clinical applications need to be investigated further. In addition, for an alternative source of pancreatic β-cell replacement therapy, the ex vivo generation of insulin-secreting cells from diverse origins of stem/progenitor cells has become an attractive option in regenerative medicine. This paper focuses on the genetic manipulation of islets during transplantation therapy and summarizes current strategies to obtain functional insulin-secreting cells from stem/progenitor cells.

  10. 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…

  11. 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

  12. 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

  13. 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.

  14. 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...

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. A specific scenario for the origin of life and the genetic code based on peptide/oligonucleotide interdependence.

    Science.gov (United States)

    Griffith, Robert W

    2009-12-01

    Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and translation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface.

  8. REVIEW: The Characteristics of Genetic Resource of Bali Cattle (Bos-bibos banteng and the Alternative of It's Conservation Methods

    Directory of Open Access Journals (Sweden)

    ACHMAD NUR CHAMDI

    2005-01-01

    Full Text Available Bali cattle is an Indonesian native beef cattle, the result of domestication of Banteng (Bos-bibos banteng. The main problem faced in the development of Bali cattle is the low quality of breed, which is predicted as the effect of inbreeding or raising management. The affects of genetic and cross breeding which usually inflict a loss are the decreasing of cattle’s endurance, fertility and birth weight. Seeing the fact, the government effort to introduce a quality bull to the breed source areas, the determination of cattle release including the controll on the cutting of productive female cattle, and to exactly count the number of Bali cattle which can be released in order to do not disturb its population balance, so it is necessary to do conservation attempt by in-situ and ex-situ. The result of this study shows that the characteristics on genetic resource of Bali cattle which comprises documentation, evaluation on reproduction and production, and attempt in increasing Bali cattle’s genetic quality in Indonesia have been done, eventhough those are still limited.

  9. A genetic algorithm-based search for parametric reform alternatives for the Turkish pension system : 2005-2060

    OpenAIRE

    Alparslan, Mustafa Artun

    2005-01-01

    Ankara : The Department of Economics, Bilkent Univ., 2005. Thesis (Master's) -- Bilkent University, 2005. Includes bibliographical references leaves 54-55. In this thesis, we search for parametric reform alternatives so as to achieve a balance in the long term accumulated difference between pension expenditures and revenues of the SSI, the largest pension fund in Turkey, from 2005 to 2060. The projected worker-retiree composition of the pension system is allowed to change al...

  10. 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)

  11. 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 ...

  12. 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.

  13. 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.

  14. Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success

    Science.gov (United States)

    Maxwell, Elisabeth A.; Marshall, Andrea D.; Christensen, Ana B.

    2015-01-01

    Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing. PMID:26413431

  15. Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success

    Directory of Open Access Journals (Sweden)

    Tom Kashiwagi

    2015-08-01

    Full Text Available Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.

  16. 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

  17. 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.

  18. 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.

  19. Fibrillin binds calcium and is coded by cDNAs that reveal a multidomain structure and alternatively spliced exons at the 5[prime] end

    Energy Technology Data Exchange (ETDEWEB)

    Corson, G.M.; Chalberg, S.C.; Charbonneau, N.L.; Sakai, L.Y. (Oregon Health Sciences Univ., Portland (United States)); Dietz, H.C. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))

    1993-08-01

    Fibrillin is an important structural protein of the extracellular matrix. It is a large cysteine-rich glycoprotein with extensive intrachain disulfide bonds, likely contributed by multiple EGF-like repeats. The authors have previously published 6.9 kb of FBN1 cDNA sequence. FBN1 cDNA clones that extend the sequence 3089 bp in the 5[prime] direction are described in this report. The deduced primary structure suggests that fibrillin in composed of multiple domains. The most predominant features the presence of 43 calcium binding EGF-like repeats. They demonstrate here that fibrillin molecules bind calcium. In addition, three alternatively spliced exons at the 5[prime] end are described. Analysis of 5.8 kb of surrounding genomic sequence revealed a 1.8-kb CpG island spanning the alternatively spliced exons and the next downstream exon. Since FBN1 is the gene responsible for Marfan syndrome, the information presented here will be useful in identifying new mutations and in understanding the function of fibrillin in the pathogenesis of the disease. 42 refs., 7 figs.

  20. 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 ...

  1. [Evaluation of visualization of biological stains with the use of alternative light source (ALS) for the purpose of genetic identification. Part I. Blood and saliva stains analysis].

    Science.gov (United States)

    Szeremeta, Michał; Pepiński, Witold; Niemcunowicz-Janica, Anna; Skawrońska, Małgorzata; Sackiewicz, Adam; Ptaszyńska-Sarosiek, Iwona; Okłota, Magdalena

    2010-01-01

    The objective of the investigation was evaluation of visualization of human blood and saliva stains with the use of alternative light source for the purpose of genetic identification. Experimental bloodstains on the bright base were the most clearly seen in the natural light and white light, up to blood dilution of 1:600. Complete typeability of AmpFISTR SGM Plus kit profiles was obtained from bloodstains at dilution 1:1500. Partial AmpFISTR SGM Plus kit profiles were typed from bloodstains at dilutions 1:1750 and 1:2000. Experimental saliva stains on the light-colored base were completely invisible in the natural light and white light, while they were visualized at wavelength range 300-415 nm through yellow goggles, and at wavelength range 300-455 nm through orange goggles at saliva dilution 1: 600. Complete typeability of AmpFISTR SGM Plus kit loci was obtained from saliva stains at dilution 1:1750. Partial AmpFISTR SGM Plus kit profiles were typed from saliva stains at dilution 1:2000. The wavelength of 455 nm and orange goggles were the optimal set for visualization of bloodstains on various, noncontrasting materials. Other useful wavelength/combinations of goggles were CSS light/red goggles. In case of saliva, the most useful general condition for visualization of stains on various, non-contrasting materials was with the wavelength set to 300-415 nm, while wearing yellow goggles. Other useful combinations of wavelength/goggles were 300-455 nm/orange or red goggles, and also CSS light/orange or red goggles.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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...

  8. Alternative security

    International Nuclear Information System (INIS)

    Weston, B.H.

    1990-01-01

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview

  9. Programming Entity Framework Code First

    CERN Document Server

    Lerman, Julia

    2011-01-01

    Take advantage of the Code First data modeling approach in ADO.NET Entity Framework, and learn how to build and configure a model based on existing classes in your business domain. With this concise book, you'll work hands-on with examples to learn how Code First can create an in-memory model and database by default, and how you can exert more control over the model through further configuration. Code First provides an alternative to the database first and model first approaches to the Entity Data Model. Learn the benefits of defining your model with code, whether you're working with an exis

  10. 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.

  11. Alternative additives; Alternative additiver

    Energy Technology Data Exchange (ETDEWEB)

    2007-08-15

    In this project a number of industrial and agricultural waste products have been characterised and evaluated in terms of alkali-getter performance. The intended use is for biomass-fired power stations aiming at reducing corrosion or slagging related problems. The following products have been obtained, characterised and evaluated: 1) Brewery draff 2) Danish de-gassed manure 3) Paper sludge 4) Moulding sand 5) Spent bleaching earth 6) Anorthosite 7) Sand 8) Clay-sludge. Most of the above alternative additive candidates are deemed unsuitable due to insufficient chemical effect and/or expensive requirements for pre-treatment (such as drying and transportation). 3 products were selected for full-scale testing: de-gassed manure, spent bleaching earth and clay slugde. The full scale tests were undertaken at the biomass-fired power stations in Koege, Slagelse and Ensted. Spent bleaching earth (SBE) and clay sludge were the only tested additive candidates that had a proven ability to react with KCl, to thereby reduce Cl-concentrations in deposits, and reduce the deposit flux to superheater tubes. Their performance was shown to nearly as good as commercial additives. De-gassed manure, however, did not evaluate positively due to inhibiting effects of Ca in the manure. Furthermore, de-gassed manure has a high concentration of heavy metals, which imposes a financial burden with regard to proper disposal of the ash by-products. Clay-sludge is a wet clay slurring, and drying and transportation of this product entails substantial costs. Spent bleaching does not require much pre-treatment and is therefore the most promising alternative additive. On the other hand, bleaching earth contains residual plant oil which means that a range of legislation relating to waste combustion comes into play. Not least a waste combustion fee of 330 DKK/tonne. For all alternative (and commercial) additives disposal costs of the increase ash by-products represents a significant cost. This is

  12. 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

  13. 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

  14. 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 ...

  15. 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

  16. 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.

  17. 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)

  18. Production of Novel Ebola Virus-Like Particles from cDNAs: an Alternative to Ebola Virus Generation by Reverse Genetics

    OpenAIRE

    Watanabe, Shinji; Watanabe, Tokiko; Noda, Takeshi; Takada, Ayato; Feldmann, Heinz; Jasenosky, Luke D.; Kawaoka, Yoshihiro

    2004-01-01

    We established a plasmid-based system for generating infectious Ebola virus-like particles (VLPs), which contain an Ebola virus-like minigenome consisting of a negative-sense copy of the green fluorescent protein gene. This system produced nearly 103 infectious particles per ml of supernatant, equivalent to the titer of Ebola virus generated by a reverse genetics system. Interestingly, infectious Ebola VLPs were generated, even without expression of VP24. Transmission and scanning electron mi...

  19. 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...

  20. 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

  1. 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.)

  2. 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...

  3. 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.

  4. 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

  5. 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 ...

  6. 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

  7. 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.

  8. The neurogenetics of alternative splicing.

    Science.gov (United States)

    Vuong, Celine K; Black, Douglas L; Zheng, Sika

    2016-05-01

    Alternative precursor-mRNA splicing is a key mechanism for regulating gene expression in mammals and is controlled by specialized RNA-binding proteins. The misregulation of splicing is implicated in multiple neurological disorders. We describe recent mouse genetic studies of alternative splicing that reveal its critical role in both neuronal development and the function of mature neurons. We discuss the challenges in understanding the extensive genetic programmes controlled by proteins that regulate splicing, both during development and in the adult brain.

  9. L'alternance de code de deux enseignants de francais dans l'enseignement assiste par ordinateur de niveau debutant de langue seconde (Codeswitching in Two French as a Second Language Teachers, Beginning Level, in Computer Assisted Instruction).

    Science.gov (United States)

    Taylor, Alan M.

    2002-01-01

    Investigates the code switching of two French teachers in a computer-assisted language learning (CALL) environment. Highlights the importance of the social dynamic and technical aspects of teachers' codeswitching behaviors. (Author/VWL)

  10. 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.

  11. Genetic analysis of complement C1s deficiency associated with systemic lupus erythematosus highlights alternative splicing of normal C1s gene

    DEFF Research Database (Denmark)

    Amano, Mariane T; Ferriani, Virgínia P L; Florido, Marlene P C

    2008-01-01

    Deficiencies of complement proteins of the classical pathway are strongly associated with the development of autoimmune diseases. Deficiency of C1r has been observed to occur concomitantly with deficiency in C1s and 9 out of 15 reported cases presented systemic lupus erythematosus (SLE). Here, we...... describe a family in which all four children are deficient in C1s but only two of them developed SLE. Hemolytic activity mediated by the alternative and the lectin pathways were normal, but classical pathway activation was absent in all children's sera. C1s was undetectable, while in the parents' sera...

  12. Genetically engineered fusion of MAP-1 and factor H domains 1-5 generates a potent dual upstream inhibitor of both the lectin and alternative complement pathways

    DEFF Research Database (Denmark)

    Nordmaj, Mie Anemone; Munthe-Fog, Lea; Hein, Estrid

    2015-01-01

    Inhibition of the complement cascade has emerged as an option for treatment of a range of diseases. Mannose-binding lectin/ficolin/collectin-associated protein (MAP-1) is a pattern recognition molecule (PRM)-associated inhibitor of the lectin pathway. The central regulator of the alternative......:4 in a solid-phase functional assay, only the first 5 N-terminal domains of complement FH fused to the C-terminal part of full-length MAP-1 chimeric construct were able to combine inhibition of lectin and AP activation with an half maximal inhibitory concentration of ∼ 100 and 20 nM, respectively. No effect...

  13. Iterative nonlinear unfolding code: TWOGO

    International Nuclear Information System (INIS)

    Hajnal, F.

    1981-03-01

    a new iterative unfolding code, TWOGO, was developed to analyze Bonner sphere neutron measurements. The code includes two different unfolding schemes which alternate on successive iterations. The iterative process can be terminated either when the ratio of the coefficient of variations in terms of the measured and calculated responses is unity, or when the percentage difference between the measured and evaluated sphere responses is less than the average measurement error. The code was extensively tested with various known spectra and real multisphere neutron measurements which were performed inside the containments of pressurized water reactors

  14. 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)

  15. 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

  16. Alternative Remedies

    Science.gov (United States)

    ... Home › Aging & Health A to Z › Alternative Remedies Font ... medical treatment prescribed by their healthcare provider. Using this type of alternative therapy along with traditional treatments is ...

  17. Alternative Fuels

    Science.gov (United States)

    Alternative fuels include gaseous fuels such as hydrogen, natural gas, and propane; alcohols such as ethanol, methanol, and butanol; vegetable and waste-derived oils; and electricity. Overview of alternative fuels is here.

  18. Alternating Hemiplegia

    Science.gov (United States)

    ... to the symptoms of the disorder. View Full Definition Treatment Drug therapy including verapamil may help to reduce the ... the more serious form of alternating hemiplegia × ... Definition Alternating hemiplegia is a rare neurological disorder that ...

  19. Efficient convolutional sparse coding

    Science.gov (United States)

    Wohlberg, Brendt

    2017-06-20

    Computationally efficient algorithms may be applied for fast dictionary learning solving the convolutional sparse coding problem in the Fourier domain. More specifically, efficient convolutional sparse coding may be derived within an alternating direction method of multipliers (ADMM) framework that utilizes fast Fourier transforms (FFT) to solve the main linear system in the frequency domain. Such algorithms may enable a significant reduction in computational cost over conventional approaches by implementing a linear solver for the most critical and computationally expensive component of the conventional iterative algorithm. The theoretical computational cost of the algorithm may be reduced from O(M.sup.3N) to O(MN log N), where N is the dimensionality of the data and M is the number of elements in the dictionary. This significant improvement in efficiency may greatly increase the range of problems that can practically be addressed via convolutional sparse representations.

  20. 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...

  1. X-ray image coding

    International Nuclear Information System (INIS)

    1974-01-01

    The invention aims at decreasing the effect of stray radiation in X-ray images. This is achieved by putting a plate between source and object with parallel zones of alternating high and low absorption coefficients for X-radiation. The image is scanned with the help of electronic circuits which decode the signal space coded by the plate, thus removing the stray radiation

  2. Surgical navigation with QR codes

    Directory of Open Access Journals (Sweden)

    Katanacho Manuel

    2016-09-01

    Full Text Available The presented work is an alternative to established measurement systems in surgical navigation. The system is based on camera based tracking of QR code markers. The application uses a single video camera, integrated in a surgical lamp, that captures the QR markers attached to surgical instruments and to the patient.

  3. Genetic selection of peptide aptamers that interact and inhibit both Small protein B and alternative ribosome-rescue factor A of Aeromonas veronii C4

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2016-08-01

    Full Text Available Aeromonas veronii is a pathogenic gram-negative bacterium, which infects a variety of animals and results in mass mortality. The stalled-ribosome rescues are reported to ensure viability and virulence under stress conditions, of which primarily include trans-translation and alternative ribosome-rescue factor A (ArfA in A. veronii. For identification of specific peptides that interact and inhibit the stalled-ribosome rescues, peptide aptamer library (pTRG-SN-peptides was constructed using pTRG as vector and Staphylococcus aureus nuclease (SN as scaffold protein, in which 16 random amino acids were introduced to form an exposed surface loop. In the meantime both Small Protein B (SmpB which acts as one of the key components in trans-translation, and alternative ribosome-rescue factor A (ArfA were inserted to pBT to constitute pBT-SmpB and pBT-ArfA, respectively. The peptide aptamer PA-2 was selected from pTRG-SN-peptides by bacterial two-hybrid system (B2H employing pBT-SmpB or pBT-ArfA as baits. The conserved sites G133K134 and D138K139R140 of C-terminal SmpB were identified by interacting with N-terminal SN, and concurrently the residue K62 of ArfA was recognized by interacting with the surface loop of the specific peptide aptamer PA-2. The expression plasmids pN-SN or pN-PA-2, which combined the duplication origin of pRE112 with the neokanamycin promoter expressing SN or PA-2, were created and transformed into A. veronii C4, separately. The engineered A. veronii C4 which endowing SN or PA-2 expression impaired growth capabilities under stress conditions including temperatures, sucrose, glucose, potassium chloride (KCl and antibiotics, and the stress-related genes rpoS and nhaP were down-regulated significantly by Quantitative Real-time PCR (qRT-PCR when treating in 2.0% KCl. Thus,the engineered A. veronii C4 conferring PA-2 expression might be potentially attenuated vaccine, and also the peptide aptamer PA-2 could develop as anti

  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. Genetic Selection of Peptide Aptamers That Interact and Inhibit Both Small Protein B and Alternative Ribosome-Rescue Factor A of Aeromonas veronii C4.

    Science.gov (United States)

    Liu, Peng; Chen, Yong; Wang, Dan; Tang, Yanqiong; Tang, Hongqian; Song, Haichao; Sun, Qun; Zhang, Yueling; Liu, Zhu

    2016-01-01

    Aeromonas veronii is a pathogenic gram-negative bacterium, which infects a variety of animals and results in mass mortality. The stalled-ribosome rescues are reported to ensure viability and virulence under stress conditions, of which primarily include trans-translation and alternative ribosome-rescue factor A (ArfA) in A. veronii. For identification of specific peptides that interact and inhibit the stalled-ribosome rescues, peptide aptamer library (pTRG-SN-peptides) was constructed using pTRG as vector and Staphylococcus aureus nuclease (SN) as scaffold protein, in which 16 random amino acids were introduced to form an exposed surface loop. In the meantime both Small Protein B (SmpB) which acts as one of the key components in trans-translation, and ArfA were inserted to pBT to constitute pBT-SmpB and pBT-ArfA, respectively. The peptide aptamer PA-2 was selected from pTRG-SN-peptides by bacterial two-hybrid system (B2H) employing pBT-SmpB or pBT-ArfA as baits. The conserved sites G133K134 and D138K139R140 of C-terminal SmpB were identified by interacting with N-terminal SN, and concurrently the residue K62 of ArfA was recognized by interacting with the surface loop of the specific peptide aptamer PA-2. The expression plasmids pN-SN or pN-PA-2, which combined the duplication origin of pRE112 with the neokanamycin promoter expressing SN or PA-2, were created and transformed into A. veronii C4, separately. The engineered A. veronii C4 which endowing SN or PA-2 expression impaired growth capabilities under stress conditions including temperatures, sucrose, glucose, potassium chloride (KCl) and antibiotics, and the stress-related genes rpoS and nhaP were down-regulated significantly by Quantitative Real-time PCR (qRT-PCR) when treating in 2.0% KCl. Thus, the engineered A. veronii C4 conferring PA-2 expression might be potentially attenuated vaccine, and also the peptide aptamer PA-2 could develop as anti-microbial drugs targeted to the ribosome rescued factors in A

  8. Adaptive decoding of convolutional codes

    Directory of Open Access Journals (Sweden)

    K. Hueske

    2007-06-01

    Full Text Available Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

  9. Adaptive decoding of convolutional codes

    Science.gov (United States)

    Hueske, K.; Geldmacher, J.; Götze, J.

    2007-06-01

    Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

  10. Alternative wastewatersystems

    DEFF Research Database (Denmark)

    Dyck-Madsen, Søren; Hoffmann, Birgitte; Gabriel, Søren

    1999-01-01

    The report:-  Communicates experiences from Swedish buildings from the establishment and running of alternative wastewater systems. Communicates pictures of alternative buildings and wastewater systems in Sweden. Gives a short evaluation of the performance and the sustainability of the systems....

  11. 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

  12. 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.

  13. How alternative are alternative fuels?

    OpenAIRE

    Soffritti, Tiziana; Danielis, Romeo

    1998-01-01

    Could alternative fuel vehicles contribute to a substantial reduction of air pollution? Is there a market for alternative fuel vehicles? Could a market be created via a pollution tax? The article answers these questions on the basis of the available estimates.

  14. Alternative detox.

    Science.gov (United States)

    Ernst, E

    2012-01-01

    The concept that alternative therapies can eliminate toxins and toxicants from the body, i.e. 'alternative detox' (AD) is popular. Selected textbooks and articles on the subject of AD. The principles of AD make no sense from a scientific perspective and there is no clinical evidence to support them. The promotion of AD treatments provides income for some entrepreneurs but has the potential to cause harm to patients and consumers. In alternative medicine, simplistic but incorrect concepts such as AD abound. AREAS TIMELY FOR RESEARCH: All therapeutic claims should be scientifically tested before being advertised-and AD cannot be an exception.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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...

  20. Acadian variant of Fanconi syndrome is caused by mitochondrial respiratory chain complex I deficiency due to a non-coding mutation in complex I assembly factor NDUFAF6

    Czech Academy of Sciences Publication Activity Database

    Hartmannová, H.; Piherová, L.; Tauchmannová, Kateřina; Kidd, K.; Acott, P. D.; Crocker, J. F. S.; Oussedik, Y.; Mallet, M.; Hodaňová, K.; Stránecký, V.; Přistoupilová, A.; Barešová, V.; Jedličková, I.; Živná, M.; Sovová, J.; Hůlková, H.; Robins, V.; Vrbacký, Marek; Pecina, Petr; Kaplanová, Vilma; Houštěk, Josef; Mráček, Tomáš; Thibeault, Y.; Bleyer, A. J.; Kmoch, S.

    2016-01-01

    Roč. 25, č. 18 (2016), s. 4062-4079 ISSN 0964-6906 R&D Projects: GA ČR(CZ) GB14-36804G; GA MŠk(CZ) LL1204 Institutional support: RVO:67985823 Keywords : Acadian variant of Fanconi syndrome * mitochondrial complex I deficiency * NDUFAF6 * C8ORF38 * non-coding mutation * alternative splicing variant * protein isoforms Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.340, year: 2016

  1. 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...

  2. 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.

  3. 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".

  4. Language Alternation in University Classrooms

    Science.gov (United States)

    Taha, T. A.

    2008-01-01

    This paper examines the alternate use of Arabic and English in the context of a university classroom, where a policy to use the former language in place of the latter was being implemented. Analysis of a sample of recorded university lectures of English and Arabic medium classes in sciences and humanities reveals that teachers use code switching,…

  5. Cosmic alternatives?

    Science.gov (United States)

    Gregory, Ruth

    2009-04-01

    "Cosmologists are often in error but never in doubt." This pithy characterization by the Soviet physicist Lev Landau sums up the raison d'être of Facts and Speculations in Cosmology. Authors Jayant Narlikar and Geoffrey Burbidge are proponents of a "steady state" theory of cosmology, and they argue that the cosmological community has become fixated on a "Big Bang" dogma, suppressing alternative viewpoints. This book very much does what it says on the tin: it sets out what is known in cosmology, and puts forward the authors' point of view on an alternative to the Big Bang.

  6. Community Perspective of Alternative Methods of keeping ...

    African Journals Online (AJOL)

    UNIBEN

    methods of keeping childhood immunization records based on community's .... An alternative home-based record keeping ... coded before computer entry. Data was managed using the Statistical ..... encounter and also work to ensure accurate.

  7. 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.

  8. 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.

  9. Death of a dogma: eukaryotic mRNAs can code for more than one protein.

    Science.gov (United States)

    Mouilleron, Hélène; Delcourt, Vivian; Roucou, Xavier

    2016-01-08

    mRNAs carry the genetic information that is translated by ribosomes. The traditional view of a mature eukaryotic mRNA is a molecule with three main regions, the 5' UTR, the protein coding open reading frame (ORF) or coding sequence (CDS), and the 3' UTR. This concept assumes that ribosomes translate one ORF only, generally the longest one, and produce one protein. As a result, in the early days of genomics and bioinformatics, one CDS was associated with each protein-coding gene. This fundamental concept of a single CDS is being challenged by increasing experimental evidence indicating that annotated proteins are not the only proteins translated from mRNAs. In particular, mass spectrometry (MS)-based proteomics and ribosome profiling have detected productive translation of alternative open reading frames. In several cases, the alternative and annotated proteins interact. Thus, the expression of two or more proteins translated from the same mRNA may offer a mechanism to ensure the co-expression of proteins which have functional interactions. Translational mechanisms already described in eukaryotic cells indicate that the cellular machinery is able to translate different CDSs from a single viral or cellular mRNA. In addition to summarizing data showing that the protein coding potential of eukaryotic mRNAs has been underestimated, this review aims to challenge the single translated CDS dogma. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Growing Alternatives

    DEFF Research Database (Denmark)

    Bagger-Petersen, Mai Corlin

    2014-01-01

    From 2014, Anhui Province will pilot a reform of the residential land market in China, thus integrating rural Anhui in the national housing market. In contrast, artist and activist Ou Ning has proposed the Bishan time money currency, intending to establish an alternative economic circuit in Bishan...

  11. Alternative Veier

    DEFF Research Database (Denmark)

    Kruse, Tove Elisabeth; Salamonsen, Anita

    reflektioner omkring patienters brug af og erfaringer med alternativ behandling. Patientorganisationer, organisatoner for alternative behandlere og organisationer for læger og medicinstuderende har læst bogens patienthistorier og deres perspektiver lægges frem. Til slut i bogen diskuteres betydningen af de...

  12. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    Science.gov (United States)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

    2015-01-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

  13. Extraordinarily adaptive properties of the genetically encoded amino acids.

    Science.gov (United States)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves, H James

    2015-03-24

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or "chemistry space." Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

  14. Multiplexed coding in the human basal ganglia

    Science.gov (United States)

    Andres, D. S.; Cerquetti, D.; Merello, M.

    2016-04-01

    A classic controversy in neuroscience is whether information carried by spike trains is encoded by a time averaged measure (e.g. a rate code), or by complex time patterns (i.e. a time code). Here we apply a tool to quantitatively analyze the neural code. We make use of an algorithm based on the calculation of the temporal structure function, which permits to distinguish what scales of a signal are dominated by a complex temporal organization or a randomly generated process. In terms of the neural code, this kind of analysis makes it possible to detect temporal scales at which a time patterns coding scheme or alternatively a rate code are present. Additionally, finding the temporal scale at which the correlation between interspike intervals fades, the length of the basic information unit of the code can be established, and hence the word length of the code can be found. We apply this algorithm to neuronal recordings obtained from the Globus Pallidus pars interna from a human patient with Parkinson’s disease, and show that a time pattern coding and a rate coding scheme co-exist at different temporal scales, offering a new example of multiplexed neuronal coding.

  15. Alternative Immune Systems

    Directory of Open Access Journals (Sweden)

    Luis Fernando Cadavid Gutierrez

    2011-09-01

    Full Text Available The immune system in animals is a complex network of molecules, cells and tissues that coordinately maintain the physiological and genetic integrity of the organism. Traditionally, two classes of immunity have been considered, the innate immunity and the adaptive immunity. The former is ancestral, with limited variability and low discrimination. The latter is highly variable, specific and limited to jawed vertebrates. Adaptive immunity is based on antigen receptors that rearrange somatically to generate a nearly unlimited diversity of molecules. Likely, this mechanism of somatic recombination arose as a consequence of a horizontal transfer of transposons and transposases from bacterial genomes in the ancestor of jawed vertebrates. The recent discovery in jawless vertebrates and invertebrates of alternative adaptive immune mechanisms, suggests during evolution different animal groups have found alternative solutions to the problem of immune recognition.

  16. 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...

  17. 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...

  18. 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.

  19. 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....

  20. 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

  1. 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

  2. Energy alternatives

    International Nuclear Information System (INIS)

    Sweet, C.

    1987-01-01

    The designated successor to fossil fuels is nuclear fission/fusion and that turns out to be problematic. Alternative Energy Systems have great potential but political forces seem to be hampering their development and introduction. The technologies are flexible in their use and scale of operation. The learning curve will not be short but neither will it be as long and as costly as nuclear power. It is time that this is recognised and some serious rethinking takes place in what presently passes for energy policies both in the industrialised countries and in the Third World. Alternative energy systems are defined and some of them which are relevant to the United Kingdom are discussed. (author)

  3. 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.

  4. 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....

  5. 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.

  6. 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

  7. Alternative detente

    International Nuclear Information System (INIS)

    Soper, K.; Ryle, M.

    1988-01-01

    The influence of the Chernobyl accident on the disarmament and anti-nuclear movements is discussed. The accident directed attention towards the areas in common rather than the areas of disagreement. It also demonstrated the environmental impact of radioactivity, strengthening the ecological case of the anti-nuclear movement. The issues are discussed for the Western and Eastern bloc countries and the relationship between the two. Sections focus on the Eco-protest, Green politics and economics and on the politics of minority protest and the Green alternative. (U.K.)

  8. 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.

  9. Alternative crops

    International Nuclear Information System (INIS)

    Andreasen, L.M.; Boon, A.D.

    1992-01-01

    Surplus cereal production in the EEC and decreasing product prices, mainly for cereals, has prompted considerable interest for new earnings in arable farming. The objective was to examine whether suggested new crops (fibre, oil, medicinal and alternative grains crops) could be considered as real alternatives. Whether a specific crop can compete economically with cereals and whether there is a market demand for the crop is analyzed. The described possibilities will result in ca. 50,000 hectares of new crops. It is expected that they would not immediately provide increased earnings, but in the long run expected price developments are more positive than for cereals. The area for new crops will not solve the current surplus cereal problem as the area used for new crops is only 3% of that used for cereals. Preconditions for many new crops is further research activities and development work as well as the establishment of processing units and organizational initiatives. Presumably, it is stated, there will then be a basis for a profitable production of new crops for some farmers. (AB) (47 refs.)

  10. 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…

  11. Alternative Fuels Data Center: Federal Laws and Incentives for Electricity

    Science.gov (United States)

    and 49 U.S. Code 47136a) Advanced Technology Vehicle (ATV) and Alternative Fuel Infrastructure Manufacturing Loan Program website and the Alternative Fuel Infrastructure fact sheet. (Reference 42 U.S. Code vehicles and infrastructure. Projects supported with CMAQ funds must demonstrate emissions reductions, be

  12. 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.

  13. Energy alternatives

    International Nuclear Information System (INIS)

    1981-01-01

    English. A special committe of the Canadian House of Commons was established on 23 May 1980 to investigate the use of alternative energy sources such as 'gasohol', liquified coal, solar energy, methanol, wind and tidal power, biomass, and propane. In its final report, the committee envisions an energy system for Canada based on hydrogen and electricity, using solar and geothermal energy for low-grade heat. The committe was not able to say which method of generating electricty would dominate in the next century, although it recommends that fossil fuels should not be used. The fission process is not specifically discussed, but the outlook for fusion was investigated, and continued governmental support of fusion research is recommended. The report proposes some improvements in governmental energy organizations and programs

  14. 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...

  15. ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

    KAUST Repository

    Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

    2012-01-01

    Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

  16. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms.

    Science.gov (United States)

    Mattick, John S

    2003-10-01

    The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoietic development and phenotypic variation. Copyright 2003 Wiley Periodicals, Inc.

  17. 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.

  18. Evaluation of practicality of ASME code, Section XI

    International Nuclear Information System (INIS)

    Mattu, R.K.; Lauderdale, J.R.; Liu, S.N.; Lance, J.J.

    2004-01-01

    Many nuclear power plants have found that it is impractical or unduly burdensome to comply with some ASME Boiler and Pressure Code provisions and have sought relief from those provisions from the Nuclear Regulatory Commission. An Electric Power Research Institute (EPRI) project is evaluating such Code provisions and alternatives to them that will meet the safety intent of the Code with less burden on utilities. The methodology is to extract data from an on-line data base of relief requests since 1980, analyse the data to identify burdensome provisions for which there are satisfactory alternatives, and recommend changes in the Code to the ASME. (author)

  19. Allele-Specific Alternative mRNA processing (ASARP) | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    A software pipeline for prediction of allele-specific alternative RNA processing events using single RNA-seq data. The current version focuses on prediction of alternative splicing and alternative polyadenylation modulated by genetic variants.

  20. 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...

  1. 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.

  2. 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.)

  3. 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 ...

  4. 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...

  5. 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

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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

  11. 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.

  12. Symbol synchronization in convolutionally coded systems

    Science.gov (United States)

    Baumert, L. D.; Mceliece, R. J.; Van Tilborg, H. C. A.

    1979-01-01

    Alternate symbol inversion is sometimes applied to the output of convolutional encoders to guarantee sufficient richness of symbol transition for the receiver symbol synchronizer. A bound is given for the length of the transition-free symbol stream in such systems, and those convolutional codes are characterized in which arbitrarily long transition free runs occur.

  13. Erasure Coded Storage on a Changing Network

    DEFF Research Database (Denmark)

    Sipos, Marton A.; Venkat, Narayan; Oran, David

    2016-01-01

    As faster storage devices become commercially viable alternatives to disk drives, the network is increasingly becoming the bottleneck in achieving good performance in distributed storage systems. This is especially true for erasure coded storage, where the reconstruction of lost data can signific...

  14. 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.

  15. Tri-code inductance control rod position indicator with several multi-coding-bars

    International Nuclear Information System (INIS)

    Shi Jibin; Jiang Yueyuan; Wang Wenran

    2004-01-01

    A control rod position indicator named as tri-code inductance control rod position indicator with multi-coding-bars, which possesses simple structure, reliable operation and high precision, is developed. The detector of the indicator is composed of K coils, a compensatory coil and K coding bars. Each coding bar consists of several sections of strong magnetic cores, several sections of weak magnetic cores and several sections of non-magnetic portions. As the control rod is withdrawn, the coding bars move in the center of the coils respectively, while the constant alternating current passes the coils and makes them to create inductance alternating voltage signals. The outputs of the coils are picked and processed, and the tri-codes indicating rod position can be gotten. Moreover, the coding principle of the detector and its related structure are introduced. The analysis shows that the indicator owns more advantage over the coils-coding rod position indicator, so it can meet the demands of the rod position indicating in nuclear heating reactor (NHR). (authors)

  16. DNA Barcoding through Quaternary LDPC Codes.

    Science.gov (United States)

    Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

    2015-01-01

    For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).

  17. DNA Barcoding through Quaternary LDPC Codes.

    Directory of Open Access Journals (Sweden)

    Elizabeth Tapia

    Full Text Available For many parallel applications of Next-Generation Sequencing (NGS technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH or have intrinsic poor error correcting abilities (Hamming. Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9 at the expense of a rate of read losses just in the order of 10(-6.

  18. 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)

  19. 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.

  20. Resolving Ethical Disputes Through Arbitration: An Alternative to Code Penalties.

    Science.gov (United States)

    Barwis, Gail Lund

    Arbitration cases involving journalism ethics can be grouped into three major categories: outside activities that lead to conflicts of interest, acceptance of gifts that compromise journalistic objectivity, and writing false or misleading information or failing to check facts or correct errors. In most instances, failure to adhere to ethical…

  1. Alternative Fuels Data Center: E85 Codes and Standards

    Science.gov (United States)

    confused with beverage alcohol. Cigarettes and other open ignition sources should never be allowed in Ethanol Incentives and Laws, by State More Ethanol Data | All Maps & Data Case Studies California Ramps Up Biofuels Infrastructure More Ethanol Case Studies | All Case Studies Publications Handbook for

  2. Coding and transmission of subband coded images on the Internet

    Science.gov (United States)

    Wah, Benjamin W.; Su, Xiao

    2001-09-01

    Subband-coded images can be transmitted in the Internet using either the TCP or the UDP protocol. Delivery by TCP gives superior decoding quality but with very long delays when the network is unreliable, whereas delivery by UDP has negligible delays but with degraded quality when packets are lost. Although images are delivered currently over the Internet by TCP, we study in this paper the use of UDP to deliver multi-description reconstruction-based subband-coded images. First, in order to facilitate recovery from UDP packet losses, we propose a joint sender-receiver approach for designing optimized reconstruction-based subband transform (ORB-ST) in multi-description coding (MDC). Second, we carefully evaluate the delay-quality trade-offs between the TCP delivery of SDC images and the UDP and combined TCP/UDP delivery of MDC images. Experimental results show that our proposed ORB-ST performs well in real Internet tests, and UDP and combined TCP/UDP delivery of MDC images provide a range of attractive alternatives to TCP delivery.

  3. 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)

  4. 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

  5. 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)

  6. 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.

  7. Vehicle Codes and Standards: Overview and Gap Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Blake, C.; Buttner, W.; Rivkin, C.

    2010-02-01

    This report identifies gaps in vehicle codes and standards and recommends ways to fill the gaps, focusing on six alternative fuels: biodiesel, natural gas, electricity, ethanol, hydrogen, and propane.

  8. 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....

  9. 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 ...

  10. 21 CFR 201.25 - Bar code label requirements.

    Science.gov (United States)

    2010-04-01

    ... Number/Uniform Code Council (EAN.UCC) or Health Industry Business Communications Council (HIBCC... alternative regulatory program or method of product use renders the bar code unnecessary for patient safety... Evaluation and Research, Food and Drug Administration, 5600 Fishers Lane, Rockville, MD 20857 (requests...

  11. Context based Coding of Quantized Alpha Planes for Video Objects

    DEFF Research Database (Denmark)

    Aghito, Shankar Manuel; Forchhammer, Søren

    2002-01-01

    In object based video, each frame is a composition of objects that are coded separately. The composition is performed through the alpha plane that represents the transparency of the object. We present an alternative to MPEG-4 for coding of alpha planes that considers their specific properties....... Comparisons in terms of rate and distortion are provided, showing that the proposed coding scheme for still alpha planes is better than the algorithms for I-frames used in MPEG-4....

  12. 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...

  13. 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.

  14. 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.)

  15. 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).

  16. 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)

  17. 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

  18. 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

  19. 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

  20. Future trends in image coding

    Science.gov (United States)

    Habibi, Ali

    1993-01-01

    The objective of this article is to present a discussion on the future of image data compression in the next two decades. It is virtually impossible to predict with any degree of certainty the breakthroughs in theory and developments, the milestones in advancement of technology and the success of the upcoming commercial products in the market place which will be the main factors in establishing the future stage to image coding. What we propose to do, instead, is look back at the progress in image coding during the last two decades and assess the state of the art in image coding today. Then, by observing the trends in developments of theory, software, and hardware coupled with the future needs for use and dissemination of imagery data and the constraints on the bandwidth and capacity of various networks, predict the future state of image coding. What seems to be certain today is the growing need for bandwidth compression. The television is using a technology which is half a century old and is ready to be replaced by high definition television with an extremely high digital bandwidth. Smart telephones coupled with personal computers and TV monitors accommodating both printed and video data will be common in homes and businesses within the next decade. Efficient and compact digital processing modules using developing technologies will make bandwidth compressed imagery the cheap and preferred alternative in satellite and on-board applications. In view of the above needs, we expect increased activities in development of theory, software, special purpose chips and hardware for image bandwidth compression in the next two decades. The following sections summarize the future trends in these areas.

  1. 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 ...

  2. 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.

  3. 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.

  4. Alternative Fuel Guidelines for Alternative Transportation Systems.

    Science.gov (United States)

    2011-01-31

    The Volpe Center documented the increased use of alternative fuels on vehicles owned and operated by federal land management agencies. For each alternative fuel type, the Volpe Center documented the availability of vehicles, fueling mechanisms and pr...

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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

  12. 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 ...

  13. 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...

  14. 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)

  15. 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)

  16. Using genetic algorithms for calibrating simplified models of nuclear reactor dynamics

    International Nuclear Information System (INIS)

    Marseguerra, Marzio; Zio, Enrico; Canetta, Raffaele

    2004-01-01

    In this paper the use of genetic algorithms for the estimation of the effective parameters of a model of nuclear reactor dynamics is investigated. The calibration of the effective parameters is achieved by best fitting the model responses of the quantities of interest (e.g., reactor power, average fuel and coolant temperatures) to the actual evolution profiles, here simulated by the Quandry based reactor kinetics (Quark) code available from the Nuclear Energy Agency. Alternative schemes of single- and multi-objective optimization are investigated. The efficiency of convergence of the algorithm with respect to the different effective parameters to be calibrated is studied with reference to the physical relationships involved

  17. Using genetic algorithms for calibrating simplified models of nuclear reactor dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Marseguerra, Marzio E-mail: marzio.marseguerra@polimi.it; Zio, Enrico E-mail: enrico.zio@polimi.it; Canetta, Raffaele

    2004-07-01

    In this paper the use of genetic algorithms for the estimation of the effective parameters of a model of nuclear reactor dynamics is investigated. The calibration of the effective parameters is achieved by best fitting the model responses of the quantities of interest (e.g., reactor power, average fuel and coolant temperatures) to the actual evolution profiles, here simulated by the Quandry based reactor kinetics (Quark) code available from the Nuclear Energy Agency. Alternative schemes of single- and multi-objective optimization are investigated. The efficiency of convergence of the algorithm with respect to the different effective parameters to be calibrated is studied with reference to the physical relationships involved.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. Distributed Electrical Power Generation: Summary of Alternative Available Technologies

    National Research Council Canada - National Science Library

    Scott, Sarah

    2003-01-01

    .... While distributed generation (DG) technologies offer many of the benefits of alternative, efficient energy sources, few DG systems can currently be commercially purchased "off the shelf", and complicated codes and standards deter potential users...

  3. 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.

  4. 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 ...

  5. 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.

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. 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 ...

  11. Fundamentals of the DIGES code

    Energy Technology Data Exchange (ETDEWEB)

    Simos, N.; Philippacopoulos, A.J.

    1994-08-01

    Recently the authors have completed the development of the DIGES code (Direct GEneration of Spectra) for the US Nuclear Regulatory Commission. This paper presents the fundamental theoretical aspects of the code. The basic modeling involves a representation of typical building-foundation configurations as multi degree-of-freedom dynamic which are subjected to dynamic inputs in the form of applied forces or pressure at the superstructure or in the form of ground motions. Both the deterministic as well as the probabilistic aspects of DIGES are described. Alternate ways of defining the seismic input for the estimation of in-structure spectra and their consequences in terms of realistically appraising the variability of the structural response is discussed in detaiL These include definitions of the seismic input by ground acceleration time histories, ground response spectra, Fourier amplitude spectra or power spectral densities. Conversions of one of these forms to another due to requirements imposed by certain analysis techniques have been shown to lead, in certain cases, in controversial results. Further considerations include the definition of the seismic input as the excitation which is directly applied at the foundation of a structure or as the ground motion of the site of interest at a given point. In the latter case issues related to the transferring of this motion to the foundation through convolution/deconvolution and generally through kinematic interaction approaches are considered.

  12. 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.

  13. 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....

  14. 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

  15. 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

  16. 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...

  17. 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)

  18. 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.

  19. 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

  20. 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...

  1. 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.

  2. 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)

  3. 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.

  4. 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 ...

  5. 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

  6. 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....

  7. 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)

  8. 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

  9. 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.

  10. 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 ...

  11. Alternating hemiplegia of childhood in Denmark

    DEFF Research Database (Denmark)

    Høi-Hansen, Christina; Dali, Christine I.; Lyngbye, Troels Johan Brünnich

    2014-01-01

    Alternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder characterized by early-onset recurrent distinctive hemiplegic episodes commonly accompanied by other paroxysmal features and developmental impairment. De novo mutations in ATP1A3 were recently identified as a genetic...

  12. Fast comparison of IS radar code sequences for lag profile inversion

    Directory of Open Access Journals (Sweden)

    M. S. Lehtinen

    2008-08-01

    Full Text Available A fast method for theoretically comparing the posteriori variances produced by different phase code sequences in incoherent scatter radar (ISR experiments is introduced. Alternating codes of types 1 and 2 are known to be optimal for selected range resolutions, but the code sets are inconveniently long for many purposes like ground clutter estimation and in cases where coherent echoes from lower ionospheric layers are to be analyzed in addition to standard F-layer spectra.

    The method is used in practice for searching binary code quads that have estimation accuracy almost equal to that of much longer alternating code sets. Though the code sequences can consist of as few as four different transmission envelopes, the lag profile estimation variances are near to the theoretical minimum. Thus the short code sequence is equally good as a full cycle of alternating codes with the same pulse length and bit length. The short code groups cannot be directly decoded, but the decoding is done in connection with more computationally expensive lag profile inversion in data analysis.

    The actual code searches as well as the analysis and real data results from the found short code searches are explained in other papers sent to the same issue of this journal. We also discuss interesting subtle differences found between the different alternating codes by this method. We assume that thermal noise dominates the incoherent scatter signal.

  13. Alternative Substrate Metabolism in Yarrowia lipolytica

    Directory of Open Access Journals (Sweden)

    Michael Spagnuolo

    2018-05-01

    Full Text Available Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.

  14. Code cases for implementing risk-based inservice testing in the ASME OM code

    Energy Technology Data Exchange (ETDEWEB)

    Rowley, C.W.

    1996-12-01

    Historically inservice testing has been reasonably effective, but quite costly. Recent applications of plant PRAs to the scope of the IST program have demonstrated that of the 30 pumps and 500 valves in the typical plant IST program, less than half of the pumps and ten percent of the valves are risk significant. The way the ASME plans to tackle this overly-conservative scope for IST components is to use the PRA and plant expert panels to create a two tier IST component categorization scheme. The PRA provides the quantitative risk information and the plant expert panel blends the quantitative and deterministic information to place the IST component into one of two categories: More Safety Significant Component (MSSC) or Less Safety Significant Component (LSSC). With all the pumps and valves in the IST program placed in MSSC or LSSC categories, two different testing strategies will be applied. The testing strategies will be unique for the type of component, such as centrifugal pump, positive displacement pump, MOV, AOV, SOV, SRV, PORV, HOV, CV, and MV. A series of OM Code Cases are being developed to capture this process for a plant to use. One Code Case will be for Component Importance Ranking. The remaining Code Cases will develop the MSSC and LSSC testing strategy for type of component. These Code Cases are planned for publication in early 1997. Later, after some industry application of the Code Cases, the alternative Code Case requirements will gravitate to the ASME OM Code as appendices.

  15. Code cases for implementing risk-based inservice testing in the ASME OM code

    International Nuclear Information System (INIS)

    Rowley, C.W.

    1996-01-01

    Historically inservice testing has been reasonably effective, but quite costly. Recent applications of plant PRAs to the scope of the IST program have demonstrated that of the 30 pumps and 500 valves in the typical plant IST program, less than half of the pumps and ten percent of the valves are risk significant. The way the ASME plans to tackle this overly-conservative scope for IST components is to use the PRA and plant expert panels to create a two tier IST component categorization scheme. The PRA provides the quantitative risk information and the plant expert panel blends the quantitative and deterministic information to place the IST component into one of two categories: More Safety Significant Component (MSSC) or Less Safety Significant Component (LSSC). With all the pumps and valves in the IST program placed in MSSC or LSSC categories, two different testing strategies will be applied. The testing strategies will be unique for the type of component, such as centrifugal pump, positive displacement pump, MOV, AOV, SOV, SRV, PORV, HOV, CV, and MV. A series of OM Code Cases are being developed to capture this process for a plant to use. One Code Case will be for Component Importance Ranking. The remaining Code Cases will develop the MSSC and LSSC testing strategy for type of component. These Code Cases are planned for publication in early 1997. Later, after some industry application of the Code Cases, the alternative Code Case requirements will gravitate to the ASME OM Code as appendices

  16. Alternate superior Julia sets

    International Nuclear Information System (INIS)

    Yadav, Anju; Rani, Mamta

    2015-01-01

    Alternate Julia sets have been studied in Picard iterative procedures. The purpose of this paper is to study the quadratic and cubic maps using superior iterates to obtain Julia sets with different alternate structures. Analytically, graphically and computationally it has been shown that alternate superior Julia sets can be connected, disconnected and totally disconnected, and also fattier than the corresponding alternate Julia sets. A few examples have been studied by applying different type of alternate structures

  17. 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.

  18. 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.)

  19. 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].

  20. 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...

  1. 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.

  2. 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

  3. 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.)

  4. 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.

  5. 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...

  6. 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 ...

  7. Automated searching for quantum subsystem codes

    International Nuclear Information System (INIS)

    Crosswhite, Gregory M.; Bacon, Dave

    2011-01-01

    Quantum error correction allows for faulty quantum systems to behave in an effectively error-free manner. One important class of techniques for quantum error correction is the class of quantum subsystem codes, which are relevant both to active quantum error-correcting schemes as well as to the design of self-correcting quantum memories. Previous approaches for investigating these codes have focused on applying theoretical analysis to look for interesting codes and to investigate their properties. In this paper we present an alternative approach that uses computational analysis to accomplish the same goals. Specifically, we present an algorithm that computes the optimal quantum subsystem code that can be implemented given an arbitrary set of measurement operators that are tensor products of Pauli operators. We then demonstrate the utility of this algorithm by performing a systematic investigation of the quantum subsystem codes that exist in the setting where the interactions are limited to two-body interactions between neighbors on lattices derived from the convex uniform tilings of the plane.

  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. Comparative study of Thermal Hydraulic Analysis Codes for Pressurized Water Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang Hoon; Jang, Mi Suk; Han, Kee Soo [Nuclear Engineering Service and Solution Co. Ltd., Daejeon (Korea, Republic of)

    2015-05-15

    Various codes are used for the thermal hydraulic analysis of nuclear reactors. The use of some codes among these is limited by user and some codes are not even open to general person. Thus, the use of alternative code is considered for some analysis. In this study, simple thermal hydraulic behaviors are analyzed using three codes to show that alternative codes are possible for the analysis of nuclear reactors. We established three models of the simple u-tube manometer using three different codes. RELAP5 (Reactor Excursion and Leak Analysis Program), SPACE (Safety and Performance Analysis CodE for nuclear power Plants), GOTHIC (Generation of Thermal Hydraulic Information for Containments) are selected for this analysis. RELAP5 is widely used codes for the analysis of system behavior of PWRs. SPACE has been developed based on RELAP5 for the analysis of system behavior of PWRs and licensing of the code is in progress. And GOTHIC code also has been widely used for the analysis of thermal hydraulic behavior in the containment system. The internal behavior of u-tube manometer was analyzed by RELAP5, SPACE and GOTHIC codes. The general transient behavior was similar among 3 codes. However, the stabilized status of the transient period analyzed by REPAP5 was different from the other codes. It would be resulted from the different physical models used in the other codes, which is specialized for the multi-phase thermal hydraulic behavior analysis.

  10. 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.

  11. 75 FR 24323 - American Society of Mechanical Engineers (ASME) Codes and New and Revised ASME Code Cases

    Science.gov (United States)

    2010-05-04

    ...The NRC proposes to amend its regulations to incorporate by reference the 2005 Addenda through 2008 Addenda of Section III, Division 1, and the 2005 Addenda through 2008 Addenda of Section XI, Division 1, of the ASME Boiler and Pressure Vessel Code (ASME B&PV Code); and the 2005 Addenda and 2006 Addenda of the ASME Code for Operation and Maintenance of Nuclear Power Plants (ASME OM Code). The NRC also proposes to incorporate by reference ASME Code Case N-722-1, ``Additional Examinations for PWR Pressure Retaining Welds in Class 1 Components Fabricated With Alloy 600/82/182 Materials Section XI, Division 1,'' and Code Case N-770, ``Alternative Examination Requirements and Acceptance Standards for Class 1 PWR [Pressurized- Water Reactor] Piping and Vessel Nozzle Butt Welds Fabricated with UNS N06082 or UNS W86182 Weld Filler Material with or without Application of Listed Mitigation Activities.''

  12. 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

  13. 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)

  14. 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.

  15. 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)

  16. 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.

  17. 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

  18. 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.

  19. 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 ...

  20. Exploring geovisualization symbology for landscape genetics

    DEFF Research Database (Denmark)

    Aoidh, Eoin Mac; Martinsohn, Jann Th.; Maes, Gregory E.

    2013-01-01

    or genetic expertise. While specialist applications exist, alternative accessible solutions do not provide adequate support for the visualization of multi‐attribute spatially referenced genetic population structure information. As a solution, we document our exploration for an appropriate symbology...... to communicate landscape genetic information through an accessible, web‐based interface. A full problem description, review of available technologies, development rationale, and discussion of the symbology exploration are provided.......Landscape genetics, which considers genetic population structure in the context of spatially referenced parameters in the surrounding landscape, has been shown to be extremely useful for wildlife management. Unfortunately its widespread uptake beyond the research community is hampered due to a lack...

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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)

  6. 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...

  7. 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...

  8. Radiological impacts of Jackpile-Paguate uranium mines: an analysis of alternatives of decommissioning

    International Nuclear Information System (INIS)

    Momeni, M.H.; Tsai, S.Y.H.; Yang, J.Y.; Gureghian, A.B.; Dungey, C.E.

    1983-03-01

    Potential pathways of radiation exposure and radiation-induced genetic and somatic effects from materials at the mine complex under five alternatives of decommissioning were analyzed using UDAD and PRIM computer codes. The principal pathways of exposure included in the analysis were inhalation of airborne radionuclides, ingestion of food and water containing radionuclides, and extended exposure to gamma and beta radiation from either airborne or ground-deposited radionuclides. The alternatives of decommissioning include (A) No Action (site will be fenced, otherwise left as it is), (B) No Future Use (site will be fenced and all disturbed area will be covered with 30 cm of soil, no grazing on the site); (C1) Grazing Land Use as developed by Anaconda Company (protore, waste piles, and open pits covered with 120 cm of soil, the remainder of the disturbed areas covered with 30 cm of soil, pits backfilled 90 cm above the equilibrium groundwater recovery level, no human habitation or farming allowed on the mine site, but grazing would be allowed); (C2) Grazing Land Use as developed by US Department of the Interior (similar to Alternative C1, but the pits covered with 300 cm of soil above the groundwater recovery level); and (D) Maximum Future Use (similar to Alternative C2, except construction of commercial and industrial facilities, storage, recreation, and further mining would be allowed). Radiation doses from atmospheric transport and ingestion of radionuclides were calculated, and somatic and genetic effects in individuals living within 80 km from the mine complex were predicted. Hydrological flow patterns in the mine area were analyzed to determine the potential for future contamination of surface water and groundwater and to determine the groundwater recovery level after reclamation, thus permitting incorporation of corrective actions into the reclamation procedures

  9. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution

    Science.gov (United States)

    Mayer, R.E.; Bofill-Mas, S.; Egle, L.; Reischer, G.H.; Schade, M.; Fernandez-Cassi, X.; Fuchs, W.; Mach, R.L.; Lindner, G.; Kirschner, A.; Gaisbauer, M.; Piringer, H.; Blaschke, A.P.; Girones, R.; Zessner, M.; Sommer, R.; Farnleitner, A.H.

    2016-01-01

    This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml−1) and biologically treated wastewater samples (median log10 6.2–6.5 ME 100 ml−1), irrespective of plant size, type and time of the season (n = 53–65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3–3.0) and treated wastewater (s* = 3.7–4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support if

  10. 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.

  11. The metaethics of nursing codes of ethics and conduct.

    Science.gov (United States)

    Snelling, Paul C

    2016-10-01

    Nursing codes of ethics and conduct are features of professional practice across the world, and in the UK, the regulator has recently consulted on and published a new code. Initially part of a professionalising agenda, nursing codes have recently come to represent a managerialist and disciplinary agenda and nursing can no longer be regarded as a self-regulating profession. This paper argues that codes of ethics and codes of conduct are significantly different in form and function similar to the difference between ethics and law in everyday life. Some codes successfully integrate these two functions within the same document, while others, principally the UK Code, conflate them resulting in an ambiguous document unable to fulfil its functions effectively. The paper analyses the differences between ethical-codes and conduct-codes by discussing titles, authorship, level, scope for disagreement, consequences of transgression, language and finally and possibly most importantly agent-centeredness. It is argued that conduct-codes cannot require nurses to be compassionate because compassion involves an emotional response. The concept of kindness provides a plausible alternative for conduct-codes as it is possible to understand it solely in terms of acts. But if kindness is required in conduct-codes, investigation and possible censure follows from its absence. Using examples it is argued that there are at last five possible accounts of the absence of kindness. As well as being potentially problematic for disciplinary panels, difficulty in understanding the features of blameworthy absence of kindness may challenge UK nurses who, following a recently introduced revalidation procedure, are required to reflect on their practice in relation to The Code. It is concluded that closer attention to metaethical concerns by code writers will better support the functions of their issuing organisations. © 2016 John Wiley & Sons Ltd.

  12. 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…

  13. 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...

  14. 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.)

  15. 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)

  16. 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

  17. 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

  18. 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...

  19. 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.

  20. 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)

  1. 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

  2. Corporate governance through codes

    NARCIS (Netherlands)

    Haxhi, I.; Aguilera, R.V.; Vodosek, M.; den Hartog, D.; McNett, J.M.

    2014-01-01

    The UK's 1992 Cadbury Report defines corporate governance (CG) as the system by which businesses are directed and controlled. CG codes are a set of best practices designed to address deficiencies in the formal contracts and institutions by suggesting prescriptions on the preferred role and

  3. Error Correcting Codes -34 ...

    Indian Academy of Sciences (India)

    information and coding theory. A large scale relay computer had failed to deliver the expected results due to a hardware fault. Hamming, one of the active proponents of computer usage, was determined to find an efficient means by which computers could detect and correct their own faults. A mathematician by train-.

  4. Broadcast Coded Slotted ALOHA

    DEFF Research Database (Denmark)

    Ivanov, Mikhail; Brännström, Frederik; Graell i Amat, Alexandre

    2016-01-01

    We propose an uncoordinated medium access control (MAC) protocol, called all-to-all broadcast coded slotted ALOHA (B-CSA) for reliable all-to-all broadcast with strict latency constraints. In B-CSA, each user acts as both transmitter and receiver in a half-duplex mode. The half-duplex mode gives ...

  5. Software Defined Coded Networking

    DEFF Research Database (Denmark)

    Di Paola, Carla; Roetter, Daniel Enrique Lucani; Palazzo, Sergio

    2017-01-01

    the quality of each link and even across neighbouring links and using simulations to show that an additional reduction of packet transmission in the order of 40% is possible. Second, to advocate for the use of network coding (NC) jointly with software defined networking (SDN) providing an implementation...

  6. New code of conduct

    CERN Multimedia

    Laëtitia Pedroso

    2010-01-01

    During his talk to the staff at the beginning of the year, the Director-General mentioned that a new code of conduct was being drawn up. What exactly is it and what is its purpose? Anne-Sylvie Catherin, Head of the Human Resources (HR) Department, talked to us about the whys and wherefores of the project.   Drawing by Georges Boixader from the cartoon strip “The World of Particles” by Brian Southworth. A code of conduct is a general framework laying down the behaviour expected of all members of an organisation's personnel. “CERN is one of the very few international organisations that don’t yet have one", explains Anne-Sylvie Catherin. “We have been thinking about introducing a code of conduct for a long time but lacked the necessary resources until now”. The call for a code of conduct has come from different sources within the Laboratory. “The Equal Opportunities Advisory Panel (read also the "Equal opportuni...

  7. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  8. Decoding Codes on Graphs

    Indian Academy of Sciences (India)

    having a probability Pi of being equal to a 1. Let us assume ... equal to a 0/1 has no bearing on the probability of the. It is often ... bits (call this set S) whose individual bits add up to zero ... In the context of binary error-correct~ng codes, specifi-.

  9. The Redox Code.

    Science.gov (United States)

    Jones, Dean P; Sies, Helmut

    2015-09-20

    The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.

  10. Spurious correlations and inference in landscape genetics

    Science.gov (United States)

    Samuel A. Cushman; Erin L. Landguth

    2010-01-01

    Reliable interpretation of landscape genetic analyses depends on statistical methods that have high power to identify the correct process driving gene flow while rejecting incorrect alternative hypotheses. Little is known about statistical power and inference in individual-based landscape genetics. Our objective was to evaluate the power of causalmodelling with partial...

  11. Complementary and Alternative Medicine

    Science.gov (United States)

    ... for Educators Search English Español Complementary and Alternative Medicine KidsHealth / For Teens / Complementary and Alternative Medicine What's ... a replacement. How Is CAM Different From Conventional Medicine? Conventional medicine is based on scientific knowledge of ...

  12. Z₂-double cyclic codes

    OpenAIRE

    Borges, J.

    2014-01-01

    A binary linear code C is a Z2-double cyclic code if the set of coordinates can be partitioned into two subsets such that any cyclic shift of the coordinates of both subsets leaves invariant the code. These codes can be identified as submodules of the Z2[x]-module Z2[x]/(x^r − 1) × Z2[x]/(x^s − 1). We determine the structure of Z2-double cyclic codes giving the generator polynomials of these codes. The related polynomial representation of Z2-double cyclic codes and its duals, and the relation...

  13. Coding for urologic office procedures.

    Science.gov (United States)

    Dowling, Robert A; Painter, Mark

    2013-11-01

    This article summarizes current best practices for documenting, coding, and billing common office-based urologic procedures. Topics covered include general principles, basic and advanced urologic coding, creation of medical records that support compliant coding practices, bundled codes and unbundling, global periods, modifiers for procedure codes, when to bill for evaluation and management services during the same visit, coding for supplies, and laboratory and radiology procedures pertinent to urology practice. Detailed information is included for the most common urology office procedures, and suggested resources and references are provided. This information is of value to physicians, office managers, and their coding staff. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  15. CONDOR: neutronic code for fuel elements calculation with rods

    International Nuclear Information System (INIS)

    Villarino, E.A.

    1990-01-01

    CONDOR neutronic code is used for the calculation of fuel elements formed by fuel rods. The method employed to obtain the neutronic flux is that of collision probabilities in a multigroup scheme on two-dimensional geometry. This code utilizes new calculation algorithms and normalization of such collision probabilities. Burn-up calculations can be made before the alternative of applying variational methods for response flux calculations or those corresponding to collision normalization. (Author) [es

  16. RADTRAN: a computer code to analyze transportation of radioactive material

    International Nuclear Information System (INIS)

    Taylor, J.M.; Daniel, S.L.

    1977-04-01

    A computer code is presented which predicts the environmental impact of any specific scheme of radioactive material transportation. Results are presented in terms of annual latent cancer fatalities and annual early fatility probability resulting from exposure, during normal transportation or transport accidents. The code is developed in a generalized format to permit wide application including normal transportation analysis; consideration of alternatives; and detailed consideration of specific sectors of industry

  17. 76 FR 36231 - American Society of Mechanical Engineers (ASME) Codes and New and Revised ASME Code Cases

    Science.gov (United States)

    2011-06-21

    ...The NRC is amending its regulations to incorporate by reference the 2005 Addenda (July 1, 2005) and 2006 Addenda (July 1, 2006) to the 2004 ASME Boiler and Pressure Vessel Code, Section III, Division 1; 2007 ASME Boiler and Pressure Vessel Code, Section III, Division 1, 2007 Edition (July 1, 2007), with 2008a Addenda (July 1, 2008); 2005 Addenda (July 1, 2005) and 2006 Addenda (July 1, 2006) to the 2004 ASME Boiler and Pressure Vessel Code, Section XI, Division 1; 2007 ASME Boiler and Pressure Vessel Code, Section XI, Division 1, 2007 Edition (July 1, 2007), with 2008a Addenda (July 1, 2008); and 2005 Addenda, ASME OMa Code-2005 (approved July 8, 2005) and 2006 Addenda, ASME OMb Code-2006 (approved July 6, 2006) to the 2004 ASME Code for Operation and Maintenance of Nuclear Power Plants (OM Code). The NRC is also incorporating by reference (with conditions on their use) ASME Boiler and Pressure Vessel Code Case N-722-1, ``Additional Examinations for PWR Pressure Retaining Welds in Class 1 Components Fabricated with Alloy 600/82/182 Materials, Section XI, Division 1,'' Supplement 8, ASME approval date: January 26, 2009, and ASME Boiler and Pressure Vessel Code Case N-770-1, ``Alternative Examination Requirements and Acceptance Standards for Class 1 PWR Piping and Vessel Nozzle Butt Welds Fabricated With UNS N06082 or UNS W86182 Weld Filler Material With or Without Application of Listed Mitigation Activities, Section XI, Division 1,'' ASME approval date: December 25, 2009.

  18. Alternative way of life

    International Nuclear Information System (INIS)

    Fischer, C.

    1980-01-01

    The volume describes the reasons why more and more people seek alternative ways of life, the theoretical background and what alternative life means in practice as well as the sociological significance and history of the alternative movement. It also contains statements of persons who have 'got out' and advice on energy-saving. (HSCH) [de

  19. Building codes as barriers to solar heating and cooling of buildings

    Energy Technology Data Exchange (ETDEWEB)

    Meeker, F.O. III

    1978-04-01

    The application of building codes to solar energy systems for heating and cooling of buildings is discussed, using as typical codes the three model building codes most widely adopted by states and localities. Some potential barriers to solar energy systems are found, federal and state programs to deal with these barriers are discussed, and alternatives are suggested. To remedy this, a federal program is needed to encourage state adoption of standards and acceptance of certification of solar systems for code approval, and to encourage revisions to codes based on model legislation prepared for the federal government by the model codes groups.

  20. Essential idempotents and simplex codes

    Directory of Open Access Journals (Sweden)

    Gladys Chalom

    2017-01-01

    Full Text Available We define essential idempotents in group algebras and use them to prove that every mininmal abelian non-cyclic code is a repetition code. Also we use them to prove that every minimal abelian code is equivalent to a minimal cyclic code of the same length. Finally, we show that a binary cyclic code is simplex if and only if is of length of the form $n=2^k-1$ and is generated by an essential idempotent.

  1. Rate-adaptive BCH codes for distributed source coding

    DEFF Research Database (Denmark)

    Salmistraro, Matteo; Larsen, Knud J.; Forchhammer, Søren

    2013-01-01

    This paper considers Bose-Chaudhuri-Hocquenghem (BCH) codes for distributed source coding. A feedback channel is employed to adapt the rate of the code during the decoding process. The focus is on codes with short block lengths for independently coding a binary source X and decoding it given its...... strategies for improving the reliability of the decoded result are analyzed, and methods for estimating the performance are proposed. In the analysis, noiseless feedback and noiseless communication are assumed. Simulation results show that rate-adaptive BCH codes achieve better performance than low...... correlated side information Y. The proposed codes have been analyzed in a high-correlation scenario, where the marginal probability of each symbol, Xi in X, given Y is highly skewed (unbalanced). Rate-adaptive BCH codes are presented and applied to distributed source coding. Adaptive and fixed checking...

  2. A novel neutron energy spectrum unfolding code using particle swarm optimization

    International Nuclear Information System (INIS)

    Shahabinejad, H.; Sohrabpour, M.

    2017-01-01

    A novel neutron Spectrum Deconvolution using Particle Swarm Optimization (SDPSO) code has been developed to unfold the neutron spectrum from a pulse height distribution and a response matrix. The Particle Swarm Optimization (PSO) imitates the bird flocks social behavior to solve complex optimization problems. The results of the SDPSO code have been compared with those of the standard spectra and recently published Two-steps Genetic Algorithm Spectrum Unfolding (TGASU) code. The TGASU code have been previously compared with the other codes such as MAXED, GRAVEL, FERDOR and GAMCD and shown to be more accurate than the previous codes. The results of the SDPSO code have been demonstrated to match well with those of the TGASU code for both under determined and over-determined problems. In addition the SDPSO has been shown to be nearly two times faster than the TGASU code. - Highlights: • Introducing a novel method for neutron spectrum unfolding. • Implementation of a particle swarm optimization code for neutron unfolding. • Comparing results of the PSO code with those of recently published TGASU code. • Match results of the PSO code with those of TGASU code. • Greater convergence rate of implemented PSO code than TGASU code.

  3. Parallel and vector implementation of APROS simulator code

    International Nuclear Information System (INIS)

    Niemi, J.; Tommiska, J.

    1990-01-01

    In this paper the vector and parallel processing implementation of a general purpose simulator code is discussed. In this code the utilization of vector processing is straightforward. In addition to the loop level parallel processing, the functional decomposition and the domain decomposition have been considered. Results represented for a PWR-plant simulation illustrate the potential speed-up factors of the alternatives. It turns out that the loop level parallelism and the domain decomposition are the most promising alternative to employ the parallel processing. (author)

  4. Economic analysis of alternative LLW disposal methods

    International Nuclear Information System (INIS)

    Foutes, C.E.

    1987-01-01

    The Environmental Protection Agency (EPA) has evaluated the costs and benefits of alternative disposal technologies as part of its program to develop generally applicable environmental standards for the land disposal of low-level radioactive waste (LLW). Costs, population health effects and Critical Population Group (CPG) exposures resulting from alternative waste treatment and disposal methods were developed and input into the analysis. The cost-effectiveness analysis took into account a number of waste streams, hydrogeologic and climatic region settings, and waste treatment and disposal methods. Total costs of each level of a standard included costs for packaging, processing, transportation, and burial of waste. Benefits are defined in terms of reductions in the general population health risk (expected fatal cancers and genetic effects) evaluated over 10,000 years. A cost-effectiveness ratio, was calculated for each alternative standard. This paper describes the alternatives considered and preliminary results of the cost-effectiveness analysis

  5. Depleted uranium management alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Hertzler, T.J.; Nishimoto, D.D.

    1994-08-01

    This report evaluates two management alternatives for Department of Energy depleted uranium: continued storage as uranium hexafluoride, and conversion to uranium metal and fabrication to shielding for spent nuclear fuel containers. The results will be used to compare the costs with other alternatives, such as disposal. Cost estimates for the continued storage alternative are based on a life-cycle of 27 years through the year 2020. Cost estimates for the recycle alternative are based on existing conversion process costs and Capital costs for fabricating the containers. Additionally, the recycle alternative accounts for costs associated with intermediate product resale and secondary waste disposal for materials generated during the conversion process.

  6. Depleted uranium management alternatives

    International Nuclear Information System (INIS)

    Hertzler, T.J.; Nishimoto, D.D.

    1994-08-01

    This report evaluates two management alternatives for Department of Energy depleted uranium: continued storage as uranium hexafluoride, and conversion to uranium metal and fabrication to shielding for spent nuclear fuel containers. The results will be used to compare the costs with other alternatives, such as disposal. Cost estimates for the continued storage alternative are based on a life-cycle of 27 years through the year 2020. Cost estimates for the recycle alternative are based on existing conversion process costs and Capital costs for fabricating the containers. Additionally, the recycle alternative accounts for costs associated with intermediate product resale and secondary waste disposal for materials generated during the conversion process

  7. Genetically Engineering Entomopathogenic Fungi.

    Science.gov (United States)

    Zhao, H; Lovett, B; Fang, W

    2016-01-01

    Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Safe genetically engineered plants

    Energy Technology Data Exchange (ETDEWEB)

    Rosellini, D; Veronesi, F [Dipartimento di Biologia Vegetale e Biotecnologie Agroambientali e Zootecniche, Universita degli Studi di Perugia, Borgo XX giugno 74, 06121 Perugia (Italy)

    2007-10-03

    The application of genetic engineering to plants has provided genetically modified plants (GMPs, or transgenic plants) that are cultivated worldwide on increasing areas. The most widespread GMPs are herbicide-resistant soybean and canola and insect-resistant corn and cotton. New GMPs that produce vaccines, pharmaceutical or industrial proteins, and fortified food are approaching the market. The techniques employed to introduce foreign genes into plants allow a quite good degree of predictability of the results, and their genome is minimally modified. However, some aspects of GMPs have raised concern: (a) control of the insertion site of the introduced DNA sequences into the plant genome and of its mutagenic effect; (b) presence of selectable marker genes conferring resistance to an antibiotic or an herbicide, linked to the useful gene; (c) insertion of undesired bacterial plasmid sequences; and (d) gene flow from transgenic plants to non-transgenic crops or wild plants. In response to public concerns, genetic engineering techniques are continuously being improved. Techniques to direct foreign gene integration into chosen genomic sites, to avoid the use of selectable genes or to remove them from the cultivated plants, to reduce the transfer of undesired bacterial sequences, and make use of alternative, safer selectable genes, are all fields of active research. In our laboratory, some of these new techniques are applied to alfalfa, an important forage plant. These emerging methods for plant genetic engineering are briefly reviewed in this work.

  9. Safe genetically engineered plants

    International Nuclear Information System (INIS)

    Rosellini, D; Veronesi, F

    2007-01-01

    The application of genetic engineering to plants has provided genetically modified plants (GMPs, or transgenic plants) that are cultivated worldwide on increasing areas. The most widespread GMPs are herbicide-resistant soybean and canola and insect-resistant corn and cotton. New GMPs that produce vaccines, pharmaceutical or industrial proteins, and fortified food are approaching the market. The techniques employed to introduce foreign genes into plants allow a quite good degree of predictability of the results, and their genome is minimally modified. However, some aspects of GMPs have raised concern: (a) control of the insertion site of the introduced DNA sequences into the plant genome and of its mutagenic effect; (b) presence of selectable marker genes conferring resistance to an antibiotic or an herbicide, linked to the useful gene; (c) insertion of undesired bacterial plasmid sequences; and (d) gene flow from transgenic plants to non-transgenic crops or wild plants. In response to public concerns, genetic engineering techniques are continuously being improved. Techniques to direct foreign gene integration into chosen genomic sites, to avoid the use of selectable genes or to remove them from the cultivated plants, to reduce the transfer of undesired bacterial sequences, and make use of alternative, safer selectable genes, are all fields of active research. In our laboratory, some of these new techniques are applied to alfalfa, an important forage plant. These emerging methods for plant genetic engineering are briefly reviewed in this work

  10. Entanglement-assisted quantum MDS codes constructed from negacyclic codes

    Science.gov (United States)

    Chen, Jianzhang; Huang, Yuanyuan; Feng, Chunhui; Chen, Riqing

    2017-12-01

    Recently, entanglement-assisted quantum codes have been constructed from cyclic codes by some scholars. However, how to determine the number of shared pairs required to construct entanglement-assisted quantum codes is not an easy work. In this paper, we propose a decomposition of the defining set of negacyclic codes. Based on this method, four families of entanglement-assisted quantum codes constructed in this paper satisfy the entanglement-assisted quantum Singleton bound, where the minimum distance satisfies q+1 ≤ d≤ n+2/2. Furthermore, we construct two families of entanglement-assisted quantum codes with maximal entanglement.

  11. Evolutionary genetics

    National Research Council Canada - National Science Library

    Maynard Smith, John

    1989-01-01

    .... It differs from other textbooks of population genetics in applying the basic theory to topics, such as social behaviour, molecular evolution, reiterated DNA, and sex, which are the main subjects...

  12. Genetic Discrimination

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  13. Arthropod Genetics.

    Science.gov (United States)

    Zumwalde, Sharon

    2000-01-01

    Introduces an activity on arthropod genetics that involves phenotype and genotype identification of the creature and the construction process. Includes a list of required materials and directions to build a model arthropod. (YDS)

  14. Suggestion for a hybrid neuro genetic system as an alternative for the assessment of electric power consumption curves; Sugestao de um sistema hibrido neuro-genetico como alternativa a avaliacao de curvas de consumo de energia eletrica

    Energy Technology Data Exchange (ETDEWEB)

    Masselli, Yvo Marcelo Chiaradia; Torres, Germano Lambert [Universidade Federal de Itajuba (UNIFEI), MG (Brazil)]. E-mails: ymcm@unifei.edu.br; germano@unifei.edu.br

    2006-07-01

    Increase the electrical distribution network quality it's a permanent interesting of energy companies. Therefore, quality services with acceptable values must be offers. In direct form this involves to manage efficiently all distribution system. Nowadays, this supervision is carried out with Geographic Information System (GIS) tools associate with calculation of demands transformers, result of correlation curve kWh versus KV A. Simple linear regression is used to estimate this curve, which make the process not too accuracy. To estimate consumers loads, the traditional methodology consider only end consumption, refusing the characteristic of different kinds of consumers: residential, commercial, industrial, rural and others. This paper present a model based hybridism between Artificial Neural Network (ANN) and Genetic Algorithm (GA), that can identify on load curve acquired any point of distribution system, the portions of consumption relatives to each one of main consumers sectors in that point. Besides, is suggested to the same application an ANN type Multi-Layer Perceptron, with the purpose to compare the showing results and to verify the advantages of hybridism use. The Hybrid System proposed use GA to the ANN training, in other words, the determination of best values to the ANN synaptic weights. Definite the work methodology, the practical valuation of the model starts, and the results presented by hybrid system are compared with those generates by ANN training by the conventional method well-know Back propagation Error (BP). The practical application propose that load curve acquired been analyze in any point of distribution system. Knowing this curve, the system should identify instant consumption quantities, relative to each one of main consumers sectors: industrial, commercial and residential. Subsequently are consider oscillations about these curves, in way to approach the real situation. The initial result indicated a best performance of conventional

  15. New tools to analyze overlapping coding regions.

    Science.gov (United States)

    Bayegan, Amir H; Garcia-Martin, Juan Antonio; Clote, Peter

    2016-12-13

    Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We

  16. Desktop Genetics

    OpenAIRE

    Hough, Soren H; Ajetunmobi, Ayokunmi; Brody, Leigh; Humphryes-Kirilov, Neil; Perello, Edward

    2016-01-01

    Desktop Genetics is a bioinformatics company building a gene-editing platform for personalized medicine. The company works with scientists around the world to design and execute state-of-the-art clustered regularly interspaced short palindromic repeats (CRISPR) experiments. Desktop Genetics feeds the lessons learned about experimental intent, single-guide RNA design and data from international genomics projects into a novel CRISPR artificial intelligence system. We believe that machine learni...

  17. JPEG2000 COMPRESSION CODING USING HUMAN VISUAL SYSTEM MODEL

    Institute of Scientific and Technical Information of China (English)

    Xiao Jiang; Wu Chengke

    2005-01-01

    In order to apply the Human Visual System (HVS) model to JPEG2000 standard,several implementation alternatives are discussed and a new scheme of visual optimization isintroduced with modifying the slope of rate-distortion. The novelty is that the method of visual weighting is not lifting the coefficients in wavelet domain, but is complemented by code stream organization. It remains all the features of Embedded Block Coding with Optimized Truncation (EBCOT) such as resolution progressive, good robust for error bit spread and compatibility of lossless compression. Well performed than other methods, it keeps the shortest standard codestream and decompression time and owns the ability of VIsual Progressive (VIP) coding.

  18. CRACKEL: a computer code for CFR fuel management calculations

    International Nuclear Information System (INIS)

    Burstall, R.F.; Ball, M.A.; Thornton, D.E.J.

    1975-12-01

    The CRACKLE computer code is designed to perform rapid fuel management surveys of CFR systems. The code calculates overall features such as reactivity, power distributions and breeding gain, and also calculates for each sub-assembly plutonium content and power output. A number of alternative options are built into the code, in order to permit different fuel management strategies to be calculated, and to perform more detailed calculations when necessary. A brief description is given of the methods of calculation, and the input facilities of CRACKLE, with examples. (author)

  19. Computer codes for beam dynamics analysis of cyclotronlike accelerators

    Science.gov (United States)

    Smirnov, V.

    2017-12-01

    Computer codes suitable for the study of beam dynamics in cyclotronlike (classical and isochronous cyclotrons, synchrocyclotrons, and fixed field alternating gradient) accelerators are reviewed. Computer modeling of cyclotron segments, such as the central zone, acceleration region, and extraction system is considered. The author does not claim to give a full and detailed description of the methods and algorithms used in the codes. Special attention is paid to the codes already proven and confirmed at the existing accelerating facilities. The description of the programs prepared in the worldwide known accelerator centers is provided. The basic features of the programs available to users and limitations of their applicability are described.

  20. Coded Network Function Virtualization

    DEFF Research Database (Denmark)

    Al-Shuwaili, A.; Simone, O.; Kliewer, J.

    2016-01-01

    Network function virtualization (NFV) prescribes the instantiation of network functions on general-purpose network devices, such as servers and switches. While yielding a more flexible and cost-effective network architecture, NFV is potentially limited by the fact that commercial off......-the-shelf hardware is less reliable than the dedicated network elements used in conventional cellular deployments. The typical solution for this problem is to duplicate network functions across geographically distributed hardware in order to ensure diversity. In contrast, this letter proposes to leverage channel...... coding in order to enhance the robustness on NFV to hardware failure. The proposed approach targets the network function of uplink channel decoding, and builds on the algebraic structure of the encoded data frames in order to perform in-network coding on the signals to be processed at different servers...

  1. The NIMROD Code

    Science.gov (United States)

    Schnack, D. D.; Glasser, A. H.

    1996-11-01

    NIMROD is a new code system that is being developed for the analysis of modern fusion experiments. It is being designed from the beginning to make the maximum use of massively parallel computer architectures and computer graphics. The NIMROD physics kernel solves the three-dimensional, time-dependent two-fluid equations with neo-classical effects in toroidal geometry of arbitrary poloidal cross section. The NIMROD system also includes a pre-processor, a grid generator, and a post processor. User interaction with NIMROD is facilitated by a modern graphical user interface (GUI). The NIMROD project is using Quality Function Deployment (QFD) team management techniques to minimize re-engineering and reduce code development time. This paper gives an overview of the NIMROD project. Operation of the GUI is demonstrated, and the first results from the physics kernel are given.

  2. Expression profile of genes coding for carotenoid biosynthetic ...

    Indian Academy of Sciences (India)

    Expression profile of genes coding for carotenoid biosynthetic pathway during ripening and their association with accumulation of lycopene in tomato fruits. Shuchi Smita, Ravi Rajwanshi, Sangram Keshari Lenka, Amit Katiyar, Viswanathan Chinnusamy and. Kailash Chander Bansal. J. Genet. 92, 363–368. Table 1.

  3. Computer code FIT

    International Nuclear Information System (INIS)

    Rohmann, D.; Koehler, T.

    1987-02-01

    This is a description of the computer code FIT, written in FORTRAN-77 for a PDP 11/34. FIT is an interactive program to decude position, width and intensity of lines of X-ray spectra (max. length of 4K channels). The lines (max. 30 lines per fit) may have Gauss- or Voigt-profile, as well as exponential tails. Spectrum and fit can be displayed on a Tektronix terminal. (orig.) [de

  4. Discrete Sparse Coding.

    Science.gov (United States)

    Exarchakis, Georgios; Lücke, Jörg

    2017-11-01

    Sparse coding algorithms with continuous latent variables have been the subject of a large number of studies. However, discrete latent spaces for sparse coding have been largely ignored. In this work, we study sparse coding with latents described by discrete instead of continuous prior distributions. We consider the general case in which the latents (while being sparse) can take on any value of a finite set of possible values and in which we learn the prior probability of any value from data. This approach can be applied to any data generated by discrete causes, and it can be applied as an approximation of continuous causes. As the prior probabilities are learned, the approach then allows for estimating the prior shape without assuming specific functional forms. To efficiently train the parameters of our probabilistic generative model, we apply a truncated expectation-maximization approach (expectation truncation) that we modify to work with a general discrete prior. We evaluate the performance of the algorithm by applying it to a variety of tasks: (1) we use artificial data to verify that the algorithm can recover the generating parameters from a random initialization, (2) use image patches of natural images and discuss the role of the prior for the extraction of image components, (3) use extracellular recordings of neurons to present a novel method of analysis for spiking neurons that includes an intuitive discretization strategy, and (4) apply the algorithm on the task of encoding audio waveforms of human speech. The diverse set of numerical experiments presented in this letter suggests that discrete sparse coding algorithms can scale efficiently to work with realistic data sets and provide novel statistical quantities to describe the structure of the data.

  5. Code of Practice

    International Nuclear Information System (INIS)

    Doyle, Colin; Hone, Christopher; Nowlan, N.V.

    1984-05-01

    This Code of Practice introduces accepted safety procedures associated with the use of alpha, beta, gamma and X-radiation in secondary schools (pupils aged 12 to 18) in Ireland, and summarises good practice and procedures as they apply to radiation protection. Typical dose rates at various distances from sealed sources are quoted, and simplified equations are used to demonstrate dose and shielding calculations. The regulatory aspects of radiation protection are outlined, and references to statutory documents are given

  6. Tokamak simulation code manual

    International Nuclear Information System (INIS)

    Chung, Moon Kyoo; Oh, Byung Hoon; Hong, Bong Keun; Lee, Kwang Won

    1995-01-01

    The method to use TSC (Tokamak Simulation Code) developed by Princeton plasma physics laboratory is illustrated. In KT-2 tokamak, time dependent simulation of axisymmetric toroidal plasma and vertical stability have to be taken into account in design phase using TSC. In this report physical modelling of TSC are described and examples of application in JAERI and SERI are illustrated, which will be useful when TSC is installed KAERI computer system. (Author) 15 refs., 6 figs., 3 tabs

  7. Status of MARS Code

    Energy Technology Data Exchange (ETDEWEB)

    N.V. Mokhov

    2003-04-09

    Status and recent developments of the MARS 14 Monte Carlo code system for simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 100 TeV are described. these include physics models both in strong and electromagnetic interaction sectors, variance reduction techniques, residual dose, geometry, tracking, histograming. MAD-MARS Beam Line Build and Graphical-User Interface.

  8. Codes of Good Governance

    DEFF Research Database (Denmark)

    Beck Jørgensen, Torben; Sørensen, Ditte-Lene

    2013-01-01

    Good governance is a broad concept used by many international organizations to spell out how states or countries should be governed. Definitions vary, but there is a clear core of common public values, such as transparency, accountability, effectiveness, and the rule of law. It is quite likely......, transparency, neutrality, impartiality, effectiveness, accountability, and legality. The normative context of public administration, as expressed in codes, seems to ignore the New Public Management and Reinventing Government reform movements....

  9. Orthopedics coding and funding.

    Science.gov (United States)

    Baron, S; Duclos, C; Thoreux, P

    2014-02-01

    The French tarification à l'activité (T2A) prospective payment system is a financial system in which a health-care institution's resources are based on performed activity. Activity is described via the PMSI medical information system (programme de médicalisation du système d'information). The PMSI classifies hospital cases by clinical and economic categories known as diagnosis-related groups (DRG), each with an associated price tag. Coding a hospital case involves giving as realistic a description as possible so as to categorize it in the right DRG and thus ensure appropriate payment. For this, it is essential to understand what determines the pricing of inpatient stay: namely, the code for the surgical procedure, the patient's principal diagnosis (reason for admission), codes for comorbidities (everything that adds to management burden), and the management of the length of inpatient stay. The PMSI is used to analyze the institution's activity and dynamism: change on previous year, relation to target, and comparison with competing institutions based on indicators such as the mean length of stay performance indicator (MLS PI). The T2A system improves overall care efficiency. Quality of care, however, is not presently taken account of in the payment made to the institution, as there are no indicators for this; work needs to be done on this topic. Copyright © 2014. Published by Elsevier Masson SAS.

  10. Code Modernization of VPIC

    Science.gov (United States)

    Bird, Robert; Nystrom, David; Albright, Brian

    2017-10-01

    The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

  11. MELCOR computer code manuals

    Energy Technology Data Exchange (ETDEWEB)

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L. [Sandia National Labs., Albuquerque, NM (United States); Hodge, S.A.; Hyman, C.R.; Sanders, R.L. [Oak Ridge National Lab., TN (United States)

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.

  12. MELCOR computer code manuals

    International Nuclear Information System (INIS)

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L.; Hodge, S.A.; Hyman, C.R.; Sanders, R.L.

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR's phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package

  13. The genetic code – Thawing the 'frozen accident'

    Indian Academy of Sciences (India)

    Madhu

    2006-10-04

    Oct 4, 2006 ... The components foremost involved in this process are the. tRNA molecules whose ... that tRNA species with dual identity (capable of being charged by two ... However, the theory has good support, as the CUG codon in ...

  14. Contrasting genetic influence of PON 1 coding gene polymorphisms ...

    African Journals Online (AJOL)

    Nadia Youssef Sadek Morcos

    2015-03-31

    Mar 31, 2015 ... toxicity primarily by inhibiting the enzyme acetylcholinesterase. (AChE) [1]. ... 3. Methods. DNA was extracted from whole blood using a QIAamp Blood .... activity. It is not clear whether this is because of a decreased stability of ...

  15. RNA-DNA sequence differences spell genetic code ambiguities

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Michael L

    2013-01-01

    A recent paper in Science by Li et al. 2011(1) reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized. ...

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

    Indian Academy of Sciences (India)

    We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS- and GC-NSF(a)-0th order ...

  17. Origins of gene, genetic code, protein and life: comprehensive view ...

    Indian Academy of Sciences (India)

    Unknown

    production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions .... using random numbers by a computer, to confirm whether main chains of ...... world on the origin of life by the pseudo-replication of. [GADV]-proteins in the absence of ...

  18. Coevolution mechanisms that adapt viruses to genetic code ...

    Indian Academy of Sciences (India)

    Recent work on virus × host inter- ... of long-term interdependent symbiotic relationship between them. ... Evolution in species of living organisms occurs based on the .... their parents (Francino and Ochman 1999; Lynn et al. 2002; ... dently some dozens of times. ... in the families of certain viruses, bacteria, fungi and inverte-.

  19. Cracking the Genetic Code | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... of interpretation, which is going to get gradually better over time, so that if somebody makes a discovery that happens to be relevant to you, you learn about it. For the complete transcript and video interview, visit http://www.pbs.org/newshour/ . Click ...

  20. Universal Fault-Tolerant Gates on Concatenated Stabilizer Codes

    Directory of Open Access Journals (Sweden)

    Theodore J. Yoder

    2016-09-01

    Full Text Available It is an oft-cited fact that no quantum code can support a set of fault-tolerant logical gates that is both universal and transversal. This no-go theorem is generally responsible for the interest in alternative universality constructions including magic state distillation. Widely overlooked, however, is the possibility of nontransversal, yet still fault-tolerant, gates that work directly on small quantum codes. Here, we demonstrate precisely the existence of such gates. In particular, we show how the limits of nontransversality can be overcome by performing rounds of intermediate error correction to create logical gates on stabilizer codes that use no ancillas other than those required for syndrome measurement. Moreover, the logical gates we construct, the most prominent examples being Toffoli and controlled-controlled-Z, often complete universal gate sets on their codes. We detail such universal constructions for the smallest quantum codes, the 5-qubit and 7-qubit codes, and then proceed to generalize the approach. One remarkable result of this generalization is that any nondegenerate stabilizer code with a complete set of fault-tolerant single-qubit Clifford gates has a universal set of fault-tolerant gates. Another is the interaction of logical qubits across different stabilizer codes, which, for instance, implies a broadly applicable method of code switching.