WorldWideScience

Sample records for alternative genetic code

  1. Polyphase alternating codes

    CERN Document Server

    Markkanen, Markku

    2007-01-01

    This work introduces a method for constructing polyphase alternating codes in which the length of a code transmission cycle can be $p^m$ or $p-1$, where $p$ is a prime number and $m$ is a positive integer. The relevant properties leading to the construction alternating codes and the algorithm for generating alternating codes is described. Examples of all practical and some not that practical polyphase code lengths are given.

  2. Polyphase alternating codes

    Directory of Open Access Journals (Sweden)

    M. Markkanen

    2008-08-01

    Full Text Available We present a new class of alternating codes. Instead of the customary binary phase codes, the new codes utilize either p or p–1 phases, where p is a prime number. The first class of codes has code length pm, where m is a positive integer, the second class has code length p–1. We give an actual construction algorithm, and explain the principles behind it. We handle a few specific examples in detail. The new codes offer an enlarged collection of code lengths for radar experiments.

  3. Polyphase alternating codes

    OpenAIRE

    M. Markkanen; Vierinen, J.; Markkanen, J.

    2007-01-01

    We present a new class of alternating codes. Instead of the customary binary phase codes, the new codes utilize either p or p–1 phases, where p is a prime number. The first class of codes has code length pm, where m is a positive integer, the second class has code length p–1. We give an actual construction algorithm, and explain the principles behind it. We ...

  4. Crystalizing the genetic code

    CERN Document Server

    Frappat, L; Sorba, Paul

    2000-01-01

    New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An operator which gives the correspondence between the amino-acids and the codons is now obtained for any known genetic code. The free energy released by base pairing of dinucleotides as well as the relative hydrophilicity and hydrophobicity of the dinucleosides are also computed. For the vertebrate series, a universal behaviour in the ratios of codon usage frequencies is put in evidence and is shown to fit nicely in our model. Then a first attempt to represent the mutations relative to the deletion of a pyrimidine by action of a suitable crystal spinor operator is proposed. Finally recent theoretical descriptions are reviewed and compared with our model.

  5. Overcoming Challenges in Engineering the Genetic Code.

    Science.gov (United States)

    Lajoie, M J; Söll, D; Church, G M

    2016-02-27

    Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code. PMID:26348789

  6. Overcoming Challenges in Engineering the Genetic Code.

    Science.gov (United States)

    Lajoie, M J; Söll, D; Church, G M

    2016-02-27

    Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code.

  7. Parallel evolution of the genetic code in arthropod mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Federico Abascal

    2006-05-01

    Full Text Available The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code or arginine (as in the standard genetic code. We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.

  8. Genomics: Evolution of the Genetic Code.

    Science.gov (United States)

    Keeling, Patrick J

    2016-09-26

    The genetic code is not quite universal. The rare variations that we know of reveal selective pressures on the code and on the translation machinery. New data suggest the code changes through ambiguous intermediates and that termination is context dependent. PMID:27676305

  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. Hacking the genetic code of mammalian cells.

    Science.gov (United States)

    Schwarzer, Dirk

    2009-07-01

    A genetic shuttle: The highlighted article, which was recently published by Schultz, Geierstanger and co-workers, describes a straightforward scheme for enlarging the genetic code of mammalian cells. An orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for a new amino acid can be evolved in E. coli and subsequently transferred into mammalian cells. The feasibility of this approach was demonstrated by adding a photocaged lysine derivative to the genetic repertoire of a human cell line.

  11. Expanding the eukaryotic genetic code

    Science.gov (United States)

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

    2013-01-22

    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.

  12. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-03

    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.

  13. Quaternionic representation of the genetic code.

    Science.gov (United States)

    Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

    2016-03-01

    A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. PMID:26751396

  14. Synthetic biology: Tailor-made genetic codes

    Science.gov (United States)

    Jewett, Michael C.; Noireaux, Vincent

    2016-04-01

    Expanding the range of amino acids polymerizable by ribosomes could enable new functionalities to be added to polypeptides. Now, the genetic code has been reprogrammed using a reconstituted in vitro translation system to enable synthesis of unnatural peptides with unmatched flexibility.

  15. Xenomicrobiology: a roadmap for genetic code engineering.

    Science.gov (United States)

    Acevedo-Rocha, Carlos G; Budisa, Nediljko

    2016-09-01

    Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non-natural building blocks in living cells. In this context, genetic code engineering respectively enables the re-design of genes/genomes and proteins/proteomes with non-canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new-to-nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a 'genetic firewall' will also allow to study and understand the relation between code evolution and horizontal gene transfer. PMID:27489097

  16. 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 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 embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely

  17. Whole Genome Sequencing: Cracking the Genetic Code for Foodborne Illness

    Science.gov (United States)

    ... For Consumers Home For Consumers Consumer Updates Whole Genome Sequencing: Cracking the Genetic Code for Foodborne Illness ... Bacteria that cause disease have millions of different genomes, or sequences of genetic code, each as unique ...

  18. Biological Information Transfer Beyond the Genetic Code: The Sugar Code

    Science.gov (United States)

    Gabius, H.-J.

    In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i

  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

    European consumers, in general, have negative attitudes towards the use of gene technology in food production. The objective of this study was to examine whether taste and health benefits influence the acceptability of genetically modified (gm) products when they are presented as real product...... 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...

  20. Non-Standard Genetic Codes Define New Concepts for Protein Engineering

    Directory of Open Access Journals (Sweden)

    Ana R. Bezerra

    2015-11-01

    Full Text Available The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.

  1. Metalloprotein design using genetic code expansion.

    Science.gov (United States)

    Hu, Cheng; Chan, Sunney I; Sawyer, Elizabeth B; Yu, Yang; Wang, Jiangyun

    2014-09-21

    More than one third of all proteins are metalloproteins. They catalyze important reactions such as photosynthesis, nitrogen fixation and CO2 reduction. Metalloproteins such as the olfactory receptors also serve as highly elaborate sensors. Here we review recent developments in functional metalloprotein design using the genetic code expansion approach. We show that, through the site-specific incorporation of metal-chelating unnatural amino acids (UAAs), proton and electron transfer mediators, and UAAs bearing bioorthogonal reaction groups, small soluble proteins can recapitulate and expand the important functions of complex metalloproteins. Further developments along this route may result in cell factories and live-cell sensors with unprecedented efficiency and selectivity.

  2. Analysis of the optimality of the standard genetic code.

    Science.gov (United States)

    Kumar, Balaji; Saini, Supreet

    2016-07-19

    Many theories have been proposed attempting to explain the origin of the genetic code. While strong reasons remain to believe that the genetic code evolved as a frozen accident, at least for the first few amino acids, other theories remain viable. In this work, we test the optimality of the standard genetic code against approximately 17 million genetic codes, and locate 29 which outperform the standard genetic code at the following three criteria: (a) robustness to point mutation; (b) robustness to frameshift mutation; and (c) ability to encode additional information in the coding region. We use a genetic algorithm to generate and score codes from different parts of the associated landscape, which are, as a result, presumably more representative of the entire landscape. Our results show that while the genetic code is sub-optimal for robustness to frameshift mutation and the ability to encode additional information in the coding region, it is very strongly selected for robustness to point mutation. This coupled with the observation that the different performance indicator scores for a particular genetic code are negatively correlated makes the standard genetic code nearly optimal for the three criteria tested in this work. PMID:27327359

  3. A Binary Representation of the Genetic Code

    CERN Document Server

    Nemzer, Louis R

    2016-01-01

    This article introduces a novel binary representation of the canonical genetic code, in which each of the four mRNA nucleotide bases is assigned a unique 2-bit identifier. These designations have a physiological meaning derived from the molecular structures of, and relationships between, the bases. In this scheme, the 64 possible triplet codons are each indexed by a 6-bit label. The order of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. Transition and transversion mutations are naturally expressed as basic binary operations, and the severity of the different types is analyzed. Using a principal component analysis, it is shown that physicochemical properties of amino acids related to protein folding also correlate with particular bit positions of their respective labels. Thus, the likelihood for a particular point mutation to be conservative, and therefore less likely to cause a change in protein functionality, can be estimated.

  4. 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...

  5. An algebraic hypothesis about the primeval genetic code

    OpenAIRE

    Sanchez, Robersy; Grau, Ricardo

    2008-01-01

    A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic cod...

  6. The degeneracy of the genetic code and Hadamard matrices

    CERN Document Server

    Petoukhov, Sergey V

    2008-01-01

    The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic matrices is investigated, which is based on the genetic matrix [C A; U G], where C, A, U, G are the letters of the genetic alphabet. This matrix in the third Kronecker power is the (8*8)-matrix, which contains 64 triplets. Peculiarities of the degeneracy of the vertebrate mitochondria genetic code are reflected in the symmetrical black-and-white mosaic of this genetic (8*8)-matrix. This mosaic matrix is connected algorithmically with Hadamard matrices unexpectedly, which are famous in the theory of signal processing, quantum mechanics and quantum computers.

  7. Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.

    Science.gov (United States)

    Hammerling, Michael J; Gollihar, Jimmy; Mortensen, Catherine; Alnahhas, Razan N; Ellington, Andrew D; Barrick, Jeffrey E

    2016-08-01

    Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to experimentally study the impact of alternative genetic codes on the evolution of biological systems. We explored how Escherichia coli strains that incorporate a 21st nonstandard amino acid (nsAA) at the recoded amber (TAG) stop codon evolve resistance to the antibiotic rifampicin. Resistance to rifampicin arises from chromosomal mutations in the β subunit of RNA polymerase (RpoB). We found that a variety of mutations that lead to substitutions of nsAAs in the essential RpoB protein confer robust rifampicin resistance. We interpret these results in a framework in which an expanded code can increase evolvability in two distinct ways: by adding a new letter with unique chemical properties to the protein alphabet and by altering the mutational connectivity of amber-adjacent codons by converting a lethal nonsense mutation into a missense mutation. Finally, we consider the implications of these results for the evolution of alternative genetic codes. In our experiments, reliance on a mutation to a reassigned codon for a vital trait is not required for the long-term maintenance of an expanded genetic code and may even destabilize incorporation of an nsAA, a result that is consistent with the codon capture model of genetic code evolution. PMID:27189550

  8. The origin and evolution of the genetic code.

    Science.gov (United States)

    Béland, P; Allen, T F

    1994-10-21

    We argue that a primitive genetic code with only 20 separate words explains that there are 20 coded amino acids in modern life. The existence of 64 words on the modern genetic code requires modern life to read almost exclusively one strand of DNA in one direction. In our primitive code, both the original and the complementary sequence are read in either direction to give the same strings of amino acids. The algebra of complements forces synonymy of primitive codons so as to reduce the 64 independent codons of the modern code to exactly 20 independent separate words in the primitive condition. The synonymy in the modern code is the result of selection rather than algebraic forcing. The primitive code has almost no resilience to base mutations, unlike the third base redundancy of the modern code. Our primitive and the modern code are orthogonal. If palindromic proteins were coded by hairpin DNA or RNA, then (i) no punctuation would be needed; (ii) the reverse reading would give the same secondarily folded protein structure; and (iii) the sugar backbone would be read in the conventional 5' to 3' direction for the original arm and its complement. Modern copying of genetic material is almost always antiparallel. However, occasional parallel copying, as does occur in modern life, would give the complementary hairpin that would also read 5' to 3' along its entire length.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7996862

  9. Preparation of materials for flexizyme reactions and genetic code reprogramming

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Yuki Goto, Takayuki Katoh & Hiroaki Suga ### Abstract Genetic code reprogramming is a method for the reassignment of arbitrary codons from proteinogenic amino acids to non-proteinogenic ones, and thus specific sequences of non-standard peptides can be ribosomally expressed according to their mRNA templates. We have developed a protocol that facilitates the genetic code reprogramming using flexizymes integrated with a custom-made in-vitro translation apparatus, referred to...

  10. Origin and evolution of the genetic code: the universal enigma

    OpenAIRE

    Eugene V Koonin; Novozhilov, Artem S

    2009-01-01

    The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physico-chemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory ...

  11. An Improved Real-Coded Genetic Algorithm and Its Application

    Institute of Scientific and Technical Information of China (English)

    Zhong-Lai Wang; Ping Yang; Dan Ling; Qiang Miao

    2008-01-01

    Real-coded genetic algorithm (RGA) usuaUy meets the demand of consecutive space problem. However, compared with simple genetic algorithm (SGA), RGA also has the inherent disadvantages such as prematurity and slow convergence when the solution is close to the optimum solution. This paper presents an improved real-coded genetic algorithm to increase the computation efficiency and avoid prematurity, especially in the optimization of multi-modal function. In this method, mutation operation and crossover operation are improved. Examples are given to demonstrate its computation efficiency and robustness.

  12. OPTIMIZATION BASED ON LMPROVED REAL—CODED GENETIC ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    ShiYu; YuShenglin

    2002-01-01

    An improved real-coded genetic algorithm is pro-posed for global optimization of functionsl.The new algo-rithm is based om the judgement of the searching perfor-mance of basic real-coded genetic algorithm.The opera-tions of basic real-coded genetic algorithm are briefly dis-cussed and selected.A kind of chaos sequence is described in detail and added in the new algorithm ad a disturbance factor.The strategy of field partition is also used to im-prove the strcture of the new algorithm.Numerical ex-periment shows that the mew genetic algorithm can find the global optimum of complex funtions with satistaiting precision.

  13. System-Level Genetic Codes Using a Transposable Element-Like Mechanism with Applications to Cancer

    OpenAIRE

    McGowan, John F.

    2000-01-01

    A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded independently. In general, a system-level genetic code requires coding discrete interacting parts such as organs or proteins in an interdependent way. Changing a single symbol or "gene" in a system-level genetic code affects two or more parts in a coordina...

  14. Unnatural reactive amino acid genetic code additions

    Science.gov (United States)

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

    2014-08-26

    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.

  15. Unnatural reactive amino acid genetic code additions

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-05-21

    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, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  16. 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.

  17. 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.

  18. 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.

  19. Alternative Living Kidney Donation Programs Boost Genetically Unrelated Donation

    Directory of Open Access Journals (Sweden)

    Rosalie A. Poldervaart

    2015-01-01

    Full Text Available Donor-recipient ABO and/or HLA incompatibility used to lead to donor decline. Development of alternative transplantation programs enabled transplantation of incompatible couples. How did that influence couple characteristics? Between 2000 and 2014, 1232 living donor transplantations have been performed. In conventional and ABO-incompatible transplantation the willing donor becomes an actual donor for the intended recipient. In kidney-exchange and domino-donation the donor donates indirectly to the intended recipient. The relationship between the donor and intended recipient was studied. There were 935 conventional and 297 alternative program transplantations. There were 66 ABO-incompatible, 68 domino-paired, 62 kidney-exchange, and 104 altruistic donor transplantations. Waiting list recipients (n=101 were excluded as they did not bring a living donor. 1131 couples remained of whom 196 participated in alternative programs. Genetically unrelated donors (486 were primarily partners. Genetically related donors (645 were siblings, parents, children, and others. Compared to genetically related couples, almost three times as many genetically unrelated couples were incompatible and participated in alternative programs (P<0.001. 62% of couples were genetically related in the conventional donation program versus 32% in alternative programs (P<0.001. Patient and graft survival were not significantly different between recipient programs. Alternative donation programs increase the number of transplantations by enabling genetically unrelated donors to donate.

  20. Optimization of energy saving device combined with a propeller using real-coded genetic algorithm

    OpenAIRE

    Ryu Tomohiro; Kanemaru Takashi; Kataoka Shiro; Arihama Kiyoshi; Yoshitake Akira; Arakawa Daijiro; Ando Jun

    2014-01-01

    This paper presents a numerical optimization method to improve the performance of the propeller with Turbo-Ring using real-coded genetic algorithm. In the presented method, Unimodal Normal Distribution Crossover (UNDX) and Minimal Generation Gap (MGG) model are used as crossover operator and generation-alternation model, respectively. Propeller characteristics are evaluated by a simple surface panel method “SQCM” in the optimization process. Blade sections of the original Turbo-Ring and prope...

  1. p-Adic Degeneracy of the Genetic Code

    CERN Document Server

    Dragovich, Branko

    2007-01-01

    Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\\mathcal{C}_5 (64) = \\{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2, 3, 4 \\} ,$ where $n_i$ are digits related to nucleotides as follows: C = 1, A = 2, T = U = 3, G = 4. The smallest 5-adic distance between codons joins them into 16 quadruplets, which under 2-adic distance decay into 32 doublets. p-Adically close codons are assigned to one of 20 amino acids, which are building blocks of proteins, or code termination of protein synthesis. We shown that genetic code multiplets are made of the p-adic nearest codons.

  2. On the possible origin and evolution of the genetic code

    Science.gov (United States)

    Jukes, T. H.

    1974-01-01

    The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

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

    OpenAIRE

    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 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 ...

  4. Load Flow Analysis Using Real Coded Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Himakar Udatha

    2014-02-01

    Full Text Available This paper presents a Real Coded Genetic Algorithm (RCGA for finding the load flow solution of electrical power systems. The proposed method is based on the minimization of the real and reactive power mismatches at various buses. The traditional methods such as Gauss-Seidel method and Newton-Raphson (NR method have certain drawbacks under abnormal operating condition. In order to overcome these problems, the load flow solution based on Real Coded Genetic Algorithm (RCGA is presented in this paper. Two cross over techniques, Arithmetic crossover and heuristic crossover are used to solve the power flow problem. The proposed method is applied for 3-bus, 5-bus and 6-bus systems and the results are presented.

  5. Physical Model for the Evolution of the Genetic Code

    Science.gov (United States)

    Yamashita, Tatsuro; Narikiyo, Osamu

    2011-12-01

    Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

  6. Preimplantational genetic diagnosis: an actual alternative with future implications

    Directory of Open Access Journals (Sweden)

    Claudia Juliana Serrano Serrano

    2005-08-01

    Full Text Available Preimplantational genetic diagnosis (PGT isa new technique, promoted as an alternative for prenatal diagnosisand eventually for the voluntary termination of pregnancy whenthe couple is willing . Essentially, they are afraid that a geneticdisease may be transmitted to their descendents. After the assistedreproduction techniques have been applied, an embryo biopsy isconducted, extracting two of the blastomeres, which are geneticallyanalyzed. Those embryos free from genetic diseases are implantedin the mother uterus. PGT has also allowed the medical communityto study different aspects of the early embryo development andthe comprehension of reproductive genetics. However these newtechniques have given rise to many ethical questions and debatesabout the moral consequences of routinely practicing PGT.

  7. Recent evidence for evolution of the genetic code

    Science.gov (United States)

    Osawa, S.; Jukes, T. H.; Watanabe, K.; Muto, A.

    1992-01-01

    The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

  8. 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.

  9. Innovations in human genetics education. Alternative methods of instruction in medical genetics.

    OpenAIRE

    King, C R

    1989-01-01

    A course in medical genetics for first-year medical students was developed with the use of alternative methods of instruction, including audiovisual materials and computer-assisted instruction. The use of this methodology enabled students to consider many significant areas of medical genetics, without a dependency on the traditional lecture-based instructional format. Seventy-eight percent of the students identified the alternative instructional methods as an enhancement to their education. T...

  10. 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.

  11. Statistical analysis of the distribution of amino acids in Borrelia burgdorferi genome under different genetic codes

    Science.gov (United States)

    García, José A.; Alvarez, Samantha; Flores, Alejandro; Govezensky, Tzipe; Bobadilla, Juan R.; José, Marco V.

    2004-10-01

    The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling properties and the maximum entropy of the distribution of distances of amino acids in sequences obtained by translating protein-coding regions from the genome of Borrelia burgdorferi, under different genetic codes. Overall our results indicate that these properties are very stable to perturbations made by altering the genetic code. We also discuss the evolutionary likely implications of the present results.

  12. A Content-Centric Organization of the Genetic Code

    Institute of Scientific and Technical Information of China (English)

    Jun Yu

    2007-01-01

    The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively. For prokaryotic genomes, when the genomic GC content increases, their amino acid contents tend to be restricted to the GC-rich quarter and the purine-content insensitive half, where all codons are fourfold degenerate and relatively mutation-tolerant. Conversely, when the genomic GC content decreases, most of the codons retract to the AU-rich quarter and the purine-content sensitive half; most of the codons not only remain encoding physicochemically diversified amino acids but also vary when transversion (between purine and pyrimidine) happens. Amino acids with sixfolddegenerate codons are distributed into all four quarters and across the two halves; their fourfold-degenerate codons are all partitioned into the purine-insensitive half in favorite of robustness against mutations. The features manifested in the rearranged codon table explain most of the intrinsic relationship between protein coding sequences (the informational content) and amino acid compositions (the functional content). The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physicochemical properties.

  13. Python code parallelization for ALMA, challenges and alternatives

    OpenAIRE

    Gonzalez, Justo; Taylor, Julian; Castro, Sandra; Kern, Jeff; Knudstrup, Jens; Zampieri, Stefano; Manning, Alisdair

    2015-01-01

    In the last few years development of Python code for science and data reduction purposes has gained significant popularity. ESO in itself uses a Python-based archiving  system for VLT and ALMA data. Also the data reduction suite for ALMA data is python-based. Rapid development is fostered by a big community and a wide range of already available packages. However Python enforces locking mechanisms, to ensure thread safety, that effectively reduce the capacity of Python to use only one cor...

  14. 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. PMID:26515765

  15. Genetic Algorithm Based Production Planning for Alternative Process Production

    Institute of Scientific and Technical Information of China (English)

    ZHANG Fa-ping; SUN Hou-fang; SHAHID I. Butt

    2009-01-01

    Production planning under flexible job shop environment is studied. A mathematic model is formulated to help improve alternative process production. This model, in which genetic algorithm is used, is expected to result in better production planning, hence towards the aim of minimizing production cost under the constraints of delivery time and other scheduling conditions. By means of this algorithm, all planning schemes which could meet all requirements of the constraints within the whole solution space are exhaustively searched so as to find the optimal one. Also, a case study is given in the end to support and validate this model. Our results show that genetic algorithm is capable of locating feasible process routes to reduce production cost for certain tasks.

  16. FREQUENCY-CODED OPTIMIZATION OF HOPPED-FREQUENCY PULSE SIGNAL BASED ON GENETIC ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    Liu Zheng; Mu Xuehua

    2005-01-01

    The Frequency-Coded Pulse (FCP) signal has good performance of range and Doppler resolution. This paper first gives the mathematical expression of the ambiguity function for FCP signals, and then presents a coding rule for optimizing FCP signal. The genetic algorithm is presented to solve this kind of problem for optimizing codes. Finally, an example for optimizing calculation is illustrated and the optimized frequency coding results are given with the code length N=64 and N=128 respectively.

  17. Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast

    DEFF Research Database (Denmark)

    Clément-Ziza, Mathieu; Marsellach, Francesc X.; Codlin, Sandra;

    2014-01-01

    Our current understanding of how natural genetic variation affects gene expression beyond well-annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci (eQTLs) has the potential to close this gap. Here, we generated...... the first recombinant strain library for fission yeast and conducted an RNA-seq-based QTL study of the coding, non-coding, and antisense transcriptomes. We show that the frequency of distal effects (trans-eQTLs) greatly exceeds the number of local effects (cis-eQTLs) and that non-coding RNAs are as likely...

  18. Optimization of energy saving device combined with a propeller using real-coded genetic algorithm

    Directory of Open Access Journals (Sweden)

    Ryu Tomohiro

    2014-06-01

    Full Text Available This paper presents a numerical optimization method to improve the performance of the propeller with Turbo-Ring using real-coded genetic algorithm. In the presented method, Unimodal Normal Distribution Crossover (UNDX and Minimal Generation Gap (MGG model are used as crossover operator and generation-alternation model, respectively. Propeller characteristics are evaluated by a simple surface panel method “SQCM” in the optimization process. Blade sections of the original Turbo-Ring and propeller are replaced by the NACA66 a = 0.8 section. However, original chord, skew, rake and maximum blade thickness distributions in the radial direction are unchanged. Pitch and maximum camber distributions in the radial direction are selected as the design variables. Optimization is conducted to maximize the efficiency of the propeller with Turbo-Ring. The experimental result shows that the efficiency of the optimized propeller with Turbo-Ring is higher than that of the original propeller with Turbo-Ring.

  19. Optimization of energy saving device combined with a propeller using real-coded genetic algorithm

    Science.gov (United States)

    Ryu, Tomohiro; Kanemaru, Takashi; Kataoka, Shiro; Arihama, Kiyoshi; Yoshitake, Akira; Arakawa, Daijiro; Ando, Jun

    2014-06-01

    This paper presents a numerical optimization method to improve the performance of the propeller with Turbo-Ring using real-coded genetic algorithm. In the presented method, Unimodal Normal Distribution Crossover (UNDX) and Minimal Generation Gap (MGG) model are used as crossover operator and generation-alternation model, respectively. Propeller characteristics are evaluated by a simple surface panel method "SQCM" in the optimization process. Blade sections of the original Turbo-Ring and propeller are replaced by the NACA66 a = 0.8 section. However, original chord, skew, rake and maximum blade thickness distributions in the radial direction are unchanged. Pitch and maximum camber distributions in the radial direction are selected as the design variables. Optimization is conducted to maximize the efficiency of the propeller with Turbo-Ring. The experimental result shows that the efficiency of the optimized propeller with Turbo-Ring is higher than that of the original propeller with Turbo-Ring.

  20. Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

    Directory of Open Access Journals (Sweden)

    J. Tze-Fei Wong

    2016-03-01

    Full Text Available The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.

  1. 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.

  2. A p-Adic Model of DNA Sequence and Genetic Code

    CERN Document Server

    Dragovich, Branko

    2007-01-01

    Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are nucleotides, codons and genes. We show that a 5-adic model is appropriate for DNA sequence. This 5-adic model, combined with 2-adic distance, is also suitable for genetic code and for a more advanced employment in genomics. We find that genetic code degeneracy is related to the p-adic distance between codons.

  3. Matrix genetics, part 2: the degeneracy of the genetic code and the octave algebra with two quasi-real units (the genetic octave Yin-Yang-algebra)

    CERN Document Server

    Petoukhov, Sergey V

    2008-01-01

    Algebraic properties of the genetic code are analyzed. The investigations of the genetic code on the basis of matrix approaches ("matrix genetics") are described. The degeneracy of the vertebrate mitochondria genetic code is reflected in the black-and-white mosaic of the (8*8)-matrix of 64 triplets, 20 amino acids and stop-signals. This mosaic genetic matrix is connected with the matrix form of presentation of the special 8-dimensional Yin-Yang-algebra and of its particular 4-dimensional case. The special algorithm, which is based on features of genetic molecules, exists to transform the mosaic genomatrix into the matrices of these algebras. Two new numeric systems are defined by these 8-dimensional and 4-dimensional algebras: genetic Yin-Yang-octaves and genetic tetrions. Their comparison with quaternions by Hamilton is presented. Elements of new "genovector calculation" and ideas of "genetic mechanics" are discussed. These algebras are considered as models of the genetic code and as its possible pre-code ba...

  4. Global Genetic Robustness of the Alternative Splicing Machinery in Caenorhabditis elegans

    NARCIS (Netherlands)

    Li, Yang; Breitling, Rainer; Snoek, L. Basten; van der Velde, K. Joeri; Swertz, Morris A.; Riksen, Joost; Jansen, Ritsert C.; Kammenga, Jan E.; Borevitz, J.

    2010-01-01

    Alternative splicing is considered a major mechanism for creating multicellular diversity from a limited repertoire of genes. Here, we performed the first study of genetic variation controlling alternative splicing patterns by comprehensively identifying quantitative trait loci affecting the differe

  5. 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

  6. A novel Lie algebra of the genetic code over the Galois field of four DNA bases.

    Science.gov (United States)

    Sánchez, Robersy; Grau, Ricardo; Morgado, Eberto

    2006-07-01

    Starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the main partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignments and physicochemical properties of amino acids. Moreover, a distance defined between codons expresses a physicochemical meaning. It was also noticed that the distance between wild type and mutant codons tends to be small in mutational variants of four genes: human phenylalanine hydroxylase, human beta-globin, HIV-1 protease and HIV-1 reverse transcriptase. These results strongly suggest that deterministic rules in genetic code origin must be involved. PMID:16780898

  7. 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.

  8. The non-power model of the genetic code: a paradigm for interpreting genomic information.

    Science.gov (United States)

    Gonzalez, Diego Luis; Giannerini, Simone; Rosa, Rodolfo

    2016-03-13

    In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications. PMID:26857679

  9. An alternative strategy to generate coding sequence of macrophage migration inhibitory factor-2 of Wuchereria bancrofti

    OpenAIRE

    Nikhil Chauhan; Hoti, S.L.

    2016-01-01

    Background & objectives: Different developmental stages of Wuchereria bancrofti, the major causal organism of lymphatic filariasis (LF), are difficult to obtain. Beside this limitation, to obtain complete coding sequence (CDS) of a gene one has to isolate mRNA and perform subsequent cDNA synthesis which is laborious and not successful at times. In this study, an alternative strategy employing polymerase chain reaction (PCR) was optimized and validated, to generate CDS of Macrophage migration ...

  10. 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 sci

  11. Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

    Indian Academy of Sciences (India)

    K Ikehara

    2002-03-01

    We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, -helix, -sheet and -turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. 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 structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages.

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

    International Nuclear Information System (INIS)

    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

  13. Genetic Searching Algorithm for Optimal Runlength—Limited Codes with Error Control

    Institute of Scientific and Technical Information of China (English)

    RenQingsheng; YeZhongxing

    1997-01-01

    A genetic searching algorithm is presented to construct arbitrarily concatenatable block code with runlength(d,k)constraints.The code also has the ability to correct error during decoding.A similar eliminating operator and an anti-symbiotic operator are suggested to improve the efficiency of the algorithm.

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

    NARCIS (Netherlands)

    Gulik, P.T.S. van der; Hoff, W.D.

    2011-01-01

    The 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 of the code and the i

  15. Problem-Based Test: An "In Vitro" Experiment to Analyze the Genetic Code

    Science.gov (United States)

    Szeberenyi, Jozsef

    2010-01-01

    Terms to be familiar with before you start to solve the test: genetic code, translation, synthetic polynucleotide, leucine, serine, filter precipitation, radioactivity measurement, template, mRNA, tRNA, rRNA, aminoacyl-tRNA synthesis, ribosomes, degeneration of the code, wobble, initiation, and elongation of protein synthesis, initiation codon.…

  16. 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.

  17. An Efficient Soft Decoder of Block Codes Based on Compact Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Ahmed Azouaoui

    2012-09-01

    Full Text Available Soft-decision decoding is an NP-hard problem with great interest to developers of communication systems. We present an efficient soft-decision decoder of linear block codes based on compact genetic algorithm (cGA and compare its performances with various other decoding algorithms including Shakeel algorithm. The proposed algorithm uses the dual code in contrast to Shakeel algorithm which uses the code itself. Hence, this new approach reduces the decoding complexity of high rates codes. The complexity and an optimized version of this new algorithm are also presented and discussed.

  18. Matrix genetics, part 3: the evolution of the genetic code from the viewpoint of the genetic octave Yin-Yang-algebra

    OpenAIRE

    Petoukhov, Sergey V.

    2008-01-01

    The set of known dialects of the genetic code (GC) is analyzed from the viewpoint of the genetic octave Yin-Yang-algebra. This algebra was described in the previous author's publications. The algebra was discovered on the basis of structural features of the GC in the matrix form of its presentation ("matrix genetics"). The octave Yin-Yang-algebra is considered as the pre-code or as the model of the GC. From the viewpoint of this algebraic model, for example, the sets of 20 amino acids and of ...

  19. Algorithm Optical Codes: An alternative to Random Optical Codes in an intra-satellite optical wireless network

    OpenAIRE

    Martín González, Jesús Ángel; Poves Valdés, Enrique; López Hernández, Francisco

    2008-01-01

    We propose a novel family of optical codes to be used in intra-satellite optical wireless networks. They are Algorithm Optical Codes (AOCs). This family is related with the recently introduced family Random Optical Codes (ROCs). Both families of codes are designed to be used in optical Code-Division Multiple-Access (OCDMA) systems. Similarly than their predecessor, i.e. ROCs, AOCs are specially suitable for optical networks where the number of channels varies, ever large, low bit rate require...

  20. 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.

  1. Multiple description video coding using GOB alternation and low quality macroblock update

    Institute of Scientific and Technical Information of China (English)

    Wang Yangli; Wu Chengke

    2005-01-01

    To combat packet loss and realize robust video transmission over Internet and wireless networks, a new multiple description (MD) video coding method is proposed. In the method, two descriptions for each video frame is first created by group of blocks (GOB) alternation. Motion information is then duplicated in both the descriptions and a process called low quality macroblock update is designed to redundantly encode textures in each frame using standard bit stream syntax. In this way, the output bit streams are standard compliant and better trade-offs between redundancy and single channel reconstruction distortion are achieved. The proposed method has much better performance than the well-known MD transform coding (MDTC) method both in terms of redundancy rate distortion, and in the packet loss scenario.

  2. Yury Borisovich Rumer and his 'biological papers' on the genetic code.

    Science.gov (United States)

    Fimmel, Elena; Strüngmann, Lutz

    2016-03-13

    Yury Borisovich Rumer was one of the most important theoretical physicists of the former Soviet Union in the early 1930s. However, he also wrote a few 'biological papers' on the standard genetic code after he read Crick's and Nirenberg's pioneering papers on the topic. Rumer's articles on the 'Systematization of Codons in the Genetic Code' (Rumer 1966 Doklady Akademii nauk SSSR 167, 1393-1394); Rumer 1968 Doklady Akademii nauk SSSR 183, 225-226; Rumer 1969 Doklady Akademii nauk SSSR 187, 937-938, where he suggested the idea of partitioning codons depending on their redundancy-the first mention of symmetry in the genetic code-were published in Russian only. Due to their importance and their frequent citation, we here present translations of these articles into English in order to make them accessible to a broader community. PMID:26857664

  3. Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

    OpenAIRE

    Woese, Carl R.; Olsen, Gary J; Ibba, Michael; Söll, Dieter

    2000-01-01

    The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the followi...

  4. Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

    Directory of Open Access Journals (Sweden)

    Steven E. Massey

    2015-04-01

    Full Text Available The standard genetic code (SGC is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of “neutral emergence”. The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these “pseudaptations”, and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P, and that its reduction in size leads to an “unfreezing” of the codon – amino acid mapping that defines the genetic code, consistent with Crick’s Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome

  5. Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach.

    Science.gov (United States)

    Eslami-Mossallam, Behrouz; Schram, Raoul D; Tompitak, Marco; van Noort, John; Schiessel, Helmut

    2016-01-01

    Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function. PMID:27272176

  6. Scientific rationality, uncertainty and the governance of human genetics: an interview study with researchers at deCODE genetics.

    Science.gov (United States)

    Hjörleifsson, Stefán; Schei, Edvin

    2006-07-01

    Technology development in human genetics is fraught with uncertainty, controversy and unresolved moral issues, and industry scientists are sometimes accused of neglecting the implications of their work. The present study was carried out to elicit industry scientists' reflections on the relationship between commercial, scientific and ethical dimensions of present day genetics and the resources needed for robust governance of new technologies. Interviewing scientists of the company deCODE genetics in Iceland, we found that in spite of optimism, the informants revealed ambiguity and uncertainty concerning the use of human genetic technologies for the prevention of common diseases. They concurred that uncritical marketing of scientific success might cause exaggerated public expectations of health benefits from genetics, with the risk of backfiring and causing resistance to genetics in the population. On the other hand, the scientists did not address dilemmas arising from the commercial nature of their own employer. Although the scientists tended to describe public fear as irrational, they identified issues where scepticism might be well founded and explored examples where they, despite expert knowledge, held ambiguous or tentative personal views on the use of predictive genetic technologies. The rationality of science was not seen as sufficient to ensure beneficial governance of new technologies. The reflexivity and suspension of judgement demonstrated in the interviews exemplify productive features of moral deliberation in complex situations. Scientists should take part in dialogues concerning the governance of genetic technologies, acknowledge any vested interests, and use their expertise to highlight, not conceal the technical and moral complexity involved. PMID:16622446

  7. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

    Science.gov (United States)

    Aggarwal, Neha; Vishwa Bandhu, Ashutosh; Sengupta, Supratim

    2016-06-01

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

  8. Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code.

    Science.gov (United States)

    Aggarwal, Neha; Bandhu, Ashutosh Vishwa; Sengupta, Supratim

    2016-05-27

    The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

  9. GENETIC ALGORITHM FOR DECODING LINEAR CODES OVER AWGN AND FADING CHANNELS

    Directory of Open Access Journals (Sweden)

    H. BERBIA

    2011-08-01

    Full Text Available This paper introduces a decoder for binary linear codes based on Genetic Algorithm (GA over the Gaussian and Rayleigh flat fading channel. The performances and compututional complexity of our decoder applied to BCH and convolutional codes are good compared to Chase-2 and Viterbi algorithm respectively. It show that our algorithm is less complex for linear block codes of large block length; furthermore it's performances can be improved by tuning the decoder's parameters, in particular the number of individuals by population and the number of generations

  10. An improved Genetic Algorithm of Bi-level Coding for Flexible Job Shop Scheduling Problems

    Directory of Open Access Journals (Sweden)

    Ye Li

    2014-07-01

    Full Text Available The current study presents an improved genetic algorithm(GA for the flexible job shop scheduling problem (FJSP. The coding is divided into working sequence level and machine level and two effective crossover operators and mutation operators are designed for the generation and reduce the disruptive effects of genetic operators. The algorithm is tested on instances of 10 working sequences and 10 machines. Computational results show that the proposed GA was successfully and efficiently applied to the FJSP. The results were compared with other approaches, such as traditional GA and GA with neural network. Compared to traditional genetic algorithm, the proposed approach yields significant improvement in solution quality.

  11. Alternate Service Delivery Models in Cancer Genetic Counseling: A Mini-Review

    OpenAIRE

    Buchanan, Adam Hudson; Rahm, Alanna Kulchak; Williams, Janet L.

    2016-01-01

    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 o...

  12. [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.

  13. Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

    NARCIS (Netherlands)

    Kumar, Vinod; Westra, Harm-Jan; Karjalainen, Juha; Zhernakova, Daria V.; Esko, Tonu; Hrdlickova, Barbara; Almeida, Rodrigo; Zhernakova, Alexandra; Reinmaa, Eva; Hofker, Marten H.; Fehrmann, Rudolf S. N.; Fu, Jingyuan; Withoff, Sebo; Metspalu, Andres; Franke, Lude; Wijmenga, Cisca; Vosa, Urmo

    2013-01-01

    Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variation

  14. Stress, Neural Systems, and Genetic Code: An Interview with Neuroscientist Judy Cameron. Perspectives

    Science.gov (United States)

    National Scientific Council on the Developing Child, 2006

    2006-01-01

    Research indicates some early life stresses can have a profound impact, resulting in changes in brain function and behavior, and even differences in the ways some genes express their particular genetic code signature. At various times during early development, different neural systems appear to have an increased sensitivity to stress and can…

  15. Genetic Variation of Pre-mRNA Alternative Splicing in Human Populations

    OpenAIRE

    Lu, Zhi-xiang; Jiang, Peng; Xing, Yi

    2011-01-01

    The precise splicing outcome of a transcribed gene is controlled by complex interactions between cis regulatory splicing signals and trans-acting regulators. In higher eukaryotes, alternative splicing is a prevalent mechanism for generating transcriptome and proteome diversity. Alternative splicing can modulate gene function, affect organismal phenotype and cause disease. Common genetic variation that affects splicing regulation can lead to differences in alternative splicing between human in...

  16. Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila.

    Directory of Open Access Journals (Sweden)

    Daniela Brites

    Full Text Available In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig domains of the Dscam protein. This diversity plays a role in the development of the nervous system and also in the immune system. Structural analysis of the protein suggested candidate epitopes where binding to pathogens could occur. These epitopes are coded by regions of the duplicated exons and are therefore diverse within individuals. Here we apply molecular population genetics and molecular evolution analyses using Daphnia magna and several Drosophila species to investigate the potential role of natural selection in the divergence between orthologs of these duplicated exons among species, as well as between paralogous exons within species. We found no evidence for a role of positive selection in the divergence of these paralogous exons. However, the power of this test was low, and the fact that no signs of gene conversion between paralogous exons were found suggests that paralog diversity may nonetheless be maintained by selection. The analysis of orthologous exons in Drosophila and in Daphnia revealed an excess of non-synonymous polymorphisms in the epitopes putatively involved in pathogen binding. This may be a sign of balancing selection. Indeed, in Dr. melanogaster the same derived non-synonymous alleles segregate in several populations around the world. Yet other hallmarks of balancing selection were not found. Hence, we cannot rule out that the excess of non-synonymous polymorphisms is caused by segregating slightly deleterious alleles, thus potentially indicating reduced selective constraints in the putative pathogen binding epitopes of Dscam.

  17. A coding-independent function of an alternative Ube3a transcript during neuronal development.

    Science.gov (United States)

    Valluy, Jeremy; Bicker, Silvia; Aksoy-Aksel, Ayla; Lackinger, Martin; Sumer, Simon; Fiore, Roberto; Wüst, Tatjana; Seffer, Dominik; Metge, Franziska; Dieterich, Christoph; Wöhr, Markus; Schwarting, Rainer; Schratt, Gerhard

    2015-05-01

    The E3 ubiquitin ligase Ube3a is an important regulator of activity-dependent synapse development and plasticity. Ube3a mutations cause Angelman syndrome and have been associated with autism spectrum disorders (ASD). However, the biological significance of alternative Ube3a transcripts generated in mammalian neurons remains unknown. We report here that Ube3a1 RNA, a transcript that encodes a truncated Ube3a protein lacking catalytic activity, prevents exuberant dendrite growth and promotes spine maturation in rat hippocampal neurons. Surprisingly, Ube3a1 RNA function was independent of its coding sequence but instead required a unique 3' untranslated region and an intact microRNA pathway. Ube3a1 RNA knockdown increased activity of the plasticity-regulating miR-134, suggesting that Ube3a1 RNA acts as a dendritic competing endogenous RNA. Accordingly, the dendrite-growth-promoting effect of Ube3a1 RNA knockdown in vivo is abolished in mice lacking miR-134. Taken together, our results define a noncoding function of an alternative Ube3a transcript in dendritic protein synthesis, with potential implications for Angelman syndrome and ASD. PMID:25867122

  18. Genetic variation in the non-coding genome : Involvement of micro-RNAs and long non-coding RNAs in disease

    NARCIS (Netherlands)

    Hrdlickova, Barbara; de Almeida, Rodrigo Coutinho; Borek, Zuzanna; Withoff, Sebo

    2014-01-01

    It has been found that the majority of disease-associated genetic variants identified by genome-wide association studies are located outside of protein-coding regions, where they seem to affect regions that control transcription (promoters, enhancers) and non-coding RNAs that also can influence gene

  19. Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code

    Directory of Open Access Journals (Sweden)

    Tate Warren P

    2008-12-01

    Full Text Available Abstract Background Transfer RNA (tRNA is the means by which the cell translates DNA sequence into protein according to the rules of the genetic code. A credible proposition is that tRNA was formed from the duplication of an RNA hairpin half the length of the contemporary tRNA molecule, with the point at which the hairpins were joined marked by the canonical intron insertion position found today within tRNA genes. If these hairpins possessed a 3'-CCA terminus with different combinations of stem nucleotides (the ancestral operational RNA code, specific aminoacylation and perhaps participation in some form of noncoded protein synthesis might have occurred. However, the identity of the first tRNA and the initial steps in the origin of the genetic code remain elusive. Results Here we show evidence that glycine tRNA was the first tRNA, as revealed by a vestigial imprint in the anticodon loop sequences of contemporary descendents. This provides a plausible mechanism for the missing first step in the origin of the genetic code. In 448 of 466 glycine tRNA gene sequences from bacteria, archaea and eukaryote cytoplasm analyzed, CCA occurs immediately upstream of the canonical intron insertion position, suggesting the first anticodon (NCC for glycine has been captured from the 3'-terminal CCA of one of the interacting hairpins as a result of an ancestral ligation. Conclusion That this imprint (including the second and third nucleotides of the glycine tRNA anticodon has been retained through billions of years of evolution suggests Crick's 'frozen accident' hypothesis has validity for at least this very first step at the dawn of the genetic code. Reviewers This article was reviewed by Dr Eugene V. Koonin, Dr Rob Knight and Dr David H Ardell.

  20. On origin of genetic code and tRNA before translation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs

    2011-02-01

    Full Text Available Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas. A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1 the fundamental veto on "foresight evolution", 2 modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3 the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code the anticodon(2-3/codon(1-2 tetramers to their anticodon(1-2/codon(2-3 counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator to the eventual 76 base

  1. An Efficient Dynamic Orthogonal Variable Spreading Factor Code Allocation Approach in WCDMA through Modified Adaptive Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    P. Kavipriya

    2014-03-01

    Full Text Available Orthogonal Variable Spreading Factor (OVSF codes would give variable data rate transmissions for different bandwidth supplies in Wideband CDMA (WCDMA networks. These OVSF codes are used for the channelization of codes in WCDMA. In WCDMA, effective utilization of OVSF codes has become an active area of research as the number of codes is very limited. It is a fact that the successor and predecessor codes of OVSF cannot be used simultaneously when a specific code is used in OVSF as their encoded sequences become indistinguishable. Consequently, OVSF code tree has inadequate number of available codes. Thus, this research study uses Adaptive Genetic Algorithm (AGA based approach for dynamic OVSF code assignment in WCDMA networks. Different from existing Conventional Code Assignment (CCA and dynamic code assignment schemes, population is adaptively constructed according to existing traffic density in the OVSF code-tree. In existing technique in order to improve the ability of the GA, ‘‘dominance and diploidy’’ structure is employed to adapt to changing traffic conditions. Because in SGA algorithm cannot convergence if the new user is included into the existing OVSF code tree while SGA is running to find optimum OVSF code tree, SGA cannot adapt its structure to this unexpected variation. This problem can be overcome by the Modified Adaptive Genetic Algorithm (MAGA. Performance of the proposed MAGA approach is evaluated in terms of blocking probability and spectral efficiency and is compared with SGA, D&D GA.

  2. Why Your ZIP Code Matters More Than Your Genetic Code: Promoting Healthy Outcomes from Mother to Child.

    Science.gov (United States)

    Graham, Garth N

    2016-10-01

    Health equity has long been the dominant theme in the work of the Aetna Foundation. Recent data have focused on disparities through another lens, particularly the correlation between where people live (i.e., ZIP code) and their quality-and length-of life. In various cities across America, average life expectancies in certain communities are 20-30 years shorter than those mere miles away. In general, health disparities are founded on a complex interplay of racial, economic, educational, and other social factors. For example, breastfeeding rates in the United States differ significantly depending upon the race and income of the mother. Government policy makers are acutely aware of these disparities, but recent health system reforms have focused predominately on the processes used to administer, finance, and deliver care. What is needed is an approach that considers the health and wellness of all people in a geographic area, beyond established patients, and that measures more than clinical factors-such as genetics, environmental health, social circumstances, and individual behaviors. Solutions also must extend beyond the traditional healthcare arena. In particular, novel technological innovations show promise to bridge gaps between our healthcare capabilities and the needs of underserved populations. Digital tools are poised to revolutionize measurement, diagnostics, treatment, and global aspect of our healthcare system. The Aetna Foundation views technology as a core strategy in reducing health inequities through an approach that addresses both clinical and social factors in populations to dismantle the persistent paradigm of ZIP code as personal health destiny.

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

    International Nuclear Information System (INIS)

    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

  4. CONGESTION MANAGEMENT IN DEREGULATED POWER SYSTEMS USING REAL CODED GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    Sujatha Balaraman

    2010-11-01

    Full Text Available In this paper, an efficient method has been proposed for transmission line over load alleviation in deregulated power system using real coded genetic algorithm (RCGA. For secure operation of power system, the network loading has to be maintained within specified limits. Transmission line congestion initiates the cascading outages which forces the system to collapse. Accurate prediction and alleviation of line overloads is the suitable corrective action to avoid network collapse. In this paper an attempt is made to explore the use of real coded genetic algorithm to find the optimal generation rescheduling for relieving congestion. The effectiveness of the proposed algorithm has been analyzed on IEEE 30 bus test system. The results obtained by the proposed method are found to be quite encouraging when compared with Simulated Annealing (SA and hence it will be useful in electrical restructuring.

  5. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code

    CERN Document Server

    Higgs, Paul G

    2009-01-01

    Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

  6. 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.

  7. The genetic code degeneracy and the amino acids chemical composition are connected

    OpenAIRE

    Negadi, Tidjani

    2009-01-01

    We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the chemical composition of the 20 canonical amino acids. As a result, several remarkable atomic patterns involving hydrogen, carbon, nucleon and atom numbers are derived. This study has no obvious practical application(s) but could, we hope, add some new know...

  8. A Modified Integer Coded Genetic Algorithm Design of Time-Variant Staggered Sampling MTI Filter

    Institute of Scientific and Technical Information of China (English)

    TAOHaihong; LIAOGuisheng; WANGLing

    2005-01-01

    The stagger time-variant sampling MTI filter design is an effective method to reject clutter and alleviate the blind speed problem. Selecting the suitable stagger-code to make the nadir shallow can avoid the loss of weak target in it. Also multi-model clutters can be suppressed by MTI filter, and blind-velocity can appear out of three times velocity of sound. So the low speed weak target can be detected out of strong multl-model clutters. The paper presents a modified Integer coded genetic algorithm (ICGA) including some strategies to select the optimal stagger-code. By comparing with other traditional algorithm, GA is a global stochastic searching method and can converge quickly. The simulation and performance analysis demonstrate the feasibility and validity of this algorithm.

  9. Two-terminal Distributed Source Coding with Alternating Messages for Function Computation

    CERN Document Server

    Ma, Nan

    2008-01-01

    A two-terminal interactive distributed source coding problem with alternating messages is studied. The focus is on function computation at both locations with a probability which tends to one as the blocklength tends to infinity. A single-letter characterization of the rate region is provided. It is observed that interaction is useless (in terms of the minimum sum-rate) if the goal is pure source reproduction at one or both locations but the gains can be arbitrarily large for (general) function computation. For doubly symmetric binary sources and any Boolean function, interaction is useless with even infinite messages, when computation is desired at only one location, but is useful, when desired at both locations. For independent Bernoulli sources and the Boolean AND function computation at both locations, an interesting achievable infinite-message sum-rate is derived. This sum-rate is expressed, in analytic closed-form, in terms of a two-dimensional definite integral with an infinitesimal rate for each messa...

  10. Application of hybrid coded genetic algorithm in fuzzy neural network controller

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Presents the fuzzy neural network optimized by hybrid coded genetic algorithm of decimal encoding and bi nary encoding, the searching ability and stability of genetic algorithms enhanced by using binary encoding during the crossover operation and decimal encoding during the mutation operation, and the way of accepting new individuals by probability adopted, by which a new individual is accepted and its parent is discarded when its fitness is higher than that of its parent, and a new individual is accepted by probability when its fitness is lower than that of its parent. And concludes with calculations made with an example that these improvements enhance the speed of genetic algorithms to optimize the fuzzy neural network controller.

  11. Genetic programming as alternative for predicting development effort of individual software projects.

    Directory of Open Access Journals (Sweden)

    Arturo Chavoya

    Full Text Available Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment.

  12. Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Lilach Soreq

    2014-03-01

    Full Text Available The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence, calling for the development of inexpensive blood-based diagnostics. Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace. However, there is lack of tools to discover novel exons, junctions and splicing events and to precisely and sensitively assess differential splicing through RNA-Seq data analysis and across RNA-Seq platforms. Here, we present a new and comprehensive computational workflow for whole-transcriptome RNA-Seq analysis, using an updated version of the software AltAnalyze, to identify both known and novel high-confidence alternative splicing events, and to integrate them with both protein-domains and microRNA binding annotations. We applied the novel workflow on RNA-Seq data from Parkinson's disease (PD patients' leukocytes pre- and post- Deep Brain Stimulation (DBS treatment and compared to healthy controls. Disease-mediated changes included decreased usage of alternative promoters and N-termini, 5'-end variations and mutually-exclusive exons. The PD regulated FUS and HNRNP A/B included prion-like domains regulated regions. We also present here a workflow to identify and analyze long non-coding RNAs (lncRNAs via RNA-Seq data. We identified reduced lncRNA expression and selective PD-induced changes in 13 of over 6,000 detected leukocyte lncRNAs, four of which were inversely altered post-DBS. These included the U1 spliceosomal lncRNA and RP11-462G22.1, each entailing sequence complementarity to numerous microRNAs. Analysis of RNA-Seq from PD and unaffected controls brains revealed over 7,000 brain-expressed lncRNAs, of which 3,495 were co-expressed in the leukocytes including U1, which showed both leukocyte and brain increases. Furthermore, qRT-PCR validations confirmed these co-increases in PD leukocytes and two brain regions, the amygdala and substantia

  13. Matrix genetics, part 3: the evolution of the genetic code from the viewpoint of the genetic octave Yin-Yang-algebra

    CERN Document Server

    Petoukhov, Sergey V

    2008-01-01

    The set of known dialects of the genetic code (GC) is analyzed from the viewpoint of the genetic octave Yin-Yang-algebra. This algebra was described in the previous author's publications. The algebra was discovered on the basis of structural features of the GC in the matrix form of its presentation ("matrix genetics"). The octave Yin-Yang-algebra is considered as the pre-code or as the model of the GC. From the viewpoint of this algebraic model, for example, the sets of 20 amino acids and of 64 triplets consist of sub-sets of "male", "female" and "androgynous" molecules, etc. This algebra permits to reveal hidden peculiarities of the structure and evolution of the GC and to propose the conception of "sexual" relationships among genetic molecules. The first results of the analysis of the GC systems from such algebraic viewpoint say about the close connection between evolution of the GC and this algebra. They include 8 evolutionary rules of the dialects of the GC. The evolution of the GC is appeared as the stru...

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

    International Nuclear Information System (INIS)

    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 CO2 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

  15. The Biosynthetic Order of Amino Acid Addition to the Genetic Code

    CERN Document Server

    Davis, B K

    2002-01-01

    The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the model indicated that the direction of code evolution changed on expansion from the N-fixers code (stage 2). Growth of the code from 16 codons in the NAN column (N, any standard nucleotide) proceeded by assignment of codons in the GNN, ANN, CNN and UNN rows. Expansion phase (stage 4 to 7) precursor/product pairs that spanned this shift included aspartate/threonine, aspartate/methionine and glutamate/proline. Both 5' and mid-base differ in the codons of each of these pairs. Second, post-expansion additions (stage 9 to 14) required codon reassignment, eliminating initial correlations. Codons for the post-expansion pair, aspartate (glutamate)/arginine, also differ at both 5' and mid-base sites. Third, the distribution of core structure groups among acceptors indicated that varia...

  16. CSD-Coded Genetic Algorithm on Robustly Stable Multiplierless IIR Filter Design

    OpenAIRE

    Shing-Tai Pan

    2012-01-01

    A Canonic-Signed-Digit-(CSD-) coded genetic algorithm (GA) is proposed to find the optimal design of robustly stable infinite impulse response digital filter (IIR). Under the characteristics of the CSD structure, the circuit of the filter can be simplified and also the calculation speed can be raised to increase the hardware’s efficiency. However, the design of CSD has a big challenge: the CSD structure of the system parameters will be destroyed by an optimal design procedure. To solve this p...

  17. Real-coded genetic algorithm for optimal vibration control of flexible structure

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Presents the study on the optimum location of actuators/sensors for active vibration control in aerospace flexible structures with the performance function first built by maximization of dissipation energy due to control action and a real-coded genetic algorithm then proposed to produce a global-optimum solution, and proves the feasibility and advantages of this algorithm with the example of a standard test function and a two-collocated actuators/sensors cantilever, and comparing the results with those given in the literatures.

  18. Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code

    OpenAIRE

    Tate Warren P; Bernhardt Harold S

    2008-01-01

    Abstract Background Transfer RNA (tRNA) is the means by which the cell translates DNA sequence into protein according to the rules of the genetic code. A credible proposition is that tRNA was formed from the duplication of an RNA hairpin half the length of the contemporary tRNA molecule, with the point at which the hairpins were joined marked by the canonical intron insertion position found today within tRNA genes. If these hairpins possessed a 3'-CCA terminus with different combinations of s...

  19. Alternative construction of interleaved RLL codes for partial response channels using multichannel methods

    Science.gov (United States)

    Swanson, Robert E.

    1994-09-01

    Current work in magnetic recording channels has demonstrated significant improvement in recording density using partial response communication methods along with maximum likelihood detection. The class IV partial response channel (PR4) behaves as the interleaving of two identical run-length limited (RLL) channels. Efficient recording codes for the PR4 channel have been made by considering a channel bit sequence to be composed of two interleaved subsequences. Finite state techniques are used to describe run-length constraints on each subsequence as well as a global run-length constraint on both sequences combined. A recent paper by Swanson and Wolf discusses multichannel run-length limited codes that turn out to be very similar to interleaved run-length limited codes. The present paper discusses the similarities between the code description of multichannel RLL codes and the interleaved RLL codes required by the PR4 channel. The extension of the techniques of multichannel RLL work to the interleaved problem is discussed. It was found that suitable code constructions are possible by viewing the problem as two distinct RLL codes that have individual maximum run-lengths onto which a global run-length is imposed. Two examples are developed to illustrate the ideas.

  20. Analysis of protein-coding genetic variation in 60,706 humans.

    Science.gov (United States)

    Lek, Monkol; Karczewski, Konrad J; Minikel, Eric V; Samocha, Kaitlin E; Banks, Eric; Fennell, Timothy; O'Donnell-Luria, Anne H; Ware, James S; Hill, Andrew J; Cummings, Beryl B; Tukiainen, Taru; Birnbaum, Daniel P; Kosmicki, Jack A; Duncan, Laramie E; Estrada, Karol; Zhao, Fengmei; Zou, James; Pierce-Hoffman, Emma; Berghout, Joanne; Cooper, David N; Deflaux, Nicole; DePristo, Mark; Do, Ron; Flannick, Jason; Fromer, Menachem; Gauthier, Laura; Goldstein, Jackie; Gupta, Namrata; Howrigan, Daniel; Kiezun, Adam; Kurki, Mitja I; Moonshine, Ami Levy; Natarajan, Pradeep; Orozco, Lorena; Peloso, Gina M; Poplin, Ryan; Rivas, Manuel A; Ruano-Rubio, Valentin; Rose, Samuel A; Ruderfer, Douglas M; Shakir, Khalid; Stenson, Peter D; Stevens, Christine; Thomas, Brett P; Tiao, Grace; Tusie-Luna, Maria T; Weisburd, Ben; Won, Hong-Hee; Yu, Dongmei; Altshuler, David M; Ardissino, Diego; Boehnke, Michael; Danesh, John; Donnelly, Stacey; Elosua, Roberto; Florez, Jose C; Gabriel, Stacey B; Getz, Gad; Glatt, Stephen J; Hultman, Christina M; Kathiresan, Sekar; Laakso, Markku; McCarroll, Steven; McCarthy, Mark I; McGovern, Dermot; McPherson, Ruth; Neale, Benjamin M; Palotie, Aarno; Purcell, Shaun M; Saleheen, Danish; Scharf, Jeremiah M; Sklar, Pamela; Sullivan, Patrick F; Tuomilehto, Jaakko; Tsuang, Ming T; Watkins, Hugh C; Wilson, James G; Daly, Mark J; MacArthur, Daniel G

    2016-08-18

    Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes. PMID:27535533

  1. Analysis of protein-coding genetic variation in 60,706 humans.

    Science.gov (United States)

    Lek, Monkol; Karczewski, Konrad J; Minikel, Eric V; Samocha, Kaitlin E; Banks, Eric; Fennell, Timothy; O'Donnell-Luria, Anne H; Ware, James S; Hill, Andrew J; Cummings, Beryl B; Tukiainen, Taru; Birnbaum, Daniel P; Kosmicki, Jack A; Duncan, Laramie E; Estrada, Karol; Zhao, Fengmei; Zou, James; Pierce-Hoffman, Emma; Berghout, Joanne; Cooper, David N; Deflaux, Nicole; DePristo, Mark; Do, Ron; Flannick, Jason; Fromer, Menachem; Gauthier, Laura; Goldstein, Jackie; Gupta, Namrata; Howrigan, Daniel; Kiezun, Adam; Kurki, Mitja I; Moonshine, Ami Levy; Natarajan, Pradeep; Orozco, Lorena; Peloso, Gina M; Poplin, Ryan; Rivas, Manuel A; Ruano-Rubio, Valentin; Rose, Samuel A; Ruderfer, Douglas M; Shakir, Khalid; Stenson, Peter D; Stevens, Christine; Thomas, Brett P; Tiao, Grace; Tusie-Luna, Maria T; Weisburd, Ben; Won, Hong-Hee; Yu, Dongmei; Altshuler, David M; Ardissino, Diego; Boehnke, Michael; Danesh, John; Donnelly, Stacey; Elosua, Roberto; Florez, Jose C; Gabriel, Stacey B; Getz, Gad; Glatt, Stephen J; Hultman, Christina M; Kathiresan, Sekar; Laakso, Markku; McCarroll, Steven; McCarthy, Mark I; McGovern, Dermot; McPherson, Ruth; Neale, Benjamin M; Palotie, Aarno; Purcell, Shaun M; Saleheen, Danish; Scharf, Jeremiah M; Sklar, Pamela; Sullivan, Patrick F; Tuomilehto, Jaakko; Tsuang, Ming T; Watkins, Hugh C; Wilson, James G; Daly, Mark J; MacArthur, Daniel G

    2016-08-17

    Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

  2. Real Coded Genetic Algorithm Based Improvement of Efficiency in Interleaved Boost Converter

    Directory of Open Access Journals (Sweden)

    K Valarmathi

    2015-02-01

    Full Text Available   The reliability, efficiency, and controllability of Photo Voltaic power systems can be increased by embedding the components of a Boost Converter. Currently, the converter technology overcomes the main problems of manufacturing cost, efficiency and mass production. Issue to limit the life span of a Photo Voltaic inverter is the huge electrolytic capacitor across the Direct Current bus for energy decoupling. This paper presents a two-phase interleaved boost converter which ensures 180 angle phase shift between the two interleaved converters. The Proportional Integral controller is used to reshape that the controller attempts to minimize the error by adjusting the control inputs and also real coded genetic algorithm is proposed for tuning of controlling parameters of Proportional Integral controller. The real coded genetic algorithm is applied in the Interleaved Boost Converter with Advanced Pulse Width Modulation Techniques for improving the results of efficiency and reduction of ripple current. Simulation results illustrate the improvement of efficiency and the diminution of ripple current.

  3. ATRX mutations and glioblastoma: Impaired DNA damage repair, alternative lengthening of telomeres, and genetic instability.

    Science.gov (United States)

    Koschmann, Carl; Lowenstein, Pedro R; Castro, Maria G

    2016-05-01

    Alpha thalassemia/mental retardation syndrome X-linked (ATRX) is mutated in nearly a third of pediatric glioblastoma (GBM) patients. We developed an animal model of ATRX-deficient GBM. Using this model combined with analysis of multiple human glioma genome-wide datasets, we determined that ATRX mutation leads to genetic instability, impaired non-homologous end joining, and alternate lengthening of telomeres (ALT). PMID:27314101

  4. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer

    Science.gov (United States)

    Timofeeva, Maria N.; Kinnersley, Ben; Farrington, Susan M.; Whiffin, Nicola; Palles, Claire; Svinti, Victoria; Lloyd, Amy; Gorman, Maggie; Ooi, Li-Yin; Hosking, Fay; Barclay, Ella; Zgaga, Lina; Dobbins, Sara; Martin, Lynn; Theodoratou, Evropi; Broderick, Peter; Tenesa, Albert; Smillie, Claire; Grimes, Graeme; Hayward, Caroline; Campbell, Archie; Porteous, David; Deary, Ian J.; Harris, Sarah E.; Northwood, Emma L.; Barrett, Jennifer H.; Smith, Gillian; Wolf, Roland; Forman, David; Morreau, Hans; Ruano, Dina; Tops, Carli; Wijnen, Juul; Schrumpf, Melanie; Boot, Arnoud; Vasen, Hans F A; Hes, Frederik J.; van Wezel, Tom; Franke, Andre; Lieb, Wolgang; Schafmayer, Clemens; Hampe, Jochen; Buch, Stephan; Propping, Peter; Hemminki, Kari; Försti, Asta; Westers, Helga; Hofstra, Robert; Pinheiro, Manuela; Pinto, Carla; Teixeira, Manuel; Ruiz-Ponte, Clara; Fernández-Rozadilla, Ceres; Carracedo, Angel; Castells, Antoni; Castellví-Bel, Sergi; Campbell, Harry; Bishop, D. Timothy; Tomlinson, Ian P M; Dunlop, Malcolm G.; Houlston, Richard S.

    2015-01-01

    Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10−7), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10−7); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10−7 and OR = 1.09, P = 7.4 × 10−8); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10−9), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 × 10−6). We found an excess of rare, damaging variants in base-excision (P = 2.4 × 10−4) and DNA mismatch repair genes (P = 6.1 × 10−4) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC. PMID:26553438

  5. Rapid communication The mental number line dominates alternative, explicit coding of number magnitude.

    Science.gov (United States)

    Dollman, Justin; Levine, William H

    2016-01-01

    Numerical judgments are facilitated for left-space responses to a smaller number and right-space responses to a larger number (the spatial-numerical association of response codes, SNARC, effect). Despite support for a mental number line (i.e., spatial) explanation of the SNARC effect, this account has been challenged by an intermediate-coding theory that makes use of a polarity-correspondence principle. The latter is a general explanatory framework whereby stimulus and response dimensions are represented in a categorical, binary manner, with complementary categories coded as having either positive or negative polarity. When stimulus and response polarity match, responding is facilitated. In the present experiment we pitted explicitly presented close-far coding against an implicit mental number line (i.e., left-right coding). Subjects categorized numbers (1, 4, 6, and 9) as greater or less than a standard (5) using keys defined only as close to and far from a starting key. We found that, despite instructing subjects to use a close-far coding scheme, they exhibited a typical SNARC effect, with small-number responses facilitated on the left and large-number responses on the right. These results are discussed in the context of results supporting the polarity explanation and with respect to representational pluralism. PMID:26445276

  6. APPLICATION OF INTEGER CODING ACCELERATING GENETIC ALGORITHM IN RECTANGULAR CUTTING STOCK PROBLEM

    Institute of Scientific and Technical Information of China (English)

    FANG Hui; YIN Guofu; LI Haiqing; PENG Biyou

    2006-01-01

    An improved genetic algorithm and its application to resolve cutting stock problem are presented. It is common to apply simple genetic algorithm (SGA) to cutting stock problem, but the huge amount of computing of SGA is a serious problem in practical application. Accelerating genetic algorithm (AGA) based on integer coding and AGA's detailed steps are developed to reduce the amount of computation, and a new kind of rectangular parts blank layout algorithm is designed for rectangular cutting stock problem. SGA is adopted to produce individuals within given evolution process, and the variation interval of these individuals is taken as initial domain of the next optimization process, thus shrinks searching range intensively and accelerates the evaluation process of SGA.To enhance the diversity of population and to avoid the algorithm stagnates at local optimization result, fixed number of individuals are produced randomly and replace the same number of parents in every evaluation process. According to the computational experiment, it is observed that this improved GA converges much sooner than SGA, and is able to get the balance of good result and high efficiency in the process of optimization for rectangular cutting stock problem.

  7. Coding Psychological Constructs in Text Using Mechanical Turk: A Reliable, Accurate, and Efficient Alternative.

    Science.gov (United States)

    Tosti-Kharas, Jennifer; Conley, Caryn

    2016-01-01

    In this paper we evaluate how to effectively use the crowdsourcing service, Amazon's Mechanical Turk (MTurk), to content analyze textual data for use in psychological research. MTurk is a marketplace for discrete tasks completed by workers, typically for small amounts of money. MTurk has been used to aid psychological research in general, and content analysis in particular. In the current study, MTurk workers content analyzed personally-written textual data using coding categories previously developed and validated in psychological research. These codes were evaluated for reliability, accuracy, completion time, and cost. Results indicate that MTurk workers categorized textual data with comparable reliability and accuracy to both previously published studies and expert raters. Further, the coding tasks were performed quickly and cheaply. These data suggest that crowdsourced content analysis can help advance psychological research. PMID:27303321

  8. Alternate Service Delivery Models in Cancer Genetic Counseling: A Mini-Review.

    Science.gov (United States)

    Buchanan, Adam Hudson; Rahm, Alanna Kulchak; Williams, Janet L

    2016-01-01

    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. PMID:27242960

  9. 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.

  10. Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation.

    Science.gov (United States)

    Weng, Lingjie; Li, Yi; Xie, Xiaohui; Shi, Yongsheng

    2016-06-01

    mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional gene regulation and is often regulated in a tissue- and/or developmental stage-specific manner. An ultimate goal for the APA field has been to be able to computationally predict APA profiles under different physiological or pathological conditions. As a first step toward this goal, we have assembled a poly(A) code for predicting tissue-specific poly(A) sites (PASs). Based on a compendium of over 600 features that have known or potential roles in PAS selection, we have generated and refined a machine-learning algorithm using multiple high-throughput sequencing-based data sets of tissue-specific and constitutive PASs. This code can predict tissue-specific PASs with >85% accuracy. Importantly, by analyzing the prediction performance based on different RNA features, we found that PAS context, including the distance between alternative PASs and the relative position of a PAS within the gene, is a key feature for determining the susceptibility of a PAS to tissue-specific regulation. Our poly(A) code provides a useful tool for not only predicting tissue-specific APA regulation, but also for studying its underlying molecular mechanisms. PMID:27095026

  11. The Optimization of Dispersion Properties of Photonic Crystal Fibers Using a Real-Coded Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    YIN Guo-Bing; LI Shu-Guang; LIU Shuo; WANG Xiao-Yan

    2011-01-01

    @@ A real-coded genetic algorithm (GA) combined with a fully vectorial effective index method (FVEIM) is employed to design structures of photonic crystal fibers (PCFs) with user defined dispersion properties theoretically.The structures of PCFs whose solid cores axe doped GeO with zero-dispersions at 0.7-3.9μm are optimized and the flat dispersion ranges through the R+L+C band and the negative dispersion is -1576.26 ps.km·nm at 1.55μm.Analyses show that the zero-dispersion wavelength (ZDW) could be one of many ZDWs for the same fiber structure; PCFs couM alter the dispersion to be flattened through the R+L+C band with a single air-hole diameter; and negative dispersion requires high air filling rate at 1.55μm.The method is proved to be elegant for solving this inverse problem.

  12. Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA).

    Science.gov (United States)

    Ramesh, S V

    2013-09-01

    Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.

  13. Genetic evidence for conserved non-coding element function across species--the ears have it

    Directory of Open Access Journals (Sweden)

    Eric E Turner

    2014-01-01

    Full Text Available Comparison of genomic sequences from diverse vertebrate species has revealed numerous highly conserved regions that do not appear to encode proteins or functional RNAs. Often these conserved non-coding elements, or CNEs, direct gene expression to specific tissues in transgenic models, demonstrating they have regulatory function. CNEs are frequently found near ‘developmental’ genes, particularly transcription factors, implying that these elements have essential regulatory roles in development. However, actual examples demonstrating CNE regulatory functions across species have been few, and recent loss-of-function studies of several CNEs in mice have shown relatively minor effects. In this Perspectives article, we discuss new findings in fancy rats and Highland cattle demonstrating that function of a CNE near the Hmx1 gene is crucial for normal external ear development and resembles loss-of function Hmx1 coding mutations in mice and humans. These findings provide important support for similar developmental roles of CNEs in divergent species, and reinforce the concept that CNEs should be examined systematically in the ongoing search for genetic causes of human developmental disorders in the era of genome-scale sequencing.

  14. Bandwidth optimization of a Planar Inverted-F Antenna using binary and real coded genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    AMEERUDDEN Mohammad Riyad; RUGHOOPUTH Harry C S

    2009-01-01

    With the exponential development of mobile communications and the miniaturization of radio frequency transceivers, the need for small and low profile antennas at mobile frequencies is constantly growing. Therefore, new antennas should be developed to provide larger bandwidth and at the same time small dimensions. Although the gain in bandwidth performances of an antenna are directly related to its dimensions in relation to the wavelength, the aim is to keep the overall size of the antenna constant and from there, find the geometry and structure that give the best performance. The design and bandwidth optimization of a Planar Inverted-F Antenna (PIFA) were introduced in order to achieve a larger bandwidth in the 2 GHz band, using two optimization techniques based upon genetic algorithms (GA), namely the Binary Coded GA (BCGA) and Real-Coded GA (RCGA). During the optimization process, the different PIFA models were evaluated using the finite-difference time domain (FDTD) method-a technique belonging to the general class of differential time domain numerical modeling methods.

  15. Search for Active-State Conformation of Drug Target GPCR Using Real-Coded Genetic Algorithm

    Science.gov (United States)

    Ishino, Yoko; Harada, Takanori; Aida, Misako

    G-Protein coupled receptors (GPCRs) comprise a large superfamily of proteins and are a target for nearly 50% of drugs in clinical use today. GPCRs have a unique structural motif, seven transmembrane helices, and it is known that agonists and antagonists dock with a GPCR in its ``active'' and ``inactive'' condition, respectively. Knowing conformations of both states is eagerly anticipated for elucidation of drug action mechanism. Since GPCRs are difficult to crystallize, the 3D structures of these receptors have not yet been determined by X-ray crystallography, except the inactive-state conformation of two proteins. The conformation of them enabled the inactive form of other GPCRs to be modeled by computer-aided homology modeling. However, to date, the active form of GPCRs has not been solved. This paper describes a novel method to predict the 3D structure of an active-state GPCR aiming at molecular docking-based virtual screening using real-coded genetic algorithm (real-coded GA), receptor-ligand docking simulations, and molecular dynamics (MD) simulations. The basic idea of the method is that the MD is first used to calculate an average 3D coordinates of all atoms of a GPCR protein against heat fluctuation on the pico- or nano- second time scale, and then real-coded GA involving receptor-ligand docking simulations functions to determine the rotation angle of each helix as a movement on wider time scale. The method was validated using human leukotriene B4 receptor BLT1 as a sample GPCR. Our study demonstrated that the established evolutionary search for the active state of the leukotriene receptor provided the appropriate 3D structure of the receptor to dock with its agonists.

  16. Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.; Watkins, C. L.; Hall, L. M.

    1986-01-01

    Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

  17. A Real-coded Genetic Algorithm Applied to Optimum Design of a Low Solidity Vaned Diffuser for Diffuser Pump

    Institute of Scientific and Technical Information of China (English)

    Jun LI; Hiroshi TSUKAMOTO

    2001-01-01

    A numerical procedure for hydrodynamic redesign of the conventional vaned diffuser into the low solidity vaned diffuser by means of a real-ceded genetic algorithm with Boltzmann, Tournament and Roulette Wheel selection is presented. In the first part, an investigation on the relative efficiency of the different real-coded genetic algorithm is carried out on a typical mathematical test function. The real-coded genetic algorithm with Boltzmann selection shows the best optimization performance compared to the Tournament and Roulette Wheel selection. In the second part, an approach to redesign the vaned diffuser profile is introduced. Goal of the optimum design is to search the highest static pressure recovery coefficient and low solidity vaned diffuser. The result of the low solidity vaned diffuser optimum design confirms that the efficiency and optimization performance of the real-coded Boltzmann selection genetic algorithm outperforms the other selection methods. A comparison between the designed low solidity vaned diffuser and original vaned diffuser shows that the diffuser pump with the redesigned low solidity vaned diffuser has the higher static pressure recovery and improved total hydrodynamic performance. In addition,the smaller outlet diameter of designed vaned diffuser tends to a more compact size of diffuser pump compared to the original diffuser pump. The obtained results also demonstrate the real-coded Boltzmann selection genetic algorithm is a promising optimization algorithm for centrifugal pumps design.

  18. Translocation Properties of Primitive Molecular Machines and Their Relevance to the Structure of the Genetic Code

    CERN Document Server

    Aldana, M; Larralde, H; Martínez-Mekler, G; Aldana, Maximino; Cocho, Germinal; Larralde, Hernan; Martinez-Mekler, Gustavo

    2002-01-01

    We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles(rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi one dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present day genetic sequences, we show that the ab...

  19. An Alternative Scalable Video Coding Scheme Used For Efficient Image Representation In Multimedia Applications

    Directory of Open Access Journals (Sweden)

    Aravinda T.V

    2010-07-01

    Full Text Available This paper describes a novel video coding scheme based on a three-dimensional Matching Pursuit algorithm. In addition to good compression performance at low bit rate, the proposed coder allows for flexible spatial, temporal and rate scalability thanks to its progressive coding structure. The Matching Pursuit algorithm generates a sparse composition of a video sequence in a series of spatio-temporal atoms, taken from an over complete dictionary of three-dimensional basis functions. The dictionary is generated by shifting, scaling and rotating two different mother atoms in order to cover the whole frequency cube. An embedded stream is then produced from the series of atoms. They are first distributed into sets through the set-partitioned position map algorithm (SPPM to form the index-map, inspired from bit plane encoding. Scalar quantization is then applied to the coefficients which are finally arithmetic coded. A completeMP3D codec has been implemented, and performances are shown to favorably compare to other scalable coders like MPEG-4 FGS and SPIHT-3D. In addition, the MP3D streams offer an incomparable flexibility for multiresolution streaming or adaptive decoding.

  20. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

    Science.gov (United States)

    Corominas, Roser; Yang, Xinping; Lin, Guan Ning; Kang, Shuli; Shen, Yun; Ghamsari, Lila; Broly, Martin; Rodriguez, Maria; Tam, Stanley; Trigg, Shelly A; Fan, Changyu; Yi, Song; Tasan, Murat; Lemmens, Irma; Kuang, Xingyan; Zhao, Nan; Malhotra, Dheeraj; Michaelson, Jacob J; Vacic, Vladimir; Calderwood, Michael A; Roth, Frederick P; Tavernier, Jan; Horvath, Steve; Salehi-Ashtiani, Kourosh; Korkin, Dmitry; Sebat, Jonathan; Hill, David E; Hao, Tong; Vidal, Marc; Iakoucheva, Lilia M

    2014-04-11

    Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases.

  1. An alternative approach to modeling genetic merit of feed efficiency in dairy cattle.

    Science.gov (United States)

    Lu, Y; Vandehaar, M J; Spurlock, D M; Weigel, K A; Armentano, L E; Staples, C R; Connor, E E; Wang, Z; Bello, N M; Tempelman, R J

    2015-09-01

    Genetic improvement of feed efficiency (FE) in dairy cattle requires greater attention given increasingly important resource constraint issues. A widely accepted yet occasionally contested measure of FE in dairy cattle is residual feed intake (RFI). The use of RFI is limiting for several reasons, including interpretation, differences in recording frequencies between the various component traits that define RFI, and potential differences in genetic versus nongenetic relationships between dry matter intake (DMI) and FE component traits. Hence, analyses focusing on DMI as the response are often preferred. We propose an alternative multiple-trait (MT) modeling strategy that exploits the Cholesky decomposition to provide a potentially more robust measure of FE. We demonstrate that our proposed FE measure is identical to RFI provided that genetic and nongenetic relationships between DMI and component traits of FE are identical. We assessed both approaches (MT and RFI) by simulation as well as by application to 26,383 weekly records from 50 to 200 d in milk on 2,470 cows from a dairy FE consortium study involving 7 institutions. Although the proposed MT model fared better than the RFI model when simulated genetic and nongenetic associations between DMI and FE component traits were substantially different from each other, no meaningful differences were found in predictive performance between the 2 models when applied to the consortium data. PMID:26210274

  2. DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts

    NARCIS (Netherlands)

    Zhernakova, Daria V.; de Klerk, Eleonora; Westra, Harm-Jan; Mastrokolias, Anastasios; Amini, Shoaib; Ariyurek, Yavuz; Jansen, Rick; Penninx, Brenda W.; Hottenga, Jouke J.; Willemsen, Gonneke; de Geus, Eco J.; Boomsma, Dorret I.; Veldink, Jan H.; van den Berg, Leonard H.; Wijmenga, Cisca; den Dunnen, Johan T.; van Ommen, Gert-Jan B.; 't Hoen, Peter A. C.; Franke, Lude

    2013-01-01

    Many disease-associated variants affect gene expression levels (expression quantitative trait loci, eQTLs) and expression profiling using next generation sequencing (NGS) technology is a powerful way to detect these eQTLs. We analyzed 94 total blood samples from healthy volunteers with DeepSAGE to g

  3. A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code

    Directory of Open Access Journals (Sweden)

    Higgs Paul G

    2009-04-01

    Full Text Available Abstract Background The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties. Hence, the effects of translational error are minimized with respect to randomly reshuffled codes. Further inspection reveals that it is amino acids in the same column of the code (i.e. same second base that are similar, whereas those in the same row show no particular similarity. We propose a 'four-column' theory for the origin of the code that explains how the action of selection during the build-up of the code leads to a final code that has the observed properties. Results The theory makes the following propositions. (i The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii These amino acids are assigned to codons with G at first position. Therefore the first code may have used only these codons. (iii The code rapidly developed into a four-column code where all codons in the same column coded for the same amino acid: NUN = Val, NCN = Ala, NAN = Asp and/or Glu, and NGN = Gly. (iv Later amino acids were added sequentially to the code by a process of subdivision of codon blocks in which a subset of the codons assigned to an early amino acid were reassigned to a later amino acid. (v Later amino acids were added into positions formerly occupied by amino acids with similar properties because this can occur with minimal disruption to the proteins already encoded by the earlier code. As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution. Conclusion The driving force during this process is not the minimization of translational error, but positive selection for the increased diversity and functionality of the proteins that can be made with a larger amino acid alphabet. Nevertheless, the code that results is one

  4. The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation*

    OpenAIRE

    Davis, Ryan; Shi, Yongsheng

    2014-01-01

    The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3′ ends through a process called mRNA alternative polyadenylation (APA). Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also prov...

  5. 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...

  6. 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.

  7. Application of Freeman Chain Codes: An Alternative Recognition Technique for Malaysian Car Plates

    CERN Document Server

    Jusoh, Nor Amizam

    2011-01-01

    Various applications of car plate recognition systems have been developed using various kinds of methods and techniques by researchers all over the world. The applications developed were only suitable for specific country due to its standard specification endorsed by the transport department of particular countries. The Road Transport Department of Malaysia also has endorsed a specification for car plates that includes the font and size of characters that must be followed by car owners. However, there are cases where this specification is not followed. Several applications have been developed in Malaysia to overcome this problem. However, there is still problem in achieving 100% recognition accuracy. This paper is mainly focused on conducting an experiment using chain codes technique to perform recognition for different types of fonts used in Malaysian car plates.

  8. Exploring the potential impact of an expanded genetic code on protein function.

    Science.gov (United States)

    Xiao, Han; Nasertorabi, Fariborz; Choi, Sei-Hyun; Han, Gye Won; Reed, Sean A; Stevens, Raymond C; Schultz, Peter G

    2015-06-01

    With few exceptions, all living organisms encode the same 20 canonical amino acids; however, it remains an open question whether organisms with additional amino acids beyond the common 20 might have an evolutionary advantage. Here, we begin to test that notion by making a large library of mutant enzymes in which 10 structurally distinct noncanonical amino acids were substituted at single sites randomly throughout TEM-1 β-lactamase. A screen for growth on the β-lactam antibiotic cephalexin afforded a unique p-acrylamido-phenylalanine (AcrF) mutation at Val-216 that leads to an increase in catalytic efficiency by increasing kcat, but not significantly affecting KM. To understand the structural basis for this enhanced activity, we solved the X-ray crystal structures of the ligand-free mutant enzyme and of the deacylation-defective wild-type and mutant cephalexin acyl-enzyme intermediates. These structures show that the Val-216-AcrF mutation leads to conformational changes in key active site residues-both in the free enzyme and upon formation of the acyl-enzyme intermediate-that lower the free energy of activation of the substrate transacylation reaction. The functional changes induced by this mutation could not be reproduced by substitution of any of the 20 canonical amino acids for Val-216, indicating that an expanded genetic code may offer novel solutions to proteins as they evolve new activities. PMID:26038548

  9. 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...

  10. Alternative Fuzzy Cluster Segmentation of Remote Sensing Images Based on Adaptive Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    WANG Jing; TANG Jilong; LIU Jibin; REN Chunying; LIU Xiangnan; FENG Jiang

    2009-01-01

    Remote sensing image segmentation is the basis of image understanding and analysis. However, the precision and the speed of segmentation can not meet the need of image analysis, due to strong uncertainty and rich texture details of remote sensing images. We proposed a new segmentation method based on Adaptive Genetic Algorithm (AGA) and Alternative Fuzzy C-Means (AFCM). Segmentation thresholds were identified by AGA. Then the image was segmented by AFCM. The results indicate that the precision and the speed of segmentation have been greatly increased, and the accuracy of threshold selection is much higher compared with traditional Otsu and Fuzzy C-Means (FCM) segmentation methods. The segmentation results also show that multi-thresholds segmentation has been achieved by combining AGA with AFCM.

  11. Deciphering the plant splicing code: Experimental and computational approaches for predicting alternative splicing and splicing regulatory elements

    Directory of Open Access Journals (Sweden)

    Anireddy S.N. Reddy

    2012-02-01

    Full Text Available Extensive alternative splicing (AS of precursor mRNAs (pre-mRNAs in multicellular eukaryotes increases the protein-coding capacity of a genome and allows novel ways to regulate gene expression. In fowering plants, up to 48% of intron-containing genes exhibit AS. However, the full extent of AS in plants is not yet known, as only a few high throughput RNA-Seq studies have been performed. As the cost of obtaining RNA-Seq reads continues to fall, it is anticipated that huge amounts of plant sequence data will accumulate and help in obtaining a more complete picture of AS in plants. Although it is not an onerous task to obtain hundreds of millions of reads using high throughput sequencing technologies, computational tools to accurately predict and visualize AS are still being developed and refined. This review will discuss the tools to predict and visualize transcriptome-wide AS in plants using short reads and highlight their limitations. Comparative studies of AS events between plants and animals have revealed that there are major differences in the most prevalent types of AS events, suggesting that plants and animals differ in the way they recognize exons and introns. Extensive studies have been performed in animals to identify cis-elements involved in regulating AS, especially in exon skipping. However, such studies are in their infancy in plants. Here, we review the current state of research on splicing regulatory elements (SREs and briefly discuss emerging experimental and computational tools to identify cis-elements involved in regulation of AS in plants. The availability of curated alternative splice forms in plants makes it possible to use computational tools to predict SREs involved in AS regulation, which can then be verified experimentally. Such studies will permit identification of plant-specific features involved in AS regulation and contribute to deciphering the splicing code in plants.

  12. 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.

  13. Biological genesis: the first step from dead matter to life. A contribution to the nature of DNA, RNA, and the genetic code

    OpenAIRE

    Schmidt FH

    2013-01-01

    Friedrich H Schmidt Retired, Schramberg, Germany Abstract: Information is understood semantically in the special case of the genetic code as the contents of news-bearing and genetically acting molecules. The connection of single molecules to groups and molecule chains can be referred to as syntactic. Well-defined information is not only exchanged between molecules in biology like nucleic and amino acids cooperating in the genetic code: the topic of this article is that an exchange of informa...

  14. Meropenem as an Alternative Antibiotic Agent for Suppression of Agrobacterium in Genetic Transformation of Orchid

    Institute of Scientific and Technical Information of China (English)

    CAO Ying; Niimi Yoshiyuki; HU Shang-lian

    2006-01-01

    A case of Meropenem as a novel antibacterial agent to suppress and eliminate Agrobacterium tumefaciens in the Agrobacterium-mediated transformation of orchid protocorm-like bodies (PLBs) has been reported in this article. The in vitro activities of meropenem and four comparator antibacterial agents against three Agrobacterium tumefaciens strains, LBA4404, EHA101, and GV3101, were assessed. In addition, the effect of meropenem on the growth of Dendrobium phalaenopsis PLBs was determined. Compared with other commonly used antibiotics (including ampicillin,carbenicillin, cefotaxime, and cefoperazone), meropenem showed the highest activity in suppressing all tested A.tumefaciens strains (minimum inhibitory concentration [MIC] < 0.5 mg L-1, which is equal to minimum bactericidal concentration [MBC]). Meropenem, at all tested concentrations, except for 10 mg L-1 concentration, had little negative effect on the growth of orchid tissues. The A. tumefaciens strain EHA101 in genetic transformation with vector pIG121Hm in infected PLBs of the orchid was visually undetectable after a two-month subculture in 1/2 MS medium with 50 mg L-1 meropenem and 25 mg L-1 hygromacin. The expression and incorporation of the transgenes were confirmed by GUS histochemical assay and PCR analysis. Meropenem may be an alternative antibiotic for the effective suppression of A. tumefaciens in genetic transformation.

  15. Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

    Science.gov (United States)

    van der Gulik, Peter T. S.; Hoff, Wouter D.

    2016-01-01

    Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA. PMID:27454314

  16. Simulation platform of economical operation and dispatch for power plant based on float-coded genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    朱奕; 伞冶; 马克茂

    2004-01-01

    This paper discusses a float-coded genetic algorithm and its application to the optimization of the power plant operation concerning the simulation problem of economical operation for power plant systems. The method proposed realizes the load optimization between generating units of power plants and their loads, solves the problem of influence of a unit plant pause spoilage and load variance on the optimal plant combination and load, and finally establishes a simulation platform for the power plant economical operation.

  17. The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

    Directory of Open Access Journals (Sweden)

    Jan C. Biro

    2006-01-01

    Full Text Available All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, which is not represented by the known genetic code. Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE than the subsequence containing only the 2nd residues (pn=81. This periodic FFE difference is not present in introns and therefore it is a specific physico-chemical characteristic of coding sequences and it might contribute to unambiguous definition of codon boundaries during translation. The FFE in the 1st and 3rd residues is additive, which suggests that these residues contain a significant number of complementary bases and contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-forming of mRNAs indicates a connection between the structure of exons and the corresponding (translated proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC base pairs at the 1st and 3rd codon positions and translated in reverse orientation are preferentially co-located in protein structures. Exons are distinguished from introns and codon boundaries are physico-chemically defined by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically interacting amino acids are coded by partially

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

    CERN Document Server

    De Geyter, Gert; Fritz, Jacopo; Camps, Peter

    2012-01-01

    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 NGC4013. This galaxy has been modeled previously by other authors using different combinations of radiative transfer codes and optimization methods. Given the different...

  19. Evaluation of gene value and heuristic function of alternate plans in multi database system using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Sambit Kumar Mishra

    2011-09-01

    Full Text Available The major tasks in multiple query processing in multi database system are common operation or expressionidentification and global execution plan construction. Each query can have several alternative evaluationplans, each with a different set of tasks. Therefore the goal of multiple query processing is to choose theright set of plans for queries which minimizes the total execution time by performing common tasks onlyonce. The objectives in the multiple query processing are to increase system throughput and decreasesingle query response time. I have retrieved the alternate plans and the tasks, estimated cost of plans andheuristic function of alternate plans in multi database system by applying the genetic algorithm technique.

  20. Play in two languages. Language alternation and code-switching in role-play in North Sámi and Norwegian

    Directory of Open Access Journals (Sweden)

    Carola Kleemann

    2013-01-01

    Full Text Available Normal 0 false false false NO-BOK JA X-NONE This article analyses how children in a Sámi kindergarten use their languages, North Sámi and Norwegian, in everyday life. My focus is on role-play in periods of free play in a kindergarten where children speak both North Sámi and Norwegian. Role-play is a bilingual context in that one sequence of play most often uses elements from both languages. Role-play as a situation is suitable for studying language alternation and code-switching because it is an in-group driven activity. The language alternation and code-switching which appears in role-play situations is discussed in light of theories advocating dividing code and language, viewing language choice as one of a cluster of codes used in role-play. I argue the children observed for this study have layers of codes to use. I discuss the language codes North Sámi, Norwegian and bilingual, which the children use in the role-play setting; the main codes used are directory utterances, role utterances, magical utterances and out-of-play-utterances. 

  1. 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.

  2. The poetics of the non-verbal : code and performance in Jean Genet's theatre

    OpenAIRE

    Finburgh, C.

    2000-01-01

    This is an extensive study of the non-verbal in Genet's dramaturgy. Non-verbal forms constitute the plural, fragmented sum of theatrical possibility. Rhythms, movements, colours and shapes highlight the ritualised form of words and actions on and off stage. In Part One I define my understanding of Genet's theory of representation, and show how this theory informs his use of the non-verbal. On the one hand the discursive limits of Genet's reality forefront closure. On the oth...

  3. 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...

  4. MassCode liquid arrays as a tool for multiplexed high-throughput genetic profiling.

    Directory of Open Access Journals (Sweden)

    Gregory S Richmond

    Full Text Available Multiplexed detection assays that analyze a modest number of nucleic acid targets over large sample sets are emerging as the preferred testing approach in such applications as routine pathogen typing, outbreak monitoring, and diagnostics. However, very few DNA testing platforms have proven to offer a solution for mid-plexed analysis that is high-throughput, sensitive, and with a low cost per test. In this work, an enhanced genotyping method based on MassCode technology was devised and integrated as part of a high-throughput mid-plexing analytical system that facilitates robust qualitative differential detection of DNA targets. Samples are first analyzed using MassCode PCR (MC-PCR performed with an array of primer sets encoded with unique mass tags. Lambda exonuclease and an array of MassCode probes are then contacted with MC-PCR products for further interrogation and target sequences are specifically identified. Primer and probe hybridizations occur in homogeneous solution, a clear advantage over micro- or nanoparticle suspension arrays. The two cognate tags coupled to resultant MassCode hybrids are detected in an automated process using a benchtop single quadrupole mass spectrometer. The prospective value of using MassCode probe arrays for multiplexed bioanalysis was demonstrated after developing a 14plex proof of concept assay designed to subtype a select panel of Salmonella enterica serogroups and serovars. This MassCode system is very flexible and test panels can be customized to include more, less, or different markers.

  5. Single nucleotide polymorphism (SNP-strings: an alternative method for assessing genetic associations.

    Directory of Open Access Journals (Sweden)

    Douglas S Goodin

    Full Text Available BACKGROUND: Genome-wide association studies (GWAS identify disease-associations for single-nucleotide-polymorphisms (SNPs from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person's SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid. For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1, representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself

  6. [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.

  7. 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

  8. 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.

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

    International Nuclear Information System (INIS)

    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

  10. Deciphering the four-letter code : The genetic basis of complex traits and common disease

    NARCIS (Netherlands)

    Pulit, S.L.

    2016-01-01

    Deoxyribonucleic acid (DNA) is made up of four bases: adenine (A), cytosine (C), guanine (G), and thymine (T). Assembled in a strategic fashion, these bases code for the unique genomes of all walks of life, from viruses, to rodents, to primates. The human genome, mapped completely for the first time

  11. Genetic Programming as Alternative for Predicting Development Effort of Individual Software Projects

    OpenAIRE

    Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R.; M.E. Meda-Campaña

    2012-01-01

    Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, wher...

  12. 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.

  13. On the evolution of the standard genetic code: vestiges of critical scale invariance from the RNA world in current prokaryote genomes.

    Directory of Open Access Journals (Sweden)

    Marco V José

    Full Text Available Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine 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. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10(-10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC.

  14. Biological genesis: the first step from dead matter to life. A contribution to the nature of DNA, RNA, and the genetic code

    Directory of Open Access Journals (Sweden)

    Schmidt FH

    2013-04-01

    Full Text Available Friedrich H Schmidt Retired, Schramberg, Germany Abstract: Information is understood semantically in the special case of the genetic code as the contents of news-bearing and genetically acting molecules. The connection of single molecules to groups and molecule chains can be referred to as syntactic. Well-defined information is not only exchanged between molecules in biology like nucleic and amino acids cooperating in the genetic code: the topic of this article is that an exchange of information could also occur between inorganic and organic substances, eg, mineral crystals interacting with organic molecules. This may have played a role in the origins of life on earth. As the origin of the genetic code and the mechanism of its translation is still an unresolved problem, so is the interaction of inorganic substances and organic substances still an open question. Stereochemical similarities existing between code and amino acids cannot explain the relationship completely and are not present between inorganic and organic molecules at all. Symmetry is a structural entity in organic chemistry and organisms, and Δ-values calculated by a mathematical algorithm and introduced in this article give an estimate of symmetry and transferred information. Symmetric Δ-values exist in minerals as well as in genetic molecules, and could thus bring dead material to life before DNA, RNA, and enzymes were developed. The fact that symmetry is important as a quality of organic matter with the function of the genetic code is pointed out in the works of other authors, who are cited in this paper. Keywords: genetic information, genetic code, symmetry in inorganic and organic molecules, calculation of Δ-values

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

    International Nuclear Information System (INIS)

    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)

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

    NARCIS (Netherlands)

    S. Stringer

    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 co

  17. Human SHBG mRNA translation is modulated by alternative 5'-non-coding exons 1A and 1B.

    Directory of Open Access Journals (Sweden)

    Tomàs Pinós

    Full Text Available BACKGROUND: The human sex hormone-binding globulin (SHBG gene comprises at least 6 different transcription units (TU-1, -1A, -1B, -1C, -1D and -1E, and is regulated by no less than 6 different promoters. The best characterized are TU-1 and TU-1A: TU-1 is responsible for producing plasma SHBG, while TU-1A is transcribed and translated in the testis. Transcription of the recently described TU-1B, -1C, and -1D has been demonstrated in human prostate tissue and prostate cancer cell lines, as well as in other human cell lines such as HeLa, HepG2, HeK 293, CW 9019 and imr 32. However, there are no reported data demonstrating their translation. In the present study, we aimed to determine whether TU-1A and TU-1B are indeed translated in the human prostate and whether 5' UTR exons 1A and 1B differently regulate SHBG translation. RESULTS: Cis-regulatory elements that could potentially regulate translation were identified within the 5'UTRs of SHBG TU-1A and TU-1B. Although full-length SHBG TU-1A and TU-1B mRNAs were present in prostate cancer cell lines, the endogenous SHBG protein was not detected by western blot in any of them. LNCaP prostate cancer cells transfected with several SHBG constructs containing exons 2 to 8 but lacking the 5'UTR sequence did show SHBG translation, whereas inclusion of the 5'UTR sequences of either exon 1A or 1B caused a dramatic decrease in SHBG protein levels. The molecular weight of SHBG did not vary between cells transfected with constructs with or without the 5'UTR sequence, thus confirming that the first in-frame ATG of exon 2 is the translation start site of TU-1A and TU-1B. CONCLUSIONS: The use of alternative SHBG first exons 1A and 1B differentially inhibits translation from the ATG situated in exon 2, which codes for methionine 30 of transcripts that begin with the exon 1 sequence.

  18. Genetic basis and selection for life-history trait plasticity on alternative host plants for the cereal aphid Sitobion avenae.

    Science.gov (United States)

    Dai, Xinjia; Gao, Suxia; Liu, Deguang

    2014-01-01

    Sitobion avenae (F.) can survive on various plants in the Poaceae, which may select for highly plastic genotypes. But phenotypic plasticity was often thought to be non-genetic, and of little evolutionary significance historically, and many problems related to adaptive plasticity, its genetic basis and natural selection for plasticity have not been well documented. To address these questions, clones of S. avenae were collected from three plants, and their phenotypic plasticity under alternative environments was evaluated. Our results demonstrated that nearly all tested life-history traits showed significant plastic changes for certain S. avenae clones with the total developmental time of nymphs and fecundity tending to have relatively higher plasticity for most clones. Overall, the level of plasticity for S. avenae clones' life-history traits was unexpectedly low. The factor 'clone' alone explained 27.7-62.3% of the total variance for trait plasticities. The heritability of plasticity was shown to be significant in nearly all the cases. Many significant genetic correlations were found between trait plasticities with a majority of them being positive. Therefore, it is evident that life-history trait plasticity involved was genetically based. There was a high degree of variation in selection coefficients for life-history trait plasticity of different S. avenae clones. Phenotypic plasticity for barley clones, but not for oat or wheat clones, was frequently found to be under significant selection. The directional selection of alternative environments appeared to act to decrease the plasticity of S. avenae clones in most cases. G-matrix comparisons showed significant differences between S. avenae clones, as well as quite a few negative covariances (i.e., trade-offs) between trait plasticities. Genetic basis and evolutionary significance of life-history trait plasticity were discussed.

  19. Genetic characterization of three novel chicken parvovirus strains based on analysis of their coding sequences.

    Science.gov (United States)

    Koo, Bon-Sang; Lee, Hae-Rim; Jeon, Eun-Ok; Han, Moo-Sung; Min, Kyeong-Cheol; Lee, Seung-Baek; Bae, Yeon-Ji; Cho, Sun-Hyung; Mo, Jong-Suk; Kwon, Hyuk Moo; Sung, Haan Woo; Kim, Jong-Nyeo; Mo, In-Pil

    2015-01-01

    Chicken parvovirus (ChPV) is one of the causative agents of viral enteritis. Recently, the genome of the ABU-P1 strain of ChPV was fully sequenced and determined to have a distinct genomic composition compared with that of vertebrate parvoviruses. However, no comparative sequence analysis of coding regions of ChPVs was possible because of the lack of other sequence information. In this study, we obtained the nucleotide sequences of all genomic coding regions of three ChPVs by polymerase chain reaction using 13 primer sets, and deduced the amino acid sequences from the nucleotide sequences. The non-structural protein 1 (NS1) gene of the three ChPVs showed 95.0 to 95.5% nucleotide sequence identity and 96.5 to 98.1% amino acid sequence identity to those of NS1 from the ABU-P1 strain, respectively, and even higher nucleotide and amino acid similarities to one another. The viral proteins (VP) gene was more divergent between the three ChPV Korean strains and ABU-P1, with 88.1 to 88.3% nucleotide identity and 93.0% amino acid identity. Analysis of the putative tertiary structure of the ChPV VP2 protein showed that variable regions with less than 80% nucleotide similarity between the three Korean strains and ABU-P1 occurred in large loops of the VP2 protein believed to be involved in antigenicity, pathogenicity, and tissue tropism in other parvoviruses. Based on our analysis of full-length coding sequences, we discovered greater variation in ChPV strains than reported previously, especially in partial regions of the VP2 protein.

  20. Symmetry Breaking and Adaptation The Genetic Code of Retroviral Env Proteins

    CERN Document Server

    Vera, S

    1996-01-01

    Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of the synonym symmetry by mutation and recombination. We conjecture that this enhances the probability to produce mutants that are well-adapted to the current environment. Evidence is found in the codon frequencies of the HIV resistant to the current immunological attack, are found with a greater frequency than their less mutable synonyms.

  1. Genetic and biomedical studies demonstrating a second gene coding for asparagine synthetase in Escherichia coli.

    OpenAIRE

    Humbert, R; Simoni, R D

    1980-01-01

    Genetic experiments have indicated that asparagine auxotrophs of Escherichias coli K-12 can be made asparagine prototrophs at either of two sites on the chromosome and that wild-type strains require both sites to be mutated to produce asparagine auxotrophy. The former asn locus is now called asnA, and the new gene is designated asnB. The asnB gene is located near gal.AsnA+ asnB and asnA asnB+ strains were constructed, and the asparagine synthetic reaction was characterized in extracts. These ...

  2. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code.

    Science.gov (United States)

    Xiao, Han; Schultz, Peter G

    2016-01-01

    The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted. PMID:27413101

  3. Optimal design of FIR high pass filter based on L1 error approximation using real coded genetic algorithm

    Directory of Open Access Journals (Sweden)

    Apoorva Aggarwal

    2015-12-01

    Full Text Available In this paper, an optimal design of linear phase digital finite impulse response (FIR highpass (HP filter using the L1-norm based real-coded genetic algorithm (RCGA is investigated. A novel fitness function based on L1 norm is adopted to enhance the design accuracy. Optimized filter coefficients are obtained by defining the filter objective function in L1 sense using RCGA. Simulation analysis unveils that the performance of the RCGA adopting this fitness function is better in terms of signal attenuation ability of the filter, flatter passband and the convergence rate. Observations are made on the percentage improvement of this algorithm over the gradient-based L1 optimization approach on various factors by a large amount. It is concluded that RCGA leads to the best solution under specified parameters for the FIR filter design on account of slight unnoticeable higher transition width.

  4. Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics.

    Science.gov (United States)

    Mank, Judith E; Avise, John C

    2004-12-01

    Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in 'populations' that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre--Bayesian clustering--using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (F(ST) and phiST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals.

  5. 重述克里克的密码起源理论%The Research on Crick’s Genetic Code Origin Theory

    Institute of Scientific and Technical Information of China (English)

    孙咏萍; 郭世荣

    2015-01-01

    利用概念分析法,从内史角度厘清了弗朗西斯·克里克在遗传密码破解以后对密码起源问题的逻辑性思考———密码的性质、密码的统一性、古密码子及立体化学作用理论和冻结偶然性理论的比较,揭示了克里克研究密码起源理论的核心是冻结偶然性,他提出的古密码子理论比较合理地推测了密码的起源与进化关系。%According to the concept analysis,the logic thinking of Francis Crick is studied in terms of the origin of genetic code from the perspective of internal history,which includes the nature of genetic code,universality,the primitive code,the contrast between stereochemical theory and frozen accident.The core of Crick’s theory on the origin of genetic code is “frozen accident”.Specifically,the primitive code he proposed was able to predict the code origin and evolution relationship in the proper sense.

  6. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

    Science.gov (United States)

    Xiong, Hui Y; Alipanahi, Babak; Lee, Leo J; Bretschneider, Hannes; Merico, Daniele; Yuen, Ryan K C; Hua, Yimin; Gueroussov, Serge; Najafabadi, Hamed S; Hughes, Timothy R; Morris, Quaid; Barash, Yoseph; Krainer, Adrian R; Jojic, Nebojsa; Scherer, Stephen W; Blencowe, Benjamin J; Frey, Brendan J

    2015-01-01

    To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation-driven aberrant splicing. Intronic disease mutations that are more than 30 nucleotides from any splice site alter splicing nine times as often as common variants, and missense exonic disease mutations that have the least impact on protein function are five times as likely as others to alter splicing. We detected tens of thousands of disease-causing mutations, including those involved in cancers and spinal muscular atrophy. Examination of intronic and exonic variants found using whole-genome sequencing of individuals with autism revealed misspliced genes with neurodevelopmental phenotypes. Our approach provides evidence for causal variants and should enable new discoveries in precision medicine.

  7. Generating Alternative Engineering Designs by Integrating Desktop VR with Genetic Algorithms

    Science.gov (United States)

    Chandramouli, Magesh; Bertoline, Gary; Connolly, Patrick

    2009-01-01

    This study proposes an innovative solution to the problem of multiobjective engineering design optimization by integrating desktop VR with genetic computing. Although, this study considers the case of construction design as an example to illustrate the framework, this method can very much be extended to other engineering design problems as well.…

  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. 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.

  10. Proposal of Functional-Specialization Multi-Objective Real-Coded Genetic Algorithm: FS-MOGA

    Science.gov (United States)

    Hamada, Naoki; Tanaka, Masaharu; Sakuma, Jun; Kobayashi, Shigenobu; Ono, Isao

    This paper presents a Genetic Algorithm (GA) for multi-objective function optimization. To find a precise and widely-distributed set of solutions in difficult multi-objective function optimization problems which have multimodality and curved Pareto-optimal set, a GA would be required conflicting behaviors in the early stage and the last stage of search. That is, in the early stage of search, GA should perform local-Pareto-optima-overcoming search which aims to overcome local Pareto-optima and converge the population to promising areas in the decision variable space. On the other hand, in the last stage of search, GA should perform Pareto-frontier-covering search which aims to spread the population along the Pareto-optimal set. NSGA-II and SPEA2, the most widely used conventional methods, have problems in local-Pareto-optima-overcoming and Pareto-frontier-covering search. In local-Pareto-optima-overcoming search, their selection pressure is too high to maintain the diversity for overcoming local Pareto-optima. In Pareto-frontier-covering search, their abilities of extrapolation-directed sampling are not enough to spread the population and they cannot sample along the Pareto-optimal set properly. To resolve above problems, the proposed method adaptively switches two search strategies, each of which is specialized for local-Pareto-optima-overcoming and Pareto-frontier-covering search, respectively. We examine the effectiveness of the proposed method using two benchmark problems. The experimental results show that our approach outperforms the conventional methods in terms of both local-Pareto-optima-overcoming and Pareto-frontier-covering search.

  11. 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.

  12. 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.

  13. Codon usage, genetic code and phylogeny of Dictyostelium discoideum mitochondrial DNA as deduced from a 7.3-kb region.

    Science.gov (United States)

    Angata, K; Kuroe, K; Yanagisawa, K; Tanaka, Y

    1995-02-01

    We have sequenced a region (7,376-bp) of the mitochondrial (mt) DNA (54 kb) of the cellular slime mold, Dictyostelium discoideum. From the DNA and amino-acid sequence comparisons with known sequences, genes for ATPase subunit 9 (ATP9), cytochrome b (CYTB), NADH dehydrogenase subunits 1, 3 and 6 (ND1, ND3 and ND6), small subunit rRNA (SSU rRNA) and seven tRNAs (Arg, Asn, Cys, Lys, f-Met, Met and Pro) have been identified. The sequenced region of the mtDNA has a high average A + T-content (70.8%). The A + T-content of protein-genes (73.6%) is considerably higher than that of RNA genes (61.3%). Even with the strong AT-bias, the genetic code employed is most probably the universal one. All seven tRNAs are able to form typical clover leaf structures. The molecular phylogenetic trees of CYTB and SSU rRNA suggest that D. discoideum is closer to green plants than to animals and fungi. PMID:7736610

  14. 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.

  15. Two Human ACAT2 mRNA Variants Produced by Alternative Splicing and Coding for Novel Isoenzymes

    Institute of Scientific and Technical Information of China (English)

    Xiao-Min YAO; Bo-Liang LI; Can-Hua WANG; Bao-Liang SONG; Xin-Ying YANG; Zhen-Zhen WANG; Wei QI; Zhi-Xin LIN; Catherine C. Y. CHANG; Ta-Yuan CHANG

    2005-01-01

    Acyl coenzyme A:cholesterol acyltransferase 2 (ACAT2) plays an important role in cholesterol absorption. Human ACAT2 is highly expressed in small intestine and fetal liver, but its expression is greatly diminished in adult liver. The full-length human ACAT2 mRNA encodes a protein, designated ACAT2a, with 522 amino acids. We have previously reported the organization of the human ACAT2 gene and the differentiation-dependent promoter activity in intestinal Caco-2 cells. In the current work, two human ACAT2 mRNA variants produced by alternative splicing are cloned and predicted to encode two novel ACAT2 isoforms,named ACAT2b and ACAT2c, with 502 and 379 amino acids, respectively. These mRNA variants differ from ACAT2a mRNA by lack of the exon 4 (ACAT2b mRNA) and exons 4-5 plus 8-9-10 (ACAT2c mRNA).Significantly, comparable amounts of the alternatively spliced ACAT2 mRNA variants were detected by RTPCR, and Western blot analysis confirmed the presence of their corresponding proteins in human liver and intestine cells. Furthermore, phosphorylation and enzymatic activity analyses demonstrated that the novel isoenzymes ACAT2b and ACAT2c lacked the phosphorylatable site SLLD, and their enzymatic activities reduced to 25%-35% of that of ACAT2a. These evidences indicate that alternative splicing produces two human ACAT2 mRNA variants that encode the novel ACAT2 isoenzymes. Our findings might help to understand the regulation of the ACAT2 gene expression under certain physiological and pathological conditions.

  16. Experimental design for stable genetic manipulation in mammalian cell lines: lentivirus and alternatives.

    Science.gov (United States)

    Shearer, Robert F; Saunders, Darren N

    2015-01-01

    The use of third-generation lentiviral vectors is now commonplace in most areas of basic biology. These systems provide a fast, efficient means for modulating gene expression, but experimental design needs to be carefully considered to minimize potential artefacts arising from off-target effects and other confounding factors. This review offers a starting point for those new to lentiviral-based vector systems, addressing the main issues involved with the use of lentiviral systems in vitro and outlines considerations which should be taken into account during experimental design. Factors such as selecting an appropriate system and controls, and practical titration of viral transduction are important considerations for experimental design. We also briefly describe some of the more recent advances in genome editing technology. TALENs and CRISPRs offer an alternative to lentivirus, providing endogenous gene editing with reduced off-target effects often at the expense of efficiency.

  17. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  18. Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA).

    Science.gov (United States)

    Miller, Daniel E; Patel, Zubin H; Lu, Xiaoming; Lynch, Arthur T; Weirauch, Matthew T; Kottyan, Leah C

    2016-01-01

    Population and family-based genetic studies typically result in the identification of genetic variants that are statistically associated with a clinical disease or phenotype. For many diseases and traits, most variants are non-coding, and are thus likely to act by impacting subtle, comparatively hard to predict mechanisms controlling gene expression. Here, we describe a general strategic approach to prioritize non-coding variants, and screen them for their function. This approach involves computational prioritization using functional genomic databases followed by experimental analysis of differential binding of transcription factors (TFs) to risk and non-risk alleles. For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. For EMSA, the oligonucleotides with or without bound nuclear factors (often TFs) are analyzed by non-denaturing electrophoresis on a tris-borate-EDTA (TBE) polyacrylamide gel. For DAPA, the oligonucleotides are bound to a magnetic column and the nuclear factors that specifically bind the DNA sequence are eluted and analyzed through mass spectrometry or with a reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blot analysis. This general approach can be widely used to study the function of non-coding genetic variants associated with any disease, trait, or phenotype. PMID:27585267

  19. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Directory of Open Access Journals (Sweden)

    Brian R. Francis

    2015-02-01

    Full Text Available Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid. Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of

  20. File Compression and Expansion of the Genetic Code by the use of the Yin/Yang Directions to find its Sphered Cube

    Science.gov (United States)

    Castro-Chavez, Fernando

    2014-01-01

    Objective The objective of this article is to demonstrate that the genetic code can be studied and represented in a 3-D Sphered Cube for bioinformatics and for education by using the graphical help of the ancient “Book of Changes” or I Ching for the comparison, pair by pair, of the three basic characteristics of nucleotides: H-bonds, molecular structure, and their tautomerism. Methods The source of natural biodiversity is the high plasticity of the genetic code, analyzable with a reverse engineering of its 2-D and 3-D representations (here illustrated), but also through the classical 64-hexagrams of the ancient I Ching, as if they were the 64-codons or words of the genetic code. Results In this article, the four elements of the Yin/Yang were found by correlating the 3×2=6 sets of Cartesian comparisons of the mentioned properties of nucleic acids, to the directionality of their resulting blocks of codons grouped according to their resulting amino acids and/or functions, integrating a 384-codon Sphered Cube whose function is illustrated by comparing six brain peptides and a promoter of osteoblasts from Humans versus Neanderthal, as well as to Negadi’s work on the importance of the number 384 within the genetic code. Conclusions Starting with the codon/anticodon correlation of Nirenberg, published in full here for the first time, and by studying the genetic code and its 3-D display, the buffers of reiteration within codons codifying for the same amino acid, displayed the two long (binary number one) and older Yin/Yang arrows that travel in opposite directions, mimicking the parental DNA strands, while annealing to the two younger and broken (binary number zero) Yin/Yang arrows, mimicking the new DNA strands; the graphic analysis of the of the genetic code and its plasticity was helpful to compare compatible sequences (human compatible to human versus neanderthal compatible to neanderthal), while further exploring the wondrous biodiversity of nature for

  1. Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code.

    Science.gov (United States)

    Bernhardt, Harold S

    2016-01-01

    We have previously proposed that tRNA(Gly) was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNA(Gly) sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNA(Ser) has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNA(Ser) is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNA(Ser) and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio's recent criticism of our proposal that tRNA(Gly) was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers. PMID:26927183

  2. Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette

    Directory of Open Access Journals (Sweden)

    Guillaume Borrel

    2014-01-01

    Full Text Available Pyrrolysine (Pyl, the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber   tRNAPyl with an imperfect anticodon stem and a shortened tRNAPyl synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.

  3. The genetic basis of early-life morphological traits and their relation to alternative male reproductive tactics in Atlantic salmon.

    Science.gov (United States)

    Páez, D J; Morrissey, M; Bernatchez, L; Dodson, J J

    2010-04-01

    Although heritability estimates for traits potentially under natural selection are increasingly being reported, their estimation remains a challenge if we are to understand the patterns of adaptive phenotypic change in nature. Given the potentially important role of selection on the early life phenotype, and thereby on future life history events in many fish species, we conducted a common garden experiment, using the Atlantic salmon (Salmo salar L.), with two major aims. The first objective is to determine how the site of origin, the paternal sexual tactic and additive genetic effects influence phenotypic variation of several morphological traits at hatching and emergence. The second aim is to test whether a link exists between phenotypic characteristics early in life and the incidence of male alternative tactics later in life. We found no evidence of a site or paternal effect on any morphological trait at hatching or emergence, suggesting that the spatial phenotypic differences observed in the natural river system from which these fish originated are mainly environmentally driven. However, we do find significant heritabilities and maternal effects for several traits, including body size. No direct evidence was found correlating the incidence of precocious maturation with early life characteristics. We suggest that under good growing conditions, body size and other traits at early developmental stages are not reliable cues for the surpassing of the threshold values associated with male sexual development. PMID:20149020

  4. 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.

  5. 无义密码对线粒体密码进化的影响%Influence of Nonsense Codons on the Evolution of Mitochondrial Genetic Codes

    Institute of Scientific and Technical Information of China (English)

    孙咏萍; 罗辽复

    2011-01-01

    遗传密码的起源与进化是理论生物学研究的一个基本问题.以线粒体密码为例,讨论密码进化关系构建的不同规则,分析密码进化中重要影响因素——无义密码子的再定义及其逆过程.终止信号与氨基酸间的距离是密码进化关系构建中的关键,在密码进化中无义密码子突变可以频繁进行,存在干涉现象,且进化倾向于无义密码子减少的方向.%The origin and evolution of the genetic code is a basic problem in the study of theory biology. As a typical case,the different rules of constructing evolutionary relationship of mitochon-drial genetic codes are discussed. An important factor affecting the evolution of codes ,namely, redefinition of nonsense codons and its reverse processes analyzed. The distance of terminator and amino acid is the key factor for the construction of evolution relationship. The nonsense mutation is frequent, there are interference phenomena, and the direction of evolution tends to the lesser nonsense codons.

  6. Real-Code Genetic Algorithm for Ground State Energies of Hydrogenic Donors in GaAs-(Ga,Al)As Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    YAN Hai-Qing; TANG Chen; LIU Ming; ZHANG Hao

    2005-01-01

    We present a global optimization method, called the real-code genetic algorithm (RGA), to the ground state energies. The proposed method does not require partial derivatives with respect to each variational parameter or solving an eigenequation, so the present method overcomes the major difficulties of the variational method. RGAs also do not require coding and encoding procedures, so the computation time and complexity are reduced. The ground state energies of hydrogenic donors in GaAs-(Ga,Al)As quantum dots have been calculated for a range of the radius of the quantum dot radii of practical interest. They are compared with those obtained by the variational method. The results obtained demonstrate the proposed method is simple, accurate, and easy implement.

  7. Product Codes for Optical Communication

    DEFF Research Database (Denmark)

    Andersen, Jakob Dahl

    2002-01-01

    Many optical communicaton systems might benefit from forward-error-correction. We present a hard-decision decoding algorithm for the "Block Turbo Codes", suitable for optical communication, which makes this coding-scheme an alternative to Reed-Solomon codes.......Many optical communicaton systems might benefit from forward-error-correction. We present a hard-decision decoding algorithm for the "Block Turbo Codes", suitable for optical communication, which makes this coding-scheme an alternative to Reed-Solomon codes....

  8. Application of Projection Pursuit Evaluation Model Based on Real-Coded Accelerating Genetic Algorithm in Evaluating Wetland Soil Quality Variations in the Sanjiang Plain,China

    Institute of Scientific and Technical Information of China (English)

    FU QIANG; XIE YONGGANG; WEI ZIMIN

    2003-01-01

    A new technique of dimension reduction named projection pursuit is applied to model and evaluatewetland soil quality variations in the Sanjiang Plain, Helongjiang Province, China. By adopting the im-proved real-coded accelerating genetic algorithm (RAGA), the projection direction is optimized and multi-dimensional indexes are converted into low-dimensional space. Classification of wetland soils and evaluationof wetland soil quality variations are realized by pursuing optimum projection direction and projection func-tion value. Therefore, by adopting this new method, any possible human interference can be avoided andsound results can be achieved in researching quality changes and classification of wetland soils.

  9. 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

  10. Quantum genetic algorithm based on multi-chain coding scheme%基于多链拓展编码方案的量子遗传算法

    Institute of Scientific and Technical Information of China (English)

    王之腾; 张宏军; 张睿; 邢英; 何健

    2012-01-01

    为了提高量子遗传算法的性能,提出了一种基于多链拓展编码方案的量子遗传算法.根据编码方案,将每个量子位分解为多个并列的基因,有效地拓展了搜索空间;结合编码方案提出量子更新策略,并引入了动态调整旋转角机制对个体进行更新,使用量子非门变异策略实现量子变异.仿真实验中,分析了使用不同变异概率[0,0.1,…,0.9,1]时对算法性能的影响,对比了分别使用普通量子遗传算法、双链编码方案、三链编码方案以及四链编码方案的量子遗传算法在优化函数极值问题时算法的性能.实验结果证明,通过增加基因链可以显著提高算法的性能,多链拓展编码方案可以提高量子遗传算法的性能,是有效的.%In order to improve the efficiency of the quantum genetic algorithm, this paper proposed a quantum genetic algorithm based on a expanded multi-chain coding scheme. The algorithm took qubit as chromosome. Each chromosome generated multiple and parallel gene chains which were mapping to multiple optimized solutions by separating qubit into multiple and parallel genes. The expanded genes chains expanded the searching space effectively and increased evolutionary rate for quantum genetic algorithm. It introduced the dynamic adjusting rotation angle mechanism to quantum rotation gate to guide individual e-volution and used quantum not-gate to prevent algorithm occurring premature convergence. The method further improved searching efficiency. In the simulation experiment, analysed the influence for the algorithm with different variation probability ( [0,0. 1 ,…,0. 9,1 ] )and used different code schemes to optimize extremal function. The simulation experiment result shows that it can obviously improve the efficiency of quantum genetic algorithm by adding gene chain, and the quantum genetic algorithm based on a expanded multi-chain coding scheme is efficient.

  11. Genetically engineered foods

    Science.gov (United States)

    ... plants or animals) inserted into their genetic codes. Genetic engineering can be done with plants, animals, or bacteria ... have been genetically engineering plants since the 1990s. Genetic engineering allows scientists to speed this process up by ...

  12. Speaking Code

    DEFF Research Database (Denmark)

    Cox, Geoff

    development, Speaking Code unfolds an argument to undermine the distinctions between criticism and practice, and to emphasize the aesthetic and political aspects of software studies. Not reducible to its functional aspects, program code mirrors the instability inherent in the relationship of speech......; alternatives to mainstream development, from performances of the live-coding scene to the organizational forms of commons-based peer production; the democratic promise of social media and their paradoxical role in suppressing political expression; and the market’s emptying out of possibilities for free...... expression in the public realm. The book’s line of argument defends language against its invasion by economics, arguing that speech continues to underscore the human condition, however paradoxical this may seem in an era of pervasive computing....

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

    International Nuclear Information System (INIS)

    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

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

    OpenAIRE

    MASOUM, M. A. S.; NABAVI S.M.H.; A. Kazemi

    2011-01-01

    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, ...

  16. 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

    regions and regions of importance for translation, as well as coding sequences of the two genes, were studied using single-strand conformation polymorphism (SSCP) analysis and DNA sequencing. The genetic analyses were performed in subgroups of 52 Caucasian NIDDM patients and 25 age-matched healthy...... 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...... in the GLUT4 cDNA was a silent polymorphism at codon 130. Southern blotting of both gene loci did not detect any major abnormalities.(ABSTRACT TRUNCATED AT 250 WORDS)...

  17. 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.

  18. Analysis of the genetic determinants coding for the S-fimbrial adhesin (sfa) in different Escherichia coli strains causing meningitis or urinary tract infections.

    Science.gov (United States)

    Ott, M; Hacker, J; Schmoll, T; Jarchau, T; Korhonen, T K; Goebel, W

    1986-12-01

    Recently we have described the molecular cloning of the genetic determinant coding for the S-fimbrial adhesin (Sfa), a sialic acid-recognizing pilus frequently found among extraintestinal Escherichia coli isolates. Fimbriae from the resulting Sfa+ E. coli K-12 clone were isolated, and an Sfa-specific antiserum was prepared. Western blots indicate that S fimbriae isolated from different uropathogenic and meningitis-associated E. coli strains, including O83:K1 isolates, were serologically related. The Sfa-specific antibodies did not cross-react with P fimbriae, but did cross-react with F1C fimbriae. Furthermore the sfa+ recombinant DNAs and some cloned sfa-flanking regions were used as probes in Southern experiments. Chromosomal DNAs isolated from O18:K1 and O83:K1 meningitis strains with and without S fimbriae and from uropathogenic O6:K+ strains were hybridized against these sfa-specific probes. Only one copy of the sfa determinant was identified on the chromosome of these strains. No sfa-specific sequences were observed on the chromosome of E. coli K-12 strains and an O7:K1 isolate. With the exception of small alterations in the sfa-coding region the genetic determinants for S fimbriae were identical in uropathogenic O6:K+ and meningitis O18:K1 and O83:K1 strains. The sfa determinant was also detected on the chromosome of K1 isolates with an Sfa-negative phenotype, and specific cross-hybridization signals were visible after blotting against F1C-specific DNA. In addition homology among the different strains was observed in the sfa-flanking regions.

  19. Risk-associated coding synonymous SNPs in type 2 diabetes and neurodegenerative diseases: genetic silence and the underrated association with splicing regulation and epigenetics.

    Science.gov (United States)

    Karambataki, M; Malousi, A; Kouidou, S

    2014-12-01

    Single nucleotide polymorphisms (SNPs) are tentatively critical with regard to disease predisposition, but coding synonymous SNPs (sSNPs) are generally considered "neutral". Nevertheless, sSNPs in serine/arginine-rich (SR) and splice-site (SS) exonic splicing enhancers (ESEs) or in exonic CpG methylation targets, could be decisive for splicing, particularly in aging-related conditions, where mis-splicing is frequently observed. We presently identified 33 genes T2D-related and 28 related to neurodegenerative diseases, by investigating the impact of the corresponding coding sSNPs on splicing and using gene ontology data and computational tools. Potentially critical (prominent) sSNPs comply with the following criteria: changing the splicing potential of prominent SR-ESEs or of significant SS-ESEs by >1.5 units (Δscore), or formation/deletion of ESEs with maximum splicing score. We also noted the formation/disruption of CpGs (tentative methylation sites of epigenetic sSNPs). All disease association studies involving sSNPs are also reported. Only 21/670 coding SNPs, mostly epigenetic, reported in 33 T2D-related genes, were found to be prominent coding synonymous. No prominent sSNPs have been recorded in three key T2D-related genes (GCGR, PPARGC1A, IGF1). Similarly, 20/366 coding synonymous were identified in ND related genes, mostly epigenetic. Meta-analysis showed that 17 of the above prominent sSNPs were previously investigated in association with various pathological conditions. Three out of four sSNPs (all epigenetic) were associated with T2D and one with NDs (branch site sSNP). Five were associated with other or related pathological conditions. None of the four sSNPs introducing new ESEs was found to be disease-associated. sSNPs introducing smaller Δscore changes (<1.5) in key proteins (INSR, IRS1, DISC1) were also correlated to pathological conditions. This data reveals that genetic variation in splicing-regulatory and particularly CpG sites might be related to

  20. Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code.

    Science.gov (United States)

    Duax, William L; Huether, Robert; Pletnev, Vladimir Z; Langs, David; Addlagatta, Anthony; Connare, Sonjay; Habegger, Lukas; Gill, Jay

    2005-12-01

    The short-chain oxidoreductase (SCOR) family of enzymes includes over 6000 members, extending from bacteria and archaea to humans. Nucleic acid sequence analysis reveals that significant numbers of these genes are remarkably free of stopcodons in reading frames other than the coding frame, including those on the antisense strand. The genes from this subset also use almost entirely the GC-rich half of the 64 codons. Analysis of a million hypothetical genes having random nucleotide composition shows that the percentage of SCOR genes having multiple open reading frames exceeds random by a factor of as much as 1 x 10(6). Nevertheless, screening the content of the SWISS-PROT TrEMBL database reveals that 15% of all genes contain multiple open reading frames. The SCOR genes having multiple open reading frames and a GC-rich coding bias exhibit a similar GC bias in the nucleotide triple composition of their DNA. This bias is not correlated with the GC content of the species in which the SCOR genes are found. One possible explanation for the conservation of multiple open reading frames and extreme bias in nucleic acid composition in the family of Rossman folds is that the primordial member of this family was encoded early using only very stable GC-rich DNA and that evolution proceeded with extremely limited introduction of any codons having two or more adenine or thymine nucleotides. These and other data suggest that the SCOR family of enzymes may even have diverged from a common ancestor before most of the AT-rich half of the genetic code was fully defined.

  1. 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.

  2. Evaluating alternate models to estimate genetic parameters of calving traits in United Kingdom Holstein-Friesian dairy cattle

    Directory of Open Access Journals (Sweden)

    Eaglen Sophie A E

    2012-07-01

    Full Text Available Abstract Background The focus in dairy cattle breeding is gradually shifting from production to functional traits and genetic parameters of calving traits are estimated more frequently. However, across countries, various statistical models are used to estimate these parameters. This study evaluates different models for calving ease and stillbirth in United Kingdom Holstein-Friesian cattle. Methods Data from first and later parity records were used. Genetic parameters for calving ease, stillbirth and gestation length were estimated using the restricted maximum likelihood method, considering different models i.e. sire (−maternal grandsire, animal, univariate and bivariate models. Gestation length was fitted as a correlated indicator trait and, for all three traits, genetic correlations between first and later parities were estimated. Potential bias in estimates was avoided by acknowledging a possible environmental direct-maternal covariance. The total heritable variance was estimated for each trait to discuss its theoretical importance and practical value. Prediction error variances and accuracies were calculated to compare the models. Results and discussion On average, direct and maternal heritabilities for calving traits were low, except for direct gestation length. Calving ease in first parity had a significant and negative direct-maternal genetic correlation. Gestation length was maternally correlated to stillbirth in first parity and directly correlated to calving ease in later parities. Multi-trait models had a slightly greater predictive ability than univariate models, especially for the lowly heritable traits. The computation time needed for sire (−maternal grandsire models was much smaller than for animal models with only small differences in accuracy. The sire (−maternal grandsire model was robust when additional genetic components were estimated, while the equivalent animal model had difficulties reaching convergence. Conclusions

  3. Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.

    Science.gov (United States)

    Lassen, Kara G; McKenzie, Craig I; Mari, Muriel; Murano, Tatsuro; Begun, Jakob; Baxt, Leigh A; Goel, Gautam; Villablanca, Eduardo J; Kuo, Szu-Yu; Huang, Hailiang; Macia, Laurence; Bhan, Atul K; Batten, Marcel; Daly, Mark J; Reggiori, Fulvio; Mackay, Charles R; Xavier, Ramnik J

    2016-06-21

    Although numerous polymorphisms have been associated with inflammatory bowel disease (IBD), identifying the function of these genetic factors has proved challenging. Here we identified a role for nine genes in IBD susceptibility loci in antibacterial autophagy and characterized a role for one of these genes, GPR65, in maintaining lysosome function. Mice lacking Gpr65, a proton-sensing G protein-coupled receptor, showed increased susceptibly to bacteria-induced colitis. Epithelial cells and macrophages lacking GPR65 exhibited impaired clearance of intracellular bacteria and accumulation of aberrant lysosomes. Similarly, IBD patient cells and epithelial cells expressing an IBD-associated missense variant, GPR65 I231L, displayed aberrant lysosomal pH resulting in lysosomal dysfunction, impaired bacterial restriction, and altered lipid droplet formation. The GPR65 I231L polymorphism was sufficient to confer decreased GPR65 signaling. Collectively, these data establish a role for GPR65 in IBD susceptibility and identify lysosomal dysfunction as a potentially causative element in IBD pathogenesis with effects on cellular homeostasis and defense. PMID:27287411

  4. 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.

  5. 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.

  6. Genetic modification of alternative respiration in Nicotiana benthamiana affects basal and salicylic acid-induced resistance to potato virus X

    Directory of Open Access Journals (Sweden)

    Verchot-Lubicz Jeanmarie

    2011-02-01

    Full Text Available Abstract Background Salicylic acid (SA regulates multiple anti-viral mechanisms, including mechanism(s that may be negatively regulated by the mitochondrial enzyme, alternative oxidase (AOX, the sole component of the alternative respiratory pathway. However, studies of this mechanism can be confounded by SA-mediated induction of RNA-dependent RNA polymerase 1, a component of the antiviral RNA silencing pathway. We made transgenic Nicotiana benthamiana plants in which alternative respiratory pathway capacity was either increased by constitutive expression of AOX, or decreased by expression of a dominant-negative mutant protein (AOX-E. N. benthamiana was used because it is a natural mutant that does not express a functional RNA-dependent RNA polymerase 1. Results Antimycin A (an alternative respiratory pathway inducer and also an inducer of resistance to viruses and SA triggered resistance to tobacco mosaic virus (TMV. Resistance to TMV induced by antimycin A, but not by SA, was inhibited in Aox transgenic plants while SA-induced resistance to this virus appeared to be stronger in Aox-E transgenic plants. These effects, which were limited to directly inoculated leaves, were not affected by the presence or absence of a transgene constitutively expressing a functional RNA-dependent RNA polymerase (MtRDR1. Unexpectedly, Aox-transgenic plants infected with potato virus X (PVX showed markedly increased susceptibility to systemic disease induction and virus accumulation in inoculated and systemically infected leaves. SA-induced resistance to PVX was compromised in Aox-transgenic plants but plants expressing AOX-E exhibited enhanced SA-induced resistance to this virus. Conclusions We conclude that AOX-regulated mechanisms not only play a role in SA-induced resistance but also make an important contribution to basal resistance against certain viruses such as PVX.

  7. Genetic variations regulate alternative splicing in the 5' untranslated regions of the mouse glioma-associated oncogene 1, Gli1

    Directory of Open Access Journals (Sweden)

    Zaphiropoulos Peter G

    2010-04-01

    Full Text Available Abstract Background Alternative splicing is one of the key mechanisms that generate biological diversity. Even though alternative splicing also occurs in the 5' and 3' untranslated regions (UTRs of mRNAs, the understanding of the significance and the regulation of these variations is rather limited. Results We investigated 5' UTR mRNA variants of the mouse Gli1 oncogene, which is the terminal transcriptional effector of the Hedgehog (HH signaling pathway. In addition to identifying novel transcription start sites, we demonstrated that the expression ratio of the Gli1 splice variants in the 5' UTR is regulated by the genotype of the mouse strain analyzed. The GT allele, which contains the consensus intronic dinucleotides at the 5' splice site of intron 1B, favors exon 1B inclusion, while the GC allele, having a weaker 5' splice site sequence, promotes exon 1B skipping. Moreover, the alternative Gli1 5' UTRs had an impact on translational capacity, with the shorter and the exon 1B-skipped mRNA variants being most effective. Conclusions Our findings implicate novel, genome-based mechanisms as regulators of the terminal events in the mouse HH signaling cascade.

  8. Blood spots as an alternative to whole blood collection and the effect of a small monetary incentive to increase participation in genetic association studies

    Directory of Open Access Journals (Sweden)

    Ringer Danny

    2009-11-01

    Full Text Available Abstract Background Collection of buccal cells from saliva for DNA extraction offers a less invasive and convenient alternative to venipuncture blood collection that may increase participation in genetic epidemiologic studies. However, dried blood spot collection, which is also a convenient method, offers a means of collecting peripheral blood samples from which analytes in addition to DNA can be obtained. Methods To determine if offering blood spot collection would increase participation in genetic epidemiologic studies, we conducted a study of collecting dried blood spot cards by mail from a sample of female cancer cases (n = 134 and controls (n = 256 who were previously selected for a breast cancer genetics study and declined to provide a venipuncture blood sample. Participants were also randomized to receive either a $2.00 bill or no incentive with the blood spot collection kits. Results The average time between the venipuncture sample refusal and recruitment for the blood spot collection was 4.4 years. Thirty-seven percent of cases and 28% of controls provided a dried blood spot card. While the incentive was not associated with participation among controls (29% for $2.00 incentive vs. 26% for no incentive, p = 0.6, it was significantly associated with participation among the breast cancer cases (48% vs. 27%, respectively, p = 0.01. There did not appear to be any bias in response since no differences between cases and controls and incentive groups were observed when examining several demographic, work history and radiation exposure variables. Conclusion This study demonstrates that collection of dried blood spot cards in addition to venipuncture blood samples may be a feasible method to increase participation in genetic case-control studies.

  9. Evaluation of the Genetic Variation of Non Coding Control Region of BK Virus Using Nested-PCR Sequencing Method in Renal Graft Patients

    Directory of Open Access Journals (Sweden)

    A Emami

    2015-05-01

    Full Text Available Background & aim: Polyomaviruses (BK is a comprehensive infection with more than of 80% prevalence in the world. One of the most important reasons of BK virus nephropathy is in the renal transplant recipients and rejection of transplanted tissue between them. Non Coding region of this virus play a regulatory role in replication and amplification of the virus. The aim of this study was to evaluate the genetic patterns of this area in renal graft at Namazi Transplantation Center, Shiraz, Iran. Methods: In the present experimental study, 380 renal allograft serums were collected. DNAs of 129 eligible samples were extracted and evaluated using a virus genome. The presence of the virus was determined by qualitative and sequencing. Of these, 129 samples were tested for the presence of virus according to the condition study, using quantitative, qualitative genomic amplification and sequencing. Results: The study showed symptoms of nephropathy, 76 (58.9% of them were males and 46 (35.7% were females with the mean age 38.0±.089 years of age. In general, 46 patients (35.7% percent were positive for BK Polyomaviruses. After comparing the genomic sequence with applications of molecular they were categorized in three groups and then recorded in gene bank. Conclusion: About 35% of renal transplant recipients with high creatinine levels were positive for the presence of BK virus. Non-coding region of respondents in the sample survey revealed that among patients with the most common genotypes were rearranged the entire transplant patients were observed at this tranplant center. Examination of these sequences indicated that this rearrangments had a specific pattern, different from the standard strain of archaea type.

  10. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2007-05-01

    Full Text Available Abstract Background The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons, through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code. Results Our main guide in constructing the models is the Darwinian Continuity Principle whereby a scenario for the evolution of a complex system must consist of plausible elementary steps, each conferring a distinct advantage on the evolving ensemble of genetic elements. Evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in a RNA World containing ribozymes with versatile activities. Since evolution has no foresight, the translation system could not evolve in the RNA World as the result of selection for protein synthesis and must have been a by-product of evolution drive by selection for another function, i.e., the translation system evolved via the exaptation route. It is proposed that the evolutionary process that eventually led to the emergence of translation started with

  11. All about Genetics (For Parents)

    Science.gov (United States)

    ... Things to Know About Zika & Pregnancy All About Genetics KidsHealth > For Parents > All About Genetics Print A ... way they pick up special laboratory dyes. continue 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. Dynamic cellular manufacturing system design considering alternative routing and part operation tradeoff using simulated annealing based genetic algorithm

    Indian Academy of Sciences (India)

    KAMAL DEEP; PARDEEP K SINGH

    2016-09-01

    In this paper, an integrated mathematical model of multi-period cell formation and part operation tradeoff in a dynamic cellular manufacturing system is proposed in consideration with multiple part process route. This paper puts emphasize on the production flexibility (production/subcontracting part operation) to satisfy the product demand requirement in different period segments of planning horizon considering production capacity shortage and/or sudden machine breakdown. The proposed model simultaneously generates machine cells and part families and selects the optimum process route instead of the user specifying predetermined routes. Conventional optimization method for the optimal cell formation problem requires substantial amount of time and memory space. Hence a simulated annealing based genetic algorithm is proposed to explore the solution regions efficiently and to expedite the solution search space. To evaluate the computability of the proposed algorithm, different problem scenarios are adopted from literature. The results approve the effectiveness of theproposed approach in designing the manufacturing cell and minimization of the overall cost, considering various manufacturing aspects such as production volume, multiple process route, production capacity, machine duplication, system reconfiguration, material handling and subcontracting part operation.

  14. Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing.

    Directory of Open Access Journals (Sweden)

    Dorothy Concepcion

    2009-05-01

    Full Text Available Cellular gene expression machinery has coevolved with molecular parasites, such as viruses and transposons, which rely on host cells for their expression and reproduction. We previously reported that a wild-derived allele of mouse Nxf1 (Tap, a key component of the host mRNA nuclear export machinery, suppresses two endogenous retrovirus-induced mutations and shows suggestive evidence of positive selection. Here we show that Nxf1(CAST suppresses a specific and frequent class of intracisternal A particle (IAP-induced mutations, including Ap3d1(mh2J, a model for Hermansky-Pudlak syndrome, and Atcay(hes, an orthologous gene model for Cayman ataxia, among others. The molecular phenotype of suppression includes approximately two-fold increase in the level of correctly-spliced mRNA and a decrease in mutant-specific, alternatively-processed RNA accumulating from the inserted allele. Insertional mutations involving ETn and LINE elements are not suppressed, demonstrating a high degree of specificity to this suppression mechanism. These results implicate Nxf1 in some instances of pre-mRNA processing, demonstrate the useful range of Nxf1(CAST alleles for manipulating existing mouse models of disease, and specifically imply a low functional threshold for therapeutic benefit in Cayman ataxia.

  15. 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

  16. Studies of the genetic variability of the coding region of the hepatocyte nuclear factor-4alpha in Caucasians with maturity onset NIDDM.

    Science.gov (United States)

    Møller, A M; Urhammer, S A; Dalgaard, L T; Reneland, R; Berglund, L; Hansen, T; Clausen, J O; Lithell, H; Pedersen, O

    1997-08-01

    Mutations in the hepatocyte nuclear factor-4alpha (HNF-4alpha) gene cause the type 1 form of maturity onset diabetes of the young (MODY1). To address the question of whether genetic variability of HNF-4alpha is associated with late onset non-insulin-dependent diabetes mellitus (NIDDM) we have sequenced the coding region and intron/exon boundaries of the gene in 36 randomly recruited Danish NIDDM patients. Two nucleotide substitutions that changed the sequence of HNF-4alpha were identified: Thr/Ile130, which has been reported previously and a novel Val/Met255. The Val/Met 255 mutation was found in 4 of 477 Danish NIDDM patients and in none of 217 glucose tolerant control subjects; thus it cannot be excluded that this mutation may have an impact on NIDDM susceptibility. Among 509 NIDDM patients the allelic frequency of the Thr/Ile130 variant was 4.7% (95% confidence interval: 3.4-6.0%) compared to 1.9% (0.7-3.1%) among 239 control subjects (p = 0.008). However, in a population sample of 942 Swedish men with an average age of 70 years the allelic frequency of the variant was similar in 246 men with either impaired glucose tolerance (5.6% [2.6-8.6%]) or NIDDM (5.4% [2.7-8.1%]) as compared to 666 glucose tolerant men (5.1% [3.9-6.3%]). Also in a population sample of 369 young healthy Danes the prevalence of the codon 130 variant (4.7% [3.2-6.2%]) was similar to what was found in Swedish Caucasians. Thus, the allelic frequency of the Thr/Ile130 variant among the control subjects in the Danish case-control study deviates from the prevalence in the two other studies which is why we consider the significant association between the codon 130 variant and NIDDM an incidental finding. In glucose tolerant subjects the codon 130 variant in its heterozygous form had no major effect on glucose-induced insulin and C-peptide release although a tendency to a lower insulin secretion during an oral glucose tolerance test was seen in middle-aged subjects. In conclusion, variability in

  17. 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.

  18. On an Alternative Cosmology

    CERN Document Server

    Vankov, A

    1998-01-01

    The suggested alternative cosmology is based on the idea of barion symmetric universe, in which our home universe is a representative of multitude of typical matter and antimatter universes. This alternative concept gives a physically reasonable explanation of all major problems of the Standard Cosmological Model. Classification Code MSC: Cosmology 524.8 Key words: standard cosmological model, alternative cosmology, barionic symmetry, typical universe, quasars, cosmic rays.

  19. Quantized Network Coding for Correlated Sources

    OpenAIRE

    Nabaee, Mahdy; Labeau, Fabrice

    2012-01-01

    Non-adaptive joint source network coding of correlated sources is discussed in this paper. By studying the information flow in the network, we propose quantized network coding as an alternative for packet forwarding. This technique has both network coding and distributed source coding advantages, simultaneously. Quantized network coding is a combination of random linear network coding in the (infinite) field of real numbers and quantization to cope with the limited capacity of links. With the...

  20. Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions

    Indian Academy of Sciences (India)

    S B Nagendrakumar; M Madhanmohan; P N Rangarajan; V A Srinivasan

    2009-03-01

    The leader protease (Lpro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968–2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups – Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classified into different genetic subgroups (< 5% divergence). Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or convergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the Lpro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identified at aa positions 23 in the Lpro ( < 0.05; 0.046*) and at aa 171 in the capsid protein VP1 ( < 0.01; 0.003**).

  1. 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.

  2. code {poems}

    Directory of Open Access Journals (Sweden)

    Ishac Bertran

    2012-08-01

    Full Text Available "Exploring the potential of code to communicate at the level of poetry," the code­ {poems} project solicited submissions from code­writers in response to the notion of a poem, written in a software language which is semantically valid. These selections reveal the inner workings, constitutive elements, and styles of both a particular software and its authors.

  3. Genetic Immunization of BALB/c mice with a Plasmid Bearing the Gene Coding for a Hybrid Merozoite Surface Protein 1-Hepatitis B Virus Surface Protein Fusion Protects Mice against Lethal Plasmodium chabaudi chabaudi PC1 Infection

    OpenAIRE

    Wunderlich, Gerhard; Moura, Ivan C.; del Portillo, Hernando A

    2000-01-01

    The genetic immunization of rodents with a plasmid coding for a Plasmodium chabaudi merozoite surface protein 1 (C terminus)-hepatitis B virus surface fusion protein (pPcMSP119-HBs) provided protection of mice against subsequent lethal challenge with P. chabaudi chabaudi PC1-infected red blood cells. The percentage of survivor mice was higher in DNA-immunized mice than in animals immunized with a recombinant rPcMSP119– glutathione S-transferase fusion protein administered in Freund adjuvant. ...

  4. Genetic polymorphism of T6235C mutation in 3 non-coding region of CYP1A1 and GSTM1 genes and lung cancer susceptibility in the Mongolian population

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Objective To estimate the relative risk for lung cancer associated with genetic polymorphism of T6235C mutation in 3' non-coding region(MspⅠ)of cytochrome P450 1A1(CYP1A1)and glutathione S-transferase M1(GSTM1)in the Mongolian population in Inner Mongolian Region of China.Methods Polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP)and multiplex PCR methods were used to analyze blood samples obtained from 263 case subjects and 263 control subjects to determine their genotypes for CYP1...

  5. 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.

  6. 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.

  7. An Alternative Life

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Young genius left school to pursue genetic code analysis University students are expected to enjoy campus life.But for more than one year, 19-year-old Zhao Bowen has assumed the leadership of a research team probing one of the world’s toughest problems—the genetic basis for human IQ.In 2009,Zhao,still a student in his third year at the High School Affiliated to Renmin

  8. Holographic codes

    CERN Document Server

    Latorre, Jose I

    2015-01-01

    There exists a remarkable four-qutrit state that carries absolute maximal entanglement in all its partitions. Employing this state, we construct a tensor network that delivers a holographic many body state, the H-code, where the physical properties of the boundary determine those of the bulk. This H-code is made of an even superposition of states whose relative Hamming distances are exponentially large with the size of the boundary. This property makes H-codes natural states for a quantum memory. H-codes exist on tori of definite sizes and get classified in three different sectors characterized by the sum of their qutrits on cycles wrapped through the boundaries of the system. We construct a parent Hamiltonian for the H-code which is highly non local and finally we compute the topological entanglement entropy of the H-code.

  9. Alternative security

    International Nuclear Information System (INIS)

    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

  10. Alternative energies; Energies alternatives

    Energy Technology Data Exchange (ETDEWEB)

    Bonal, J.; Rossetti, P

    2007-07-01

    The earth took millions years to made the petroleum, the gas the coal and the uranium. Only a few centuries will be needed to exhaust these fossil fuels and some years to reach expensive prices. Will the wold continue on this way of energy compulsive consumption? The renewable energies and some citizen attitudes are sufficient to break this spiral. This book proposes to discuss these alternative energies. It shows that this attitude must be supported by the government. It takes stock on the more recent information concerning the renewable energies. it develops three main points: the electricity storage, the housing and the transports. (A.L.B.)

  11. 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

  12. A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer

    Science.gov (United States)

    Yuan, Hua; Liu, Hongliang; Liu, Zhensheng; Owzar, Kouros; Han, Younghun; Su, Li; Wei, Yongyue; Hung, Rayjean J.; McLaughlin, John; Brhane, Yonathan; Brennan, Paul; Bickeboeller, Heike; Rosenberger, Albert; Houlston, Richard S.; Caporaso, Neil; Landi, Maria Teresa; Heinrich, Joachim; Risch, Angela; Christiani, David C.; Gümüş, Zeynep H.; Klein, Robert J.; Amos, Christopher I.; Wei, Qingyi

    2016-01-01

    Lung cancer etiology is multifactorial, and growing evidence has indicated that long non-coding RNAs (lncRNAs) are important players in lung carcinogenesis. We performed a large-scale meta-analysis of 690,564 SNPs in 15,531 autosomal lncRNAs by using datasets from six previously published genome-wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium in populations of European ancestry. Previously unreported significant SNPs (P value < 1 × 10−7) were further validated in two additional independent lung cancer GWAS datasets from Harvard University and deCODE. In the final meta-analysis of all eight GWAS datasets with 17,153 cases and 239,337 controls, a novel risk SNP rs114020893 in the lncRNA NEXN-AS1 region at 1p31.1 remained statistically significant (odds ratio = 1.17; 95% confidence interval = 1.11–1.24; P = 8.31 × 10−9). In further in silico analysis, rs114020893 was predicted to change the secondary structure of the lncRNA. Our finding indicates that SNP rs114020893 of NEXN-AS1 at 1p31.1 may contribute to lung cancer susceptibility. PMID:27713484

  13. 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

  14. 格雷码混合遗传算法求解0-1背包问题%Gray coded hybrid genetic algorithm for 0-1 knapsack problem

    Institute of Scientific and Technical Information of China (English)

    王则林; 吴志健

    2012-01-01

    This paper gave an athematic mode of 0-1 knapsack problem,and modified the binary coding to establish a gray coded hybrid genetic algorithm used greedy algorithm to handle with the constraint conditions, And this paper proposed a value density operator to the individual, which could improve the search effciency, used the elitism mechanism to accelerate the convergence process, The numerical experiment proves the affectivity of the algorithm.%给出0-1背包问题的数学模型,修改传统二进制编码为格雷码混合遗传算法,使用贪心算法来解决约束问题,对每个个体使用价值密度来衡量,提高了算法搜索效率,同时使用精英保留机制来加速算法收敛的速度.最后通过数值实验证明了算法的有效性.

  15. Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg's and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula.

    Science.gov (United States)

    Castro-Chavez, Fernando

    2012-01-01

    BACKGROUND: Three binary representations of the genetic code according to the ancient I Ching of Fu-Xi will be presented, depending on their defragging capabilities by pairing based on three biochemical properties of the nucleic acids: H-bonds, Purine/Pyrimidine rings, and the Keto-enol/Amino-imino tautomerism, yielding the last pair a 32/32 single-strand self-annealed genetic code and I Ching tables. METHODS: Our working tool is the ancient binary I Ching's resulting genetic code chromosomes defragged by vertical and by horizontal pairing, reverse engineered into non-binaries of 2D rotating 4×4×4 circles and 8×8 squares and into one 3D 100% symmetrical 16×4 tetrahedron coupled to a functional tetrahedron with apical signaling and central hydrophobicity (codon formula: 4[1(1)+1(3)+1(4)+4(2)]; 5:5, 6:6 in man) forming a stella octangula, and compared to Nirenberg's 16×4 codon table (1965) pairing the first two nucleotides of the 64 codons in axis y. RESULTS: One horizontal and one vertical defragging had the start Met at the center. Two, both horizontal and vertical pairings produced two pairs of 2×8×4 genetic code chromosomes naturally arranged (M and I), rearranged by semi-introversion of central purines or pyrimidines (M' and I') and by clustering hydrophobic amino acids; their quasi-identity was disrupted by amino acids with odd codons (Met and Tyr pairing to Ile and TGA Stop); in all instances, the 64-grid 90° rotational ability was restored. CONCLUSIONS: We defragged three I Ching representations of the genetic code while emphasizing Nirenberg's historical finding. The synthetic genetic code chromosomes obtained reflect the protective strategy of enzymes with a similar function, having both humans and mammals a biased G-C dominance of three H-bonds in the third nucleotide of their most used codons per amino acid, as seen in one chromosome of the i, M and M' genetic codes, while a two H-bond A-T dominance was found in their complementary chromosome, as

  16. Alternative Splice in Alternative Lice.

    Science.gov (United States)

    Tovar-Corona, Jaime M; Castillo-Morales, Atahualpa; Chen, Lu; Olds, Brett P; Clark, John M; Reynolds, Stuart E; Pittendrigh, Barry R; Feil, Edward J; Urrutia, Araxi O

    2015-10-01

    Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial diseases; epidemictyphus, trench fever, and relapsing fever. In order to gain insights into the molecular bases for these differences, we analyzed alternative splicing (AS) using next-generation sequencing data for one strain of head lice and one strain of body lice. We identified a total of 3,598 AS events which were head or body lice specific. Exon skipping AS events were overrepresented among both head and body lice, whereas intron retention events were underrepresented in both. However, both the enrichment of exon skipping and the underrepresentation of intron retention are significantly stronger in body lice compared with head lice. Genes containing body louse-specific AS events were found to be significantly enriched for functions associated with development of the nervous system, salivary gland, trachea, and ovarian follicle cells, as well as regulation of transcription. In contrast, no functional categories were overrepresented among genes with head louse-specific AS events. Together, our results constitute the first evidence for transcript pool differences in head and body lice, providing insights into molecular adaptations that enabled human lice to adapt to clothing, and representing a powerful illustration of the pivotal role AS can play in functional adaptation. PMID:26169943

  17. 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 path...

  18. 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

  19. The neurogenetics of alternative splicing

    OpenAIRE

    Vuong, CK; Black, DL; S. Zheng

    2016-01-01

    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 r...

  20. 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

  1. 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.

  2. 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.)

  3. 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...... the codes succinctly using Gröbner bases....

  4. MCNP code

    International Nuclear Information System (INIS)

    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

  5. ANIMAL code

    International Nuclear Information System (INIS)

    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

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

    DEFF Research Database (Denmark)

    Armano, MT; Ferriani, VP; Florido, MP;

    2008-01-01

    ' fibroblasts when analyzed by confocal microscopy. We show that all four siblings are homozygous for a mutation at position 938 in exon 6 of the C1s cDNA that creates a premature stop codon. Our investigations led us to reveal the presence of previously uncharacterized splice variants of C1s mRNA transcripts...... in normal human cells. These variants are derived from the skipping of exon 3 and from the use of an alternative 3' splice site within intron 1 which increases the size of exon 2 by 87 nucleotides....

  7. Correct Code Containing Containers

    OpenAIRE

    Dross, Claire; Filliâtre, Jean-Christophe; Moy, Yannick

    2011-01-01

    For critical software development, containers such as lists, vectors, sets or maps are an attractive alternative to ad-hoc data structures based on pointers. As standards like DO-178C put formal verification and testing on an equal footing, it is important to give users the ability to apply both to the verification of code using containers. In this paper, we present a definition of containers whose aim is to facilitate their use in certified software, using modern proof technology and novel s...

  8. NOVEL BIPHASE CODE -INTEGRATED SIDELOBE SUPPRESSION CODE

    Institute of Scientific and Technical Information of China (English)

    Wang Feixue; Ou Gang; Zhuang Zhaowen

    2004-01-01

    A kind of novel binary phase code named sidelobe suppression code is proposed in this paper. It is defined to be the code whose corresponding optimal sidelobe suppression filter outputs the minimum sidelobes. It is shown that there do exist sidelobe suppression codes better than the conventional optimal codes-Barker codes. For example, the sidelobe suppression code of length 11 with filter of length 39 has better sidelobe level up to 17dB than that of Barker code with the same code length and filter length.

  9. 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...... in trees....

  10. Concatenated codes with convolutional inner codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Thommesen, Christian; Zyablov, Viktor

    1988-01-01

    The minimum distance of concatenated codes with Reed-Solomon outer codes and convolutional inner codes is studied. For suitable combinations of parameters the minimum distance can be lower-bounded by the product of the minimum distances of the inner and outer codes. For a randomized ensemble of...... concatenated codes a lower bound of the Gilbert-Varshamov type is proved...

  11. 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.

    Science.gov (United States)

    Nordmaj, Mie Anemone; Munthe-Fog, Lea; Hein, Estrid; Skjoedt, Mikkel-Ole; Garred, Peter

    2015-12-01

    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 pathway (AP) is complement factor H (FH). Our aim was to design a dual upstream inhibitor of both human lectin and APs by fusing MAP-1 with a part of FH. There were 2 different recombinant chimeric proteins comprising full-length human MAP-1 and the first 5 N-terminal domains of human FH designed. The FH domains were orientated either in the N- or C-terminal part of MAP-1. The complement inhibition potential in human serum was assessed. Both chimeric constructs displayed the characteristics of the native molecules and bound to the PRMs with an EC50 of ∼ 2 nM. However, when added to serum diluted 1:4 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 was seen on the classical pathway. Fusion of MAP-1 with FH domains represents a novel therapeutic approach for selective targeting upstream and central complement activation at sites of inflammation.

  12. Quantum Cyclic Code

    CERN Document Server

    Dutta, Sagarmoy

    2010-01-01

    In this paper, we define and study \\emph{quantum cyclic codes}, a generalisation of cyclic codes to the quantum setting. Previously studied examples of quantum cyclic codes were all quantum codes obtained from classical cyclic codes via the CSS construction. However, the codes that we study are much more general. In particular, we construct cyclic stabiliser codes with parameters $[[5,1,3

  13. [Perspectives of RNA interference application in the therapy of diseases associated with defects in alternative RNA splicing].

    Science.gov (United States)

    Wysokiński, Daniel; Błasiak, Janusz

    2012-09-18

    The primary transcript of an eukaryotic gene (pre-mRNA) is composed of coding regions--exons intervened by non-coding introns--which are removed in the RNA splicing process, leading to the formation of mature, intron-free mRNA. Alternative splicing of pre-mRNA is responsible for high complexity of the cellular proteome and expresses effective use of genetic information contained in genomic DNA. Alternative splicing plays important roles in the organism, including apoptosis regulation or development and plasticity of the nervous system. The main role of alternative splicing is differential, dependent on conditions and the cell type, splicing of mRNA, generating diverse transcripts from one gene, and, after the translation, different isoforms of a particular protein. Because of the high complexity of this mechanism, alternative splicing is particularly prone to errors. The perturbations resulting from mutations in the key sequences for splicing regulations are especially harmful. The pathogenesis of numerous diseases results from disturbed alternative RNA splicing, and those include cancers and neurodegenerative disorders. The treatment of these conditions is problematic due to their genetic background and currently RNA interference, which is a common mechanism of eukaryotic gene regulation, is being studied. Initial successes in the attempts of silencing the expression of faulty protein isoforms support the idea of using RNA interference in targeting disease related to disturbances in alternative splicing of RNA.

  14. 连续交替共前缀长度码测试数据压缩和解压方案%Scheme of Test Data Compression and Decompression Based on Continuous Alternation Sharing-Prefix Length Code

    Institute of Scientific and Technical Information of China (English)

    暴阳; 吴琼

    2016-01-01

    This paper proposes a new coding method.The method further explores the correlation between the adjacent run on the basis of continuous sequence coding meanwhile if the two have the same prefix .This scheme uses 1 bit to represent the whole prefix.%本文提出了一种新的编码方法,对连续序列进行编码,如果前后两个编码组有相同的前缀,那么用一个标记位1,就可以代替后一个游程很长的前缀。如果两个游程不在同一组,就用一个标记位0隔开,后面按源代码编码。

  15. Quantum algorithms and the genetic code

    Indian Academy of Sciences (India)

    Apoorva Patel

    2001-02-01

    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 solutions to an optimisation problem. Components of the DNA structure which implement Grover’s algorithm are identified, and a physical scenario is presented for the execution of the quantum algorithm. It is proposed that enzymes play a crucial role in maintaining quantum coherence of the process. Experimental tests that can verify this scenario are pointed out.

  16. Quantum Algorithms and the Genetic Code

    CERN Document Server

    Patel, A D

    2001-01-01

    Replication of DNA and synthesis of proteins are studied from the view-pointof quantum database search. Identification of a base-pairing with a quantumquery gives a natural (and first ever!) explanation of why living organismshave 4 nucleotide bases and 20 amino acids. It is amazing that these numbersarise as solutions to an optimisation problem. Components of the DNA structurewhich implement Grover's algorithm are identified, and a physical scenario ispresented for the execution of the quantum algorithm. It is proposed thatenzymes play a crucial role in maintaining quantum coherence of the process.Experimental tests that can verify this scenario are pointed out.

  17. STRUCTURAL OPTIMIZATION OF COMPOSITE PROPELLER WITH INTEGER-CODED PARALLEL GENETIC ALGORITHM%基于整数编码并行遗传算法的复合材料螺旋桨结构优化设计

    Institute of Scientific and Technical Information of China (English)

    金朋; 钟小平; 宋笔锋; 安伟刚; 李凯

    2012-01-01

    An integer-coded parallel genetic algorithm is presented for solving large scale composite structures optimization problem. This optimization method, which is applied to the structure optimization of a composite propeller, makes staking sequence and staking thickness be optimized simultaneously. First, on the basis of region division, a length-control factor for every ply is added to decide the regions of composite plies. Second, the GA( genetic algorithm) is improved to make it a high-efficiency algorithm that can optimize staking sequence and staking thickness simultaneously. Then, MPI (message-passing interface) is adopted to build parallel program environment and master-slave parallel GA to fulfill the parallel calculation of GA through single computer multi-process method. Finally, the optimization method proposed is used to optimize a composite propeller to demonstrate the high efficiency. The acceleration effect of the parallel GA is also analyzed.%提出一种针对大型复合材料结构铺层厚度和铺层顺序同时进行优化的整数编码并行遗传算法,并将该优化方法应用于复合材料螺旋桨结构优化问题.首先,在区域划分的基础上,对每一单层设定一个长度控制因子来决定单层的铺设区域,以实现对大型复合材料结构的整体一次性优化.然后对遗传算法进行改进,使之成为一种能同时优化铺层厚度和铺层顺序的高效算法.并采用并行编程语言标准MPI( message passing interface)构建并行编程环境,利用主从式并行遗传算法框架,实现遗传算法在单机多进程上的并行计算.最后针对复合材料螺旋桨结构进行优化设计,以验证该方法的高效性,并分析并行遗传算法的加速效果.

  18. Alternative Treatments

    Science.gov (United States)

    ... Find your chapter: search by state Home > Alzheimer's Disease > Treatments > Alternative Treatments Overview What Is Dementia? What Is Alzheimer's? Younger/Early Onset Facts and Figures Know the 10 Signs Stages Inside the Brain: ...

  19. Seleção recorrente intrapopulacional no maracujazeiro amarelo: alternativa de capitalização de ganhos genéticos Intrapopulation recurrent selection in yellow passion fruit: alternative to accumulate genetic gains

    Directory of Open Access Journals (Sweden)

    Marcelo Geraldo de Morais Silva

    2009-02-01

    evaluated, which represents the improved population, UENF/MA1. The randomized complete block design with two replications and five plants per plot was used. Evaluations were made from February to July 2007 for five agronomic traits. Data of plot means were considered for statistical analysis. The genetic parameter estimates and correlations, as well as the selection based on the selection index made possible the identification of progenies with high performance for several traits, simultaneously. Besides, the strategy may constitute an alternative of accumulating genetic gains in yellow passion fruit recurrent selection, increasing the efficiency of the selective process and its use in fruit improvement programs, once it allows genetic gain in two (generation and progeny tests of the three recurrent selection steps.

  20. 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

  1. ["Matreshka" Genes with Alternative Reading Frames].

    Science.gov (United States)

    Sheshukova, E V; Shindyapina, A V; Komarova, T V; Dorokhov, Yu L

    2016-02-01

    Although a relatively small part of the human genome contains protein encoding genes, the latest data on the discovery of alternative open reading frames (ORFs) in conventional mRNAs has highlighted the expanded coding potential of these genes. Until recently, it was believed that each mRNA transcript encodes a single protein. Recent proteogenomics data indicate the existence of exceptions to this rule, which greatly changes the usual meaning of the term "gene". The topology of a gene with overlapping ORFs resembles a Russian "matreshka" toy. There are two levels of "matreshka" genetic systems. First, the chromosomal level, when the "nested" gene is located within introns and exons of the main chromosomal gene, both in the sense and antisense orientation relative to the external gene. The second level is a mature mRNA molecule containing overlapping ORFs or an ORF with an alternative-start codon. In this review we will focus on the properties of "matreshka" genes of the second type and methods for their detection and verification. Particular attention is paid to the biological properties of the polypeptides encoded by these genes. PMID:27215029

  2. Regulation of Coding and Non-coding Genes : New insights obtained through analysis of high-throughput sequencing data

    NARCIS (Netherlands)

    K. Rooijers (Koos)

    2016-01-01

    markdownabstractThe genetic code of a cell is kept in its DNA. However, a vast number of functions of a cell are carried out by proteins. Through gene expression the genetic code can be expressed and give rise to proteins. The expression of genes into proteins follows two steps: transcription of DNA

  3. Strong Trinucleotide Circular Codes

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2011-01-01

    Full Text Available Recently, we identified a hierarchy relation between trinucleotide comma-free codes and trinucleotide circular codes (see our previous works. Here, we extend our hierarchy with two new classes of codes, called DLD and LDL codes, which are stronger than the comma-free codes. We also prove that no circular code with 20 trinucleotides is a DLD code and that a circular code with 20 trinucleotides is comma-free if and only if it is a LDL code. Finally, we point out the possible role of the symmetric group ∑4 in the mathematical study of trinucleotide circular codes.

  4. 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.

  5. Foundations of genetic algorithms 1991

    CERN Document Server

    FOGA

    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

  6. 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...

  7. Joint source channel coding using arithmetic codes

    CERN Document Server

    Bi, Dongsheng

    2009-01-01

    Based on the encoding process, arithmetic codes can be viewed as tree codes and current proposals for decoding arithmetic codes with forbidden symbols belong to sequential decoding algorithms and their variants. In this monograph, we propose a new way of looking at arithmetic codes with forbidden symbols. If a limit is imposed on the maximum value of a key parameter in the encoder, this modified arithmetic encoder can also be modeled as a finite state machine and the code generated can be treated as a variable-length trellis code. The number of states used can be reduced and techniques used fo

  8. Model Children's Code.

    Science.gov (United States)

    New Mexico Univ., Albuquerque. American Indian Law Center.

    The Model Children's Code was developed to provide a legally correct model code that American Indian tribes can use to enact children's codes that fulfill their legal, cultural and economic needs. Code sections cover the court system, jurisdiction, juvenile offender procedures, minor-in-need-of-care, and termination. Almost every Code section is…

  9. 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". PMID:27048216

  10. 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.

  11. Genetic background of phenotypic variation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A noteworthy feature of the living world is its bewildering variability. A key issue in several biological disciplines is the achievement of an understanding of the hereditary basis of this variability. Two opposing, but not necessarily irreconcilable conceptions attempt to explain the underlying mechanism. The gene function paradigm postulates that phenotypic variance is generated by the polymorphism in the coding sequences of genes. However, comparisons of a great number of homologous gene and protein sequences have revealed that they predominantly remained functionally conserved even across distantly related phylogenic taxa. Alternatively, the gene regulation paradigm assumes that differences in the cis-regulatory region of genes do account for phenotype variation within species. An extension of this latter concept is that phenotypic variability is generated by the polyrnorphism in the overall gene expression profiles of gene networks.In other words, the activity of a particular gene is a system property determined both by the cis-regulatory sequences of the given genes and by the other genes of a gene network, whose expressions vary among individuals, too. Novel proponents of gene function paradigm claim that functional genetic variance within the coding sequences of regulatory genes is critical for the generation of morphological polymorphism. Note, however, that these developmental genes play direct regulatory roles in the control of gene expression.

  12. Nonbinary quantum codes

    OpenAIRE

    Eric M. Rains

    1997-01-01

    We present several results on quantum codes over general alphabets (that is, in which the fundamental units may have more than 2 states). In particular, we consider codes derived from finite symplectic geometry assumed to have additional global symmetries. From this standpoint, the analogues of Calderbank-Shor-Steane codes and of GF(4)-linear codes turn out to be special cases of the same construction. This allows us to construct families of quantum codes from certain codes over number fields...

  13. 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....

  14. Affine Grassmann codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Beelen, Peter; Ghorpade, Sudhir Ramakant

    2010-01-01

    We consider a new class of linear codes, called affine Grassmann codes. These can be viewed as a variant of generalized Reed-Muller codes and are closely related to Grassmann codes.We determine the length, dimension, and the minimum distance of any affine Grassmann code. Moreover, we show that...... affine Grassmann codes have a large automorphism group and determine the number of minimum weight codewords....

  15. 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

  16. 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

  17. RNA Editing Dynamically Rewrites the Cancer Code

    Science.gov (United States)

    Rayon-Estrada, Violeta; Papavasiliou, F. Nina; Harjanto, Dewi

    2016-01-01

    Global analyses of cancer transcriptomes demonstrate that ADAR (adenosine deaminase, RNA-specific)-mediated RNA editing dynamically contributes to genetic alterations in cancer, and directly correlates with progression and prognosis. RNA editing is abundant and frequently elevated in cancer, and affects functionally and clinically relevant sites in both coding and non-coding regions of the transcriptome. Therefore, ADAR and differentially edited transcripts may be promising biomarkers or targets for therapy.

  18. The optimal code searching method with an improved criterion of coded exposure for remote sensing image restoration

    Science.gov (United States)

    He, Lirong; Cui, Guangmang; Feng, Huajun; Xu, Zhihai; Li, Qi; Chen, Yueting

    2015-03-01

    Coded exposure photography makes the motion de-blurring a well-posed problem. The integration pattern of light is modulated using the method of coded exposure by opening and closing the shutter within the exposure time, changing the traditional shutter frequency spectrum into a wider frequency band in order to preserve more image information in frequency domain. The searching method of optimal code is significant for coded exposure. In this paper, an improved criterion of the optimal code searching is proposed by analyzing relationship between code length and the number of ones in the code, considering the noise effect on code selection with the affine noise model. Then the optimal code is obtained utilizing the method of genetic searching algorithm based on the proposed selection criterion. Experimental results show that the time consuming of searching optimal code decreases with the presented method. The restoration image is obtained with better subjective experience and superior objective evaluation values.

  19. Coupling CFD code with system code and neutron kinetic code

    International Nuclear Information System (INIS)

    Highlights: • Coupling interface between CFD code Fluent and system code Athlet was created. • Athlet code is internally coupled with neutron kinetic code Dyn3D. • Explicit coupling of overlapped computational domains was used. • A coupled system of Athlet/Dyn3D+Fluent codes was successfully tested on a real case. - Abstract: The aim of this work was to develop the coupling interface between CFD code Fluent and system code Athlet internally coupled with neutron kinetic code Dyn3D. The coupling interface is intended for simulation of complex transients such as Main Steam Line Break scenarios, which cannot be modeled separately first by system and neutron kinetic code and then by CFD code, because of the feedback between the codes. In the first part of this article, the coupling method is described. Explicit coupling of overlapped computational domains is used in this work. The second part of the article presents a demonstration simulation performed by the coupled system of Athlet/Dyn3D and Fluent. The “Opening a Steam Dump to the Atmosphere” test carried out at the Temelin NPP (VVER-1000) was simulated by the coupled system. In this simulation, the primary and secondary circuits were modeled by Athlet, mixing in downcomer and lower plenum was simulated by Fluent and heat generation in the core was calculated by Dyn3D. The results of the simulation with Athlet/Dyn3D+Fluent were compared with the experimental data and the results from a calculation performed with Athlet/Dyn3D without Fluent

  20. One Twenty Phase Code Design for Radar

    Directory of Open Access Journals (Sweden)

    E.N.V. Purna Chandra Rao

    2013-12-01

    Full Text Available Sequences with good autocorrelation Properties are useful for radar and communication applications. In this paper One Twenty Phase sequences are synthesized using Modified Genetic Algorithm (MGA. MGA is used as a statistical technique for obtaining approximate solutions to combinatorial optimization problems. This algorithm combines the good methodologies of the two algorithms like global minimum converging property of Genetic Algorithm (GA and fast convergence rate of Hamming scan algorithm. The synthesized sequences have autocorrelation Properties better than well-known binary MPS code and Frank codes. The synthesized sequences also have complex signal structure which is difficult to detect and analyze by enemy electronics support measure.

  1. Robot path planning using genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Presents a strategy for soccer robot path planning using genetic algorithms for which, real number coding method is used, to overcome the defects of binary coding method, and the double crossover operation a dopted, to avoid the common defect of early convergence and converge faster than the standard genetic algo rithms concludes from simulation results that the method is effective for robot path planning.

  2. Alternative crops

    International Nuclear Information System (INIS)

    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.)

  3. [Genetics and genetic counseling].

    Science.gov (United States)

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  4. [The genetic language: grammar, semantics, evolution].

    Science.gov (United States)

    Ratner, V A

    1993-05-01

    The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering.

  5. [The genetic language: grammar, semantics, evolution].

    Science.gov (United States)

    Ratner, V A

    1993-05-01

    The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering. PMID:8335231

  6. Locally Orderless Registration Code

    DEFF Research Database (Denmark)

    2012-01-01

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

  7. Alternative Energies

    Energy Technology Data Exchange (ETDEWEB)

    Planting, A.; De saint Jacob, Y.; Verwijs, H.; Belin, H.; Preesman, L.

    2009-03-15

    In two articles, one interview and one column attention is paid to alternative energies. The article 'A new light on saving energy' discusses the option to save energy by modernising lighting systems in urban areas. The column 'View from Paris' focuses on investment decisions in France with regard to renewable energy and energy savings. The article 'Europe turns a blind eye to big battery' discusses developments in batteries to store energy. The interview concerns fuel cell expert and formerly President of UTC Power Jan van Dokkum. The last article gives a brief overview of the European Energy Research Alliance (EERA) and the challenges this alliance will have to face with regard to climate change and energy security.

  8. Energy alternatives

    International Nuclear Information System (INIS)

    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

  9. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  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. Constructing quantum codes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Quantum error correcting codes are indispensable for quantum information processing and quantum computation.In 1995 and 1996,Shor and Steane gave first several examples of quantum codes from classical error correcting codes.The construction of efficient quantum codes is now an active multi-discipline research field.In this paper we review the known several constructions of quantum codes and present some examples.

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

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    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.

  13. Turbo Codes Extended with Outer BCH Code

    DEFF Research Database (Denmark)

    Andersen, Jakob Dahl

    1996-01-01

    The "error floor" observed in several simulations with the turbo codes is verified by calculation of an upper bound to the bit error rate for the ensemble of all interleavers. Also an easy way to calculate the weight enumerator used in this bound is presented. An extended coding scheme is proposed...

  14. Nonbinary quantum codes

    CERN Document Server

    Rains, E M

    1997-01-01

    We present several results on quantum codes over general alphabets (that is, in which the fundamental units may have more than 2 states). In particular, we consider codes derived from finite symplectic geometry assumed to have additional global symmetries. From this standpoint, the analogues of Calderbank-Shor-Steane codes and of GF(4)-linear codes turn out to be special cases of the same construction. This allows us to construct families of quantum codes from certain codes over number fields; in particular, we get analogues of quadratic residue codes, including a single-error correcting code encoding one letter in five, for any alphabet size. We also consider the problem of fault-tolerant computation through such codes, generalizing ideas of Gottesman.

  15. Defining the genetics of thrombotic microangiopathies.

    Science.gov (United States)

    Vieira-Martins, Paula; El Sissy, Carine; Bordereau, Pauline; Gruber, Aurelia; Rosain, Jeremie; Fremeaux-Bacchi, Veronique

    2016-04-01

    The spectrum of the thrombotic microangiopathies (TMA) encompasses a heterogeneous group of disorders with hereditary and acquired forms. Endothelial cell injury in the microvasculature is common to all TMAs, whatever the pathophysiological process. In this review we describe genetic mutations characteristic of certain TMAs and review their contributions to disease. Recent identification of novel pathologic mutations has been enabled by exome studies. The monogenic forms of TMA are more frequently caused by recessive alterations in von Willebrand factor cleaving protease ADAMST13, leading to congenital thrombotic thrombocytopenic purpura, or cobalamine C and DGKE genes, leading to an atypical hemolytic-uremic syndrome (aHUS)-like TMA. aHUS, whether idiopathic or linked to a known complement amplifying condition, is a TMA that primarily affects kidney function. It often results from a combination of an underlying genetic susceptibility with environmental factors activating the alternative complement pathway. Pathogenic variants in at least five complement genes coding for complement factor H (CFH) complement factor I (CFI), MCP (CD46), C3 and complement factor B (CFB) have been demonstrated to increase the risk of developing aHUS, but several more genes have been implicated. A new challenge is to separate disease-associated genetic variants from the broader background of variants or polymorphisms present in all human genomes that are rare, potentially functional, but may or may not be pathogenic.

  16. Network coding for computing: Linear codes

    CERN Document Server

    Appuswamy, Rathinakumar; Karamchandani, Nikhil; Zeger, Kenneth

    2011-01-01

    In network coding it is known that linear codes are sufficient to achieve the coding capacity in multicast networks and that they are not sufficient in general to achieve the coding capacity in non-multicast networks. In network computing, Rai, Dey, and Shenvi have recently shown that linear codes are not sufficient in general for solvability of multi-receiver networks with scalar linear target functions. We study single receiver networks where the receiver node demands a target function of the source messages. We show that linear codes may provide a computing capacity advantage over routing only when the receiver demands a `linearly-reducible' target function. % Many known target functions including the arithmetic sum, minimum, and maximum are not linearly-reducible. Thus, the use of non-linear codes is essential in order to obtain a computing capacity advantage over routing if the receiver demands a target function that is not linearly-reducible. We also show that if a target function is linearly-reducible,...

  17. Construction of Codes for Network Coding

    CERN Document Server

    Elsenhans, Andreas-Stephan; Wassermann, Alfred

    2010-01-01

    Based on ideas of K\\"otter and Kschischang we use constant dimension subspaces as codewords in a network. We show a connection to the theory of q-analogues of a combinatorial designs, which has been studied in Braun, Kerber and Laue as a purely combinatorial object. For the construction of network codes we successfully modified methods (construction with prescribed automorphisms) originally developed for the q-analogues of a combinatorial designs. We then give a special case of that method which allows the construction of network codes with a very large ambient space and we also show how to decode such codes with a very small number of operations.

  18. TIPONLINE Code Table

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Coded items are entered in the tiponline data entry program. The codes and their explanations are necessary in order to use the data

  19. SEVERO code - user's manual

    International Nuclear Information System (INIS)

    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.)

  20. Unfolding the color code

    OpenAIRE

    Kubica, Aleksander; Yoshida, Beni; Pastawski, Fernando

    2015-01-01

    The topological color code and the toric code are two leading candidates for realizing fault-tolerant quantum computation. Here we show that the color code on a $d$-dimensional closed manifold is equivalent to multiple decoupled copies of the $d$-dimensional toric code up to local unitary transformations and adding or removing ancilla qubits. Our result not only generalizes the proven equivalence for $d=2$, but also provides an explicit recipe of how to decouple independent components of the ...

  1. Looking for an Alternative.

    Science.gov (United States)

    Kennedy, Jack

    1999-01-01

    Argues that high school newspapers might do well to create stronger ties with alternative weeklies. Discusses issues of niche marketing, alternative content, and alternative presentation. Notes that high school papers could learn a lot from alternative newspapers. (SR)

  2. The materiality of Code

    DEFF Research Database (Denmark)

    Soon, Winnie

    2014-01-01

    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...

  3. Informal control code logic

    OpenAIRE

    Bergstra, J. A.

    2010-01-01

    General definitions as well as rules of reasoning regarding control code production, distribution, deployment, and usage are described. The role of testing, trust, confidence and risk analysis is considered. A rationale for control code testing is sought and found for the case of safety critical embedded control code.

  4. Refactoring test code

    NARCIS (Netherlands)

    Deursen, A. van; Moonen, L.M.F.; Bergh, A. van den; Kok, G.

    2001-01-01

    Two 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 refactoring product

  5. Informal Control code logic

    CERN Document Server

    Bergstra, Jan A

    2010-01-01

    General definitions as well as rules of reasoning regarding control code production, distribution, deployment, and usage are described. The role of testing, trust, confidence and risk analysis is considered. A rationale for control code testing is sought and found for the case of safety critical embedded control code.

  6. 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 the...

  7. High performance word level sequential and parallel coding methods and architectures for bit plane coding

    Institute of Scientific and Technical Information of China (English)

    XIONG ChengYi; TIAN JinWen; LIU Jian

    2008-01-01

    This paper introduced a novel high performance algorithm and VLSI architectures for achieving bit plane coding (BPC) in word level sequential and parallel mode. The proposed BPC algorithm adopts the techniques of coding pass prediction and par-allel & pipeline to reduce the number of accessing memory and to increase the ability of concurrently processing of the system, where all the coefficient bits of a code block could be coded by only one scan. A new parallel bit plane architecture (PA) was proposed to achieve word-level sequential coding. Moreover, an efficient high-speed architecture (HA) was presented to achieve multi-word parallel coding. Compared to the state of the art, the proposed PA could reduce the hardware cost more efficiently, though the throughput retains one coefficient coded per clock. While the proposed HA could perform coding for 4 coefficients belonging to a stripe column at one intra-clock cycle, so that coding for an N×N code-block could be completed in approximate N2/4 intra-clock cycles. Theoretical analysis and ex-perimental results demonstrate that the proposed designs have high throughput rate with good performance in terms of speedup to cost, which can be good alter-natives for low power applications.

  8. ARC Code TI: CODE Software Framework

    Data.gov (United States)

    National Aeronautics and Space Administration — CODE is a software framework for control and observation in distributed environments. The basic functionality of the framework allows a user to observe a...

  9. ARC Code TI: ROC Curve Code Augmentation

    Data.gov (United States)

    National Aeronautics and Space Administration — ROC (Receiver Operating Characteristic) curve Code Augmentation was written by Rodney Martin and John Stutz at NASA Ames Research Center and is a modification of...

  10. The Procions` code; Le code Procions

    Energy Technology Data Exchange (ETDEWEB)

    Deck, D.; Samba, G.

    1994-12-19

    This paper presents a new code to simulate plasmas generated by inertial confinement. This multi-kinds kinetic code is done with no angular approximation concerning ions and will work in plan and spherical geometry. First, the physical model is presented, using Fokker-Plank. Then, the numerical model is introduced in order to solve the Fokker-Plank operator under the Rosenbluth form. At the end, several numerical tests are proposed. (TEC). 17 refs., 27 figs.

  11. 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.

  12. 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…

  13. Universal Rateless Codes From Coupled LT Codes

    CERN Document Server

    Aref, Vahid

    2011-01-01

    It was recently shown that spatial coupling of individual low-density parity-check codes improves the belief-propagation threshold of the coupled ensemble essentially to the maximum a posteriori threshold of the underlying ensemble. We study the performance of spatially coupled low-density generator-matrix ensembles when used for transmission over binary-input memoryless output-symmetric channels. We show by means of density evolution that the threshold saturation phenomenon also takes place in this setting. Our motivation for studying low-density generator-matrix codes is that they can easily be converted into rateless codes. Although there are already several classes of excellent rateless codes known to date, rateless codes constructed via spatial coupling might offer some additional advantages. In particular, by the very nature of the threshold phenomenon one expects that codes constructed on this principle can be made to be universal, i.e., a single construction can uniformly approach capacity over the cl...

  14. (Sigma-Delta) Codes

    OpenAIRE

    Boulagouaz, M.; Leroy, A

    2013-01-01

    In this paper we introduce the notion of cyclic ($f(t),\\sigma,\\delta$)-codes for $f(t)\\in \\Ore$. These codes generalize the $\\theta$-codes as introduced by D. Boucher, F. Ulmer, W. Geiselmann \\cite{BGU}. We construct generic and control matrices for these codes. As a particular case the ($\\si,\\de$)-$W$-code associated to a Wedderburn polynomial are defined and we show that their control matrices are given by generalized Vandermonde matrices. All the Wedderburn polynomials of $\\mathbb F_q[t;\\t...

  15. Genetic Counseling

    Science.gov (United States)

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  16. Testing algebraic geometric codes

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Property testing was initially studied from various motivations in 1990’s. A code C  GF (r)n is locally testable if there is a randomized algorithm which can distinguish with high possibility the codewords from a vector essentially far from the code by only accessing a very small (typically constant) number of the vector’s coordinates. The problem of testing codes was firstly studied by Blum, Luby and Rubinfeld and closely related to probabilistically checkable proofs (PCPs). How to characterize locally testable codes is a complex and challenge problem. The local tests have been studied for Reed-Solomon (RS), Reed-Muller (RM), cyclic, dual of BCH and the trace subcode of algebraicgeometric codes. In this paper we give testers for algebraic geometric codes with linear parameters (as functions of dimensions). We also give a moderate condition under which the family of algebraic geometric codes cannot be locally testable.

  17. Noisy Network Coding

    CERN Document Server

    Lim, Sung Hoon; Gamal, Abbas El; Chung, Sae-Young

    2010-01-01

    A noisy network coding scheme for sending multiple sources over a general noisy network is presented. For multi-source multicast networks, the scheme naturally extends both network coding over noiseless networks by Ahlswede, Cai, Li, and Yeung, and compress-forward coding for the relay channel by Cover and El Gamal to general discrete memoryless and Gaussian networks. The scheme also recovers as special cases the results on coding for wireless relay networks and deterministic networks by Avestimehr, Diggavi, and Tse, and coding for wireless erasure networks by Dana, Gowaikar, Palanki, Hassibi, and Effros. The scheme involves message repetition coding, relay signal compression, and simultaneous decoding. Unlike previous compress--forward schemes, where independent messages are sent over multiple blocks, the same message is sent multiple times using independent codebooks as in the network coding scheme for cyclic networks. Furthermore, the relays do not use Wyner--Ziv binning as in previous compress-forward sch...

  18. Testing algebraic geometric codes

    Institute of Scientific and Technical Information of China (English)

    CHEN Hao

    2009-01-01

    Property testing was initially studied from various motivations in 1990's.A code C (∩)GF(r)n is locally testable if there is a randomized algorithm which can distinguish with high possibility the codewords from a vector essentially far from the code by only accessing a very small (typically constant) number of the vector's coordinates.The problem of testing codes was firstly studied by Blum,Luby and Rubinfeld and closely related to probabilistically checkable proofs (PCPs).How to characterize locally testable codes is a complex and challenge problem.The local tests have been studied for Reed-Solomon (RS),Reed-Muller (RM),cyclic,dual of BCH and the trace subcode of algebraicgeometric codes.In this paper we give testers for algebraic geometric codes with linear parameters (as functions of dimensions).We also give a moderate condition under which the family of algebraic geometric codes cannot be locally testable.

  19. Chinese remainder codes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Aili; LIU Xiufeng

    2006-01-01

    Chinese remainder codes are constructed by applying weak block designs and the Chinese remainder theorem of ring theory.The new type of linear codes take the congruence class in the congruence class ring R/I1 ∩ I2 ∩…∩ In for the information bit,embed R/Ji into R/I1 ∩ I2 ∩…∩ In,and assign the cosets of R/Ji as the subring of R/I1 ∩ I2 ∩…∩ In and the cosets of R/Ji in R/I1 ∩ I2 ∩…∩ In as check lines.Many code classes exist in the Chinese remainder codes that have high code rates.Chinese remainder codes are the essential generalization of Sun Zi codes.

  20. Chinese Remainder Codes

    Institute of Scientific and Technical Information of China (English)

    张爱丽; 刘秀峰; 靳蕃

    2004-01-01

    Chinese Remainder Codes are constructed by applying weak block designs and Chinese Remainder Theorem of ring theory. The new type of linear codes take the congruence class in the congruence class ring R/I1∩I2∩…∩In for the information bit, embed R/Ji into R/I1∩I2∩…∩In, and asssign the cosets of R/Ji as the subring of R/I1∩I2∩…∩In and the cosets of R/Ji in R/I1∩I2∩…∩In as check lines. There exist many code classes in Chinese Remainder Codes, which have high code rates. Chinese Remainder Codes are the essential generalization of Sun Zi Codes.

  1. 应用UCC/EAN-128编码技术对转基因植物产品进行溯源研究%Tracing of genetically modified crops and their derived products by UCC/EAN-128 bar code

    Institute of Scientific and Technical Information of China (English)

    王醒宇; 杨捷琳; 陈勇; 潘良文; 丁卓平

    2013-01-01

    This paper gathered information from the five sections including the planting origin, products category, harvesting, processing and packaging stages. Based on the national standard and coding rules, the tracing of genetically modified crops by UCC/EAN-128 bar code about five sections was designed and encipher. As the example of soybeans, the five sections were combined to make the integrity the UCC/EAN bar code. The consumer can obtain the information and trace the products through scanning the UCC/EAN-128 bar code, combining with the data received and the data from the computer database.%该文对转基因植物产品从产地、产品、采收、加工、包装等5个环节收集信息,并根据国家标准中规定相应编码规则对这5个环节进行UCC/EAN-128码的设计与编码。最后,以大豆为例,将这5个编码结合,形成一个完整UCC/EAN-128码。消费者通过扫描条形码,获取相关数据,并将获得数据与计算机建立的数据库相结合,进行信息读取,了解转基因植物产品的生产、加工、包装等信息,从而对转基因植物产品进行有效的溯源。

  2. University Hate Speech Codes: Toward an Approach Restricting Verbal Attack.

    Science.gov (United States)

    Hanson, Jim

    This paper reviews events leading to the University of Michigan speech codes, identifies the state of the law following the Doe v. the University of Michigan decision, points out problems in suggested alternatives to the code, and outlines an approach that protects students from hate speech while maintaining first amendment rights. The paper first…

  3. 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....

  4. Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei

    Directory of Open Access Journals (Sweden)

    Schmid Solveig

    2012-03-01

    Full Text Available Abstract Background Alternative sigma factors trigger various adaptive responses. Lactobacillus sakei, a non-sporulating meat-borne bacterium, carries an alternative sigma factor seemingly orthologous to σH of Bacillus subtilis, best known for its contribution to the initiation of a large starvation response ultimately leading to sporulation. As the role of σH-like factors has been little studied in non-sporulating bacteria, we investigated the function of σH in L. sakei. Results Transcription of sigH coding for σH was hardly affected by entry into stationary phase in our laboratory conditions. Twenty-five genes potentially regulated by σH in L. sakei 23 K were revealed by genome-wide transcriptomic profiling of sigH overexpression and/or quantitative PCR analysis. More than half of them are involved in the synthesis of a DNA uptake machinery linked to genetic competence, and in DNA metabolism; however, σH overproduction did not allow detectable genetic transformation. σH was found to be conserved in the L. sakei species. Conclusion Our results are indicative of the existence of a genetic competence state activated by σH in L. sakei, and sustain the hypothesis that σH-like factors in non sporulating Firmicutes share this common function with the well-known ComX of naturally transformable streptococci.

  5. 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....... Instead we propose that the promise of coding-based research lies in its ability to open up new qualitative questions.......We welcome Tanya Stivers’s discussion (Stivers, 2015/this issue) of coding social interaction and find that her descriptions of the processes of coding open up important avenues for discussion, among other things of the precise ad hoc considerations that researchers need to bear in mind, both when...

  6. On Polynomial Remainder Codes

    CERN Document Server

    Yu, Jiun-Hung

    2012-01-01

    Polynomial remainder codes are a large class of codes derived from the Chinese remainder theorem that includes Reed-Solomon codes as a special case. In this paper, we revisit these codes and study them more carefully than in previous work. We explicitly allow the code symbols to be polynomials of different degrees, which leads to two different notions of weight and distance. Algebraic decoding is studied in detail. If the moduli are not irreducible, the notion of an error locator polynomial is replaced by an error factor polynomial. We then obtain a collection of gcd-based decoding algorithms, some of which are not quite standard even when specialized to Reed-Solomon codes.

  7. The Aesthetics of Coding

    DEFF Research Database (Denmark)

    Andersen, Christian Ulrik

    2007-01-01

    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......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...

  8. Generating code adapted for interlinking legacy scalar code and extended vector code

    Science.gov (United States)

    Gschwind, Michael K

    2013-06-04

    Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

  9. The Research Progress on The Contributions of Crick in Genetic Code Field%克里克对遗传密码领域之贡献的研究进展

    Institute of Scientific and Technical Information of China (English)

    孙咏萍; 郭世荣

    2011-01-01

    The historical merit of Crick on life code research is investigated. With the respect to the achievements of Crick in the field,books,biographies and papers of the domestic and the foreign are studied n the paper. The scientific activities of Crick on life code research, especially the origin and essence of scientific thinking after his getting the structure of DNA,are indeed worth studying further as an important listorical theme.%考察了克里克在生命密码领域的历史功绩,整理了国内外生物学史论著、名人传记以及研究性论文中关于克里克在生命密码研究领域所取得的成就,指出克里克在生命密码研究中的全部科学活动.特别是其密码研究思想形成的过程和本质是克里克发现DNA结构后的又一个值得深入研究的历史课题.

  10. 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.

  11. Security of QR Codes

    OpenAIRE

    Kapsalis, Ioannis

    2013-01-01

    The 2-dimensional barcodes known as QR (Quick Response) Codesare increasing their popularity as they appear in more places in theurban environment. QR Codes can be considered as physical hyper-linksthat give the ability to users to access, through their mobile devicesthat are able to scan QR Codes, additional information located in aweb-page. Apart from marketing, QR Codes have been also adopted indifferent areas such as the on-line payments. This development alongwith the trend that some of ...

  12. Practices in Code Discoverability

    OpenAIRE

    Teuben, Peter; Allen, Alice; Nemiroff, Robert J.; Shamir, Lior

    2012-01-01

    Much of scientific progress now hinges on the reliability, falsifiability and reproducibility of computer source codes. Astrophysics in particular is a discipline that today leads other sciences in making useful scientific components freely available online, including data, abstracts, preprints, and fully published papers, yet even today many astrophysics source codes remain hidden from public view. We review the importance and history of source codes in astrophysics and previous efforts to d...

  13. 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)

  14. Progressive fractal coding

    OpenAIRE

    Kopilovic, Ivan; Saupe, Dietmar; Hamzaoui, Raouf

    2001-01-01

    Progressive coding is an important feature of compression schemes. Wavelet coders are well suited for this purpose because the wavelet coefficients can be naturally ordered according to decreasing importance. Progressive fractal coding is feasible, but it was proposed only for hybrid fractal-wavelet schemes. We introduce a progressive fractal image coder in the spatial domain. A Lagrange optimization based on rate-distortion performance estimates determines an optimal ordering of the code bit...

  15. A New Evolutionary Algorithm Based on the Decimal Coding

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Traditional Evolutionary Algorithm (EAs) is based on the binary code, real number code, structure code and so on. But these coding strategies have their own advantages and disadvantages for the optimization of functions. In this paper a new Decimal Coding Strategy (DCS) ,which is convenient for space division and alterable precision, was proposed, and the theory analysis of its implicit parallelism and convergence was also discussed. We also redesign several genetic operators for the decimal code. In order to utilize the historical information of the existing individuals in the process of evolution and avoid repeated exploring,the strategies of space shrinking and precision alterable, are adopted. Finally, the evolutionary algorithm based on decimal coding (DCEAs) was applied to the optimization of functions, the optimization of parameter, mixed-integer nonlinear programming. Comparison with traditional GAs was made and the experimental results show that the performances of DCEAS are better than the tradition GAs.

  16. Genetic diversity in Entamoeba histolytica

    Indian Academy of Sciences (India)

    C Graham Clark; Mehreen Zaki; Ibne Karim Md Ali

    2002-11-01

    Genetic diversity within Entamoeba histolytica led to the re-description of the species 10 years ago. However, more recent investigation has revealed significant diversity within the re-defined species. Both protein-coding and non-coding sequences show variability, but the common feature in all cases is the presence of short tandem repeats of varying length and sequence. The ability to identify strains of E. histolytica may lead to insights into the population structure and epidemiology of the organism.

  17. Tokamak Systems Code

    International Nuclear Information System (INIS)

    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

  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. ARC Code TI: ACCEPT

    Data.gov (United States)

    National Aeronautics and Space Administration — ACCEPT consists of an overall software infrastructure framework and two main software components. The software infrastructure framework consists of code written to...

  20. 75 FR 56015 - Vessel Inspection Alternatives

    Science.gov (United States)

    2010-09-15

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND SECURITY Coast Guard 46 CFR Part 8 Vessel Inspection Alternatives CFR Correction In Title 46 of the Code of... delegated function related to general vessel safety assessment, as defined in Sec. 8.100 of this part, for...

  1. Research on universal combinatorial coding.

    Science.gov (United States)

    Lu, Jun; Zhang, Zhuo; Mo, Juan

    2014-01-01

    The conception of universal combinatorial coding is proposed. Relations exist more or less in many coding methods. It means that a kind of universal coding method is objectively existent. It can be a bridge connecting many coding methods. Universal combinatorial coding is lossless and it is based on the combinatorics theory. The combinational and exhaustive property make it closely related with the existing code methods. Universal combinatorial coding does not depend on the probability statistic characteristic of information source, and it has the characteristics across three coding branches. It has analyzed the relationship between the universal combinatorial coding and the variety of coding method and has researched many applications technologies of this coding method. In addition, the efficiency of universal combinatorial coding is analyzed theoretically. The multicharacteristic and multiapplication of universal combinatorial coding are unique in the existing coding methods. Universal combinatorial coding has theoretical research and practical application value.

  2. Schizophyllum commune has an extensive and functional alternative splicing repertoire

    Science.gov (United States)

    Gehrmann, Thies; Pelkmans, Jordi F.; Lugones, Luis G.; Wösten, Han A. B.; Abeel, Thomas; Reinders, Marcel J. T.

    2016-01-01

    Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically. PMID:27659065

  3. Code Generation = A* + BURS

    NARCIS (Netherlands)

    Nymeyer, A.; Katoen, J.P.; Westra, Y.; Alblas, H.; Gyimóthy, T.

    1996-01-01

    A system called BURS that is based on term rewrite systems and a search algorithm A* are combined to produce a code generator that generates optimal code. The theory underlying BURS is re-developed, formalised and explained in this work. The search algorithm uses a cost heuristic that is derived fro

  4. Nuremberg code turns 60

    OpenAIRE

    Thieren, Michel; Mauron, Alex

    2007-01-01

    This month marks sixty years since the Nuremberg code – the basic text of modern medical ethics – was issued. The principles in this code were articulated in the context of the Nuremberg trials in 1947. We would like to use this anniversary to examine its ability to address the ethical challenges of our time.

  5. 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…

  6. Codes of Conduct

    Science.gov (United States)

    Million, June

    2004-01-01

    Most schools have a code of conduct, pledge, or behavioral standards, set by the district or school board with the school community. In this article, the author features some schools that created a new vision of instilling code of conducts to students based on work quality, respect, safety and courtesy. She suggests that communicating the code…

  7. Code A1 Revised

    CERN Multimedia

    SC Secretariat

    2004-01-01

    Please note that the revised safety code A1 entitled 'MEDICAL CODE' is available on the web at the following url: https://edms.cern.ch/document/335476/last_released Paper copies can also be obtained from the SC Secretariat, e-mail : sc.secretariat@cern.ch SC Secretariat

  8. Safety Code A12

    CERN Multimedia

    SC Secretariat

    2005-01-01

    Please note that the Safety Code A12 (Code A12) entitled "THE SAFETY COMMISSION (SC)" is available on the web at the following url: https://edms.cern.ch/document/479423/LAST_RELEASED Paper copies can also be obtained from the SC Unit Secretariat, e-mail: sc.secretariat@cern.ch SC Secretariat

  9. Computerized mega code recording.

    Science.gov (United States)

    Burt, T W; Bock, H C

    1988-04-01

    A system has been developed to facilitate recording of advanced cardiac life support mega code testing scenarios. By scanning a paper "keyboard" using a bar code wand attached to a portable microcomputer, the person assigned to record the scenario can easily generate an accurate, complete, timed, and typewritten record of the given situations and the obtained responses. PMID:3354937

  10. READING A NEURAL CODE

    NARCIS (Netherlands)

    BIALEK, W; RIEKE, F; VANSTEVENINCK, RRD; WARLAND, D

    1991-01-01

    Traditional approaches to neural coding characterize the encoding of known stimuli in average neural responses. Organisms face nearly the opposite task - extracting information about an unknown time-dependent stimulus from short segments of a spike train. Here the neural code was characterized from

  11. AZIMUT code abstract

    International Nuclear Information System (INIS)

    The brief description of the AZIMUT code for calculation the neutron flux in a cluster cell is presented. Code takes into account 1 and 2 azimuthal harmonics in the one-group P3-approximation and uses the heterogeneous approach. 2 refs

  12. Astrophysics Source Code Library

    CERN Document Server

    Allen, Alice; Berriman, Bruce; Hanisch, Robert J; Mink, Jessica; Teuben, Peter J

    2012-01-01

    The Astrophysics Source Code Library (ASCL), founded in 1999, is a free on-line registry for source codes of interest to astronomers and astrophysicists. The library is housed on the discussion forum for Astronomy Picture of the Day (APOD) and can be accessed at http://ascl.net. The ASCL has a comprehensive listing that covers a significant number of the astrophysics source codes used to generate results published in or submitted to refereed journals and continues to grow. The ASCL currently has entries for over 500 codes; its records are citable and are indexed by ADS. The editors of the ASCL and members of its Advisory Committee were on hand at a demonstration table in the ADASS poster room to present the ASCL, accept code submissions, show how the ASCL is starting to be used by the astrophysics community, and take questions on and suggestions for improving the resource.

  13. Fracture flow code

    International Nuclear Information System (INIS)

    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)

  14. Combustion chamber analysis code

    Science.gov (United States)

    Przekwas, A. J.; Lai, Y. G.; Krishnan, A.; Avva, R. K.; Giridharan, M. G.

    1993-05-01

    A three-dimensional, time dependent, Favre averaged, finite volume Navier-Stokes code has been developed to model compressible and incompressible flows (with and without chemical reactions) in liquid rocket engines. The code has a non-staggered formulation with generalized body-fitted-coordinates (BFC) capability. Higher order differencing methodologies such as MUSCL and Osher-Chakravarthy schemes are available. Turbulent flows can be modeled using any of the five turbulent models present in the code. A two-phase, two-liquid, Lagrangian spray model has been incorporated into the code. Chemical equilibrium and finite rate reaction models are available to model chemically reacting flows. The discrete ordinate method is used to model effects of thermal radiation. The code has been validated extensively against benchmark experimental data and has been applied to model flows in several propulsion system components of the SSME and the STME.

  15. Transformation invariant sparse coding

    DEFF Research Database (Denmark)

    Mørup, Morten; Schmidt, Mikkel Nørgaard

    2011-01-01

    Sparse coding is a well established principle for unsupervised learning. Traditionally, features are extracted in sparse coding in specific locations, however, often we would prefer invariant representation. This paper introduces a general transformation invariant sparse coding (TISC) model....... The model decomposes images into features invariant to location and general transformation by a set of specified operators as well as a sparse coding matrix indicating where and to what degree in the original image these features are present. The TISC model is in general overcomplete and we therefore invoke...... sparse coding to estimate its parameters. We demonstrate how the model can correctly identify components of non-trivial artificial as well as real image data. Thus, the model is capable of reducing feature redundancies in terms of pre-specified transformations improving the component identification....

  16. 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

    OpenAIRE

    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.; A. P. Blaschke; Girones, R; M. Zessner

    2015-01-01

    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...

  17. The structural diversity of artificial genetic polymers

    OpenAIRE

    Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

    2015-01-01

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeg...

  18. The Appliance of Code Switching in the SM Language

    Institute of Scientific and Technical Information of China (English)

    LI Chang

    2014-01-01

    Code-switching, a natural phenomenon that consists of alternating two or more languages in bilinguals ’discourse, has traditionally been examined in its oral production. For over three decades, much attention has been emphasized on its form, meaning, and grammatical patterns. However, very little research focuses on code-switching in short message form. Code switch-ing is a quite common phenomenon. As cell phones become the communication tools used by people more frequently, short mes-sage language (SM) attracts more attention by people. Through analyzing the code switching in the SM language, it will help us understand more about its use and explore more information for our study.

  19. Transmission code optimization method for incoherent scatter radar

    Directory of Open Access Journals (Sweden)

    J. Vierinen

    2008-09-01

    Full Text Available When statistical inversion of a lag profile is used to determine an incoherent scatter target, the posterior variance of the estimated target can be used to determine how well a set of transmission codes perform. In this work we present an incoherent scatter radar transmission code optimization search method suitable for different modulation types, including binary phase, polyphase and amplitude modulation. We found that the combination of amplitude and phase modulation provides better performance than traditional binary phase coding, in some cases giving better accuracy than alternating codes.

  20. Transmission code optimization method for incoherent scatter radar

    CERN Document Server

    Vierinen, Juha; Orispaa, Mikko; Virtanen, Ilkka I

    2008-01-01

    When statistical inversion of a lag profile is used to determine an incoherent scatter target, the posterior variance of the estimated target can be used to determine how well a certain set of transmission codes perform. In this work we present an incoherent scatter radar transmission code optimization search method suitable for different modulation types, including binary phase, polyphase and amplitude modulation. We find that the combination of amplitude and phase modulation provides better performance than traditional binary phase coding, in some cases giving better accuracy than alternating codes.

  1. Network Coding: Is zero error always possible?

    CERN Document Server

    Langberg, Michael

    2011-01-01

    In this work we study the zero vs. epsilon-error capacity in network coding instances. For "multicast" network coding it is well known that there is no advantage in capacity when one allows communication at epsilon-error when compared to zero error. For general network coding instances in which the source nodes are co-located, it has been recently shown by Chan and Grant [ISIT 2010] that, again, there is no advantage in epsilon-error over zero error communication. In this work, we revisit the setting of co-located sources, and present an alternative and constructive proof complementing that of Chan and Grant. We stress, that the core ideas in the proof of Chan and Grant seem similar to ours. Nevertheless, we believe that the presentation at hand could be useful for potential readers that find the problem of interest. We extend our results to the setting of "index coding", a special and representative form of network coding that encapsulates the "source coding with side information" problem.

  2. Prospective and therapeutic screening value of non-coding RNA as biomarkers in cardiovascular disease.

    Science.gov (United States)

    Busch, Albert; Eken, Suzanne M; Maegdefessel, Lars

    2016-06-01

    Non-coding RNA (ncRNA) is a class of genetic, epigenetic and translational regulators, containing short and long transcripts with intriguing abilities for use as biomarkers due to their superordinate role in disease development. In the past five years many of these have been investigated in cardiovascular diseases (CVD), mainly myocardial infarction (MI) and heart failure. To extend this view, we summarize the existing data about ncRNA as biomarker in the whole entity of CVDs by literature-based review and comparison of the identified candidates. The myomirs miRNA-1, -133a/b, -208a, -499 with well-defined cellular functions have proven equal to classic protein biomarkers for disease detection in MI. Other microRNAs (miRNAs) were reproducibly found to correlate with disease, disease severity and outcome in heart failure, stroke, coronary artery disease (CAD) and aortic aneurysm. An additional utilization has been discovered for therapeutic monitoring. The function of long non-coding transcripts is only about to be unraveled, yet shows great potential for outcome prediction. ncRNA biomarkers have a distinct role if no alternative test is available or has is performing poorly. With increasing mechanistic understanding, circulating miRNA and long non-coding transcripts will provide useful disease information with high predictive power. PMID:27429962

  3. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Thomas Julie

    2010-02-01

    Full Text Available Abstract Background Genome-wide computational analysis of alternative splicing (AS in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in Chlamydomonas reinhardtii using its recently completed genome sequence and all available ESTs and cDNAs. Results Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at http://combi.cs.colostate.edu/as/chlamy. Conclusions The extent of AS in Chlamydomonas that we observed is much

  4. Application of RS Codes in Decoding QR Code

    Institute of Scientific and Technical Information of China (English)

    Zhu Suxia(朱素霞); Ji Zhenzhou; Cao Zhiyan

    2003-01-01

    The QR Code is a 2-dimensional matrix code with high error correction capability. It employs RS codes to generate error correction codewords in encoding and recover errors and damages in decoding. This paper presents several QR Code's virtues, analyzes RS decoding algorithm and gives a software flow chart of decoding the QR Code with RS decoding algorithm.

  5. Report number codes

    International Nuclear Information System (INIS)

    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

  6. 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 net...... 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.......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...

  7. 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.

  8. 长链非编码RNA多态性与肿瘤遗传易感性%Association between long non-coding RNA polymorphisms and genetic susceptibility of cancers

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    长链非编码RNAs(Long non-coding RNAs,LncRNAs)是一类长度超过200个核苷酸且不能翻译成蛋白质的RNA分子.作为一类新的调控分子,LncRNAs可通过转录、转录后和表观遗传学等多水平调控基因表达,参与人类疾病的发生发展进程.LncRNAs基因存在广泛的单核甘酸多态位点(Single Nucleotide Polymorphism,SNPs),这些位点的变异可能影响LncRNAs的调控功能,从而导致个体对某些疾病包括肿瘤的遗传易感性改变.本文就国内外最新研究进展,对LncRNAs SNPs与人类恶性肿瘤发生发展的关系作一综述.

  9. 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.

  10. FORIST unfolding code

    International Nuclear Information System (INIS)

    The FERDOR method is widely used to unfold neutron energy spectra from pulse-height distributions measured with NE-213 spectrometers. Two unfolding codes COOLC (developed at ORNL) and FORIST (modified version of COOLC developed at UIUC) implement the FERDOR method and are distributed by RSIC. Each code package contains an NE-213 response matrix, sample input data, and sample output. The smoothing (window) widths which are distributed with COOLC are not the most appropriate for all neutron spectrum measurements. The FORIST code determines an optimum set of window widths according to the desired statistical error in the smoothed spectrum

  11. Classical Holographic Codes

    CERN Document Server

    Brehm, Enrico M

    2016-01-01

    In this work, we introduce classical holographic codes. These can be understood as concatenated probabilistic codes and can be represented as networks uniformly covering hyperbolic space. In particular, classical holographic codes can be interpreted as maps from bulk degrees of freedom to boundary degrees of freedom. Interestingly, they are shown to exhibit features similar to those expected from the AdS/CFT correspondence. Among these are a version of the Ryu-Takayanagi formula and intriguing properties regarding bulk reconstruction and boundary representations of bulk operations. We discuss the relation of our findings with expectations from AdS/CFT and, in particular, with recent results from quantum error correction.

  12. Distributed multiple description coding

    CERN Document Server

    Bai, Huihui; Zhao, Yao

    2011-01-01

    This book examines distributed video coding (DVC) and multiple description coding (MDC), two novel techniques designed to address the problems of conventional image and video compression coding. Covering all fundamental concepts and core technologies, the chapters can also be read as independent and self-sufficient, describing each methodology in sufficient detail to enable readers to repeat the corresponding experiments easily. Topics and features: provides a broad overview of DVC and MDC, from the basic principles to the latest research; covers sub-sampling based MDC, quantization based MDC,

  13. Laser propagation code study

    OpenAIRE

    Rockower, Edward B.

    1985-01-01

    A number of laser propagation codes have been assessed as to their suitability for modeling Army High Energy Laser (HEL) weapons used in an anti- sensor mode. We identify a number of areas in which systems analysis HEL codes are deficient. Most notably, available HEL scaling law codes model the laser aperture as circular, possibly with a fixed (e.g. 10%) obscuration. However, most HELs have rectangular apertures with up to 30% obscuration. We present a beam-quality/aperture shape scaling rela...

  14. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  15. Optimal Selection of Nonuniform Code of Radar Based on Euclidean Distance-adaptive Genetic Algorithm%基于欧式距离约束自适应遗传算法的参差码搜索

    Institute of Scientific and Technical Information of China (English)

    张明博; 罗丰

    2009-01-01

    提出了一种基于欧式距离约束的自适应遗传算法(Euclidean distance-Adaptive Genetic Algorithm,EAGA),该算法将欧式距离引入自适应交叉概率,使交叉概率随适应度和个体之间的相似度自适应变化,更好地增强种群的多样性,保存优良个体;为了防止EAGA在优化过程中出现退化现象,通过融合按照一定规则产生的新个体对算法进行了改进.采用EAGA选择最优参差比,使滤波器的零点尽可能的浅,在有效抑制杂波的同时避免目标丢失.同标准遗传算法相比,EAGA表现出了较好的搜索性能.

  16. 78 FR 37721 - Approval of American Society of Mechanical Engineers' Code Cases

    Science.gov (United States)

    2013-06-24

    ...-1232, ``Operation and Maintenance code Case, Acceptability, ASME OM Code.'' The subject DGs list the... acceptable voluntary alternative to the mandatory American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel (BPV) Code and Operation and Maintenance (OM) of nuclear power plant provisions approved...

  17. 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.

  18. Genetic Counseling

    Science.gov (United States)

    ... go for genetic counseling, such as: A family history of a genetic condition To learn about genetic screening for diseases that are more common in certain ethnic groups (e.g., sickle cell disease in African Americans and Tay-Sachs disease in Ashkenazi Jews) To discuss abnormal results ...

  19. Genetic principles.

    Science.gov (United States)

    Abuelo, D

    1987-01-01

    The author discusses the basic principles of genetics, including the classification of genetic disorders and a consideration of the rules and mechanisms of inheritance. The most common pitfalls in clinical genetic diagnosis are described, with emphasis on the problem of the negative or misleading family history.

  20. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  1. 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...

  2. Der Code der Transparenz

    OpenAIRE

    Alloa, Emmanuel

    2015-01-01

    In allen Bereichen der Gesellschaft werden gegenwärtig Forderungen nach mehr Transparenz laut. Was steht hinter diesem Wort? Für Emmanuel Alloa wohnt der Transparenzforderung die Paradoxie inne, ein "codefreier Code" sein zu wollen.

  3. 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)

  4. 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....

  5. Code-Pointer Integrity

    OpenAIRE

    Volodymyr Kuznetsov; Laszlo Szekeres; Mathias Payer; George Candea; Sekar, R.; Dawn Song

    2014-01-01

    Systems code is often written in low-level languages like C/C++, which offer many benefits but also delegate memory management to programmers. This invites memory safety bugs that attackers can exploit to divert control flow and compromise the system. Deployed defense mechanisms (e.g., ASLR, DEP) are incomplete, and stronger defense mechanisms (e.g., CFI) often have high overhead and limited guarantees [19, 15, 9]. We introduce code-pointer integrity (CPI), a new design point that guarantees...

  6. Secure Fractal Image Coding

    OpenAIRE

    Lian, Shiguo

    2007-01-01

    In recent work, various fractal image coding methods are reported, which adopt the self-similarity of images to compress the size of images. However, till now, no solutions for the security of fractal encoded images have been provided. In this paper, a secure fractal image coding scheme is proposed and evaluated, which encrypts some of the fractal parameters during fractal encoding, and thus, produces the encrypted and encoded image. The encrypted image can only be recovered by the correct ke...

  7. 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...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  8. Coding of auditory space

    OpenAIRE

    Konishi­, Masakazu

    2003-01-01

    Behavioral, anatomical, and physiological approaches can be integrated in the study of sound localization in barn owls. Space representation in owls provides a useful example for discussion of place and ensemble coding. Selectivity for space is broad and ambiguous in low-order neurons. Parallel pathways for binaural cues and for different frequency bands converge on high-order space-specific neurons, which encode space more precisely. An ensemble of broadly tuned place-coding neurons may conv...

  9. KENO-V code

    International Nuclear Information System (INIS)

    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 P1 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

  10. Genetics Home Reference: Genetic Conditions

    Science.gov (United States)

    Skip to main content Your Guide to Understanding Genetic Conditions Enable Javascript for addthis links to activate. ... Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Home Health Conditions Health Conditions Explore the signs ...

  11. 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.

  12. Eggplant (Solanum melongena L.: tissue culture, genetic transformation and use as an alternative model plant Berinjela (Solanum melongena L.: cultura de tecidos, transformação genética e uso como planta modelo

    Directory of Open Access Journals (Sweden)

    Claudia Magioli

    2005-03-01

    Full Text Available Eggplant is an agronomically important non-tuberous solanaceous crop grown primarily for its large oval fruit. In popular medicine, eggplant is indicated for the treatment of several diseases, including diabetes, arthritis, asthma and bronchitis. Eggplant is susceptible to a number of diseases and pests capable of causing serious crop losses. This problem has been addressed by hybridizing eggplant with wild resistant Solanum species, which present a wide genetic diversity and are source of useful agronomic traits. The application of in vitro methodologies to eggplant has resulted in considerable success. Eggplant tissues present a high morphogenetic potential that is useful for developmental studies as well as for establishing biotechnological approaches to produce improved varieties, such as embryo rescue, in vitro selection, somatic hybridization and genetic transformation. Taken together, these characteristics also make eggplant a complete model for studies on different areas of plant science, including control of gene expression and assessment of genetic stability of somaclones derived from different morphogenetic processes. In the present study, important factors that affect the efficiency of in vitro regeneration through organogenesis and embryogenesis as well as genetic transformation are analyzed. The potential of this species as a model plant for studying various aspects of plant genetics and physiology is also discussed.A berinjela é uma espécie solanácea não tuberosa de importância agronômica, cultivada principalmente por seus frutos. Na medicina popular, a berinjela é indicada para o tratamento de várias doenças, incluindo diabetes, artrite, asma e bronquite. A berinjela é suscetível a várias doenças e pragas que causam perdas econômicas significativas. Esse problema tem sido abordado com técnicas convencionais de melhoramento, utilizando espécies silvestres resistentes de Solanum, que possuem uma grande diversidade

  13. Polyphase-coded incoherent scatter measurements at Millstone Hill

    Science.gov (United States)

    Virtanen, Ilkka I.; Lind, Frank D.; Roininen, Lassi; Erickson, Philip J.; Rideout, William C.; Orispää, Mikko; Vierinen, Juha; Lehtinen, Markku S.

    2013-09-01

    We report first results of polyphase-coded incoherent scatter measurements at Millstone Hill. To our knowledge, these are the first incoherent scatter measurements with polyphase alternating codes of Markkanen et al. (2008) and optimal quadriphase sequences of Damtie et al. (2008). The results demonstrate that an arbitrary waveform generator recently installed at the Millstone Hill incoherent scatter radar, part of the National Science Foundation Geospace Facility operated by the Massachusetts Institute of Technology Haystack Observatory, is capable of reproducing the polyphase waveforms with an accuracy sufficient for incoherent scatter measurements. Polyphase codes will allow incoherent scatter radar experiments to be better optimized, because they provide a larger variety of code and code cycle lengths than the traditional binary codes.

  14. The natural variation of a neural code.

    Science.gov (United States)

    Kfir, Yoav; Renan, Ittai; Schneidman, Elad; Segev, Ronen

    2012-01-01

    The way information is represented by sequences of action potentials of spiking neurons is determined by the input each neuron receives, but also by its biophysics, and the specifics of the circuit in which it is embedded. Even the "code" of identified neurons can vary considerably from individual to individual. Here we compared the neural codes of the identified H1 neuron in the visual systems of two families of flies, blow flies and flesh flies, and explored the effect of the sensory environment that the flies were exposed to during development on the H1 code. We found that the two families differed considerably in the temporal structure of the code, its content and energetic efficiency, as well as the temporal delay of neural response. The differences in the environmental conditions during the flies' development had no significant effect. Our results may thus reflect an instance of a family-specific design of the neural code. They may also suggest that individual variability in information processing by this specific neuron, in terms of both form and content, is regulated genetically.

  15. Accumulative Landings System Code Tables

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Code Tables Used In Landings System. These tables assign meanings to the codes that appear in the data tables. Code tables exist for species, gear, state, county,...

  16. Algebraic geometric codes with applications

    Institute of Scientific and Technical Information of China (English)

    CHEN Hao

    2007-01-01

    The theory of linear error-correcting codes from algebraic geomet-ric curves (algebraic geometric (AG) codes or geometric Goppa codes) has been well-developed since the work of Goppa and Tsfasman, Vladut, and Zink in 1981-1982. In this paper we introduce to readers some recent progress in algebraic geometric codes and their applications in quantum error-correcting codes, secure multi-party computation and the construction of good binary codes.

  17. Key Frames Extraction Based on the Improved Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHOU Dong-sheng; JIANG Wei; YI Peng-fei; LIURui

    2014-01-01

    In order toovercomethe poor local search ability of genetic algorithm, resulting in the basic genetic algorithm is time-consuming, and low search abilityin the late evolutionary, we use thegray coding instead ofbinary codingatthebeginning of the coding;we use multi-point crossoverto replace the originalsingle-point crossoveroperation.Finally, theexperimentshows that the improved genetic algorithmnot only has a strong search capability, but also thestability has been effectively improved.

  18. Association Rule Mining Strategy Based on Three-Sectional Coding Immune Genetic Algorithm%三段式编码的改进的IGA关联规则挖掘算法

    Institute of Scientific and Technical Information of China (English)

    王晓光; 张永健

    2014-01-01

    There are some shortcomings of low mining accuracy and falling into local convergence easily in the lat-est intelligence algorithm on the mining association rules mining. To solve these problems, a TIGA strategy was pro-pose. Firstly, a three-step encoding was used to encode continuous association rule mining in order to educe the seg-mentation point of mining influence. Secondly, an immune algorithm was used to mine the association rules. A multi-dimensional mining plan was proposed based on vector distance of genetic algorithm, which can increase the diversity of population and the accuracy of mining rules. Finally, the adaptive crossover and mutation factors were uses to re-duce the interference of artificial setting parameters on the mining results. The experimental results show that, com-pared with the latest mining algorithm, the proposed algorithm has the advantages of high precision and global conver-gence based on mining association rules.%最新智能算法在关联规则挖掘上存在挖掘精度低,易陷入局部收敛,运行时间较长等弊端,针对以上问题,提出了求解连续属性关联规则挖掘的三段式的改进的免疫遗传挖掘算法( TIIGA),首先使用三段式编码方案降低分割点的选取对挖掘的影响,其次提出了基于矢量矩浓度的TIIGA的选择方案,可以提高挖掘规则的多样性和挖掘的精度,最后使用了自适应的交叉与变异因子降低人工设置参数对挖掘结果的干扰。实验结果表明,与最新智能算法相比,提出的TIIGA算法在关联规则连续属性挖掘上具有挖掘精度高、全局收敛,挖掘时间短等优势。

  19. Optical coding theory with Prime

    CERN Document Server

    Kwong, Wing C

    2013-01-01

    Although several books cover the coding theory of wireless communications and the hardware technologies and coding techniques of optical CDMA, no book has been specifically dedicated to optical coding theory-until now. Written by renowned authorities in the field, Optical Coding Theory with Prime gathers together in one volume the fundamentals and developments of optical coding theory, with a focus on families of prime codes, supplemented with several families of non-prime codes. The book also explores potential applications to coding-based optical systems and networks. Learn How to Construct

  20. Polynomial weights and code constructions

    DEFF Research Database (Denmark)

    Massey, J; Costello, D; Justesen, Jørn

    1973-01-01

    that are subcodes of the binary Reed-Muller codes and can be very simply instrumented, 3) a new class of constacyclic codes that are subcodes of thep-ary "Reed-Muller codes," 4) two new classes of binary convolutional codes with large "free distance" derived from known binary cyclic codes, 5) two new classes...... of long constraint length binary convolutional codes derived from2^r-ary Reed-Solomon codes, and 6) a new class ofq-ary "repeated-root" constacyclic codes with an algebraic decoding algorithm....

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

    International Nuclear Information System (INIS)

    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

  2. Complementary and Alternative Medicine

    Science.gov (United States)

    ... Help a Friend Who Cuts? Complementary and Alternative Medicine KidsHealth > For Teens > Complementary and Alternative Medicine Print ... replacement. continue How Is CAM Different From Conventional Medicine? Conventional medicine is based on scientific knowledge of ...

  3. Alternative medicine - pain relief

    Science.gov (United States)

    Alternative medicine refers to treatments that are used instead of conventional (standard) ones. If you use an alternative ... considered complementary therapy. There are many forms of ... Acupuncture involves stimulating certain acupoints on the body ...

  4. Error coding simulations

    Science.gov (United States)

    Noble, Viveca K.

    1993-01-01

    There are various elements such as radio frequency interference (RFI) which may induce errors in data being transmitted via a satellite communication link. When a transmission is affected by interference or other error-causing elements, the transmitted data becomes indecipherable. It becomes necessary to implement techniques to recover from these disturbances. The objective of this research is to develop software which simulates error control circuits and evaluate the performance of these modules in various bit error rate environments. The results of the evaluation provide the engineer with information which helps determine the optimal error control scheme. The Consultative Committee for Space Data Systems (CCSDS) recommends the use of Reed-Solomon (RS) and convolutional encoders and Viterbi and RS decoders for error correction. The use of forward error correction techniques greatly reduces the received signal to noise needed for a certain desired bit error rate. The use of concatenated coding, e.g. inner convolutional code and outer RS code, provides even greater coding gain. The 16-bit cyclic redundancy check (CRC) code is recommended by CCSDS for error detection.

  5. Physical Layer Network Coding

    CERN Document Server

    Shengli, Zhang; Lam, Patrick P K

    2007-01-01

    A main distinguishing feature of a wireless network compared with a wired network is its broadcast nature, in which the signal transmitted by a node may reach several other nodes, and a node may receive signals from several other nodes simultaneously. Rather than a blessing, this feature is treated more as an interference-inducing nuisance in most wireless networks today (e.g., IEEE 802.11). This paper shows that the concept of network coding can be applied at the physical layer to turn the broadcast property into a capacity-boosting advantage in wireless ad hoc networks. Specifically, we propose a physical-layer network coding (PNC) scheme to coordinate transmissions among nodes. In contrast to straightforward network coding which performs coding arithmetic on digital bit streams after they have been received, PNC makes use of the additive nature of simultaneously arriving electromagnetic (EM) waves for equivalent coding operation. And in doing so, PNC can potentially achieve 100% and 50% throughput increase...

  6. To Code or Not To Code in Multi-Hop Relay Channels

    OpenAIRE

    Vaze, Rahul; Robert W. Heath Jr.

    2008-01-01

    Multi-hop relay channels use multiple relay stages, each with multiple relay nodes, to facilitate communication between a source and destination. Previously, distributed space-time coding was used to maximize diversity gain. Assuming a low-rate feedback link from the destination to each relay stage and the source, this paper proposes end-to-end antenna selection strategies as an alternative to distributed space-time coding. One-way (where only the source has data for destination) and two-way ...

  7. Nested Quantum Error Correction Codes

    CERN Document Server

    Wang, Zhuo; Fan, Hen; Vedral, Vlatko

    2009-01-01

    The theory of quantum error correction was established more than a decade ago as the primary tool for fighting decoherence in quantum information processing. Although great progress has already been made in this field, limited methods are available in constructing new quantum error correction codes from old codes. Here we exhibit a simple and general method to construct new quantum error correction codes by nesting certain quantum codes together. The problem of finding long quantum error correction codes is reduced to that of searching several short length quantum codes with certain properties. Our method works for all length and all distance codes, and is quite efficient to construct optimal or near optimal codes. Two main known methods in constructing new codes from old codes in quantum error-correction theory, the concatenating and pasting, can be understood in the framework of nested quantum error correction codes.

  8. 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.

  9. Graph Codes with Reed-Solomon Component Codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Justesen, Jørn

    2006-01-01

    We treat a specific case of codes based on bipartite expander graphs coming from finite geometries. The code symbols are associated with the branches and the symbols connected to a given node are restricted to be codewords in a Reed-Solomon code. We give results on the parameters of the codes and...

  10. Phase-coded pulse aperiodic transmitter coding

    Directory of Open Access Journals (Sweden)

    I. I. Virtanen

    2009-07-01

    Full Text Available Both ionospheric and weather radar communities have already adopted the method of transmitting radar pulses in an aperiodic manner when measuring moderately overspread targets. Among the users of the ionospheric radars, this method is called Aperiodic Transmitter Coding (ATC, whereas the weather radar users have adopted the term Simultaneous Multiple Pulse-Repetition Frequency (SMPRF. When probing the ionosphere at the carrier frequencies of the EISCAT Incoherent Scatter Radar facilities, the range extent of the detectable target is typically of the order of one thousand kilometers – about seven milliseconds – whereas the characteristic correlation time of the scattered signal varies from a few milliseconds in the D-region to only tens of microseconds in the F-region. If one is interested in estimating the scattering autocorrelation function (ACF at time lags shorter than the F-region correlation time, the D-region must be considered as a moderately overspread target, whereas the F-region is a severely overspread one. Given the technical restrictions of the radar hardware, a combination of ATC and phase-coded long pulses is advantageous for this kind of target. We evaluate such an experiment under infinitely low signal-to-noise ratio (SNR conditions using lag profile inversion. In addition, a qualitative evaluation under high-SNR conditions is performed by analysing simulated data. The results show that an acceptable estimation accuracy and a very good lag resolution in the D-region can be achieved with a pulse length long enough for simultaneous E- and F-region measurements with a reasonable lag extent. The new experiment design is tested with the EISCAT Tromsø VHF (224 MHz radar. An example of a full D/E/F-region ACF from the test run is shown at the end of the paper.

  11. Adjoint code generator

    Institute of Scientific and Technical Information of China (English)

    CHENG Qiang; CAO JianWen; WANG Bin; ZHANG HaiBin

    2009-01-01

    The adjoint code generator (ADG) is developed to produce the adjoint codes, which are used to analytically calculate gradients and the Hessian-vector products with the costs independent of the number of the independent variables. Different from other automatic differentiation tools, the implementation of ADG has advantages of using the least program behavior decomposition method and several static dependence analysis techniques. In this paper we first address the concerned concepts and fundamentals, and then introduce the functionality and the features of ADG. In particular, we also discuss the design architecture of ADG and implementation details including the recomputation and storing strategy and several techniques for code optimization. Some experimental results in several applications are presented at the end.

  12. MHD Generation Code

    CERN Document Server

    Frutos-Alfaro, Francisco

    2015-01-01

    A program to generate codes in Fortran and C of the full Magnetohydrodynamic equations is shown. The program used the free computer algebra system software REDUCE. This software has a package called EXCALC, which is an exterior calculus program. The advantage of this program is that it can be modified to include another complex metric or spacetime. The output of this program is modified by means of a LINUX script which creates a new REDUCE program to manipulate the MHD equations to obtain a code that can be used as a seed for a MHD code for numerical applications. As an example, we present part of output of our programs for Cartesian coordinates and how to do the discretization.

  13. 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.

  14. Genetic barcodes

    Science.gov (United States)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  15. Quantitative regulation of alternative splicing in evolution and development

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Roy, Scott W;

    2009-01-01

    Alternative splicing (AS) is a widespread mechanism with an important role in increasing transcriptome and proteome diversity by generating multiple different products from the same gene. Evolutionary studies of AS have focused primarily on the conservation of alternatively spliced sequences...... layer in complex gene regulatory networks and in the emergence of genetic novelties....

  16. Aeroacoustic Prediction Codes

    Science.gov (United States)

    Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

    2000-01-01

    This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor

  17. Securing mobile code.

    Energy Technology Data Exchange (ETDEWEB)

    Link, Hamilton E.; Schroeppel, Richard Crabtree; Neumann, William Douglas; Campbell, Philip LaRoche; Beaver, Cheryl Lynn; Pierson, Lyndon George; Anderson, William Erik

    2004-10-01

    If software is designed so that the software can issue functions that will move that software from one computing platform to another, then the software is said to be 'mobile'. There are two general areas of security problems associated with mobile code. The 'secure host' problem involves protecting the host from malicious mobile code. The 'secure mobile code' problem, on the other hand, involves protecting the code from malicious hosts. This report focuses on the latter problem. We have found three distinct camps of opinions regarding how to secure mobile code. There are those who believe special distributed hardware is necessary, those who believe special distributed software is necessary, and those who believe neither is necessary. We examine all three camps, with a focus on the third. In the distributed software camp we examine some commonly proposed techniques including Java, D'Agents and Flask. For the specialized hardware camp, we propose a cryptographic technique for 'tamper-proofing' code over a large portion of the software/hardware life cycle by careful modification of current architectures. This method culminates by decrypting/authenticating each instruction within a physically protected CPU, thereby protecting against subversion by malicious code. Our main focus is on the camp that believes that neither specialized software nor hardware is necessary. We concentrate on methods of code obfuscation to render an entire program or a data segment on which a program depends incomprehensible. The hope is to prevent or at least slow down reverse engineering efforts and to prevent goal-oriented attacks on the software and execution. The field of obfuscation is still in a state of development with the central problem being the lack of a basis for evaluating the protection schemes. We give a brief introduction to some of the main ideas in the field, followed by an in depth analysis of a technique called &apos

  18. 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

  19. Modular optimization code package: MOZAIK

    Science.gov (United States)

    Bekar, Kursat B.

    This dissertation addresses the development of a modular optimization code package, MOZAIK, for geometric shape optimization problems in nuclear engineering applications. MOZAIK's first mission, determining the optimal shape of the D2O moderator tank for the current and new beam tube configurations for the Penn State Breazeale Reactor's (PSBR) beam port facility, is used to demonstrate its capabilities and test its performance. MOZAIK was designed as a modular optimization sequence including three primary independent modules: the initializer, the physics and the optimizer, each having a specific task. By using fixed interface blocks among the modules, the code attains its two most important characteristics: generic form and modularity. The benefit of this modular structure is that the contents of the modules can be switched depending on the requirements of accuracy, computational efficiency, or compatibility with the other modules. Oak Ridge National Laboratory's discrete ordinates transport code TORT was selected as the transport solver in the physics module of MOZAIK, and two different optimizers, Min-max and Genetic Algorithms (GA), were implemented in the optimizer module of the code package. A distributed memory parallelism was also applied to MOZAIK via MPI (Message Passing Interface) to execute the physics module concurrently on a number of processors for various states in the same search. Moreover, dynamic scheduling was enabled to enhance load balance among the processors while running MOZAIK's physics module thus improving the parallel speedup and efficiency. In this way, the total computation time consumed by the physics module is reduced by a factor close to M, where M is the number of processors. This capability also encourages the use of MOZAIK for shape optimization problems in nuclear applications because many traditional codes related to radiation transport do not have parallel execution capability. A set of computational models based on the

  20. 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

    2016-03-01

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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)

  3. SEQassembly: A Practical Tools Program for Coding Sequences Splicing

    Science.gov (United States)

    Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

    CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

  4. 毛细管电泳——基因突变及多态性分析新方法%Capillary Electrophoresis——An Attractive Alternative Tool for Analyses ofGenetic Mutations/Polymorphisms

    Institute of Scientific and Technical Information of China (English)

    任吉存

    2001-01-01

    Recently, capillary electrophoresis (CE) has been successfully used for genetic analysis instead of conventional slab gel electrophoresis. This article will give an overview of the fundamental aspects on mutation/polymorphism analyses in combination with capillary electrophoresis (CE), which mainly includes single strand conformation polymorphism analysis, denaturing gradient-gel electrophoresis, heteroduplex analysis, chemical mismatch cleavage, restriction fragment length polymorphism, allele specific oligonucleotide hybridization, allele specific amplification, primer extension, and minisatellite and microsatellite analyses. A number of key applications are summarized.%摘要着重介绍基因突变及多态性分析方法以及毛细管电泳在该领域中的应用。主要包括单链构象多态性分析,变性梯度及温度梯度电泳,杂合子分析,限制性片段多态性分析,等位基因特异性扩增,核酸杂交,引物扩展及小卫星和微卫星分析。

  5. New code match strategy for wideband code division multiple access code tree management

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Orthogonal variable spreading factor channelization codes are widely used to provide variable data rates for supporting different bandwidth requirements in wideband code division multiple access (WCDMA) systems. A new code match scheme for WCDMA code tree management was proposed. The code match scheme is similar to the existing crowed-first scheme. When choosing a code for a user, the code match scheme only compares the one up layer of the allocated codes, unlike the crowed-first scheme which perhaps compares all up layers. So the operation of code match scheme is simple, and the average time delay is decreased by 5.1%. The simulation results also show that the code match strategy can decrease the average code blocking probability by 8.4%.

  6. 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.

  7. Coded Random Access

    DEFF Research Database (Denmark)

    Paolini, Enrico; Stefanovic, Cedomir; Liva, Gianluigi;

    2015-01-01

    as waste. However, if the common receiver (e.g., base station) is capable to store the collision slots and use them in a transmission recovery process based on successive interference cancellation, the design space for access protocols is radically expanded. We present the paradigm of coded random access...

  8. 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...

  9. Physical Layer Network Coding

    DEFF Research Database (Denmark)

    Fukui, Hironori; Yomo, Hironori; Popovski, Petar

    2013-01-01

    Physical layer network coding (PLNC) has the potential to improve throughput of multi-hop networks. However, most of the works are focused on the simple, three-node model with two-way relaying, not taking into account the fact that there can be other neighboring nodes that can cause...

  10. 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...

  11. On Asymmetric Quantum MDS Codes

    CERN Document Server

    Ezerman, Martianus Frederic; Ling, San

    2010-01-01

    Assuming the validity of the MDS Conjecture, the weight distribution of all MDS codes is known. Using a recently-established characterization of asymmetric quantum error-correcting codes, linear MDS codes can be used to construct asymmetric quantum MDS codes with $d_{z} \\geq d_{x}\\geq 2$ for all possible values of length $n$ for which linear MDS codes over $\\F_{q}$ are known to exist.

  12. 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)

  13. 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 inclu...... 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...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 4.2 Affine variety codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 4.3 Some Gr¨obner basis theoretical tools . . . . . . . . . . . . . . . . . . . . . . . 155 4.4 A bound on the minimum distance of C(I,L) . . . . . . . . . . . . . . . . . . 157 4.5 The Feng-Rao bound...... for C(I,L)? . . . . . . . . . . . . . . . . . . . . . . . . 160 4.6 Using weighted degree orderings . . . . . . . . . . . . . . . . . . . . . . . . . 163 4.7 The order domain conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 4.8 Weight functions and order domains...

  14. 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...... 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...... 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...

  15. Non-coding genome functions in diabetes.

    Science.gov (United States)

    Cebola, Inês; Pasquali, Lorenzo

    2016-01-01

    Most of the genetic variation associated with diabetes, through genome-wide association studies, does not reside in protein-coding regions, making the identification of functional variants and their eventual translation to the clinic challenging. In recent years, high-throughput sequencing-based methods have enabled genome-scale high-resolution epigenomic profiling in a variety of human tissues, allowing the exploration of the human genome outside of the well-studied coding regions. These experiments unmasked tens of thousands of regulatory elements across several cell types, including diabetes-relevant tissues, providing new insights into their mechanisms of gene regulation. Regulatory landscapes are highly dynamic and cell-type specific and, being sensitive to DNA sequence variation, can vary with individual genomes. The scientific community is now in place to exploit the regulatory maps of tissues central to diabetes etiology, such as pancreatic progenitors and adult islets. This giant leap forward in the understanding of pancreatic gene regulation is revolutionizing our capacity to discriminate between functional and non-functional non-coding variants, opening opportunities to uncover regulatory links between sequence variation and diabetes susceptibility. In this review, we focus on the non-coding regulatory landscape of the pancreatic endocrine cells and provide an overview of the recent developments in this field. PMID:26438568

  16. 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.

  17. Renewable Energy Requirements for Future Building Codes: Options for Compliance

    Energy Technology Data Exchange (ETDEWEB)

    Dillon, Heather E.; Antonopoulos, Chrissi A.; Solana, Amy E.; Russo, Bryan J.

    2011-09-30

    As the model energy codes are improved to reach efficiency levels 50 percent greater than current codes, use of on-site renewable energy generation is likely to become a code requirement. This requirement will be needed because traditional mechanisms for code improvement, including envelope, mechanical and lighting, have been pressed to the end of reasonable limits. Research has been conducted to determine the mechanism for implementing this requirement (Kaufman 2011). Kaufmann et al. determined that the most appropriate way to structure an on-site renewable requirement for commercial buildings is to define the requirement in terms of an installed power density per unit of roof area. This provides a mechanism that is suitable for the installation of photovoltaic (PV) systems on future buildings to offset electricity and reduce the total building energy load. Kaufmann et al. suggested that an appropriate maximum for the requirement in the commercial sector would be 4 W/ft{sup 2} of roof area or 0.5 W/ft{sup 2} of conditioned floor area. As with all code requirements, there must be an alternative compliance path for buildings that may not reasonably meet the renewables requirement. This might include conditions like shading (which makes rooftop PV arrays less effective), unusual architecture, undesirable roof pitch, unsuitable building orientation, or other issues. In the short term, alternative compliance paths including high performance mechanical equipment, dramatic envelope changes, or controls changes may be feasible. These options may be less expensive than many renewable systems, which will require careful balance of energy measures when setting the code requirement levels. As the stringency of the code continues to increase however, efficiency trade-offs will be maximized, requiring alternative compliance options to be focused solely on renewable electricity trade-offs or equivalent programs. One alternate compliance path includes purchase of Renewable Energy

  18. 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

  19. Alternative Solar Indices

    Energy Technology Data Exchange (ETDEWEB)

    Lantz, L.J.

    1980-07-01

    Possible alternative Solar Indices which could either be a perturbation from the currently defined Solar Index or possible indices based on current technologies for other media markets are discussed. An overview is given of the current project, including the logic that was utilized in defining its current structure and then alternative indices and definitions are presented and finally, recommendations are made for adopting alternative indices.

  20. Complex Alternative Splicing

    OpenAIRE

    Park, Jung Woo; Graveley, Brenton R.

    2007-01-01

    Alternative splicing is a powerful means of controlling gene expression and increasing protein diversity. Most genes express a limited number of mRNA isoforms, but there are several examples of genes that use alternative splicing to generate hundreds, thousands, and even tens of thousands of isoforms. Collectively such genes are considered to undergo complex alternative splicing. The best example is the Drosophila Down syndrome cell adhesion molecule (Dscam) gene, which can generate 38,016 is...

  1. Decoding Generalized Concatenated Codes Using Interleaved Reed-Solomon Codes

    CERN Document Server

    Senger, Christian; Bossert, Martin; Zyablov, Victor

    2008-01-01

    Generalized Concatenated codes are a code construction consisting of a number of outer codes whose code symbols are protected by an inner code. As outer codes, we assume the most frequently used Reed-Solomon codes; as inner code, we assume some linear block code which can be decoded up to half its minimum distance. Decoding up to half the minimum distance of Generalized Concatenated codes is classically achieved by the Blokh-Zyablov-Dumer algorithm, which iteratively decodes by first using the inner decoder to get an estimate of the outer code words and then using an outer error/erasure decoder with a varying number of erasures determined by a set of pre-calculated thresholds. In this paper, a modified version of the Blokh-Zyablov-Dumer algorithm is proposed, which exploits the fact that a number of outer Reed-Solomon codes with average minimum distance d can be grouped into one single Interleaved Reed-Solomon code which can be decoded beyond d/2. This allows to skip a number of decoding iterations on the one...

  2. CTI Correction Code

    Science.gov (United States)

    Massey, Richard; Stoughton, Chris; Leauthaud, Alexie; Rhodes, Jason; Koekemoer, Anton; Ellis, Richard; Shaghoulian, Edgar

    2013-07-01

    Charge Transfer Inefficiency (CTI) due to radiation damage above the Earth's atmosphere creates spurious trailing in images from Charge-Coupled Device (CCD) imaging detectors. Radiation damage also creates unrelated warm pixels, which can be used to measure CTI. This code provides pixel-based correction for CTI and has proven effective in Hubble Space Telescope Advanced Camera for Surveys raw images, successfully reducing the CTI trails by a factor of ~30 everywhere in the CCD and at all flux levels. The core is written in java for speed, and a front-end user interface is provided in IDL. The code operates on raw data by returning individual electrons to pixels from which they were unintentionally dragged during readout. Correction takes about 25 minutes per ACS exposure, but is trivially parallelisable to multiple processors.

  3. 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.

  4. Sinusoidal transform coding

    Science.gov (United States)

    Mcaulay, Robert J.; Quatieri, Thomas F.

    1988-01-01

    It has been shown that an analysis/synthesis system based on a sinusoidal representation of speech leads to synthetic speech that is essentially perceptually indistinguishable from the original. Strategies for coding the amplitudes, frequencies and phases of the sine waves have been developed that have led to a multirate coder operating at rates from 2400 to 9600 bps. The encoded speech is highly intelligible at all rates with a uniformly improving quality as the data rate is increased. A real-time fixed-point implementation has been developed using two ADSP2100 DSP chips. The methods used for coding and quantizing the sine-wave parameters for operation at the various frame rates are described.

  5. Epetra developers coding guidelines.

    Energy Technology Data Exchange (ETDEWEB)

    Heroux, Michael Allen; Sexton, Paul Michael

    2003-12-01

    Epetra is a package of classes for the construction and use of serial and distributed parallel linear algebra objects. It is one of the base packages in Trilinos. This document describes guidelines for Epetra coding style. The issues discussed here go beyond correct C++ syntax to address issues that make code more readable and self-consistent. The guidelines presented here are intended to aid current and future development of Epetra specifically. They reflect design decisions that were made in the early development stages of Epetra. Some of the guidelines are contrary to more commonly used conventions, but we choose to continue these practices for the purposes of self-consistency. These guidelines are intended to be complimentary to policies established in the Trilinos Developers Guide.

  6. Confocal coded aperture imaging

    Energy Technology Data Exchange (ETDEWEB)

    Tobin, Jr., Kenneth William (Harriman, TN); Thomas, Jr., Clarence E. (Knoxville, TN)

    2001-01-01

    A method for imaging a target volume comprises the steps of: radiating a small bandwidth of energy toward the target volume; focusing the small bandwidth of energy into a beam; moving the target volume through a plurality of positions within the focused beam; collecting a beam of energy scattered from the target volume with a non-diffractive confocal coded aperture; generating a shadow image of said aperture from every point source of radiation in the target volume; and, reconstructing the shadow image into a 3-dimensional image of the every point source by mathematically correlating the shadow image with a digital or analog version of the coded aperture. The method can comprise the step of collecting the beam of energy scattered from the target volume with a Fresnel zone plate.

  7. Code of Practice

    International Nuclear Information System (INIS)

    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

  8. MELCOR computer code manuals

    International Nuclear Information System (INIS)

    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

  9. 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.

  10. The expanded genetic alphabet.

    Science.gov (United States)

    Malyshev, Denis A; Romesberg, Floyd E

    2015-10-01

    All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information. PMID:26304162

  11. 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. PMID:27131325

  12. Safe genetically engineered plants

    International Nuclear Information System (INIS)

    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

  13. Safe genetically engineered plants

    Science.gov (United States)

    Rosellini, D.; Veronesi, F.

    2007-10-01

    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.

  14. 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.

  15. 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.

  16. Structural coding versus free-energy predictive coding.

    Science.gov (United States)

    van der Helm, Peter A

    2016-06-01

    Focusing on visual perceptual organization, this article contrasts the free-energy (FE) version of predictive coding (a recent Bayesian approach) to structural coding (a long-standing representational approach). Both use free-energy minimization as metaphor for processing in the brain, but their formal elaborations of this metaphor are fundamentally different. FE predictive coding formalizes it by minimization of prediction errors, whereas structural coding formalizes it by minimization of the descriptive complexity of predictions. Here, both sides are evaluated. A conclusion regarding competence is that FE predictive coding uses a powerful modeling technique, but that structural coding has more explanatory power. A conclusion regarding performance is that FE predictive coding-though more detailed in its account of neurophysiological data-provides a less compelling cognitive architecture than that of structural coding, which, for instance, supplies formal support for the computationally powerful role it attributes to neuronal synchronization. PMID:26407895

  17. Alternative energy and environmental concerns

    International Nuclear Information System (INIS)

    The New Brunswick Market Design Committee will address environmental concerns within the context of the new energy policy and market rules for the newly restructured electric power industry. The new rules that come with power restructuring will in some ways facilitate environmental protection but they can also complicate it. With open access markets, it will be possible to coordinate evolving energy frameworks with current environmental objectives. Restructuring provides an opportunity to create incentives and guidelines to operate in an environmentally sustainable manner, as suggested in the New Brunswick Energy Policy, White Paper which outlines green pricing, the development of a provincial Climate Change Action Plan, and promotion of alternative energy. The Market Design Committee examined the environmental concerns listed within the White Paper that pertain to the generation and transmission of electricity. These include the integration of energy and environmental policy. Other issues addressed in this report were trans-boundary and global air emissions, the development of a provincial climate change action plan, and a federal-provincial climate change framework agreement. New Brunswick will encourage the development of pilot studies that demonstrate the benefits of renewable and alternative technologies and that help promote the market to manufacture, sell and maintain renewable and alternative technologies in small-scale on-site power generation. This report also discussed the 4 key air pollutants for which specific treatment has been defined, including sulphur dioxide, nitrogen oxides, mercury and carbon dioxide. Recommendations for reducing these emissions include the use of renewable energy sources, the use of lower carbon fuels, increased efficiency of power transmission/generation/distribution systems, reducing power demand by the industrial sector, and promoting energy efficient building codes. 34 refs., 1 tab

  18. Decoding of concatenated codes with interleaved outer codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Thommesen, Christian; Høholdt, Tom

    2004-01-01

    Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved Reed/Solomon codes, which allows close to errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes. (NK) N-K......Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved Reed/Solomon codes, which allows close to errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes. (NK) N-K...

  19. Coding Opportunity Densification Strategies for Instantly Decodable Network Coding

    OpenAIRE

    Sorour, Sameh; Valaee, Shahrokh

    2012-01-01

    In this paper, we aim to identify the strategies that can maximize and monotonically increase the density of the coding opportunities in instantly decodable network coding (IDNC).Using the well-known graph representation of IDNC, first derive an expression for the exact evolution of the edge set size after the transmission of any arbitrary coded packet. From the derived expressions, we show that sending commonly wanted packets for all the receivers can maximize the number of coding opportunit...

  20. TASS code topical report. V.1 TASS code technical manual

    International Nuclear Information System (INIS)

    TASS 1.0 code has been developed at KAERI for the initial and reload non-LOCA safety analysis for the operating PWRs as well as the PWRs under construction in Korea. TASS code will replace various vendor's non-LOCA safety analysis codes currently used for the Westinghouse and ABB-CE type PWRs in Korea. This can be achieved through TASS code input modifications specific to each reactor type. The TASS code can be run interactively through the keyboard operation. A simimodular configuration used in developing the TASS code enables the user easily implement new models. TASS code has been programmed using FORTRAN77 which makes it easy to install and port for different computer environments. The TASS code can be utilized for the steady state simulation as well as the non-LOCA transient simulations such as power excursions, reactor coolant pump trips, load rejections, loss of feedwater, steam line breaks, steam generator tube ruptures, rod withdrawal and drop, and anticipated transients without scram (ATWS). The malfunctions of the control systems, components, operator actions and the transients caused by the malfunctions can be easily simulated using the TASS code. This technical report describes the TASS 1.0 code models including reactor thermal hydraulic, reactor core and control models. This TASS code models including reactor thermal hydraulic, reactor core and control models. This TASS code technical manual has been prepared as a part of the TASS code manual which includes TASS code user's manual and TASS code validation report, and will be submitted to the regulatory body as a TASS code topical report for a licensing non-LOCA safety analysis for the Westinghouse and ABB-CE type PWRs operating and under construction in Korea. (author). 42 refs., 29 tabs., 32 figs

  1. Doctors Look for Liver Transplant Alternatives

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ Robert Pennington, a 19 - year - old boy, suffers from liver disease. His name was put on a transplant waiting list, but no livers were available. Then Dr. Marlon Levy, a transplant surgeon at Baylor University Medical Center, offered an alternative: a procedure2 using a dead pig's liver. But not a liver from an ordinary pig, "They're genetically modified3 to try to prevent a reaction between the human blood and the pig liver" , Levy said.

  2. Containment Code Validation Matrix

    International Nuclear Information System (INIS)

    The Committee on the Safety of Nuclear Installations (CSNI) formed the CCVM (Containment Code Validation Matrix) task group in 2002. The objective of this group was to define a basic set of available experiments for code validation, covering the range of containment (ex-vessel) phenomena expected in the course of light and heavy water reactor design basis accidents and beyond design basis accidents/severe accidents. It was to consider phenomena relevant to pressurised heavy water reactor (PHWR), pressurised water reactor (PWR) and boiling water reactor (BWR) designs of Western origin as well as of Eastern European VVER types. This work would complement the two existing CSNI validation matrices for thermal hydraulic code validation (NEA/CSNI/R(1993)14) and In-vessel core degradation (NEA/CSNI/R(2001)21). The report initially provides a brief overview of the main features of a PWR, BWR, CANDU and VVER reactors. It also provides an overview of the ex-vessel corium retention (core catcher). It then provides a general overview of the accident progression for light water and heavy water reactors. The main focus is to capture most of the phenomena and safety systems employed in these reactor types and to highlight the differences. This CCVM contains a description of 127 phenomena, broken down into 6 categories: - Containment Thermal-hydraulics Phenomena; - Hydrogen Behaviour (Combustion, Mitigation and Generation) Phenomena; - Aerosol and Fission Product Behaviour Phenomena; - Iodine Chemistry Phenomena; - Core Melt Distribution and Behaviour in Containment Phenomena; - Systems Phenomena. A synopsis is provided for each phenomenon, including a description, references for further information, significance for DBA and SA/BDBA and a list of experiments that may be used for code validation. The report identified 213 experiments, broken down into the same six categories (as done for the phenomena). An experiment synopsis is provided for each test. Along with a test description

  3. Combinatorial neural codes from a mathematical coding theory perspective.

    Science.gov (United States)

    Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L

    2013-07-01

    Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli. PMID:23724797

  4. Genetic Breakthrough

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new calf breeding technique shows promise for treating malignant tumors Chinese scientists have successfully bred a genetically altered cow capable of producing cancer-curing proteins for human beings.

  5. Genetic Discrimination

    Science.gov (United States)

    ... Care Online Health Resources For Health Professionals Competency & Curricular Resources Genetics 101 Genomic Medicine and Health Care ... Role of the NHGRI in the Federal Legislative Process Genome Statute and Legislation Database Human Subjects Research ...

  6. Genetic Mapping

    Science.gov (United States)

    ... Care Online Health Resources For Health Professionals Competency & Curricular Resources Genetics 101 Genomic Medicine and Health Care ... of DNA. Think of it as a shuffling process, called recombination. The single chromosome in a reproductive ...

  7. Genetic Disorders

    Science.gov (United States)

    ... 21 (Down syndrome) . Other trisomies include trisomy 13 (Patau syndrome) and trisomy 18 (Edwards syndrome) . Monosomy is ... which there is an extra chromosome. Trisomy 13 (Patau Syndrome): A genetic disorder that causes serious heart ...

  8. 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. ...

  9. Cracking the Genetic Code | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... research has already had a profound impact on scientific progress." In what ways? FRANCIS COLLINS: A graduate student today cannot imagine how you did research without access to the human genome sequence. It is so fundamental, something you're looking at many times a ...

  10. Alternative Devices for Taking Insulin

    Science.gov (United States)

    ... KB). Alternate Language URL Alternative Devices for Taking Insulin Page Content On this page: What alternative devices ... the skin. [ Top ] What alternative devices for taking insulin are available? Insulin pens provide a convenient, easy- ...

  11. Alternative health insurance schemes

    DEFF Research Database (Denmark)

    Keiding, Hans; Hansen, Bodil O.

    2002-01-01

    In this paper, we present a simple model of health insurance with asymmetric information, where we compare two alternative ways of organizing the insurance market. Either as a competitive insurance market, where some risks remain uninsured, or as a compulsory scheme, where however, the level...... competitive insurance; this situation turns out to be at least as good as either of the alternatives...

  12. Ciona Genetics

    OpenAIRE

    Veeman, Michael T.; Chiba, Shota; Smith, William C.

    2011-01-01

    Ascidians, such as Ciona, are invertebrate chordates with simple embryonic body plans and small, relatively non-redundant genomes. Ciona genetics is in its infancy compared to many other model systems, but it provides a powerful method for studying this important vertebrate outgroup. Here we give basic methods for genetic analysis of Ciona, including protocols for controlled crosses both by natural spawning and by the surgical isolation of gametes; the identification and propagation of mutant...

  13. High Energy Transport Code HETC

    International Nuclear Information System (INIS)

    The physics contained in the High Energy Transport Code (HETC), in particular the collision models, are discussed. An application using HETC as part of the CALOR code system is also given. 19 refs., 5 figs., 3 tabs

  14. The Tap code - a code similar to Morse code for communication by tapping

    OpenAIRE

    Rafler, Stephan

    2013-01-01

    A code is presented for fast, easy and efficient communication over channels that allow only two signal types: a single sound (e.g. a knock), or no sound (i.e. silence). This is a true binary code while Morse code is a ternary code and does not work in such situations. Thus the presented code is more universal than Morse and can be used in much more situations. Additionally it is very tolerant to variations in signal strength or duration. The paper contains various ways in which the code can ...

  15. Erasure Coded Storage on a Changing Network: the Untold Story

    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...

  16. Scalable-to-lossless transform domain distributed video coding

    DEFF Research Database (Denmark)

    Huang, Xin; Ukhanova, Ann; Veselov, Anton;

    2010-01-01

    TransformDomain Wyner-Ziv (TDWZ) distributed video codec with feedback.The lossless coding is obtained by using a reversible integer DCT.Experimental results show that the performance of the proposed scalable-to-lossless TDWZ video codec can outperform alternatives based on the JPEG 2000 standard. The TDWZ...

  17. Interface requirements for coupling a containment code to a reactor system thermal hydraulic codes

    Energy Technology Data Exchange (ETDEWEB)

    Baratta, A.J.

    1997-07-01

    To perform a complete analysis of a reactor transient, not only the primary system response but the containment response must also be accounted for. Such transients and accidents as a loss of coolant accident in both pressurized water and boiling water reactors and inadvertent operation of safety relief valves all challenge the containment and may influence flows because of containment feedback. More recently, the advanced reactor designs put forth by General Electric and Westinghouse in the US and by Framatome and Seimens in Europe rely on the containment to act as the ultimate heat sink. Techniques used by analysts and engineers to analyze the interaction of the containment and the primary system were usually iterative in nature. Codes such as RELAP or RETRAN were used to analyze the primary system response and CONTAIN or CONTEMPT the containment response. The analysis was performed by first running the system code and representing the containment as a fixed pressure boundary condition. The flows were usually from the primary system to the containment initially and generally under choked conditions. Once the mass flows and timing are determined from the system codes, these conditions were input into the containment code. The resulting pressures and temperatures were then calculated and the containment performance analyzed. The disadvantage of this approach becomes evident when one performs an analysis of a rapid depressurization or a long term accident sequence in which feedback from the containment can occur. For example, in a BWR main steam line break transient, the containment heats up and becomes a source of energy for the primary system. Recent advances in programming and computer technology are available to provide an alternative approach. The author and other researchers have developed linkage codes capable of transferring data between codes at each time step allowing discrete codes to be coupled together.

  18. Decoding Xing-Ling codes

    DEFF Research Database (Denmark)

    Nielsen, Rasmus Refslund

    2002-01-01

    This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed.......This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed....

  19. Multiple LDPC decoding for distributed source coding and video coding

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Luong, Huynh Van; Huang, Xin

    2011-01-01

    Distributed source coding (DSC) is a coding paradigm for systems which fully or partly exploit the source statistics at the decoder to reduce the computational burden at the encoder. Distributed video coding (DVC) is one example. This paper considers the use of Low Density Parity Check Accumulate...... (LDPCA) codes in a DSC scheme with feed-back. To improve the LDPC coding performance in the context of DSC and DVC, while retaining short encoder blocks, this paper proposes multiple parallel LDPC decoding. The proposed scheme passes soft information between decoders to enhance performance. Experimental...

  20. Exploring geovisualization symbology for landscape genetics

    DEFF Research Database (Denmark)

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

    2013-01-01

    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 la...... 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...... 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...