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Sample records for alternative genetic code

  1. Can the genetic code be mathematically described?

    Science.gov (United States)

    Gonzalez, Diego L

    2004-04-01

    From a mathematical point of view, the genetic code is a surjective mapping between the set of the 64 possible three-base codons and the set of 21 elements composed of the 20 amino acids plus the Stop signal. Redundancy and degeneracy therefore follow. In analogy with the genetic code, non-power integer-number representations are also surjective mappings between sets of different cardinality and, as such, also redundant. However, none of the non-power arithmetics studied so far nor other alternative redundant representations are able to match the actual degeneracy of the genetic code. In this paper we develop a slightly more general framework that leads to the following surprising results: i) the degeneracy of the genetic code is mathematically described, ii) a new symmetry is uncovered within this degeneracy, iii) by assigning a binary string to each of the codons, their classification into definite parity classes according to the corresponding sequence of bases is made possible. This last result is particularly appealing in connection with the fact that parity coding is the basis of the simplest strategies devised for error correction in man-made digital data transmission systems.

  2. 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.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

    acids allows only for the superimposition of punctual and loosely positioned signals to conserved amino acid sequences. The degree of flexibility of the genetic code is low or average with respect to several classes of alternative codes. This result is consistent with the view that DNA structure...

  4. Future of the Genetic Code

    Directory of Open Access Journals (Sweden)

    Hong Xue

    2017-02-01

    Full Text Available The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA in addition to canonical amino acids (CAA include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments of nonsense codons and sense codons are also under development. These methods enable the application of NCAAs to enrich both fundamental and applied aspects of protein chemistry and biology. Sense codon reassignment to NCAA could incur problems arising from the usage of anticodons as identity elements on tRNA, and possible misreading of NNY codons by UNN anticodons. Evidence suggests that the problem of anticodon as identity elements can be diminished or resolved through removal from the tRNA of all identity elements besides the anticodons, and the problem of misreading of NNY codons by UNN anticodon can be resolved by the retirement of both the UNN anticodon and its complementary NNA codon from the proteome in the event that a restrictive post-transcriptional modification of the UNN anticodon by host enzymes to prevent the misreading cannot be obtained.

  5. 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

  6. Hacking the genetic code of mammalian cells.

    Science.gov (United States)

    Schwarzer, Dirk

    2009-07-06

    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.

  7. 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.

  8. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-28

    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.

  9. The puzzling origin of the genetic code.

    Science.gov (United States)

    Cedergren, R; Miramontes, P

    1996-06-01

    Recent results add to the mystery of the origin of the genetic code. In spite of early doubts, RNA can discriminate between hydrophobic amino acids under certain contexts. Moreover, codon reassignment, which has taken place in several organisms and mitochondria, is not a random process. Finally, phylogenies of some aminoacyl-tRNA synthetases suggest that the entire code was not completely assigned at the time of the divergence of bacteria from nucleated cells.

  10. 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.

  11. 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

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    alternatives. Consumers in Denmark, Finland, Norway and Sweden (n=738) assessed two cheeses: one was labelled as genetically modified (preferred in an earlier product test) and the other as conventional (neutral in an ealier product test). A smaller control group received two cheeses with blind codes......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...

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

    Directory of Open Access Journals (Sweden)

    Monteagudo Ángel

    2011-02-01

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

  14. 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.

  15. Optimality properties of a proposed precursor to the genetic code.

    Science.gov (United States)

    Butler, Thomas; Goldenfeld, Nigel

    2009-09-01

    We calculate the optimality score of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the proposed precursor is much less optimal than that of the canonical code. Our results render unlikely the notion that the doublet precursor was an intermediate state in the evolution of the canonical genetic code. These findings support the notion that code optimality reflects evolutionary dynamics, and that if such a doublet code originally had a biochemical significance, it arose before the emergence of translation.

  16. 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.

  17. 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.

  18. Expanding the genetic code of Mus musculus

    Science.gov (United States)

    Han, Songmi; Yang, Aerin; Lee, Soonjang; Lee, Han-Woong; Park, Chan Bae; Park, Hee-Sung

    2017-01-01

    Here we report the expansion of the genetic code of Mus musculus with various unnatural amino acids including Nɛ-acetyl-lysine. Stable integration of transgenes encoding an engineered Nɛ-acetyl-lysyl-tRNA synthetase (AcKRS)/tRNAPyl pair into the mouse genome enables site-specific incorporation of unnatural amino acids into a target protein in response to the amber codon. We demonstrate temporal and spatial control of protein acetylation in various organs of the transgenic mouse using a recombinant green fluorescent protein (GFPuv) as a model protein. This strategy will provide a powerful tool for systematic in vivo study of cellular proteins in the most commonly used mammalian model organism for human physiology and disease. PMID:28220771

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

    OpenAIRE

    Bezerra, Ana R; Guimarães, Ana R.; Santos, Manuel A. S.

    2015-01-01

    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 reporte...

  20. Some mathematical refinements concerning error minimization in the genetic code.

    Science.gov (United States)

    Buhrman, Harry; van der Gulik, Peter T S; Kelk, Steven M; Koolen, Wouter M; Stougie, Leen

    2011-01-01

    The genetic code is known to have a high level of error robustness and has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimization problem as a Quadratic Assignment Problem and use this to formally verify that the code found by the heuristic algorithm is the global optimum. We also argue that it is strongly misleading to compare the genetic code only with codes sampled from the fixed block model, because the real code space is orders of magnitude larger. We thus enlarge the space from which random codes can be sampled from approximately 2.433 × 10(18) codes to approximately 5.908 × 10(45) codes. We do this by leaving the fixed block model, and using the wobble rules to formulate the characteristics acceptable for a genetic code. By relaxing more constraints, three larger spaces are also constructed. Using a modified error function, the genetic code is found to be more error robust compared to a background of randomly generated codes with increasing space size. We point out that these results do not necessarily imply that the code was optimized during evolution for error minimization, but that other mechanisms could be the reason for this error robustness.

  1. 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.

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

    Science.gov (United States)

    Komar, Anton A

    2016-01-01

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

  3. Origin and evolutionary process of the genetic code.

    Science.gov (United States)

    Ikehara, Kenji; Niihara, Yuka

    2007-01-01

    The genetic code plots the relationship between a triplet base sequence on RNA and an amino acid that corresponds to a protein associated with a required function in organisms. Accurate knowledge about the genetic code, including its origin and evolutionary process, would be helpful for determining the causes of genetic disorders and discovering new medical treatments, as well as for understanding the origin of life. This review begins with discussion of several well-known theories on the origin of the genetic code. Then, a GNC-SNS primitive genetic code hypothesis, which we originally proposed, is explained in relation to the weak points of other theories. S and N denote G or C and any of the four bases, respectively. We also introduce our hypothesis of the GADV-protein world hypothesis on the origin of life, where GADV stands for the four amino acids, Gly[G], Ala[A], Asp[D] and Val[V]. Next, we discuss the reason why genetic disorders, which should be triggered by base replacements, are repressed at a low level under the universal genetic code. Finally, we explain the current difficulties we faced in treating genetic disorders, suggesting a prospect for a new type of treatments of these disorders.

  4. Genetics Home Reference: alternating hemiplegia of childhood

    Science.gov (United States)

    ... Home Health Conditions alternating hemiplegia of childhood alternating hemiplegia of childhood Enable Javascript to view the expand/ ... Download PDF Open All Close All Description Alternating hemiplegia of childhood is a neurological condition characterized by ...

  5. Improving the efficiency of the genetic code by varying the codon length--the perfect genetic code.

    Science.gov (United States)

    Doig, A J

    1997-10-07

    The function of DNA is to specify protein sequences. The four-base "alphabet" used in nucleic acids is translated to the 20 base alphabet of proteins (plus a stop signal) via the genetic code. The code is neither overlapping nor punctuated, but has mRNA sequences read in successive triplet codons until reaching a stop codon. The true genetic code uses three bases for every amino acid. The efficiency of the genetic code can be significantly increased if the requirement for a fixed codon length is dropped so that the more common amino acids have shorter codon lengths and rare amino acids have longer codon lengths. More efficient codes can be derived using the Shannon-Fano and Huffman coding algorithms. The compression achieved using a Huffman code cannot be improved upon. I have used these algorithms to derive efficient codes for representing protein sequences using both two and four bases. The length of DNA required to specify the complete set of protein sequences could be significantly shorter if transcription used a variable codon length. The restriction to a fixed codon length of three bases means that it takes 42% more DNA than the minimum necessary, and the genetic code is 70% efficient. One can think of many reasons why this maximally efficient code has not evolved: there is very little redundancy so almost any mutation causes an amino acid change. Many mutations will be potentially lethal frame-shift mutations, if the mutation leads to a change in codon length. It would be more difficult for the machinery of transcription to cope with a variable codon length. Nevertheless, in the strict and narrow sense of coding for protein sequences using the minimum length of DNA possible, the Huffman code derived here is perfect.

  6. 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.

  7. Unnatural reactive amino acid genetic code additions

    Science.gov (United States)

    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.

  8. 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.

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Koonin, Eugene V; Novozhilov, Artem S

    2009-02-01

    The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly nonrandom. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physicochemical 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 under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code's evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, that is, the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.

  12. Horizontal symmetry in the algebraic approach of genetic code

    CERN Document Server

    Godina-Nava, J J

    2013-01-01

    Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a horizontal symmetry used in gauge theories to fit the contents of the multiplets of the genetic code. It is used the algebraic approch of Hornos et. al. \\cite{main,PRL71,PRE,MPLB}. We propose an example for the incorporation of horizontal symmetry to study mixtures of elements of the multiplets.

  13. Horizontal symmetry in the algebraic approach of genetic code

    OpenAIRE

    Godina-Nava, J. J.

    2013-01-01

    Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a horizontal symmetry used in gauge theories to fit the contents of the multiplets of the genetic code. It is used the algebraic approch of Hornos et. al. \\cite{main,PRL71,PRE,MPLB}. We propose an example for the incorporation of horizontal symmetry to study mixtu...

  14. The Genetic Code as a Periodic Table Algebraic Aspects

    CERN Document Server

    Bashford, J D

    2000-01-01

    The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of protein conformational parameters. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

  15. On the Organizational Dynamics of the Genetic Code

    KAUST Repository

    Zhang, Zhang

    2011-06-07

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

  16. On the organizational dynamics of the genetic code.

    Science.gov (United States)

    Zhang, Zhang; Yu, Jun

    2011-04-01

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

  17. 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.

  18. 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.

  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. Exceptional error minimization in putative primordial genetic codes

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2009-11-01

    Full Text Available Abstract Background The standard genetic code is redundant and has a highly non-random structure. Codons for the same amino acids typically differ only by the nucleotide in the third position, whereas similar amino acids are encoded, mostly, by codon series that differ by a single base substitution in the third or the first position. As a result, the code is highly albeit not optimally robust to errors of translation, a property that has been interpreted either as a product of selection directed at the minimization of errors or as a non-adaptive by-product of evolution of the code driven by other forces. Results We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage as the measure of a code's robustness to mistranslation. It is shown that, when the 16-supercodon table is populated with 10 putative primordial amino acids, inferred from the results of abiotic synthesis experiments and other evidence independent of the code's evolution, and with minimal assumptions used to assign the remaining supercodons, the resulting 2-letter codes are nearly optimal in terms of the error minimization level. Conclusion The results of the computational experiments with putative primordial genetic codes that contained only two meaningful letters in all codons and encoded 10 to 16 amino acids indicate that such codes are likely to have been nearly optimal with respect to the minimization of translation errors. This near-optimality could be the outcome of extensive early selection during the co-evolution of the code with the primordial, error-prone translation system, or a result of a unique, accidental event. Under this hypothesis, the subsequent expansion of the code resulted in a decrease of the error minimization level that became sustainable owing to the evolution of a high

  1. Linguistic Alternants and Code Selection in Baba Malay.

    Science.gov (United States)

    Pakir, Anne

    1989-01-01

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

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

    Science.gov (United States)

    Bashford, J D; Jarvis, P D

    2000-01-01

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

  3. 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.

  4. A Scenario on the Stepwise Evolution of the Genetic Code

    Institute of Scientific and Technical Information of China (English)

    Jing-Fa; Xiao; Jun; Yu

    2007-01-01

    It is believed that in the RNA world the operational (ribozymes) and the infor- mational (riboscripts) RNA molecules were created with only three (adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigor- ous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12, 15, and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine. Therefore, the maturation of the genetic code also coincided with (1) the departure of aminoacyl-tRNA synthetases (AARSs) from the primordial translation machinery, (2) the replacement of informational RNA by DNA, and (3) the co-evolution of AARSs and their cognate tRNAs. This model predicts gradual replacements of RNA-made molecular mechanisms, cellular processes by proteins, and informational exploitation by DNA.

  5. The Genetic Codes: Mathematical Formulae and an Inverse Symmetry-Information Relationship

    Directory of Open Access Journals (Sweden)

    Tidjani Négadi

    2016-12-01

    Full Text Available First, mathematical formulae faithfully describing the distributions of amino acids and codons and reproducing the degeneracies in the various known genetic codes, including the standard genetic code, are constructed, by hand. Second, we summarize another mathematical approach relying on the use of q-deformations to describe these same genetic codes, and add a new application not considered before. Third, by considering these same genetic codes, we find, qualitatively, that an inverse symmetry-information relationship exists.

  6. 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.

  7. 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.

  8. An Autotrophic Origin for the Coded Amino Acids is Concordant with the Coevolution Theory of the Genetic Code.

    Science.gov (United States)

    Di Giulio, Massimo

    2016-10-01

    The coevolution theory of the origin of the genetic code maintains that the biosynthetic relationships between amino acids co-evolved with the genetic code organization. In other words, the metabolism of amino acids co-evolved with the organization of the genetic code because the biosynthetic pathways of amino acids occurred on tRNA-like molecules. Thus, a heterotrophic origin of amino acids-also only of those involved in the early phase of the structuring of the genetic code-would seem to contradict the main postulate of the coevolution theory. As a matter of fact, this origin not being linked to the metabolism of amino acids in any way-being taken from a physical setting-would seem to remove the possibility that this metabolism had instead heavily contributed to the structuring of the genetic code. Therefore, I have analyzed the structure of the genetic code and mechanisms that brought to its structuring for understanding if the coevolution theory is compatible with autotrophic or heterotrophic conditions. One of the arguments was that an autotrophic origin of amino acids would have the advantage to be able to directly link their metabolism to the structure of the genetic code if-as hypothesized by the coevolution theory-the biosyntheses of amino acids occurred on tRNA-like molecules. Simultaneously, a heterotrophic origin would not have been able to link the metabolism of amino acids to the structure of the genetic code for the absence of a precise determinism of allocation of amino acids, that is to say of a clear mechanism-linked to tRNA-like molecules, for example-that would have determined the specific pattern observed in the genetic code of the biosynthetic relationships between amino acids. The conclusion is that an autotrophic origin of coded amino acids would seem to be the condition under which the genetic code originated.

  9. Genetic algorithms with permutation coding for multiple sequence alignment.

    Science.gov (United States)

    Ben Othman, Mohamed Tahar; Abdel-Azim, Gamil

    2013-08-01

    Multiple sequence alignment (MSA) is one of the topics of bio informatics that has seriously been researched. It is known as NP-complete problem. It is also considered as one of the most important and daunting tasks in computational biology. Concerning this a wide number of heuristic algorithms have been proposed to find optimal alignment. Among these heuristic algorithms are genetic algorithms (GA). The GA has mainly two major weaknesses: it is time consuming and can cause local minima. One of the significant aspects in the GA process in MSA is to maximize the similarities between sequences by adding and shuffling the gaps of Solution Coding (SC). Several ways for SC have been introduced. One of them is the Permutation Coding (PC). We propose a hybrid algorithm based on genetic algorithms (GAs) with a PC and 2-opt algorithm. The PC helps to code the MSA solution which maximizes the gain of resources, reliability and diversity of GA. The use of the PC opens the area by applying all functions over permutations for MSA. Thus, we suggest an algorithm to calculate the scoring function for multiple alignments based on PC, which is used as fitness function. The time complexity of the GA is reduced by using this algorithm. Our GA is implemented with different selections strategies and different crossovers. The probability of crossover and mutation is set as one strategy. Relevant patents have been probed in the topic.

  10. Different types of secondary information in the genetic code.

    Science.gov (United States)

    Maraia, Richard J; Iben, James R

    2014-07-01

    Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code. Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information: codon-specific translational pauses that can be used by particular proteins toward their unique folding and biased codon patterns shared by groups of functionally related mRNAs with coordinate regulation. AGI is important to genetics in general and to human disease; here, we consider influences of its three major components, biased codon use itself, variations in the tRNAome, and anticodon modifications that distinguish synonymous decoding. AGI is plastic and can be used by different species to different extents, with tissue-specificity and in stress responses. Because AGI is species-specific, it is important to consider codon-sensitive experiments when using heterologous systems; for this we focus on the tRNA anticodon loop modification enzyme, CDKAL1, and its link to type 2 diabetes. Newly uncovered tRNAome variability among humans suggests roles in penetrance and as a genetic modifier and disease modifier. Development of experimental and bioinformatics methods are needed to uncover additional means of auxiliary genetic information.

  11. Interleaver Design Method for Turbo Codes Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    Tan Ying; Sun Hong; Zhou Huai-bei

    2004-01-01

    This paper describes a new interleaver construction technique for turbo code. The technique searches as much as possible pseudo-random interleaving patterns under a certain condition using genetic algorithms(GAs). The new interleavers have the superiority of the S-random interleavers and this interleaver construction technique can reduce the time taken to generate pseudo-random interleaving patterns under a certain condition. Tbe results obtained indicate that the new interleavers yield an equal to or better performance than the Srandom interleavers. Compared to the S-random interleaver,this design requires a lower level of computational complexity.

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

    Science.gov (United States)

    Domínguez-Serna, Francisco; Rojas, Fernando

    2015-06-01

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

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

    Science.gov (United States)

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

    2016-06-21

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

  14. 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.

  15. 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...

  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. 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.

  18. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement.

    Science.gov (United States)

    Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida

    2009-06-01

    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.

  19. 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.

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

    Science.gov (United States)

    Wong, J Tze-Fei; Ng, Siu-Kin; Mat, Wai-Kin; Hu, Taobo; Xue, Hong

    2016-03-16

    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. 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.

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

    Directory of Open Access Journals (Sweden)

    Aqsa Tahir

    2016-11-01

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

  4. 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

  5. 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...

  6. 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

  7. Identification of common genetic variation that modulates alternative splicing.

    Directory of Open Access Journals (Sweden)

    Jeremy Hull

    2007-06-01

    Full Text Available Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs. In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.

  8. A new neutron energy spectrum unfolding code using a two steps genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Shahabinejad, H., E-mail: shahabinejad1367@yahoo.com; Hosseini, S.A.; Sohrabpour, M.

    2016-03-01

    A new neutron spectrum unfolding code TGASU (Two-steps Genetic Algorithm Spectrum Unfolding) has been developed to unfold the neutron spectrum from a pulse height distribution which was calculated using the MCNPX-ESUT computational Monte Carlo code. To perform the unfolding process, the response matrices were generated using the MCNPX-ESUT computational code. Both one step (common GA) and two steps GAs have been implemented to unfold the neutron spectra. According to the obtained results, the new two steps GA code results has shown closer match in all energy regions and particularly in the high energy regions. The results of the TGASU code have been compared with those of the standard spectra, LSQR method and GAMCD code. The results of the TGASU code have been demonstrated to be more accurate than that of the existing computational codes for both under-determined and over-determined problems.

  9. 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.

  10. 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.

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  12. Recurrent Coding Sequence Variation Explains only A Small Fraction of the Genetic Architecture of Colorectal Cancer

    NARCIS (Netherlands)

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

    2015-01-01

    textabstractWhilst 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 ca

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

    NARCIS (Netherlands)

    Timofeeva, Maria N.; Ben Kinnersley, [Unknown; 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; Foersti, Asta; Westers, Helga; Hofstra, Robert; Pinheiro, Manuela; Pinto, Carla; Teixeira, Manuel; Ruiz-Ponte, Clara; Fernandez-Rozadilla, Ceres; Carracedo, Angel; Castells, Antoni; Castellvi-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 29,0

  14. 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.

  15. 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.

  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. 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.

  19. An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

    Science.gov (United States)

    Cedergren, R J

    1982-04-01

    Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

  20. Mean-Adaptive Real-Coding Genetic Algorithm and its Applications to Electromagnetic Optimization (Part One

    Directory of Open Access Journals (Sweden)

    Z. Raida

    2007-09-01

    Full Text Available In the paper, a novel instance of the real-coding steady-state genetic algorithm, called the Mean-adaptive real-coding genetic algorithm, is put forward. In this instance, three novel implementations of evolution operators are incorporated. Those are a recombination and two mutation operators. All of the evolution operators are designed with the aim of possessing a big explorative power. Moreover, one of the mutation operators exhibits self-adaptive behavior and the other exhibits adaptive behavior, thereby allowing the algorithm to self-control its own mutability as the search advances. This algorithm also takes advantage of population-elitist selection, acting as a replacement policy, being adopted from evolution strategies. The purpose of this paper (i.e., the first part is to provide theoretical foundations of a robust and advanced instance of the real-coding genetic algorithm having the big potential of being successfully applied to electromagnetic optimization.

  1. Expanding the genetic code of Salmonella with non-canonical amino acids

    Science.gov (United States)

    Gan, Qinglei; Lehman, Brent P.; Bobik, Thomas A.; Fan, Chenguang

    2016-01-01

    The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella. PMID:28008993

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Two proofreading steps amplify the accuracy of genetic code translation.

    Science.gov (United States)

    Ieong, Ka-Weng; Uzun, Ülkü; Selmer, Maria; Ehrenberg, Måns

    2016-11-29

    Aminoacyl-tRNAs (aa-tRNAs) are selected by the messenger RNA programmed ribosome in ternary complex with elongation factor Tu (EF-Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF-Tu. We use tRNA mutants with different affinities for EF-Tu to demonstrate that proofreading of aa-tRNAs occurs in two consecutive steps. First, aa-tRNAs in ternary complex with EF-Tu·GDP are selected in a step where the accuracy increases linearly with increasing aa-tRNA affinity to EF-Tu. Then, following dissociation of EF-Tu·GDP from the ribosome, the accuracy is further increased in a second and apparently EF-Tu-independent step. Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of EF-Tu for fast and accurate protein synthesis, and illustrate the importance of multistep substrate selection in intracellular processing of genetic information.

  7. 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.

  8. On models of the genetic code generated by binary dichotomic algorithms.

    Science.gov (United States)

    Gumbel, Markus; Fimmel, Elena; Danielli, Alberto; Strüngmann, Lutz

    2015-02-01

    In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher.

  9. 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…

  10. 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

  11. [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.

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

    Directory of Open Access Journals (Sweden)

    Jianyong Liu

    2015-01-01

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

  13. Micropropagation and cryopreservation: alternative techniques for conserving plant genetic resources

    Science.gov (United States)

    Genetic resources of vegetatively propagated crops are maintained as growing plants and are often at risk of loss from disease, and environmental hazards. Micropropagation and cryopreservation are used for backup of the temperate fruit, nut and specialty crops held at the National Clonal Germplasm R...

  14. 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

  15. 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.

  16. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-15

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

  18. A probabilistic coding based quantum genetic algorithm for multiple sequence alignment.

    Science.gov (United States)

    Huo, Hongwei; Xie, Qiaoluan; Shen, Xubang; Stojkovic, Vojislav

    2008-01-01

    This paper presents an original Quantum Genetic algorithm for Multiple sequence ALIGNment (QGMALIGN) that combines a genetic algorithm and a quantum algorithm. A quantum probabilistic coding is designed for representing the multiple sequence alignment. A quantum rotation gate as a mutation operator is used to guide the quantum state evolution. Six genetic operators are designed on the coding basis to improve the solution during the evolutionary process. The features of implicit parallelism and state superposition in quantum mechanics and the global search capability of the genetic algorithm are exploited to get efficient computation. A set of well known test cases from BAliBASE2.0 is used as reference to evaluate the efficiency of the QGMALIGN optimization. The QGMALIGN results have been compared with the most popular methods (CLUSTALX, SAGA, DIALIGN, SB_PIMA, and QGMALIGN) results. The QGMALIGN results show that QGMALIGN performs well on the presenting biological data. The addition of genetic operators to the quantum algorithm lowers the cost of overall running time.

  19. Genetic control of the alternative pathway of complement in humans and age-related macular degeneration.

    Science.gov (United States)

    Hecker, Laura A; Edwards, Albert O; Ryu, Euijung; Tosakulwong, Nirubol; Baratz, Keith H; Brown, William L; Charbel Issa, Peter; Scholl, Hendrik P; Pollok-Kopp, Beatrix; Schmid-Kubista, Katharina E; Bailey, Kent R; Oppermann, Martin

    2010-01-01

    Activation of the alternative pathway of complement is implicated in common neurodegenerative diseases including age-related macular degeneration (AMD). We explored the impact of common variation in genes encoding proteins of the alternative pathway on complement activation in human blood and in AMD. Genetic variation across the genes encoding complement factor H (CFH), factor B (CFB) and component 3 (C3) was determined. The influence of common haplotypes defining transcriptional and translational units on complement activation in blood was determined in a quantitative genomic association study. Individual haplotypes in CFH and CFB were associated with distinct and novel effects on plasma levels of precursors, regulators and activation products of the alternative pathway of complement in human blood. Further, genetic variation in CFH thought to influence cell surface regulation of complement did not alter plasma complement levels in human blood. Plasma markers of chronic activation (split-products Ba and C3d) and an activating enzyme (factor D) were elevated in AMD subjects. Most of the elevation in AMD was accounted for by the genetic variation controlling complement activation in human blood. Activation of the alternative pathway of complement in blood is under genetic control and increases with age. The genetic variation associated with increased activation of complement in human blood also increased the risk of AMD. Our data are consistent with a disease model in which genetic variation in the complement system increases the risk of AMD by a combination of systemic complement activation and abnormal regulation of complement activation in local tissues.

  20. 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.

  1. 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.

  2. A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis

    Directory of Open Access Journals (Sweden)

    Van Leeuwen Thomas

    2009-09-01

    Full Text Available Abstract Background Mitochondria (mt contain their own autonomously replicating DNA, constituted as a small circular genome encoding essential subunits of the respiratory chain. Mt DNA is characterized by a genetic code which differs from the standard one. Interestingly, the mt genome of nematodes share some peculiar features, such as small transfer RNAs, truncated ribosomal RNAs and - in the class of Chromadorean nematodes - unidirectional transcription. Findings We present the complete mt genomic sequence (16,791 bp of the plant-parasitic nematode Radopholus similis (class Chromadorea. Although it has a gene content similar to most other nematodes, many idiosyncrasies characterize the extremely AT-rich mt genome of R. similis (85.4% AT. The secondary structure of the large (16S rRNA is further reduced, the gene order is unique, the large non-coding region contains two large repeats, and most interestingly, the UAA codon is reassigned from translation termination to tyrosine. In addition, 7 out of 12 protein-coding genes lack a canonical stop codon and analysis of transcriptional data showed the absence of polyadenylation. Northern blot analysis confirmed that only one strand is transcribed and processed. Furthermore, using nucleotide content bias methods, regions for the origin of replication are suggested. Conclusion The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution.

  3. 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.

  4. 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

  5. A quantum-inspired genetic algorithm based on probabilistic coding for multiple sequence alignment.

    Science.gov (United States)

    Huo, Hong-Wei; Stojkovic, Vojislav; Xie, Qiao-Luan

    2010-02-01

    Quantum parallelism arises from the ability of a quantum memory register to exist in a superposition of base states. Since the number of possible base states is 2(n), where n is the number of qubits in the quantum memory register, one operation on a quantum computer performs what an exponential number of operations on a classical computer performs. The power of quantum algorithms comes from taking advantages of quantum parallelism. Quantum algorithms are exponentially faster than classical algorithms. Genetic optimization algorithms are stochastic search algorithms which are used to search large, nonlinear spaces where expert knowledge is lacking or difficult to encode. QGMALIGN--a probabilistic coding based quantum-inspired genetic algorithm for multiple sequence alignment is presented. A quantum rotation gate as a mutation operator is used to guide the quantum state evolution. Six genetic operators are designed on the coding basis to improve the solution during the evolutionary process. The experimental results show that QGMALIGN can compete with the popular methods, such as CLUSTALX and SAGA, and performs well on the presenting biological data. Moreover, the addition of genetic operators to the quantum-inspired algorithm lowers the cost of overall running time.

  6. 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.

  7. An algorithm for the study of DNA sequence evolution based on the genetic code.

    Science.gov (United States)

    Sirakoulis, G Ch; Karafyllidis, I; Sandaltzopoulos, R; Tsalides, Ph; Thanailakis, A

    2004-11-01

    Recent studies of the quantum-mechanical processes in the DNA molecule have seriously challenged the principle that mutations occur randomly. The proton tunneling mechanism causes tautomeric transitions in base pairs resulting in mutations during DNA replication. The meticulous study of the quantum-mechanical phenomena in DNA may reveal that the process of mutagenesis is not completely random. We are still far away from a complete quantum-mechanical model of DNA sequence mutagenesis because of the complexity of the processes and the complex three-dimensional structure of the molecule. In this paper we have developed a quantum-mechanical description of DNA evolution and, following its outline, we have constructed a classical model for DNA evolution assuming that some aspects of the quantum-mechanical processes have influenced the determination of the genetic code. Conversely, our model assumes that the genetic code provides information about the quantum-mechanical mechanisms of mutagenesis, as the current code is the product of an evolutionary process that tries to minimize the spurious consequences of mutagenesis. Based on this model we develop an algorithm that can be used to study the accumulation of mutations in a DNA sequence. The algorithm has a user-friendly interface and the user can change key parameters in order to study relevant hypotheses.

  8. 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...

  9. Genetic Code Expansion as a Tool to Study Regulatory Processes of Transcription

    Science.gov (United States)

    Schmidt, Moritz; Summerer, Daniel

    2014-02-01

    The expansion of the genetic code with noncanonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-01

    China is the second largest building energy user in the world, ranking first and third in residential and commercial energy consumption. Beginning in the early 1980s, the Chinese government has developed a variety of building energy codes to improve building energy efficiency and reduce total energy demand. This paper studies the impact of building energy codes on energy use and 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.

  11. 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...

  12. Genetic algorithms applied to reconstructing coded imaging of neutrons and analysis of residual watermark.

    Science.gov (United States)

    Zhang, Tiankui; Hu, Huasi; Jia, Qinggang; Zhang, Fengna; Chen, Da; Li, Zhenghong; Wu, Yuelei; Liu, Zhihua; Hu, Guang; Guo, Wei

    2012-11-01

    Monte-Carlo simulation of neutron coded imaging based on encoding aperture for Z-pinch of large field-of-view with 5 mm radius has been investigated, and then the coded image has been obtained. Reconstruction method of source image based on genetic algorithms (GA) has been established. "Residual watermark," which emerges unavoidably in reconstructed image, while the peak normalization is employed in GA fitness calculation because of its statistical fluctuation amplification, has been discovered and studied. Residual watermark is primarily related to the shape and other parameters of the encoding aperture cross section. The properties and essential causes of the residual watermark were analyzed, while the identification on equivalent radius of aperture was provided. By using the equivalent radius, the reconstruction can also be accomplished without knowing the point spread function (PSF) of actual aperture. The reconstruction result is close to that by using PSF of the actual aperture.

  13. Rate-prediction structure complexity analysis for multi-view video coding using hybrid genetic algorithms

    Science.gov (United States)

    Liu, Yebin; Dai, Qionghai; You, Zhixiang; Xu, Wenli

    2007-01-01

    Efficient exploitation of the temporal and inter-view correlation is critical to multi-view video coding (MVC), and the key to it relies on the design of prediction chain structure according to the various pattern of correlations. In this paper, we propose a novel prediction structure model to design optimal MVC coding schemes along with tradeoff analysis in depth between compression efficiency and prediction structure complexity for certain standard functionalities. Focusing on the representation of the entire set of possible chain structures rather than certain typical ones, the proposed model can given efficient MVC schemes that adaptively vary with the requirements of structure complexity and video source characteristics (the number of views, the degrees of temporal and interview correlations). To handle large scale problem in model optimization, we deploy a hybrid genetic algorithm which yields satisfactory results shown in the simulations.

  14. 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.

  15. Improvements of real coded genetic algorithms based on differential operators preventing premature convergence

    CERN Document Server

    Hrstka, O; 10.1016/S0965-9978(03)00113-3

    2009-01-01

    This paper presents several types of evolutionary algorithms (EAs) used for global optimization on real domains. The interest has been focused on multimodal problems, where the difficulties of a premature convergence usually occurs. First the standard genetic algorithm (SGA) using binary encoding of real values and its unsatisfactory behavior with multimodal problems is briefly reviewed together with some improvements of fighting premature convergence. Two types of real encoded methods based on differential operators are examined in detail: the differential evolution (DE), a very modern and effective method firstly published by R. Storn and K. Price, and the simplified real-coded differential genetic algorithm SADE proposed by the authors. In addition, an improvement of the SADE method, called CERAF technology, enabling the population of solutions to escape from local extremes, is examined. All methods are tested on an identical set of objective functions and a systematic comparison based on a reliable method...

  16. 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.

  17. 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.

  18. Simple association of the genetic code with hexagrams of the Book of Changes (I Ching

    Directory of Open Access Journals (Sweden)

    Sergey P. Fedotov

    2016-11-01

    Full Text Available Article "Simple association of the genetic code and hexagrams of the Book of Changes (I Ching" is based on the provisions of previous paper "The genetic code as a structure of the Five elements in Chinese philosophy" where the hypothesis regarding the principles of formation of digrams and trigrams in Chinese philosophy are proposed. It allowed to suggest an idea of digrams and trigrams as a tool for description of DNA codons in the process of their interaction, each with others as an independent oscillator (objects, generating its own natural frequency. On the basis of this hypothesis it is considered the logic of structure of trigrams from the Book of Changes (I Ching, the properties of Start and Stop codons, and the properties of their position in the general order of the King Wen. It is suggested that hexagrams order of King Wen describes dynamics of pulse process in the human body as a process of interaction of amino acids which are programmed by codons on the base of frequency (wavelength peculiarities. In addition, a comparative study of the properties between peptide products (manufactured on the base of research of Institute of Gerontology and Bioregulation – St. Petersburg and the scheme of daily activity of codons are represented.

  19. 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.

  20. Polar body biopsy: a viable alternative to preimplantation genetic diagnosis and screening.

    Science.gov (United States)

    Montag, M; van der Ven, K; Rösing, B; van der Ven, H

    2009-01-01

    Polar body diagnosis (PBD) is a diagnostic method for the indirect genetic analysis of oocytes. Polar bodies are by-products of the meiotic cell cycle, which have no influence on further embryo development. The biopsy of polar bodies can be accomplished either by zona drilling or laser drilling within a very short time period. However, the paternal contribution to the genetic constitution of the developing embryo cannot be diagnosed by PBD. The major application of PBD is the detection of maternally derived chromosomal aneuploidies and translocations in oocytes. For these indications, PBD may offer a viable alternative to blastomere biopsy as the embryo's integrity remains unaffected, in contrast to preimplantation genetic diagnosis (PGD) by blastomere biopsy. The rapid pace of developments in the field of molecular diagnostics will also influence the advantages of PBD, and probably allow more general diagnostic applications in the future.

  1. The clinical and molecular genetic features of idiopathic infantile periodic alternating nystagmus.

    Science.gov (United States)

    Thomas, Mervyn G; Crosier, Moira; Lindsay, Susan; Kumar, Anil; Thomas, Shery; Araki, Masasuke; Talbot, Chris J; McLean, Rebecca J; Surendran, Mylvaganam; Taylor, Katie; Leroy, Bart P; Moore, Anthony T; Hunter, David G; Hertle, Richard W; Tarpey, Patrick; Langmann, Andrea; Lindner, Susanne; Brandner, Martina; Gottlob, Irene

    2011-03-01

    Periodic alternating nystagmus consists of involuntary oscillations of the eyes with cyclical changes of nystagmus direction. It can occur during infancy (e.g. idiopathic infantile periodic alternating nystagmus) or later in life. Acquired forms are often associated with cerebellar dysfunction arising due to instability of the optokinetic-vestibular systems. Idiopathic infantile periodic alternating nystagmus can be familial or occur in isolation; however, very little is known about the clinical characteristics, genetic aetiology and neural substrates involved. Five loci (NYS1-5) have been identified for idiopathic infantile nystagmus; three are autosomal (NYS2, NYS3 and NYS4) and two are X-chromosomal (NYS1 and NYS5). We previously identified the FRMD7 gene on chromosome Xq26 (NYS1 locus); mutations of FRMD7 are causative of idiopathic infantile nystagmus influencing neuronal outgrowth and development. It is unclear whether the periodic alternating nystagmus phenotype is linked to NYS1, NYS5 (Xp11.4-p11.3) or a separate locus. From a cohort of 31 X-linked families and 14 singletons (70 patients) with idiopathic infantile nystagmus we identified 10 families and one singleton (21 patients) with periodic alternating nystagmus of which we describe clinical phenotype, genetic aetiology and neural substrates involved. Periodic alternating nystagmus was not detected clinically but only on eye movement recordings. The cycle duration varied from 90 to 280 s. Optokinetic reflex was not detectable horizontally. Mutations of the FRMD7 gene were found in all 10 families and the singleton (including three novel mutations). Periodic alternating nystagmus was predominantly associated with missense mutations within the FERM domain. There was significant sibship clustering of the phenotype although in some families not all affected members had periodic alternating nystagmus. In situ hybridization studies during mid-late human embryonic stages in normal tissue showed restricted

  2. An Alternative Coding System Defining the Total and Severity of Wear

    Science.gov (United States)

    1996-04-01

    of fluid which may be retated to the severity of wear that has occurred in the sampled machine. A 20 to 30ml plastic bottle provides an adequate...University of Wales Swansea Abstract: A ferrous debris monitor is described which is capable of measuring the concentration of ferrous wear debris ...suspended in a lubricant and the severity of wear associated with particle size of this suspended debris . A coding system is proposed : PQ index(total

  3. 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.

  4. Nonlinear System Identification with a Real–Coded Genetic Algorithm (RCGA

    Directory of Open Access Journals (Sweden)

    Cherif Imen

    2015-12-01

    Full Text Available This paper is devoted to the blind identification problem of a special class of nonlinear systems, namely, Volterra models, using a real-coded genetic algorithm (RCGA. The model input is assumed to be a stationary Gaussian sequence or an independent identically distributed (i.i.d. process. The order of the Volterra series is assumed to be known. The fitness function is defined as the difference between the calculated cumulant values and analytical equations in which the kernels and the input variances are considered. Simulation results and a comparative study for the proposed method and some existing techniques are given. They clearly show that the RCGA identification method performs better in terms of precision, time of convergence and simplicity of programming.

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    Adam Hudson Buchanan

    2016-05-01

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

  7. Analysis of genetic interaction networks shows that alternatively spliced genes are highly versatile.

    Science.gov (United States)

    Talavera, David; Sheoran, Ritika; Lovell, Simon C

    2013-01-01

    Alternative splicing has the potential to increase the diversity of the transcriptome and proteome. Where more than one transcript arises from a gene they are often so different that they are quite unlikely to have the same function. However, it remains unclear if alternative splicing generally leads to a gene being involved in multiple biological processes or whether it alters the function within a single process. Knowing that genetic interactions occur between functionally related genes, we have used them as a proxy for functional versatility, and have analysed the sets of genes of two well-characterised model organisms: Caenorhabditis elegans and Drosophila melanogaster. Using network analyses we find that few genes are functionally homogenous (only involved in a few functionally-related biological processes). Moreover, there are differences between alternatively spliced genes and genes with a single transcript; specifically, genes with alternatively splicing are, on average, involved in more biological processes. Finally, we suggest that factors other than specific functional classes determine whether a gene is alternatively spliced.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

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

    Science.gov (United States)

    Ezzat, Shereen

    2008-10-01

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

  14. 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...

  15. An orthogonalized platform for genetic code expansion in both bacteria and eukaryotes.

    Science.gov (United States)

    Italia, James S; Addy, Partha Sarathi; Wrobel, Chester J J; Crawford, Lisa A; Lajoie, Marc J; Zheng, Yunan; Chatterjee, Abhishek

    2017-02-13

    In this study, we demonstrate the feasibility of expanding the genetic code of Escherichia coli using its own tryptophanyl-tRNA synthetase and tRNA (TrpRS-tRNA(Trp)) pair. This was made possible by first functionally replacing this endogenous pair with an E. coli-optimized counterpart from Saccharomyces cerevisiae, and then reintroducing the liberated E. coli TrpRS-tRNA(Trp) pair into the resulting strain as a nonsense suppressor, which was then followed by its directed evolution to genetically encode several new unnatural amino acids (UAAs). These engineered TrpRS-tRNA(Trp) variants were also able to drive efficient UAA mutagenesis in mammalian cells. Since bacteria-derived aminoacyl-tRNA synthetase (aaRS)-tRNA pairs are typically orthogonal in eukaryotes, our work provides a general strategy to develop additional aaRS-tRNA pairs that can be used for UAA mutagenesis of proteins expressed in both E. coli and eukaryotes.

  16. 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

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

    Science.gov (United States)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.

    1983-01-01

    A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

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

    CERN Document Server

    Baianu,I C

    2004-01-01

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

  3. 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.

  4. 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.

  5. [New alternatives in the prevention of iron deficiency. Use of genetic engineering in food modification].

    Science.gov (United States)

    García-Casal, M N

    1999-09-01

    This article reviews the possible applications of new food biotechnology techniques to introduce some compounds into plants or animals. The potential for these plant modification methods has ample applications ranging from improvements in food production and development for human consumption, production of antibodies or therapeutic proteins, inclusion of nutrients to improve nutritional value of the food to production of vaccines. It must be clear though that currently the scope and consequences of such modifications are not completely clear. There is some concern about potential secondary effects and the hypothesis of the appearance of new viruses due to recombinant genetical transformations that have not been totally rejected. However the tendency is towards considering the process as safe. Finally some evidence is presented about the possibility of introducing the capacity to synthesize vitamin A in vegetables or produce rice with high content of iron as real alternatives to fight some of the nutritional deficiencies most common worldwide.

  6. 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.

  7. 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

  8. 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 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.

  9. 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.

  10. 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...

  11. 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...

  12. Annual review of genetics. Volume 21

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, A.

    1987-01-01

    This book contains 20 articles on genetics. Some of the titles are: Behavioral Genetics of Paramecium, Natural Variation in the Genetic Code, Alternative Promoters in Developmental Gene Expression, Oncogene Activation by Chromosome Translocation in Human Malignancy, The Genetic System, the Deme, and the Origin of the Species, and RNA 3' End Formation in the Control of Gene Expression.

  13. 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.

  14. Clinical and genetic analysis in alternating hemiplegia of childhood: ten new patients from Southern Europe.

    Science.gov (United States)

    Vila-Pueyo, Marta; Pons, Roser; Raspall-Chaure, Miquel; Marcé-Grau, Anna; Carreño, Oriel; Sintas, Cèlia; Cormand, Bru; Pineda-Marfà, Mercè; Macaya, Alfons

    2014-09-15

    Alternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder featuring attacks of hemiplegia and other paroxysmal and non-paroxysmal manifestations leading to progressive neurological impairment. De novo mutations in ATP1A3 have been identified in up to 80% of patients. AHC is also associated with rare mutations in other genes involved in episodic neurological disorders. We sought to find mutations in ATP1A3, CACNA1A, ATP1A2, SCN1A and SLC2A1 in a cohort of ten unrelated patients from Spain and Greece. All patients fulfilled AHC diagnostic criteria. All five genes were amplified by PCR and Sanger sequenced. Copy number variation (CNV) analysis of SLC2A1 and CACNA1A was performed using two different approaches. We identified three previously described heterozygous missense ATP1A3 mutations (p.Asp801Asn, p.Glu815Lys and p.Gly947Arg) in five patients. No disease-causing mutations were found in the remaining genes. All mutations occurred de novo; carriers presented on average earlier than non-carriers. Intellectual disability was more severe with the p.Glu815Lys variant. A p.Gly947Arg carrier harbored a maternally-inherited CACNA1A p.Ala454Thr variant. Of note, three of our patients exhibited remarkable clinical responses to the ketogenic diet. We confirmed ATP1A3 mutations in half of our patients. Further AHC genetic studies will need to investigate large rearrangements in ATP1A3 or consider greater genetic heterogeneity than previously suspected.

  15. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis.

    Science.gov (United States)

    Cavalier-Smith, T

    2001-01-01

    I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later

  16. 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.

  17. 利用遗传算法构造QC-LDPC码%Construction of QC-LDPC Codes with Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    郑丹玲; 穆攀; 田凯; 袁建国

    2015-01-01

    A new method is proposed to construct a large girth quasi-cyclic low density parity check( QC-LDPC) code with Genetic Algorithm( GA) by consideration of LDPC codes under the influence of girth. This method depends on computer search,uses GA repeatedly,improves girth step by step. A large girth is obtained,at the same time LDPC codes with a quasi-cyclic structure is constructed. Analysis shows its complexity has a linear relationship with code length. Simulation results illustrate that when the bit error rate(BER) is 10-6 QC-LDPC codes constructed with the new method has net coding gain(NCG) of 0. 15 dB,0. 5 dB,0. 2 dB over LDPC code based on Euclidean Geometry,Gallager random codes and Mackay random codes,respectively,and it is easy to restore and be implemented in hardware because of quasi-cy-clic structure.%考虑到围长(girth)对低密度奇偶校验(LDPC)码的影响,提出了一种利用遗传算法构造大girth的准循环LDPC( QC-LDPC)码的新方法。该方法借助于计算机搜索,多次运用遗传算法,分步提高girth,在得到大girth 的同时,构造出具有准循环结构的LDPC码。分析发现,该构造方法的复杂度与码长成线性关系。仿真结果表明:在误码率( BER)为10-6时,新方法构造的QC-LDPC码比基于欧式几何构造方法、Gallager和Mackay构造法分别获得约0.15 dB、0.5 dB和0.2 dB的净编码增益( NCG),且因具有准循环结构更易于存储和硬件实现。

  18. Genetic analysis of coding SNPs in blood-brain barrier transporter MDR1 in European Parkinson's disease patients.

    Science.gov (United States)

    Funke, Claudia; Soehn, Anne S; Tomiuk, Juergen; Riess, Olaf; Berg, Daniela

    2009-04-01

    Parkinson's disease (PD) is characterized by the loss of dopaminergic neurons and the presence of intracytoplasmic inclusions (Lewy bodies). Iron, which is elevated in the substantia nigra of PD patients, seems to be of pivotal importance, because of its capacity to enhance the amplification of reactive oxygen species. As iron enters and exits the brain via transport proteins in the blood-brain barrier (BBB), these proteins may represent candidates for a genetic susceptibility to PD. P-glycoprotein (P-gp) is one important efflux pump in the BBB. There is evidence that the function of P-gp is impaired in PD patients. In the current study we examined ten coding single nucleotide polymorphisms in the multidrug resistance gene 1 (MDR1) encoding P-gp to assess whether certain genotypes are associated with PD. However, genotyping of 300 PD patients and 302 healthy controls did not reveal a significant association between coding MDR1 gene polymorphisms and PD.

  19. [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.

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

    Science.gov (United States)

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

    2015-08-01

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

  1. 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

  2. An automatic modeling system of the reaction mechanisms for chemical vapor deposition processes using real-coded genetic algorithms.

    Science.gov (United States)

    Takahashi, Takahiro; Nakai, Hiroyuki; Kinpara, Hiroki; Ema, Yoshinori

    2011-09-01

    The identification of appropriate reaction models is very helpful for developing chemical vapor deposition (CVD) processes. In this study, we have developed an automatic system to model reaction mechanisms in the CVD processes by analyzing the experimental results, which are cross-sectional shapes of the deposited films on substrates with micrometer- or nanometer-sized trenches. We designed the inference engine to model the reaction mechanism in the system by the use of real-coded genetic algorithms (RCGAs). We studied the dependence of the system performance on two methods using simple genetic algorithms (SGAs) and the RCGAs; the one involves the conventional GA operators and the other involves the blend crossover operator (BLX-alpha). Although we demonstrated that the systems using both the methods could successfully model the reaction mechanisms, the RCGAs showed the better performance with respect to the accuracy and the calculation cost for identifying the models.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.)

    Science.gov (United States)

    Lepais, Olivier; Manicki, Aurélie; Glise, Stéphane; Buoro, Mathieu; Bardonnet, Agnès

    2017-01-01

    Alternative mating tactics have important ecological and evolutionary implications and are determined by complex interactions between environmental and genetic factors. Here, we study the genetic effect and architecture of the variability in reproductive tactics among Atlantic salmon males which can either mature sexually early in life in freshwater or more commonly only after completing a migration at sea. We applied the latent environmental threshold model (LETM), which provides a conceptual framework linking individual status to a threshold controlling the decision to develop alternative traits, in an innovative experimental design using a semi-natural river which allowed for ecologically relevant phenotypic expression. Early male parr maturation rates varied greatly across families (10 to 93%) which translated into 90% [64–100%] of the phenotypic variation explained by genetic variation. Three significant QTLs were found for the maturation status, however only one collocated with a highly significant QTL explaining 20.6% of the variability of the maturation threshold located on chromosome 25 and encompassing a locus previously shown to be linked to sea age at maturity in anadromous Atlantic salmon. These results provide new empirical illustration of the relevance of the LETM for a better understanding of alternative mating tactics evolution in natural populations. PMID:28281522

  9. 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.

  10. 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.

  11. 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.

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

    Science.gov (United States)

    Wohlin, Åsa

    2015-03-21

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

  13. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection

    Science.gov (United States)

    Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

    2012-01-01

    Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg2+ concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon–anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell. PMID:22190491

  14. Functional testing strategy for coding genetic variants of unclear significance in MLH1 in Lynch syndrome diagnosis.

    Science.gov (United States)

    Hinrichsen, Inga; Schäfer, Dieter; Langer, Deborah; Köger, Nicole; Wittmann, Margarethe; Aretz, Stefan; Steinke, Verena; Holzapfel, Stefanie; Trojan, Jörg; König, Rainer; Zeuzem, Stefan; Brieger, Angela; Plotz, Guido

    2015-02-01

    Lynch syndrome is caused by inactivating mutations in the MLH1 gene, but genetic variants of unclear significance frequently preclude diagnosis. Functional testing can reveal variant-conferred defects in gene or protein function. Based on functional defect frequencies and clinical applicability of test systems, we developed a functional testing strategy aimed at efficiently detecting pathogenic defects in coding MLH1 variants. In this strategy, tests of repair activity and expression are prioritized over analyses of subcellular protein localization and messenger RNA (mRNA) formation. This strategy was used for four unclear coding MLH1 variants (p.Asp41His, p.Leu507Phe, p.Gln689Arg, p.Glu605del + p.Val716Met). Expression was analyzed using a transfection system, mismatch repair (MMR) activity by complementation in vitro, mRNA formation by reverse transcriptase-PCR in carrier lymphocyte mRNA, and subcellular localization with dye-labeled fusion constructs. All tests included clinically meaningful controls. The strategy enabled efficient identification of defects in two unclear variants: the p.Asp41His variant showed loss of MMR activity, whereas the compound variant p.Glu605del + p.Val716Met had a defect of expression. This expression defect was significantly stronger than the pathogenic expression reference variant analyzed in parallel, therefore the defect of the compound variant is also pathogenic. Interestingly, the expression defect was caused additively by both of the compound variants, at least one of which is non-pathogenic when occurring by itself. Tests were neutral for p.Leu507Phe and p.Gln689Arg, and the results were consistent with available clinical data. We finally discuss the improved sensitivity and efficiency of the applied strategy and its limitations in analyzing unclear coding MLH1 variants.

  15. 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.

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

    OpenAIRE

    Carola Kleemann

    2013-01-01

    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 a...

  17. 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.

  18. A Genetic Variant (COMT) Coding Dopaminergic Activity Predicts Personality Traits in Healthy Elderly.

    Science.gov (United States)

    Kotyuk, Eszter; Duchek, Janet; Head, Denise; Szekely, Anna; Goate, Alison M; Balota, David A

    2015-08-01

    Association studies between the NEO five factor personality inventory and COMT rs4680 have focused on young adults and the results have been inconsistent. However, personality and cortical changes with age may put older adults in a more sensitive range for detecting a relationship. The present study examined associations of COMT rs4680 and personality in older adults. Genetic association analyses were carried out between the NEO and the targeted COMT rs4680 in a large, well-characterized sample of healthy, cognitively normal older adults (N = 616, mean age = 69.26 years). Three significant associations were found: participants with GG genotype showed lower mean scores on Neuroticism (p = 0.039) and higher scores on Agreeableness (p = 0.020) and Conscientiousness (p = 0.006) than participants with AA or AG genotypes. These results suggest that older adults with higher COMT enzymatic activity (GG), therefore lower dopamine level, have lower Neuroticism scores, and higher Agreeableness and Conscientiousness scores. This is consistent with a recent model of phasic and tonic dopamine release suggesting that even though GG genotype is associated with lower tonic dopamine release, the phasic release of dopamine might be optimal for a more adaptive personality profile.

  19. 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.…

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Game Bozo – genetics: a didactic proposal as an alternative to DNA replication of teaching in high school

    Directory of Open Access Journals (Sweden)

    Letícia de Oliveira Rosa

    2016-12-01

    Full Text Available Today, despite hearing much talking about the DNA molecule in newspapers, magazines, news and TV programs, it is still perceived many difficulties for the students to assimilate the concepts and understand the gene processes. Faced with this reality is that the idea of creating a playful activity arose, as a methodological tool, in order to arouse the interest of students to study scientific concepts addressed in genetics education, including those involved in the DNA replication process. The game was developed by students of Biological Sciences Degree, the IFAM (Federal Institute of Science and Technology Amazon in Molecular Genetics discipline. Which, inspired by the traditional game Bozó, created the Bozó-genetic game, which consists of playing the dice, adding the numbers present on the faces of the dice and score according to the rules of the game. A simple, low cost and efficient alternative in transmission of scientific knowledge easily and interactively, with the possibility of aid student and teacher in the teaching-learning process.

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

    Science.gov (United States)

    Mitchison, A

    1997-01-01

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

  7. Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.

    Directory of Open Access Journals (Sweden)

    Feng-Jie Sun

    Full Text Available Transfer RNA (tRNA molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.

  8. 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.

  9. Symptom dimensions as alternative phenotypes to address genetic heterogeneity in schizophrenia and bipolar disorder.

    Science.gov (United States)

    Labbe, Aurélie; Bureau, Alexandre; Moreau, Isabel; Roy, Marc-André; Chagnon, Yvon; Maziade, Michel; Merette, Chantal

    2012-11-01

    This study introduces a novel way to use the lifetime ratings of symptoms of psychosis, mania and depression in genetic linkage analysis of schizophrenia (SZ) and bipolar disorder (BP). It suggests using a latent class model developed for family data to define more homogeneous symptom subtypes that are influenced by a smaller number of genes that will thus be more easily detectable. In a two-step approach, we proposed: (i) to form homogeneous clusters of subjects based on the symptom dimensions and (ii) to use the information from these homogeneous clusters in linkage analysis. This framework was applied to a unique SZ and BP sample composed of 1278 subjects from 48 large kindreds from the Eastern Quebec population. The results suggest that our strategy has the power to increase linkage signals previously obtained using the diagnosis as phenotype and allows for a better characterization of the linkage signals. This is the case for a linkage signal, which we formerly obtained in chromosome 13q and enhanced using the dimension mania. The analysis also suggests that the methods may detect new linkage signals not previously uncovered by using diagnosis alone, as in chromosomes 2q (delusion), 15q (bizarre behavior), 7p (anhedonia) and 9q (delusion). In the case of the 15q and 2q region, the results coincide with linkage signals detected in other studies. Our results support the view that dissecting phenotypic heterogeneity by modeling symptom dimensions may provide new insights into the genetics of SZ and BP.

  10. Simulation of alternative genetic control systems for Aedes aegypti in outdoor cages and with a computer

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, C.F.; Lorimer, N.; Rai, K.S.; Suguna, S.G.; Uppal, D.K.; Kazmi, S.J.; Hallinan, E.; Dietz, K.

    1976-06-01

    Cycling populations of A. aegypti of wild origin were established in outdoor cages. Releases were then made for 32 to 43 days of either males carrying chromosome translocations cr males of the sex ratio distorter type. The translocation caused a maximum of 50% sterility, but this declined rapidly after termination of releases. The distorter males depressed the proportion of females among the pupae produced in the cage to a minimum of 35% and the distortion of sex ratio persisted for 13 weeks following termination of releases. It was possible to simulate the effects of the releases with a computer. Simulations were aslo made of standard release schedules of three types of genetic material. A strain carrying both sex ratio distortion and a translocation gave the most effective population suppression.

  11. 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.

  12. Newborn genetic identification: a protocol using microsatellite DNA as an alternative to footprinting.

    Science.gov (United States)

    de Pancorbo, M M; Rodríguez-Alarcón, J; Castro, A; Fernández-Fernández, I; Melchor, J C; Linares, A; García-Orad, A; Fernández-Llebrez del Rey, L; Aranguren, G; Santillana, L

    1997-07-04

    Newborn identification by foot- or finger-printing presents serious drawbacks. This study proposes an alternative method based on DNA analysis of blood-spots taken from the newborn child. CSF1PO, TPOX and TH01 microsatellite loci were chosen to develop a fast and reliable protocol to be applied in cases where it is suspected that newborn children have been exchanged. The advantage of these loci is that one can simultaneously amplify them by PCR multiplex reaction and determine their alleles, thereby reducing the time needed for identification tests. Moreover, the amplification products of these loci are very small (< 350 bp) and so can be analyzed in samples with degraded DNA. We have been able to prove that it is possible to obtain results in blood-spots taken from newborns up to 13 years before and kept at room temperature. Thus the protocol proposed here can be applied in long-term post-natal identification cases.

  13. Genetic parameters and alternatives for evaluation and ranking of Nellore young bulls in pasture performance tests

    Directory of Open Access Journals (Sweden)

    Breno de Oliveira Fragomeni

    2013-08-01

    Full Text Available The objective of this study was to estimate (covariance components for weight at 550 days, average daily gain and an index with both traits, and to compare alternatives for evaluation and ranking of Nellore young bulls in pasture performance tests. The heritability estimates were 0.73, 0.31 and 0.44 for weight at 550 days, average daily gain and index, respectively. Animals were ranked according to their predicted breeding values or the phenotypic deviations in relation to the mean of the test. Although the correlations between breeding values and phenotypic deviations were high, there were differences in the number of animals selected in common when the selection criteria were the predicted breeding values or the phenotypic deviations. Mixed models are more appropriate than the least squares method and should be utilized in the evaluation of young bulls in performance tests.

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

    Science.gov (United States)

    Francis, Brian R.

    2015-01-01

    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 polyesters and

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

    Science.gov (United States)

    Francis, Brian R

    2015-02-11

    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 polyesters and

  16. 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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Daniel San Juan Orta

    2016-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

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

  20. MATLAB code to estimate landslide volume from single remote sensed image using genetic algorithm and imagery similarity measurement

    Science.gov (United States)

    Wang, Ting-Shiuan; Yu, Teng-To; Lee, Shing-Tsz; Peng, Wen-Fei; Lin, Wei-Ling; Li, Pei-Ling

    2014-09-01

    Information regarding the scale of a hazard is crucial for the evaluation of its associated impact. Quantitative analysis of landslide volume immediately following the event can offer better understanding and control of contributory factors and their relative importance. Such information cannot be gathered for each landslide event, owing to limitations in obtaining useable raw data and the necessary procedures of each applied technology. Empirical rules are often used to predict volume change, but the resulting accuracy is very low. Traditional methods use photogrammetry or light detection and ranging (LiDAR) to produce a post-event digital terrain model (DTM). These methods are both costly and time-intensive. This study presents a technique to estimate terrain change volumes quickly and easily, not only reducing waiting time but also offering results with less than 25% error. A genetic algorithm (GA) programmed MATLAB is used to intelligently predict the elevation change for each pixel of an image. This deviation from the pre-event DTM becomes a candidate for the post-event DTM. Thus, each changed DTM is converted into a shadow relief image and compared with a single post-event remotely sensed image for similarity ranking. The candidates ranked in the top two thirds are retained as parent chromosomes to produce offspring in the next generation according to the rules of GAs. When the highest similarity index reaches 0.75, the DTM corresponding to that hillshade image is taken as the calculated post-event DTM. As an example, a pit with known volume is removed from a flat, inclined plane to demonstrate the theoretical capability of the code. The method is able to rapidly estimate the volume of terrain change within an error of 25%, without the delays involved in obtaining stereo image pairs, or the need for ground control points (GCPs) or professional photogrammetry software.

  1. 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.

  2. 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 ...

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  4. The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework.

    Science.gov (United States)

    Gile, Gillian H; Novis, Philip M; Cragg, David S; Zuccarello, Giuseppe C; Keeling, Patrick J

    2009-01-01

    The systematics of the green algal class Ulvophyceae have been difficult to resolve with ultrastructural and molecular phylogenetic analyses. Therefore, we investigated relationships among ulvophycean orders by determining the distribution of two discrete genetic characters previously identified only in the order Dasycladales. First, Acetabularia acetabulum uses the core translation GTPase Elongation Factor 1alpha (EF-1alpha) while most Chlorophyta instead possess the related GTPase Elongation Factor-Like (EFL). Second, the nuclear genomes of dasycladaleans A. acetabulum and Batophora oerstedii use a rare non-canonical genetic code in which the canonical termination codons TAA and TAG instead encode glutamine. Representatives of Ulvales and Ulotrichales were found to encode EFL, while Caulerpales, Dasycladales, Siphonocladales, and Ignatius tetrasporus were found to encode EF-1alpha, in congruence with the two major lineages previously proposed for the Ulvophyceae. The EF-1alpha of I. tetrasporus supports its relationship with Caulerpales/Dasycladales/Siphonocladales, in agreement with ultrastructural evidence, but contrary to certain small subunit rRNA analyses that place it with Ulvales/Ulotrichales. The same non-canonical genetic code previously described in A. acetabulum was observed in EF-1alpha sequences from Parvocaulis pusillus (Dasycladales), Chaetomorpha coliformis, and Cladophora cf. crinalis (Siphonocladales), whereas Caulerpales use the universal code. This supports a sister relationship between Siphonocladales and Dasycladales and further refines our understanding of ulvophycean phylogeny.

  5. 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.

  6. 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....

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

    Science.gov (United States)

    Plomin, Robert; Davis, Oliver S. P.

    2009-01-01

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

  8. 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......'-untranslated region, and the coding region of the GLUT4 gene showed four polymorphisms, all single nucleotide substitutions, positioned at -581, 1, 30, and 582. None of the three changes in the regulatory region of the gene had any major influence on expression of the GLUT4 gene in muscle. The variant at 582...... 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...

  9. 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.

  10. 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

  11. 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.

  12. Speaking Code

    DEFF Research Database (Denmark)

    Cox, Geoff

    ; 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...... 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...... 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. 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.

  14. Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology.

    Science.gov (United States)

    Scherrer, Klaus; Jost, Jürgen

    2007-10-01

    , as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon.

  15. 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.

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

    NARCIS (Netherlands)

    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.

    2016-01-01

    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 the

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

    Science.gov (United States)

    Demongeot, J; Hazgui, H

    2016-12-01

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

  18. Synthetic lethal genetic interactions that decrease somatic cell proliferation in Caenorhabditis elegans identify the alternative RFC CTF18 as a candidate cancer drug target.

    Science.gov (United States)

    McLellan, Jessica; O'Neil, Nigel; Tarailo, Sanja; Stoepel, Jan; Bryan, Jennifer; Rose, Ann; Hieter, Philip

    2009-12-01

    Somatic mutations causing chromosome instability (CIN) in tumors can be exploited for selective killing of cancer cells by knockdown of second-site genes causing synthetic lethality. We tested and statistically validated synthetic lethal (SL) interactions between mutations in six Saccharomyces cerevisiae CIN genes orthologous to genes mutated in colon tumors and five additional CIN genes. To identify which SL interactions are conserved in higher organisms and represent potential chemotherapeutic targets, we developed an assay system in Caenorhabditis elegans to test genetic interactions causing synthetic proliferation defects in somatic cells. We made use of postembryonic RNA interference and the vulval cell lineage of C. elegans as a readout for somatic cell proliferation defects. We identified SL interactions between members of the cohesin complex and CTF4, RAD27, and components of the alternative RFC(CTF18) complex. The genetic interactions tested are highly conserved between S. cerevisiae and C. elegans and suggest that the alternative RFC components DCC1, CTF8, and CTF18 are ideal therapeutic targets because of their mild phenotype when knocked down singly in C. elegans. Furthermore, the C. elegans assay system will contribute to our knowledge of genetic interactions in a multicellular animal and is a powerful approach to identify new cancer therapeutic targets.

  19. Linkage relationships among five enzyme-coding gene loci in the copepod Tigriopus californicus: a genetic confirmation of achiasmiatic meiosis.

    Science.gov (United States)

    Burton, R S; Feldman, M W; Swisher, S G

    1981-12-01

    Linkage relationships among five polymorphic enzyme-coding gene loci in the marine copepod Tigriopus californicus have been determined using electrophoretic analysis of progeny from laboratory matings. Phosphoglucose isomerase (PGI; EC 5.3.1.9) was found to be tightly linked to glutamate-pyruvate transaminase (GPT; EC 2.6..1.2), with only one recombinant observed in 364 progeny; glutamate-oxaloacetate transaminase (GOT; EC 2.6.1.1) is linked to the PGI-GPT pair, with a recombination fraction of approximately 0.20 in male double heterozygotes. Phosphoglucomutase (PGM; EC 2.7.5.1) and an esterase (EST; EC 3.1.1.1) are not linked to the PGI, GPT, GOT grouping, which has been designated linkage group I. Reciprocal crosses have revealed that no recombination occurs in female T. californicus; this observation confirms a previous report that meiosis in female Tigriopus is achiasmatic.

  20. 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.

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

    Science.gov (United States)

    Pierrel, Jérôme

    2012-01-01

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

  2. 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.

  3. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA editing, and a novel genetic code.

    Science.gov (United States)

    Lavrov, Dennis V; Pett, Walker; Voigt, Oliver; Wörheide, Gert; Forget, Lise; Lang, B Franz; Kayal, Ehsan

    2013-04-01

    Sponges (phylum Porifera) are a large and ancient group of morphologically simple but ecologically important aquatic animals. Although their body plan and lifestyle are relatively uniform, sponges show extensive molecular and genetic diversity. In particular, mitochondrial genomes from three of the four previously studied classes of Porifera (Demospongiae, Hexactinellida, and Homoscleromorpha) have distinct gene contents, genome organizations, and evolutionary rates. Here, we report the mitochondrial genome of Clathrina clathrus (Calcinea, Clathrinidae), a representative of the fourth poriferan class, the Calcarea, which proves to be the most unusual. Clathrina clathrus mitochondrial DNA (mtDNA) consists of six linear chromosomes 7.6-9.4 kb in size and encodes at least 37 genes: 13 protein codings, 2 ribosomal RNAs (rRNAs), and 24 transfer RNAs (tRNAs). Protein genes include atp9, which has now been found in all major sponge lineages, but no atp8. Our analyses further reveal the presence of a novel genetic code that involves unique reassignments of the UAG codons from termination to tyrosine and of the CGN codons from arginine to glycine. Clathrina clathrus mitochondrial rRNAs are encoded in three (srRNA) and ≥6 (lrRNA) fragments distributed out of order and on several chromosomes. The encoded tRNAs contain multiple mismatches in the aminoacyl acceptor stems that are repaired posttranscriptionally by 3'-end RNA editing. Although our analysis does not resolve the phylogenetic position of calcareous sponges, likely due to their high rates of mitochondrial sequence evolution, it confirms mtDNA as a promising marker for population studies in this group. The combination of unusual mitochondrial features in C. clathrus redefines the extremes of mtDNA evolution in animals and further argues against the idea of a "typical animal mtDNA."

  4. 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.

  5. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

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

  6. Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 (MC1R) gene in Tibetan pigs and Landrace pigs.

    Science.gov (United States)

    Liu, Rui; Jin, Long; Long, Keren; Chai, Jie; Ma, Jideng; Tang, Qianzi; Tian, Shilin; Hu, Yaodong; Lin, Ling; Wang, Xun; Jiang, Anan; Li, Xuewei; Li, Mingzhou

    2016-01-10

    Domestication and subsequent selective pressures have produced a large variety of pig coat colors in different regions and breeds. The melanocortin 1 receptor (MC1R) gene plays a crucial role in determining coat color of mammals. Here, we investigated genetic diversity and selection at the coding region of the porcine melanocortin receptor 1 (MC1R) in Tibetan pigs and Landrace pigs. By contrast, genetic variability was much lower in Landrace pigs than in Tibetan pigs. Meanwhile, haplotype analysis showed that Tibetan pigs possessed shared haplotypes, suggesting a possibility of recent introgression event by way of crossbreeding with neighboring domestic pigs or shared ancestral polymorphism. Additionally, we detected positive selection at the MC1R in both Tibetan pigs and Landrace pigs through the dN/dS analysis. These findings suggested that novel phenotypic change (dark coat color) caused by novel mutations may help Tibetan pigs against intensive solar ultraviolet (UV) radiation and camouflage in wild environment, whereas white coat color in Landrace were intentionally selected by human after domestication. Furthermore, both the phylogenetic analysis and the network analysis provided clues that MC1R in Asian and European wild boars may have initially experienced different selective pressures, and MC1R alleles diversified in modern domesticated pigs.

  7. Genetics of gliadins coded by the group 1 chromosomes in the high-quality bread wheat cultivar Neepawa.

    Science.gov (United States)

    Dachkevitch, T; Redaelli, R; Biancardi, A M; Metakovsky, E V; Pogna, N E

    1993-04-01

    The inheritance and biochemical properties of gliadins controlled by the group 1 chromosomes of the high-quality bread wheat cultivar Neepawa were studied in the progeny of the cross Neepawa x Costantino by six different electrophoretic procedures. Chromosome 1B of Neepawa contains two gliadin loci, one (Gli-B1) coding for at least six ω- or γ-gliadins, the other (Gli-B3) controlling the synthesis of gliadin N6 only. The map distance between these loci was calculated as 22.1 cM. Amongst the chromosome 1A gliadins, three proteins are encoded at the Gli-A1 locus whereas polypeptides N14-N15-N16 are controlled by a remote locus which recombines with Gli-A1. Six other gliadins are controlled by a gene cluster at Gli-D1 on chromosome 1D. Canadian wheat cultivars sharing the Gli-B1 allele of Neepawa were found to differ in the presence or absence of gliadin N6. The electrophoretic mobilities of proteins N6 and N14-N15-N16 were unaffected by the addition of a reducing agent during two-dimensional sodium dodecyl sulphate polyacrylamid-gel electrophoresis, suggesting the absence of intra-chain disulphide bonds in their structure.

  8. 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.

  9. 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

  10. 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.

  11. Expression of Drosophila mushroom body mutations in alternative genetic backgrounds: a case study of the mushroom body miniature gene (mbm).

    Science.gov (United States)

    de Belle, J S; Heisenberg, M

    1996-01-01

    Mutations in 12 genes regulating Drosophila melanogaster mushroom body (MB) development were each studied in two genetic backgrounds. In all cases, brain structure was qualitatively or quantitatively different after replacement of the "original" genetic background with that of the Canton Special wild-type strain. The mushroom body miniature gene (mbm) was investigated in detail. mbm supports the maintenance of MB Kenyon cell fibers in third instar larvae and their regrowth during metamorphosis. Adult mbm1 mutant females are lacking many or most Kenyon cell fibers and are impaired in MB-mediated associative odor learning. We show here that structural defects in mbm1 are apparent only in combination with an X-linked, dosage-dependent modifier (or modifiers). In the Canton Special genetic background, the mbm1 anatomical phenotype is suppressed, and MBs develop to a normal size. However, the olfactory learning phenotype is not fully restored, suggesting that submicroscopic defects persist in the MBs. Mutant mbm1 flies with full-sized MBs have normal retention but show a specific acquisition deficit that cannot be attributed to reductions in odor avoidance, shock reactivity, or locomotor behavior. We propose that polymorphic gene interactions (in addition to ontogenetic factors) determine MB size and, concomitantly, the ability to recognize and learn odors. Images Fig. 1 Fig. 2 Fig. 3 PMID:8790424

  12. Expression of Drosophila mushroom body mutations in alternative genetic backgrounds: a case study of the mushroom body miniature gene (mbm).

    Science.gov (United States)

    de Belle, J S; Heisenberg, M

    1996-09-03

    Mutations in 12 genes regulating Drosophila melanogaster mushroom body (MB) development were each studied in two genetic backgrounds. In all cases, brain structure was qualitatively or quantitatively different after replacement of the "original" genetic background with that of the Canton Special wild-type strain. The mushroom body miniature gene (mbm) was investigated in detail. mbm supports the maintenance of MB Kenyon cell fibers in third instar larvae and their regrowth during metamorphosis. Adult mbm1 mutant females are lacking many or most Kenyon cell fibers and are impaired in MB-mediated associative odor learning. We show here that structural defects in mbm1 are apparent only in combination with an X-linked, dosage-dependent modifier (or modifiers). In the Canton Special genetic background, the mbm1 anatomical phenotype is suppressed, and MBs develop to a normal size. However, the olfactory learning phenotype is not fully restored, suggesting that submicroscopic defects persist in the MBs. Mutant mbm1 flies with full-sized MBs have normal retention but show a specific acquisition deficit that cannot be attributed to reductions in odor avoidance, shock reactivity, or locomotor behavior. We propose that polymorphic gene interactions (in addition to ontogenetic factors) determine MB size and, concomitantly, the ability to recognize and learn odors.

  13. 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.

  14. Use of genetic algorithms for optimization of subchannel simulations; Application des algorithmes genetiques pour l'optimisation d'un code d'analyse des sous-canaux d'une grappe de combustible nucleaire

    Energy Technology Data Exchange (ETDEWEB)

    Nava Dominguez, A

    2004-07-01

    To facilitate the modeling of a rod fuel bundle, the most common used method consist in dividing the complex cross-sectional area in small subsections called subchannels. To close the system equations, a mixture model is used to represent the intersubchannel interactions. These interactions are as follows: diversion cross-flow, turbulent void diffusion, void drift and buoyancy drift. Amongst these mechanisms, the turbulent void diffusion and void drift are frequently modelled using diffusion coefficients. In this work, a novel approach has been employed where an existing subchannel code coupled to a genetic algorithm code which were used to optimize these coefficients. After several numerical simulations, a new objective function based in the principle of minimum dissipated energy was developed. The use of this function in the genetic algorithm coupled to the subchannel code, gave results in good agreement with the experimental data.

  15. 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.

  16. 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.

  17. The potential of genetically-engineered pigs in providing an alternative source of organs and cells for transplantation.

    Science.gov (United States)

    Cooper, David K C; Hara, Hidetaka; Ezzelarab, Mohamed; Bottino, Rita; Trucco, Massimo; Phelps, Carol; Ayares, David; Dai, Yifan

    2013-07-01

    There is a critical shortage of organs, cells, and corneas from deceased human donors worldwide. There are also shortages of human blood for transfusion. A potential solution to all of these problems is the transplantation of organs, cells, and corneas from a readily available animal species, such as the pig, and the transfusion of red blood cells from pigs into humans. However, to achieve these ends, major immunologic and other barriers have to be overcome. Considerable progress has been made in this respect by the genetic modification of pigs to protect their tissues from the primate immune response and to correct several molecular incompatibilities that exist between pig and primate. These have included knockout of genes responsible for the expression of major antigenic targets for primate natural anti-pig antibodies, insertion of human complement- and coagulation-regulatory transgenes, and knockdown of swine leukocyte antigens that stimulate the primate's adaptive immune response. As a result of these manipulations, the administration of novel immunosuppressive agents, and other innovations, pig hearts have now functioned in baboons for 6-8 months, pig islets have maintained normoglycemia in diabetic monkeys for > 1 year, and pig corneas have maintained transparency for several months. Clinical trials of pig islet transplantation are already in progress. Future developments will involve further genetic manipulations of the organ-source pig, with most of the genes that are likely to be beneficial already identified.

  18. Structural and spectroscopic studies of water-alkaline earth ion micro clusters: an alternate approach using genetic algorithm in conjunction with quantum chemical methods

    Science.gov (United States)

    Ganguly Neogi, S.; Chaudhury, P.

    2014-08-01

    We present an approach of using a stochastic optimization technique namely genetic algorithm in association with quantum chemical methods to first elucidate structure and then infrared spectroscopy and thermochemistry of water-alkaline earth metal ion clusters. We show that an initial determination of structure using stochastic techniques and following it up with quantum chemical calculation can lead to much faster convergence to high quality structures for these systems. Infrared spectroscopic, thermochemical calculations and natural population analysis based charges on the central metal ions are done to further ascertain the correctness of the structures using our technique. We have done a comparative study with a pure density functional theory calculation and have shown that even for very poor starting guess geometries genetic algorithm in conjunction with density functional theory indeed converges to global structure while pure density functional theory can encounter problems in certain situations to arrive at global geometry. We have also discussed usefulness of Unimodal Normal distribution crossover for handling situation with real coded variables.

  19. 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.

  20. Natural genetic and induced plant resistance, as a control strategy to plant-parasitic nematodes alternative to pesticides.

    Science.gov (United States)

    Molinari, Sergio

    2011-03-01

    Plant-parasitic nematodes are pests of a wide range of economically important crops, causing severe losses to agriculture. Natural genetic resistance of plants is expected to be a valid solution of the many problems nematodes cause all over the world. Progress in resistance applications is particularly important for the less-developed countries of tropical and subtropical regions, since use of resistant cultivars may be the only possible and economically feasible control strategy in those farming systems. Resistance is being considered of particular importance also in modern high-input production systems of developed countries, as the customary reliance on chemical nematicides has been restricted or has come to an end. This review briefly describes the genetic bases of resistance to nematodes in plants and focuses on the chances and problems of its exploitation as a key element in an integrated management program. Much space is dedicated to the major problem of resistance durability, in that the intensive use of resistant cultivars is likely to increasingly induce the selection of virulent populations able to "break" the resistance. Protocols of pest-host suitability are described, as bioassays are being used to evaluate local nematode populations in their potential to be selected on resistant germplasm and endanger resistant crops. The recent progress in using robust and durable resistances against nematodes as an efficient method for growers in vegetable cropping systems is reported, as well as the possible use of chemicals that do not show any unfavorable impact on environment, to induce in plants resistance against plant-parasitic nematodes.

  1. 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

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

    Directory of Open Access Journals (Sweden)

    Tom Kashiwagi

    2015-08-01

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

  3. 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.

  4. Validation of alternative capillary electrophoresis detection of STRs using POP-6 polymer and a 22cm array on a 3130xl genetic analyzer.

    Science.gov (United States)

    Connon, Catherine C; LeFebvre, Aaron K; Benjamin, Robert C

    2016-05-01

    The goal of this project was to reduce capillary electrophoresis detection time on a 3130xl Genetic Analyzer for amplification product obtained from 4-dye and 5-dye STR amplification kits while still generating high quality STR profiles. This was accomplished by utilizing a more viscous polymer (POP-6™) and a shorter array (22 cm) than that which are typically used (POP-4(®) polymer and a 36 cm array) for human identification purposes. Spatial calibration and detection run modules were modified in response to the use of this polymer/array combination and to reduce detection time. Alternative detection resulted in 24-28 min run times, as compared to ∼45 min using traditional POP-4(®)/36 cm detection methods. POP-6™/22 cm detection run modules were validated for use with 4-dye Promega STR kits (e.g., PowerPlex(®) 16 and PowerPlex(®) 16HS) and 5-dye Life Technologies kits (e.g., Identifiler(®) and Identifiler(®) Plus). Three hundred ninety-five samples, controls and allelic ladders were used for the validation studies, which consisted of a comparison of alternative POP-6™/22 cm detection to traditional POP-4(®)/36 cm (including reproducibility/concordance of allele calls, resolution, ILS sizing quality, peak height and pass rates), a sizing study (precision and accuracy) and a sensitivity study to obtain a usable range of injection times. Compared to traditional POP-4(®)/36 cm detection, alternative detection resulted in 100% reproducible and concordant alleles, the ability to achieve one base resolution, slightly reduced ILS sizing quality, slightly reduced peak height and statistically similar pass rates (α=0.05). It should be noted that alternative detection offered improved resolution over that of traditional for amplicons less than ∼200 b, but had reduced resolution for products greater than ∼200 b. Additionally, alternative detection yielded acceptable precision and accuracy of sizing using Life Technologies criteria (POP-6™ polymer on a

  5. 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.

  6. Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.

    Science.gov (United States)

    Viollet, Louis; Glusman, Gustavo; Murphy, Kelley J; Newcomb, Tara M; Reyna, Sandra P; Sweney, Matthew; Nelson, Benjamin; Andermann, Frederick; Andermann, Eva; Acsadi, Gyula; Barbano, Richard L; Brown, Candida; Brunkow, Mary E; Chugani, Harry T; Cheyette, Sarah R; Collins, Abigail; DeBrosse, Suzanne D; Galas, David; Friedman, Jennifer; Hood, Lee; Huff, Chad; Jorde, Lynn B; King, Mary D; LaSalle, Bernie; Leventer, Richard J; Lewelt, Aga J; Massart, Mylynda B; Mérida, Mario R; Ptáček, Louis J; Roach, Jared C; Rust, Robert S; Renault, Francis; Sanger, Terry D; Sotero de Menezes, Marcio A; Tennyson, Rachel; Uldall, Peter; Zhang, Yue; Zupanc, Mary; Xin, Winnie; Silver, Kenneth; Swoboda, Kathryn J

    2015-01-01

    Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clusteredin exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K(26%) and 11 had G947R (8%) mutations [corrected].Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

  7. 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.

  8. 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.

  9. Autocatalysis, information and coding.

    Science.gov (United States)

    Wills, P R

    2001-01-01

    Autocatalytic self-construction in macromolecular systems requires the existence of a reflexive relationship between structural components and the functional operations they perform to synthesise themselves. The possibility of reflexivity depends on formal, semiotic features of the catalytic structure-function relationship, that is, the embedding of catalytic functions in the space of polymeric structures. Reflexivity is a semiotic property of some genetic sequences. Such sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts. Autocatalytic selection is a mechanism whereby matter becomes differentiated in primitive biochemical systems. In the case of coding self-organisation, it corresponds to the creation of symbolic information. Prions are present-day entities whose replication through autocatalysis reflects aspects of biological semiotics less obvious than genetic coding.

  10. PI Parameter Optimization Method Based on the Floating-Point Coded Genetic Algorithm%基于浮点数编码遗传算法的PI参数优化算法

    Institute of Scientific and Technical Information of China (English)

    何同祥; 韩宁青; 李洪亮; 常保春

    2011-01-01

    This article introduces PID parameter optimization method based on the floating-point coded genetic algorithm, using the performance index -time squared integral of the error as the objective function, making use of the global search ability of genetic algorithm to achieve an optimum solution of the optimization, to reduce the difficulty to design PID performance, and overall improve system performance. The simulation results show that coded by floating-point genetic algorithm parameter optimization enables system PI has a good dynamic quality and steady state characteristics.%本文介绍了基于浮点数编码遗传算法寻优的PID参数优化方法,采用误差绝对值时间平方积分性能指标作为参数选择的目标函数,利用遗传算法的全局搜索能力,实现对全局最优解的寻优,以降低PID参数整定的难度,达到总体提高系统性能的目的.仿真结果表明,通过浮点数编码遗传算法进行PI参数优化可使系统具有很好的动态品质和稳态特性.

  11. 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**).

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. Study on Bar-coding of Wheat Variety Based on Genetic Diversity of Seed Storage Protein%基于籽粒贮藏蛋白遗传多样性的小麦条形码研究

    Institute of Scientific and Technical Information of China (English)

    康志钰; 王建军

    2012-01-01

    为便于小麦品种管理及保护,针对植物DNA条形码研制存在的问题,以36份品种为材料,分析其HMW-GS和醇溶蛋白组分,并根据谱带的有无,对谱带进行数量化处理,存在的谱带标为1,不存在的谱带标为0,建立谱带二进制代码,再转化为十进制代码,最后通过数据整合,建立了小麦品种身份识别码,并将其转换为条形码,研制出基于籽粒贮藏蛋白遗传多样性的小麦身份识别码制作方法,使原来需要用119位数字表明的品种间差距现在只需37位数字即可表示出来。%To be convenient for the management and protection of wheat varieties, and aimed at the problems on DNA bar-coding of plant, the high molecular weight gluten subunit (HMW-GS) and gli- adin of 36 wheat varieties were investigated and used to establish their codes. By number processing, according to the presence and absence of the bands as presence of band was signed with "1" and ab- sence of band was signed with "0", the binary code system was established and then the binary code system was translated into decimal code system, finally, the identification code system of wheat varie- ty was established through the conformity of data, and translated the identification code for bar-cod- ing. An method for the identification code system of wheat was built based on the genetic diversity of seed storage protein. In this way, the difference between the varieties could be distinguished by 37 digits, instead of 119 digits used in the past.

  17. 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

  18. Polar Codes

    Science.gov (United States)

    2014-12-01

    QPSK Gaussian channels . .......................................................................... 39 vi 1. INTRODUCTION Forward error correction (FEC...Capacity of BSC. 7 Figure 5. Capacity of AWGN channel . 8 4. INTRODUCTION TO POLAR CODES Polar codes were introduced by E. Arikan in [1]. This paper...Under authority of C. A. Wilgenbusch, Head ISR Division EXECUTIVE SUMMARY This report describes the results of the project “More reliable wireless

  19. Differential expression of long non-coding RNAs in three genetic lines of rainbow trout (Oncorhynchus mykiss) in response to infection with Flavobacterium psychrophilum

    Science.gov (United States)

    Bacterial cold-water disease caused by Flavobacterium psychrophilum is one of the major causes of mortality of salmonids. Three genetic lines of rainbow trout designated as ARS-Fp-R (resistant), ARS-Fp-C (control) and ARS-Fp-S (susceptible) have significant differences in survival rate following F. ...

  20. 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.)

  1. Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory.

    Science.gov (United States)

    Balázs, András

    2006-08-01

    A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.

  2. 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

  3. 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

  4. 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

  5. Quantum Genetic Algorithm Based on Angle Coding of 3D%基于3D角度编码的量子遗传算法

    Institute of Scientific and Technical Information of China (English)

    钱国红; 黄德才

    2012-01-01

    为了充分利用量子态在算法中的量子特性,提高算法的搜索效率,减少存储空间,提出了一种基于3D角度编码的量子遗传算法.该算法将量子位描述为3D球面坐标下的一对相位角,充分利用了量子的空间运动特性,并引入一种自适应旋转角大小和方向的确定方案,从而进一步简化了染色体的更新和变异过程,而且使算法的量子特性、存储性能、时间性能都得到很大的提高.仿真结果表明,其在算法优化效率和搜索能力上都优于简单遗传算法和普通量子遗传算法.%In order to make full use of the quantum characteristics of the quantum state in the algorithm, and improve the search efficiency,reduce storage space,a new quantum genetic algorithm called 3D-AQGA was proposed. The algorithm describes quantum bit as a pair of angles in 3D spherical coordinate, makes full use of the quantum space motion characteristics,and introduces a kind of adaptive scheme to calculate the rotation angle size and direction which not only makes the process of chromosome's update and variation simplified,but also improves quantum characteristics,storage properties and time performance of the algorithm greatly . The simulation results show that the efficiency of the algorithm and the search ability are superior to the simple genetic algorithm and common quantum genetic algorithm.

  6. Some possible codes for encrypting data in DNA.

    Science.gov (United States)

    Smith, Geoff C; Fiddes, Ceridwyn C; Hawkins, Jonathan P; Cox, Jonathan P L

    2003-07-01

    Three codes are reported for storing written information in DNA. We refer to these codes as the Huffman code, the comma code and the alternating code. The Huffman code was devised using Huffman's algorithm for constructing economical codes. The comma code uses a single base to punctuate the message, creating an automatic reading frame and DNA which is obviously artificial. The alternating code comprises an alternating sequence of purines and pyrimidines, again creating DNA that is clearly artificial. The Huffman code would be useful for routine, short-term storage purposes, supposing--not unrealistically--that very fast methods for assembling and sequencing large pieces of DNA can be developed. The other two codes would be better suited to archiving data over long periods of time (hundreds to thousands of years).

  7. 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.)

  8. 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.

  9. 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....

  10. 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 seen

  11. 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

  12. Genetic identification of cryptic genospecies of Haemophilus causing urogenital and neonatal infections by PCR using specific primers targeting genes coding for 16S rRNA.

    Science.gov (United States)

    Quentin, R; Ruimy, R; Rosenau, A; Musser, J M; Christen, R

    1996-06-01

    Previous genetic analysis of Haemophilus influenzae strains isolated from genital and neonatal infections identified a group of biotype IV that constitutes a cryptic genospecies only distantly related to H. influenzae and H. Haemolyticus. Small-subunit rRNA genes of two representative strains of this genital Haemophilus genospecies (strains 16N and 2406) were sequenced. The analysis indicated that these strains form a monophyletic unit with H. haemolyticus and H. influenzae biogroups Influenzae and Aegyptius and are more closely related to H. haemolyticus than to H. influenzae biogroups Influenzae and Aegyptius. 16S rRNA gene sequences were used to formulate primers for PCR-based identification of cryptic genital Haemophilus organisms. A 242-bp fragment was amplified from strains belonging to the genital Haemophilus genospecies but not from strains of 12 other Haemophilus species, including strains of H. influenzae biotype IV sensu stricto.

  13. A NOVEL VARIABLE-LENGTH CODE FOR ROBUST VIDEO CODING

    Institute of Scientific and Technical Information of China (English)

    Ma Linhua; Chang Yilin

    2006-01-01

    A novel Variable-Length Code (VLC), called Alternate VLC (AVLC), is proposed in this letter,which employs two types of VLC to encode source symbols alternately. Its advantage is that it can not only stop the symbol error propagation effect, but also correct symbol insertion errors and avoid symbol deletion errors, so the original sequence number of symbols can be kept correctly, which is very important in video communication.

  14. i-Review: Sharing Code

    Directory of Open Access Journals (Sweden)

    Jonas Kubilius

    2014-02-01

    Full Text Available Sharing code is becoming increasingly important in the wake of Open Science. In this review I describe and compare two popular code-sharing utilities, GitHub and Open Science Framework (OSF. GitHub is a mature, industry-standard tool but lacks focus towards researchers. In comparison, OSF offers a one-stop solution for researchers but a lot of functionality is still under development. I conclude by listing alternative lesser-known tools for code and materials sharing.

  15. 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...

  16. 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

  17. 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.

  18. Does the human brain have unique genetically determined networks coding logical and ethical principles and aesthetics? From Plato to novel mirror networks.

    Science.gov (United States)

    Agnati, Luigi Francesco; Agnati, Achille; Mora, Francisco; Fuxe, Kjell

    2007-08-01

    Starting from the assumption that philosophers carry out "experiments" not on concrete objects, but on concepts and relationships between concepts, it could be postulated that the philosopher's way to proceed is not basically different from that followed by scientists. From this similarity of approaches it can be considered that some philosophical problems and theories have a high impact on how to address scientific investigations. One of these issues is certainly the philosophical debate over innate ideas, which is central to the conflict between rationalist and empiricist epistemologies. We started our reflections on the possible presence of innate ideas in the human brain from the observation that there exists strong experimental support for the view that not only complex behaviours (e.g., sexual courtship, parental care) but also aesthetic and ethic judgements can be, at least in part, genetically determined. On these grounds it is suggested that neurobiological findings can give important contributions to the philosophical debate on innatism by putting forward possible explanatory models and heuristic hypotheses.

  19. Decoding the productivity code

    DEFF Research Database (Denmark)

    Hansen, David

    .e., to be prepared to initiate improvement. The study shows how the effectiveness of the improvement system depends on the congruent fit between the five elements as well as the bridging coherence between the improvement system and the work system. The bridging coherence depends on how improvements are activated...... approach often ends up with demanding intense employee focus to sustain improvement and engagement. Likewise, a single-minded employee development approach often ends up demanding rationalization to achieve the desired financial results. These ineffective approaches make organizations react like pendulums...... that swing between rationalization and employee development. The productivity code is the lack of alternatives to this ineffective approach. This thesis decodes the productivity code based on the results from a 3-year action research study at a medium-sized manufacturing facility. During the project period...

  20. Pol II CTD Code Light.

    Science.gov (United States)

    Corden, Jeffry L

    2016-01-21

    In this issue of Molecular Cell, Schüller et al. (2016) and Suh et al. (2016) describe genetic and mass spectrometry methodologies for mapping phosphorylation sites on the tandem repeats of the RNA polymerase II CTD. The results suggest that the CTD Code may be simpler than expected.

  1. 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.

  2. Surgical navigation with QR codes

    Directory of Open Access Journals (Sweden)

    Katanacho Manuel

    2016-09-01

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

  3. 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...

  4. Function Optimization Based on Quantum Genetic Algorithm

    OpenAIRE

    Ying Sun; Hegen Xiong

    2014-01-01

    Optimization method is important in engineering design and application. Quantum genetic algorithm has the characteristics of good population diversity, rapid convergence and good global search capability and so on. It combines quantum algorithm with genetic algorithm. A novel quantum genetic algorithm is proposed, which is called Variable-boundary-coded Quantum Genetic Algorithm (vbQGA) in which qubit chromosomes are collapsed into variable-boundary-coded chromosomes instead of binary-coded c...

  5. Function Optimization Based on Quantum Genetic Algorithm

    OpenAIRE

    Ying Sun; Yuesheng Gu; Hegen Xiong

    2013-01-01

    Quantum genetic algorithm has the characteristics of good population diversity, rapid convergence and good global search capability and so on.It combines quantum algorithm with genetic algorithm. A novel quantum genetic algorithm is proposed ,which is called variable-boundary-coded quantum genetic algorithm (vbQGA) in which qubit chromosomes are collapsed into variableboundary- coded chromosomes instead of binary-coded chromosomes. Therefore much shorter chromosome strings can be gained.The m...

  6. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2016-08-01

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

  8. The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts.

    Directory of Open Access Journals (Sweden)

    Luboš Majeský

    Full Text Available Dandelions (genus Taraxacum comprise a group of sexual diploids and apomictic polyploids with a complicated reticular evolution. Apomixis (clonal reproduction through seeds in this genus is considered to be obligate, and therefore represent a good model for studying the role of asexual reproduction in microevolutionary processes of apomictic genera. In our study, a total of 187 apomictic individuals composing a set of nine microspecies (sampled across wide geographic area in Europe were genotyped for six microsatellite loci and for 162 amplified fragment length polymorphism (AFLP markers. Our results indicated that significant genetic similarity existed within accessions with low numbers of genotypes. Genotypic variability was high among accessions but low within accessions. Clustering methods discriminated individuals into nine groups corresponding to their phenotypes. Furthermore, two groups of apomictic genotypes were observed, which suggests that they had different asexual histories. A matrix compatibility test suggests that most of the variability within accession groups was mutational in origin. However, the presence of recombination was also detected. The accumulation of mutations in asexual clones leads to the establishment of a network of clone mates. However, this study suggests that the clones primarily originated from the hybridisation between sexual and apomicts.

  9. The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts.

    Science.gov (United States)

    Majeský, Luboš; Vašut, Radim J; Kitner, Miloslav; Trávníček, Bohumil

    2012-01-01

    Dandelions (genus Taraxacum) comprise a group of sexual diploids and apomictic polyploids with a complicated reticular evolution. Apomixis (clonal reproduction through seeds) in this genus is considered to be obligate, and therefore represent a good model for studying the role of asexual reproduction in microevolutionary processes of apomictic genera. In our study, a total of 187 apomictic individuals composing a set of nine microspecies (sampled across wide geographic area in Europe) were genotyped for six microsatellite loci and for 162 amplified fragment length polymorphism (AFLP) markers. Our results indicated that significant genetic similarity existed within accessions with low numbers of genotypes. Genotypic variability was high among accessions but low within accessions. Clustering methods discriminated individuals into nine groups corresponding to their phenotypes. Furthermore, two groups of apomictic genotypes were observed, which suggests that they had different asexual histories. A matrix compatibility test suggests that most of the variability within accession groups was mutational in origin. However, the presence of recombination was also detected. The accumulation of mutations in asexual clones leads to the establishment of a network of clone mates. However, this study suggests that the clones primarily originated from the hybridisation between sexual and apomicts.

  10. [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.

  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. Space Time Codes from Permutation Codes

    CERN Document Server

    Henkel, Oliver

    2006-01-01

    A new class of space time codes with high performance is presented. The code design utilizes tailor-made permutation codes, which are known to have large minimal distances as spherical codes. A geometric connection between spherical and space time codes has been used to translate them into the final space time codes. Simulations demonstrate that the performance increases with the block lengths, a result that has been conjectured already in previous work. Further, the connection to permutation codes allows for moderate complex en-/decoding algorithms.

  13. 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

  14. Alternative metrics

    Science.gov (United States)

    2012-11-01

    As the old 'publish or perish' adage is brought into question, additional research-impact indices, known as altmetrics, are offering new evaluation alternatives. But such metrics may need to adjust to the evolution of science publishing.

  15. Simulation of life-cycle efficiency of lamb and wool production for genetic levels of component traits and alternative management options.

    Science.gov (United States)

    Wang, C T; Dickerson, G E

    1991-11-01

    A deterministic computer model was used to predict effects of genetic improvements in performance and of management options on life-cycle flock TDN input per unit of empty body weight (EBW) or carcass lean (CLN) equivalent value of market lamb, cull ewe, and wool output from a pure breeding system of sheep production for sheep fed to maintain normal weight. Relative values per kilogram for market lambs, cull ewes, and clean wool were 1 to .33 to 2.04 in lamb empty body equivalent, but 1 to .33 to 1 in lamb carcass lean equivalent. A 10% increase in lamb viability improved TDN/EBW or CLN by -15 to -20% for high to low lambing rates. Corresponding smaller gains were -7 to -11% for fertility, -3 to -13% for lambing rate, -1 to -3% for wool growth rate, -1 to -5% for milk production without creep feeding, -2 to -1% for mature size to about 70 kg, and -.6 to -.9% for precocity of fertility. Increasing leanness 10% improved TDN/CLN by -3 to -1% but increased TDN/EBW 3% because of higher maintenance requirements of leaner sheep. Higher protein requirements for increased lambing rate, milk production or leanness, or greater increases in non-feed than in feed costs, would mean only slightly less reduction of TDN/output than shown. Creep feeding was beneficial only for prolific, low-milking stock. Flushing reduced adverse effects of restricted feeding. Different values for wool vs meat or for costs of feed vs non-feed inputs would change results. These estimates for relative economic importance of traits apply to derivation of optimum criteria for selection among breeds or crosses, or within-breeds used in rotation crossbreeding, but would differ for specialized terminal-sire or maternal breed roles.

  16. 用EXCEL中的VBA编写“质量性状遗传分析”相关程序及其在农业上的应用%Coding Programs in Genetic Analysis of Quality Traits by VBA of EXCEL Applied in Agriculture

    Institute of Scientific and Technical Information of China (English)

    杨振宇; 杨海智; 杨信东

    2012-01-01

    Excel是常用的电子表格处理软件,笔者采用基于Excel的VBA编程方法,编写了“质量性状遗传分析”有关程序,经教学和农业科研工作中使用,获得了理想的效果.%The Excel is a commonly used sheet-processing software. Using Excel-based VBA programming methods, we coded programs for genetic analysis of quality traits. The programs have been used successfully in our teaching and agricultural research work. This article discussed the source code and application methods of the programs.

  17. 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.

  18. Imaging The Genetic Code of a Virus

    Science.gov (United States)

    Graham, Jenna; Link, Justin

    2013-03-01

    Atomic Force Microscopy (AFM) has allowed scientists to explore physical characteristics of nano-scale materials. However, the challenges that come with such an investigation are rarely expressed. In this research project a method was developed to image the well-studied DNA of the virus lambda phage. Through testing and integrating several sample preparations described in literature, a quality image of lambda phage DNA can be obtained. In our experiment, we developed a technique using the Veeco Autoprobe CP AFM and mica substrate with an appropriate absorption buffer of HEPES and NiCl2. This presentation will focus on the development of a procedure to image lambda phage DNA at Xavier University. The John A. Hauck Foundation and Xavier University

  19. Genetic code expansion for multiprotein complex engineering.

    Science.gov (United States)

    Koehler, Christine; Sauter, Paul F; Wawryszyn, Mirella; Girona, Gemma Estrada; Gupta, Kapil; Landry, Jonathan J M; Fritz, Markus Hsi-Yang; Radic, Ksenija; Hoffmann, Jan-Erik; Chen, Zhuo A; Zou, Juan; Tan, Piau Siong; Galik, Bence; Junttila, Sini; Stolt-Bergner, Peggy; Pruneri, Giancarlo; Gyenesei, Attila; Schultz, Carsten; Biskup, Moritz Bosse; Besir, Hueseyin; Benes, Vladimir; Rappsilber, Juri; Jechlinger, Martin; Korbel, Jan O; Berger, Imre; Braese, Stefan; Lemke, Edward A

    2016-12-01

    We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, 'MultiBacTAG', (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure-function studies of novel eukaryotic complexes using single-molecule Förster resonance energy transfer as well as site-specific crosslinking strategies.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. Magnetostrictive Alternator

    Science.gov (United States)

    Dyson, Rodger; Bruder, Geoffrey

    2013-01-01

    This innovation replaces the linear alternator presently used in Stirling engines with a continuous-gradient, impedance-matched, oscillating magnetostrictive transducer that eliminates all moving parts via compression, maintains high efficiency, costs less to manufacture, reduces mass, and eliminates the need for a bearing system. The key components of this new technology are the use of stacked magnetostrictive materials, such as Terfenol-D, under a biased magnetic and stress-induced compression, continuous-gradient impedance-matching material, coils, force-focusing metallic structure, and supports. The acoustic energy from the engine travels through an impedancematching layer that is physically connected to the magnetostrictive mass. Compression bolts keep the structure under compressive strain, allowing for the micron-scale compression of the magnetostrictive material and eliminating the need for bearings. The relatively large millimeter displacement of the pressure side of the impedance-matching material is reduced to micron motion, and undergoes stress amplification at the magnetostrictive interface. The alternating compression and expansion of the magnetostrictive material creates an alternating magnetic field that then induces an electric current in a coil that is wound around the stack. This produces electrical power from the acoustic pressure wave and, if the resonant frequency is tuned to match the engine, can replace the linear alternator that is commonly used.

  5. 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...

  6. Alternative Treatments

    Science.gov (United States)

    ... triglyceride (fat) produced by processing coconut oil or palm kernel oil. The body breaks down caprylic acid into substances called “ketone bodies.” The theory behind Axona is that the ketone bodies derived from caprylic acid may provide an alternative energy source for brain cells that have lost ...

  7. 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...... including an outer BCH code correcting a few bit errors....

  8. 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.

  9. Code domains in tandem repetitive DNA sequence structures.

    Science.gov (United States)

    Vogt, P

    1992-10-01

    Traditionally, many people doing research in molecular biology attribute coding properties to a given DNA sequence if this sequence contains an open reading frame for translation into a sequence of amino acids. This protein coding capability of DNA was detected about 30 years ago. The underlying genetic code is highly conserved and present in every biological species studied so far. Today, it is obvious that DNA has a much larger coding potential for other important tasks. Apart from coding for specific RNA molecules such as rRNA, snRNA and tRNA molecules, specific structural and sequence patterns of the DNA chain itself express distinct codes for the regulation and expression of its genetic activity. A chromatin code has been defined for phasing of the histone-octamer protein complex in the nucleosome. A translation frame code has been shown to exist that determines correct triplet counting at the ribosome during protein synthesis. A loop code seems to organize the single stranded interaction of the nascent RNA chain with proteins during the splicing process, and a splicing code phases successive 5' and 3' splicing sites. Most of these DNA codes are not exclusively based on the primary DNA sequence itself, but also seem to include specific features of the corresponding higher order structures. Based on the view that these various DNA codes are genetically instructive for specific molecular interactions or processes, important in the nucleus during interphase and during cell division, the coding capability of tandem repetitive DNA sequences has recently been reconsidered.

  10. 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....

  11. 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

  12. 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

  13. Genetic Discrimination

    Science.gov (United States)

    ... in Genetics Archive Regulation of Genetic Tests Genetic Discrimination Overview Genetic Information Nondiscrimination Act Genetic Discrimination and ... gov/employees/process.cfm Top of page Genetic Discrimination and Other Laws Bill Clinton's Executive Order Prohibiting ...

  14. 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.

  15. 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

  16. [Felines: an alternative in genetic toxicology studies?].

    Science.gov (United States)

    Zamora-Perez, Ana; Gómez-Meda, Belinda C; Ramos-Ibarra, Maria L; Batista-González, Cecilia M; Luna-Aguirre, Jaime; González-Rodríguez, Andrés; Rodríguez-Avila, José L; Zúñiga-González, Guillermo M

    2008-06-01

    The micronuclei (MN) test carry out in peripheral blood is fast, simple, economic and it is used to detect genotoxic environmental agents. MN are fragments of chromosomes or complete chromosomes remaining in the cytoplasm after cell division, which increase when organisms are exposed to genotoxic agents. Therefore, species with the highest values of spontaneous micronucleated erythrocytes (MNE) are the most suitable to be potentials biomonitor of micronucleogenic agents, using a drop of blood. Nine species of Felines that present spontaneous MNE in peripheral blood are shown. From these species, the cat has been previously proven, with positive results and also lion (Panthera leo), yaguaroundi (Felis yagoaroundi), lynx (Lynx ruffus), jaguar (Panthera onca), puma (Puma concolor), tiger (Panthera tigris), ocelote (Felis padalis) and leopard (Panthera pardus) display spontaneous MNE, and with this characteristic this Family can be propose like a potential group to be used in toxicogenetic studies.

  17. 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....

  18. 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....

  19. [The genetics of spinocerebellar ataxias].

    Science.gov (United States)

    Jacobi, H; Minnerop, M; Klockgether, T

    2013-02-01

    Spinocerebellar ataxias are genetically heterogeneous autosomal dominant ataxia disorders. To date more than 30 different subtypes are known. In Germany particularly SCA1, SCA2, SCA3 and SCA6 are prevalent, as well as the less frequent subtypes SCA5, SCA14, SCA15, SCA17 and SCA28. Genetic causes range from coding repeat expansions (polyglutamine diseases), to non-coding expansions as well as conventional mutations. In some subtypes the genetic background is currently unknown. Age of onset, typical clinical findings and geographic distribution may help to reach a correct diagnosis; however a definitive diagnosis requires molecular genetic testing.

  20. 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…

  1. 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.

  2. 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.

  3. Alternative splicing interference by xenobiotics.

    Science.gov (United States)

    Zaharieva, Emanuela; Chipman, J Kevin; Soller, Matthias

    2012-06-14

    The protein coding sequence of most eukaryotic genes (exons) is interrupted by non-coding parts (introns), which are excised in a process termed splicing. To generate a mature messenger RNA (mRNA) hundreds of combinatorial protein-protein and RNA-protein interactions are required to splice out often very large introns with high fidelity and accuracy. Inherent to splicing is the use of alternative splice sites generating immense proteomic diversity from a limited number of genes. In humans, alternative splicing is a major mode of regulating gene expression, occurs in over 90% of genes and is particularly abundant in the brain. Only recently, it has been recognized that the complexity of the splicing process makes it susceptible to interference by various xenobiotics. These compounds include antineoplastic substances, commonly used drugs and food supplements and cause a spectrum of effects ranging from deleterious inhibition of general splicing to highly specific modifications of alternative splicing affecting only certain genes. Alterations in splicing have been implicated in numerous diseases such as cancer and neurodegeneration. Splicing regulation plays an important role in the execution of programmed cell death. The switch between anti- and pro-apoptotic isoforms by alternative splice site selection and misregulation of a number of splicing factors impacts on cell survival and disease. Here, our current knowledge is summarized on compounds interfering with general and alternative splicing and of the current methodology to study changes in these processes relevant to the field of toxicology and future risk assessments.

  4. 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.

  5. 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.

  6. 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.

  7. 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,...

  8. Practices in Code Discoverability

    CERN Document Server

    Teuben, Peter; 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 develop ways in which information about astrophysics codes can be shared. We also discuss why some scientist coders resist sharing or publishing their codes, the reasons for and importance of overcoming this resistance, and alert the community to a reworking of one of the first attempts for sharing codes, the Astrophysics Source Code Library (ASCL). We discuss the implementation of the ASCL in an accompanying poster paper. We suggest that code could be given a similar level of referencing as data gets in repositories such ...

  9. Enhancing QR Code Security

    OpenAIRE

    Zhang, Linfan; Zheng, Shuang

    2015-01-01

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

  10. 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...

  11. 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.

  12. 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

  13. Fountain Codes: LT And Raptor Codes Implementation

    Directory of Open Access Journals (Sweden)

    Ali Bazzi, Hiba Harb

    2017-01-01

    Full Text Available Digital fountain codes are a new class of random error correcting codes designed for efficient and reliable data delivery over erasure channels such as internet. These codes were developed to provide robustness against erasures in a way that resembles a fountain of water. A digital fountain is rateless in a way that sender can send limitless number of encoded packets. The receiver doesn’t care which packets are received or lost as long as the receiver gets enough packets to recover original data. In this paper, the design of the fountain codes is explored with its implementation of the encoding and decoding algorithm so that the performance in terms of encoding/decoding symbols, reception overhead, data length, and failure probability is studied.

  14. 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 ROC...

  15. 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 distributed...

  16. Model and algorithm of optimizing alternate traffic restriction scheme in urban traffic network

    Institute of Scientific and Technical Information of China (English)

    徐光明; 史峰; 刘冰; 黄合来

    2014-01-01

    An optimization model and its solution algorithm for alternate traffic restriction (ATR) schemes were introduced in terms of both the restriction districts and the proportion of restricted automobiles. A bi-level programming model was proposed to model the ATR scheme optimization problem by aiming at consumer surplus maximization and overload flow minimization at the upper-level model. At the lower-level model, elastic demand, mode choice and multi-class user equilibrium assignment were synthetically optimized. A genetic algorithm involving prolonging codes was constructed, demonstrating high computing efficiency in that it dynamically includes newly-appearing overload links in the codes so as to reduce the subsequent searching range. Moreover, practical processing approaches were suggested, which may improve the operability of the model-based solutions.

  17. [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.

  18. 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.

  19. Software Certification - Coding, Code, and Coders

    Science.gov (United States)

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

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

  20. 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...

  1. 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.

  2. 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…

  3. 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.

  4. 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.

  5. 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.

  6. Code of Ethics

    DEFF Research Database (Denmark)

    Adelstein, Jennifer; Clegg, Stewart

    2016-01-01

    Ethical codes have been hailed as an explicit vehicle for achieving more sustainable and defensible organizational practice. Nonetheless, when legal compliance and corporate governance codes are conflated, codes can be used to define organizational interests ostentatiously by stipulating norms...... for employee ethics. Such codes have a largely cosmetic and insurance function, acting subtly and strategically to control organizational risk management and protection. In this paper, we conduct a genealogical discourse analysis of a representative code of ethics from an international corporation...... to understand how management frames expectations of compliance. Our contribution is to articulate the problems inherent in codes of ethics, and we make some recommendations to address these to benefit both an organization and its employees. In this way, we show how a code of ethics can provide a foundation...

  7. 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...

  8. 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.

  9. Serially Concatenated IRA Codes

    CERN Document Server

    Cheng, Taikun; Belzer, Benjamin J

    2007-01-01

    We address the error floor problem of low-density parity check (LDPC) codes on the binary-input additive white Gaussian noise (AWGN) channel, by constructing a serially concatenated code consisting of two systematic irregular repeat accumulate (IRA) component codes connected by an interleaver. The interleaver is designed to prevent stopping-set error events in one of the IRA codes from propagating into stopping set events of the other code. Simulations with two 128-bit rate 0.707 IRA component codes show that the proposed architecture achieves a much lower error floor at higher SNRs, compared to a 16384-bit rate 1/2 IRA code, but incurs an SNR penalty of about 2 dB at low to medium SNRs. Experiments indicate that the SNR penalty can be reduced at larger blocklengths.

  10. 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)

  11. MOLECULAR STRUCTURE RELATED TO GENETIC CODE DEGENERACY AND TWO DIMENSION CLASSIFICATION OF AMINO ACIDS%氨基酸的分子结构与遗传密码简并及二维集合分类

    Institute of Scientific and Technical Information of China (English)

    陈志华; 陈惟昌; 邱红霞; 王自强

    2001-01-01

    According to the degree of degeneracy of genetic codes,64 geneticcodons can be subdivided into two groups,the high degenerate group (3,4,6 triplets degeneracy)and the low degenerate group (single and 2 triplets degeneracy).There are 9 amino acids which belong to the high degenerate group (G,A,S,P,V,T,L,I,R)and 11 amino acids to the low degenerate group (C,N,D,Q,K,E,M,H,F,Y,W).Amino acids of the high degenerate group have relatively simple molecular structure,rather small molecular weights and comparatively concentrated distribution of isoelectric points.While in the low degenerate group,molecular structure is more complex,with relatively large molecular weights,and the distribution of their isoelectric points is more dispersed.Based on the two dimension distribution of molecular weights (M)and isoelectric points (P)of amino acids,a set of classification graph (Venn's diagram)of amino acids can be obtained.The MP classification graph can demonstrate many chemical properties of amino acids,such as:size of molecular weights,degree of degeneracy,polar or non-polar,charged or non-charged,hydrophobic or hydrophilic,and the functional groups of the residues.It is suggested that the amino acids of high degenerate group are mostly small and simple,and constitute the transmembranic structure or the structural domains of protein molecules.So,amino acids of high degenerate group might appear in the early evolution stage.On the other hand,the amino acids of low degenerate group are rather large and complex,and ultimately correlate to the functional domains of protein molecules,then,the amino acids of low degenerate group might appear more lately during evolution.%根据氨基酸遗传密码子的简并程度,可将64个遗传密码子分为高简并度类(3,4,6度简并组)和低简并度类(1,2度简并组)两大类[1]。高简并度类有9个氨基酸,其分子量比较小,等电点的分布比较集中。低简并度类有11个氨基酸,其分子结构

  12. 76 FR 33994 - Alternative Simplified Credit Under Section 41(c)(5)

    Science.gov (United States)

    2011-06-10

    ... Internal Revenue Service 26 CFR Part 1 RIN 1545-BH32 Alternative Simplified Credit Under Section 41(c)(5... alternative simplified credit under section 41(c)(5) of the Internal Revenue Code (Code). The final... alternative simplified credit (ASC) under section 41(c)(5). The ASC was added by the Tax Relief and...

  13. 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 ...

  14. 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....

  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. 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.

  17. 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.

  18. Industrial Computer Codes

    Science.gov (United States)

    Shapiro, Wilbur

    1996-01-01

    This is an overview of new and updated industrial codes for seal design and testing. GCYLT (gas cylindrical seals -- turbulent), SPIRALI (spiral-groove seals -- incompressible), KTK (knife to knife) Labyrinth Seal Code, and DYSEAL (dynamic seal analysis) are covered. CGYLT uses G-factors for Poiseuille and Couette turbulence coefficients. SPIRALI is updated to include turbulence and inertia, but maintains the narrow groove theory. KTK labyrinth seal code handles straight or stepped seals. And DYSEAL provides dynamics for the seal geometry.

  19. The aeroelastic code FLEXLAST

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-09-01

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

  20. Opening up codings?

    DEFF Research Database (Denmark)

    Steensig, Jakob; Heinemann, Trine

    2015-01-01

    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....... Instead we propose that the promise of coding-based research lies in its ability to open up new qualitative questions....

  1. 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...

  2. 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

  3. MORSE Monte Carlo code

    Energy Technology Data Exchange (ETDEWEB)

    Cramer, S.N.

    1984-01-01

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

  4. 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。

  5. Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming.

    Science.gov (United States)

    Ruiz, Sergio; Gore, Athurva; Li, Zhe; Panopoulos, Athanasia D; Montserrat, Nuria; Fung, Ho-Lim; Giorgetti, Alessandra; Bilic, Josipa; Batchelder, Erika M; Zaehres, Holm; Schöler, Hans R; Zhang, Kun; Izpisua Belmonte, Juan Carlos

    2013-01-01

    Recent studies indicate that human-induced pluripotent stem cells contain genomic structural variations and point mutations in coding regions. However, these studies have focused on fibroblast-derived human induced pluripotent stem cells, and it is currently unknown whether the use of alternative somatic cell sources with varying reprogramming efficiencies would result in different levels of genetic alterations. Here we characterize the genomic integrity of eight human induced pluripotent stem cell lines derived from five different non-fibroblast somatic cell types. We show that protein-coding mutations are a general feature of the human induced pluripotent stem cell state and are independent of somatic cell source. Furthermore, we analyse a total of 17 point mutations found in human induced pluripotent stem cells and demonstrate that they do not generally facilitate the acquisition of pluripotency and thus are not likely to provide a selective advantage for reprogramming.

  6. 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.

  7. Modifier effects between regulatory and protein-coding variation.

    Directory of Open Access Journals (Sweden)

    Antigone S Dimas

    2008-10-01

    Full Text Available Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs. We predict that about 18% (1,502 out of 8,233 nsSNPs of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.

  8. Modifier effects between regulatory and protein-coding variation.

    Science.gov (United States)

    Dimas, Antigone S; Stranger, Barbara E; Beazley, Claude; Finn, Robert D; Ingle, Catherine E; Forrest, Matthew S; Ritchie, Matthew E; Deloukas, Panos; Tavaré, Simon; Dermitzakis, Emmanouil T

    2008-10-01

    Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis) is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs). We predict that about 18% (1,502 out of 8,233 nsSNPs) of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants.

  9. 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.

  10. The Study of Parallel Genetic Algorithm Based on Hybrid Coding of Coarse-Grained in Highway Route Optimization%基于混合编码的粗粒度并行遗传算法在公路选线优化中的研究

    Institute of Scientific and Technical Information of China (English)

    刘超群; 陈国; 胡文华

    2016-01-01

    This paper analyzes the necessity of computer software algorithms optimizing highway route design,pointed out as the industry particularity on the highway route optimization,there are still limi-tations in computational efficiency;and proposes a hybrid-purpose-coding coarse-grained parallel ge-netic algorithm to highway route optimization,the use of hybrid-coding technology to streamline the traffic code and sub-thread,the use of coarse-grained parallel genetic algorithm improves the utiliza-tion rate of multi-core CPU,and ultimately improve highway route optimization algorithm efficiency. This paper introduces the principle and process of the algorithm,and develop computer software sys-tems applied to the actual project;and finally,the article summarize that the use of parallel genetic algorithm to solve the optimization problem of highway route is to study the technology used in artifi-cial intelligence algorithms highway route optimization areas, which can mostly improve efficiency and achieve the effect.%首先分析公路选线设计中,采用计算机软件算法进行优化的必要性,指出由于公路选线优化上的行业特殊性,目前在提高计算效率中还存在局限性;提出一种基于混合编码的粗粒度并行遗传算法来进行公路选线优化,利用混合编码技术精简编码和子线程的通信量,利用粗粒度并行遗传算法提高多核心CPU的应用率,最终达到提高公路路线优化算法效率的目的。详细介绍了整个算法的原理和过程,并开发计算机软件系统应用到实际工程中;最后,在总结中认为,采用并行遗传算法来解决公路选线优化问题,是研究人工智能算法技术运用在公路选线优化领域中,最能提升效率并取得效果的一种途径。

  11. Scrum Code Camps

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  12. Pseudonoise code tracking loop

    Science.gov (United States)

    Laflame, D. T. (Inventor)

    1980-01-01

    A delay-locked loop is presented for tracking a pseudonoise (PN) reference code in an incoming communication signal. The loop is less sensitive to gain imbalances, which can otherwise introduce timing errors in the PN reference code formed by the loop.

  13. 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

  14. The materiality of Code

    DEFF Research Database (Denmark)

    Soon, Winnie

    2014-01-01

    , Twitter and Facebook). The focus is not to investigate the functionalities and efficiencies of the code, but to study and interpret the program level of code in order to trace the use of various technological methods such as third-party libraries and platforms’ interfaces. These are important...

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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....

  20. The Aesthetics of Coding

    DEFF Research Database (Denmark)

    Andersen, Christian Ulrik

    2007-01-01

    discusses code as the artist’s material and, further, formulates a critique of Cramer. The seductive magic in computer-generated art does not lie in the magical expression, but nor does it lie in the code/material/text itself. It lies in the nature of code to do something – as if it was magic......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...... 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...

  1. The SIFT Code Specification

    Science.gov (United States)

    1983-01-01

    The specification of Software Implemented Fault Tolerance (SIFT) consists of two parts, the specifications of the SIFT models and the specifications of the SIFT PASCAL program which actually implements the SIFT system. The code specifications are the last of a hierarchy of models describing the operation of the SIFT system and are related to the SIFT models as well as the PASCAL program. These Specifications serve to link the SIFT models to the running program. The specifications are very large and detailed and closely follow the form and organization of the PASCAL code. In addition to describing each of the components of the SIFT code, the code specifications describe the assumptions of the upper SIFT models which are required to actually prove that the code will work as specified. These constraints are imposed primarily on the schedule tables.

  2. 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.

  3. 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.

  4. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

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

  5. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  6. 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 ... with conventional medicine or therapy, it is considered complementary therapy. There are many forms of alternative medicine. Acupuncture ...

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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.

  13. Embedded foveation image coding.

    Science.gov (United States)

    Wang, Z; Bovik, A C

    2001-01-01

    The human visual system (HVS) is highly space-variant in sampling, coding, processing, and understanding. The spatial resolution of the HVS is highest around the point of fixation (foveation point) and decreases rapidly with increasing eccentricity. By taking advantage of this fact, it is possible to remove considerable high-frequency information redundancy from the peripheral regions and still reconstruct a perceptually good quality image. Great success has been obtained previously by a class of embedded wavelet image coding algorithms, such as the embedded zerotree wavelet (EZW) and the set partitioning in hierarchical trees (SPIHT) algorithms. Embedded wavelet coding not only provides very good compression performance, but also has the property that the bitstream can be truncated at any point and still be decoded to recreate a reasonably good quality image. In this paper, we propose an embedded foveation image coding (EFIC) algorithm, which orders the encoded bitstream to optimize foveated visual quality at arbitrary bit-rates. A foveation-based image quality metric, namely, foveated wavelet image quality index (FWQI), plays an important role in the EFIC system. We also developed a modified SPIHT algorithm to improve the coding efficiency. Experiments show that EFIC integrates foveation filtering with foveated image coding and demonstrates very good coding performance and scalability in terms of foveated image quality measurement.

  14. 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. ...

  15. Role of stem cells in large animal genetic engineering in the TALENs-CRISPR era.

    Science.gov (United States)

    Park, Ki-Eun; Telugu, Bhanu Prakash V L

    2013-01-01

    The establishment of embryonic stem cells (ESCs) and gene targeting technologies in mice has revolutionised the field of genetics. The relative ease with which genes can be knocked out, and exogenous sequences introduced, has allowed the mouse to become the prime model for deciphering the genetic code. Not surprisingly, the lack of authentic ESCs has hampered the livestock genetics field and has forced animal scientists into adapting alternative technologies for genetic engineering. The recent discovery of the creation of induced pluripotent stem cells (iPSCs) by upregulation of a handful of reprogramming genes has offered renewed enthusiasm to animal geneticists. However, much like ESCs, establishing authentic iPSCs from the domestic animals is still beset with problems, including (but not limited to) the persistent expression of reprogramming genes and the lack of proven potential for differentiation into target cell types both in vitro and in vivo. Site-specific nucleases comprised of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regulated interspaced short palindromic repeats (CRISPRs) emerged as powerful genetic tools for precisely editing the genome, usurping the need for ESC-based genetic modifications even in the mouse. In this article, in the aftermath of these powerful genome editing technologies, the role of pluripotent stem cells in livestock genetics is discussed.

  16. Coded MapReduce

    OpenAIRE

    Li, Songze; Maddah-Ali, Mohammad Ali; Avestimehr, A. Salman

    2015-01-01

    MapReduce is a commonly used framework for executing data-intensive jobs on distributed server clusters. We introduce a variant implementation of MapReduce, namely "Coded MapReduce", to substantially reduce the inter-server communication load for the shuffling phase of MapReduce, and thus accelerating its execution. The proposed Coded MapReduce exploits the repetitive mapping of data blocks at different servers to create coding opportunities in the shuffling phase to exchange (key,value) pair...

  17. 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,

  18. 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.

  19. 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.

  20. Importance of Building Code

    Directory of Open Access Journals (Sweden)

    Reshmi Banerjee

    2015-06-01

    Full Text Available A building code, or building control, is a set of rules that specify the minimum standards for constructed objects such as buildings and non building structures. The main purpose of building codes are to protect public health, safety and general welfare as they relate to the construction and occupancy of buildings and structures. The building code becomes law of a particular jurisdiction when formally enacted by the appropriate governmental or private authority. Building codes are generally intended to be applied by architects, engineers, constructors and regulators but are also used for various purposes by safety inspectors, environmental scientists, real estate developers, subcontractors, manufacturers of building products and materials, insurance companies, facility managers, tenants and others.

  1. Bandwidth efficient coding

    CERN Document Server

    Anderson, John B

    2017-01-01

    Bandwidth Efficient Coding addresses the major challenge in communication engineering today: how to communicate more bits of information in the same radio spectrum. Energy and bandwidth are needed to transmit bits, and bandwidth affects capacity the most. Methods have been developed that are ten times as energy efficient at a given bandwidth consumption as simple methods. These employ signals with very complex patterns and are called "coding" solutions. The book begins with classical theory before introducing new techniques that combine older methods of error correction coding and radio transmission in order to create narrowband methods that are as efficient in both spectrum and energy as nature allows. Other topics covered include modulation techniques such as CPM, coded QAM and pulse design.

  2. Code Disentanglement: Initial Plan

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbier, John Greaton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kelley, Timothy M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockefeller, Gabriel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Calef, Matthew Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-27

    The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

  3. 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....

  4. 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)

  5. Coded Random Access

    DEFF Research Database (Denmark)

    Paolini, Enrico; Stefanovic, Cedomir; Liva, Gianluigi

    2015-01-01

    , in which the structure of the access protocol can be mapped to a structure of an erasure-correcting code defined on graph. This opens the possibility to use coding theory and tools for designing efficient random access protocols, offering markedly better performance than ALOHA. Several instances of coded......The rise of machine-to-machine communications has rekindled the interest in random access protocols as a support for a massive number of uncoordinatedly transmitting devices. The legacy ALOHA approach is developed under a collision model, where slots containing collided packets are considered...... 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...

  6. 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.

  7. Annotated Raptor Codes

    CERN Document Server

    Mahdaviani, Kaveh; Tellambura, Chintha

    2011-01-01

    In this paper, an extension of raptor codes is introduced which keeps all the desirable properties of raptor codes, including the linear complexity of encoding and decoding per information bit, unchanged. The new design, however, improves the performance in terms of the reception rate. Our simulations show a 10% reduction in the needed overhead at the benchmark block length of 64,520 bits and with the same complexity per information bit.

  8. 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.

  9. On Expanded Cyclic Codes

    CERN Document Server

    Wu, Yingquan

    2008-01-01

    The paper has a threefold purpose. The first purpose is to present an explicit description of expanded cyclic codes defined in $\\GF(q^m)$. The proposed explicit construction of expanded generator matrix and expanded parity check matrix maintains the symbol-wise algebraic structure and thus keeps many important original characteristics. The second purpose of this paper is to identify a class of constant-weight cyclic codes. Specifically, we show that a well-known class of $q$-ary BCH codes excluding the all-zero codeword are constant-weight cyclic codes. Moreover, we show this class of codes achieve the Plotkin bound. The last purpose of the paper is to characterize expanded cyclic codes utilizing the proposed expanded generator matrix and parity check matrix. We analyze the properties of component codewords of a codeword and particularly establish the precise conditions under which a codeword can be represented by a subbasis. With the new insights, we present an improved lower bound on the minimum distance of...

  10. Robust Nonlinear Neural Codes

    Science.gov (United States)

    Yang, Qianli; Pitkow, Xaq

    2015-03-01

    Most interesting natural sensory stimuli are encoded in the brain in a form that can only be decoded nonlinearly. But despite being a core function of the brain, nonlinear population codes are rarely studied and poorly understood. Interestingly, the few existing models of nonlinear codes are inconsistent with known architectural features of the brain. In particular, these codes have information content that scales with the size of the cortical population, even if that violates the data processing inequality by exceeding the amount of information entering the sensory system. Here we provide a valid theory of nonlinear population codes by generalizing recent work on information-limiting correlations in linear population codes. Although these generalized, nonlinear information-limiting correlations bound the performance of any decoder, they also make decoding more robust to suboptimal computation, allowing many suboptimal decoders to achieve nearly the same efficiency as an optimal decoder. Although these correlations are extremely difficult to measure directly, particularly for nonlinear codes, we provide a simple, practical test by which one can use choice-related activity in small populations of neurons to determine whether decoding is suboptimal or optimal and limited by correlated noise. We conclude by describing an example computation in the vestibular system where this theory applies. QY and XP was supported by a grant from the McNair foundation.

  11. All About Alternatives

    Science.gov (United States)

    Barr, Robert D.; And Others

    1972-01-01

    A primer on alternative schools. Described are existing programs in different areas, philosophy of the alternative schools, funding, student behavior, community relations, accountability, State regulations, management, and the environment of the alternative school. A list of sources of additional information on alternative schools is included.…

  12. 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

  13. 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.

  14. 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.

  15. Polynomial weights and code constructions

    DEFF Research Database (Denmark)

    Massey, J; Costello, D; Justesen, Jørn

    1973-01-01

    polynomial included. This fundamental property is then used as the key to a variety of code constructions including 1) a simplified derivation of the binary Reed-Muller codes and, for any primepgreater than 2, a new extensive class ofp-ary "Reed-Muller codes," 2) a new class of "repeated-root" cyclic codes...... 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....

  16. Distributed Video Coding: Iterative Improvements

    DEFF Research Database (Denmark)

    Luong, Huynh Van

    Nowadays, emerging applications such as wireless visual sensor networks and wireless video surveillance are requiring lightweight video encoding with high coding efficiency and error-resilience. Distributed Video Coding (DVC) is a new coding paradigm which exploits the source statistics...

  17. 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.

  18. The implications of alternative splicing in the ENCODE protein complement

    DEFF Research Database (Denmark)

    Tress, Michael L.; Martelli, Pier Luigi; Frankish, Adam;

    2007-01-01

    Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been...

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

  1. Algebraic and stochastic coding theory

    CERN Document Server

    Kythe, Dave K

    2012-01-01

    Using a simple yet rigorous approach, Algebraic and Stochastic Coding Theory makes the subject of coding theory easy to understand for readers with a thorough knowledge of digital arithmetic, Boolean and modern algebra, and probability theory. It explains the underlying principles of coding theory and offers a clear, detailed description of each code. More advanced readers will appreciate its coverage of recent developments in coding theory and stochastic processes. After a brief review of coding history and Boolean algebra, the book introduces linear codes, including Hamming and Golay codes.

  2. Optical coding theory with Prime

    CERN Document Server

    Kwong, Wing C

    2013-01-01

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

  3. 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.

  4. Golden Coded Multiple Beamforming

    CERN Document Server

    Li, Boyu

    2010-01-01

    The Golden Code is a full-rate full-diversity space-time code, which achieves maximum coding gain for Multiple-Input Multiple-Output (MIMO) systems with two transmit and two receive antennas. Since four information symbols taken from an M-QAM constellation are selected to construct one Golden Code codeword, a maximum likelihood decoder using sphere decoding has the worst-case complexity of O(M^4), when the Channel State Information (CSI) is available at the receiver. Previously, this worst-case complexity was reduced to O(M^(2.5)) without performance degradation. When the CSI is known by the transmitter as well as the receiver, beamforming techniques that employ singular value decomposition are commonly used in MIMO systems. In the absence of channel coding, when a single symbol is transmitted, these systems achieve the full diversity order provided by the channel. Whereas this property is lost when multiple symbols are simultaneously transmitted. However, uncoded multiple beamforming can achieve the full div...

  5. Coded source neutron imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bingham, Philip R [ORNL; Santos-Villalobos, Hector J [ORNL

    2011-01-01

    Coded aperture techniques have been applied to neutron radiography to address limitations in neutron flux and resolution of neutron detectors in a system labeled coded source imaging (CSI). By coding the neutron source, a magnified imaging system is designed with small spot size aperture holes (10 and 100 m) for improved resolution beyond the detector limits and with many holes in the aperture (50% open) to account for flux losses due to the small pinhole size. An introduction to neutron radiography and coded aperture imaging is presented. A system design is developed for a CSI system with a development of equations for limitations on the system based on the coded image requirements and the neutron source characteristics of size and divergence. Simulation has been applied to the design using McStas to provide qualitative measures of performance with simulations of pinhole array objects followed by a quantitative measure through simulation of a tilted edge and calculation of the modulation transfer function (MTF) from the line spread function. MTF results for both 100um and 10um aperture hole diameters show resolutions matching the hole diameters.

  6. Coded source neutron imaging

    Science.gov (United States)

    Bingham, Philip; Santos-Villalobos, Hector; Tobin, Ken

    2011-03-01

    Coded aperture techniques have been applied to neutron radiography to address limitations in neutron flux and resolution of neutron detectors in a system labeled coded source imaging (CSI). By coding the neutron source, a magnified imaging system is designed with small spot size aperture holes (10 and 100μm) for improved resolution beyond the detector limits and with many holes in the aperture (50% open) to account for flux losses due to the small pinhole size. An introduction to neutron radiography and coded aperture imaging is presented. A system design is developed for a CSI system with a development of equations for limitations on the system based on the coded image requirements and the neutron source characteristics of size and divergence. Simulation has been applied to the design using McStas to provide qualitative measures of performance with simulations of pinhole array objects followed by a quantitative measure through simulation of a tilted edge and calculation of the modulation transfer function (MTF) from the line spread function. MTF results for both 100μm and 10μm aperture hole diameters show resolutions matching the hole diameters.

  7. Speech coding code- excited linear prediction

    CERN Document Server

    Bäckström, Tom

    2017-01-01

    This book provides scientific understanding of the most central techniques used in speech coding both for advanced students as well as professionals with a background in speech audio and or digital signal processing. It provides a clear connection between the whys hows and whats thus enabling a clear view of the necessity purpose and solutions provided by various tools as well as their strengths and weaknesses in each respect Equivalently this book sheds light on the following perspectives for each technology presented Objective What do we want to achieve and especially why is this goal important Resource Information What information is available and how can it be useful and Resource Platform What kind of platforms are we working with and what are their capabilities restrictions This includes computational memory and acoustic properties and the transmission capacity of devices used. The book goes on to address Solutions Which solutions have been proposed and how can they be used to reach the stated goals and ...

  8. 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.

  9. 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.

  10. 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...

  11. 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.

  12. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...... 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....

  13. 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.

  14. Code query by example

    Science.gov (United States)

    Vaucouleur, Sebastien

    2011-02-01

    We introduce code query by example for customisation of evolvable software products in general and of enterprise resource planning systems (ERPs) in particular. The concept is based on an initial empirical study on practices around ERP systems. We motivate our design choices based on those empirical results, and we show how the proposed solution helps with respect to the infamous upgrade problem: the conflict between the need for customisation and the need for upgrade of ERP systems. We further show how code query by example can be used as a form of lightweight static analysis, to detect automatically potential defects in large software products. Code query by example as a form of lightweight static analysis is particularly interesting in the context of ERP systems: it is often the case that programmers working in this field are not computer science specialists but more of domain experts. Hence, they require a simple language to express custom rules.

  15. The 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.

  16. The Planning of Urban Medium Voltage Distribution Network Based on Dual-coding Immune Genetic Algorithm%基于双重编码免疫遗传算法城市中压配电网规划

    Institute of Scientific and Technical Information of China (English)

    崔凤仙; 刘阳

    2011-01-01

    针对配电网络规划中出现的中压配电站容量和位置不确定的情况,提出将中压配电站容量和位置连同网架结构、导线型号、线路回数等一起作为变量,采用整数编码与矩阵实数编码相结合的双重编码方式进行中压配电网络规划,其中整数编码用以确定网架结构、导线型号以及线路回数,而矩阵实数编码用以调整虚拟负荷点所带负荷量。设计了用于该规划的各项免疫遗传算法操作,并通过算例验证了该算法的有效性。%Considering the uncertainty of the capacities and the locations of the medium-voltage distribution stations in contribution network planning,this paper proposes a method for the planning,which employs a dual encoding way that takes the capacities and positions of the distribution stations,together with the structure of network,the types of the transmission lines and the number of circuit lines as parameters,and combines the integer encoding and real-matrix encoding.Here the integer encoding is for the structure of network,the types of the transmission lines and the number of circuit lines while the real-matrix encoding is for optimizing loads on the virtual load points.The operators of immune genetic algorithm for medium-voltage network planning are designed and applied to a real power distribution system,and it proves that the algorithm is effective.

  17. Distinguishing protein-coding from non-coding RNAs through support vector machines.

    Directory of Open Access Journals (Sweden)

    Jinfeng Liu

    2006-04-01

    Full Text Available RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in general. Increasing evidence points to the important cellular roles of such non-coding RNAs (ncRNAs. The distinction of protein-coding RNA transcripts from ncRNA transcripts is therefore an important problem in understanding the transcriptome and carrying out its annotation. Very few in silico methods have specifically addressed this problem. Here, we introduce CONC (for "coding or non-coding", a novel method based on support vector machines that classifies transcripts according to features they would have if they were coding for proteins. These features include peptide length, amino acid composition, predicted secondary structure content, predicted percentage of exposed residues, compositional entropy, number of homologs from database searches, and alignment entropy. Nucleotide frequencies are also incorporated into the method. Confirmed coding cDNAs for eukaryotic proteins from the Swiss-Prot database constituted the set of true positives, ncRNAs from RNAdb and NONCODE the true negatives. Ten-fold cross-validation suggested that CONC distinguished coding RNAs from ncRNAs at about 97% specificity and 98% sensitivity. Applied to 102,801 mouse cDNAs from the FANTOM3 dataset, our method reliably identified over 14,000 ncRNAs and estimated the total number of ncRNAs to be about 28,000.

  18. 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

  19. 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

  20. Multiband Asymmetric Transmission of Airborne Sound by Coded Metasurfaces

    Science.gov (United States)

    Xie, Boyang; Cheng, Hua; Tang, Kun; Liu, Zhengyou; Chen, Shuqi; Tian, Jianguo

    2017-02-01

    We present the design, characterization, and theoretical and experimental demonstration of multiband asymmetric transmission of airborne sound using an ultrathin coded metasurface formed by an alternating arrangement of the coding elements 0 and 1. The asymmetric transmission effect can be easily controlled to selectively achieve off and on by coding different patterns. Both frequency- and angle-selective transmission is discussed. The proposed multiband asymmetric transmission stems from the constructive and destructive interferences of acoustic-wave coupling between the coded elements. The experimental results are in relative agreement with numerical simulations. This work opens an alternative path for ultrathin acoustic-device design and shows promise for application in acoustic rectification and noise control.

  1. 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

  2. Discovery of Proteomic Code with mRNA Assisted Protein Folding

    Directory of Open Access Journals (Sweden)

    Jan C. Biro

    2008-12-01

    Full Text Available The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.

  3. Consumer Health: Alternative Therapy

    Science.gov (United States)

    Healthy Lifestyle Consumer health What's considered an alternative therapy is a moving target. Get the facts about what CAM means and ... Original article: http://www.mayoclinic.org/healthy-lifestyle/consumer-health/in-depth/alternative-medicine/art-20045267 . Mayo ...

  4. 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%.

  5. Reed-Solomon convolutional codes

    NARCIS (Netherlands)

    Gluesing-Luerssen, H; Schmale, W

    2005-01-01

    In this paper we will introduce a specific class of cyclic convolutional codes. The construction is based on Reed-Solomon block codes. The algebraic parameters as well as the distance of these codes are determined. This shows that some of these codes are optimal or near optimal.

  6. 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

  7. Ptolemy Coding Style

    Science.gov (United States)

    2014-09-05

    Laboratory (NRL #N0013-12-1-015), and the following companies: Denso, National Instruments, and Toyota ). Ptolemy Coding Style ∗ Christopher Brooks1, Edward A...Instruments, and Toyota ). 1As reported on September 3, 2014 by https://www.openhub.net/p/12005/factoids 1 In addition, OpenHub.net indicates that the

  8. Polar Code Validation

    Science.gov (United States)

    1989-09-30

    SUMMARY OF POLAR ACHIEVEMENTS ..... .......... 3 3. POLAR CODE PHYSICAL MODELS ..... ............. 5 3.1 PL- ASMA Su ^"ru5 I1LS SH A...of this problem. 1.1. The Charge-2 Rocket The Charge-2 payload was launched on a Black Brant VB from White Sands Mis- sile Range in New Mexico in

  9. Physical layer network coding

    DEFF Research Database (Denmark)

    Fukui, Hironori; Popovski, Petar; Yomo, Hiroyuki

    2014-01-01

    Physical layer network coding (PLNC) has been proposed to improve throughput of the two-way relay channel, where two nodes communicate with each other, being assisted by a relay node. Most of the works related to PLNC are focused on a simple three-node model and they do not take into account...

  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. 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...

  12. Corporate governance through codes

    NARCIS (Netherlands)

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

    2014-01-01

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

  13. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

    Energy Technology Data Exchange (ETDEWEB)

    Hasin-Brumshtein, Yehudit; Khan, Arshad H.; Hormozdiari, Farhad; Pan, Calvin; Parks, Brian W.; Petyuk, Vladislav A.; Piehowski, Paul D.; Brümmer, Anneke; Pellegrini, Matteo; Xiao, Xinshu; Eskin, Eleazar; Smith, Richard D.; Lusis, Aldons J.; Smith, Desmond J.

    2016-09-13

    Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals bothlocalandtransexpression Quantitative Trait Loci (eQTLs) demonstrating 2transeQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.

  14. Genetic manipulation in biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Sherwood, R.; Atkinson, T.

    1981-04-04

    The role of genetic manipulation in opening up new possibilities in biotechnology is discussed and the basic steps in a recombinant DNA experiment are summarized. Some current and future applications of this technology in the fields of medicine, industry and agriculture are presented, including, conversion of wastes to SCP, chemicals and alcohols, plant improvement and the introduction of nitrogen fixation genes into plants as an alternative to the use of nitrogen fertilizers.

  15. 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.

  16. 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.

  17. 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...

  18. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

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

  19. 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 ...

  20. Genetic counseling

    Science.gov (United States)

    ... will want to think about your personal desires, religious beliefs, and family circumstances. Some people have a ... purpose of genetic counseling is simply to help parents make informed decisions. A genetic counselor will help ...

  1. Genetic modification and genetic determinism.

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-06-26

    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.

  2. On primordial sense-antisense coding.

    Science.gov (United States)

    Rodin, Andrei S; Rodin, Sergei N; Carter, Charles W

    2009-11-01

    The genetic code is implemented by aminoacyl-tRNA synthetases (aaRS). These 20 enzymes are divided into two classes that, despite performing same functions, have nothing common in structure. The mystery of this striking partition of aaRSs might have been concealed in their sterically complementary modes of tRNA recognition that, as we have found recently, protect the tRNAs with complementary anticodons from confusion in translation. This finding implies that, in the beginning, life increased its coding repertoire by the pairs of complementary codons (rather than one-by-one) and used both complementary strands of genes as templates for translation. The class I and class II aaRSs may represent one of the most important examples of such primordial sense-antisense (SAS) coding (Rodin and Ohno, Orig Life Evol Biosph 25:565-589, 1995). In this report, we address the issue of SAS coding in a wider scope. We suggest a variety of advantages that such coding would have had in exploring a wider sequence space before translation became highly specific. In particular, we confirm that in Achlya klebsiana a single gene might have originally coded for an HSP70 chaperonin (class II aaRS homolog) and an NAD-specific GDH-like enzyme (class I aaRS homolog) via its sense and antisense strands. Thus, in contrast to the conclusions in Williams et al. (Mol Biol Evol 26:445-450, 2009), this could indeed be a "Rosetta stone" gene (Carter and Duax, Mol Cell 10:705-708, 2002) (eroded somewhat, though) for the SAS origin of the two aaRS classes.

  3. 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.

  4. 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.

  5. 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.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    Distributed video coding (DVC) is a novel approach providing new features as low complexity encoding by mainly exploiting the source statistics at the decoder based on the availability of decoder side information. In this paper, scalable-tolossless DVC is presented based on extending a lossy...... 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...... codec provides frame by frame encoding. Comparing the lossless coding efficiency, the proposed scalable-to-lossless TDWZ video codec can save up to 5%-13% bits compared to JPEG LS and H.264 Intra frame lossless coding and do so as a scalable-to-lossless coding....

  7. 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....

  8. 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.

  9. Manometer Behavior Analysis using CATHENA, RELAP and GOTHIC Codes

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-15

    In this presentation, simple thermal hydraulic behavior is analyzed using three codes to show the possibility of using alternative codes. We established three models of simple u-tube manometer using three different codes. CATHENA (Canadian Algorithm for Thermal hydraulic Network Analysis), RELAP (Reactor Excursion and Leak Analysis Program), GOTHIC (Generation of Thermal Hydraulic Information for Containments) are used for this analysis. CATHENA and RELAP are widely used codes for the analysis of system behavior of CANDU and PWR. And GOTHIC code also has been widely used for the analysis of thermal hydraulic behavior in the containment system. In this paper, the internal behavior of u-tube manometer was analyzed using 3 codes, CATHENA, RELAP and GOTHIC. The general transient behavior is similar among 3 codes. However, the behavior simulated using GOTHIC shows some different trend compared with the results from the other 2 codes at the end of the transient. It would be resulted from the use of different physical model in GOTHIC, which is specialized for the multi-phase thermal hydraulic behavior analysis of containment system unlike the other two codes.

  10. Reserved-Length Prefix Coding

    CERN Document Server

    Baer, Michael B

    2008-01-01

    Huffman coding finds an optimal prefix code for a given probability mass function. Consider situations in which one wishes to find an optimal code with the restriction that all codewords have lengths that lie in a user-specified set of lengths (or, equivalently, no codewords have lengths that lie in a complementary set). This paper introduces a polynomial-time dynamic programming algorithm that finds optimal codes for this reserved-length prefix coding problem. This has applications to quickly encoding and decoding lossless codes. In addition, one modification of the approach solves any quasiarithmetic prefix coding problem, while another finds optimal codes restricted to the set of codes with g codeword lengths for user-specified g (e.g., g=2).

  11. 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...

  12. 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.

  13. 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.

  14. Codes of Good Governance

    DEFF Research Database (Denmark)

    Beck Jørgensen, Torben; Sørensen, Ditte-Lene

    2013-01-01

    Good governance is a broad concept used by many international organizations to spell out how states or countries should be governed. Definitions vary, but there is a clear core of common public values, such as transparency, accountability, effectiveness, and the rule of law. It is quite likely......, however, that national views of good governance reflect different political cultures and institutional heritages. Fourteen national codes of conduct are analyzed. The findings suggest that public values converge and that they match model codes from the United Nations and the European Council as well...... as conceptions of good governance from other international organizations. While values converge, they are balanced and communicated differently, and seem to some extent to be translated into the national cultures. The set of global public values derived from this analysis include public interest, regime dignity...

  15. 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.

  16. Evaluation of Extended CCSDS Reed-Solomon Codes for Bandwidth efficiency

    DEFF Research Database (Denmark)

    Andersen, Jakob Dahl; Justesen, Jørn; Larsen, Knud J.;

    1999-01-01

    of the recommendation. For that purpose we have investigated a number of topics: We give the performance of Reed-Solomon codes with less error-correcting capability than in the present recommendation, and we give suggestions for selection of the generator polynomial for such codes. We provide some comments...... on the recommendation aimed at improving the presentation in the recommendation. We comment on the selection of a pseudo-randomiser sequence in the recommendation and suggest an alternative with better properties. An alternative to higher rate Reed-Solomon codes is investigated by puncturing the convolutional codes...

  17. The Hunstad Code

    DEFF Research Database (Denmark)

    Abraham, Anders; Capetillo, Christina

    2016-01-01

    With modern technology and levels of prosperity making many of us increasingly self-sufficient, architects Anders Abraham and Christina Capetillo argue that a rural ‘town’ is defined by the level of interactivity within it rather than merely by population figures. In collaboration with curators A...... Annesofie Becker and Martin Christiansen, they have developed the Hunstad Code to offer guidelines for the construction of environments that can encourage the development of relationships between residents even while remaining low-density....

  18. The Liege Oscillation Code

    CERN Document Server

    Scuflaire, R; Théado, S; Bourge, P -O; Miglio, A; Godart, M; Thoul, A; Noels, A

    2007-01-01

    The Liege Oscillation code can be used as a stand-alone program or as a library of subroutines that the user calls from a Fortran main program of his own to compute radial and non-radial adiabatic oscillations of stellar models. We describe the variables and the equations used by the program and the methods used to solve them. A brief account is given of the use and the output of the program.

  19. The Phantom SPH code

    Science.gov (United States)

    Price, Daniel; Wurster, James; Nixon, Chris

    2016-05-01

    I will present the capabilities of the Phantom SPH code for global simulations of dust and gas in protoplanetary discs. I will present our new algorithms for simulating both small and large grains in discs, as well as our progress towards simulating evolving grain populations and coupling with radiation. Finally, I will discuss our recent applications to HL Tau and the physics of dust gap opening.

  20. Genetic modification and genetic determinism

    OpenAIRE

    Vorhaus Daniel B; Resnik David B

    2006-01-01

    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....

  1. 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.

  2. 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...

  3. Random linear codes in steganography

    Directory of Open Access Journals (Sweden)

    Kamil Kaczyński

    2016-12-01

    Full Text Available Syndrome coding using linear codes is a technique that allows improvement in the steganographic algorithms parameters. The use of random linear codes gives a great flexibility in choosing the parameters of the linear code. In parallel, it offers easy generation of parity check matrix. In this paper, the modification of LSB algorithm is presented. A random linear code [8, 2] was used as a base for algorithm modification. The implementation of the proposed algorithm, along with practical evaluation of algorithms’ parameters based on the test images was made.[b]Keywords:[/b] steganography, random linear codes, RLC, LSB

  4. 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

  5. Convolutional coding techniques for data protection

    Science.gov (United States)

    Massey, J. L.

    1975-01-01

    Results of research on the use of convolutional codes in data communications are presented. Convolutional coding fundamentals are discussed along with modulation and coding interaction. Concatenated coding systems and data compression with convolutional codes are described.

  6. 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。

  7. Code flows : Visualizing structural evolution of source code

    NARCIS (Netherlands)

    Telea, Alexandru; Auber, David

    2008-01-01

    Understanding detailed changes done to source code is of great importance in software maintenance. We present Code Flows, a method to visualize the evolution of source code geared to the understanding of fine and mid-level scale changes across several file versions. We enhance an existing visual met

  8. Code Flows : Visualizing Structural Evolution of Source Code

    NARCIS (Netherlands)

    Telea, Alexandru; Auber, David

    2008-01-01

    Understanding detailed changes done to source code is of great importance in software maintenance. We present Code Flows, a method to visualize the evolution of source code geared to the understanding of fine and mid-level scale changes across several file versions. We enhance an existing visual met

  9. On alternating quantum walks

    Science.gov (United States)

    Rousseva, Jenia; Kovchegov, Yevgeniy

    2017-03-01

    We study an inhomogeneous quantum walk on a line that evolves according to alternating coins, each a rotation matrix. For the quantum walk with the coin alternating between clockwise and counterclockwise rotations by the same angle, we derive a closed form solution for the propagation of probabilities, and provide its asymptotic approximation via the method of stationary phase. Finally, we observe that for a x03c0;/4 angle, this alternating rotation walk will replicate the renown Hadamard walk.

  10. 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.

  11. Brandmodstandsbidrag for alternative isoleringsmaterialer

    DEFF Research Database (Denmark)

    Hansen, Ernst Jan de Place

    2001-01-01

    Resume af rapport om alternative isoleringsmaterialers brandmodstandsbidrag, udarbejdet af Dansk Brandteknisk Institut under Energistyrelsens udviklingsprogram "Miljø- og arbejdsmiljøvenlig isolering"...

  12. The path of code linting

    CERN Document Server

    CERN. Geneva

    2017-01-01

    Join the path of code linting and discover how it can help you reach higher levels of programming enlightenment. Today we will cover how to embrace code linters to offload cognitive strain on preserving style standards in your code base as well as avoiding error-prone constructs. Additionally, I will show you the journey ahead for integrating several code linters in the programming tools your already use with very little effort.

  13. IRIG Serial Time Code Formats

    Science.gov (United States)

    2016-08-01

    Standard This standard consists of a family of rate-scaled serial time codes with formats containing up to four coded expressions or words. All time...time code formats is designated A, B, D, E, G, and H. Various combinations of subwords and signal forms make up a time code word. To differentiate...ARE leap years. Additional information can be found at the following USNO web sites. • http://timeanddate.com/ date /leapyear.html • http

  14. 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...

  15. 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.

  16. Information, Genetics and Entropy

    Directory of Open Access Journals (Sweden)

    Julio Ernesto Rubio Barrios

    2015-04-01

    Full Text Available The consolidation of the informational paradigm in molecular biology research concluded on a system to convert the epistemic object into an operational technological object and a stable epistemic product. However, the acceptance of the informational properties of genetic acids failed to clarify the meaning of the concept of information. The “information”’ as a property of the genetic molecules remained as an informal notion that allows the description of the mechanism of inheritance, but it was not specified in a logic–semantic structure. The metaphorical implications associated with the idea of genes as molecules with meaning, questioned the linguistics that seemed too foreign to molecular biology. A reformulation of the concept of information in molecular biology was developed upon the theory of Claude Shannon. The node for the structural coupling between biology, physics and information theory was the identification of an analog structure between the coded messages of Shannon’s theory.

  17. Tagalog-English Code Switching as a Mode of Discourse

    Science.gov (United States)

    Bautista, Maria Lourdes S.

    2004-01-01

    The alternation of Tagalog and English in informal discourse is a feature of the linguistic repertoire of educated, middle- and upper-class Filipinos. This paper describes the linguistic structure and sociolinguistic functions of Tagalog-English code switching (Taglish) as provided by various researchers through the years. It shows that the…

  18. 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...

  19. Improved code-tracking loop

    Science.gov (United States)

    Laflame, D. T.

    1980-01-01

    Delay-locked loop tracks pseudonoise codes without introducing dc timing errors, because it is not sensitive to gain imbalance between signal processing arms. "Early" and "late" reference codes pass in combined form through both arms, and each arm acts on both codes. Circuit accomodates 1 dB weaker input signals with tracking ability equal to that of tau-dither loops.

  20. Order functions and evaluation codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Pellikaan, Ruud; van Lint, Jack

    1997-01-01

    Based on the notion of an order function we construct and determine the parameters of a class of error-correcting evaluation codes. This class includes the one-point algebraic geometry codes as wella s the generalized Reed-Muller codes and the parameters are detremined without using the heavy...... machinery of algebraic geometry....