On the Organizational Dynamics of the Genetic Code

KAUST Repository

Zhang, Zhang; Yu, Jun

2011-01-01

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

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

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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.

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

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Sella, Guy; Ardell, David H

2006-09-01

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

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

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

2007-10-31

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

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

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Santos, José; Monteagudo, Angel

2011-02-21

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

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

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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

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

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Sergey V. Petoukhov

2016-12-01

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

Real coded genetic algorithm for fuzzy time series prediction

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

2017-10-01

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

The Genetic Code: Yesterday, Today and Tomorrow

Indian Academy of Sciences (India)

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

The "Wow! signal" of the terrestrial genetic code

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shCherbak, Vladimir I.; Makukov, Maxim A.

2013-05-01

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

Representation mutations from standard genetic codes

Science.gov (United States)

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

2018-03-01

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

Efficient Dual Domain Decoding of Linear Block Codes Using Genetic Algorithms

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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.

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

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Isabel Miranda

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

HOW TO REPRESENT THE GENETIC CODE?

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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

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

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Kubyshkin, Vladimir; Budisa, Nediljko

2017-08-01

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

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

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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.

Programming peptidomimetic syntheses by translating genetic codes designed de novo.

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

2003-05-27

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

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

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

2018-02-01

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

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

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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.

Origins of gene, genetic code, protein and life

Indian Academy of Sciences (India)

Unknown

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

A symbiotic liaison between the genetic and epigenetic code

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Holger eHeyn

2014-05-01

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

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

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Carter, Charles W; Wills, Peter R

2018-01-01

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

The genetic code as a periodic table: algebraic aspects.

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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.

The Search for Symmetries in the Genetic Code:

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

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

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

Science.gov (United States)

Zamudio, Gabriel S.; José, Marco V.

2018-03-01

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

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

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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.

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

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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.

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

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

Science.gov (United States)

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

2014-03-01

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

[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.

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

Science.gov (United States)

Barr, C L; Misener, V L

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

J.H. Vermeulen

2003-11-01

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

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

Science.gov (United States)

Błażej, Paweł; Wnȩtrzak, Małgorzata; Mackiewicz, Paweł

2016-12-01

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

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

Directory of Open Access Journals (Sweden)

Gao Lin

2012-06-01

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

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

Directory of Open Access Journals (Sweden)

Steven J. Schrodi

2017-01-01

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

Automation of RELAP5 input calibration and code validation using genetic algorithm

International Nuclear Information System (INIS)

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

2016-01-01

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

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

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

Science.gov (United States)

Goldstein, Bob

2018-04-02

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

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

Science.gov (United States)

Santos, José; Monteagudo, Ángel

2017-03-27

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

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

Science.gov (United States)

Di Giulio, Massimo

2017-11-07

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

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.

Amino acid fermentation at the origin of the genetic code.

Science.gov (United States)

de Vladar, Harold P

2012-02-10

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

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

Directory of Open Access Journals (Sweden)

Novosljska-Dragovič Aleksandra

2005-01-01

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

Quantum control using genetic algorithms in quantum communication: superdense coding

International Nuclear Information System (INIS)

Domínguez-Serna, Francisco; Rojas, Fernando

2015-01-01

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

Amino acid fermentation at the origin of the genetic code

Science.gov (United States)

2012-01-01

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

Amino acid fermentation at the origin of the genetic code

Directory of Open Access Journals (Sweden)

de Vladar Harold P

2012-02-01

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

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

NARCIS (Netherlands)

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

2011-01-01

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

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

Science.gov (United States)

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

2016-07-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1995-05-20

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

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.

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

Science.gov (United States)

Koonin, Eugene V

2017-05-23

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

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

Science.gov (United States)

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

2013-02-01

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

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

Science.gov (United States)

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

2017-01-01

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

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

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

2017-12-01

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

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

NARCIS (Netherlands)

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

2017-01-01

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

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

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Petoukhov, Sergey V

2017-08-01

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

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

Directory of Open Access Journals (Sweden)

Antoine Danchin

2017-06-01

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

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

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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.

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

Science.gov (United States)

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

2017-09-19

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

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

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

2016-01-01

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

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.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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.

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.

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

International Nuclear Information System (INIS)

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

2004-10-01

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

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

International Nuclear Information System (INIS)

Ortiz, Juan Jose; Requena, Ignacio

2004-01-01

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

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

Science.gov (United States)

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

2015-03-01

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

[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.

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

International Nuclear Information System (INIS)

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

2009-01-01

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

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

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

2018-04-18

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

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.

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

Science.gov (United States)

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

2015-08-01

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

Theory of epigenetic coding.

Science.gov (United States)

Elder, D

1984-06-07

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

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

Science.gov (United States)

Witzany, Guenther

2016-02-01

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

Bistability in self-activating genes regulated by non-coding RNAs

International Nuclear Information System (INIS)

Miro-Bueno, Jesus

2015-01-01

Non-coding RNA molecules are able to regulate gene expression and play an essential role in cells. On the other hand, bistability is an important behaviour of genetic networks. Here, we propose and study an ODE model in order to show how non-coding RNA can produce bistability in a simple way. The model comprises a single gene with positive feedback that is repressed by non-coding RNA molecules. We show how the values of all the reaction rates involved in the model are able to control the transitions between the high and low states. This new model can be interesting to clarify the role of non-coding RNA molecules in genetic networks. As well, these results can be interesting in synthetic biology for developing new genetic memories and biomolecular devices based on non-coding RNAs

Self-complementary circular codes in coding theory.

Science.gov (United States)

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

2018-04-01

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

All about Genetics (For Parents)

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

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

Science.gov (United States)

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

2016-09-01

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

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

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

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

International Nuclear Information System (INIS)

Ponnamperuma, C.

1992-01-01

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

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.

Quantum algorithms and the genetic code

Indian Academy of Sciences (India)

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

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

International Nuclear Information System (INIS)

Momeni, M.H.

1983-01-01

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

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

Science.gov (United States)

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

2006-07-01

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

Genetics researchers’ and iRB professionals’ attitudes toward genetic research review: a comparative analysis

Science.gov (United States)

Edwards, Karen L.; Lemke, Amy A.; Trinidad, Susan B.; Lewis, Susan M.; Starks, Helene; Snapinn, Katherine W.; Griffin, Mary Quinn; Wiesner, Georgia L.; Burke, Wylie

2012-01-01

Purpose Genetic research involving human participants can pose challenging questions related to ethical and regulatory standards for research oversight. However, few empirical studies describe how genetic researchers and institutional review board (IRB) professionals conceptualize ethical issues in genetic research or where common ground might exist. Methods Parallel online surveys collected information from human genetic researchers (n = 351) and IRB professionals (n = 208) regarding their views about human participant oversight for genetic protocols. Results A range of opinions were observed within groups on most issues. In both groups, a minority thought it likely that people would be harmed by participation in genetic research or identified from coded genetic data. A majority of both groups agreed that reconsent should be required for four of the six scenarios presented. Statistically significant differences were observed between groups on some issues, with more genetic researcher respondents trusting the confidentiality of coded data, fewer expecting harms from reidentification, and fewer considering reconsent necessary in certain scenarios. Conclusions The range of views observed within and between IRB and genetic researcher groups highlights the complexity and unsettled nature of many ethical issues in genome research. Our findings also identify areas where researcher and IRB views diverge and areas of common ground. PMID:22241102

Function and Application Areas in Medicine of Non-Coding RNA

Directory of Open Access Journals (Sweden)

Figen Guzelgul

2009-06-01

Full Text Available RNA is the genetic material converting the genetic code that it gets from DNA into protein. While less than 2 % of RNA is converted into protein , more than 98 % of it can not be converted into protein and named as non-coding RNAs. 70 % of noncoding RNAs consists of introns , however, the rest part of them consists of exons. Non-coding RNAs are examined in two classes according to their size and functions. Whereas they are classified as long non-coding and small non-coding RNAs according to their size , they are grouped as housekeeping non-coding RNAs and regulating non-coding RNAs according to their function. For long years ,these non-coding RNAs have been considered as non-functional. However, today, it has been proved that these non-coding RNAs play role in regulating genes and in structural, functional and catalitic roles of RNAs converted into protein. Due to its taking a role in gene silencing mechanism, particularly in medical world , non-coding RNAs have led to significant developments. RNAi technolgy , which is used in designing drugs to be used in treatment of various diseases , is a ray of hope for medical world. [Archives Medical Review Journal 2009; 18(3.000: 141-155

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

Directory of Open Access Journals (Sweden)

John P McCutcheon

2009-07-01

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

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...

Foundations of genetic algorithms 1991

CERN Document Server

1991-01-01

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

Unnatural reactive amino acid genetic code additions

Energy Technology Data Exchange (ETDEWEB)

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

2017-10-25

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

The Genetic Privacy Act and commentary

Energy Technology Data Exchange (ETDEWEB)

Annas, G.J.; Glantz, L.H.; Roche, P.A.

1995-02-28

The Genetic Privacy Act is a proposal for federal legislation. The Act is based on the premise that genetic information is different from other types of personal information in ways that require special protection. The DNA molecule holds an extensive amount of currently indecipherable information. The major goal of the Human Genome Project is to decipher this code so that the information it contains is accessible. The privacy question is, accessible to whom? The highly personal nature of the information contained in DNA can be illustrated by thinking of DNA as containing an individual`s {open_quotes}future diary.{close_quotes} A diary is perhaps the most personal and private document a person can create. It contains a person`s innermost thoughts and perceptions, and is usually hidden and locked to assure its secrecy. Diaries describe the past. The information in one`s genetic code can be thought of as a coded probabilistic future diary because it describes an important part of a unique and personal future. This document presents an introduction to the proposal for federal legislation `the Genetic Privacy Act`; a copy of the proposed act; and comment.

Annotating pathogenic non-coding variants in genic regions.

Science.gov (United States)

Gelfman, Sahar; Wang, Quanli; McSweeney, K Melodi; Ren, Zhong; La Carpia, Francesca; Halvorsen, Matt; Schoch, Kelly; Ratzon, Fanni; Heinzen, Erin L; Boland, Michael J; Petrovski, Slavé; Goldstein, David B

2017-08-09

Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes.While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

Health effects estimation code development for accident consequence analysis

International Nuclear Information System (INIS)

Togawa, O.; Homma, T.

1992-01-01

As part of a computer code system for nuclear reactor accident consequence analysis, two computer codes have been developed for estimating health effects expected to occur following an accident. Health effects models used in the codes are based on the models of NUREG/CR-4214 and are revised for the Japanese population on the basis of the data from the reassessment of the radiation dosimetry and information derived from epidemiological studies on atomic bomb survivors of Hiroshima and Nagasaki. The health effects models include early and continuing effects, late somatic effects and genetic effects. The values of some model parameters are revised for early mortality. The models are modified for predicting late somatic effects such as leukemia and various kinds of cancers. The models for genetic effects are the same as those of NUREG. In order to test the performance of one of these codes, it is applied to the U.S. and Japanese populations. This paper provides descriptions of health effects models used in the two codes and gives comparisons of the mortality risks from each type of cancer for the two populations. (author)

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

Science.gov (United States)

Hoffmann, Robert D; Palmgren, Michael

2016-06-13

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

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

Directory of Open Access Journals (Sweden)

Adi Oron-Gottesman

2016-11-01

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

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

Science.gov (United States)

Wei, Chengying; Xiong, Cuilian; Liu, Huanlin

2017-12-01

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

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

Science.gov (United States)

Wohlin, Åsa

2015-03-21

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

I-Ching, dyadic groups of binary numbers and the geno-logic coding in living bodies.

Science.gov (United States)

Hu, Zhengbing; Petoukhov, Sergey V; Petukhova, Elena S

2017-12-01

The ancient Chinese book I-Ching was written a few thousand years ago. It introduces the system of symbols Yin and Yang (equivalents of 0 and 1). It had a powerful impact on culture, medicine and science of ancient China and several other countries. From the modern standpoint, I-Ching declares the importance of dyadic groups of binary numbers for the Nature. The system of I-Ching is represented by the tables with dyadic groups of 4 bigrams, 8 trigrams and 64 hexagrams, which were declared as fundamental archetypes of the Nature. The ancient Chinese did not know about the genetic code of protein sequences of amino acids but this code is organized in accordance with the I-Ching: in particularly, the genetic code is constructed on DNA molecules using 4 nitrogenous bases, 16 doublets, and 64 triplets. The article also describes the usage of dyadic groups as a foundation of the bio-mathematical doctrine of the geno-logic code, which exists in parallel with the known genetic code of amino acids but serves for a different goal: to code the inherited algorithmic processes using the logical holography and the spectral logic of systems of genetic Boolean functions. Some relations of this doctrine with the I-Ching are discussed. In addition, the ratios of musical harmony that can be revealed in the parameters of DNA structure are also represented in the I-Ching book. Copyright © 2017 Elsevier Ltd. All rights reserved.

Allele coding in genomic evaluation

DEFF Research Database (Denmark)

Standen, Ismo; Christensen, Ole Fredslund

2011-01-01

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

On fuzzy semantic similarity measure for DNA coding.

Science.gov (United States)

Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin

2016-02-01

A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-06-15

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

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics. Amit Katiyar. Articles written in Journal of Genetics. Volume 92 Issue 3 December 2013 pp 363-368 Research Article. Expression profile of genes coding for carotenoid biosynthetic pathway during ripening and their association with accumulation of lycopene in tomato fruits.

Trends in genetic patent applications: The commercialization of academic intellectual property

NARCIS (Netherlands)

Kers, J.G.; van Burg, J.C.; Stoop, T.; Cornel, M.C.

2014-01-01

We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications

Emergence of a code in the polymerization of amino acids along RNA templates.

Directory of Open Access Journals (Sweden)

Jean Lehmann

2009-06-01

Full Text Available The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.

Clinical application of antenatal genetic diagnosis of osteogenesis imperfecta type IV.

Science.gov (United States)

Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

2015-04-02

Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families.

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

Directory of Open Access Journals (Sweden)

Hassan Abdullah Kubba

2015-05-01

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

Preimplantation genetic screening.

Science.gov (United States)

Harper, Joyce C

2018-03-01

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

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

Science.gov (United States)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

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

Quantum-genetic theory of the hafure of malignant tumors

International Nuclear Information System (INIS)

Ovsyannikov, V.A.

1984-01-01

It is shown, that all interactions, which can cause a transformation in genetic code of a cell, from energy viewpoint should possess quantum energy from 4 to 10 eV, i.e. they should be referred to radiations of UV range. All the reasons known presently, which cause initial carcinomas, are accompanied by UV radiation in the range. The mechanism of UV radiation interaction with living cells, mechanism of genetic code transformation and mechanism of appearance and development of initial and secondary carcinomas are considered

Expression profile of genes coding for carotenoid biosynthetic ...

Indian Academy of Sciences (India)

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

A SNP panel and online tool for checking genotype concordance through comparing QR codes.

Directory of Open Access Journals (Sweden)

Yonghong Du

Full Text Available In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech, nicknamed QRC (for QR code based Concordance check, which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

A SNP panel and online tool for checking genotype concordance through comparing QR codes.

Science.gov (United States)

Du, Yonghong; Martin, Joshua S; McGee, John; Yang, Yuchen; Liu, Eric Yi; Sun, Yingrui; Geihs, Matthias; Kong, Xuejun; Zhou, Eric Lingfeng; Li, Yun; Huang, Jie

2017-01-01

In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

Evolving a Dynamic Predictive Coding Mechanism for Novelty Detection

OpenAIRE

Haggett, Simon J.; Chu, Dominique; Marshall, Ian W.

2007-01-01

Novelty detection is a machine learning technique which identifies new or unknown information in data sets. We present our current work on the construction of a new novelty detector based on a dynamical version of predictive coding. We compare three evolutionary algorithms, a simple genetic algorithm, NEAT and FS-NEAT, for the task of optimising the structure of an illustrative dynamic predictive coding neural network to improve its performance over stimuli from a number of artificially gener...

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

A novel neutron energy spectrum unfolding code using particle swarm optimization

International Nuclear Information System (INIS)

Shahabinejad, H.; Sohrabpour, M.

2017-01-01

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

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

Science.gov (United States)

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

2013-10-01

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

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

DEFF Research Database (Denmark)

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

2015-01-01

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

Development of a graphical interface computer code for reactor fuel reloading optimization

International Nuclear Information System (INIS)

Do Quang Binh; Nguyen Phuoc Lan; Bui Xuan Huy

2007-01-01

This report represents the results of the project performed in 2007. The aim of this project is to develop a graphical interface computer code that allows refueling engineers to design fuel reloading patterns for research reactor using simulated graphical model of reactor core. Besides, this code can perform refueling optimization calculations based on genetic algorithms as well as simulated annealing. The computer code was verified based on a sample problem, which relies on operational and experimental data of Dalat research reactor. This code can play a significant role in in-core fuel management practice at nuclear research reactor centers and in training. (author)

Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

Science.gov (United States)

2015-10-01

AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John... encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

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.

Use of genetic algorithms for optimization of subchannel simulations

International Nuclear Information System (INIS)

Nava Dominguez, A.

2004-01-01

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

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.

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 ...

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

Science.gov (United States)

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

2015-01-01

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

Extraordinarily adaptive properties of the genetically encoded amino acids.

Science.gov (United States)

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

2015-03-24

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

How to measure genetic heterogeneity

International Nuclear Information System (INIS)

Yamada, Ryo

2009-01-01

Genetic information of organisms is coded as a string of four letters, A, T, G and C, a sequence in macromolecules called deoxyribonucleic acid (DNA). DNA sequence offers blueprint of organisms and its heterogeneity determines identity and variation of species. The quantitation of this genetic heterogeneity is fundamental to understand biology. We compared previously-reported three measures, covariance matrix expression of list of loci (pair-wise r 2 ), the most popular index in genetics, and its multi-dimensional form, Ψ, and entropy-based index, ε. Thereafter we proposed two methods so that we could handle the diplotypic heterogeneity and quantitate the conditions where the number of DNA sequence samples is much smaller than the number of possible variants.

[Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

Science.gov (United States)

Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

2014-12-01

In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

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

Science.gov (United States)

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

2018-05-17

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

Call for consistent coding in diabetes mellitus using the Royal College of General Practitioners and NHS pragmatic classification of diabetes

Directory of Open Access Journals (Sweden)

Simon de Lusignan

2013-03-01

Full Text Available Background The prevalence of diabetes is increasing with growing levels of obesity and an aging population. New practical guidelines for diabetes provide an applicable classification. Inconsistent coding of diabetes hampers the use of computerised disease registers for quality improvement, and limits the monitoring of disease trends.Objective To develop a consensus set of codes that should be used when recording diabetes diagnostic data.Methods The consensus approach was hierarchical, with a preference for diagnostic/disorder codes, to define each type of diabetes and non-diabetic hyperglycaemia, which were listed as being completely, partially or not readily mapped to available codes. The practical classification divides diabetes into type 1 (T1DM, type 2 (T2DM, genetic, other, unclassified and non-diabetic fasting hyperglycaemia. We mapped the classification to Read version 2, Clinical Terms version 3 and SNOMED CT.Results T1DMand T2DM were completely mapped to appropriate codes. However, in other areas only partial mapping is possible. Genetics is a fast-moving field and there were considerable gaps in the available labels for genetic conditions; what the classification calls ‘other’ the coding system labels ‘secondary’ diabetes. The biggest gap was the lack of a code for diabetes where the type of diabetes was uncertain. Notwithstanding these limitations we were able to develop a consensus list.Conclusions It is a challenge to develop codes that readily map to contemporary clinical concepts. However, clinicians should adopt the standard recommended codes; and audit the quality of their existing records.

Genetic algorithms - A new technique for solving the neutron spectrum unfolding problem

International Nuclear Information System (INIS)

Freeman, David W.; Edwards, D. Ray; Bolon, Albert E.

1999-01-01

A new technique utilizing genetic algorithms has been applied to the Bonner sphere neutron spectrum unfolding problem. Genetic algorithms are part of a relatively new field of 'evolutionary' solution techniques that mimic living systems with computer-simulated 'chromosome' solutions. Solutions mate and mutate to create better solutions. Several benchmark problems, considered representative of radiation protection environments, have been evaluated using the newly developed UMRGA code which implements the genetic algorithm unfolding technique. The results are compared with results from other well-established unfolding codes. The genetic algorithm technique works remarkably well and produces solutions with relatively high spectral qualities. UMRGA appears to be a superior technique in the absence of a priori data - it does not rely on 'lucky' guesses of input spectra. Calculated personnel doses associated with the unfolded spectra match benchmark values within a few percent

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

KAUST Repository

Alam, Tanvir

2014-10-02

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection

Science.gov (United States)

It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs ...

Therapeutic targeting of non-coding RNAs in cancer

Czech Academy of Sciences Publication Activity Database

Slabý, O.; Laga, Richard; Sedláček, Ondřej

2017-01-01

Roč. 474, č. 24 (2017), s. 4219-4251 ISSN 0264-6021 R&D Projects: GA MŠk(CZ) LQ1604; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 Keywords : non-coding RNA * RNA delivery * polymer carriers Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemical research methods Impact factor: 3.797, year: 2016

Genetics of immune-mediated disorders : from genome-wide association to molecular mechanism

NARCIS (Netherlands)

Kumar, Vinod; Wijmenga, Cisca; Xavier, Ramnik J.

2014-01-01

Genetic association studies have identified not only hundreds of susceptibility loci to immune-mediated diseases but also pinpointed causal amino-acid variants of HLA genes that contribute to many autoimmune reactions. Majority of non-HLA genetic variants are located within non-coding regulatory

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

NARCIS (Netherlands)

Stringer, S.

2015-01-01

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

The in-core fuel management code system for VVER reactors

International Nuclear Information System (INIS)

Cada, R.; Krysl, V.; Mikolas, P.; Sustek, J.; Svarny, J.

2004-01-01

The structure and methodology of a fuel management system for NPP VVER 1000 (NPP Temelin) and VVER 440 (NPP Dukovany) is described. It is under development in SKODA JS a.s. and is followed by practical applications. The general objectives of the system are maximization of end of cycle reactivity, the minimization of fresh fuel inventory for the minimization of fed enrichment and minimization of burnable poisons (BPs) inventory. They are also safety related constraints in witch minimization of power peaking plays a dominant role. General structure of the system consists in preparation of input data for macrocode calculation, algorithms (codes) for optimization of fuel loading, calculation of fuel enrichment and BPs assignment. At present core loading can be calculated (optimized) by Tabu search algorithm (code ATHENA), genetic algorithm (code Gen1) and hybrid algorithm - simplex procedure with application of Tabu search algorithm on binary shuffling (code OPAL B ). Enrichment search is realized by the application of simplex algorithm (OPAL B code) and BPs assignment by module BPASS and simplex algorithm in OPAL B code. Calculations of the real core loadings are presented and a comparison of different optimization methods is provided. (author)

Integrated analysis of genetic data with R

Directory of Open Access Journals (Sweden)

Zhao Jing

2006-01-01

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

Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval

DEFF Research Database (Denmark)

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

2018-01-01

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

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...

Privacy rules for DNA databanks. Protecting coded 'future diaries'.

Science.gov (United States)

Annas, G J

1993-11-17

In privacy terms, genetic information is like medical information. But the information contained in the DNA molecule itself is more sensitive because it contains an individual's probabilistic "future diary," is written in a code that has only partially been broken, and contains information about an individual's parents, siblings, and children. Current rules for protecting the privacy of medical information cannot protect either genetic information or identifiable DNA samples stored in DNA databanks. A review of the legal and public policy rationales for protecting genetic privacy suggests that specific enforceable privacy rules for DNA databanks are needed. Four preliminary rules are proposed to govern the creation of DNA databanks, the collection of DNA samples for storage, limits on the use of information derived from the samples, and continuing obligations to those whose DNA samples are in the databanks.

Genetic structure of arbuscular mycorrhizal populations in fallow and cultivated soils

DEFF Research Database (Denmark)

Rosendahl, Søren; Matzen, Hans

2008-01-01

protein-coding genes GmFOX2 and GmTOR2 were used as co-dominant genetic markers together with the large subunit (LSU) rDNA. The gene diversity and genetic structure of Glomus mosseae, Glomus geosporum and Glomus caledonium were compared within and between the fields. •  Spores of G. caledonium and G...

Assessment of genetic diversity among maize accessions using inter ...

African Journals Online (AJOL)

NRCC

2011-11-07

Nov 7, 2011 ... Key words: Zea mays, Tripsacum sp., genetic narrowing, gene pool, DNA markers. INTRODUCTION ... coding, genomic mapping and evolutionary biology (Reddy et al., 2002). ... (http://www.r-project.org). RESULTS AND ...

Open Genetic Code: on open source in the life sciences

OpenAIRE

Deibel, Eric

2014-01-01

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

A novel progressively swarmed mixed integer genetic algorithm for ...

African Journals Online (AJOL)

MIGA) which inherits the advantages of binary and real coded Genetic Algorithm approach. The proposed algorithm is applied for the conventional generation cost minimization Optimal Power Flow (OPF) problem and for the Security ...

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

DEFF Research Database (Denmark)

Hansen, Johan Peder

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

Time-Delay System Identification Using Genetic Algorithm

DEFF Research Database (Denmark)

Yang, Zhenyu; Seested, Glen Thane

2013-01-01

problem through an identification approach using the real coded Genetic Algorithm (GA). The desired FOPDT/SOPDT model is directly identified based on the measured system's input and output data. In order to evaluate the quality and performance of this GA-based approach, the proposed method is compared...

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

https://www.ias.ac.in/article/fulltext/jgen/095/01/0003-0012. Keywords. codon usage; eukaryotes; nonstandard genetic code; phages; prokaryotes; transfer RNA; translation factors; viruses. Author Affiliations. Sushil Kumar1 2 Renu Kumari2 Vishakha Sharma1 2. SKA Institution for Research, Education and Development, ...

WONOEP appraisal: new genetic approaches to study epilepsy

Science.gov (United States)

Rossignol, Elsa; Kobow, Katja; Simonato, Michele; Loeb, Jeffrey A.; Grisar, Thierry; Gilby, Krista L.; Vinet, Jonathan; Kadam, Shilpa D.; Becker, Albert J.

2014-01-01

Objective New genetic investigation techniques, including next-generation sequencing, epigenetic profiling, cell lineage mapping, targeted genetic manipulation of specific neuronal cell types, stem cell reprogramming and optogenetic manipulations within epileptic networks are progressively unravelling the mysteries of epileptogenesis and ictogenesis. These techniques have opened new avenues to discover the molecular basis of epileptogenesis and to study the physiological impacts of mutations in epilepsy-associated genes on a multilayer level, from cells to circuits. Methods This manuscript reviews recently published applications of these new genetic technologies in the study of epilepsy, as well as work presented by the authors at the genetic session of the XII Workshop on the Neurobiology of Epilepsy in Quebec, Canada. Results Next-generation sequencing is providing investigators with an unbiased means to assess the molecular causes of sporadic forms of epilepsy and have revealed the complexity and genetic heterogeneity of sporadic epilepsy disorders. To assess the functional impact of mutations in these newly identified genes on specific neuronal cell-types during brain development, new modeling strategies in animals, including conditional genetics in mice and in utero knockdown approaches, are enabling functional validation with exquisite cell-type and temporal specificity. In addition, optogenetics, using cell-type specific Cre recombinase driver lines, is enabling investigators to dissect networks involved in epilepsy. Genetically-encoded cell-type labeling is also providing new means to assess the role of the non-neuronal components of epileptic networks such as glial cells. Furthermore, beyond its role in revealing coding variants involved in epileptogenesis, next-generation sequencing can be used to assess the epigenetic modifications that lead to sustained network hyperexcitability in epilepsy, including methylation changes in gene promoters and non-coding

Automatic coding method of the ACR Code

International Nuclear Information System (INIS)

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

1993-01-01

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

Development of a BWR loading pattern design system based on modified genetic algorithms and knowledge

International Nuclear Information System (INIS)

Martin-del-Campo, Cecilia; Francois, Juan Luis; Avendano, Linda; Gonzalez, Mario

2004-01-01

An optimization system based on Genetic Algorithms (GAs), in combination with expert knowledge coded in heuristics rules, was developed for the design of optimized boiling water reactor (BWR) fuel loading patterns. The system was coded in a computer program named Loading Pattern Optimization System based on Genetic Algorithms, in which the optimization code uses GAs to select candidate solutions, and the core simulator code CM-PRESTO to evaluate them. A multi-objective function was built to maximize the cycle energy length while satisfying power and reactivity constraints used as BWR design parameters. Heuristic rules were applied to satisfy standard fuel management recommendations as the Control Cell Core and Low Leakage loading strategies, and octant symmetry. To test the system performance, an optimized cycle was designed and compared against an actual operating cycle of Laguna Verde Nuclear Power Plant, Unit I

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

Science.gov (United States)

Mattick, John S

2003-10-01

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

Something about Genetics in Psychiatry

Directory of Open Access Journals (Sweden)

Bakir Mehić

2012-11-01

of the brain functioning and connect them with the hereditary basis. An important advantage of the endophenotype evaluation is also, that it can work in small groups of respondents. Endophenotype evaluation includes an assessment of cognitive deficits, EEG abnormalities, and data obtained by the method of neuroimaging. Considering the current cognition about the genetics of psychiatric disorders, especially schizophrenia [2], it can be said that no single gene by itself causes brain dysfunction. Many gene variants that have proved to be risky for psychiatric disorders have also been found in many healthy individuals. Strength of correlation of the detected genetic polymorphisms is estimated to be relatively low. This means: COMT genes’ polymorphisms (catecho-O-methyltransferase, but also many other genes, modulate cognitive functions, but they do not represent the primary cause of disease[3],genetic risk variants for psychiatric disorders are also found in many healthy people,“Strength” of correlation of detected genetic polymorphisms and diseases is estimated as relative. Except for the primary sequence of nucleotides in our genome, there is also likely a hidden genetic code, which does not determine the sequence of amino acids in proteins, but it determines the time when a gene turns on or off (rewrites or not. The problem with this code is that it is more or less changeable. It is because of the modification of the genome (DNA. The modification with metillization of cytosine in CpG dinucleotide turns off the gene, whereas the acetylation of histones alters the structure of chromatin and turns on the genes. Epigenetics studies[4] such modifications of genomes. Epigenetics may explain the large variability of phenotypes in human population, and why monozygotic twins are not quite identical. They do not differ in the sequence of nucleotides in DNA, but they have different modifications of DNA, because they occur and change by the effect of environmental

Coding in pigeons: Multiple-coding versus single-code/default strategies.

Science.gov (United States)

Pinto, Carlos; Machado, Armando

2015-05-01

To investigate the coding strategies that pigeons may use in a temporal discrimination tasks, pigeons were trained on a matching-to-sample procedure with three sample durations (2s, 6s and 18s) and two comparisons (red and green hues). One comparison was correct following 2-s samples and the other was correct following both 6-s and 18-s samples. Tests were then run to contrast the predictions of two hypotheses concerning the pigeons' coding strategies, the multiple-coding and the single-code/default. According to the multiple-coding hypothesis, three response rules are acquired, one for each sample. According to the single-code/default hypothesis, only two response rules are acquired, one for the 2-s sample and a "default" rule for any other duration. In retention interval tests, pigeons preferred the "default" key, a result predicted by the single-code/default hypothesis. In no-sample tests, pigeons preferred the key associated with the 2-s sample, a result predicted by multiple-coding. Finally, in generalization tests, when the sample duration equaled 3.5s, the geometric mean of 2s and 6s, pigeons preferred the key associated with the 6-s and 18-s samples, a result predicted by the single-code/default hypothesis. The pattern of results suggests the need for models that take into account multiple sources of stimulus control. © Society for the Experimental Analysis of Behavior.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

This noticeable hot spot regions hold higher frequency (50%) of pathogenic / likely pathogenic genetic variants constituting single nucleotide variants than large deletion and insertion that actually represents only 41.08% of coding sequence ofPKD2. Statistically significant association for IVS3-22AA genotype was observed ...

Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

Energy Technology Data Exchange (ETDEWEB)

Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S. [Univ. of Bonn (Germany)] [and others

1995-10-09

In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains a functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.

Code Cactus; Code Cactus

Energy Technology Data Exchange (ETDEWEB)

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

1966-09-01

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

Genetic variation in KCNA5

DEFF Research Database (Denmark)

Christophersen, Ingrid E; Olesen, Morten S; Liang, Bo

2012-01-01

AimsGenetic factors may be important in the development of atrial fibrillation (AF) in the young. KCNA5 encodes the potassium channel a-subunit K(V)1.5, which underlies the voltage-gated atrial-specific potassium current I(Kur). KCNAB2 encodes K(V)ß2, a ß-subunit of K(V)1.5, which increases I......(Kur). Three studies have identified loss-of-function mutations in KCNA5 in patients with idiopathic AF. We hypothesized that early-onset lone AF is associated with high prevalence of genetic variants in KCNA5 and KCNAB2.Methods and resultsThe coding sequences of KCNA5 and KCNAB2 were sequenced in 307 patients...

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Cotranslational protein folding reveals the selective use of synonymous codons along the coding sequence of a low expression gene ... Genetic analysis to identify good combiners for ToLCV resistance and yield components in tomato ... The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, ...

Evaluation Codes from an Affine Veriety Code Perspective

DEFF Research Database (Denmark)

Geil, Hans Olav

2008-01-01

Evaluation codes (also called order domain codes) are traditionally introduced as generalized one-point geometric Goppa codes. In the present paper we will give a new point of view on evaluation codes by introducing them instead as particular nice examples of affine variety codes. Our study...... includes a reformulation of the usual methods to estimate the minimum distances of evaluation codes into the setting of affine variety codes. Finally we describe the connection to the theory of one-pointgeometric Goppa codes. Contents 4.1 Introduction...... . . . . . . . . . . . . . . . . . . . . . . . 171 4.9 Codes form order domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 4.10 One-point geometric Goppa codes . . . . . . . . . . . . . . . . . . . . . . . . 176 4.11 Bibliographical Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 References...

Kinetic models of gene expression including non-coding RNAs

Energy Technology Data Exchange (ETDEWEB)

Zhdanov, Vladimir P., E-mail: zhdanov@catalysis.r

2011-03-15

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury.

Science.gov (United States)

Arthur-Farraj, Peter J; Morgan, Claire C; Adamowicz, Martyna; Gomez-Sanchez, Jose A; Fazal, Shaline V; Beucher, Anthony; Razzaghi, Bonnie; Mirsky, Rhona; Jessen, Kristjan R; Aitman, Timothy J

2017-09-12

Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A new coding system for metabolic disorders demonstrates gaps in the international disease classifications ICD-10 and SNOMED-CT, which can be barriers to genotype-phenotype data sharing.

Science.gov (United States)

Sollie, Annet; Sijmons, Rolf H; Lindhout, Dick; van der Ploeg, Ans T; Rubio Gozalbo, M Estela; Smit, G Peter A; Verheijen, Frans; Waterham, Hans R; van Weely, Sonja; Wijburg, Frits A; Wijburg, Rudolph; Visser, Gepke

2013-07-01

Data sharing is essential for a better understanding of genetic disorders. Good phenotype coding plays a key role in this process. Unfortunately, the two most widely used coding systems in medicine, ICD-10 and SNOMED-CT, lack information necessary for the detailed classification and annotation of rare and genetic disorders. This prevents the optimal registration of such patients in databases and thus data-sharing efforts. To improve care and to facilitate research for patients with metabolic disorders, we developed a new coding system for metabolic diseases with a dedicated group of clinical specialists. Next, we compared the resulting codes with those in ICD and SNOMED-CT. No matches were found in 76% of cases in ICD-10 and in 54% in SNOMED-CT. We conclude that there are sizable gaps in the SNOMED-CT and ICD coding systems for metabolic disorders. There may be similar gaps for other classes of rare and genetic disorders. We have demonstrated that expert groups can help in addressing such coding issues. Our coding system has been made available to the ICD and SNOMED-CT organizations as well as to the Orphanet and HPO organizations for further public application and updates will be published online (www.ddrmd.nl and www.cineas.org). © 2013 WILEY PERIODICALS, INC.

An Optimal Linear Coding for Index Coding Problem

OpenAIRE

Pezeshkpour, Pouya

2015-01-01

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

Single nucleotide polymorphisms (SNPs in coding regions of canine dopamine- and serotonin-related genes

Directory of Open Access Journals (Sweden)

Lingaas Frode

2008-01-01

Full Text Available Abstract Background Polymorphism in genes of regulating enzymes, transporters and receptors of the neurotransmitters of the central nervous system have been associated with altered behaviour, and single nucleotide polymorphisms (SNPs represent the most frequent type of genetic variation. The serotonin and dopamine signalling systems have a central influence on different behavioural phenotypes, both of invertebrates and vertebrates, and this study was undertaken in order to explore genetic variation that may be associated with variation in behaviour. Results Single nucleotide polymorphisms in canine genes related to behaviour were identified by individually sequencing eight dogs (Canis familiaris of different breeds. Eighteen genes from the dopamine and the serotonin systems were screened, revealing 34 SNPs distributed in 14 of the 18 selected genes. A total of 24,895 bp coding sequence was sequenced yielding an average frequency of one SNP per 732 bp (1/732. A total of 11 non-synonymous SNPs (nsSNPs, which may be involved in alteration of protein function, were detected. Of these 11 nsSNPs, six resulted in a substitution of amino acid residue with concomitant change in structural parameters. Conclusion We have identified a number of coding SNPs in behaviour-related genes, several of which change the amino acids of the proteins. Some of the canine SNPs exist in codons that are evolutionary conserved between five compared species, and predictions indicate that they may have a functional effect on the protein. The reported coding SNP frequency of the studied genes falls within the range of SNP frequencies reported earlier in the dog and other mammalian species. Novel SNPs are presented and the results show a significant genetic variation in expressed sequences in this group of genes. The results can contribute to an improved understanding of the genetics of behaviour.

Genetic maps and physical units

International Nuclear Information System (INIS)

Karunakaran, V.; Holt, G.

1976-01-01

The relationships between physical and genetic units are examined. Genetic mapping involves the detection of linkage of genes and the measurement of recombination frequencies. The genetic distance is measured in map units and is proportional to the recombination frequencies between linked markers. Physical mapping of genophores, particularly the simple genomes of bacteriophages and bacterial plasmids can be achieved through heteroduplex analysis. Genetic distances are dependent on recombination frequencies and, therefore, can only be correlated accurately with physical unit lengths if the recombination frequency is constant throughout the entire genome. Methods are available to calculate the equivalent length of DNA per average map unit in different organisms. Such estimates indicate significant differences from one organism to another. Gene lengths can also be calculated from the number of amino acids in a specified polypeptide and relating this to the number of nucleotides required to code for such a polypeptide. Many attempts have been made to relate microdosimetric measurements to radiobiological data. For irradiation effects involving deletion of genetic material such a detailed correlation may be possible in systems where heteroduplex analysis or amino acid sequencing can be performed. The problems of DNA packaging and other functional associations within the cell in interpreting data is discussed

Innovation of genetic algorithm code GenA for WWER fuel loading optimization

International Nuclear Information System (INIS)

Sustek, J.

2005-01-01

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

Use of Contemporary Genetics in Cardiovascular Diagnosis

Science.gov (United States)

George, Alfred L.

2015-01-01

An explosion of knowledge regarding the genetic and genomic basis for rare and common diseases has provided a framework for revolutionizing the practice of medicine. Achieving the reality of a genomic medicine era requires that basic discoveries are effectively translated into clinical practice through implementation of genetic and genomic testing. Clinical genetic tests have become routine for many inherited disorders and can be regarded as the standard-of-care in many circumstances including disorders affecting the cardiovascular system. New, high-throughput methods for determining the DNA sequence of all coding exons or complete genomes are being adopted for clinical use to expand the speed and breadth of genetic testing. Along with these extraordinary advances have emerged new challenges to practicing physicians for understanding when and how to use genetic testing along with how to appropriately interpret test results. This review will acquaint readers with general principles of genetic testing including newer technologies, test interpretation and pitfalls. The focus will be on testing genes responsible for monogenic disorders and on other emerging applications such as pharmacogenomic profiling. The discussion will be extended to the new paradigm of direct-to-consumer genetic testing and the value of assessing genomic risk for common diseases. PMID:25421045

[MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

Science.gov (United States)

Liu, Ren-Hu; Meng, Jin-Ling

2003-05-01

MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

Rate-adaptive BCH codes for distributed source coding

DEFF Research Database (Denmark)

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

2013-01-01

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

Diagonal Eigenvalue Unity (DEU) code for spectral amplitude coding-optical code division multiple access

Science.gov (United States)

Ahmed, Hassan Yousif; Nisar, K. S.

2013-08-01

Code with ideal in-phase cross correlation (CC) and practical code length to support high number of users are required in spectral amplitude coding-optical code division multiple access (SAC-OCDMA) systems. SAC systems are getting more attractive in the field of OCDMA because of its ability to eliminate the influence of multiple access interference (MAI) and also suppress the effect of phase induced intensity noise (PIIN). In this paper, we have proposed new Diagonal Eigenvalue Unity (DEU) code families with ideal in-phase CC based on Jordan block matrix with simple algebraic ways. Four sets of DEU code families based on the code weight W and number of users N for the combination (even, even), (even, odd), (odd, odd) and (odd, even) are constructed. This combination gives DEU code more flexibility in selection of code weight and number of users. These features made this code a compelling candidate for future optical communication systems. Numerical results show that the proposed DEU system outperforms reported codes. In addition, simulation results taken from a commercial optical systems simulator, Virtual Photonic Instrument (VPI™) shown that, using point to multipoint transmission in passive optical network (PON), DEU has better performance and could support long span with high data rate.

How Sensitive Is Genetic Data?

Science.gov (United States)

Sariyar, Murat; Suhr, Stephanie; Schlünder, Irene

2017-12-01

The rising demand to use genetic data for research goes hand in hand with an increased awareness of privacy issues related to its use. Using human genetic data in a legally compliant way requires an examination of the legal basis as well as an assessment of potential disclosure risks. Focusing on the relevant legal framework in the European Union, we discuss open questions and uncertainties around the handling of genetic data in research, which can result in the introduction of unnecessary hurdles for data sharing. First, we discuss defining features and relative disclosure risks of some DNA-related biomarkers, distinguishing between the risk for disclosure of (1) the identity of an individual, (2) information about an individual's health and behavior, including previously unknown phenotypes, and (3) information about an individual's blood relatives. Second, we discuss the European legal framework applicable to the use of DNA-related biomarkers in research, the implications of including both inherited and acquired traits in the legal definition, as well as the issue of "genetic exceptionalism"-the notion that genetic information has inherent characteristics that require different considerations than other health and medical information. Finally, by mapping the legal to specific technical definitions, we draw some initial conclusions concerning how sensitive different types of "genetic data" may actually be. We argue that whole genome sequences may justifiably be considered "exceptional" and require special protection, whereas other genetic data that do not fulfill the same criteria should be treated in a similar manner to other clinical data. This kind of differentiation should be reflected by the law and/or other governance frameworks as well as agreed Codes of Conduct when using the term "genetic data."

List Decoding of Matrix-Product Codes from nested codes: an application to Quasi-Cyclic codes

DEFF Research Database (Denmark)

Hernando, Fernando; Høholdt, Tom; Ruano, Diego

2012-01-01

A list decoding algorithm for matrix-product codes is provided when $C_1,..., C_s$ are nested linear codes and $A$ is a non-singular by columns matrix. We estimate the probability of getting more than one codeword as output when the constituent codes are Reed-Solomon codes. We extend this list...... decoding algorithm for matrix-product codes with polynomial units, which are quasi-cyclic codes. Furthermore, it allows us to consider unique decoding for matrix-product codes with polynomial units....

Genetic Testing for Respiratory Disease: Are We There Yet?

Directory of Open Access Journals (Sweden)

Peter D Paré

2012-01-01

Full Text Available The human genome project promised a revolution in health care – the development of ‘personalized medicine’, where knowledge of an individual’s genetic code enables the prediction of risk for specific diseases and the potential to alter that risk based on preventive measures and lifestyle modification. The present brief review provides a report card on the progress toward that goal with respect to respiratory disease. Should generalized population screening for genetic risk factors for respiratory disease be instituted? Or not?

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.

The genetic basis of DOORS syndrome : an exome-sequencing study

NARCIS (Netherlands)

Campeau, Philippe M.; Kasperaviciute, Dalia; Lu, James T.; Burrage, Lindsay C.; Kim, Choel; Hori, Mutsuki; Powell, Berkley R.; Stewart, Fiona; Felix, Temis Maria; van den Ende, Jenneke; Wisniewska, Marzena; Kayserili, Huelya; Rump, Patrick; Nampoothiri, Sheela; Aftimos, Salim; Mey, Antje; Nair, Lal D. V.; Begleiter, Michael L.; De Bie, Isabelle; Meenakshi, Girish; Murray, Mitzi L.; Repetto, Gabriela M.; Golabi, Mahin; Blair, Edward; Male, Alison; Giuliano, Fabienne; Kariminejad, Ariana; Newman, William G.; Bhaskar, Sanjeev S.; Dickerson, Jonathan E.; Kerr, Bronwyn; Banka, Siddharth; Giltay, Jacques C.; Wieczorek, Dagmar; Tostevin, Anna; Wiszniewska, Joanna; Cheung, Sau Wai; Hennekam, Raoul C.; Gibbs, Richard A.; Lee, Brendan H.; Sisodiya, Sanjay M.

Background Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome is a rare autosomal recessive disorder of unknown cause. We aimed to identify the genetic basis of this syndrome by sequencing most coding exons in affected individuals. Methods Through a search

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.

Combinatorial neural codes from a mathematical coding theory perspective.

Science.gov (United States)

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

2013-07-01

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

A Hybrid Genetic Algorithm Approach for Optimal Power Flow

Directory of Open Access Journals (Sweden)

Sydulu Maheswarapu

2011-08-01

Full Text Available This paper puts forward a reformed hybrid genetic algorithm (GA based approach to the optimal power flow. In the approach followed here, continuous variables are designed using real-coded GA and discrete variables are processed as binary strings. The outcomes are compared with many other methods like simple genetic algorithm (GA, adaptive genetic algorithm (AGA, differential evolution (DE, particle swarm optimization (PSO and music based harmony search (MBHS on a IEEE30 bus test bed, with a total load of 283.4 MW. Its found that the proposed algorithm is found to offer lowest fuel cost. The proposed method is found to be computationally faster, robust, superior and promising form its convergence characteristics.

LDGM Codes for Channel Coding and Joint Source-Channel Coding of Correlated Sources

Directory of Open Access Journals (Sweden)

Javier Garcia-Frias

2005-05-01

Full Text Available We propose a coding scheme based on the use of systematic linear codes with low-density generator matrix (LDGM codes for channel coding and joint source-channel coding of multiterminal correlated binary sources. In both cases, the structures of the LDGM encoder and decoder are shown, and a concatenated scheme aimed at reducing the error floor is proposed. Several decoding possibilities are investigated, compared, and evaluated. For different types of noisy channels and correlation models, the resulting performance is very close to the theoretical limits.

Non-coding RNAs and epigenome: de novo DNA methylation, allelic exclusion and X-inactivation

Directory of Open Access Journals (Sweden)

V. A. Halytskiy

2013-12-01

Full Text Available Non-coding RNAs are widespread class of cell RNAs. They participate in many important processes in cells – signaling, posttranscriptional silencing, protein biosynthesis, splicing, maintenance of genome stability, telomere lengthening, X-inactivation. Nevertheless, activity of these RNAs is not restricted to posttranscriptional sphere, but cover also processes that change or maintain the epigenetic information. Non-coding RNAs can directly bind to the DNA targets and cause their repression through recruitment of DNA methyltransferases as well as chromatin modifying enzymes. Such events constitute molecular mechanism of the RNA-dependent DNA methylation. It is possible, that the RNA-DNA interaction is universal mechanism triggering DNA methylation de novo. Allelic exclusion can be also based on described mechanism. This phenomenon takes place, when non-coding RNA, which precursor is transcribed from one allele, triggers DNA methylation in all other alleles present in the cell. Note, that miRNA-mediated transcriptional silencing resembles allelic exclusion, because both miRNA gene and genes, which can be targeted by this miRNA, contain elements with the same sequences. It can be assumed that RNA-dependent DNA methylation and allelic exclusion originated with the purpose of counteracting the activity of mobile genetic elements. Probably, thinning and deregulation of the cellular non-coding RNA pattern allows reactivation of silent mobile genetic elements resulting in genome instability that leads to ageing and carcinogenesis. In the course of X-inactivation, DNA methylation and subsequent hete­rochromatinization of X chromosome can be triggered by direct hybridization of 5′-end of large non-coding RNA Xist with DNA targets in remote regions of the X chromosome.

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.

Discussion on LDPC Codes and Uplink Coding

Science.gov (United States)

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

2007-01-01

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

A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.

Science.gov (United States)

Blair, David R; Lyttle, Christopher S; Mortensen, Jonathan M; Bearden, Charles F; Jensen, Anders Boeck; Khiabanian, Hossein; Melamed, Rachel; Rabadan, Raul; Bernstam, Elmer V; Brunak, Søren; Jensen, Lars Juhl; Nicolae, Dan; Shah, Nigam H; Grossman, Robert L; Cox, Nancy J; White, Kevin P; Rzhetsky, Andrey

2013-09-26

Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to complex disease risk. We detect thousands of associations between Mendelian and complex diseases, revealing a nondegenerate, phenotypic code that links each complex disorder to a unique collection of Mendelian loci. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this "Mendelian code." Finally, we detect hundreds of comorbidity associations among Mendelian disorders, and we use probabilistic genetic modeling to demonstrate that Mendelian variants likely contribute nonadditively to the risk for a subset of complex diseases. Overall, this study illustrates a complementary approach for mapping complex disease loci and provides unique predictions concerning the etiologies of specific diseases. Copyright © 2013 Elsevier Inc. All rights reserved.

Conceptual Approach to Forming the Basic Code of Neo-Industrial Development of a Region

Directory of Open Access Journals (Sweden)

Elena Leonidovna Andreeva

2017-09-01

Full Text Available In the article, the authors propose the conceptual fundamentals of the “code approach” to the regional neo-industrial development. The purpose of the research is to reveal the essence of the transition to a new type of industrial and economic relations through a prism of “genetic codes” of the region. We consider these codes as a system of the “racial memory” of a territory, which determines the specificity and features of neo-industrialization realization. We substantiated the hypothesis about the influence of the “genetic codes” of the region on the effectiveness of the neo-industrialization. We have defined the participants, or else the carriers of the codes in the transformation of regional inheritance for the stimulation of the neoindustrial development of region’s economy. The subject matter of the research is the distinctive features of the functioning of the determinative region’s codes. Their content determines the socio-economic specificity of the region and the features of innovative, informational, value-based and competence-based development of the territory. The determinative codes generate the dynamic codes of the region, which are understood as their derivatives. They have a high probability of occurrence, higher speed of development and distribution, internal forces that make possible the self-development of the region. The scientific contribution is the substantiation of the basic code of the regional neo-industrial development. It represents the evolutionary accumulation of the rapid changes of its innovative, informational, value-based and competence-based codes stimulating the generation and implementation of new ideas regarding to economic entities adapted to the historical and cultural conditions. The article presents the code model of neo-industrial development of the region described by formulas. We applied the system analysis methods, historical and civilization approaches, evolutionary and

Optimization of multicast optical networks with genetic algorithm

Science.gov (United States)

Lv, Bo; Mao, Xiangqiao; Zhang, Feng; Qin, Xi; Lu, Dan; Chen, Ming; Chen, Yong; Cao, Jihong; Jian, Shuisheng

2007-11-01

In this letter, aiming to obtain the best multicast performance of optical network in which the video conference information is carried by specified wavelength, we extend the solutions of matrix games with the network coding theory and devise a new method to solve the complex problems of multicast network switching. In addition, an experimental optical network has been testified with best switching strategies by employing the novel numerical solution designed with an effective way of genetic algorithm. The result shows that optimal solutions with genetic algorithm are accordance with the ones with the traditional fictitious play method.

The genetic basis of DOORS syndrome: an exome-sequencing study

NARCIS (Netherlands)

Campeau, Philippe M.; Kasperaviciute, Dalia; Lu, James T.; Burrage, Lindsay C.; Kim, Choel; Hori, Mutsuki; Powell, Berkley R.; Stewart, Fiona; Félix, Têmis Maria; van den Ende, Jenneke; Wisniewska, Marzena; Kayserili, Hülya; Rump, Patrick; Nampoothiri, Sheela; Aftimos, Salim; Mey, Antje; Nair, Lal D. V.; Begleiter, Michael L.; de Bie, Isabelle; Meenakshi, Girish; Murray, Mitzi L.; Repetto, Gabriela M.; Golabi, Mahin; Blair, Edward; Male, Alison; Giuliano, Fabienne; Kariminejad, Ariana; Newman, William G.; Bhaskar, Sanjeev S.; Dickerson, Jonathan E.; Kerr, Bronwyn; Banka, Siddharth; Giltay, Jacques C.; Wieczorek, Dagmar; Tostevin, Anna; Wiszniewska, Joanna; Cheung, Sau Wai; Hennekam, Raoul C.; Gibbs, Richard A.; Lee, Brendan H.; Sisodiya, Sanjay M.

2014-01-01

Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome is a rare autosomal recessive disorder of unknown cause. We aimed to identify the genetic basis of this syndrome by sequencing most coding exons in affected individuals. Through a search of available case

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…

Genetic diagnosis of a Chinese multiple endocrine neoplasia type ...

Indian Academy of Sciences (India)

However, different families with MEN 2A due to the same RET mutation often have significant variability inthe clinical exhibition of disease and aggressiveness of the MTC, which implies additional genetic loci exsit beyondRET coding region. Whole genome sequencing (WGS) greatly expands the breadth of screening from ...

Genetically Modified (GM) Foods and Ethical Eating.

Science.gov (United States)

Dizon, Francis; Costa, Sarah; Rock, Cheryl; Harris, Amanda; Husk, Cierra; Mei, Jenny

2016-02-01

The ability to manipulate and customize the genetic code of living organisms has brought forth the production of genetically modified organisms (GMOs) and consumption of genetically modified (GM) foods. The potential for GM foods to improve the efficiency of food production, increase customer satisfaction, and provide potential health benefits has contributed to the rapid incorporation of GM foods into the American diet. However, GM foods and GMOs are also a topic of ethical debate. The use of GM foods and GM technology is surrounded by ethical concerns and situational judgment, and should ideally adhere to the ethical standards placed upon food and nutrition professionals, such as: beneficence, nonmaleficence, justice and autonomy. The future of GM foods involves many aspects and trends, including enhanced nutritional value in foods, strict labeling laws, and potential beneficial economic conditions in developing nations. This paper briefly reviews the origin and background of GM foods, while delving thoroughly into 3 areas: (1) GMO labeling, (2) ethical concerns, and (3) health and industry applications. This paper also examines the relationship between the various applications of GM foods and their corresponding ethical issues. Ethical concerns were evaluated in the context of the code of ethics developed by the Academy of Nutrition and Dietetics (AND) that govern the work of food and nutrition professionals. Overall, there is a need to stay vigilant about the many ethical implications of producing and consuming GM foods and GMOs. © 2015 Institute of Food Technologists®

Genetics of Congenital Heart Disease: Past and Present.

Science.gov (United States)

Muntean, Iolanda; Togănel, Rodica; Benedek, Theodora

2017-04-01

Congenital heart disease is the most common congenital anomaly, representing an important cause of infant morbidity and mortality. Congenital heart disease represents a group of heart anomalies that include septal defects, valve defects, and outflow tract anomalies. The exact genetic, epigenetic, or environmental basis of congenital heart disease remains poorly understood, although the exact mechanism is likely multifactorial. However, the development of new technologies including copy number variants, single-nucleotide polymorphism, next-generation sequencing are accelerating the detection of genetic causes of heart anomalies. Recent studies suggest a role of small non-coding RNAs, micro RNA, in congenital heart disease. The recently described epigenetic factors have also been found to contribute to cardiac morphogenesis. In this review, we present past and recent genetic discoveries in congenital heart disease.

New quantum codes constructed from quaternary BCH codes

Science.gov (United States)

Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

2016-10-01

In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

Entanglement-assisted quantum MDS codes from negacyclic codes

Science.gov (United States)

Lu, Liangdong; Li, Ruihu; Guo, Luobin; Ma, Yuena; Liu, Yang

2018-03-01

The entanglement-assisted formalism generalizes the standard stabilizer formalism, which can transform arbitrary classical linear codes into entanglement-assisted quantum error-correcting codes (EAQECCs) by using pre-shared entanglement between the sender and the receiver. In this work, we construct six classes of q-ary entanglement-assisted quantum MDS (EAQMDS) codes based on classical negacyclic MDS codes by exploiting two or more pre-shared maximally entangled states. We show that two of these six classes q-ary EAQMDS have minimum distance more larger than q+1. Most of these q-ary EAQMDS codes are new in the sense that their parameters are not covered by the codes available in the literature.

Visualizing code and coverage changes for code review

NARCIS (Netherlands)

Oosterwaal, Sebastiaan; van Deursen, A.; De Souza Coelho, R.; Sawant, A.A.; Bacchelli, A.

2016-01-01

One of the tasks of reviewers is to verify that code modifications are well tested. However, current tools offer little support in understanding precisely how changes to the code relate to changes to the tests. In particular, it is hard to see whether (modified) test code covers the changed code.

Homological stabilizer codes

Energy Technology Data Exchange (ETDEWEB)

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

2013-03-15

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

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

Science.gov (United States)

Sawamura, Jitsuki; Morishita, Shigeru; Ishigooka, Jun

2014-05-07

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

SPECTRAL AMPLITUDE CODING OCDMA SYSTEMS USING ENHANCED DOUBLE WEIGHT CODE

Directory of Open Access Journals (Sweden)

F.N. HASOON

2006-12-01

Full Text Available A new code structure for spectral amplitude coding optical code division multiple access systems based on double weight (DW code families is proposed. The DW has a fixed weight of two. Enhanced double-weight (EDW code is another variation of a DW code family that can has a variable weight greater than one. The EDW code possesses ideal cross-correlation properties and exists for every natural number n. A much better performance can be provided by using the EDW code compared to the existing code such as Hadamard and Modified Frequency-Hopping (MFH codes. It has been observed that theoretical analysis and simulation for EDW is much better performance compared to Hadamard and Modified Frequency-Hopping (MFH codes.

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.

A field release of genetically engineered gypsy moth (Lymantria dispar L.) Nuclear Polyhedrosis Virus (LdNPV)

Science.gov (United States)

Vincent D' Amico; Joseph S. Elkinton; John D. Podgwaite; James M. Slavicek; Michael L. McManus; John P. Burand

1999-01-01

The gypsy moth (Lymantria dispar L.) nuclear polyhedrosis virus was genetically engineered for nonpersistence by removal of the gene coding for polyhedrin production and stabilized using a coocclusion process. A β-galactosidase marker gene was inserted into the genetically engineered virus (LdGEV) so that infected larvae could be tested for...

RESEARCH NOTE Genetic Analyses for Deciphering the Status and ...

Indian Academy of Sciences (India)

Precision breeding for developing varieties for a specific area would involve ... Presently India is the fifth largest soybean producing country after US, Brazil, ... Genetic analysis at E3 and E4 loci and assessment of effect of photoperiodic ... outsourced (Scigenom, Banglore) for Sanger sequencing of coding region of E1.

Genetic algorithm for the optimization of the loading pattern for reactor core fuel management

International Nuclear Information System (INIS)

Zhou Sheng; Hu Yongming; zheng Wenxiang

2000-01-01

The paper discusses the application of a genetic algorithm to the optimization of the loading pattern for in-core fuel management with the NP characteristics. The algorithm develops a matrix model for the fuel assembly loading pattern. The burnable poisons matrix was assigned randomly considering the distributed nature of the poisons. A method based on the traveling salesman problem was used to solve the problem. A integrated code for in-core fuel management was formed by combining this code with a reactor physics code

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

Science.gov (United States)

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

2018-01-01

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

The conservation of forest genetic resources: case histories from Canada, Mexico, and the United States

Science.gov (United States)

F. Thomas Ledig; J. Jesús Vargas-Hernández; Kurt H. Johnsen

1998-01-01

The genetic codes of living organisms are natural resources no less than soil, air, and water. Genetic resources-from nucleotide sequences in DNA to selected genotypes, populations, and species-are the raw material in forestry: for breeders, for the forest manager who produces an economic crop, for society that reaps the environmental benefits provided by forests, and...

DLLExternalCode

Energy Technology Data Exchange (ETDEWEB)

2014-05-14

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

High efficiency video coding coding tools and specification

CERN Document Server

Wien, Mathias

2015-01-01

The video coding standard High Efficiency Video Coding (HEVC) targets at improved compression performance for video resolutions of HD and beyond, providing Ultra HD video at similar compressed bit rates as for HD video encoded with the well-established video coding standard H.264 | AVC. Based on known concepts, new coding structures and improved coding tools have been developed and specified in HEVC. The standard is expected to be taken up easily by established industry as well as new endeavors, answering the needs of todays connected and ever-evolving online world. This book presents the High Efficiency Video Coding standard and explains it in a clear and coherent language. It provides a comprehensive and consistently written description, all of a piece. The book targets at both, newbies to video coding as well as experts in the field. While providing sections with introductory text for the beginner, it suits as a well-arranged reference book for the expert. The book provides a comprehensive reference for th...

Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis

Directory of Open Access Journals (Sweden)

Angela D. Millar

2018-05-01

Full Text Available Background: Draft and complete genome sequences from bacteria are key tools to understand genetic determinants involved in pathogenesis in several disease models. Piscirickettsia salmonis is a Gram-negative bacterium responsible for the Salmon Rickettsial Syndrome (SRS, a bacterial disease that threatens the sustainability of the Chilean salmon industry. In previous reports, complete and draft genome sequences have been generated and annotated. However, the lack of transcriptome data underestimates the genetic potential, does not provide information about transcriptional units and contributes to disseminate annotation errors. Results: Here we present the draft genome and transcriptome sequences of four P. salmonis strains. We have identified the transcriptional architecture of previously characterized virulence factors and trait-specific genes associated to cation uptake, metal efflux, antibiotic resistance, secretion systems and other virulence factors. Conclusions: This data has provided a refined genome annotation and also new insights on the transcriptional structures and coding potential of this fish pathogen.How to cite: Millar AD, Tapia P, Gomez FA, et al. Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis. Electron J Biotechnol 2018;33. https://doi.org/10.1016/j.ejbt.2018.04.002. Keywords: Bacterial genomes, Coding potential, Comparative analysis, Draft genome, Piscirickettsia salmonis, Reference transcriptome, Refined annotation, Salmon Rickettsial Syndrome, Salmonids

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.

Converter of a continuous code into the Grey code

International Nuclear Information System (INIS)

Gonchar, A.I.; TrUbnikov, V.R.

1979-01-01

Described is a converter of a continuous code into the Grey code used in a 12-charged precision amplitude-to-digital converter to decrease the digital component of spectrometer differential nonlinearity to +0.7% in the 98% range of the measured band. To construct the converter of a continuous code corresponding to the input signal amplitude into the Grey code used is the regularity in recycling of units and zeroes in each discharge of the Grey code in the case of a continuous change of the number of pulses of a continuous code. The converter is constructed on the elements of 155 series, the frequency of continuous code pulse passing at the converter input is 25 MHz

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

Science.gov (United States)

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

2009-01-01

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

Application of genetic algorithm in reactor fuel management

International Nuclear Information System (INIS)

Peng Gang

2002-01-01

The genetic algorithm (GA) has been used in reactor fuel management of core arrangement optimal calculation. The chromosome coding method has been selected, and the parameters in GA operators have been improved, so the quality and efficiency of calculation in GA program have been greatly improved. According to the result, better core fuel position arrangement can be obtained from the GA calculation

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.)

A novel approach to correct the coded aperture misalignment for fast neutron imaging

Energy Technology Data Exchange (ETDEWEB)

Zhang, F. N.; Hu, H. S., E-mail: huasi-hu@mail.xjtu.edu.cn; Wang, D. M.; Jia, J. [School of Energy and Power Engineering, Xi’an Jiaotong University, Xi’an 710049 (China); Zhang, T. K. [Laser Fusion Research Center, CAEP, Mianyang, 621900 Sichuan (China); Jia, Q. G. [Institute of Applied Physics and Computational Mathematics, Beijing 100094 (China)

2015-12-15

Aperture alignment is crucial for the diagnosis of neutron imaging because it has significant impact on the coding imaging and the understanding of the neutron source. In our previous studies on the neutron imaging system with coded aperture for large field of view, “residual watermark,” certain extra information that overlies reconstructed image and has nothing to do with the source is discovered if the peak normalization is employed in genetic algorithms (GA) to reconstruct the source image. Some studies on basic properties of residual watermark indicate that the residual watermark can characterize coded aperture and can thus be used to determine the location of coded aperture relative to the system axis. In this paper, we have further analyzed the essential conditions for the existence of residual watermark and the requirements of the reconstruction algorithm for the emergence of residual watermark. A gamma coded imaging experiment has been performed to verify the existence of residual watermark. Based on the residual watermark, a correction method for the aperture misalignment has been studied. A multiple linear regression model of the position of coded aperture axis, the position of residual watermark center, and the gray barycenter of neutron source with twenty training samples has been set up. Using the regression model and verification samples, we have found the position of the coded aperture axis relative to the system axis with an accuracy of approximately 20 μm. Conclusively, a novel approach has been established to correct the coded aperture misalignment for fast neutron coded imaging.

Entanglement-assisted quantum MDS codes constructed from negacyclic codes

Science.gov (United States)

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

2017-12-01

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

The efficiency of mitochondrial DNA markers in constructing genetic ...

African Journals Online (AJOL)

Administrator

2011-05-30

May 30, 2011 ... To date, only parts of mitochondrial DNA from cytochrome b, 12S rRNA, 16S rRNA and non-coding D- loop had been sequenced for different species of Oryx. Discrepancy in the genetic relationship among. Oryx species was previously revealed when combinations of these sequences were analyzed. In the.

Estimating Propensity Parameters using Google PageRank and Genetic Algorithms

Directory of Open Access Journals (Sweden)

David Murrugarra

2016-11-01

Full Text Available Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at~href{http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html}{http://www.ms.uky.edu/$sim$dmu228GeneticAlgCode.html}.

Cyclic Concatenated Genetic Encoder: A mathematical proposal for biological inferences.

Science.gov (United States)

Duarte-González, M E; Echeverri, O Y; Guevara, J M; Palazzo, R

2018-01-01

The organization of the genetic information and its ability to be conserved and translated to proteins with low error rates have been the subject of study by scientists from different disciplines. Recently, it has been proposed that living organisms display an intra-cellular transmission system of genetic information, similar to a model of digital communication system, in which there is the ability to detect and correct errors. In this work, the concept of Concatenated Genetic Encoder is introduced and applied to the analysis of protein sequences as a tool for exploring evolutionary relationships. For such purposes Error Correcting Codes (ECCs) are used to represent proteins. A methodology for representing or identifying proteins by use of BCH codes over ℤ 20 and F 4 ×ℤ 5 is proposed and cytochrome b6-f complex subunit 6-OS sequences, corresponding to different plants species, are analyzed according to the proposed methodology and results are contrasted to phylogenetic and taxonomic analyses. Through the analyses, it was observed that using BCH codes only some sequences are identified, all of which differ in one amino acid from the original sequence. In addition, mathematical relationships among identified sequences are established by considering minimal polynomials, where such sequences showed a close relationship as revealed in the phylogenetic reconstruction. Results, here shown, point out that communication theory may provide biology of interesting and useful tools to identify biological relationships among proteins, however the proposed methodology needs to be improved and rigorously tested in order to become into an applicable tool for biological analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Error-correction coding

Science.gov (United States)

Hinds, Erold W. (Principal Investigator)

1996-01-01

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

Genetic algorithms used for PWRs refuel management automatic optimization: a new modelling

International Nuclear Information System (INIS)

Chapot, Jorge Luiz C.; Schirru, Roberto; Silva, Fernando Carvalho da

1996-01-01

A Genetic Algorithms-based system, linking the computer codes GENESIS 5.0 and ANC through the interface ALGER, has been developed aiming the PWRs fuel management optimization. An innovative codification, the Lists Model, has been incorporated to the genetic system, which avoids the use of variants of the standard crossover operator and generates only valid loading patterns in the core. The GENESIS/ALGER/ANC system has been successfully tested in an optimization study for Angra-1 second cycle. (author)

Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry.

Science.gov (United States)

Ronquillo, Jay G; Weng, Chunhua; Lester, William T

2017-11-17

  Precision medicine involves three major innovations currently taking place in healthcare:  electronic health records, genomics, and big data.  A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine.   To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats.   We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry.  Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC) database, and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT).  We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting. There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes.  Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring.  Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering.  Conclusion:  While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.

Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry

Directory of Open Access Journals (Sweden)

Jay G Ronquillo

2017-11-01

Full Text Available Background:  Precision medicine involves three major innovations currently taking place in healthcare:  electronic health records, genomics, and big data.  A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine. Objective:  To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats. Methods:  We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry.  Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC database, and Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT.  We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting. Results: There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes.  Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring.  Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering.   Conclusion:  While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.

Turbo-Gallager Codes: The Emergence of an Intelligent Coding ...

African Journals Online (AJOL)

Today, both turbo codes and low-density parity-check codes are largely superior to other code families and are being used in an increasing number of modern communication systems including 3G standards, satellite and deep space communications. However, the two codes have certain distinctive characteristics that ...

The genetic origins of the Andaman Islanders

DEFF Research Database (Denmark)

Endicott, Phillip; Gilbert, M Thomas P; Stringer, Chris

2002-01-01

Mitochondrial sequences were retrieved from museum specimens of the enigmatic Andaman Islanders to analyze their evolutionary history. D-loop and protein-coding data reveal that phenotypic similarities with African pygmoid groups are convergent. Genetic and epigenetic data are interpreted as favo...... of humans through Asia. The results demonstrate that Victorian anthropological collections can be used to study extinct, or seriously admixed populations, to provide new data about early human origins....

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

International Nuclear Information System (INIS)

Sim, Suk K.; Chang, W. P.; Kim, K. D.; Kim, H. C.; Yoon, H. Y.

1997-02-01

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

The Future is Noisy: The Role of Spatial Fluctuations in Genetic Switching

International Nuclear Information System (INIS)

Metzler, Ralf

2001-01-01

A genetic switch may be realized by a certain operator sector on the DNA strand from which either genetic code, to the left or to the right of this operator sector, can be transcribed and the corresponding information processed. This switch is controlled by messenger molecules, i.e., they determine to which side the switch is flipped. Recently, it has been realized that noise plays an elementary role in genetic switching, and the effect of number fluctuations of the messenger molecules have been explored. Here we argue that the assumption of well stirredness taken in the previous models may not be sufficient to characterize the influence of noise: spatial fluctuations play a non-negligible part in cellular genetic switching processes

gPGA: GPU Accelerated Population Genetics Analyses.

Directory of Open Access Journals (Sweden)

Chunbao Zhou

Full Text Available The isolation with migration (IM model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC simulations of gene genealogies. But computational burden of IM program has placed limits on its application.With strong computational power, Graphics Processing Unit (GPU has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA, which we call gPGA.Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

Science.gov (United States)

Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

2010-02-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

Decoding of concatenated codes with interleaved outer codes

DEFF Research Database (Denmark)

Justesen, Jørn; Høholdt, Tom; Thommesen, Christian

2004-01-01

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

Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding

OpenAIRE

Gao, Yuan; Liu, Pengyu; Wu, Yueying; Jia, Kebin; Gao, Guandong

2016-01-01

In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content ...

Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

Science.gov (United States)

Chen, C.; Xia, J.; Liu, J.; Feng, G.

2006-01-01

Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant

Codes Over Hyperfields

Directory of Open Access Journals (Sweden)

Atamewoue Surdive

2017-12-01

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

Amino acid codes in mitochondria as possible clues to primitive codes

Science.gov (United States)

Jukes, T. H.

1981-01-01

Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a 'frozen accident.' The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.

Analysis of quantum error-correcting codes: Symplectic lattice codes and toric codes

Science.gov (United States)

Harrington, James William

Quantum information theory is concerned with identifying how quantum mechanical resources (such as entangled quantum states) can be utilized for a number of information processing tasks, including data storage, computation, communication, and cryptography. Efficient quantum algorithms and protocols have been developed for performing some tasks (e.g. , factoring large numbers, securely communicating over a public channel, and simulating quantum mechanical systems) that appear to be very difficult with just classical resources. In addition to identifying the separation between classical and quantum computational power, much of the theoretical focus in this field over the last decade has been concerned with finding novel ways of encoding quantum information that are robust against errors, which is an important step toward building practical quantum information processing devices. In this thesis I present some results on the quantum error-correcting properties of oscillator codes (also described as symplectic lattice codes) and toric codes. Any harmonic oscillator system (such as a mode of light) can be encoded with quantum information via symplectic lattice codes that are robust against shifts in the system's continuous quantum variables. I show the existence of lattice codes whose achievable rates match the one-shot coherent information over the Gaussian quantum channel. Also, I construct a family of symplectic self-dual lattices and search for optimal encodings of quantum information distributed between several oscillators. Toric codes provide encodings of quantum information into two-dimensional spin lattices that are robust against local clusters of errors and which require only local quantum operations for error correction. Numerical simulations of this system under various error models provide a calculation of the accuracy threshold for quantum memory using toric codes, which can be related to phase transitions in certain condensed matter models. I also present

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

Detecting non-coding selective pressure in coding regions

Directory of Open Access Journals (Sweden)

Blanchette Mathieu

2007-02-01

Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

Dynamic Shannon Coding

OpenAIRE

Gagie, Travis

2005-01-01

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

The correspondence between projective codes and 2-weight codes

NARCIS (Netherlands)

Brouwer, A.E.; Eupen, van M.J.M.; Tilborg, van H.C.A.; Willems, F.M.J.

1994-01-01

The hyperplanes intersecting a 2-weight code in the same number of points obviously form the point set of a projective code. On the other hand, if we have a projective code C, then we can make a 2-weight code by taking the multiset of points E PC with multiplicity "Y(w), where W is the weight of

Quality Improvement of MARS Code and Establishment of Code Coupling

International Nuclear Information System (INIS)

Chung, Bub Dong; Jeong, Jae Jun; Kim, Kyung Doo

2010-04-01

The improvement of MARS code quality and coupling with regulatory auditing code have been accomplished for the establishment of self-reliable technology based regulatory auditing system. The unified auditing system code was realized also by implementing the CANDU specific models and correlations. As a part of the quality assurance activities, the various QA reports were published through the code assessments. The code manuals were updated and published a new manual which describe the new models and correlations. The code coupling methods were verified though the exercise of plant application. The education-training seminar and technology transfer were performed for the code users. The developed MARS-KS is utilized as reliable auditing tool for the resolving the safety issue and other regulatory calculations. The code can be utilized as a base technology for GEN IV reactor applications

Heuristic rules embedded genetic algorithm for in-core fuel management optimization

Science.gov (United States)

Alim, Fatih

The objective of this study was to develop a unique methodology and a practical tool for designing loading pattern (LP) and burnable poison (BP) pattern for a given Pressurized Water Reactor (PWR) core. Because of the large number of possible combinations for the fuel assembly (FA) loading in the core, the design of the core configuration is a complex optimization problem. It requires finding an optimal FA arrangement and BP placement in order to achieve maximum cycle length while satisfying the safety constraints. Genetic Algorithms (GA) have been already used to solve this problem for LP optimization for both PWR and Boiling Water Reactor (BWR). The GA, which is a stochastic method works with a group of solutions and uses random variables to make decisions. Based on the theories of evaluation, the GA involves natural selection and reproduction of the individuals in the population for the next generation. The GA works by creating an initial population, evaluating it, and then improving the population by using the evaluation operators. To solve this optimization problem, a LP optimization package, GARCO (Genetic Algorithm Reactor Code Optimization) code is developed in the framework of this thesis. This code is applicable for all types of PWR cores having different geometries and structures with an unlimited number of FA types in the inventory. To reach this goal, an innovative GA is developed by modifying the classical representation of the genotype. To obtain the best result in a shorter time, not only the representation is changed but also the algorithm is changed to use in-core fuel management heuristics rules. The improved GA code was tested to demonstrate and verify the advantages of the new enhancements. The developed methodology is explained in this thesis and preliminary results are shown for the VVER-1000 reactor hexagonal geometry core and the TMI-1 PWR. The improved GA code was tested to verify the advantages of new enhancements. The core physics code

Application of genetic algorithm in the fuel management optimization for the high flux engineering test reactor

International Nuclear Information System (INIS)

Shi Xueming; Wu Hongchun; Sun Shouhua; Liu Shuiqing

2003-01-01

The in-core fuel management optimization model based on the genetic algorithm has been established. An encode/decode technique based on the assemblies position is presented according to the characteristics of HFETR. Different reproduction strategies have been studied. The expert knowledge and the adaptive genetic algorithms are incorporated into the code to get the optimized loading patterns that can be used in HFETR

Multiple component codes based generalized LDPC codes for high-speed optical transport.

Science.gov (United States)

Djordjevic, Ivan B; Wang, Ting

2014-07-14

A class of generalized low-density parity-check (GLDPC) codes suitable for optical communications is proposed, which consists of multiple local codes. It is shown that Hamming, BCH, and Reed-Muller codes can be used as local codes, and that the maximum a posteriori probability (MAP) decoding of these local codes by Ashikhmin-Lytsin algorithm is feasible in terms of complexity and performance. We demonstrate that record coding gains can be obtained from properly designed GLDPC codes, derived from multiple component codes. We then show that several recently proposed classes of LDPC codes such as convolutional and spatially-coupled codes can be described using the concept of GLDPC coding, which indicates that the GLDPC coding can be used as a unified platform for advanced FEC enabling ultra-high speed optical transport. The proposed class of GLDPC codes is also suitable for code-rate adaption, to adjust the error correction strength depending on the optical channel conditions.

Computer simulation f the genetic controller for the EB flue gas treatment process

International Nuclear Information System (INIS)

Moroz, Z.; Bouzyk, J.; Sowinski, M.; Chmielewski, A.G.

2001-01-01

The use of computer genetic algorithm (GA) for driving a controller device for the industrial flue gas purification systems employing the electron beam irradiation, has been studied. As the mathematical model of the installation the properly trained artificial neural net (ANN) was used. Various cost functions and optimising strategies of the genetic code were tested. These computer simulations proved, that ANN + GA controller can be sufficiently precise and fast to be applied in real installations. (author)

Biocontainment of genetically modified organisms by synthetic protein design

Science.gov (United States)

Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.; Takeuchi, Ryo; Kuznetsov, Gleb; Norville, Julie E.; Gregg, Christopher J.; Stoddard, Barry L.; Church, George M.

2015-02-01

Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.

Vector Network Coding

OpenAIRE

Ebrahimi, Javad; Fragouli, Christina

2010-01-01

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

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....

Attitudes Towards Prenatal Genetic Counseling, Prenatal Genetic Testing, and Termination of Pregnancy among Southeast and East Asian Women in the United States.

Science.gov (United States)

Tsai, Ginger J; Cameron, Carrie A; Czerwinski, Jennifer L; Mendez-Figueroa, Hector; Peterson, Susan K; Noblin, Sarah Jane

2017-10-01

Recognizing the heterogeneity of the Asian population with regards to acculturation, education, health awareness, and cultural values is vital for tailoring culturally sensitive and appropriate care. Prior studies show that cultural values influence perceptions of genetics within Asian populations. The reputation of the family unit factors into decisions such as pregnancy termination and disclosure of family medical history, and the nondirective model of American genetic counseling may conflict with the historical Asian model of paternalistic health care. Previous studies also provide conflicting evidence regarding correlations between education, acculturation, age, and awareness and perceptions of genetic testing. The aims of this study were to describe attitudes towards prenatal genetics among Southeast and East Asian women living in the United States for varying amounts of time and to explore sociocultural factors influencing those attitudes. Twenty-three Asian women who were members of Asian cultural organizations in the United States were interviewed via telephone about their attitudes towards prenatal genetic counseling, prenatal genetic testing, and termination of pregnancy. Responses were transcribed and coded for common themes using a thematic analysis approach. Four major themes emerged. In general, participants: (1) had diverse expectations for genetic counselors; (2) tended to weigh risks and benefits with regards to genetic testing decisions; (3) had mixed views on termination for lethal and non-lethal genetic conditions; and (4) identified cultural factors which influenced testing and termination such as lack of available resources, societal shame and stigma, and family pressure. These findings may allow prenatal genetic counselors to gain a richer, more nuanced understanding of their Asian patients and to offer culturally tailored prenatal genetic counseling.

New quantum codes derived from a family of antiprimitive BCH codes

Science.gov (United States)

Liu, Yang; Li, Ruihu; Lü, Liangdong; Guo, Luobin

The Bose-Chaudhuri-Hocquenghem (BCH) codes have been studied for more than 57 years and have found wide application in classical communication system and quantum information theory. In this paper, we study the construction of quantum codes from a family of q2-ary BCH codes with length n=q2m+1 (also called antiprimitive BCH codes in the literature), where q≥4 is a power of 2 and m≥2. By a detailed analysis of some useful properties about q2-ary cyclotomic cosets modulo n, Hermitian dual-containing conditions for a family of non-narrow-sense antiprimitive BCH codes are presented, which are similar to those of q2-ary primitive BCH codes. Consequently, via Hermitian Construction, a family of new quantum codes can be derived from these dual-containing BCH codes. Some of these new antiprimitive quantum BCH codes are comparable with those derived from primitive BCH codes.

Surface acoustic wave coding for orthogonal frequency coded devices

Science.gov (United States)

Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

2011-01-01

Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

Directory of Open Access Journals (Sweden)

Burr Alister

2009-01-01

Full Text Available Abstract This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are and . The performances of both systems with high ( and low ( BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

Seventy-five genetic loci influencing the human red blood cell.

Science.gov (United States)

van der Harst, Pim; Zhang, Weihua; Mateo Leach, Irene; Rendon, Augusto; Verweij, Niek; Sehmi, Joban; Paul, Dirk S; Elling, Ulrich; Allayee, Hooman; Li, Xinzhong; Radhakrishnan, Aparna; Tan, Sian-Tsung; Voss, Katrin; Weichenberger, Christian X; Albers, Cornelis A; Al-Hussani, Abtehale; Asselbergs, Folkert W; Ciullo, Marina; Danjou, Fabrice; Dina, Christian; Esko, Tõnu; Evans, David M; Franke, Lude; Gögele, Martin; Hartiala, Jaana; Hersch, Micha; Holm, Hilma; Hottenga, Jouke-Jan; Kanoni, Stavroula; Kleber, Marcus E; Lagou, Vasiliki; Langenberg, Claudia; Lopez, Lorna M; Lyytikäinen, Leo-Pekka; Melander, Olle; Murgia, Federico; Nolte, Ilja M; O'Reilly, Paul F; Padmanabhan, Sandosh; Parsa, Afshin; Pirastu, Nicola; Porcu, Eleonora; Portas, Laura; Prokopenko, Inga; Ried, Janina S; Shin, So-Youn; Tang, Clara S; Teumer, Alexander; Traglia, Michela; Ulivi, Sheila; Westra, Harm-Jan; Yang, Jian; Zhao, Jing Hua; Anni, Franco; Abdellaoui, Abdel; Attwood, Antony; Balkau, Beverley; Bandinelli, Stefania; Bastardot, François; Benyamin, Beben; Boehm, Bernhard O; Cookson, William O; Das, Debashish; de Bakker, Paul I W; de Boer, Rudolf A; de Geus, Eco J C; de Moor, Marleen H; Dimitriou, Maria; Domingues, Francisco S; Döring, Angela; Engström, Gunnar; Eyjolfsson, Gudmundur Ingi; Ferrucci, Luigi; Fischer, Krista; Galanello, Renzo; Garner, Stephen F; Genser, Bernd; Gibson, Quince D; Girotto, Giorgia; Gudbjartsson, Daniel Fannar; Harris, Sarah E; Hartikainen, Anna-Liisa; Hastie, Claire E; Hedblad, Bo; Illig, Thomas; Jolley, Jennifer; Kähönen, Mika; Kema, Ido P; Kemp, John P; Liang, Liming; Lloyd-Jones, Heather; Loos, Ruth J F; Meacham, Stuart; Medland, Sarah E; Meisinger, Christa; Memari, Yasin; Mihailov, Evelin; Miller, Kathy; Moffatt, Miriam F; Nauck, Matthias; Novatchkova, Maria; Nutile, Teresa; Olafsson, Isleifur; Onundarson, Pall T; Parracciani, Debora; Penninx, Brenda W; Perseu, Lucia; Piga, Antonio; Pistis, Giorgio; Pouta, Anneli; Puc, Ursula; Raitakari, Olli; Ring, Susan M; Robino, Antonietta; Ruggiero, Daniela; Ruokonen, Aimo; Saint-Pierre, Aude; Sala, Cinzia; Salumets, Andres; Sambrook, Jennifer; Schepers, Hein; Schmidt, Carsten Oliver; Silljé, Herman H W; Sladek, Rob; Smit, Johannes H; Starr, John M; Stephens, Jonathan; Sulem, Patrick; Tanaka, Toshiko; Thorsteinsdottir, Unnur; Tragante, Vinicius; van Gilst, Wiek H; van Pelt, L Joost; van Veldhuisen, Dirk J; Völker, Uwe; Whitfield, John B; Willemsen, Gonneke; Winkelmann, Bernhard R; Wirnsberger, Gerald; Algra, Ale; Cucca, Francesco; d'Adamo, Adamo Pio; Danesh, John; Deary, Ian J; Dominiczak, Anna F; Elliott, Paul; Fortina, Paolo; Froguel, Philippe; Gasparini, Paolo; Greinacher, Andreas; Hazen, Stanley L; Jarvelin, Marjo-Riitta; Khaw, Kay Tee; Lehtimäki, Terho; Maerz, Winfried; Martin, Nicholas G; Metspalu, Andres; Mitchell, Braxton D; Montgomery, Grant W; Moore, Carmel; Navis, Gerjan; Pirastu, Mario; Pramstaller, Peter P; Ramirez-Solis, Ramiro; Schadt, Eric; Scott, James; Shuldiner, Alan R; Smith, George Davey; Smith, J Gustav; Snieder, Harold; Sorice, Rossella; Spector, Tim D; Stefansson, Kari; Stumvoll, Michael; Tang, W H Wilson; Toniolo, Daniela; Tönjes, Anke; Visscher, Peter M; Vollenweider, Peter; Wareham, Nicholas J; Wolffenbuttel, Bruce H R; Boomsma, Dorret I; Beckmann, Jacques S; Dedoussis, George V; Deloukas, Panos; Ferreira, Manuel A; Sanna, Serena; Uda, Manuela; Hicks, Andrew A; Penninger, Josef Martin; Gieger, Christian; Kooner, Jaspal S; Ouwehand, Willem H; Soranzo, Nicole; Chambers, John C

2012-12-20

Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.

Codes and curves

CERN Document Server

Walker, Judy L

2000-01-01

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

German politics of genetic engineering and its deconstruction.

Science.gov (United States)

Gottweis, H

1995-05-01

Policy-making, as exemplified by biotechnology policy, can be understood as an attempt to manage a field of discursivity, to construct regularity in a dispersed multitude of combinable elements. Following this perspective of politics as a textual process, the paper interprets the politicization of genetic engineering in Germany as a defence of the political as a regime of heterogeneity, as a field of 'dissensus' rather than 'consensus', and a rejection of the idea that the framing of technological transformation is an autonomous process. From its beginning in the early 1970s, genetic engineering was symbolically entrenched as a key technology of the future, and as an integral element of the German politics of modernization. Attempts by new social movements and the Green Party to displace the egalitarian imaginary of democratic discourse into the politics of genetic engineering were construed by the political élites as an attack on the political order of post-World War II Germany. The 1990 Genetic Engineering Law attempted a closure of this controversy. But it is precisely the homogenizing idiom of this 'settlement' which continues to nourish the social movements and their radical challenge to the definitions and codings of the politics of genetic engineering.

Bitter taste stimuli induce differential neural codes in mouse brain.

Directory of Open Access Journals (Sweden)

David M Wilson

Full Text Available A growing literature suggests taste stimuli commonly classified as "bitter" induce heterogeneous neural and perceptual responses. Here, the central processing of bitter stimuli was studied in mice with genetically controlled bitter taste profiles. Using these mice removed genetic heterogeneity as a factor influencing gustatory neural codes for bitter stimuli. Electrophysiological activity (spikes was recorded from single neurons in the nucleus tractus solitarius during oral delivery of taste solutions (26 total, including concentration series of the bitter tastants quinine, denatonium benzoate, cycloheximide, and sucrose octaacetate (SOA, presented to the whole mouth for 5 s. Seventy-nine neurons were sampled; in many cases multiple cells (2 to 5 were recorded from a mouse. Results showed bitter stimuli induced variable gustatory activity. For example, although some neurons responded robustly to quinine and cycloheximide, others displayed concentration-dependent activity (p<0.05 to quinine but not cycloheximide. Differential activity to bitter stimuli was observed across multiple neurons recorded from one animal in several mice. Across all cells, quinine and denatonium induced correlated spatial responses that differed (p<0.05 from those to cycloheximide and SOA. Modeling spatiotemporal neural ensemble activity revealed responses to quinine/denatonium and cycloheximide/SOA diverged during only an early, at least 1 s wide period of the taste response. Our findings highlight how temporal features of sensory processing contribute differences among bitter taste codes and build on data suggesting heterogeneity among "bitter" stimuli, data that challenge a strict monoguesia model for the bitter quality.

Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

Directory of Open Access Journals (Sweden)

Lei Ye

2009-01-01

Full Text Available This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are 1/2 and 1/3. The performances of both systems with high (10−2 and low (10−4 BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

Quantum Codes From Cyclic Codes Over The Ring R 2

International Nuclear Information System (INIS)

Altinel, Alev; Güzeltepe, Murat

2016-01-01

Let R 2 denotes the ring F 2 + μF 2 + υ 2 + μυ F 2 + wF 2 + μwF 2 + υwF 2 + μυwF 2 . In this study, we construct quantum codes from cyclic codes over the ring R 2 , for arbitrary length n, with the restrictions μ 2 = 0, υ 2 = 0, w 2 = 0, μυ = υμ, μw = wμ, υw = wυ and μ (υw) = (μυ) w. Also, we give a necessary and sufficient condition for cyclic codes over R 2 that contains its dual. As a final point, we obtain the parameters of quantum error-correcting codes from cyclic codes over R 2 and we give an example of quantum error-correcting codes form cyclic codes over R 2 . (paper)

Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

Directory of Open Access Journals (Sweden)

Roshan Mascarenhas

Full Text Available mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs, and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs in lymphoblast cell lines (LCL and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T in ABCB1 (MDR1 on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

A New Prime Code for Synchronous Optical Code Division Multiple-Access Networks

Directory of Open Access Journals (Sweden)

Huda Saleh Abbas

2018-01-01

Full Text Available A new spreading code based on a prime code for synchronous optical code-division multiple-access networks that can be used in monitoring applications has been proposed. The new code is referred to as “extended grouped new modified prime code.” This new code has the ability to support more terminal devices than other prime codes. In addition, it patches subsequences with “0s” leading to lower power consumption. The proposed code has an improved cross-correlation resulting in enhanced BER performance. The code construction and parameters are provided. The operating performance, using incoherent on-off keying modulation and incoherent pulse position modulation systems, has been analyzed. The performance of the code was compared with other prime codes. The results demonstrate an improved performance, and a BER floor of 10−9 was achieved.

Understanding Mixed Code and Classroom Code-Switching: Myths and Realities

Science.gov (United States)

Li, David C. S.

2008-01-01

Background: Cantonese-English mixed code is ubiquitous in Hong Kong society, and yet using mixed code is widely perceived as improper. This paper presents evidence of mixed code being socially constructed as bad language behavior. In the education domain, an EDB guideline bans mixed code in the classroom. Teachers are encouraged to stick to…

An expanding universe of the non-coding genome in cancer biology.

Science.gov (United States)

Xue, Bin; He, Lin

2014-06-01

Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

MetaRanker 2.0: a web server for prioritization of genetic variation data.

Science.gov (United States)

Pers, Tune H; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

2013-07-01

MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein-protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRanker-2.0.

Development of a coupled code system based on system transient code, RETRAN, and 3-D neutronics code, MASTER

International Nuclear Information System (INIS)

Kim, K. D.; Jung, J. J.; Lee, S. W.; Cho, B. O.; Ji, S. K.; Kim, Y. H.; Seong, C. K.

2002-01-01

A coupled code system of RETRAN/MASTER has been developed for best-estimate simulations of interactions between reactor core neutron kinetics and plant thermal-hydraulics by incorporation of a 3-D reactor core kinetics analysis code, MASTER into system transient code, RETRAN. The soundness of the consolidated code system is confirmed by simulating the MSLB benchmark problem developed to verify the performance of a coupled kinetics and system transient codes by OECD/NEA

A New Coding System for Metabolic Disorders Demonstrates Gaps in the International Disease Classifications ICD-10 and SNOMED-CT, Which Can Be Barriers to Genotype-Phenotype Data Sharing

NARCIS (Netherlands)

Sollie, Annet; Sijmons, Rolf H.; Lindhout, Dick; van der Ploeg, Ans T.; Gozalbo, M. Estela Rubio; Smit, G. Peter A.; Verheijen, Frans; Waterham, Hans R.; van Weely, Sonja; Wijburg, Frits A.; Wijburg, Rudolph; Visser, Gepke

Data sharing is essential for a better understanding of genetic disorders. Good phenotype coding plays a key role in this process. Unfortunately, the two most widely used coding systems in medicine, ICD-10 and SNOMED-CT, lack information necessary for the detailed classification and annotation of

Depauperate genetic variability detected in the American and European bison using genomic techniques

DEFF Research Database (Denmark)

Pertoldi, Cino; Tokarska, Magorzata; Wójcik, Jan M

2009-01-01

, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow...

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…

Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

DEFF Research Database (Denmark)

Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen

2015-01-01

are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...

Genetic diversity of b-glucuronidase activity among 14 strains of the dominant human gut anaerobe Ruminococcus gnavus

Directory of Open Access Journals (Sweden)

Diane Beaud

2006-01-01

Full Text Available Bacterial beta-glucuronidase activity in the gut increases the enterohepatic circulation of toxic compounds and plays a major role in the etiology of colon cancer. Previously, we had found that the gus gene, which codes for beta-glucuronidase in a dominant anaerobic species of the gut microbiota, Ruminococcus gnavus strain E1, is transcribed as part of an operon that includes three ORFs that code for beta-glucoside permeases of the phosphotransferase systems. This genetic organization had never been described. We have now compared beta-glucuronidase activity and the genetic environment of the gus gene in 14 strains of Ruminococcus gnavus.We found that five out of the seven glucuronidase-positive R. gnavus strains possessed another glucuronidase gene different from the gusA operon of R. gnavus E1. This dominant commensal intestinal species appears to have a high degree of genetic diversity in the genes that control beta-glucuronidase activity.

Some Families of Asymmetric Quantum MDS Codes Constructed from Constacyclic Codes

Science.gov (United States)

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

2018-02-01

Quantum maximal-distance-separable (MDS) codes that satisfy quantum Singleton bound with different lengths have been constructed by some researchers. In this paper, seven families of asymmetric quantum MDS codes are constructed by using constacyclic codes. We weaken the case of Hermitian-dual containing codes that can be applied to construct asymmetric quantum MDS codes with parameters [[n,k,dz/dx

Theoretical Atomic Physics code development II: ACE: Another collisional excitation code

International Nuclear Information System (INIS)

Clark, R.E.H.; Abdallah, J. Jr.; Csanak, G.; Mann, J.B.; Cowan, R.D.

1988-12-01

A new computer code for calculating collisional excitation data (collision strengths or cross sections) using a variety of models is described. The code uses data generated by the Cowan Atomic Structure code or CATS for the atomic structure. Collisional data are placed on a random access file and can be displayed in a variety of formats using the Theoretical Atomic Physics Code or TAPS. All of these codes are part of the Theoretical Atomic Physics code development effort at Los Alamos. 15 refs., 10 figs., 1 tab

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...

Genetic variation in steelhead (Salmo gairdneri) from the north coast of Washington

Science.gov (United States)

Reisenbichler, R.R.; Phelps, S.R.

1989-01-01

Steelhead (Salmo gairdneri) collected from various sites in nine drainages in northwestern Washington were genetically characterized at 65 protein-coding loci by starch-gel electrophoresis. Genetic differentiation within and among drainages was not significant, and genetic variation among drainages was much less than that reported in British Columbia; these results may be the consequence of gene flow from hatchery stocks that have been released in Washington since the 1940's. Allele frequencies varied significantly among year-classes (hence, genetic characterization studies must include data from several year-classes), and also between hatchery fish (including a stock developed with local wild fish) and wild fish, indicating that few wild fish have been successfully and routinely included in hatchery brood stocks. Conservation of genetic diversity along the north coast of Washington should be facilitated by reducing the numbers of hatchery fish that spawn in streams and by including wild fish in hatchery brood stocks.

Genetic variability in five species of Anostomidae (Ostariophysi - Characiformes

Directory of Open Access Journals (Sweden)

Chiari Lucimara

1999-01-01

Full Text Available Genetic variability was studied in five fish species (Anostomidae: Schizodon intermedius and S. nasutus and Leporinus friderici, L. elongatus and L. obtusidens, collected at one location on the Tibagi River (Paraná, Brazil. The protein data from seven systems coded collectively for 19 loci in the liver, muscle and heart. Nine of these loci were polymorphic. The estimated proportion of polymorphism loci ( varied from 16.7% in S. intermedius to 36.9% in L. friderici; the mean heterozygosity observed (o was 0.027 ± 0.015 and 0.109 ± 0.042, respectively. The estimated value of the genetic identity among L. friderici and S. intermedius (0.749 and S. nasutus (0.787 suggested that these are "congeneric" species. Morphological characteristics indicate that these species belong to distinct genera, while isoenzymatic data show that they are very similar at the genetic/biochemical level.

Genetic diagnosis for congenital hemolytic anemia.

Science.gov (United States)

Ohga, Shouichi

2016-01-01

Congenital hemolytic anemia is a group of monogenic diseases presenting with anemia due to increased destruction of circulating erythrocytes. The etiology of inherited anemia accounts for germline mutations of the responsible genes coding for the structural components of erythrocytes and extra-erythrocytes. The erythrocyte abnormalities are classified into three major disorders of red cell membrane defects, hemoglobinopathies, and red cell enzymopathies. The extra-erythrocyte abnormalities, typified by consumption coagulopathy and intravascular hemolysis, include Upshaw-Schulman syndrome and atypical hemolytic uremic syndrome. The clinical manifestations of congenital hemolytic anemia are anemia, jaundice, cholelithiasis and splenomegaly, while the onset mode and severity are both variable. Genetic overlapping of red cell membrane protein disorders, and distinct frequency and mutation spectra differing among races make it difficult to understand this disease entity. On the other hand, genetic modifiers for the phenotype of β-globin diseases provide useful information for selecting the optimal treatment and for long-term management. Recently, next generation sequencing techniques have enabled us to determine the novel causative genes in patients with undiagnosed hemolytic anemias. We herein review the concept and strategy for genetic diagnosis of inherited hemolytic anemias.

Genetic bases of the nutritional approach to migraine.

Science.gov (United States)

De Marchis, Maria Laura; Guadagni, Fiorella; Silvestris, Erica; Lovero, Domenica; Della-Morte, David; Ferroni, Patrizia; Barbanti, Piero; Palmirotta, Raffaele

2018-03-08

Migraine is a common multifactorial and polygenic neurological disabling disorder characterized by a genetic background and associated to environmental, hormonal and food stimulations. A large series of evidence suggest a strong correlation between nutrition and migraine and indicates several commonly foods, food additives and beverages that may be involved in the mechanisms triggering the headache attack in migraine-susceptible persons. There are foods and drinks, or ingredients of the same, that can trigger the migraine crisis as well as some foods play a protective function depending on the specific genetic sensitivity of the subject. The recent biotechnological advances have enhanced the identification of some genetic factors involved in onset diseases and the identification of sequence variants of genes responsible for the individual sensitivity to migraine trigger-foods. Therefore many studies are aimed at the analysis of polymorphisms of genes coding for the enzymes involved in the metabolism of food factors in order to clarify the different ways in which people respond to foods based on their genetic constitution. This review discusses the latest knowledge and scientific evidence of the role of gene variants and nutrients, food additives and nutraceuticals interactions in migraine.

Trends in genetic patent applications: the commercialization of academic intellectual property.

Science.gov (United States)

Kers, Jannigje G; Van Burg, Elco; Stoop, Tom; Cornel, Martina C

2014-10-01

We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications data from the PATSTAT database from 1990 until 2009 were analyzed for time trends and regional distribution. Overall, the number of patent applications has been growing. In 2009, 152 000 patent applications were submitted under the Patent Cooperation Treaty (PCT) and within the EP (European Patent) system of the European Patent Office (EPO). The number of genetic patent applications increased until a peak was reached in the year 2000, with >8000 applications, after which it declined by almost 50%. Continents show different patterns over time, with the global peak in 2000 mainly explained by the USA and Europe, while Asia shows a stable number of >1000 per year. Nine countries together account for 98.9% of the total number of genetic patent applications. In The Netherlands, 26.7% of the genetic patent applications originate from public research institutions. After the year 2000, the number of genetic patent applications dropped significantly. Academic leadership and policy as well as patent regulations seem to have an important role in the trend differences. The ongoing investment in genetic research in the past decade is not reflected by an increase of patent applications.

Error-correction coding and decoding bounds, codes, decoders, analysis and applications

CERN Document Server

Tomlinson, Martin; Ambroze, Marcel A; Ahmed, Mohammed; Jibril, Mubarak

2017-01-01

This book discusses both the theory and practical applications of self-correcting data, commonly known as error-correcting codes. The applications included demonstrate the importance of these codes in a wide range of everyday technologies, from smartphones to secure communications and transactions. Written in a readily understandable style, the book presents the authors’ twenty-five years of research organized into five parts: Part I is concerned with the theoretical performance attainable by using error correcting codes to achieve communications efficiency in digital communications systems. Part II explores the construction of error-correcting codes and explains the different families of codes and how they are designed. Techniques are described for producing the very best codes. Part III addresses the analysis of low-density parity-check (LDPC) codes, primarily to calculate their stopping sets and low-weight codeword spectrum which determines the performance of these codes. Part IV deals with decoders desi...

A fielded wiki for personality genetics

DEFF Research Database (Denmark)

Nielsen, Finn Årup

2010-01-01

I describe a fielded wiki, where a Web form interface allows the entry, analysis and visualization of results from scientific papers in the personality genetics domain. Papers in this domain typically report the mean and standard deviation of multiple personality trait scores from statistics...... on human subjects grouped based on genotype. The wiki organizes the basic data in a single table with fixed columns, each row recording statistical values with respect to a specific personality trait reported in a specific paper with a specific genotype group. From this basic data hard-coded meta...

Error floor behavior study of LDPC codes for concatenated codes design

Science.gov (United States)

Chen, Weigang; Yin, Liuguo; Lu, Jianhua

2007-11-01

Error floor behavior of low-density parity-check (LDPC) codes using quantized decoding algorithms is statistically studied with experimental results on a hardware evaluation platform. The results present the distribution of the residual errors after decoding failure and reveal that the number of residual error bits in a codeword is usually very small using quantized sum-product (SP) algorithm. Therefore, LDPC code may serve as the inner code in a concatenated coding system with a high code rate outer code and thus an ultra low error floor can be achieved. This conclusion is also verified by the experimental results.

Evaluating the Role of Genetic Markers in Prostate Cancer Progression: A Multiethnic Cohort Experience

Science.gov (United States)

2011-10-01

presentation of prostate tumors by a novel genetic variant in CYP3A4 . [see comment] [erratum appears in J Natl Cancer Inst 1999 Jun 16;91(12):1082...European ancestry18. Sequencing of the five coding exons of ZNF652 in 48 subjects (with an oversampling of risk allele carriers; Online Methods...the five coding exons of ZNF652 was performed in 48 subjects (20 homozygous for the risk vari- ant, 20 heterozygous for the risk variant and 8

High genetic diversity in the coat protein and 3' untranslated regions

Indian Academy of Sciences (India)

The 3′ terminal region consisting of the coat protein (CP) coding sequence and 3′ untranslated region (3′UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3′UTR, making CdMV one of the highly variable members ...

Reactor lattice codes

International Nuclear Information System (INIS)

Kulikowska, T.

1999-01-01

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

Exome sequencing and genetic testing for MODY.

Directory of Open Access Journals (Sweden)

Stefan Johansson

Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

CodeArmor : Virtualizing the Code Space to Counter Disclosure Attacks

NARCIS (Netherlands)

Chen, Xi; Bos, Herbert; Giuffrida, Cristiano

2017-01-01

Code diversification is an effective strategy to prevent modern code-reuse exploits. Unfortunately, diversification techniques are inherently vulnerable to information disclosure. Recent diversification-aware ROP exploits have demonstrated that code disclosure attacks are a realistic threat, with an

A program for undergraduate research into the mechanisms of sensory coding and memory decay

Energy Technology Data Exchange (ETDEWEB)

Calin-Jageman, R J

2010-09-28

This is the final technical report for this DOE project, entitltled "A program for undergraduate research into the mechanisms of sensory coding and memory decay". The report summarizes progress on the three research aims: 1) to identify phyisological and genetic correlates of long-term habituation, 2) to understand mechanisms of olfactory coding, and 3) to foster a world-class undergraduate neuroscience program. Progress on the first aim has enabled comparison of learning-regulated transcripts across closely related learning paradigms and species, and results suggest that only a small core of transcripts serve truly general roles in long-term memory. Progress on the second aim has enabled testing of several mutant phenotypes for olfactory behaviors, and results show that responses are not fully consistent with the combinitoral coding hypothesis. Finally, 14 undergraduate students participated in this research, the neuroscience program attracted extramural funding, and we completed a successful summer program to enhance transitions for community-college students into 4-year colleges to persue STEM fields.

Nuclear reactors project optimization based on neural network and genetic algorithm

International Nuclear Information System (INIS)

Pereira, Claudio M.N.A.; Schirru, Roberto; Martinez, Aquilino S.

1997-01-01

This work presents a prototype of a system for nuclear reactor core design optimization based on genetic algorithms and artificial neural networks. A neural network is modeled and trained in order to predict the flux and the neutron multiplication factor values based in the enrichment, network pitch and cladding thickness, with average error less than 2%. The values predicted by the neural network are used by a genetic algorithm in this heuristic search, guided by an objective function that rewards the high flux values and penalizes multiplication factors far from the required value. Associating the quick prediction - that may substitute the reactor physics calculation code - with the global optimization capacity of the genetic algorithm, it was obtained a quick and effective system for nuclear reactor core design optimization. (author). 11 refs., 8 figs., 3 tabs

An Evaluation of Automated Code Generation with the PetriCode Approach

DEFF Research Database (Denmark)

Simonsen, Kent Inge

2014-01-01

Automated code generation is an important element of model driven development methodologies. We have previously proposed an approach for code generation based on Coloured Petri Net models annotated with textual pragmatics for the network protocol domain. In this paper, we present and evaluate thr...... important properties of our approach: platform independence, code integratability, and code readability. The evaluation shows that our approach can generate code for a wide range of platforms which is integratable and readable....

Characteristics of genetics-related news content in Black weekly newspapers.

Science.gov (United States)

Caburnay, C A; Babb, P; Kaphingst, K A; Roberts, J; Rath, S

2014-01-01

BACKGROUND/AIMS/OBJECTIVES: The media are an important source of health information, especially for those with less access to regular health care. Black news outlets such as Black newspapers are a source of health information for African Americans. This study characterized media coverage of genetics-related information in Black weekly newspapers and general audience newspapers from the same communities. All health stories in a sample of 24 Black weekly newspapers and 12 general audience newspapers from January 2004 to December 2007 were reviewed for genetics-related stories. These stories were further coded for both journalistic and public health variables. Of all health-related stories identified, only 2% (n = 357) were considered genetics related. Genetics-related stories in Black newspapers - compared to those in general audience newspapers - were larger, more locally and racially relevant, and more likely to contain recommendations or action steps to improve health or reduce disease risks and to mention the importance of knowing one's family history. Stories in general audience newspapers were more likely to discuss causes of disease, mention genetic testing or therapy, and suggest a high/moderate degree of genetic determinism. Black newspapers are a viable communication channel to disseminate findings and implications of human genome research to African American audiences.

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

Genetic algorithms and artificial neural networks for loading pattern optimisation of advanced gas-cooled reactors

Energy Technology Data Exchange (ETDEWEB)

Ziver, A.K. E-mail: a.k.ziver@imperial.ac.uk; Pain, C.C; Carter, J.N.; Oliveira, C.R.E. de; Goddard, A.J.H.; Overton, R.S

2004-03-01

A non-generational genetic algorithm (GA) has been developed for fuel management optimisation of Advanced Gas-Cooled Reactors, which are operated by British Energy and produce around 20% of the UK's electricity requirements. An evolutionary search is coded using the genetic operators; namely selection by tournament, two-point crossover, mutation and random assessment of population for multi-cycle loading pattern (LP) optimisation. A detailed description of the chromosomes in the genetic algorithm coded is presented. Artificial Neural Networks (ANNs) have been constructed and trained to accelerate the GA-based search during the optimisation process. The whole package, called GAOPT, is linked to the reactor analysis code PANTHER, which performs fresh fuel loading, burn-up and power shaping calculations for each reactor cycle by imposing station-specific safety and operational constraints. GAOPT has been verified by performing a number of tests, which are applied to the Hinkley Point B and Hartlepool reactors. The test results giving loading pattern (LP) scenarios obtained from single and multi-cycle optimisation calculations applied to realistic reactor states of the Hartlepool and Hinkley Point B reactors are discussed. The results have shown that the GA/ANN algorithms developed can help the fuel engineer to optimise loading patterns in an efficient and more profitable way than currently available for multi-cycle refuelling of AGRs. Research leading to parallel GAs applied to LP optimisation are outlined, which can be adapted to present day LWR fuel management problems.

Cracking the code: the accuracy of coding shoulder procedures and the repercussions.

Science.gov (United States)

Clement, N D; Murray, I R; Nie, Y X; McBirnie, J M

2013-05-01

Coding of patients' diagnosis and surgical procedures is subject to error levels of up to 40% with consequences on distribution of resources and financial recompense. Our aim was to explore and address reasons behind coding errors of shoulder diagnosis and surgical procedures and to evaluate a potential solution. A retrospective review of 100 patients who had undergone surgery was carried out. Coding errors were identified and the reasons explored. A coding proforma was designed to address these errors and was prospectively evaluated for 100 patients. The financial implications were also considered. Retrospective analysis revealed the correct primary diagnosis was assigned in 54 patients (54%) had an entirely correct diagnosis, and only 7 (7%) patients had a correct procedure code assigned. Coders identified indistinct clinical notes and poor clarity of procedure codes as reasons for errors. The proforma was significantly more likely to assign the correct diagnosis (odds ratio 18.2, p code (odds ratio 310.0, p coding department. High error levels for coding are due to misinterpretation of notes and ambiguity of procedure codes. This can be addressed by allowing surgeons to assign the diagnosis and procedure using a simplified list that is passed directly to coding.

Predicting mining activity with parallel genetic algorithms

Science.gov (United States)

Talaie, S.; Leigh, R.; Louis, S.J.; Raines, G.L.; Beyer, H.G.; O'Reilly, U.M.; Banzhaf, Arnold D.; Blum, W.; Bonabeau, C.; Cantu-Paz, E.W.; ,; ,

2005-01-01

We explore several different techniques in our quest to improve the overall model performance of a genetic algorithm calibrated probabilistic cellular automata. We use the Kappa statistic to measure correlation between ground truth data and data predicted by the model. Within the genetic algorithm, we introduce a new evaluation function sensitive to spatial correctness and we explore the idea of evolving different rule parameters for different subregions of the land. We reduce the time required to run a simulation from 6 hours to 10 minutes by parallelizing the code and employing a 10-node cluster. Our empirical results suggest that using the spatially sensitive evaluation function does indeed improve the performance of the model and our preliminary results also show that evolving different rule parameters for different regions tends to improve overall model performance. Copyright 2005 ACM.

A multi-perspective view of genetic variation in Cameroon.

Science.gov (United States)

Coia, V; Brisighelli, F; Donati, F; Pascali, V; Boschi, I; Luiselli, D; Battaggia, C; Batini, C; Taglioli, L; Cruciani, F; Paoli, G; Capelli, C; Spedini, G; Destro-Bisol, G

2009-11-01

In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration Nnu ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon.

Construction of new quantum MDS codes derived from constacyclic codes

Science.gov (United States)

Taneja, Divya; Gupta, Manish; Narula, Rajesh; Bhullar, Jaskaran

Obtaining quantum maximum distance separable (MDS) codes from dual containing classical constacyclic codes using Hermitian construction have paved a path to undertake the challenges related to such constructions. Using the same technique, some new parameters of quantum MDS codes have been constructed here. One set of parameters obtained in this paper has achieved much larger distance than work done earlier. The remaining constructed parameters of quantum MDS codes have large minimum distance and were not explored yet.

Vector Network Coding Algorithms

OpenAIRE

Ebrahimi, Javad; Fragouli, Christina

2010-01-01

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

Code-Mixing and Code Switchingin The Process of Learning

Directory of Open Access Journals (Sweden)

Diyah Atiek Mustikawati

2016-09-01

Full Text Available This study aimed to describe a form of code switching and code mixing specific form found in the teaching and learning activities in the classroom as well as determining factors influencing events stand out that form of code switching and code mixing in question.Form of this research is descriptive qualitative case study which took place in Al Mawaddah Boarding School Ponorogo. Based on the analysis and discussion that has been stated in the previous chapter that the form of code mixing and code switching learning activities in Al Mawaddah Boarding School is in between the use of either language Java language, Arabic, English and Indonesian, on the use of insertion of words, phrases, idioms, use of nouns, adjectives, clauses, and sentences. Code mixing deciding factor in the learning process include: Identification of the role, the desire to explain and interpret, sourced from the original language and its variations, is sourced from a foreign language. While deciding factor in the learning process of code, includes: speakers (O1, partners speakers (O2, the presence of a third person (O3, the topic of conversation, evoke a sense of humour, and just prestige. The significance of this study is to allow readers to see the use of language in a multilingual society, especially in AL Mawaddah boarding school about the rules and characteristics variation in the language of teaching and learning activities in the classroom. Furthermore, the results of this research will provide input to the ustadz / ustadzah and students in developing oral communication skills and the effectiveness of teaching and learning strategies in boarding schools.

Using Coding Apps to Support Literacy Instruction and Develop Coding Literacy

Science.gov (United States)

Hutchison, Amy; Nadolny, Larysa; Estapa, Anne

2016-01-01

In this article the authors present the concept of Coding Literacy and describe the ways in which coding apps can support the development of Coding Literacy and disciplinary and digital literacy skills. Through detailed examples, we describe how coding apps can be integrated into literacy instruction to support learning of the Common Core English…

Low Complexity List Decoding for Polar Codes with Multiple CRC Codes

Directory of Open Access Journals (Sweden)

Jong-Hwan Kim

2017-04-01

Full Text Available Polar codes are the first family of error correcting codes that provably achieve the capacity of symmetric binary-input discrete memoryless channels with low complexity. Since the development of polar codes, there have been many studies to improve their finite-length performance. As a result, polar codes are now adopted as a channel code for the control channel of 5G new radio of the 3rd generation partnership project. However, the decoder implementation is one of the big practical problems and low complexity decoding has been studied. This paper addresses a low complexity successive cancellation list decoding for polar codes utilizing multiple cyclic redundancy check (CRC codes. While some research uses multiple CRC codes to reduce memory and time complexity, we consider the operational complexity of decoding, and reduce it by optimizing CRC positions in combination with a modified decoding operation. Resultingly, the proposed scheme obtains not only complexity reduction from early stopping of decoding, but also additional reduction from the reduced number of decoding paths.

Majorana fermion codes

International Nuclear Information System (INIS)

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

2010-01-01

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

DISP1 code

International Nuclear Information System (INIS)

Vokac, P.

1999-12-01

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

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

Analysis of t(9;17)(q33.2;q25.3) chromosomal breakpoint regions and genetic association reveals novel candidate genes for bipolar disorder

DEFF Research Database (Denmark)

Rajkumar, Anto P; Christensen, Jane H; Mattheisen, Manuel

2015-01-01

,856) data. Genetic associations between these disorders and single nucleotide polymorphisms within these breakpoint regions were analysed by BioQ, FORGE, and RegulomeDB programmes. RESULTS: Four protein-coding genes [coding for (endonuclease V (ENDOV), neuronal pentraxin I (NPTX1), ring finger protein 213...

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

Science.gov (United States)

2013-03-26

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

Two-terminal video coding.

Science.gov (United States)

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

The network code

International Nuclear Information System (INIS)

1997-01-01

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

XSOR codes users manual

International Nuclear Information System (INIS)

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

1993-11-01

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

Rate-adaptive BCH coding for Slepian-Wolf coding of highly correlated sources

DEFF Research Database (Denmark)

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

2012-01-01

This paper considers using BCH codes for distributed source coding using feedback. The focus is on coding using short block lengths for a binary source, X, having a high correlation between each symbol to be coded and a side information, Y, such that the marginal probability of each symbol, Xi in X......, given Y is highly skewed. In the analysis, noiseless feedback and noiseless communication are assumed. A rate-adaptive BCH code is presented and applied to distributed source coding. Simulation results for a fixed error probability show that rate-adaptive BCH achieves better performance than LDPCA (Low......-Density Parity-Check Accumulate) codes for high correlation between source symbols and the side information....

Coding in Muscle Disease.

Science.gov (United States)

Jones, Lyell K; Ney, John P

2016-12-01

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

Generalized concatenated quantum codes

International Nuclear Information System (INIS)

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

2009-01-01

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

Synthesizing Certified Code

OpenAIRE

Whalen, Michael; Schumann, Johann; Fischer, Bernd

2002-01-01

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

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.

Coding Labour

Directory of Open Access Journals (Sweden)

Anthony McCosker

2014-03-01

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

Weight optimization of plane truss using genetic algorithm

Science.gov (United States)

Neeraja, D.; Kamireddy, Thejesh; Santosh Kumar, Potnuru; Simha Reddy, Vijay

2017-11-01

Optimization of structure on basis of weight has many practical benefits in every engineering field. The efficiency is proportionally related to its weight and hence weight optimization gains prime importance. Considering the field of civil engineering, weight optimized structural elements are economical and easier to transport to the site. In this study, genetic optimization algorithm for weight optimization of steel truss considering its shape, size and topology aspects has been developed in MATLAB. Material strength and Buckling stability have been adopted from IS 800-2007 code of construction steel. The constraints considered in the present study are fabrication, basic nodes, displacements, and compatibility. Genetic programming is a natural selection search technique intended to combine good solutions to a problem from many generations to improve the results. All solutions are generated randomly and represented individually by a binary string with similarities of natural chromosomes, and hence it is termed as genetic programming. The outcome of the study is a MATLAB program, which can optimise a steel truss and display the optimised topology along with element shapes, deflections, and stress results.

Interface requirements to couple thermal-hydraulic codes to 3D neutronic codes

Energy Technology Data Exchange (ETDEWEB)

Langenbuch, S.; Austregesilo, H.; Velkov, K. [GRS, Garching (Germany)] [and others

1997-07-01

The present situation of thermalhydraulics codes and 3D neutronics codes is briefly described and general considerations for coupling of these codes are discussed. Two different basic approaches of coupling are identified and their relative advantages and disadvantages are discussed. The implementation of the coupling for 3D neutronics codes in the system ATHLET is presented. Meanwhile, this interface is used for coupling three different 3D neutronics codes.

Interface requirements to couple thermal-hydraulic codes to 3D neutronic codes

International Nuclear Information System (INIS)

Langenbuch, S.; Austregesilo, H.; Velkov, K.

1997-01-01

The present situation of thermalhydraulics codes and 3D neutronics codes is briefly described and general considerations for coupling of these codes are discussed. Two different basic approaches of coupling are identified and their relative advantages and disadvantages are discussed. The implementation of the coupling for 3D neutronics codes in the system ATHLET is presented. Meanwhile, this interface is used for coupling three different 3D neutronics codes

Synthesizing Certified Code

Science.gov (United States)

Whalen, Michael; Schumann, Johann; Fischer, Bernd

2002-01-01

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

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.

Report number codes

International Nuclear Information System (INIS)

Nelson, R.N.

1985-05-01

This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name

Performance Analysis of CRC Codes for Systematic and Nonsystematic Polar Codes with List Decoding

Directory of Open Access Journals (Sweden)

Takumi Murata

2018-01-01

Full Text Available Successive cancellation list (SCL decoding of polar codes is an effective approach that can significantly outperform the original successive cancellation (SC decoding, provided that proper cyclic redundancy-check (CRC codes are employed at the stage of candidate selection. Previous studies on CRC-assisted polar codes mostly focus on improvement of the decoding algorithms as well as their implementation, and little attention has been paid to the CRC code structure itself. For the CRC-concatenated polar codes with CRC code as their outer code, the use of longer CRC code leads to reduction of information rate, whereas the use of shorter CRC code may reduce the error detection probability, thus degrading the frame error rate (FER performance. Therefore, CRC codes of proper length should be employed in order to optimize the FER performance for a given signal-to-noise ratio (SNR per information bit. In this paper, we investigate the effect of CRC codes on the FER performance of polar codes with list decoding in terms of the CRC code length as well as its generator polynomials. Both the original nonsystematic and systematic polar codes are considered, and we also demonstrate that different behaviors of CRC codes should be observed depending on whether the inner polar code is systematic or not.

GRFT – Genetic records family tree web applet

Directory of Open Access Journals (Sweden)

Samuel ePimentel

2011-03-01

Full Text Available Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: 1 a family tree view which displays a color-coded family tree for an individual, 2 a sequential list of crosses, and 3 a list of crosses matching user-defined search criteria. Each feature contains options to specify the number of records shown and the latter two contain an option to filter results by the owner of the cross. The family tree feature is interactive, displaying a popup box with genetic information when the user mouses over an individual and allowing the user to draw a new tree by clicking on any individual in the current tree. The applet is written in Javascript and reads genetic records from a tab-delimited text file on the server, so it is cross-platform, can be accessed by anyone with an Internet connection, and supports almost instantaneous generation of new trees and table lists. Researchers can use the tool with their own genetic cross records for any sexually-reproducing organism. No additional software is required and with only minor modifications to the script, researchers can add their own custom columns. GRFT's speed, versatility, and low overhead make it an effective and innovative visualization method for genetic records. A sample tool is available at http://stanford.edu/~walbot/grft-sample.html.

[The genetics of thrombosis in cancer].

Science.gov (United States)

Soria, José Manuel; López, Sonia

2015-01-01

Venous thromboembolism (VTE) is a multifactorial and complex disease in which the interaction of genetic factors (estimated at 60%) and environmental factors (e.g., the use of oral contraceptives, pregnancy, immobility and cancer) determine the risk of thrombosis for each individual. In particular, the association between thrombosis and cancer is well established. Approximately 20% of patients with cancer develop a thromboembolic event over the course of the natural history of the tumor process, with thrombosis being the second leading cause of death for these patients. One of the greatest challenges currently facing the field of oncology is the identification of patients at high risk of VTE who can benefit from thromboprophylaxis. Currently, there is a VTE risk prediction model for patients with cancer (the Khorana risk score); however, its ability to identify patients at high risk is very low. It is important to note that this score, which is based on five clinical parameters, ignores the genetic variability associated with VTE risk. In this article, we present the preliminary results of the Oncothromb study, whose objective is to develop an individual VTE risk prediction model for patients with cancer who are treated with outpatient chemotherapy. Our model includes the clinical and genetic data on each patient (Thrombo inCode(®) genetic profile). Only by integrating multiple layers of biological information (clinical, plasmatic and genetic) we could obtain models that provide accurate information as to which patients are at high risk of developing a thromboembolic event associated with cancer so as to take appropriate prophylactic measures. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Genetic engineering: a matter that requires further refinement in Spanish secondary school textbooks

Science.gov (United States)

Martínez-Gracia, M. V.; Gil-Quýlez, M. J.

2003-09-01

Genetic engineering is now an integral part of many high school textbooks but little work has been done to assess whether it is being properly addressed. A checklist with 19 items was used to analyze how genetic engineering is presented in biology textbooks commonly used in Spanish high schools, including the content, its relationship with fundamental genetic principles, and how it aims to improve the genetic literacy of students. The results show that genetic engineering was normally introduced without a clear reference to the universal genetic code, protein expression or the genetic material shared by all species. In most cases it was poorly defined, without a clear explanation of all the relevant processes involved. Some procedures (such as vectors) were explained in detail without considering previous student knowledge or skills. Some books emphasized applications such as the human genome project without describing DNA sequencing. All books included possible repercussions, but in most cases only fashionable topics such as human cloning. There was an excess of information that was not always well founded and hence was unsuitable to provide a meaningful understanding of DNA technology required for citizens in the twenty-first century.

Z₂-double cyclic codes

OpenAIRE

Borges, J.

2014-01-01

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

Strict optical orthogonal codes for purely asynchronous code-division multiple-access applications

Science.gov (United States)

Zhang, Jian-Guo

1996-12-01

Strict optical orthogonal codes are presented for purely asynchronous optical code-division multiple-access (CDMA) applications. The proposed code can strictly guarantee the peaks of its cross-correlation functions and the sidelobes of any of its autocorrelation functions to have a value of 1 in purely asynchronous data communications. The basic theory of the proposed codes is given. An experiment on optical CDMA systems is also demonstrated to verify the characteristics of the proposed code.

Entropy Coding in HEVC

OpenAIRE

Sze, Vivienne; Marpe, Detlev

2014-01-01

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

Quantum Codes From Negacyclic Codes over Group Ring ( Fq + υFq) G

International Nuclear Information System (INIS)

Koroglu, Mehmet E.; Siap, Irfan

2016-01-01

In this paper, we determine self dual and self orthogonal codes arising from negacyclic codes over the group ring ( F q + υF q ) G . By taking a suitable Gray image of these codes we obtain many good parameter quantum error-correcting codes over F q . (paper)

Trellis and turbo coding iterative and graph-based error control coding

CERN Document Server

Schlegel, Christian B

2015-01-01

This new edition has been extensively revised to reflect the progress in error control coding over the past few years. Over 60% of the material has been completely reworked, and 30% of the material is original. Convolutional, turbo, and low density parity-check (LDPC) coding and polar codes in a unified framework. Advanced research-related developments such as spatial coupling. A focus on algorithmic and implementation aspects of error control coding.

Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

Science.gov (United States)

Ancheta, T. C., Jr.

1976-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

An Improved Hierarchical Genetic Algorithm for Sheet Cutting Scheduling with Process Constraints

Directory of Open Access Journals (Sweden)

Yunqing Rao

2013-01-01

Full Text Available For the first time, an improved hierarchical genetic algorithm for sheet cutting problem which involves n cutting patterns for m non-identical parallel machines with process constraints has been proposed in the integrated cutting stock model. The objective of the cutting scheduling problem is minimizing the weighted completed time. A mathematical model for this problem is presented, an improved hierarchical genetic algorithm (ant colony—hierarchical genetic algorithm is developed for better solution, and a hierarchical coding method is used based on the characteristics of the problem. Furthermore, to speed up convergence rates and resolve local convergence issues, a kind of adaptive crossover probability and mutation probability is used in this algorithm. The computational result and comparison prove that the presented approach is quite effective for the considered problem.

An improved hierarchical genetic algorithm for sheet cutting scheduling with process constraints.

Science.gov (United States)

Rao, Yunqing; Qi, Dezhong; Li, Jinling

2013-01-01

For the first time, an improved hierarchical genetic algorithm for sheet cutting problem which involves n cutting patterns for m non-identical parallel machines with process constraints has been proposed in the integrated cutting stock model. The objective of the cutting scheduling problem is minimizing the weighted completed time. A mathematical model for this problem is presented, an improved hierarchical genetic algorithm (ant colony--hierarchical genetic algorithm) is developed for better solution, and a hierarchical coding method is used based on the characteristics of the problem. Furthermore, to speed up convergence rates and resolve local convergence issues, a kind of adaptive crossover probability and mutation probability is used in this algorithm. The computational result and comparison prove that the presented approach is quite effective for the considered problem.

Novel classes of non-coding RNAs and cancer

Directory of Open Access Journals (Sweden)

Sana Jiri

2012-05-01

Full Text Available Abstract For the many years, the central dogma of molecular biology has been that RNA functions mainly as an informational intermediate between a DNA sequence and its encoded protein. But one of the great surprises of modern biology was the discovery that protein-coding genes represent less than 2% of the total genome sequence, and subsequently the fact that at least 90% of the human genome is actively transcribed. Thus, the human transcriptome was found to be more complex than a collection of protein-coding genes and their splice variants. Although initially argued to be spurious transcriptional noise or accumulated evolutionary debris arising from the early assembly of genes and/or the insertion of mobile genetic elements, recent evidence suggests that the non-coding RNAs (ncRNAs may play major biological roles in cellular development, physiology and pathologies. NcRNAs could be grouped into two major classes based on the transcript size; small ncRNAs and long ncRNAs. Each of these classes can be further divided, whereas novel subclasses are still being discovered and characterized. Although, in the last years, small ncRNAs called microRNAs were studied most frequently with more than ten thousand hits at PubMed database, recently, evidence has begun to accumulate describing the molecular mechanisms by which a wide range of novel RNA species function, providing insight into their functional roles in cellular biology and in human disease. In this review, we summarize newly discovered classes of ncRNAs, and highlight their functioning in cancer biology and potential usage as biomarkers or therapeutic targets.

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

KAUST Repository

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

2012-01-01

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

[Algorithm of toxigenic genetically altered Vibrio cholerae El Tor biovar strain identification].

Science.gov (United States)

Smirnova, N I; Agafonov, D A; Zadnova, S P; Cherkasov, A V; Kutyrev, V V

2014-01-01

Development of an algorithm of genetically altered Vibrio cholerae biovar El Tor strai identification that ensures determination of serogroup, serovar and biovar of the studied isolate based on pheno- and genotypic properties, detection of genetically altered cholera El Tor causative agents, their differentiation by epidemic potential as well as evaluation of variability of key pathogenicity genes. Complex analysis of 28 natural V. cholerae strains was carried out by using traditional microbiological methods, PCR and fragmentary sequencing. An algorithm of toxigenic genetically altered V. cholerae biovar El Tor strain identification was developed that includes 4 stages: determination of serogroup, serovar and biovar based on phenotypic properties, confirmation of serogroup and biovar based on molecular-genetic properties determination of strains as genetically altered, differentiation of genetically altered strains by their epidemic potential and detection of ctxB and tcpA key pathogenicity gene polymorphism. The algorithm is based on the use of traditional microbiological methods, PCR and sequencing of gene fragments. The use of the developed algorithm will increase the effectiveness of detection of genetically altered variants of the cholera El Tor causative agent, their differentiation by epidemic potential and will ensure establishment of polymorphism of genes that code key pathogenicity factors for determination of origins of the strains and possible routes of introduction of the infection.

ComboCoding: Combined intra-/inter-flow network coding for TCP over disruptive MANETs

Directory of Open Access Journals (Sweden)

Chien-Chia Chen

2011-07-01

Full Text Available TCP over wireless networks is challenging due to random losses and ACK interference. Although network coding schemes have been proposed to improve TCP robustness against extreme random losses, a critical problem still remains of DATA–ACK interference. To address this issue, we use inter-flow coding between DATA and ACK to reduce the number of transmissions among nodes. In addition, we also utilize a “pipeline” random linear coding scheme with adaptive redundancy to overcome high packet loss over unreliable links. The resulting coding scheme, ComboCoding, combines intra-flow and inter-flow coding to provide robust TCP transmission in disruptive wireless networks. The main contributions of our scheme are twofold; the efficient combination of random linear coding and XOR coding on bi-directional streams (DATA and ACK, and the novel redundancy control scheme that adapts to time-varying and space-varying link loss. The adaptive ComboCoding was tested on a variable hop string topology with unstable links and on a multipath MANET with dynamic topology. Simulation results show that TCP with ComboCoding delivers higher throughput than with other coding options in high loss and mobile scenarios, while introducing minimal overhead in normal operation.

Performance analysis of WS-EWC coded optical CDMA networks with/without LDPC codes

Science.gov (United States)

Huang, Chun-Ming; Huang, Jen-Fa; Yang, Chao-Chin

2010-10-01

One extended Welch-Costas (EWC) code family for the wavelength-division-multiplexing/spectral-amplitude coding (WDM/SAC; WS) optical code-division multiple-access (OCDMA) networks is proposed. This system has a superior performance as compared to the previous modified quadratic congruence (MQC) coded OCDMA networks. However, since the performance of such a network is unsatisfactory when the data bit rate is higher, one class of quasi-cyclic low-density parity-check (QC-LDPC) code is adopted to improve that. Simulation results show that the performance of the high-speed WS-EWC coded OCDMA network can be greatly improved by using the LDPC codes.

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan; Gao, Xin

2014-01-01

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan

2014-07-06

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

Science.gov (United States)

Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

2016-03-01

In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

Coupling the severe accident code SCDAP with the system thermal hydraulic code MARS

Energy Technology Data Exchange (ETDEWEB)

Lee, Young Jin; Chung, Bub Dong [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

2004-07-01

MARS is a best-estimate system thermal hydraulics code with multi-dimensional modeling capability. One of the aims in MARS code development is to make it a multi-functional code system with the analysis capability to cover the entire accident spectrum. For this purpose, MARS code has been coupled with a number of other specialized codes such as CONTEMPT for containment analysis, and MASTER for 3-dimensional kinetics. And in this study, the SCDAP code has been coupled with MARS to endow the MARS code system with severe accident analysis capability. With the SCDAP, MARS code system now has acquired the capability to simulate such severe accident related phenomena as cladding oxidation, melting and slumping of fuel and reactor structures.

Coupling the severe accident code SCDAP with the system thermal hydraulic code MARS

International Nuclear Information System (INIS)

Lee, Young Jin; Chung, Bub Dong

2004-01-01

MARS is a best-estimate system thermal hydraulics code with multi-dimensional modeling capability. One of the aims in MARS code development is to make it a multi-functional code system with the analysis capability to cover the entire accident spectrum. For this purpose, MARS code has been coupled with a number of other specialized codes such as CONTEMPT for containment analysis, and MASTER for 3-dimensional kinetics. And in this study, the SCDAP code has been coupled with MARS to endow the MARS code system with severe accident analysis capability. With the SCDAP, MARS code system now has acquired the capability to simulate such severe accident related phenomena as cladding oxidation, melting and slumping of fuel and reactor structures

Distributed Video Coding for Multiview and Video-plus-depth Coding

DEFF Research Database (Denmark)

Salmistraro, Matteo

The interest in Distributed Video Coding (DVC) systems has grown considerably in the academic world in recent years. With DVC the correlation between frames is exploited at the decoder (joint decoding). The encoder codes the frame independently, performing relatively simple operations. Therefore......, with DVC the complexity is shifted from encoder to decoder, making the coding architecture a viable solution for encoders with limited resources. DVC may empower new applications which can benefit from this reversed coding architecture. Multiview Distributed Video Coding (M-DVC) is the application...... of the to-be-decoded frame. Another key element is the Residual estimation, indicating the reliability of the SI, which is used to calculate the parameters of the correlation noise model between SI and original frame. In this thesis new methods for Inter-camera SI generation are analyzed in the Stereo...

Diagnostic Coding for Epilepsy.

Science.gov (United States)

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

2016-02-01

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

Coding of Neuroinfectious Diseases.

Science.gov (United States)

Barkley, Gregory L

2015-12-01

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

Genetic similarity among commercial oil palm materials based on microsatellite markers

Directory of Open Access Journals (Sweden)

Diana Arias

2012-08-01

Full Text Available Microsatellite markers are used to determine genetic similarities among individuals and might be used in various applications in breeding programs. For example, knowing the genetic similarity relationships of commercial planting materials helps to better understand their responses to environmental, agronomic and plant health factors. This study assessed 17 microsatellite markers in 9 crosses (D x P of Elaeis guineensis Jacq. from various commercial companies in Malaysia, France, Costa Rica and Colombia, in order to find possible genetic differences and/or similarities. Seventy-seven alleles were obtained, with an average of 4.5 alleles per primer and a range of 2-8 amplified alleles. The results show a significant reduction of alleles, compared to the number of alleles reported for wild oil palm populations. The obtained dendrogram shows the formation of two groups based on their genetic similarity. Group A, with ~76% similarity, contains the commercial material of 3 codes of Deli x La Mé crosses produced in France and Colombia, and group B, with ~66% genetic similarity, includes all the materials produced by commercial companies in Malaysia, France, Costa Rica and Colombia

Immune Genetic Learning of Fuzzy Cognitive Map

Institute of Scientific and Technical Information of China (English)

LIN Chun-mei; HE Yue; TANG Bing-yong

2006-01-01

This paper presents a hybrid methodology of automatically constructing fuzzy cognitive map (FCM). The method uses immune genetic algorithm to learn the connection matrix of FCM. In the algorithm, the DNA coding method is used and an immune operator based on immune mechanism is constructed. The characteristics of the system and the experts' knowledge are abstracted as vaccine for restraining the degenerative phenomena during evolution so as to improve the algorithmic efficiency. Finally, an illustrative example is provided, and its results suggest that the method is capable of automatically generating FCM model.

A study on climatic adaptation of dipteran mitochondrial protein coding genes

Directory of Open Access Journals (Sweden)

Debajyoti Kabiraj

2017-10-01

Full Text Available Diptera, the true flies are frequently found in nature and their habitat is found all over the world including Antarctica and Polar Regions. The number of documented species for order diptera is quite high and thought to be 14% of the total animal present in the earth [1]. Most of the study in diptera has focused on the taxa of economic and medical importance, such as the fruit flies Ceratitis capitata and Bactrocera spp. (Tephritidae, which are serious agricultural pests; the blowflies (Calliphoridae and oestrid flies (Oestridae, which can cause myiasis; the anopheles mosquitoes (Culicidae, are the vectors of malaria; and leaf-miners (Agromyzidae, vegetable and horticultural pests [2]. Insect mitochondrion consists of 13 protein coding genes, 22 tRNAs and 2 rRNAs, are the remnant portion of alpha-proteobacteria is responsible for simultaneous function of energy production and thermoregulation of the cell through the bi-genomic system thus different adaptability in different climatic condition might have compensated by complementary changes is the both genomes [3,4]. In this study we have collected complete mitochondrial genome and occurrence data of one hundred thirteen such dipteran insects from different databases and literature survey. Our understanding of the genetic basis of climatic adaptation in diptera is limited to the basic information on the occurrence location of those species and mito genetic factors underlying changes in conspicuous phenotypes. To examine this hypothesis, we have taken an approach of Nucleotide substitution analysis for 13 protein coding genes of mitochondrial DNA individually and combined by different software for monophyletic group as well as paraphyletic group of dipteran species. Moreover, we have also calculated codon adaptation index for all dipteran mitochondrial protein coding genes. Following this work, we have classified our sample organisms according to their location data from GBIF (https

Refactoring test code

NARCIS (Netherlands)

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

2001-01-01

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

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...

Opening up codings?

DEFF Research Database (Denmark)

Steensig, Jakob; Heinemann, Trine

2015-01-01

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

The materiality of Code

DEFF Research Database (Denmark)

Soon, Winnie

2014-01-01

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

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

Functional characterization of genetic enzyme variations in human lipoxygenases

Directory of Open Access Journals (Sweden)

Thomas Horn

2013-01-01

Full Text Available Mammalian lipoxygenases play a role in normal cell development and differentiation but they have also been implicated in the pathogenesis of cardiovascular, hyperproliferative and neurodegenerative diseases. As lipid peroxidizing enzymes they are involved in the regulation of cellular redox homeostasis since they produce lipid hydroperoxides, which serve as an efficient source for free radicals. There are various epidemiological correlation studies relating naturally occurring variations in the six human lipoxygenase genes (SNPs or rare mutations to the frequency for various diseases in these individuals, but for most of the described variations no functional data are available. Employing a combined bioinformatical and enzymological strategy, which included structural modeling and experimental site-directed mutagenesis, we systematically explored the structural and functional consequences of non-synonymous genetic variations in four different human lipoxygenase genes (ALOX5, ALOX12, ALOX15, and ALOX15B that have been identified in the human 1000 genome project. Due to a lack of a functional expression system we resigned to analyze the functionality of genetic variations in the hALOX12B and hALOXE3 gene. We found that most of the frequent non-synonymous coding SNPs are located at the enzyme surface and hardly alter the enzyme functionality. In contrast, genetic variations which affect functional important amino acid residues or lead to truncated enzyme variations (nonsense mutations are usually rare with a global allele frequency<0.1%. This data suggest that there appears to be an evolutionary pressure on the coding regions of the lipoxygenase genes preventing the accumulation of loss-of-function variations in the human population.

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

International Nuclear Information System (INIS)

Shi Jibin; Jiang Yueyuan; Wang Wenran

2004-01-01

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

The mGA1.0: A common LISP implementation of a messy genetic algorithm

Science.gov (United States)

Goldberg, David E.; Kerzic, Travis

1990-01-01

Genetic algorithms (GAs) are finding increased application in difficult search, optimization, and machine learning problems in science and engineering. Increasing demands are being placed on algorithm performance, and the remaining challenges of genetic algorithm theory and practice are becoming increasingly unavoidable. Perhaps the most difficult of these challenges is the so-called linkage problem. Messy GAs were created to overcome the linkage problem of simple genetic algorithms by combining variable-length strings, gene expression, messy operators, and a nonhomogeneous phasing of evolutionary processing. Results on a number of difficult deceptive test functions are encouraging with the mGA always finding global optima in a polynomial number of function evaluations. Theoretical and empirical studies are continuing, and a first version of a messy GA is ready for testing by others. A Common LISP implementation called mGA1.0 is documented and related to the basic principles and operators developed by Goldberg et. al. (1989, 1990). Although the code was prepared with care, it is not a general-purpose code, only a research version. Important data structures and global variations are described. Thereafter brief function descriptions are given, and sample input data are presented together with sample program output. A source listing with comments is also included.

Perceptron Genetic to Recognize Openning Strategy Ruy Lopez

Science.gov (United States)

Azmi, Zulfian; Mawengkang, Herman

2018-01-01

The application of Perceptron method is not effective for coding on hardware based systems because it is not real time learning. With Genetic algorithm approach in calculating and searching the best weight (fitness value) system will do learning only one iteration. And the results of this analysis were tested in the case of the introduction of the opening pattern of chess Ruy Lopez. The Analysis with Perceptron Model with Algorithm Approach Genetics from group Artificial Neural Network for open Ruy Lopez. The data is processed with base open chess, with step eight a position white Pion from end open chess. Using perceptron method have many input and one output process many weight and refraction until output equal goal. Data trained and test with software Matlab and system can recognize the chess opening Ruy Lopez or Not open Ruy Lopez with Real time.

Research and Applications of Shop Scheduling Based on Genetic Algorithms

Directory of Open Access Journals (Sweden)

Hang ZHAO

Full Text Available ABSTRACT Shop Scheduling is an important factor affecting the efficiency of production, efficient scheduling method and a research and application for optimization technology play an important role for manufacturing enterprises to improve production efficiency, reduce production costs and many other aspects. Existing studies have shown that improved genetic algorithm has solved the limitations that existed in the genetic algorithm, the objective function is able to meet customers' needs for shop scheduling, and the future research should focus on the combination of genetic algorithm with other optimized algorithms. In this paper, in order to overcome the shortcomings of early convergence of genetic algorithm and resolve local minimization problem in search process,aiming at mixed flow shop scheduling problem, an improved cyclic search genetic algorithm is put forward, and chromosome coding method and corresponding operation are given.The operation has the nature of inheriting the optimal individual ofthe previous generation and is able to avoid the emergence of local minimum, and cyclic and crossover operation and mutation operation can enhance the diversity of the population and then quickly get the optimal individual, and the effectiveness of the algorithm is validated. Experimental results show that the improved algorithm can well avoid the emergency of local minimum and is rapid in convergence.

Fracture flow code

International Nuclear Information System (INIS)

Dershowitz, W; Herbert, A.; Long, J.

1989-03-01

The hydrology of the SCV site will be modelled utilizing discrete fracture flow models. These models are complex, and can not be fully cerified by comparison to analytical solutions. The best approach for verification of these codes is therefore cross-verification between different codes. This is complicated by the variation in assumptions and solution techniques utilized in different codes. Cross-verification procedures are defined which allow comparison of the codes developed by Harwell Laboratory, Lawrence Berkeley Laboratory, and Golder Associates Inc. Six cross-verification datasets are defined for deterministic and stochastic verification of geometric and flow features of the codes. Additional datasets for verification of transport features will be documented in a future report. (13 figs., 7 tabs., 10 refs.) (authors)

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

Directory of Open Access Journals (Sweden)

Jing Qian

Full Text Available Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs.We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT, to identify protein-coding gene association with 14 cardiometabolic (CMD related traits across 6 publicly available genome wide association (GWA meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1.We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes.We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and

The roles of non-coding RNAs in cardiac regenerative medicine

Directory of Open Access Journals (Sweden)

Oi Kuan Choong

2017-06-01

Full Text Available The emergence of non-coding RNAs (ncRNAs has challenged the central dogma of molecular biology that dictates that the decryption of genetic information starts from transcription of DNA to RNA, with subsequent translation into a protein. Large numbers of ncRNAs with biological significance have now been identified, suggesting that ncRNAs are important in their own right and their roles extend far beyond what was originally envisaged. ncRNAs do not only regulate gene expression, but are also involved in chromatin architecture and structural conformation. Several studies have pointed out that ncRNAs participate in heart disease; however, the functions of ncRNAs still remain unclear. ncRNAs are involved in cellular fate, differentiation, proliferation and tissue regeneration, hinting at their potential therapeutic applications. Here, we review the current understanding of both the biological functions and molecular mechanisms of ncRNAs in heart disease and describe some of the ncRNAs that have potential heart regeneration effects. Keywords: Non-coding RNAs, Cardiac regeneration, Cardiac fate, Proliferation, Differentiation, Reprograming

Eddy current testing probe optimization using a parallel genetic algorithm

Directory of Open Access Journals (Sweden)

Dolapchiev Ivaylo

2008-01-01

Full Text Available This paper uses the developed parallel version of Michalewicz's Genocop III Genetic Algorithm (GA searching technique to optimize the coil geometry of an eddy current non-destructive testing probe (ECTP. The electromagnetic field is computed using FEMM 2D finite element code. The aim of this optimization was to determine coil dimensions and positions that improve ECTP sensitivity to physical properties of the tested devices.

NAGRADATA. Code key. Geology

International Nuclear Information System (INIS)

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

1984-01-01

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

RFQ simulation code

International Nuclear Information System (INIS)

Lysenko, W.P.

1984-04-01

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

The Visual Code Navigator : An Interactive Toolset for Source Code Investigation

NARCIS (Netherlands)

Lommerse, Gerard; Nossin, Freek; Voinea, Lucian; Telea, Alexandru

2005-01-01

We present the Visual Code Navigator, a set of three interrelated visual tools that we developed for exploring large source code software projects from three different perspectives, or views: The syntactic view shows the syntactic constructs in the source code. The symbol view shows the objects a

Joint source-channel coding using variable length codes

NARCIS (Netherlands)

Balakirsky, V.B.

2001-01-01

We address the problem of joint source-channel coding when variable-length codes are used for information transmission over a discrete memoryless channel. Data transmitted over the channel are interpreted as pairs (m k ,t k ), where m k is a message generated by the source and t k is a time instant

Tokamak Systems Code

International Nuclear Information System (INIS)

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

1985-03-01

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

Blahut-Arimoto algorithm and code design for action-dependent source coding problems

DEFF Research Database (Denmark)

Trillingsgaard, Kasper Fløe; Simeone, Osvaldo; Popovski, Petar

2013-01-01

The source coding problem with action-dependent side information at the decoder has recently been introduced to model data acquisition in resource-constrained systems. In this paper, an efficient Blahut-Arimoto-type algorithm for the numerical computation of the rate-distortion-cost function...... for this problem is proposed. Moreover, a simplified two-stage code structure based on multiplexing is put forth, whereby the first stage encodes the actions and the second stage is composed of an array of classical Wyner-Ziv codes, one for each action. Leveraging this structure, specific coding/decoding...... strategies are designed based on LDGM codes and message passing. Through numerical examples, the proposed code design is shown to achieve performance close to the rate-distortion-cost function....

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

Science.gov (United States)

Deibel, Eric

2014-01-01

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

DNA watermarks in non-coding regulatory sequences

Directory of Open Access Journals (Sweden)

Pyka Martin

2009-07-01

Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

On the Combination of Multi-Layer Source Coding and Network Coding for Wireless Networks

DEFF Research Database (Denmark)

Krigslund, Jeppe; Fitzek, Frank; Pedersen, Morten Videbæk

2013-01-01

quality is developed. A linear coding structure designed to gracefully encapsulate layered source coding provides both low complexity of the utilised linear coding while enabling robust erasure correction in the form of fountain coding capabilities. The proposed linear coding structure advocates efficient...

Coding Class

DEFF Research Database (Denmark)

Ejsing-Duun, Stine; Hansbøl, Mikala

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

Criminal Code, Federal District, 16 February 1971.

Science.gov (United States)

1988-01-01

Article 320 of the Criminal Code of the Federal District of Mexico defines "abortion" as the death of the conceptus at any time during pregnancy. Articles 320-32 specify penalties for inducing abortion, and Articles 333-34 exempt punishment if the abortion resulted from failure of the woman to take proper care, if the pregnancy was the result of rape, or if the pregnancy endangered the life of the woman. The abortion provisions of the criminal codes of the Mexican states of Baja California, Chiapas, Mexico, Sinoala, Sonora, Tabasco, and Tamaulipas are nearly identical to those of the Federal District Code. Certain states also give immunity from prosecution for abortion 1) if the pregnancy resulted from artificial insemination neither requested or assented to by the woman, provided that the abortion is carried out within the first 90 days of pregnancy; 2) if there is good reason to believe that the unborn child suffers from severe physical or mental disabilities of genetic or congenital origin; 3) if the health of the woman would be seriously jeopardized by the pregnancy, and 4) if the abortion is carried out for serious and substantiated economic reasons in cases where the woman has at least three children. Guanajuato and Queretaro allow abortions only when the pregnancy is the result of rape. Guerrero authorizes abortions only when the pregnancy is the result of rape, when the pregnancy results from an unlawful artificial insemination, or for eugenic reasons. Hidalgo, Nuevo Leon, and San Luis Potosi allows abortions only when the pregnancy is the result of rape or when the continuation of the pregnancy would seriously jeopardize the woman's health. In Chihuahua, Coahuila, Durango, Oaxaca, and Veracruz, abortions allowed because the pregnancy resulted from rape must be performed in the first 90 days of pregnancy.

KENO-V code

International Nuclear Information System (INIS)

Cramer, S.N.

1984-01-01

The KENO-V code is the current release of the Oak Ridge multigroup Monte Carlo criticality code development. The original KENO, with 16 group Hansen-Roach cross sections and P 1 scattering, was one ot the first multigroup Monte Carlo codes and it and its successors have always been a much-used research tool for criticality studies. KENO-V is able to accept large neutron cross section libraries (a 218 group set is distributed with the code) and has a general P/sub N/ scattering capability. A supergroup feature allows execution of large problems on small computers, but at the expense of increased calculation time and system input/output operations. This supergroup feature is activated automatically by the code in a manner which utilizes as much computer memory as is available. The primary purpose of KENO-V is to calculate the system k/sub eff/, from small bare critical assemblies to large reflected arrays of differing fissile and moderator elements. In this respect KENO-V neither has nor requires the many options and sophisticated biasing techniques of general Monte Carlo codes

PEAR code review

International Nuclear Information System (INIS)

De Wit, R.; Jamieson, T.; Lord, M.; Lafortune, J.F.

1997-07-01

As a necessary component in the continuous improvement and refinement of methodologies employed in the nuclear industry, regulatory agencies need to periodically evaluate these processes to improve confidence in results and ensure appropriate levels of safety are being achieved. The independent and objective review of industry-standard computer codes forms an essential part of this program. To this end, this work undertakes an in-depth review of the computer code PEAR (Public Exposures from Accidental Releases), developed by Atomic Energy of Canada Limited (AECL) to assess accidental releases from CANDU reactors. PEAR is based largely on the models contained in the Canadian Standards Association (CSA) N288.2-M91. This report presents the results of a detailed technical review of the PEAR code to identify any variations from the CSA standard and other supporting documentation, verify the source code, assess the quality of numerical models and results, and identify general strengths and weaknesses of the code. The version of the code employed in this review is the one which AECL intends to use for CANDU 9 safety analyses. (author)

Manually operated coded switch

International Nuclear Information System (INIS)

Barnette, J.H.

1978-01-01

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

Phonological coding during reading.

Science.gov (United States)

Leinenger, Mallorie

2014-11-01

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

Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder.

Directory of Open Access Journals (Sweden)

René A W Frank

2011-04-01

Full Text Available Current models of schizophrenia and bipolar disorder implicate multiple genes, however their biological relationships remain elusive. To test the genetic role of glutamate receptors and their interacting scaffold proteins, the exons of ten glutamatergic 'hub' genes in 1304 individuals were re-sequenced in case and control samples. No significant difference in the overall number of non-synonymous single nucleotide polymorphisms (nsSNPs was observed between cases and controls. However, cluster analysis of nsSNPs identified two exons encoding the cysteine-rich domain and first transmembrane helix of GRM1 as a risk locus with five mutations highly enriched within these domains. A new splice variant lacking the transmembrane GPCR domain of GRM1 was discovered in the human brain and the GRM1 mutation cluster could perturb the regulation of this variant. The predicted effect on individuals harbouring multiple mutations distributed in their ten hub genes was also examined. Diseased individuals possessed an increased load of deleteriousness from multiple concurrent rare and common coding variants. Together, these data suggest a disease model in which the interplay of compound genetic coding variants, distributed among glutamate receptors and their interacting proteins, contribute to the pathogenesis of schizophrenia and bipolar disorders.

Codes maintained by the LAACG [Los Alamos Accelerator Code Group] at the NMFECC

International Nuclear Information System (INIS)

Wallace, R.; Barts, T.

1990-01-01

The Los Alamos Accelerator Code Group (LAACG) maintains two groups of design codes at the National Magnetic Fusion Energy Computing Center (NMFECC). These codes, principally electromagnetic field solvers, are used for the analysis and design of electromagnetic components for accelerators, e.g., magnets, rf structures, pickups, etc. In this paper, the status and future of the installed codes will be discussed with emphasis on an experimental version of one set of codes, POISSON/SUPERFISH

Effect of Duplicate Genes on Mouse Genetic Robustness: An Update

Directory of Open Access Journals (Sweden)

Zhixi Su

2014-01-01

Full Text Available In contrast to S. cerevisiae and C. elegans, analyses based on the current knockout (KO mouse phenotypes led to the conclusion that duplicate genes had almost no role in mouse genetic robustness. It has been suggested that the bias of mouse KO database toward ancient duplicates may possibly cause this knockout duplicate puzzle, that is, a very similar proportion of essential genes (PE between duplicate genes and singletons. In this paper, we conducted an extensive and careful analysis for the mouse KO phenotype data and corroborated a strong effect of duplicate genes on mouse genetics robustness. Moreover, the effect of duplicate genes on mouse genetic robustness is duplication-age dependent, which holds after ruling out the potential confounding effect from coding-sequence conservation, protein-protein connectivity, functional bias, or the bias of duplicates generated by whole genome duplication (WGD. Our findings suggest that two factors, the sampling bias toward ancient duplicates and very ancient duplicates with a proportion of essential genes higher than that of singletons, have caused the mouse knockout duplicate puzzle; meanwhile, the effect of genetic buffering may be correlated with sequence conservation as well as protein-protein interactivity.

Concatenated coding systems employing a unit-memory convolutional code and a byte-oriented decoding algorithm

Science.gov (United States)

Lee, L.-N.

1977-01-01

Concatenated coding systems utilizing a convolutional code as the inner code and a Reed-Solomon code as the outer code are considered. In order to obtain very reliable communications over a very noisy channel with relatively modest coding complexity, it is proposed to concatenate a byte-oriented unit-memory convolutional code with an RS outer code whose symbol size is one byte. It is further proposed to utilize a real-time minimal-byte-error probability decoding algorithm, together with feedback from the outer decoder, in the decoder for the inner convolutional code. The performance of the proposed concatenated coding system is studied, and the improvement over conventional concatenated systems due to each additional feature is isolated.

Benchmark studies of BOUT++ code and TPSMBI code on neutral transport during SMBI

Energy Technology Data Exchange (ETDEWEB)

Wang, Y.H. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Center for Magnetic Fusion Theory, Chinese Academy of Sciences, Hefei 230031 (China); Wang, Z.H., E-mail: zhwang@swip.ac.cn [Southwestern Institute of Physics, Chengdu 610041 (China); Guo, W., E-mail: wfguo@ipp.ac.cn [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Center for Magnetic Fusion Theory, Chinese Academy of Sciences, Hefei 230031 (China); Ren, Q.L. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Sun, A.P.; Xu, M.; Wang, A.K. [Southwestern Institute of Physics, Chengdu 610041 (China); Xiang, N. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Center for Magnetic Fusion Theory, Chinese Academy of Sciences, Hefei 230031 (China)

2017-06-09

SMBI (supersonic molecule beam injection) plays an important role in tokamak plasma fuelling, density control and ELM mitigation in magnetic confinement plasma physics, which has been widely used in many tokamaks. The trans-neut module of BOUT++ code is the only large-scale parallel 3D fluid code used to simulate the SMBI fueling process, while the TPSMBI (transport of supersonic molecule beam injection) code is a recent developed 1D fluid code of SMBI. In order to find a method to increase SMBI fueling efficiency in H-mode plasma, especially for ITER, it is significant to first verify the codes. The benchmark study between the trans-neut module of BOUT++ code and the TPSMBI code on radial transport dynamics of neutral during SMBI has been first successfully achieved in both slab and cylindrical coordinates. The simulation results from the trans-neut module of BOUT++ code and TPSMBI code are consistent very well with each other. Different upwind schemes have been compared to deal with the sharp gradient front region during the inward propagation of SMBI for the code stability. The influence of the WENO3 (weighted essentially non-oscillatory) and the third order upwind schemes on the benchmark results has also been discussed. - Highlights: • A 1D model of SMBI has developed. • Benchmarks of BOUT++ and TPSMBI codes have first been finished. • The influence of the WENO3 and the third order upwind schemes on the benchmark results has also been discussed.

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.

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

Introduction to focus issue: quantitative approaches to genetic networks.

Science.gov (United States)

Albert, Réka; Collins, James J; Glass, Leon

2013-06-01

All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

Identification of coding and non-coding mutational hotspots in cancer genomes.

Science.gov (United States)

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

On the Performance of a Multi-Edge Type LDPC Code for Coded Modulation

NARCIS (Netherlands)

Cronie, H.S.

2005-01-01

We present a method to combine error-correction coding and spectral-efficient modulation for transmission over the Additive White Gaussian Noise (AWGN) channel. The code employs signal shaping which can provide a so-called shaping gain. The code belongs to the family of sparse graph codes for which

Insurance billing and coding.

Science.gov (United States)

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

2008-07-01

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

Speaking Code

DEFF Research Database (Denmark)

Cox, Geoff

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

DNA Mapping Made Simple: An Intellectual Activity about the Genetic Modification of Organisms

Science.gov (United States)

Marques, Miguel; Arrabaca, Joao; Chagas, Isabel

2004-01-01

Since the discovery of the DNA double helix (in 1953 by Watson and Crick), technologies have been developed that allow scientists to manipulate the genome of bacteria to produce human hormones, as well as the genome of crop plants to achieve high yield and enhanced flavor. The universality of the genetic code has allowed DNA isolated from a…

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....

Decoding Codes on Graphs

Indian Academy of Sciences (India)

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

Induction, by thymidylate stress, of genetic recombination as evidenced by deletion of a transferred genetic marker in mouse FM3A cells

International Nuclear Information System (INIS)

Ayusawa, D.; Koyama, H.; Shimizu, K.; Kaneda, S.; Takeishi, K.; Seno, T.

1986-01-01

Studies were made on the genetic consequences of methotrexate-directed thymidylate stress, focusing attention on a human thymidylate synthase gene that was introduced as a heterologous genetic marker into mouse thymidylate synthase-negative mutant cells. Thymidylate stress induced thymidylate synthase-negative segregants with concomitant loss of human thymidylate synthase activity with frequencies 1 to 2 orders of magnitude higher than the uninduced spontaneous level in some but not all transformant lines. Induction of the segregants was suppressed almost completely by cycloheximide and partially by caffeine. Thymidylate stress did not, however, induce mutations, as determined by measuring resistance to ouabain or 6-thioguanine. Thymidylate synthase-negative segregants were also induced by other means such as bromodeoxyuridine treatment and X-ray irradiation. In each of the synthase-negative segregants induced by thymidylate stress, a DNA segment including almost the whole coding region of the transferred human thymidylate synthase gene was deleted in a very specific manner, as shown by Southern blot analysis with a human Alu sequence and a human thymidylate synthase cDNA as probes. In the segregants that emerged spontaneously at low frequency, the entire transferred genetic marker was lost. In the segregants induced by X-ray irradiation, structural alterations of the genetic marker were random. These results show that thymidylate stress is a physiological factor that provokes the instability of this exogenously incorporated DNA in some specific manner and produces nonrandom genetic recombination in mammalian cells

Genetic and Environmental Influences on Retinopathy of Prematurity

Science.gov (United States)

Ortega-Molina, J. M.; Anaya-Alaminos, R.; Uberos-Fernández, J.; Solans-Pérez de Larraya, A.; Chaves-Samaniego, M. J.; Salgado-Miranda, A.; Piñar-Molina, R.; Jerez-Calero, A.; García-Serrano, J. L.

2015-01-01

Objective. The goals were to isolate and study the genetic susceptibility to retinopathy of prematurity (ROP), as well as the gene-environment interaction established in this disease. Methods. A retrospective study (2000–2014) was performed about the heritability of retinopathy of prematurity in 257 infants who were born at a gestational age of ≤32 weeks. The ROP was studied and treated by a single pediatric ophthalmologist. A binary logistic regression analysis was completed between the presence or absence of ROP and the predictor variables. Results. Data obtained from 38 monozygotic twins, 66 dizygotic twins, and 153 of simple birth were analyzed. The clinical features of the cohorts of monozygotic and dizygotic twins were not significantly different. Genetic factors represented 72.8% of the variability in the stage of ROP, environmental factors 23.08%, and random factors 4.12%. The environmental variables representing the highest risk of ROP were the number of days of tracheal intubation (p < 0.001), postnatal weight gain (p = 0.001), and development of sepsis (p = 0.0014). Conclusion. The heritability of ROP was found to be 0.73. The environmental factors regulate and modify the expression of the genetic code. PMID:26089603

Utilization of genetic tests: analysis of gene-specific billing in Medicare claims data.

Science.gov (United States)

Lynch, Julie A; Berse, Brygida; Dotson, W David; Khoury, Muin J; Coomer, Nicole; Kautter, John

2017-08-01

We examined the utilization of precision medicine tests among Medicare beneficiaries through analysis of gene-specific tier 1 and 2 billing codes developed by the American Medical Association in 2012. We conducted a retrospective cross-sectional study. The primary source of data was 2013 Medicare 100% fee-for-service claims. We identified claims billed for each laboratory test, the number of patients tested, expenditures, and the diagnostic codes indicated for testing. We analyzed variations in testing by patient demographics and region of the country. Pharmacogenetic tests were billed most frequently, accounting for 48% of the expenditures for new codes. The most common indications for testing were breast cancer, long-term use of medications, and disorders of lipid metabolism. There was underutilization of guideline-recommended tumor mutation tests (e.g., epidermal growth factor receptor) and substantial overutilization of a test discouraged by guidelines (methylenetetrahydrofolate reductase). Methodology-based tier 2 codes represented 15% of all claims billed with the new codes. The highest rate of testing per beneficiary was in Mississippi and the lowest rate was in Alaska. Gene-specific billing codes significantly improved our ability to conduct population-level research of precision medicine. Analysis of these data in conjunction with clinical records should be conducted to validate findings.Genet Med advance online publication 26 January 2017.

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.

Structured parenting of toddlers at high versus low genetic risk: two pathways to child problems.

Science.gov (United States)

Leve, Leslie D; Harold, Gordon T; Ge, Xiaojia; Neiderhiser, Jenae M; Shaw, Daniel; Scaramella, Laura V; Reiss, David

2009-11-01

Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for psychopathology. The sample included 290 linked sets of adoptive families and birth mothers and 95 linked birth fathers. Genetic risk was assessed via birth mother and birth father psychopathology (anxiety, depression, antisociality, and drug use). Structured parenting was assessed via microsocial coding of adoptive mothers' behavior during a cleanup task. Toddler behavior problems were assessed with the Child Behavior Checklist. Controlling for temperamental risk at 9 months, there was an interaction between birth mother psychopathology and adoptive mothers' parenting on toddler behavior problems at 18 months. The interaction indicated two pathways to child problems: structured parenting was beneficial for toddlers at high genetic risk but was related to behavior problems for toddlers at low genetic risk. This crossover interaction pattern was replicated with birth father psychopathology as the index of genetic risk. The effects of structured parenting on toddler behavior problems varied as a function of genetic risk. Children at genetic risk might benefit from parenting interventions during toddlerhood that enhance structured parenting.

Sub-Transport Layer Coding

DEFF Research Database (Denmark)

Hansen, Jonas; Krigslund, Jeppe; Roetter, Daniel Enrique Lucani

2014-01-01

Packet losses in wireless networks dramatically curbs the performance of TCP. This paper introduces a simple coding shim that aids IP-layer traffic in lossy environments while being transparent to transport layer protocols. The proposed coding approach enables erasure correction while being...... oblivious to the congestion control algorithms of the utilised transport layer protocol. Although our coding shim is indifferent towards the transport layer protocol, we focus on the performance of TCP when ran on top of our proposed coding mechanism due to its widespread use. The coding shim provides gains...

Utility experience in code updating of equipment built to 1974 code, Section 3, Subsection NF

International Nuclear Information System (INIS)

Rao, K.R.; Deshpande, N.

1990-01-01

This paper addresses changes to ASME Code Subsection NF and reconciles the differences between the updated codes and the as built construction code, of ASME Section III, 1974 to which several nuclear plants have been built. Since Section III is revised every three years and replacement parts complying with the construction code are invariably not available from the plant stock inventory, parts must be procured from vendors who comply with the requirements of the latest codes. Aspects of the ASME code which reflect Subsection NF are identified and compared with the later Code editions and addenda, especially up to and including the 1974 ASME code used as the basis for the plant qualification. The concern of the regulatory agencies is that if later code allowables and provisions are adopted it is possible to reduce the safety margins of the construction code. Areas of concern are highlighted and the specific changes of later codes are discerned; adoption of which, would not sacrifice the intended safety margins of the codes to which plants are licensed

Reloading pattern optimization of VVER-1000 reactors in transient cycles using genetic algorithm

International Nuclear Information System (INIS)

Rahmani, Yashar

2017-01-01

Highlights: • The genetic algorithm (GA) and the innovative weighting factors method were used. • The coupling of WIMSD5-B and CITATION-LDI2 neutronic codes with the thermohydraulic WERL code was employed. • Optimization of reloading patterns was carried out in two states. • First an arrangement with satisfactory excess reactivity and the flattest power distribution was searched. • Second, it is tried to obtain an arrangement with satisfactory safety threshold and the maximum K_e_f_f. - Abstract: The present paper proposes application of the genetic algorithm (GA) and the innovative weighting factor method to optimize the reloading pattern of Bushehr VVER-1000 reactor in the second cycle. To estimate the composition of fuel assemblies remaining from the first cycle and precisely calculate the objective parameters of each reloading pattern in the second cycle, coupling of WIMSD5-B and CITATION-LDI2 codes in the neutronic section and the WERL code in the thermo-hydraulic section was employed. Optimization of the reloading patterns was carried out in two states. To meet the mentioned objective, with application of the weighting factor method in the first state, the type and quantity of the loadable fresh assemblies were determined to enable the reactor core to maintain the core criticality over the entire cycle length. Afterwards, the genetic algorithm was used to optimize the reloading pattern of the reactor to obtain an arrangement with flat radial power distribution. In the second state, the optimization algorithm was free to select the type and number of fresh fuel assemblies to be able to search for an arrangement with the maximum effective multiplication factor and the safe power peaking factor. In addition, in order to ensure the safety and desirability of the proposed patterns in both states, a time-dependent examination of the thermo-neutronic behavior of the reactor core was carried out during the second cycle. With consideration of the new

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

Science.gov (United States)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

ETR/ITER systems code

Energy Technology Data Exchange (ETDEWEB)

Barr, W.L.; Bathke, C.G.; Brooks, J.N.; Bulmer, R.H.; Busigin, A.; DuBois, P.F.; Fenstermacher, M.E.; Fink, J.; Finn, P.A.; Galambos, J.D.; Gohar, Y.; Gorker, G.E.; Haines, J.R.; Hassanein, A.M.; Hicks, D.R.; Ho, S.K.; Kalsi, S.S.; Kalyanam, K.M.; Kerns, J.A.; Lee, J.D.; Miller, J.R.; Miller, R.L.; Myall, J.O.; Peng, Y-K.M.; Perkins, L.J.; Spampinato, P.T.; Strickler, D.J.; Thomson, S.L.; Wagner, C.E.; Willms, R.S.; Reid, R.L. (ed.)

1988-04-01

A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs.

ETR/ITER systems code

International Nuclear Information System (INIS)

Barr, W.L.; Bathke, C.G.; Brooks, J.N.

1988-04-01

A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs

Autism and genetics: Clinical approach and association study with two markers of HRAS gene

Energy Technology Data Exchange (ETDEWEB)

Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

1995-08-14

Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

Coding and decoding for code division multiple user communication systems

Science.gov (United States)

Healy, T. J.

1985-01-01

A new algorithm is introduced which decodes code division multiple user communication signals. The algorithm makes use of the distinctive form or pattern of each signal to separate it from the composite signal created by the multiple users. Although the algorithm is presented in terms of frequency-hopped signals, the actual transmitter modulator can use any of the existing digital modulation techniques. The algorithm is applicable to error-free codes or to codes where controlled interference is permitted. It can be used when block synchronization is assumed, and in some cases when it is not. The paper also discusses briefly some of the codes which can be used in connection with the algorithm, and relates the algorithm to past studies which use other approaches to the same problem.

Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia

Science.gov (United States)

Khaw, Yam Sim; Chan, Yoke Fun; Jafar, Faizatul Lela; Othman, Norlijah; Chee, Hui Yee

2016-01-01

Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection. PMID:27199901

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

Science.gov (United States)

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

2016-08-19

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

Hermitian self-dual quasi-abelian codes

Directory of Open Access Journals (Sweden)

Herbert S. Palines

2017-12-01

Full Text Available Quasi-abelian codes constitute an important class of linear codes containing theoretically and practically interesting codes such as quasi-cyclic codes, abelian codes, and cyclic codes. In particular, the sub-class consisting of 1-generator quasi-abelian codes contains large families of good codes. Based on the well-known decomposition of quasi-abelian codes, the characterization and enumeration of Hermitian self-dual quasi-abelian codes are given. In the case of 1-generator quasi-abelian codes, we offer necessary and sufficient conditions for such codes to be Hermitian self-dual and give a formula for the number of these codes. In the case where the underlying groups are some $p$-groups, the actual number of resulting Hermitian self-dual quasi-abelian codes are determined.